/**
* This class implements user defined special replacement rules of the form
- * ${=name}. See <a
- * href="http://javaregex.com/code/trans2.java.html">trans2.java</a> and <a
- * href="http://javaregex.com/code/trans2a.java.html">trans2a.java</a>.
+ * ${=name}. See
+ * <a href="http://javaregex.com/code/trans2.java.html">trans2.java</a> and
+ * <a href="http://javaregex.com/code/trans2a.java.html">trans2a.java</a>.
*/
public class ChangeRule extends SpecialRule
{
(char) 14, (char) 15, (char) 16, (char) 17, (char) 18, (char) 19,
(char) 20, (char) 21, (char) 22, (char) 23, (char) 24, (char) 25,
(char) 26, (char) 27, (char) 27, (char) 29, (char) 30, (char) 31,
- (char) 32, (char) 1, (char) 2, (char) 3, (char) 4, (char) 5,
- (char) 6, (char) 7, (char) 8, (char) 9, (char) 10, (char) 11,
- (char) 12, (char) 13, (char) 14, (char) 15, (char) 16, (char) 17,
- (char) 18, (char) 19, (char) 20, (char) 21, (char) 22, (char) 23,
- (char) 24, (char) 25, (char) 26, (char) 59, (char) 60, (char) 61,
- (char) 62, (char) 63, (char) 192, (char) 193, (char) 194, (char) 195,
- (char) 196, (char) 197, (char) 198, (char) 199, (char) 200,
- (char) 201, (char) 202, (char) 203, (char) 204, (char) 205,
- (char) 206, (char) 207, (char) 208, (char) 209, (char) 210,
- (char) 211, (char) 212, (char) 213, (char) 214, (char) 215,
- (char) 216, (char) 217, (char) 218, (char) 219, (char) 220,
- (char) 221, (char) 222, (char) 223, (char) 224, (char) 225,
- (char) 226, (char) 227, (char) 228, (char) 229, (char) 230,
- (char) 231, (char) 232, (char) 233, (char) 234, (char) 235,
- (char) 236, (char) 237, (char) 238, (char) 239, (char) 240,
- (char) 241, (char) 242, (char) 243, (char) 244, (char) 245,
- (char) 246, (char) 247, (char) 248, (char) 249, (char) 250,
- (char) 251, (char) 252, (char) 253, (char) 254, (char) 255,
- (char) 128, (char) 129, (char) 130, (char) 131, (char) 132,
- (char) 133, (char) 134, (char) 135, (char) 136, (char) 137,
- (char) 138, (char) 139, (char) 140, (char) 141, (char) 142,
- (char) 143, (char) 144, (char) 145, (char) 146, (char) 147,
- (char) 148, (char) 149, (char) 150, (char) 151, (char) 152,
- (char) 153, (char) 154, (char) 155, (char) 156, (char) 157,
- (char) 158, (char) 159, (char) 160, (char) 161, (char) 162,
- (char) 163, (char) 164, (char) 165, (char) 166, (char) 167,
- (char) 168, (char) 169, (char) 170, (char) 171, (char) 172,
- (char) 173, (char) 174, (char) 175, (char) 176, (char) 177,
- (char) 178, (char) 179, (char) 180, (char) 181, (char) 182,
- (char) 183, (char) 184, (char) 185, (char) 186, (char) 187,
- (char) 188, (char) 189, (char) 190, (char) 191 };
+ (char) 32, (char) 1, (char) 2, (char) 3, (char) 4, (char) 5, (char) 6,
+ (char) 7, (char) 8, (char) 9, (char) 10, (char) 11, (char) 12,
+ (char) 13, (char) 14, (char) 15, (char) 16, (char) 17, (char) 18,
+ (char) 19, (char) 20, (char) 21, (char) 22, (char) 23, (char) 24,
+ (char) 25, (char) 26, (char) 59, (char) 60, (char) 61, (char) 62,
+ (char) 63, (char) 192, (char) 193, (char) 194, (char) 195, (char) 196,
+ (char) 197, (char) 198, (char) 199, (char) 200, (char) 201,
+ (char) 202, (char) 203, (char) 204, (char) 205, (char) 206,
+ (char) 207, (char) 208, (char) 209, (char) 210, (char) 211,
+ (char) 212, (char) 213, (char) 214, (char) 215, (char) 216,
+ (char) 217, (char) 218, (char) 219, (char) 220, (char) 221,
+ (char) 222, (char) 223, (char) 224, (char) 225, (char) 226,
+ (char) 227, (char) 228, (char) 229, (char) 230, (char) 231,
+ (char) 232, (char) 233, (char) 234, (char) 235, (char) 236,
+ (char) 237, (char) 238, (char) 239, (char) 240, (char) 241,
+ (char) 242, (char) 243, (char) 244, (char) 245, (char) 246,
+ (char) 247, (char) 248, (char) 249, (char) 250, (char) 251,
+ (char) 252, (char) 253, (char) 254, (char) 255, (char) 128,
+ (char) 129, (char) 130, (char) 131, (char) 132, (char) 133,
+ (char) 134, (char) 135, (char) 136, (char) 137, (char) 138,
+ (char) 139, (char) 140, (char) 141, (char) 142, (char) 143,
+ (char) 144, (char) 145, (char) 146, (char) 147, (char) 148,
+ (char) 149, (char) 150, (char) 151, (char) 152, (char) 153,
+ (char) 154, (char) 155, (char) 156, (char) 157, (char) 158,
+ (char) 159, (char) 160, (char) 161, (char) 162, (char) 163,
+ (char) 164, (char) 165, (char) 166, (char) 167, (char) 168,
+ (char) 169, (char) 170, (char) 171, (char) 172, (char) 173,
+ (char) 174, (char) 175, (char) 176, (char) 177, (char) 178,
+ (char) 179, (char) 180, (char) 181, (char) 182, (char) 183,
+ (char) 184, (char) 185, (char) 186, (char) 187, (char) 188,
+ (char) 189, (char) 190, (char) 191 };
}
import java.util.Hashtable;
/**
- * Simple custom patterns. See <a
- * href="http://javaregex.com/code/deriv2.java.html">deriv2.java</a> and <a
- * href="http://javaregex.com/code/deriv3.java.html">deriv3.java</a> in the test
- * directory.
+ * Simple custom patterns. See
+ * <a href="http://javaregex.com/code/deriv2.java.html">deriv2.java</a> and
+ * <a href="http://javaregex.com/code/deriv3.java.html">deriv3.java</a> in the
+ * test directory.
*
* @see com.stevesoft.pat.CustomEndpoint
*/
// is appropriate.
final static Pattern mkelem(char lo, char hi) throws RegSyntax
{
- return lo == hi ? (Pattern) (new oneChar(lo)) : (Pattern) (new Range(
- lo, hi));
+ return lo == hi ? (Pattern) (new oneChar(lo))
+ : (Pattern) (new Range(lo, hi));
}
static final char min(char a, char b)
return -1;
}
char c = pt.src.charAt(pos);
- return (neg ^ (c >= min && c <= max && bs.get(c - min))) ? nextMatch(
- pos + 1, pt) : -1;
+ return (neg ^ (c >= min && c <= max && bs.get(c - min)))
+ ? nextMatch(pos + 1, pt)
+ : -1;
}
}
{
if (p == null)
{
- RegSyntaxError.endItAll("Null length pattern "
- + "followed by *, +, or other Multi.");
+ RegSyntaxError.endItAll(
+ "Null length pattern " + "followed by *, +, or other Multi.");
}
fewestMatches = a;
mostMatches = b;
{
try
{
- FastMulti fm = new FastMulti(fewestMatches, mostMatches, sub.clone(h));
+ FastMulti fm = new FastMulti(fewestMatches, mostMatches,
+ sub.clone(h));
fm.matchFewest = matchFewest;
return fm;
} catch (RegSyntax rs)
* </center> Note that a FileRegex pattern always ends with the Regex pattern
* element "$". If you like to experiment, try making FileRegex's and then
* printing them out. The toString() method does a decompile of the pattern to a
- * standard Regex. Here are some more complete examples: <center>
- * <table * border=3>
+ * standard Regex. Here are some more complete examples: <center> <table *
+ * border=3>
* <tr>
* <td>FileRegex</td>
* <td>Regex</td>
return sa;
}
- final static Regex root = new Regex(File.separatorChar == '/' ? "/$"
- : "(?:.:|)\\\\$");
+ final static Regex root = new Regex(
+ File.separatorChar == '/' ? "/$" : "(?:.:|)\\\\$");
static void list1(String path, Vector v, int df, boolean rec)
{
Pattern clone1(Hashtable h)
{
throw new Error(MessageManager.formatMessage(
- "error.no_such_method_as_clone1_for", new String[] { getClass()
- .getName() }));
+ "error.no_such_method_as_clone1_for", new String[]
+ { getClass().getName() }));
}
Pattern clone(Hashtable h)
package com.stevesoft.pat;
/**
- * Implements substitution rule $POP. See the example file <a
- * href="http://javaregex.com/code/trans3.java.html">trans3.html</a>.
+ * Implements substitution rule $POP. See the example file
+ * <a href="http://javaregex.com/code/trans3.java.html">trans3.html</a>.
*/
public class PopRule extends SpecialRule
{
package com.stevesoft.pat;
/**
- * Get Unicode properties for a character. See <a
- * href="http://unicode.org">http://unicode.org</a>.
+ * Get Unicode properties for a character. See
+ * <a href="http://unicode.org">http://unicode.org</a>.
*/
public class Prop
{
package com.stevesoft.pat;
/**
- * See the example file <a
- * href="http://javaregex.com/code/trans3.java.html">trans3.java</a> for further
- * examples of how this is used. You will probably not want to call it directly.
+ * See the example file
+ * <a href="http://javaregex.com/code/trans3.java.html">trans3.java</a> for
+ * further examples of how this is used. You will probably not want to call it
+ * directly.
*/
public class PushRule extends SpecialRule
{
public int matchInternal(int p, Pthings pt)
{
- return (p < pt.src.length() && pt.src.charAt(p) == c) ? nextMatch(
- p + 1, pt) : -1;
+ return (p < pt.src.length() && pt.src.charAt(p) == c)
+ ? nextMatch(p + 1, pt)
+ : -1;
}
Pattern clone1(Hashtable h)
Pattern pp = (Pattern) v.elementAt(i);
// We want to have at least two oneChar's in
// the Or Object to consider making a Branch.
- if (pp instanceof oneChar
- && (b.h.size() >= 1 || (i + 1 < v.size() && v
- .elementAt(i + 1) instanceof oneChar)))
+ if (pp instanceof oneChar && (b.h.size() >= 1 || (i + 1 < v.size()
+ && v.elementAt(i + 1) instanceof oneChar)))
{
b.addc((oneChar) pp, ignoreCase, dontMinQ);
}
for (int i = 0; i < numSubs(); i++)
{
int n = i + 1;
- sb.append(" sub(" + n + ")=" + matchedFrom(n) + ":" + charsMatched(n));
+ sb.append(
+ " sub(" + n + ")=" + matchedFrom(n) + ":" + charsMatched(n));
}
return sb.toString();
}
public String stringMatched()
{
int mf = matchedFrom(), cm = charsMatched();
- return !didMatch_ || mf < 0 || cm < 0 ? null : src.substring(mf, mf
- + cm);
+ return !didMatch_ || mf < 0 || cm < 0 ? null
+ : src.substring(mf, mf + cm);
}
/**
public String stringMatched(int i)
{
int mf = matchedFrom(i), cm = charsMatched(i);
- return !didMatch_ || mf < 0 || cm < 0 ? null : src.substring(mf, mf
- + cm);
+ return !didMatch_ || mf < 0 || cm < 0 ? null
+ : src.substring(mf, mf + cm);
}
/**
public String right()
{
int mf = matchedFrom(), cm = charsMatched();
- return !didMatch_ || mf < 0 || cm < 0 ? null : src.substring(mf + cm,
- src.length());
+ return !didMatch_ || mf < 0 || cm < 0 ? null
+ : src.substring(mf + cm, src.length());
}
/**
public String right(int i)
{
int mf = matchedFrom(i), cm = charsMatched(i);
- return !didMatch_ || mf < 0 || cm < 0 ? null : src.substring(mf + cm,
- src.length());
+ return !didMatch_ || mf < 0 || cm < 0 ? null
+ : src.substring(mf + cm, src.length());
}
/**
return -1;
}
char c = s.charAt(from);
- return !(Prop.isAlphabetic(c) || Prop.isDecimalDigit(c) || c == '_') ? to
+ return !(Prop.isAlphabetic(c) || Prop.isDecimalDigit(c) || c == '_')
+ ? to
: -1;
}
}
* small differences as well. I will either make my package conform or note them
* as I become aware of them.
* <p>
- * This package supports additional patterns not in perl5: <center>
- * <table * border=1>
+ * This package supports additional patterns not in perl5: <center> <table *
+ * border=1>
* <tr>
* <td>(?@())</td>
* <td>Group</td>
* beginning of the string. "x(?<1)" is equivalent to "(?=x)". The number, 1
* in this example, is the number of characters to move backwards.</td>
* </table>
- * </center> </dl>
+ * </center>
+ * </dl>
*
* @author Steven R. Brandt
* @version package com.stevesoft.pat, release 1.5.3
{
pt.lastPos = 0;
}
- if ((s == null ? null : s.unwrap()) != (src == null ? null : s.unwrap()))
+ if ((s == null ? null : s.unwrap()) != (src == null ? null
+ : s.unwrap()))
{
pt.lastPos = 0;
}
{
if (s == null)
{
- throw new NullPointerException(
- MessageManager
- .getString("exception.null_string_given_to_regex_search"));
+ throw new NullPointerException(MessageManager
+ .getString("exception.null_string_given_to_regex_search"));
}
return _search(s, 0, s.length());
}
{
if (sl == null)
{
- throw new NullPointerException(
- MessageManager
- .getString("exception.null_string_like_given_to_regex_search"));
+ throw new NullPointerException(MessageManager.getString(
+ "exception.null_string_like_given_to_regex_search"));
}
return _search(sl, 0, sl.length());
}
{
if (s == null)
{
- throw new NullPointerException(
- MessageManager
- .getString("exception.null_string_given_to_regex_reverse_search"));
+ throw new NullPointerException(MessageManager.getString(
+ "exception.null_string_given_to_regex_reverse_search"));
}
return _reverseSearch(s, 0, s.length());
}
{
if (sl == null)
{
- throw new NullPointerException(
- MessageManager
- .getString("exception.null_string_like_given_to_regex_reverse_search"));
+ throw new NullPointerException(MessageManager.getString(
+ "exception.null_string_like_given_to_regex_reverse_search"));
}
return _reverseSearch(sl, 0, sl.length());
}
{
if (s == null)
{
- throw new NullPointerException(
- MessageManager
- .getString("exception.null_string_like_given_to_regex_search_from"));
+ throw new NullPointerException(MessageManager.getString(
+ "exception.null_string_like_given_to_regex_search_from"));
}
return _search(s, start, s.length());
}
{
if (s == null)
{
- throw new NullPointerException(
- MessageManager
- .getString("exception.null_string_like_given_to_regex_search_from"));
+ throw new NullPointerException(MessageManager.getString(
+ "exception.null_string_like_given_to_regex_search_from"));
}
return _search(s, start, s.length());
}
{
if (s == null)
{
- throw new NullPointerException(
- MessageManager
- .getString("exception.null_string_like_given_to_regex_search_region"));
+ throw new NullPointerException(MessageManager.getString(
+ "exception.null_string_like_given_to_regex_search_region"));
}
return _search(s, start, end);
}
* optimized() method.
* <p>
* This method will attempt to rewrite your pattern in a way that makes it
- * faster (not all patterns execute at the same speed). In general,
- * "(?: ... )" will be faster than "( ... )" so if you don't need the
- * backreference, you should group using the former pattern.
+ * faster (not all patterns execute at the same speed). In general, "(?: ...
+ * )" will be faster than "( ... )" so if you don't need the backreference,
+ * you should group using the former pattern.
* <p>
* It will also introduce new pattern elements that you can't get to
* otherwise, for example if you have a large table of strings, i.e. the
boolean isHexDigit(StrPos sp)
{
- boolean r = !sp.eos
- && !sp.dontMatch
- && ((sp.c >= '0' && sp.c <= '9')
- || (sp.c >= 'a' && sp.c <= 'f') || (sp.c >= 'A' && sp.c <= 'F'));
+ boolean r = !sp.eos && !sp.dontMatch
+ && ((sp.c >= '0' && sp.c <= '9') || (sp.c >= 'a' && sp.c <= 'f')
+ || (sp.c >= 'A' && sp.c <= 'F'));
return r;
}
if (r.substring() != null)
{
v.addElement(r.substring(i + offset));
- vi.addElement(Integer.valueOf(r.matchFrom(i + offset)
- + r.charsMatched(i + offset)));
+ vi.addElement(Integer.valueOf(
+ r.matchFrom(i + offset) + r.charsMatched(i + offset)));
}
}
pos = r.matchFrom() + r.charsMatched();
* an ending (the whole pattern is a String formed by adding the beginning and
* ending), and a ReplaceRule.
* <p>
- * An illustration of this is given in the this <a
- * href="../test/trans.java">example.</a>
+ * An illustration of this is given in the this
+ * <a href="../test/trans.java">example.</a>
*/
public class RegexWriter extends Writer
{
* default methods) that are needed by the clone() or toString() methods on this
* class. During the replacement process, each ReplaceRule tells the replacer
* what to add to StringBuffer and uses the contents of the Regular expression
- * result to get the information it needs to do this. Here is an <a
- * href="http://javaregex.com/code/fancy.java.html">example</a>
+ * result to get the information it needs to do this. Here is an
+ * <a href="http://javaregex.com/code/fancy.java.html">example</a>
*
* @see com.stevesoft.pat.NullRule
* @see com.stevesoft.pat.AmpersandRule
}
else if (tmp instanceof Transformer)
{
- head = add(head, new PushRule(var.substring(1),
- (Transformer) tmp));
+ head = add(head,
+ new PushRule(var.substring(1), (Transformer) tmp));
}
else
{
}
else if (tmp instanceof Transformer)
{
- head = add(head, new ChangeRule(var.substring(1),
- (Transformer) tmp));
+ head = add(head,
+ new ChangeRule(var.substring(1), (Transformer) tmp));
}
else
{
* <p>
* The only potential difference between using the methods of Replacer to do the
* replacing is that Replacer remembers changes to the replacing object between
- * calls to replaceAll, replaceFirst etc. For details, see the example file <a
- * href="http://javaregex.com/code/trans3.java.html">trans3.java</a>.
+ * calls to replaceAll, replaceFirst etc. For details, see the example file
+ * <a href="http://javaregex.com/code/trans3.java.html">trans3.java</a>.
*
* @see com.stevesoft.pat.Transformer
* @see com.stevesoft.pat.Regex
{
}
- public StringLike replaceFirstRegion(String s, Regex r, int start, int end)
+ public StringLike replaceFirstRegion(String s, Regex r, int start,
+ int end)
{
return replaceFirstRegion(new StringWrap(s), r, start, end);
}
{
while (x != null)
{
- if (x instanceof SpecialRule
- || (x instanceof RuleHolder && ((RuleHolder) x).held instanceof SpecialRule))
+ if (x instanceof SpecialRule || (x instanceof RuleHolder
+ && ((RuleHolder) x).held instanceof SpecialRule))
{
return true;
}
lastMatchedTo = 0;
if (rh.me == null)
{
- throw new NullPointerException(
- MessageManager
- .getString("exception.replace_null_regex_pointer"));
+ throw new NullPointerException(MessageManager
+ .getString("exception.replace_null_regex_pointer"));
}
if (rh.me._search(s, start, end))
{
apply(rh.me);
if (!first)
{
- for (int i = rmn; !want_more_text && rh.me._search(s, i, end); i = rmn)
+ for (int i = rmn; !want_more_text
+ && rh.me._search(s, i, end); i = rmn)
{
rmn = rh.me.matchedTo();
if (rh.me.charsMatched() == 0)
static int mkmask(int c)
{
char x = (char) c;
- return ~(CaseMgr.toUpperCase(x) | CaseMgr.toLowerCase(x) | CaseMgr
- .toTitleCase(x));
+ return ~(CaseMgr.toUpperCase(x) | CaseMgr.toLowerCase(x)
+ | CaseMgr.toTitleCase(x));
}
String src;
}
return sk;
}
- else if (p instanceof Or
- && ((Or) p).v.size() == 1
+ else if (p instanceof Or && ((Or) p).v.size() == 1
&& !((Or) p).leftForm().equals("(?!")
&& null != (subsk = findSkip(
(Pattern) ((Or) p).v.elementAt(0), ignoreCase, trnc)))
}
else
{
- return skipc < 0 ? null : new Skip("" + (char) skipc, ignoreCase,
- skipoff);
+ return skipc < 0 ? null
+ : new Skip("" + (char) skipc, ignoreCase, skipoff);
}
}
return null;
import com.stevesoft.pat.wrap.StringWrap;
/**
- * Like Skip, but implements a <a
- * href="http://www.dcc.uchile.cl/~rbaeza/handbook/algs/7/713b.srch.p.html">
+ * Like Skip, but implements a
+ * <a href="http://www.dcc.uchile.cl/~rbaeza/handbook/algs/7/713b.srch.p.html">
* Boyer-Moore-Horspool</a> type search method that has been modified to be more
* like a "T-search" (see the Michael Tamm''s article in <i>C'T, magazin fuer
* computer und technic</i>, August 97 p 292). Yet another important source of
- * information for me was the <a
- * href="http://www.go2net.com/people/paulp/deep/1997/05/14/"> Deep Magic</a>
+ * information for me was the
+ * <a href="http://www.go2net.com/people/paulp/deep/1997/05/14/"> Deep Magic</a>
* article on string searching. As of this writing, I can beat String's indexOf
* method in many cases.
*
public int matchInternal(int pos, Pthings pt)
{
// if(pt.no_check || s.regionMatches(pt.ignoreCase,0,pt.src,pos,s.length()))
- if (pt.no_check
- || CaseMgr.regionMatches(s, pt.ignoreCase, 0, pt.src, pos,
- s.length()))
+ if (pt.no_check || CaseMgr.regionMatches(s, pt.ignoreCase, 0, pt.src,
+ pos, s.length()))
{
return nextMatch(pos + s.length(), pt);
}
{
if (i >= tp.ra_len)
{
- throw new ArrayIndexOutOfBoundsException("i=" + i + ">=" + patterns());
+ throw new ArrayIndexOutOfBoundsException(
+ "i=" + i + ">=" + patterns());
}
if (i < 0)
{
{
if (i >= tp.ra_len)
{
- throw new ArrayIndexOutOfBoundsException("i=" + i + ">=" + patterns());
+ throw new ArrayIndexOutOfBoundsException(
+ "i=" + i + ">=" + patterns());
}
if (i < 0)
{
if (r == null)
{
throw new NullPointerException(MessageManager.formatMessage(
- "exception.bad_pattern_to_regex_perl_code",
- new String[] { rs }));
+ "exception.bad_pattern_to_regex_perl_code", new String[]
+ { rs }));
}
add(r);
}
/**
* This class makes it easy to create your own patterns and integrate them into
- * Regex. For more detail, see the example file <a
- * href="http://javaregex.com/code/deriv2.java.html">deriv2.java</a> or <a
- * href="http://javaregex.com/code/deriv3.java.html">deriv3.java</a>.
+ * Regex. For more detail, see the example file
+ * <a href="http://javaregex.com/code/deriv2.java.html">deriv2.java</a> or
+ * <a href="http://javaregex.com/code/deriv3.java.html">deriv3.java</a>.
*/
public class Validator
/**
* Triggers the reading of another line of text, allowing a longer pattern to
- * match -- for details see <a
- * href="http://javaregex.com/code/WantMore.java.html">WantMore.java</a>.
+ * match -- for details see
+ * <a href="http://javaregex.com/code/WantMore.java.html">WantMore.java</a>.
*/
public class WantMoreTextReplaceRule extends SpecialRule
{
{
char p;
int ret = -1;
- if (pos < pt.src.length()
- && !Masked(pos, pt)
- && ((p = pt.src.charAt(pos)) == c || (pt.ignoreCase && (p == altc || p == altc2))))
+ if (pos < pt.src.length() && !Masked(pos, pt)
+ && ((p = pt.src.charAt(pos)) == c
+ || (pt.ignoreCase && (p == altc || p == altc2))))
{
ret = nextMatch(pos + 1, pt);
}
return codify(s, 0, s.length(), keepbs);
}
- final public static String codify(String s, int i0, int iN, boolean keepbs)
+ final public static String codify(String s, int i0, int iN,
+ boolean keepbs)
{
StringBuffer sb = new StringBuffer();
boolean ucmode = false, lcmode = false, litmode = false;
{
}
- throw new ArrayIndexOutOfBoundsException(MessageManager.formatMessage(
- "exception.out_of_bounds_for_file", new String[] {
- Integer.valueOf(i).toString(),
- Integer.valueOf(i0).toString(),
+ throw new ArrayIndexOutOfBoundsException(MessageManager
+ .formatMessage("exception.out_of_bounds_for_file", new String[]
+ { Integer.valueOf(i).toString(), Integer.valueOf(i0).toString(),
Integer.valueOf(iend).toString() }));
}
{
if (decimal > 0)
{
- subModelNumber = Integer.parseInt(inputLine.substring(decimal
- + hash + 2, space));
+ subModelNumber = Integer
+ .parseInt(inputLine.substring(decimal + hash + 2, space));
space = decimal + hash + 1;
}
modelNumber = Integer.parseInt(inputLine.substring(hash + 1, space));
{
if (decimal > 0)
{
- subModelNumber = Integer.parseInt(inputLine.substring(decimal
- + hash + 2, space));
+ subModelNumber = Integer
+ .parseInt(inputLine.substring(decimal + hash + 2, space));
space = decimal + hash + 1;
}
modelNumber = Integer.parseInt(inputLine.substring(hash + 1, space));
{
try
{
- chimeraModel = chimeraManager.getChimeraModel(
- Integer.valueOf(model), 0);
+ chimeraModel = chimeraManager
+ .getChimeraModel(Integer.valueOf(model), 0);
} catch (NumberFormatException ex)
{
// ignore
if (modelIDNoResChain[0] != null)
{
String modelID = modelIDNoResChain[0];
- List<ChimeraModel> models = chimeraManager.getChimeraModels(
- modelID, ModelType.PDB_MODEL);
+ List<ChimeraModel> models = chimeraManager.getChimeraModels(modelID,
+ ModelType.PDB_MODEL);
if (models.size() == 1)
{ // usual case with only one model
chimeraModel = models.get(0);
// TODO: [Optional] What is this doing?
try
{
- chimeraModel = chimeraManager.getChimeraModel(
- Integer.valueOf(modelID), 0);
+ chimeraModel = chimeraManager
+ .getChimeraModel(Integer.valueOf(modelID), 0);
} catch (NumberFormatException ex)
{
// ignore
}
else if (chimeraModel.getChainCount() == 1)
{
- chimeraResidue = chimeraModel.getResidue(chimeraModel
- .getChainNames().iterator().next(), residue);
+ chimeraResidue = chimeraModel.getResidue(
+ chimeraModel.getChainNames().iterator().next(), residue);
}
// System.out.println("ChimeraResidue = " + chimeraResidue);
}
aaNames.put("LYS", "K Lys Lysine N[C@](CCCCN)([H])C(O)=O");
aaNames.put("DLY", "K Dly D-Lysine NCCCC[C@@H](N)C(O)=O");
aaNames.put("MET", "M Met Methionine N[C@](CCSC)([H])C(O)=O");
- aaNames.put("PHE", "F Phe Phenylalanine N[C@](CC1=CC=CC=C1)([H])C(O)=O");
+ aaNames.put("PHE",
+ "F Phe Phenylalanine N[C@](CC1=CC=CC=C1)([H])C(O)=O");
aaNames.put("PRO", "P Pro Proline OC([C@@]1([H])NCCC1)=O");
aaNames.put("SER", "S Ser Serine OC[C@](C(O)=O)([H])N");
aaNames.put("THR", "T Thr Threonine O[C@H](C)[C@](C(O)=O)([H])N");
displayName = displayName.substring(0, 13) + "...";
if (chainId.equals("_"))
{
- return (displayName + " Chain (no ID) (" + getResidueCount() + " residues)");
+ return (displayName + " Chain (no ID) (" + getResidueCount()
+ + " residues)");
}
else
{
- return (displayName + " Chain " + chainId + " (" + getResidueCount() + " residues)");
+ return (displayName + " Chain " + chainId + " (" + getResidueCount()
+ + " residues)");
}
}
* Select something in Chimera
*
* @param command
- * the selection command to pass to Chimera
+ * the selection command to pass to Chimera
*/
public void select(String command)
{
/**
* Return the list of depiction presets available from within Chimera. Chimera
- * will return the list as a series of lines with the format: Preset type number
- * "description"
+ * will return the list as a series of lines with the format: Preset type
+ * number "description"
*
* @return list of presets
*/
}
/**
- * Launch Chimera, unless an instance linked to this object is already running.
- * Returns true if chimera is successfully launched, or already running, else
- * false.
+ * Launch Chimera, unless an instance linked to this object is already
+ * running. Returns true if chimera is successfully launched, or already
+ * running, else false.
*
* @param chimeraPaths
* @return
* Determine the color that Chimera is using for this model.
*
* @param model
- * the ChimeraModel we want to get the Color for
+ * the ChimeraModel we want to get the Color for
* @return the default model Color for this model in Chimera
*/
public Color getModelColor(ChimeraModel model)
/**
*
* Get information about the residues associated with a model. This uses the
- * Chimera listr command. We don't return the resulting residues, but we add the
- * residues to the model.
+ * Chimera listr command. We don't return the resulting residues, but we add
+ * the residues to the model.
*
* @param model
- * the ChimeraModel to get residue information for
+ * the ChimeraModel to get residue information for
*
*/
public void addResidues(ChimeraModel model)
* Send a command to Chimera.
*
* @param command
- * Command string to be send.
+ * Command string to be send.
* @param reply
- * Flag indicating whether the method should return the reply
- * from Chimera or not.
+ * Flag indicating whether the method should return the reply from
+ * Chimera or not.
* @return List of Strings corresponding to the lines in the Chimera reply or
* <code>null</code>.
*/
*
*/
-public class ChimeraResidue implements ChimeraStructuralObject,
- Comparable<ChimeraResidue>
+public class ChimeraResidue
+ implements ChimeraStructuralObject, Comparable<ChimeraResidue>
{
/* Constants */
this.subModelNumber = 0;
if (decimalOffset > 0)
{
- this.subModelNumber = Integer.parseInt(model
- .substring(decimalOffset + 1));
- this.modelNumber = Integer.parseInt(model.substring(0,
- decimalOffset));
+ this.subModelNumber = Integer
+ .parseInt(model.substring(decimalOffset + 1));
+ this.modelNumber = Integer
+ .parseInt(model.substring(0, decimalOffset));
}
else
{
}
} catch (Exception e)
{
- LoggerFactory.getLogger(ChimeraResidue.class).error(
- "Unexpected return from Chimera: " + model);
+ LoggerFactory.getLogger(ChimeraResidue.class)
+ .error("Unexpected return from Chimera: " + model);
this.modelNumber = -1;
}
private DefaultMutableTreeNode buildTree()
{
int modelCount = chimeraManager.getChimeraModelsCount(true);
- DefaultMutableTreeNode rootNode = new DefaultMutableTreeNode(modelCount
- + " Open Chimera Models");
+ DefaultMutableTreeNode rootNode = new DefaultMutableTreeNode(
+ modelCount + " Open Chimera Models");
TreePath rootPath = new TreePath(rootNode);
TreePath path = null;
/**
* This is called by the selectionListener to let us know that the user has
- * changed their selection in Chimera. We need to go back to Chimera to find out
- * what is currently selected and update our list.
+ * changed their selection in Chimera. We need to go back to Chimera to find
+ * out what is currently selected and update our list.
*/
public void chimeraSelectionChanged()
{
}
/**
- * Add a selection to the selection list. This is called primarily by the Model
- * Navigator Dialog to keep the selections in sync
+ * Add a selection to the selection list. This is called primarily by the
+ * Model Navigator Dialog to keep the selections in sync
*
* @param selectionToAdd
- * the selection to add to our list
+ * the selection to add to our list
*/
public void addChimSelection(ChimeraStructuralObject selectionToAdd)
{
* Model Navigator Dialog to keep the selections in sync
*
* @param selectionToRemove
- * the selection to remove from our list
+ * the selection to remove from our list
*/
public void removeChimSelection(ChimeraStructuralObject selectionToRemove)
{
// Add default installation paths
if (os.startsWith("Linux"))
{
- // ChimeraX .deb and .rpm packages put symbolic link from /usr/bin/chimerax
- pathList.add(String.format("/usr/bin/%s", chimeraExe.toLowerCase(Locale.ROOT)));
+ // ChimeraX .deb and .rpm packages put symbolic link from
+ // /usr/bin/chimerax
+ pathList.add(String.format("/usr/bin/%s",
+ chimeraExe.toLowerCase(Locale.ROOT)));
pathList.add(String.format("/usr/bin/%s", chimeraExe));
- pathList.add(
- String.format("/usr/local/bin/%s", chimeraExe.toLowerCase(Locale.ROOT)));
+ pathList.add(String.format("/usr/local/bin/%s",
+ chimeraExe.toLowerCase(Locale.ROOT)));
pathList.add(String.format("/usr/local/bin/%s", chimeraExe));
// these paths also used by .deb and .rpm
pathList.add(String.format("/usr/local/chimera/bin/%s", chimeraExe));
// user home paths
- pathList.add(String.format("%s/bin/%s",
- System.getProperty("user.home"), chimeraExe.toLowerCase(Locale.ROOT)));
+ pathList.add(
+ String.format("%s/bin/%s", System.getProperty("user.home"),
+ chimeraExe.toLowerCase(Locale.ROOT)));
pathList.add(String.format("%s/bin/%s",
System.getProperty("user.home"), chimeraExe));
pathList.add(String.format("%s/opt/bin/%s",
- System.getProperty("user.home"), chimeraExe.toLowerCase(Locale.ROOT)));
+ System.getProperty("user.home"),
+ chimeraExe.toLowerCase(Locale.ROOT)));
pathList.add(String.format("%s/opt/bin/%s",
System.getProperty("user.home"), chimeraExe));
pathList.add(String.format("%s/local/bin/%s",
- System.getProperty("user.home"), chimeraExe.toLowerCase(Locale.ROOT)));
+ System.getProperty("user.home"),
+ chimeraExe.toLowerCase(Locale.ROOT)));
pathList.add(String.format("%s/local/bin/%s",
System.getProperty("user.home"), chimeraExe));
}
// Get a line-oriented reader
InputStream readChan = chimera.getInputStream();
lineReader = new BufferedReader(new InputStreamReader(readChan));
- logger = LoggerFactory
- .getLogger(ext.edu.ucsf.rbvi.strucviz2.port.ListenerThreads.class);
+ logger = LoggerFactory.getLogger(
+ ext.edu.ucsf.rbvi.strucviz2.port.ListenerThreads.class);
}
/**
throw new javax.xml.rpc.ServiceException(t);
}
throw new javax.xml.rpc.ServiceException(MessageManager.formatMessage(
- "exception.no_stub_implementation_for_interface",
- new String[] { (serviceEndpointInterface == null ? "null"
+ "exception.no_stub_implementation_for_interface", new String[]
+ { (serviceEndpointInterface == null ? "null"
: serviceEndpointInterface.getName()) }));
}
}
else
{ // Unknown Port Name
- throw new javax.xml.rpc.ServiceException(
- MessageManager.formatMessage(
- "exception.cannot_set_endpoint_address_unknown_port",
- new String[] { portName }));
+ throw new javax.xml.rpc.ServiceException(MessageManager.formatMessage(
+ "exception.cannot_set_endpoint_address_unknown_port",
+ new String[]
+ { portName }));
}
}
public vamsas.objects.simple.Secstructpred getpredict(
java.lang.String job_id) throws java.rmi.RemoteException;
- public vamsas.objects.simple.JpredResult getresult(java.lang.String job_id)
- throws java.rmi.RemoteException;
+ public vamsas.objects.simple.JpredResult getresult(
+ java.lang.String job_id) throws java.rmi.RemoteException;
}
throw new javax.xml.rpc.ServiceException(t);
}
throw new javax.xml.rpc.ServiceException(MessageManager.formatMessage(
- "exception.no_stub_implementation_for_interface",
- new String[] { (serviceEndpointInterface == null ? "null"
+ "exception.no_stub_implementation_for_interface", new String[]
+ { (serviceEndpointInterface == null ? "null"
: serviceEndpointInterface.getName()) }));
}
}
else
{ // Unknown Port Name
- throw new javax.xml.rpc.ServiceException(
- MessageManager.formatMessage(
- "exception.cannot_set_endpoint_address_unknown_port",
- new String[] { portName }));
+ throw new javax.xml.rpc.ServiceException(MessageManager.formatMessage(
+ "exception.cannot_set_endpoint_address_unknown_port",
+ new String[]
+ { portName }));
}
}
oper.setName("predict");
oper.addParameter(new javax.xml.namespace.QName("", "seq"),
new javax.xml.namespace.QName("simple.objects.vamsas",
- "Sequence"), vamsas.objects.simple.Sequence.class,
+ "Sequence"),
+ vamsas.objects.simple.Sequence.class,
org.apache.axis.description.ParameterDesc.IN, false, false);
oper.setReturnType(new javax.xml.namespace.QName(
"http://www.w3.org/2001/XMLSchema", "string"));
oper.setReturnType(new javax.xml.namespace.QName(
"http://www.w3.org/2001/XMLSchema", "string"));
oper.setReturnClass(java.lang.String.class);
- oper.setReturnQName(new javax.xml.namespace.QName("",
- "predictOnMsaReturn"));
+ oper.setReturnQName(
+ new javax.xml.namespace.QName("", "predictOnMsaReturn"));
oper.setStyle(org.apache.axis.constants.Style.RPC);
oper.setUse(org.apache.axis.constants.Use.ENCODED);
_operations[1] = oper;
oper.setReturnType(new javax.xml.namespace.QName(
"http://simple.objects.vamsas", "Secstructpred"));
oper.setReturnClass(vamsas.objects.simple.Secstructpred.class);
- oper.setReturnQName(new javax.xml.namespace.QName("",
- "getpredictReturn"));
+ oper.setReturnQName(
+ new javax.xml.namespace.QName("", "getpredictReturn"));
oper.setStyle(org.apache.axis.constants.Style.RPC);
oper.setUse(org.apache.axis.constants.Use.ENCODED);
_operations[2] = oper;
oper.setReturnType(new javax.xml.namespace.QName(
"http://simple.objects.vamsas", "JpredResult"));
oper.setReturnClass(vamsas.objects.simple.JpredResult.class);
- oper.setReturnQName(new javax.xml.namespace.QName("", "getresultReturn"));
+ oper.setReturnQName(
+ new javax.xml.namespace.QName("", "getresultReturn"));
oper.setStyle(org.apache.axis.constants.Style.RPC);
oper.setUse(org.apache.axis.constants.Use.ENCODED);
_operations[3] = oper;
cachedSerFactories.add(beansf);
cachedDeserFactories.add(beandf);
- qName = new javax.xml.namespace.QName("simple.objects.vamsas", "Result");
+ qName = new javax.xml.namespace.QName("simple.objects.vamsas",
+ "Result");
cachedSerQNames.add(qName);
cls = vamsas.objects.simple.Result.class;
cachedSerClasses.add(cls);
if (firstCall())
{
// must set encoding style before registering serializers
- _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
+ _call.setSOAPVersion(
+ org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
_call.setEncodingStyle(org.apache.axis.Constants.URI_SOAP11_ENC);
for (int i = 0; i < cachedSerFactories.size(); ++i)
{
_call.setOperation(_operations[0]);
_call.setUseSOAPAction(true);
_call.setSOAPActionURI("");
- _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
- _call.setOperationName(new javax.xml.namespace.QName("vamsas",
- "predict"));
+ _call.setSOAPVersion(
+ org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
+ _call.setOperationName(
+ new javax.xml.namespace.QName("vamsas", "predict"));
setRequestHeaders(_call);
setAttachments(_call);
return (java.lang.String) _resp;
} catch (java.lang.Exception _exception)
{
- return (java.lang.String) org.apache.axis.utils.JavaUtils.convert(
- _resp, java.lang.String.class);
+ return (java.lang.String) org.apache.axis.utils.JavaUtils
+ .convert(_resp, java.lang.String.class);
}
}
}
_call.setOperation(_operations[1]);
_call.setUseSOAPAction(true);
_call.setSOAPActionURI("");
- _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
- _call.setOperationName(new javax.xml.namespace.QName("vamsas",
- "predictOnMsa"));
+ _call.setSOAPVersion(
+ org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
+ _call.setOperationName(
+ new javax.xml.namespace.QName("vamsas", "predictOnMsa"));
setRequestHeaders(_call);
setAttachments(_call);
return (java.lang.String) _resp;
} catch (java.lang.Exception _exception)
{
- return (java.lang.String) org.apache.axis.utils.JavaUtils.convert(
- _resp, java.lang.String.class);
+ return (java.lang.String) org.apache.axis.utils.JavaUtils
+ .convert(_resp, java.lang.String.class);
}
}
}
_call.setOperation(_operations[2]);
_call.setUseSOAPAction(true);
_call.setSOAPActionURI("");
- _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
- _call.setOperationName(new javax.xml.namespace.QName("vamsas",
- "getpredict"));
+ _call.setSOAPVersion(
+ org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
+ _call.setOperationName(
+ new javax.xml.namespace.QName("vamsas", "getpredict"));
setRequestHeaders(_call);
setAttachments(_call);
java.lang.Object _resp = _call
- .invoke(new java.lang.Object[] { job_id });
+ .invoke(new java.lang.Object[]
+ { job_id });
if (_resp instanceof java.rmi.RemoteException)
{
}
}
- public vamsas.objects.simple.JpredResult getresult(java.lang.String job_id)
- throws java.rmi.RemoteException
+ public vamsas.objects.simple.JpredResult getresult(
+ java.lang.String job_id) throws java.rmi.RemoteException
{
if (super.cachedEndpoint == null)
{
_call.setOperation(_operations[3]);
_call.setUseSOAPAction(true);
_call.setSOAPActionURI("");
- _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
- _call.setOperationName(new javax.xml.namespace.QName("vamsas",
- "getresult"));
+ _call.setSOAPVersion(
+ org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
+ _call.setOperationName(
+ new javax.xml.namespace.QName("vamsas", "getresult"));
setRequestHeaders(_call);
setAttachments(_call);
java.lang.Object _resp = _call
- .invoke(new java.lang.Object[] { job_id });
+ .invoke(new java.lang.Object[]
+ { job_id });
if (_resp instanceof java.rmi.RemoteException)
{
}
throw new javax.xml.rpc.ServiceException(MessageManager.formatMessage(
- "exception.no_stub_implementation_for_interface",
- new String[] { (serviceEndpointInterface == null ? "null"
+ "exception.no_stub_implementation_for_interface", new String[]
+ { (serviceEndpointInterface == null ? "null"
: serviceEndpointInterface.getName()) }));
}
}
else
{ // Unknown Port Name
- throw new javax.xml.rpc.ServiceException(
- MessageManager.formatMessage(
- "exception.cannot_set_endpoint_address_unknown_port",
- new String[] { portName }));
+ throw new javax.xml.rpc.ServiceException(MessageManager.formatMessage(
+ "exception.cannot_set_endpoint_address_unknown_port",
+ new String[]
+ { portName }));
}
}
cachedSerFactories.add(beansf);
cachedDeserFactories.add(beandf);
- qName = new javax.xml.namespace.QName("vamsas", "ArrayOf_tns1_Sequence");
+ qName = new javax.xml.namespace.QName("vamsas",
+ "ArrayOf_tns1_Sequence");
cachedSerQNames.add(qName);
cls = vamsas.objects.simple.Sequence[].class;
cachedSerClasses.add(cls);
cachedSerFactories.add(arraysf);
cachedDeserFactories.add(arraydf);
- qName = new javax.xml.namespace.QName("simple.objects.vamsas", "Result");
+ qName = new javax.xml.namespace.QName("simple.objects.vamsas",
+ "Result");
cachedSerQNames.add(qName);
cls = vamsas.objects.simple.Result.class;
cachedSerClasses.add(cls);
oper.setReturnType(new javax.xml.namespace.QName(
"simple.objects.vamsas", "Alignment"));
oper.setReturnClass(vamsas.objects.simple.Alignment.class);
- oper.setReturnQName(new javax.xml.namespace.QName("", "getalignReturn"));
+ oper.setReturnQName(
+ new javax.xml.namespace.QName("", "getalignReturn"));
oper.setStyle(org.apache.axis.constants.Style.RPC);
oper.setUse(org.apache.axis.constants.Use.ENCODED);
_operations[1] = oper;
oper.setReturnType(new javax.xml.namespace.QName(
"simple.objects.vamsas", "MsaResult"));
oper.setReturnClass(vamsas.objects.simple.MsaResult.class);
- oper.setReturnQName(new javax.xml.namespace.QName("", "getResultReturn"));
+ oper.setReturnQName(
+ new javax.xml.namespace.QName("", "getResultReturn"));
oper.setStyle(org.apache.axis.constants.Style.RPC);
oper.setUse(org.apache.axis.constants.Use.ENCODED);
_operations[2] = oper;
if (firstCall())
{
// must set encoding style before registering serializers
- _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
+ _call.setSOAPVersion(
+ org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
_call.setEncodingStyle(org.apache.axis.Constants.URI_SOAP11_ENC);
for (int i = 0; i < cachedSerFactories.size(); ++i)
_call.setOperation(_operations[0]);
_call.setUseSOAPAction(true);
_call.setSOAPActionURI("");
- _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
- _call.setOperationName(new javax.xml.namespace.QName("vamsas", "align"));
+ _call.setSOAPVersion(
+ org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
+ _call.setOperationName(
+ new javax.xml.namespace.QName("vamsas", "align"));
setRequestHeaders(_call);
setAttachments(_call);
java.lang.Object _resp = _call
- .invoke(new java.lang.Object[] { seqSet });
+ .invoke(new java.lang.Object[]
+ { seqSet });
if (_resp instanceof java.rmi.RemoteException)
{
_call.setOperation(_operations[1]);
_call.setUseSOAPAction(true);
_call.setSOAPActionURI("");
- _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
- _call.setOperationName(new javax.xml.namespace.QName("vamsas",
- "getalign"));
+ _call.setSOAPVersion(
+ org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
+ _call.setOperationName(
+ new javax.xml.namespace.QName("vamsas", "getalign"));
setRequestHeaders(_call);
setAttachments(_call);
java.lang.Object _resp = _call
- .invoke(new java.lang.Object[] { job_id });
+ .invoke(new java.lang.Object[]
+ { job_id });
if (_resp instanceof java.rmi.RemoteException)
{
_call.setOperation(_operations[2]);
_call.setUseSOAPAction(true);
_call.setSOAPActionURI("");
- _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
- _call.setOperationName(new javax.xml.namespace.QName("vamsas",
- "getResult"));
+ _call.setSOAPVersion(
+ org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
+ _call.setOperationName(
+ new javax.xml.namespace.QName("vamsas", "getResult"));
setRequestHeaders(_call);
setAttachments(_call);
java.lang.Object _resp = _call
- .invoke(new java.lang.Object[] { job_id });
+ .invoke(new java.lang.Object[]
+ { job_id });
if (_resp instanceof java.rmi.RemoteException)
{
_call.setOperation(_operations[3]);
_call.setUseSOAPAction(true);
_call.setSOAPActionURI("");
- _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
- _call.setOperationName(new javax.xml.namespace.QName("vamsas", "cancel"));
+ _call.setSOAPVersion(
+ org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
+ _call.setOperationName(
+ new javax.xml.namespace.QName("vamsas", "cancel"));
setRequestHeaders(_call);
setAttachments(_call);
*/
package ext.vamsas;
-public class RegistryServiceSoapBindingStub extends
- org.apache.axis.client.Stub implements ext.vamsas.IRegistry
+public class RegistryServiceSoapBindingStub
+ extends org.apache.axis.client.Stub implements ext.vamsas.IRegistry
{
private java.util.Vector cachedSerClasses = new java.util.Vector();
oper.setReturnType(new javax.xml.namespace.QName(
"registry.objects.vamsas", "ServiceHandles"));
oper.setReturnClass(ext.vamsas.ServiceHandles.class);
- oper.setReturnQName(new javax.xml.namespace.QName("",
- "getServicesReturn"));
+ oper.setReturnQName(
+ new javax.xml.namespace.QName("", "getServicesReturn"));
oper.setStyle(org.apache.axis.constants.Style.RPC);
oper.setUse(org.apache.axis.constants.Use.ENCODED);
_operations[0] = oper;
if (firstCall())
{
// must set encoding style before registering serializers
- _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
+ _call.setSOAPVersion(
+ org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
_call.setEncodingStyle(org.apache.axis.Constants.URI_SOAP11_ENC);
for (int i = 0; i < cachedSerFactories.size(); ++i)
{
_call.setOperation(_operations[0]);
_call.setUseSOAPAction(true);
_call.setSOAPActionURI("");
- _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
- _call.setOperationName(new javax.xml.namespace.QName("vamsas",
- "getServices"));
+ _call.setSOAPVersion(
+ org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
+ _call.setOperationName(
+ new javax.xml.namespace.QName("vamsas", "getServices"));
setRequestHeaders(_call);
setAttachments(_call);
throw new javax.xml.rpc.ServiceException(t);
}
throw new javax.xml.rpc.ServiceException(MessageManager.formatMessage(
- "exception.no_stub_implementation_for_interface",
- new String[] { (serviceEndpointInterface == null ? "null"
+ "exception.no_stub_implementation_for_interface", new String[]
+ { (serviceEndpointInterface == null ? "null"
: serviceEndpointInterface.getName()) }));
}
}
else
{ // Unknown Port Name
- throw new javax.xml.rpc.ServiceException(
- MessageManager.formatMessage(
- "exception.cannot_set_endpoint_address_unknown_port",
- new String[] { portName }));
+ throw new javax.xml.rpc.ServiceException(MessageManager.formatMessage(
+ "exception.cannot_set_endpoint_address_unknown_port",
+ new String[]
+ { portName }));
}
}
*/
package ext.vamsas;
-public class SeqSearchServiceSoapBindingStub extends
- org.apache.axis.client.Stub implements ext.vamsas.SeqSearchI
+public class SeqSearchServiceSoapBindingStub
+ extends org.apache.axis.client.Stub implements ext.vamsas.SeqSearchI
{
private java.util.Vector cachedSerClasses = new java.util.Vector();
oper.setReturnType(new javax.xml.namespace.QName(
"http://www.w3.org/2001/XMLSchema", "string"));
oper.setReturnClass(java.lang.String.class);
- oper.setReturnQName(new javax.xml.namespace.QName("",
- "getDatabaseReturn"));
+ oper.setReturnQName(
+ new javax.xml.namespace.QName("", "getDatabaseReturn"));
oper.setStyle(org.apache.axis.constants.Style.RPC);
oper.setUse(org.apache.axis.constants.Use.ENCODED);
_operations[0] = oper;
oper.setReturnType(new javax.xml.namespace.QName(
"simple.objects.vamsas", "SeqSearchResult"));
oper.setReturnClass(vamsas.objects.simple.SeqSearchResult.class);
- oper.setReturnQName(new javax.xml.namespace.QName("", "getResultReturn"));
+ oper.setReturnQName(
+ new javax.xml.namespace.QName("", "getResultReturn"));
oper.setStyle(org.apache.axis.constants.Style.RPC);
oper.setUse(org.apache.axis.constants.Use.ENCODED);
_operations[1] = oper;
oper.setName("psearch");
oper.addParameter(new javax.xml.namespace.QName("", "al"),
new javax.xml.namespace.QName("simple.objects.vamsas",
- "Alignment"), vamsas.objects.simple.Alignment.class,
+ "Alignment"),
+ vamsas.objects.simple.Alignment.class,
org.apache.axis.description.ParameterDesc.IN, false, false);
oper.addParameter(new javax.xml.namespace.QName("", "database"),
new javax.xml.namespace.QName(
oper.setName("search");
oper.addParameter(new javax.xml.namespace.QName("", "s"),
new javax.xml.namespace.QName("simple.objects.vamsas",
- "Sequence"), vamsas.objects.simple.Sequence.class,
+ "Sequence"),
+ vamsas.objects.simple.Sequence.class,
org.apache.axis.description.ParameterDesc.IN, false, false);
oper.addParameter(new javax.xml.namespace.QName("", "database"),
new javax.xml.namespace.QName(
java.lang.Class simpledf = org.apache.axis.encoding.ser.SimpleDeserializerFactory.class;
java.lang.Class simplelistsf = org.apache.axis.encoding.ser.SimpleListSerializerFactory.class;
java.lang.Class simplelistdf = org.apache.axis.encoding.ser.SimpleListDeserializerFactory.class;
- qName = new javax.xml.namespace.QName("simple.objects.vamsas", "Result");
+ qName = new javax.xml.namespace.QName("simple.objects.vamsas",
+ "Result");
cachedSerQNames.add(qName);
cls = vamsas.objects.simple.Result.class;
cachedSerClasses.add(cls);
cachedSerFactories.add(beansf);
cachedDeserFactories.add(beandf);
- qName = new javax.xml.namespace.QName("vamsas", "ArrayOf_tns1_Sequence");
+ qName = new javax.xml.namespace.QName("vamsas",
+ "ArrayOf_tns1_Sequence");
cachedSerQNames.add(qName);
cls = vamsas.objects.simple.Sequence[].class;
cachedSerClasses.add(cls);
if (firstCall())
{
// must set encoding style before registering serializers
- _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
+ _call.setSOAPVersion(
+ org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
_call.setEncodingStyle(org.apache.axis.Constants.URI_SOAP11_ENC);
for (int i = 0; i < cachedSerFactories.size(); ++i)
{
_call.setOperation(_operations[0]);
_call.setUseSOAPAction(true);
_call.setSOAPActionURI("");
- _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
- _call.setOperationName(new javax.xml.namespace.QName("vamsas",
- "getDatabase"));
+ _call.setSOAPVersion(
+ org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
+ _call.setOperationName(
+ new javax.xml.namespace.QName("vamsas", "getDatabase"));
setRequestHeaders(_call);
setAttachments(_call);
return (java.lang.String) _resp;
} catch (java.lang.Exception _exception)
{
- return (java.lang.String) org.apache.axis.utils.JavaUtils.convert(
- _resp, java.lang.String.class);
+ return (java.lang.String) org.apache.axis.utils.JavaUtils
+ .convert(_resp, java.lang.String.class);
}
}
}
_call.setOperation(_operations[1]);
_call.setUseSOAPAction(true);
_call.setSOAPActionURI("");
- _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
- _call.setOperationName(new javax.xml.namespace.QName("vamsas",
- "getResult"));
+ _call.setSOAPVersion(
+ org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
+ _call.setOperationName(
+ new javax.xml.namespace.QName("vamsas", "getResult"));
setRequestHeaders(_call);
setAttachments(_call);
java.lang.Object _resp = _call
- .invoke(new java.lang.Object[] { job_id });
+ .invoke(new java.lang.Object[]
+ { job_id });
if (_resp instanceof java.rmi.RemoteException)
{
} catch (java.lang.Exception _exception)
{
return (vamsas.objects.simple.SeqSearchResult) org.apache.axis.utils.JavaUtils
- .convert(_resp, vamsas.objects.simple.SeqSearchResult.class);
+ .convert(_resp,
+ vamsas.objects.simple.SeqSearchResult.class);
}
}
}
_call.setOperation(_operations[2]);
_call.setUseSOAPAction(true);
_call.setSOAPActionURI("");
- _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
- _call.setOperationName(new javax.xml.namespace.QName("vamsas",
- "psearch"));
+ _call.setSOAPVersion(
+ org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
+ _call.setOperationName(
+ new javax.xml.namespace.QName("vamsas", "psearch"));
setRequestHeaders(_call);
setAttachments(_call);
- java.lang.Object _resp = _call.invoke(new java.lang.Object[] { al,
- database });
+ java.lang.Object _resp = _call
+ .invoke(new java.lang.Object[]
+ { al, database });
if (_resp instanceof java.rmi.RemoteException)
{
_call.setOperation(_operations[3]);
_call.setUseSOAPAction(true);
_call.setSOAPActionURI("");
- _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
- _call.setOperationName(new javax.xml.namespace.QName("vamsas", "search"));
+ _call.setSOAPVersion(
+ org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
+ _call.setOperationName(
+ new javax.xml.namespace.QName("vamsas", "search"));
setRequestHeaders(_call);
setAttachments(_call);
- java.lang.Object _resp = _call.invoke(new java.lang.Object[] { s,
- database });
+ java.lang.Object _resp = _call
+ .invoke(new java.lang.Object[]
+ { s, database });
if (_resp instanceof java.rmi.RemoteException)
{
_call.setOperation(_operations[4]);
_call.setUseSOAPAction(true);
_call.setSOAPActionURI("");
- _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
- _call.setOperationName(new javax.xml.namespace.QName("vamsas", "cancel"));
+ _call.setSOAPVersion(
+ org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
+ _call.setOperationName(
+ new javax.xml.namespace.QName("vamsas", "cancel"));
setRequestHeaders(_call);
setAttachments(_call);
__equalsCalc = obj;
boolean _equals;
_equals = true
- && ((this.abstractName == null && other.getAbstractName() == null) || (this.abstractName != null && this.abstractName
- .equals(other.getAbstractName())))
- && ((this.description == null && other.getDescription() == null) || (this.description != null && this.description
- .equals(other.getDescription())))
- && ((this.endpointURL == null && other.getEndpointURL() == null) || (this.endpointURL != null && this.endpointURL
- .equals(other.getEndpointURL())))
- && ((this.name == null && other.getName() == null) || (this.name != null && this.name
- .equals(other.getName())));
+ && ((this.abstractName == null
+ && other.getAbstractName() == null)
+ || (this.abstractName != null && this.abstractName
+ .equals(other.getAbstractName())))
+ && ((this.description == null && other.getDescription() == null)
+ || (this.description != null && this.description
+ .equals(other.getDescription())))
+ && ((this.endpointURL == null && other.getEndpointURL() == null)
+ || (this.endpointURL != null && this.endpointURL
+ .equals(other.getEndpointURL())))
+ && ((this.name == null && other.getName() == null)
+ || (this.name != null
+ && this.name.equals(other.getName())));
__equalsCalc = null;
return _equals;
}
}
__equalsCalc = obj;
boolean _equals;
- _equals = true && ((this.services == null && other.getServices() == null) || (this.services != null && java.util.Arrays
- .equals(this.services, other.getServices())));
+ _equals = true
+ && ((this.services == null && other.getServices() == null)
+ || (this.services != null && java.util.Arrays
+ .equals(this.services, other.getServices())));
__equalsCalc = null;
return _equals;
}
int _hashCode = 1;
if (getServices() != null)
{
- for (int i = 0; i < java.lang.reflect.Array.getLength(getServices()); i++)
+ for (int i = 0; i < java.lang.reflect.Array
+ .getLength(getServices()); i++)
{
- java.lang.Object obj = java.lang.reflect.Array
- .get(getServices(), i);
+ java.lang.Object obj = java.lang.reflect.Array.get(getServices(),
+ i);
if (obj != null && !obj.getClass().isArray())
{
_hashCode += obj.hashCode();
* @return
*/
public static int[] extractCdnaProfile(
- Hashtable<String, Object> hashtable,
- boolean ignoreGaps)
+ Hashtable<String, Object> hashtable, boolean ignoreGaps)
{
// this holds #seqs, #ungapped, and then codon count, indexed by encoded
// codon triplet
*/
public static void completeCdnaConsensus(
AlignmentAnnotation consensusAnnotation,
- Hashtable<String, Object>[] consensusData, boolean showProfileLogo,
- int nseqs)
+ Hashtable<String, Object>[] consensusData,
+ boolean showProfileLogo, int nseqs)
{
if (consensusAnnotation == null
|| consensusAnnotation.annotations == null
public AlignSeq(SequenceI s1, String string1, SequenceI s2,
String string2, String type)
{
- seqInit(s1, string1.toUpperCase(Locale.ROOT), s2, string2.toUpperCase(Locale.ROOT), type);
+ seqInit(s1, string1.toUpperCase(Locale.ROOT), s2,
+ string2.toUpperCase(Locale.ROOT), type);
}
/**
for (int j = 1; j < m; j++)
{
// What should these values be? 0 maybe
- E[0][j] = max(score[0][j - 1] - GAP_OPEN_COST, E[0][j - 1] - GAP_EXTEND_COST);
+ E[0][j] = max(score[0][j - 1] - GAP_OPEN_COST,
+ E[0][j - 1] - GAP_EXTEND_COST);
F[0][j] = -GAP_EXTEND_COST;
float pairwiseScore = scoreMatrix.getPairwiseScore(s1str.charAt(0),
s2str.charAt(j));
- score[0][j] = max(pairwiseScore * 10, -GAP_OPEN_COST, -GAP_EXTEND_COST);
+ score[0][j] = max(pairwiseScore * 10, -GAP_OPEN_COST,
+ -GAP_EXTEND_COST);
traceback[0][j] = 1;
}
for (int i = 1; i < n; i++)
{
E[i][0] = -GAP_OPEN_COST;
- F[i][0] = max(score[i - 1][0] - GAP_OPEN_COST, F[i - 1][0] - GAP_EXTEND_COST);
+ F[i][0] = max(score[i - 1][0] - GAP_OPEN_COST,
+ F[i - 1][0] - GAP_EXTEND_COST);
float pairwiseScore = scoreMatrix.getPairwiseScore(s1str.charAt(i),
s2str.charAt(0));
{
for (int j = 1; j < m; j++)
{
- E[i][j] = max(score[i][j - 1] - GAP_OPEN_COST, E[i][j - 1] - GAP_EXTEND_COST);
- F[i][j] = max(score[i - 1][j] - GAP_OPEN_COST, F[i - 1][j] - GAP_EXTEND_COST);
+ E[i][j] = max(score[i][j - 1] - GAP_OPEN_COST,
+ E[i][j - 1] - GAP_EXTEND_COST);
+ F[i][j] = max(score[i - 1][j] - GAP_OPEN_COST,
+ F[i - 1][j] - GAP_EXTEND_COST);
float pairwiseScore = scoreMatrix.getPairwiseScore(s1str.charAt(i),
s2str.charAt(j));
if (method != FEATURE_SCORE && method != FEATURE_LABEL
&& method != FEATURE_DENSITY)
{
- String msg = String
- .format("Implementation Error - sortByFeature method must be either '%s' or '%s'",
- FEATURE_SCORE, FEATURE_DENSITY);
+ String msg = String.format(
+ "Implementation Error - sortByFeature method must be either '%s' or '%s'",
+ FEATURE_SCORE, FEATURE_DENSITY);
System.err.println(msg);
return;
}
- flipFeatureSortIfUnchanged(method, featureTypes, groups, startCol, endCol);
+ flipFeatureSortIfUnchanged(method, featureTypes, groups, startCol,
+ endCol);
SequenceI[] seqs = alignment.getSequencesArray();
* get sequence residues overlapping column region
* and features for residue positions and specified types
*/
- String[] types = featureTypes == null ? null : featureTypes
- .toArray(new String[featureTypes.size()]);
+ String[] types = featureTypes == null ? null
+ : featureTypes.toArray(new String[featureTypes.size()]);
List<SequenceFeature> sfs = seqs[i].findFeatures(startCol + 1,
endCol + 1, types);
.getSequence(s.getStart() - 1 - ustream_ds, s.getStart() - 1))
.toLowerCase(Locale.ROOT).toCharArray();
char[] downstream = new String(
- ds.getSequence(s_end - 1, s_end + dstream_ds)).toLowerCase(Locale.ROOT)
- .toCharArray();
+ ds.getSequence(s_end - 1, s_end + dstream_ds))
+ .toLowerCase(Locale.ROOT).toCharArray();
char[] coreseq = s.getSequence();
char[] nseq = new char[offset + upstream.length + downstream.length
+ coreseq.length];
if (cdnaLength != mappedLength && cdnaLength > 2)
{
String lastCodon = String.valueOf(cdnaSeqChars,
- cdnaLength - CODON_LENGTH, CODON_LENGTH).toUpperCase(Locale.ROOT);
+ cdnaLength - CODON_LENGTH, CODON_LENGTH)
+ .toUpperCase(Locale.ROOT);
for (String stop : ResidueProperties.STOP_CODONS)
{
if (lastCodon.equals(stop))
*/
int startOffset = 0;
if (cdnaLength != mappedLength && cdnaLength > 2
- && String.valueOf(cdnaSeqChars, 0, CODON_LENGTH).toUpperCase(Locale.ROOT)
+ && String.valueOf(cdnaSeqChars, 0, CODON_LENGTH)
+ .toUpperCase(Locale.ROOT)
.equals(ResidueProperties.START))
{
startOffset += CODON_LENGTH;
mapList = mapList.getInverse();
}
final int cdsLength = cdsDss.getLength();
- int mappedFromLength = MappingUtils.getLength(mapList
- .getFromRanges());
+ int mappedFromLength = MappingUtils
+ .getLength(mapList.getFromRanges());
int mappedToLength = MappingUtils
.getLength(mapList.getToRanges());
boolean addStopCodon = (cdsLength == mappedFromLength
productSeqs = new HashSet<>();
for (SequenceI seq : products)
{
- productSeqs.add(seq.getDatasetSequence() == null ? seq : seq
- .getDatasetSequence());
+ productSeqs.add(seq.getDatasetSequence() == null ? seq
+ : seq.getDatasetSequence());
}
}
dataset.addSequence(cdsSeqDss);
AlignedCodonFrame cdsToProteinMapping = new AlignedCodonFrame();
cdsToProteinMapping.addMap(cdsSeqDss, proteinProduct,
- cdsToProteinMap);
+ cdsToProteinMap);
/*
* guard against duplicating the mapping if repeating this action
List<DBRefEntry> primrefs = dnaDss.getPrimaryDBRefs();
for (int ip = 0, np = primrefs.size(); ip < np; ip++)
{
- DBRefEntry primRef = primrefs.get(ip);
+ DBRefEntry primRef = primrefs.get(ip);
/*
* create a cross-reference from CDS to the source sequence's
* primary reference and vice versa
*/
String source = primRef.getSource();
String version = primRef.getVersion();
- DBRefEntry cdsCrossRef = new DBRefEntry(source, source + ":"
- + version, primRef.getAccessionId());
- cdsCrossRef.setMap(new Mapping(dnaDss, new MapList(cdsToDnaMap)));
+ DBRefEntry cdsCrossRef = new DBRefEntry(source,
+ source + ":" + version, primRef.getAccessionId());
+ cdsCrossRef
+ .setMap(new Mapping(dnaDss, new MapList(cdsToDnaMap)));
cdsSeqDss.addDBRef(cdsCrossRef);
- dnaSeq.addDBRef(new DBRefEntry(source, version, cdsSeq
- .getName(), new Mapping(cdsSeqDss, dnaToCdsMap)));
+ dnaSeq.addDBRef(new DBRefEntry(source, version,
+ cdsSeq.getName(), new Mapping(cdsSeqDss, dnaToCdsMap)));
// problem here is that the cross-reference is synthesized -
// cdsSeq.getName() may be like 'CDS|dnaaccession' or
// 'CDS|emblcdsacc'
DBRefEntry proteinToCdsRef = new DBRefEntry(source, version,
cdsSeq.getName());
//
- proteinToCdsRef.setMap(new Mapping(cdsSeqDss, cdsToProteinMap
- .getInverse()));
+ proteinToCdsRef.setMap(
+ new Mapping(cdsSeqDss, cdsToProteinMap.getInverse()));
proteinProduct.addDBRef(proteinToCdsRef);
}
/*
}
}
- AlignmentI cds = new Alignment(cdsSeqs.toArray(new SequenceI[cdsSeqs
- .size()]));
+ AlignmentI cds = new Alignment(
+ cdsSeqs.toArray(new SequenceI[cdsSeqs.size()]));
cds.setDataset(dataset);
return cds;
else
{
Console.error(
- "JAL-2154 regression: warning - found (and ignored) a duplicate CDS sequence:" + mtch.toString());
+ "JAL-2154 regression: warning - found (and ignored) a duplicate CDS sequence:"
+ + mtch.toString());
}
}
}
/*
* get features, optionally restricted by an ontology term
*/
- List<SequenceFeature> sfs = select == null ? fromSeq.getFeatures()
- .getPositionalFeatures() : fromSeq.getFeatures()
- .getFeaturesByOntology(select);
+ List<SequenceFeature> sfs = select == null
+ ? fromSeq.getFeatures().getPositionalFeatures()
+ : fromSeq.getFeatures().getFeaturesByOntology(select);
int count = 0;
for (SequenceFeature sf : sfs)
{
List<int[]> result = new ArrayList<>();
- List<SequenceFeature> sfs = dnaSeq.getFeatures().getFeaturesByOntology(
- SequenceOntologyI.CDS);
+ List<SequenceFeature> sfs = dnaSeq.getFeatures()
+ .getFeaturesByOntology(SequenceOntologyI.CDS);
if (sfs.isEmpty())
{
return result;
int phase = 0;
try
{
- String s = sf.getPhase();
- if (s != null)
- {
- phase = Integer.parseInt(s);
- }
+ String s = sf.getPhase();
+ if (s != null)
+ {
+ phase = Integer.parseInt(s);
+ }
} catch (NumberFormatException e)
{
// leave as zero
SequenceIdMatcher matcher = new SequenceIdMatcher(seqs);
if (xrefs != null)
{
- // BH 2019.01.25 recoded to remove iterators
-
+ // BH 2019.01.25 recoded to remove iterators
+
for (int ix = 0, nx = xrefs.length; ix < nx; ix++)
{
- SequenceI xref = xrefs[ix];
+ SequenceI xref = xrefs[ix];
List<DBRefEntry> dbrefs = xref.getDBRefs();
if (dbrefs != null)
{
* true; else returns false
*
* @param unaligned
- * - sequences to be aligned based on aligned
+ * - sequences to be aligned based on aligned
* @param aligned
- * - 'guide' alignment containing sequences derived from same
- * dataset as unaligned
+ * - 'guide' alignment containing sequences derived from same dataset
+ * as unaligned
* @return
*/
static boolean alignAsSameSequences(AlignmentI unaligned,
{
return false;
}
- SequenceI alignedSeq = alignedDatasets.get(ds)
- .get(0);
+ SequenceI alignedSeq = alignedDatasets.get(ds).get(0);
int startCol = alignedSeq.findIndex(seq.getStart()); // 1..
leftmost = Math.min(leftmost, startCol);
}
{
return 1;
}
- return label1.toUpperCase(Locale.ROOT).compareTo(label2.toUpperCase(Locale.ROOT));
+ return label1.toUpperCase(Locale.ROOT)
+ .compareTo(label2.toUpperCase(Locale.ROOT));
}
/**
public static void decodeCodon2(int encoded, char[] result)
{
- result[2] = decodeNucleotide(encoded & 3);
+ result[2] = decodeNucleotide(encoded & 3);
encoded = encoded >>> CODON_ENCODING_BITSHIFT;
result[1] = decodeNucleotide(encoded & 3);
encoded = encoded >>> CODON_ENCODING_BITSHIFT;
float vprop = value - qmin;
vprop /= qmax;
String description = FORMAT_3DP.form(value);
- quality2.annotations[i] = new Annotation(" ", description,
- ' ', value, new Color(minR + (maxR * vprop),
+ quality2.annotations[i] = new Annotation(" ", description, ' ',
+ value, new Color(minR + (maxR * vprop),
minG + (maxG * vprop), minB + (maxB * vprop)));
}
}
/*
* first find seq's xrefs (dna-to-peptide or peptide-to-dna)
*/
- List<DBRefEntry> rfs = DBRefUtils.selectDbRefs(!fromDna, seq.getDBRefs());
+ List<DBRefEntry> rfs = DBRefUtils.selectDbRefs(!fromDna,
+ seq.getDBRefs());
addXrefsToSources(rfs, sources);
if (dataset != null)
{
/*
* find sequence's direct (dna-to-dna, peptide-to-peptide) xrefs
*/
- List<DBRefEntry> lrfs = DBRefUtils.selectDbRefs(fromDna, seq.getDBRefs());
+ List<DBRefEntry> lrfs = DBRefUtils.selectDbRefs(fromDna,
+ seq.getDBRefs());
List<SequenceI> foundSeqs = new ArrayList<>();
/*
{
// do a bit more work - search for sequences with references matching
// xrefs on this sequence.
- found = searchDataset(fromDna, dss, xref, rseqs, cf, false, DBRefUtils.SEARCH_MODE_FULL);
+ found = searchDataset(fromDna, dss, xref, rseqs, cf, false,
+ DBRefUtils.SEARCH_MODE_FULL);
}
if (found)
{
addedXref |= importCrossRefSeq(cf, newDsSeqs, doNotAdd, dss,
retrievedDss);
}
- // JBPNote: What assumptions are made for dbref structures on
+ // JBPNote: What assumptions are made for dbref structures on
// retrieved sequences ?
- // addedXref will be true means importCrossRefSeq found
- // sequences with dbrefs with mappings to sequences congruent with dss
+ // addedXref will be true means importCrossRefSeq found
+ // sequences with dbrefs with mappings to sequences congruent with dss
if (!addedXref)
{
// protein
if (sq.isProtein() == fromDna)
{
- List<DBRefEntry> sqdbrefs = sq.getPrimaryDBRefs();
+ List<DBRefEntry> sqdbrefs = sq.getPrimaryDBRefs();
for (int idb = 0, ndb = sqdbrefs.size(); idb < ndb; idb++)
{
- DBRefEntry dbr = sqdbrefs.get(idb);
- List<DBRefEntry> searchrefs = DBRefUtils.searchRefs(dbrSourceSet, dbr, DBRefUtils.SEARCH_MODE_FULL);
+ DBRefEntry dbr = sqdbrefs.get(idb);
+ List<DBRefEntry> searchrefs = DBRefUtils.searchRefs(dbrSourceSet,
+ dbr, DBRefUtils.SEARCH_MODE_FULL);
for (int isr = 0, nsr = searchrefs.size(); isr < nsr; isr++)
{
sourceRefs.remove(searchrefs.get(isr));
/**
* Returns null or the first sequence in the dataset which is identical to
* xref.mapTo, and has a) a primary dbref matching xref, or if none found, the
- * first one with an ID source|xrefacc
- * JBPNote: Could refactor this to AlignmentI/DatasetI
+ * first one with an ID source|xrefacc JBPNote: Could refactor this to
+ * AlignmentI/DatasetI
+ *
* @param xref
* with map and mapped-to sequence
* @return
for (SequenceI seq : dataset.getSequences())
{
// first check primary refs.
- List<DBRefEntry> match = DBRefUtils.searchRefs(
- seq.getPrimaryDBRefs(), template, DBRefUtils.SEARCH_MODE_FULL);
+ List<DBRefEntry> match = DBRefUtils.searchRefs(seq.getPrimaryDBRefs(),
+ template, DBRefUtils.SEARCH_MODE_FULL);
if (match != null && match.size() == 1 && sameSequence(seq, dss))
{
return seq;
/**
* Updates any empty mappings in the cross-references with one to a compatible
* retrieved sequence if found, and adds any new mappings to the
- * AlignedCodonFrame
- * JBPNote: TODO: this relies on sequence IDs like UNIPROT|ACCESSION - which do not always happen.
+ * AlignedCodonFrame JBPNote: TODO: this relies on sequence IDs like
+ * UNIPROT|ACCESSION - which do not always happen.
+ *
* @param mapFrom
* @param xrefs
* @param retrieved
}
for (int i = 0, n = lrfs.size(); i < n; i++)
{
-// DBRefEntry xref = new DBRefEntry(lrfs.get(i));
-// // add in wildcards
-// xref.setVersion(null);
-// xref.setMap(null);
+ // DBRefEntry xref = new DBRefEntry(lrfs.get(i));
+ // // add in wildcards
+ // xref.setVersion(null);
+ // xref.setMap(null);
found |= searchDataset(fromDna, sequenceI, lrfs.get(i), foundSeqs, cf,
false, DBRefUtils.SEARCH_MODE_NO_MAP_NO_VERSION);
}
* sequenceI or all the returned sequences (eg a genomic reference
* associated with a locus and one or more transcripts)</li>
* </ul>
- * @param mode SEARCH_MODE_FULL for all; SEARCH_MODE_NO_MAP_NO_VERSION optional
+ * @param mode
+ * SEARCH_MODE_FULL for all; SEARCH_MODE_NO_MAP_NO_VERSION optional
* @return true if relationship found and sequence added.
*/
boolean searchDataset(boolean fromDna, SequenceI fromSeq, DBRefEntry xrf,
* @param ac2
* @return
*/
- public static final int compareCodonPos(AlignedCodon ac1, AlignedCodon ac2)
+ public static final int compareCodonPos(AlignedCodon ac1,
+ AlignedCodon ac2)
{
return comparator.compare(ac1, ac2);
// return jalview_2_8_2compare(ac1, ac2);
mappedrefs.add(ref); // add translated protein maps
}
}
- dnarefs = mappedrefs;//.toArray(new DBRefEntry[mappedrefs.size()]);
+ dnarefs = mappedrefs;// .toArray(new DBRefEntry[mappedrefs.size()]);
for (int d = 0, nd = dnarefs.size(); d < nd; d++)
{
Mapping mp = dnarefs.get(d).getMap();
/*
* Filled up a reading frame...
*/
- AlignedCodon alignedCodon = new AlignedCodon(cdp[0], cdp[1], cdp[2]);
+ AlignedCodon alignedCodon = new AlignedCodon(cdp[0], cdp[1],
+ cdp[2]);
String aa = codeTable.translate(new String(codon));
rf = 0;
final String gapString = String.valueOf(gapChar);
private static void transferCodedFeatures(SequenceI dna, SequenceI pep,
MapList map)
{
- // BH 2019.01.25 nop?
-// List<DBRefEntry> dnarefs = DBRefUtils.selectRefs(dna.getDBRefs(),
-// DBRefSource.DNACODINGDBS);
-// if (dnarefs != null)
-// {
-// // intersect with pep
-// for (int d = 0, nd = dnarefs.size(); d < nd; d++)
-// {
-// Mapping mp = dnarefs.get(d).getMap();
-// if (mp != null)
-// {
-// }
-// }
-// }
+ // BH 2019.01.25 nop?
+ // List<DBRefEntry> dnarefs = DBRefUtils.selectRefs(dna.getDBRefs(),
+ // DBRefSource.DNACODINGDBS);
+ // if (dnarefs != null)
+ // {
+ // // intersect with pep
+ // for (int d = 0, nd = dnarefs.size(); d < nd; d++)
+ // {
+ // Mapping mp = dnarefs.get(d).getMap();
+ // if (mp != null)
+ // {
+ // }
+ // }
+ // }
for (SequenceFeature sf : dna.getFeatures().getAllFeatures())
{
- if (FeatureProperties.isCodingFeature(null, sf.getType()))
+ if (FeatureProperties.isCodingFeature(null, sf.getType()))
+ {
+ // if (map.intersectsFrom(sf[f].begin, sf[f].end))
{
- // if (map.intersectsFrom(sf[f].begin, sf[f].end))
- {
- }
}
+ }
}
}
{
doFind(theSearchString, matchCase, searchDescription, false,
ignoreHidden);
-
+
if (searchResults.isEmpty() && idMatches.isEmpty())
{
/*
}
/**
- * Calculates and saves the sequence string to search. The string is restricted
- * to the current selection region if there is one, and is saved with all gaps
- * removed.
+ * Calculates and saves the sequence string to search. The string is
+ * restricted to the current selection region if there is one, and is saved
+ * with all gaps removed.
* <p>
* If there are hidden columns, and option {@ignoreHidden} is selected, then
* only visible positions of the sequence are included, and a mapping is also
}
/**
- * Returns a string consisting of only the visible residues of {@code seq} from
- * alignment column {@ fromColumn}, restricted to the current selection region
- * if there is one.
+ * Returns a string consisting of only the visible residues of {@code seq}
+ * from alignment column {@ fromColumn}, restricted to the current selection
+ * region if there is one.
* <p>
- * As a side-effect, also computes the mapping from the true sequence positions
- * to the positions (1, 2, ...) of the returned sequence. This is to allow
- * search matches in the visible sequence to be converted to sequence positions.
+ * As a side-effect, also computes the mapping from the true sequence
+ * positions to the positions (1, 2, ...) of the returned sequence. This is to
+ * allow search matches in the visible sequence to be converted to sequence
+ * positions.
*
* @param seq
* @return
/**
* Advances the search to the next sequence in the alignment. Sequences not in
- * the current selection group (if there is one) are skipped. The (sub-)sequence
- * to be searched is extracted, gaps removed, and saved, or set to null if there
- * are no more sequences to search.
+ * the current selection group (if there is one) are skipped. The
+ * (sub-)sequence to be searched is extracted, gaps removed, and saved, or set
+ * to null if there are no more sequences to search.
* <p>
* Returns true if a sequence could be found, false if end of alignment was
* reached
* @param ignoreHidden
* @return
*/
- protected boolean findNextMatch(String searchString,
- Regex searchPattern, boolean matchDescription,
- boolean ignoreHidden)
+ protected boolean findNextMatch(String searchString, Regex searchPattern,
+ boolean matchDescription, boolean ignoreHidden)
{
if (residueIndex < 0)
{
* at start of sequence; try find by residue number, in sequence id,
* or (optionally) in sequence description
*/
- if (doNonMotifSearches(searchString, searchPattern,
- matchDescription))
+ if (doNonMotifSearches(searchString, searchPattern, matchDescription))
{
return true;
}
*/
int offset = searchPattern.matchedFrom();
int matchStartPosition = this.searchedSequenceStartPosition + offset;
- int matchEndPosition = matchStartPosition
- + searchPattern.charsMatched() - 1;
+ int matchEndPosition = matchStartPosition + searchPattern.charsMatched()
+ - 1;
/*
* update residueIndex to next position after the start of the match
* (findIndex returns a value base 1, columnIndex is held base 0)
*/
- residueIndex = searchPattern.matchedFrom()+1;
+ residueIndex = searchPattern.matchedFrom() + 1;
/*
* return false if the match is entirely in a hidden region
}
/**
- * Adds one match to the stored list. If hidden residues are being skipped, then
- * the match may need to be split into contiguous positions of the sequence (so
- * it does not include skipped residues).
+ * Adds one match to the stored list. If hidden residues are being skipped,
+ * then the match may need to be split into contiguous positions of the
+ * sequence (so it does not include skipped residues).
*
* @param seq
* @param matchStartPosition
* @param searchPattern
* @return
*/
- protected boolean searchSequenceDescription(SequenceI seq, Regex searchPattern)
+ protected boolean searchSequenceDescription(SequenceI seq,
+ Regex searchPattern)
{
String desc = seq.getDescription();
- if (desc != null && searchPattern.search(desc) && !idMatches.contains(seq))
+ if (desc != null && searchPattern.search(desc)
+ && !idMatches.contains(seq))
{
idMatches.add(seq);
return true;
/**
* If the residue position is valid for the sequence, and in a visible column,
- * adds the position to the search results and returns true, else answers false.
+ * adds the position to the search results and returns true, else answers
+ * false.
*
* @param seq
* @param resNo
return true;
}
int col = seq.findIndex(res); // base 1
- return viewport.getAlignment().getHiddenColumns().isVisible(col - 1); // base 0
+ return viewport.getAlignment().getHiddenColumns().isVisible(col - 1); // base
+ // 0
}
@Override
}
} catch (IOException | NullPointerException e)
{
- Console.error(
- "Error reading genetic codes data file " + fileName + ": "
- + e.getMessage());
+ Console.error("Error reading genetic codes data file " + fileName
+ + ": " + e.getMessage());
}
if (codeTables.isEmpty())
{
String[] tokens = line.split("\\t");
if (tokens.length == 2)
{
- ambiguityCodes.put(tokens[0].toUpperCase(Locale.ROOT),
- tokens[1].toUpperCase(Locale.ROOT));
+ ambiguityCodes.put(tokens[0].toUpperCase(Locale.ROOT),
+ tokens[1].toUpperCase(Locale.ROOT));
}
else
{
}
} catch (IOException e)
{
- Console.error(
- "Error reading nucleotide ambiguity codes data file: "
- + e.getMessage());
+ Console.error("Error reading nucleotide ambiguity codes data file: "
+ + e.getMessage());
}
}
* @param sm
* @param options
*/
- public PCA(AlignmentView sequences, ScoreModelI sm, SimilarityParamsI options)
+ public PCA(AlignmentView sequences, ScoreModelI sm,
+ SimilarityParamsI options)
{
this.seqs = sequences;
this.scoreModel = sm;
sb.append("PCA calculation using ").append(scoreModel.getName())
.append(" sequence similarity matrix\n========\n\n");
PrintStream ps = wrapOutputBuffer(sb);
-
+
/*
* pairwise similarity scores
*/
sb.append(" --- OrigT * Orig ---- \n");
pairwiseScores.print(ps, "%8.2f");
-
+
/*
* tridiagonal matrix, with D and E vectors
*/
sb.append("--- E vector ---\n");
tridiagonal.printE(ps, "%15.4e");
ps.println();
-
+
/*
* eigenvalues matrix, with D vector
*/
sb.append(" --- Eigenvalues ---\n");
eigenMatrix.printD(ps, "%15.4e");
ps.println();
-
+
return sb.toString();
}
return pairs;
}
-
-
-
-
/**
* Function to get the end position corresponding to a given start position
*
dbseq = dbseq.getDatasetSequence();
}
// add in any interesting identifiers
- List<DBRefEntry> dbr = dbseq.getDBRefs();
+ List<DBRefEntry> dbr = dbseq.getDBRefs();
if (dbr != null)
{
SeqIdName sid = null;
* position is not a gap
*/
Set<String> types = new HashSet<>();
- List<SequenceFeature> sfs = fr.findFeaturesAtResidue(
- seq.getRefSeq(), spos, spos);
+ List<SequenceFeature> sfs = fr
+ .findFeaturesAtResidue(seq.getRefSeq(), spos, spos);
for (SequenceFeature sf : sfs)
{
types.add(sf.getType());
* regions of the alignment
*
* @param selectedRegionOnly
- * if true, and the view has a selection region,
- * then only the intersection of visible columns
- * with the selection region is returned
+ * if true, and the view has a selection region, then only the
+ * intersection of visible columns with the selection region is
+ * returned
* @return
*/
Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly);
boolean isOutwithThreshold(SequenceFeature sf);
/**
- * Answers a human-readable text description of the colour, suitable for display
- * as a tooltip, possibly internationalised for the user's locale.
+ * Answers a human-readable text description of the colour, suitable for
+ * display as a tooltip, possibly internationalised for the user's locale.
*
* @return
*/
/**
* Returns visible features at the specified aligned column on the given
- * sequence. Non-positional features are not included. If the column has a gap,
- * then enclosing features are included (but not contact features).
+ * sequence. Non-positional features are not included. If the column has a
+ * gap, then enclosing features are included (but not contact features).
*
* @param sequence
* @param column
* aligned column position (1..)
* @return
*/
- List<SequenceFeature> findFeaturesAtColumn(SequenceI sequence, int column);
+ List<SequenceFeature> findFeaturesAtColumn(SequenceI sequence,
+ int column);
/**
* Returns features at the specified residue positions on the given sequence.
/**
* Answers a bean containing a mapping, and a list of visible features in this
- * alignment at a position (or range) which is mappable from the given sequence
- * residue position in a mapped alignment. Features are returned in render order
- * of feature type (on top last), with order within feature type undefined. If
- * no features or mapping are found, answers null.
+ * alignment at a position (or range) which is mappable from the given
+ * sequence residue position in a mapped alignment. Features are returned in
+ * render order of feature type (on top last), with order within feature type
+ * undefined. If no features or mapping are found, answers null.
*
* @param sequence
* @param pos
* @return
*/
- MappedFeatures findComplementFeaturesAtResidue(SequenceI sequence, int pos);
+ MappedFeatures findComplementFeaturesAtResidue(SequenceI sequence,
+ int pos);
/**
* Sends a message to let any registered parties know that something about
/**
* Performs a find for the given search string (interpreted as a regular
* expression). Search may optionally be case-sensitive, and may optionally
- * including match in sequence description (sequence id is always searched). If
- * the viewport has an active selection, then the find is restricted to the
- * selection region. Sequences matched by id or description can be retrieved by
- * getIdMatches(), and matched residue patterns by getSearchResults().
+ * including match in sequence description (sequence id is always searched).
+ * If the viewport has an active selection, then the find is restricted to the
+ * selection region. Sequences matched by id or description can be retrieved
+ * by getIdMatches(), and matched residue patterns by getSearchResults().
* <p>
* If {@code ignoreHidden} is true, then any residues in hidden columns are
* ignored (skipped) when matching, so for example pattern {@code KRT} would
* Finds the next match for the given search string (interpreted as a regular
* expression), starting from the position after the last match found. Search
* may optionally be case-sensitive, and may optionally including match in
- * sequence description (sequence id is always searched). If the viewport has an
- * active selection, then the find is restricted to the selection region.
+ * sequence description (sequence id is always searched). If the viewport has
+ * an active selection, then the find is restricted to the selection region.
* Sequences matched by id or description can be retrieved by getIdMatches(),
* and matched residue patterns by getSearchResults().
* <p>
- * If {@code ignoreHidden} is true, any hidden residues are skipped (matches may
- * span them). If false, they are included for matching purposes. In either
- * cases, entirely hidden matches are not returned.
+ * If {@code ignoreHidden} is true, any hidden residues are skipped (matches
+ * may span them). If false, they are included for matching purposes. In
+ * either cases, entirely hidden matches are not returned.
*
* @param theSearchString
* @param caseSensitive
* get the 'other' alignFrame in the SplitFrame
*
* @param alignFrame
- * @return the complement alignFrame - or null if alignFrame wasn't held by this
- * frame
+ * @return the complement alignFrame - or null if alignFrame wasn't held by
+ * this frame
*/
AlignViewControllerGuiI getComplementAlignFrame(
AlignViewControllerGuiI alignFrame);
* @param featureSettings
* @return
*/
- void addFeatureSettingsUI(
- FeatureSettingsControllerGuiI featureSettings);
+ void addFeatureSettingsUI(FeatureSettingsControllerGuiI featureSettings);
/**
* Request to close all feature settings originating from a particular panel.
*
* @param featureSettings
* @param closeContainingFrame
- * - if false then the tab containing the feature
- * settings will be 'reset' ready for a new
- * feature settings
+ * - if false then the tab containing the feature settings will be
+ * 'reset' ready for a new feature settings
*/
void closeFeatureSettings(FeatureSettingsControllerI featureSettings,
boolean closeContainingFrame);
if (start <= end)
{
seqs.add(sg.getSequenceAt(i));
- features.add(new SequenceFeature(null, null, start, end,
- "Jalview"));
+ features.add(
+ new SequenceFeature(null, null, start, end, "Jalview"));
}
}
}
else
{
- new mc_view.AppletPDBViewer(entry, new SequenceI[] { seq }, null, ap,
- DataSourceType.URL);
+ new mc_view.AppletPDBViewer(entry, new SequenceI[] { seq }, null,
+ ap, DataSourceType.URL);
}
}
hydrophobicityColour
.setName(JalviewColourScheme.Hydrophobic.toString());
hydrophobicityColour.addItemListener(this);
- helixColour.setLabel(MessageManager
- .getString("label.colourScheme_helixpropensity"));
+ helixColour.setLabel(
+ MessageManager.getString("label.colourScheme_helixpropensity"));
helixColour.setName(JalviewColourScheme.Helix.toString());
helixColour.addItemListener(this);
strandColour.setLabel(MessageManager
case KeyEvent.VK_F2:
viewport.cursorMode = !viewport.cursorMode;
- setStatus(MessageManager
- .formatMessage("label.keyboard_editing_mode", new String[]
+ setStatus(MessageManager.formatMessage("label.keyboard_editing_mode",
+ new String[]
{ (viewport.cursorMode ? "on" : "off") }));
if (viewport.cursorMode)
{
}
else
{
- features = formatter.printGffFormat(viewport.getAlignment()
- .getSequencesArray(), alignPanel.getFeatureRenderer(), true,
- false);
+ features = formatter.printGffFormat(
+ viewport.getAlignment().getSequencesArray(),
+ alignPanel.getFeatureRenderer(), true, false);
}
if (displayTextbox)
catch (java.net.MalformedURLException ex)
{
url = viewport.applet.getCodeBase() + url;
- }
- catch (UnsupportedEncodingException ex)
+ } catch (UnsupportedEncodingException ex)
{
System.err.println(
"WARNING = IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "
column, al);
}
- setStatus(MessageManager
- .formatMessage("label.removed_columns", new String[]
+ setStatus(MessageManager.formatMessage("label.removed_columns",
+ new String[]
{ Integer.valueOf(trimRegion.getSize()).toString() }));
addHistoryItem(trimRegion);
addHistoryItem(removeGapCols);
- setStatus(MessageManager
- .formatMessage("label.removed_empty_columns", new String[]
+ setStatus(MessageManager.formatMessage("label.removed_empty_columns",
+ new String[]
{ Integer.valueOf(removeGapCols.getSize()).toString() }));
// This is to maintain viewport position on first residue
hydrophobicityColour.setLabel(
MessageManager.getString("label.colourScheme_hydrophobic"));
hydrophobicityColour.addActionListener(this);
- helixColour.setLabel(MessageManager
- .getString("label.colourScheme_helixpropensity"));
+ helixColour.setLabel(
+ MessageManager.getString("label.colourScheme_helixpropensity"));
helixColour.addActionListener(this);
strandColour.setLabel(MessageManager
.getString("label.colourScheme_strandpropensity"));
{
// register the association(s) and quit, don't create any windows.
if (StructureSelectionManager.getStructureSelectionManager(applet)
- .setMapping(seqs, chains, pdb.getFile(), protocol, null) == null)
+ .setMapping(seqs, chains, pdb.getFile(), protocol,
+ null) == null)
{
System.err.println("Failed to map " + pdb.getFile() + " ("
+ protocol + ") to any sequences");
if (colour != null)
{
- residueShading = new ResidueShader(
- ColourSchemeProperty.getColourScheme(this, alignment,
- colour));
+ residueShading = new ResidueShader(ColourSchemeProperty
+ .getColourScheme(this, alignment, colour));
if (residueShading != null)
{
residueShading.setConsensus(hconsensus);
}
/**
- * Applies the supplied feature settings descriptor to currently known features.
- * This supports an 'initial configuration' of feature colouring based on a
- * preset or user favourite. This may then be modified in the usual way using
- * the Feature Settings dialogue. NOT IMPLEMENTED FOR APPLET
+ * Applies the supplied feature settings descriptor to currently known
+ * features. This supports an 'initial configuration' of feature colouring
+ * based on a preset or user favourite. This may then be modified in the usual
+ * way using the Feature Settings dialogue. NOT IMPLEMENTED FOR APPLET
*
* @param featureSettings
*/
}
/**
- * Merges the supplied feature settings descriptor with existing feature styles.
- * This supports an 'initial configuration' of feature colouring based on a
- * preset or user favourite. This may then be modified in the usual way using
- * the Feature Settings dialogue. NOT IMPLEMENTED FOR APPLET
+ * Merges the supplied feature settings descriptor with existing feature
+ * styles. This supports an 'initial configuration' of feature colouring based
+ * on a preset or user favourite. This may then be modified in the usual way
+ * using the Feature Settings dialogue. NOT IMPLEMENTED FOR APPLET
*
* @param featureSettings
*/
public boolean scrollTo(int ostart, int end, int seqIndex,
boolean scrollToNearest, boolean redrawOverview)
{
- int startv, endv, starts, ends;//, width;
+ int startv, endv, starts, ends;// , width;
int start = -1;
if (av.hasHiddenColumns())
public static int GRAPH_HEIGHT = 40;
-// boolean MAC = false;
+ // boolean MAC = false;
public final AnnotationRenderer renderer;
public AnnotationPanel(AlignmentPanel ap)
{
new jalview.util.Platform();
-// MAC = Platform.isAMac();
+ // MAC = Platform.isAMac();
this.ap = ap;
av = ap.av;
setLayout(null);
AlignmentPanel ap;
List<AlignmentPanel> _aps = new ArrayList<>(); // remove? never
- // added to
+ // added to
String fileLoadingError;
slider.addAdjustmentListener(this);
slider.addMouseListener(this);
owner = (af != null) ? af : fs.frame;
- frame = new JVDialog(owner, MessageManager.formatMessage(
- "label.variable_color_for", new String[] { type }), true, 480,
- 248);
+ frame = new JVDialog(owner, MessageManager
+ .formatMessage("label.variable_color_for", new String[]
+ { type }), true, 480, 248);
frame.setMainPanel(this);
validate();
frame.setVisible(true);
newEnd = Integer.parseInt(end.getText());
} catch (NumberFormatException ex)
{
- //
+ //
}
/*
ffile.parseDescriptionHTML(newSf, false);
// amend features dialog only updates one sequence at a time
sequences.get(0).addSequenceFeature(newSf);
- boolean typeOrGroupChanged = (!featureType.equals(newSf.getType()) || !featureGroup
- .equals(newSf.getFeatureGroup()));
+ boolean typeOrGroupChanged = (!featureType.equals(newSf.getType())
+ || !featureGroup.equals(newSf.getFeatureGroup()));
ffile.parseDescriptionHTML(sf, false);
if (typeOrGroupChanged)
{
if (doFindAll)
{
- String message = (idMatches.size() > 0) ? "" + idMatches.size() + " IDs"
+ String message = (idMatches.size() > 0)
+ ? "" + idMatches.size() + " IDs"
: "";
if (idMatches.size() > 0 && searchResults != null
&& searchResults.getCount() > 0)
}
else
{
- this.getParent()
- .setCursor(
- Cursor.getPredefinedCursor(Cursor.CROSSHAIR_CURSOR));
+ this.getParent().setCursor(
+ Cursor.getPredefinedCursor(Cursor.CROSSHAIR_CURSOR));
}
}
// (wait to see if it's a drag instead)
// otherwise update the viewport
if (!od.isPositionInBox(evt.getX(), evt.getY()))
- {
- draggingBox = false;
+ {
+ draggingBox = false;
// display drag cursor at mouse position
setCursor(Cursor.getPredefinedCursor(Cursor.MOVE_CURSOR));
@Override
public void mouseDragged(MouseEvent evt)
{
- if (Platform.isWinRightButton(evt))
+ if (Platform.isWinRightButton(evt))
{
- showPopupMenu(evt);
- return;
+ showPopupMenu(evt);
+ return;
}
if (SwingUtilities.isRightMouseButton(evt))
- {
- return;
+ {
+ return;
+ }
+
+ if (draggingBox)
+ {
+ // set the mouse position as a fixed point in the box
+ // and drag relative to that position
+ od.adjustViewportFromMouse(evt.getX(), evt.getY(),
+ av.getAlignment().getHiddenSequences(),
+ av.getAlignment().getHiddenColumns());
+ }
+ else
+ {
+ od.updateViewportFromMouse(evt.getX(), evt.getY(),
+ av.getAlignment().getHiddenSequences(),
+ av.getAlignment().getHiddenColumns());
}
-
- if (draggingBox)
- {
- // set the mouse position as a fixed point in the box
- // and drag relative to that position
- od.adjustViewportFromMouse(evt.getX(), evt.getY(),
- av.getAlignment().getHiddenSequences(),
- av.getAlignment().getHiddenColumns());
- }
- else
- {
- od.updateViewportFromMouse(evt.getX(), evt.getY(),
- av.getAlignment().getHiddenSequences(),
- av.getAlignment().getHiddenColumns());
- }
- ap.paintAlignment(false, false);
+ ap.paintAlignment(false, false);
}
/**
for (int i = 0; i < 3; i++)
{
g.drawLine(getSize().width / 2, getSize().height / 2,
- (int) (axisEndPoints[i].x * scale * max[0] + getSize().width / 2),
- (int) (axisEndPoints[i].y * scale * max[1] + getSize().height / 2));
+ (int) (axisEndPoints[i].x * scale * max[0]
+ + getSize().width / 2),
+ (int) (axisEndPoints[i].y * scale * max[1]
+ + getSize().height / 2));
}
}
sequenceColour == Color.black ? Color.white : sequenceColour);
if (av.getSelectionGroup() != null)
{
- if (av.getSelectionGroup().getSequences(null)
- .contains(sequence))
+ if (av.getSelectionGroup().getSequences(null).contains(sequence))
{
g.setColor(Color.gray);
}
{
if (av != null)
{
- if (!av.getSelectionGroup().getSequences(null)
- .contains(sequence))
+ if (!av.getSelectionGroup().getSequences(null).contains(sequence))
{
av.getSelectionGroup().addSequence(sequence, true);
}
{
SequencePoint sp = points.get(i);
- int px = (int) ((sp.coord.x - centre.x) * scale)
- + halfwidth;
- int py = (int) ((sp.coord.y - centre.y) * scale)
- + halfheight;
+ int px = (int) ((sp.coord.x - centre.x) * scale) + halfwidth;
+ int py = (int) ((sp.coord.y - centre.y) * scale) + halfheight;
if (Math.abs(px - x) < 3 && Math.abs(py - y) < 3)
{
{
return;
}
-
+
/*
* get the identity transformation...
*/
RotatableMatrix rotmat = new RotatableMatrix();
-
+
/*
* rotate around the X axis for change in Y
* (mouse movement up/down); note we are equating a
{
rotmat.rotate(y, Axis.X);
}
-
+
/*
* rotate around the Y axis for change in X
* (mouse movement left/right)
{
rotmat.rotate(x, Axis.Y);
}
-
+
/*
* apply the composite transformation to sequence points
*/
// Now translate back again
sp.translate(centre.x, centre.y, centre.z);
}
-
+
/*
* rotate the x/y/z axis positions
*/
});
pop.add(item);
- if (av.getAlignment().getHiddenColumns().hasMultiHiddenColumnRegions())
+ if (av.getAlignment().getHiddenColumns()
+ .hasMultiHiddenColumnRegions())
{
item = new MenuItem(MessageManager.getString("action.reveal_all"));
item.addActionListener(new ActionListener()
gg.fillPolygon(
new int[]
- { -1 + res * avCharWidth - avcharHeight / 4, -1 + res * avCharWidth + avcharHeight / 4,
- -1 + res * avCharWidth }, new int[]
- { y, y, y + 2 * yOf }, 3);
+ { -1 + res * avCharWidth - avcharHeight / 4,
+ -1 + res * avCharWidth + avcharHeight / 4,
+ -1 + res * avCharWidth },
+ new int[]
+ { y, y, y + 2 * yOf }, 3);
}
}
}
int canvasHeight, int startRes)
{
AlignmentI al = av.getAlignment();
-
+
FontMetrics fm = getFontMetrics(av.getFont());
-
+
LABEL_EAST = 0;
LABEL_WEST = 0;
-
+
if (av.getScaleRightWrapped())
{
LABEL_EAST = fm.stringWidth(getMask());
}
-
+
if (av.getScaleLeftWrapped())
{
LABEL_WEST = fm.stringWidth(getMask());
}
-
+
int hgap = avcharHeight;
if (av.getScaleAboveWrapped())
{
hgap += avcharHeight;
}
-
+
int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / avcharWidth;
int cHeight = av.getAlignment().getHeight() * avcharHeight;
-
+
av.setWrappedWidth(cWidth);
-
+
av.getRanges().setViewportStartAndWidth(startRes, cWidth);
-
+
int endx;
int ypos = hgap;
-
+
int maxwidth = av.getAlignment().getVisibleWidth();
-
+
while ((ypos <= canvasHeight) && (startRes < maxwidth))
{
endx = startRes + cWidth - 1;
-
+
if (endx > maxwidth)
{
endx = maxwidth;
}
-
+
g.setColor(Color.black);
-
+
if (av.getScaleLeftWrapped())
{
drawWestScale(g, startRes, endx, ypos);
}
-
+
if (av.getScaleRightWrapped())
{
g.translate(canvasWidth - LABEL_EAST, 0);
drawEastScale(g, startRes, endx, ypos);
g.translate(-(canvasWidth - LABEL_EAST), 0);
}
-
+
g.translate(LABEL_WEST, 0);
-
+
if (av.getScaleAboveWrapped())
{
drawNorthScale(g, startRes, endx, ypos);
res = it.next() - startRes;
gg.fillPolygon(
new int[]
- { res * avcharWidth - avcharHeight / 4, res * avcharWidth + avcharHeight / 4, res * avcharWidth },
+ { res * avcharWidth - avcharHeight / 4,
+ res * avcharWidth + avcharHeight / 4,
+ res * avcharWidth },
new int[]
- { ypos - (avcharHeight / 2), ypos - (avcharHeight / 2), ypos - (avcharHeight / 2) + 8 }, 3);
+ { ypos - (avcharHeight / 2), ypos - (avcharHeight / 2),
+ ypos - (avcharHeight / 2) + 8 },
+ 3);
}
}
-
+
if (g.getClip() == null)
{
g.setClip(0, 0, cWidth * avcharWidth, canvasHeight);
}
-
+
drawPanel(g, startRes, endx, 0, al.getHeight() - 1, ypos);
g.setClip(null);
-
+
if (av.isShowAnnotation())
{
g.translate(0, cHeight + ypos + 4);
{
annotations = new AnnotationPanel(av);
}
-
+
annotations.drawComponent(g, startRes, endx + 1);
g.translate(0, -cHeight - ypos - 4);
}
g.translate(-LABEL_WEST, 0);
-
+
ypos += cHeight + getAnnotationHeight() + hgap;
-
+
startRes += cWidth;
}
-
+
}
AnnotationPanel annotations;
*/
List<SequenceFeature> findFeaturesAtColumn(SequenceI sequence, int column)
{
- return seqCanvas.getFeatureRenderer().findFeaturesAtColumn(sequence, column);
+ return seqCanvas.getFeatureRenderer().findFeaturesAtColumn(sequence,
+ column);
}
Tooltip tooltip;
{
if (sg.getSize() == av.getAlignment().getHeight())
{
- if ((av.hasHiddenColumns() && startres < av.getAlignment()
- .getHiddenColumns()
- .getNextHiddenBoundary(false, startres)))
+ if ((av.hasHiddenColumns()
+ && startres < av.getAlignment().getHiddenColumns()
+ .getNextHiddenBoundary(false, startres)))
{
endEditing();
return;
// TODO replace 8 or so code duplications with calls to this method
// (refactored as needed)
return resColourFinder.getResidueColour(av.getShowBoxes(),
- av.getResidueShading(),
- allGroups, seq, position, finder);
+ av.getResidueShading(), allGroups, seq, position, finder);
}
public Color findSequenceColour(SequenceI seq, int i)
if (currentSequenceGroup.getDisplayBoxes())
{
resBoxColour = resColourFinder.getBoxColour(
- currentSequenceGroup.getGroupColourScheme(), seq,
- i);
+ currentSequenceGroup.getGroupColourScheme(), seq, i);
}
}
else if (av.getShowBoxes())
return sequenceChar;
}
- public void drawHighlightedText(SequenceI seq, int start, int end,
- int x1, int y1)
+ public void drawHighlightedText(SequenceI seq, int start, int end, int x1,
+ int y1)
{
int avCharWidth = av.getCharWidth(), avCharHeight = av.getCharHeight();
int pady = avCharHeight / 5;
{
cs = ColourSchemeProperty.getColourScheme(av, sg,
ColourSchemeProperty
- .getColourName(av.getGlobalColourScheme()));
+ .getColourName(av.getGlobalColourScheme()));
}
// cs is null if shading is an annotationColourGradient
// if (cs != null)
if (jalview.jbgui.GDesktop.class.getClassLoader()
.loadClass("uk.ac.vamsas.client.VorbaId") != null)
{
- Console.debug("Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
+ Console.debug(
+ "Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
vamsasJarsArePresent = 1;
JLoggerLog4j lvclient = JLoggerLog4j.getLogger("uk.ac.vamsas",
Console.getCachedLogLevel("logs.Vamsas.Level"));
- JLoggerLog4j.addAppender(lvclient, Console.log, JALVIEW_LOGGER_NAME);
+ JLoggerLog4j.addAppender(lvclient, Console.log,
+ JALVIEW_LOGGER_NAME);
// Tell the user that debug is enabled
lvclient.debug(ChannelProperties.getProperty("app_name")
+ " Vamsas Client Debugging Output Follows.");
if (Cache.class.getClassLoader()
.loadClass("groovy.lang.GroovyObject") != null)
{
- Console.debug("Found Groovy (groovy.lang.GroovyObject can be loaded)");
+ Console.debug(
+ "Found Groovy (groovy.lang.GroovyObject can be loaded)");
groovyJarsArePresent = 1;
JLoggerLog4j lgclient = JLoggerLog4j.getLogger("groovy",
Console.getCachedLogLevel("logs.Groovy.Level"));
- JLoggerLog4j.addAppender(lgclient, Console.log, JALVIEW_LOGGER_NAME);
+ JLoggerLog4j.addAppender(lgclient, Console.log,
+ JALVIEW_LOGGER_NAME);
// Tell the user that debug is enabled
lgclient.debug(ChannelProperties.getProperty("app_name")
+ " Groovy Client Debugging Output Follows.");
.loadClass("com.boxysystems.jgoogleanalytics.FocusPoint");
} catch (Exception e)
{
- Console.debug("com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
+ Console.debug(
+ "com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
tracker = null;
jgoogleanalyticstracker = null;
trackerfocus = null;
{
if (re != null)
{
- Console.debug("Caught runtime exception in googletracker init:", re);
+ Console.debug("Caught runtime exception in googletracker init:",
+ re);
}
if (ex != null)
{
- Console.warn("Failed to initialise GoogleTracker for Jalview Desktop with version "
- + vrs, ex);
+ Console.warn(
+ "Failed to initialise GoogleTracker for Jalview Desktop with version "
+ + vrs,
+ ex);
}
if (err != null)
{
- Console.error("Whilst initing GoogleTracker for Jalview Desktop version "
- + vrs, err);
+ Console.error(
+ "Whilst initing GoogleTracker for Jalview Desktop version "
+ + vrs,
+ err);
}
}
else
Color col = ColorUtils.parseColourString(colprop);
if (col == null)
{
- Console.warn("Couldn't parse '" + colprop + "' as a colour for " + property);
+ Console.warn("Couldn't parse '" + colprop + "' as a colour for "
+ + property);
}
return (col == null) ? defcolour : col;
}
char[] displayHttpPw = new char[httpPassword == null ? 0
: httpPassword.length];
Arrays.fill(displayHttpPw, '*');
- Console.debug("CACHE Proxy: setting new Authenticator with httpUser='"
- + httpUser + "' httpPassword='" + displayHttpPw + "'");
+ Console.debug(
+ "CACHE Proxy: setting new Authenticator with httpUser='"
+ + httpUser + "' httpPassword='" + displayHttpPw
+ + "'");
if (!Platform.isJS())
/* *
* java.net.Authenticator not implemented in SwingJS yet
*
*/
{
- Console.debug("AUTHENTICATOR setting default Authenticator to null");
+ Console.debug(
+ "AUTHENTICATOR setting default Authenticator to null");
Authenticator.setDefault(null);
}
}
// nonProxyHosts not currently configurable in Preferences
- Console.debug("AUTHENTICATOR setting property 'http.nonProxyHosts' to \""
- + nonProxyHosts + "\"");
+ Console.debug(
+ "AUTHENTICATOR setting property 'http.nonProxyHosts' to \""
+ + nonProxyHosts + "\"");
setOrClearSystemProperty("http.nonProxyHosts", nonProxyHosts);
}
System.out.println(message);
t.printStackTrace();
}
-
+
}
public static void info(String message)
{
System.out.println(message);
}
-
+
}
public static void trace(String message, Throwable t)
{
System.out.println(message);
}
-
+
}
public static void info(String message, Throwable t)
System.out.println(message);
t.printStackTrace();
}
-
+
}
public static void warn(String message)
{
System.out.println(message);
}
-
+
}
public static void trace(String message)
System.out.println(message);
t.printStackTrace();
}
-
+
}
public static void error(String message)
{
System.err.println(message);
}
-
+
}
public static void error(String message, Throwable t)
System.err.println(message);
t.printStackTrace(System.err);
}
-
+
}
public static void fatal(String message)
{
System.err.println(message);
}
-
+
}
public static void fatal(String message, Throwable t)
System.err.println(message);
t.printStackTrace(System.err);
}
-
+
}
public static boolean isDebugEnabled()
// is laxis used? Does getLogger do anything without a Logger object?
// Logger laxis = Log4j.getLogger("org.apache.axis", myLevel);
JLoggerLog4j.getLogger("org.apache.axis", cachedLevel);
-
+
// The main application logger
log = JLoggerLog4j.getLogger(Cache.JALVIEW_LOGGER_NAME, cachedLevel);
} catch (NoClassDefFoundError e)
System.err.println("Could not initialise the logger framework");
e.printStackTrace();
}
-
+
// Test message
if (log != null)
{
int dimensionScale = 1 + (mindimension / bigScreenThreshold);
// reject outrageous values -- dpiScale in particular could be mistaken
- if (dpiScale > MAX_SCALE) {
+ if (dpiScale > MAX_SCALE)
+ {
dpiScale = 1;
}
- if (dimensionScale > MAX_SCALE) {
+ if (dimensionScale > MAX_SCALE)
+ {
dimensionScale = 1;
}
import javax.swing.Timer;
/**
- * Entry point for JalviewJS development.
+ * Entry point for JalviewJS development.
*
*
*
public class JalviewJS2
{
- static {
+ static
+ {
/**
* @j2sNative
*
public static void main(String[] args) throws Exception
{
Jalview.main(args);
- //showFocusTimer();
-}
+ // showFocusTimer();
+ }
-protected static int focusTime = 0;
+ protected static int focusTime = 0;
private static void showFocusTimer()
{
}
}
-
}
final StructureSelectionManagerProvider me = this;
final int pos = apos;
// use vamsas listener to broadcast to all listeners in scope
- if (alignedPosition != null && (alignedPosition.trim().length() == 0
- || alignedPosition.toLowerCase(Locale.ROOT).indexOf("false") > -1))
+ if (alignedPosition != null
+ && (alignedPosition.trim().length() == 0 || alignedPosition
+ .toLowerCase(Locale.ROOT).indexOf("false") > -1))
{
java.awt.EventQueue.invokeLater(new Runnable()
{
String externalsviewer = getParameter("externalstructureviewer");
if (externalsviewer != null)
{
- useXtrnalSviewer = externalsviewer.trim().toLowerCase(Locale.ROOT).equals(TRUE);
+ useXtrnalSviewer = externalsviewer.trim().toLowerCase(Locale.ROOT)
+ .equals(TRUE);
}
/**
* if true disable the check for jmol
if ((caseChange == TO_UPPER && doCommand)
|| (caseChange == TO_LOWER && !doCommand))
{
- newSeq.append(sequence.substring(start, end).toUpperCase(Locale.ROOT));
+ newSeq.append(
+ sequence.substring(start, end).toUpperCase(Locale.ROOT));
}
else if ((caseChange == TO_LOWER && doCommand)
|| (caseChange == TO_UPPER && !doCommand))
{
- newSeq.append(sequence.substring(start, end).toLowerCase(Locale.ROOT));
+ newSeq.append(
+ sequence.substring(start, end).toLowerCase(Locale.ROOT));
}
else
return null;
}
};
+
public abstract Action getUndoAction();
};
ContiguousI cutPositions = sequence.findPositions(
command.position + 1, command.position + command.number);
boolean cutIsInternal = cutPositions != null
- && sequence.getStart() != cutPositions
- .getBegin() && sequence.getEnd() != cutPositions.getEnd();
+ && sequence.getStart() != cutPositions.getBegin()
+ && sequence.getEnd() != cutPositions.getEnd();
/*
* perform the cut; if this results in a new dataset sequence, add
* that to the alignment dataset
*/
SequenceI ds = sequence.getDatasetSequence();
- sequence.deleteChars(command.position, command.position
- + command.number);
+ sequence.deleteChars(command.position,
+ command.position + command.number);
if (command.oldds != null && command.oldds[i] != null)
{
command.oldds[i] = oldds;// todo not if !cutIsInternal?
// do we need to edit sequence features for new sequence ?
- if (oldds != sequence.getDatasetSequence()
- || (cutIsInternal
- && sequence.getFeatures().hasFeatures()))
+ if (oldds != sequence.getDatasetSequence() || (cutIsInternal
+ && sequence.getFeatures().hasFeatures()))
// todo or just test cutIsInternal && cutPositions != null ?
{
if (cutPositions != null)
{
cutFeatures(command, sequence, cutPositions.getBegin(),
- cutPositions.getEnd(), cutIsInternal);
+ cutPositions.getEnd(), cutIsInternal);
}
}
}
{
boolean newDSWasNeeded = command.oldds != null
&& command.oldds[i] != null;
- boolean newStartEndWasNeeded = command.oldStartEnd!=null && command.oldStartEnd[i]!=null;
+ boolean newStartEndWasNeeded = command.oldStartEnd != null
+ && command.oldStartEnd[i] != null;
/**
* cut addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT,
start);
ContiguousI afterEditedPositions = command.seqs[i]
.findPositions(end + 1, command.seqs[i].getLength());
-
+
oldstring = command.seqs[i].getSequenceAsString();
tmp = new StringBuilder(oldstring.substring(0, start));
tmp.append(command.string[i]);
String nogapold = AlignSeq.extractGaps(Comparison.GapChars,
new String(command.string[i]));
- if (!nogaprep.toLowerCase(Locale.ROOT).equals(nogapold.toLowerCase(Locale.ROOT)))
+ if (!nogaprep.toLowerCase(Locale.ROOT)
+ .equals(nogapold.toLowerCase(Locale.ROOT)))
{
// we may already have dataset and limits stashed...
if (newDSWasNeeded || newStartEndWasNeeded)
{
if (newDSWasNeeded)
{
- // then just switch the dataset sequence
- SequenceI oldds = command.seqs[i].getDatasetSequence();
- command.seqs[i].setDatasetSequence(command.oldds[i]);
- command.oldds[i] = oldds;
+ // then just switch the dataset sequence
+ SequenceI oldds = command.seqs[i].getDatasetSequence();
+ command.seqs[i].setDatasetSequence(command.oldds[i]);
+ command.oldds[i] = oldds;
}
if (newStartEndWasNeeded)
{
command.seqs[i].setEnd(newStart.getEnd());
}
}
- else
+ else
{
// decide if we need a new dataset sequence or modify start/end
// first edit the original dataset sequence string
? afterEditedPositions.getBegin() - 1
: oldstartend.getBegin()
+ nogapold.length())
- : beforeEditedPositions.getEnd()
- );
+ : beforeEditedPositions.getEnd());
int afterEndOfEdit = -oldds.getStart() + 1
- + ((afterEditedPositions == null)
- ? oldstartend.getEnd()
+ + ((afterEditedPositions == null) ? oldstartend.getEnd()
: afterEditedPositions.getBegin() - 1);
- String fullseq = osp.substring(0,
- beforeStartOfEdit)
- + nogaprep
+ String fullseq = osp.substring(0, beforeStartOfEdit) + nogaprep
+ osp.substring(afterEndOfEdit);
// and check if new sequence data is different..
&& afterEditedPositions == null)
{
// modification at end
- command.seqs[i].setEnd(
- beforeEditedPositions.getEnd() + nogaprep.length()
- - nogapold.length());
+ command.seqs[i].setEnd(beforeEditedPositions.getEnd()
+ + nogaprep.length() - nogapold.length());
}
else if (afterEditedPositions != null
&& beforeEditedPositions == null)
// new
// start/end
String nogapalseq = AlignSeq.extractGaps(Comparison.GapChars,
- command.seqs[i].getSequenceAsString().toUpperCase(Locale.ROOT));
+ command.seqs[i].getSequenceAsString()
+ .toUpperCase(Locale.ROOT));
int newStart = command.seqs[i].getDatasetSequence()
.getSequenceAsString().indexOf(nogapalseq);
if (newStart == -1)
}
// and then duplicate added annotation on every other alignment
// view
- for (int vnum = 0; views != null && vnum < views.length; vnum++)
+ for (int vnum = 0; views != null
+ && vnum < views.length; vnum++)
{
if (views[vnum] != command.al)
{
* feature was shifted left to cut position (not truncated),
* so shift it back right
*/
- SequenceFeature shifted = new SequenceFeature(sf, sf.getBegin()
- + length, sf.getEnd() + length, sf.getFeatureGroup(),
- sf.getScore());
+ SequenceFeature shifted = new SequenceFeature(sf,
+ sf.getBegin() + length, sf.getEnd() + length,
+ sf.getFeatureGroup(), sf.getScore());
seq.addSequenceFeature(shifted);
seq.deleteFeature(sf);
}
*/
private boolean systemGenerated;
- public Edit(Action cmd, SequenceI[] sqs, int pos, int count,
- char gap)
+ public Edit(Action cmd, SequenceI[] sqs, int pos, int count, char gap)
{
this.command = cmd;
this.seqs = sqs;
this.gapChar = gap;
}
- Edit(Action cmd, SequenceI[] sqs, int pos, int count,
- AlignmentI align)
+ Edit(Action cmd, SequenceI[] sqs, int pos, int count, AlignmentI align)
{
this(cmd, sqs, pos, count, align.getGapCharacter());
* @param align
* @param replace
*/
- Edit(Action cmd, SequenceI[] sqs, int pos, int count,
- AlignmentI align, String replace)
+ Edit(Action cmd, SequenceI[] sqs, int pos, int count, AlignmentI align,
+ String replace)
{
this(cmd, sqs, pos, count, align);
}
List<SequenceFeature> added = new ArrayList<>();
List<SequenceFeature> removed = new ArrayList<>();
-
+
SequenceFeaturesI featureStore = seq.getFeatures();
if (toPosition < fromPosition || featureStore == null)
{
return;
}
-
+
int cutStartPos = fromPosition;
int cutEndPos = toPosition;
int cutWidth = cutEndPos - cutStartPos + 1;
-
+
synchronized (featureStore)
{
/*
* get features that overlap the cut region
*/
- List<SequenceFeature> toAmend = featureStore.findFeatures(
- cutStartPos, cutEndPos);
-
+ List<SequenceFeature> toAmend = featureStore.findFeatures(cutStartPos,
+ cutEndPos);
+
/*
* add any contact features that span the cut region
* (not returned by findFeatures)
int newEnd = sfEnd;
boolean toDelete = false;
boolean follows = false;
-
+
if (sfBegin >= cutStartPos && sfEnd <= cutEndPos)
{
/*
toDelete = true;
}
}
-
+
seq.deleteFeature(sf);
if (!follows)
{
}
}
}
-
+
/*
* and left shift any features lying to the right of the cut region
*/
BitSet bs = new BitSet();
boolean searchSelection = viewport.getSelectionGroup() != null
&& !extendCurrent;
- SequenceCollectionI sqcol = searchSelection ? viewport
- .getSelectionGroup() : viewport.getAlignment();
+ SequenceCollectionI sqcol = searchSelection
+ ? viewport.getSelectionGroup()
+ : viewport.getAlignment();
int nseq = findColumnsWithFeature(featureType, sqcol, bs);
{
String key = searchSelection ? "label.no_feature_found_selection"
: "label.no_feature_of_type_found";
- avcg.setStatus(MessageManager.formatMessage(key,
- new String[] { featureType }));
+ avcg.setStatus(
+ MessageManager.formatMessage(key, new String[]
+ { featureType }));
if (!extendCurrent)
{
cs.clear();
* @param bs
* @return
*/
- int findColumnsWithFeature(String featureType,
- SequenceCollectionI sqcol, BitSet bs)
+ int findColumnsWithFeature(String featureType, SequenceCollectionI sqcol,
+ BitSet bs)
{
- FeatureRenderer fr = alignPanel == null ? null : alignPanel
- .getFeatureRenderer();
+ FeatureRenderer fr = alignPanel == null ? null
+ : alignPanel.getFeatureRenderer();
final int startColumn = sqcol.getStartRes() + 1; // converted to base 1
final int endColumn = sqcol.getEndRes() + 1;
if (sq != null)
{
// int ist = sq.findPosition(sqcol.getStartRes());
- List<SequenceFeature> sfs = sq.findFeatures(startColumn,
- endColumn, featureType);
+ List<SequenceFeature> sfs = sq.findFeatures(startColumn, endColumn,
+ featureType);
boolean found = false;
for (SequenceFeature sf : sfs)
}
/**
- * Sorts the alignment (or current selection) by either average score or density
- * of the specified feature types, and adds to the command history. If
- * {@code types} is null, all visible feature types are used for the sort. If no
- * feature types apply, does nothing.
+ * Sorts the alignment (or current selection) by either average score or
+ * density of the specified feature types, and adds to the command history. If
+ * {@code types} is null, all visible feature types are used for the sort. If
+ * no feature types apply, does nothing.
*
* @param types
* @param methodText
- * - text shown in Undo/Redo command
+ * - text shown in Undo/Redo command
* @param method
- * - passed to
- * jalview.analysis.AlignmentSorter.sortByFeatures()
+ * - passed to jalview.analysis.AlignmentSorter.sortByFeatures()
*/
protected void sortByFeatures(List<String> types, String methodText,
final String method)
}
else
{
- avcg.setStatus(MessageManager.getString("label.no_highlighted_regions_marked"));
+ avcg.setStatus(MessageManager
+ .getString("label.no_highlighted_regions_marked"));
if (!extendCurrent)
{
cs.clear();
void featureSettings_isClosed();
/**
- * undo any changes made to feature settings whilst the dialog has been visible,
- * since the last 'apply'
+ * undo any changes made to feature settings whilst the dialog has been
+ * visible, since the last 'apply'
*/
void revert();
*/
public boolean covers(SequenceI seq)
{
- return covers(seq,false,false);
+ return covers(seq, false, false);
}
+
/**
*
* @param seq
- * @param localCover - when true - compare extent of seq's dataset sequence rather than the local extent
- * @param either - when true coverage is required for either seq or the mapped sequence
- * @return true if mapping covers full length of given sequence (or the other if either==true)
+ * @param localCover
+ * - when true - compare extent of seq's dataset sequence rather
+ * than the local extent
+ * @param either
+ * - when true coverage is required for either seq or the mapped
+ * sequence
+ * @return true if mapping covers full length of given sequence (or the
+ * other if either==true)
*/
- public boolean covers(SequenceI seq, boolean localCover,boolean either)
+ public boolean covers(SequenceI seq, boolean localCover, boolean either)
{
- List<int[]> mappedRanges = null,otherRanges=null;
+ List<int[]> mappedRanges = null, otherRanges = null;
MapList mapList = mapping.getMap();
- int mstart=seq.getStart(),mend=seq.getEnd(),ostart,oend;
- ;
+ int mstart = seq.getStart(), mend = seq.getEnd(), ostart, oend;
+ ;
if (fromSeq == seq || fromSeq == seq.getDatasetSequence())
{
- if (localCover && fromSeq !=seq)
+ if (localCover && fromSeq != seq)
{
- mstart=fromSeq.getStart();
- mend=fromSeq.getEnd();
+ mstart = fromSeq.getStart();
+ mend = fromSeq.getEnd();
}
mappedRanges = mapList.getFromRanges();
- otherRanges=mapList.getToRanges();
- ostart=mapping.to.getStart();
- oend=mapping.to.getEnd();
+ otherRanges = mapList.getToRanges();
+ ostart = mapping.to.getStart();
+ oend = mapping.to.getEnd();
}
else if (mapping.to == seq || mapping.to == seq.getDatasetSequence())
{
- if (localCover && mapping.to !=seq)
+ if (localCover && mapping.to != seq)
{
- mstart=mapping.to.getStart();
- mend=mapping.to.getEnd();
+ mstart = mapping.to.getStart();
+ mend = mapping.to.getEnd();
}
mappedRanges = mapList.getToRanges();
- otherRanges=mapList.getFromRanges();
- ostart=fromSeq.getStart();
- oend=fromSeq.getEnd();
+ otherRanges = mapList.getFromRanges();
+ ostart = fromSeq.getStart();
+ oend = fromSeq.getEnd();
}
else
{
* (necessary for circular CDS - example EMBL:J03321:AAA91567)
* and mapped length covers (at least) sequence length
*/
- int length = countRange(mappedRanges,mstart,mend);
+ int length = countRange(mappedRanges, mstart, mend);
if (length != -1)
{
}
return false;
}
- private int countRange(List<int[]> mappedRanges,int mstart,int mend)
+
+ private int countRange(List<int[]> mappedRanges, int mstart, int mend)
{
- int length=0;
+ int length = 0;
for (int[] range : mappedRanges)
{
int from = Math.min(range[0], range[1]);
/**
* Adds any regions mapped to or from position {@code pos} in sequence
- * {@code seq} to the given search results
- * Note: recommend first using the .covers(,true,true) to ensure mapping covers both sequences
+ * {@code seq} to the given search results Note: recommend first using the
+ * .covers(,true,true) to ensure mapping covers both sequences
+ *
* @param seq
* @param pos
* @param sr
{
ds = seq;
}
-
+
if (this.fromSeq == seq || this.fromSeq == ds)
{
codon = this.mapping.map.locateInTo(pos, pos);
}
for (SequenceToSequenceMapping ssm : mappings)
{
- if (ssm.covers(seq,true,true)) {
+ if (ssm.covers(seq, true, true))
+ {
ssm.markMappedRegion(ds, index, results);
}
}
{
synchronized (sequences)
{
-
+
if (i > -1 && i < sequences.size())
{
return sequences.get(i);
public int getWidth()
{
int maxLength = -1;
-
+
for (int i = 0; i < sequences.size(); i++)
{
maxLength = Math.max(maxLength, getSequenceAt(i).getLength());
return rnaSecondaryStructureEquivalent(that, true);
}
- public boolean rnaSecondaryStructureEquivalent(AlignmentAnnotation that, boolean compareType)
+ public boolean rnaSecondaryStructureEquivalent(AlignmentAnnotation that,
+ boolean compareType)
{
SequenceFeature[] thisSfArray = this.getRnaSecondaryStructure();
SequenceFeature[] thatSfArray = that.getRnaSecondaryStructure();
return false;
}
Arrays.sort(thisSfArray, new SFSortByEnd()); // probably already sorted
- // like this
+ // like this
Arrays.sort(thatSfArray, new SFSortByEnd()); // probably already sorted
- // like this
- for (int i=0; i < thisSfArray.length; i++) {
+ // like this
+ for (int i = 0; i < thisSfArray.length; i++)
+ {
SequenceFeature thisSf = thisSfArray[i];
SequenceFeature thatSf = thatSfArray[i];
- if (compareType) {
- if (thisSf.getType() == null || thatSf.getType() == null) {
- if (thisSf.getType() == null && thatSf.getType() == null) {
+ if (compareType)
+ {
+ if (thisSf.getType() == null || thatSf.getType() == null)
+ {
+ if (thisSf.getType() == null && thatSf.getType() == null)
+ {
continue;
- } else {
+ }
+ else
+ {
return false;
}
}
- if (! thisSf.getType().equals(thatSf.getType())) {
+ if (!thisSf.getType().equals(thatSf.getType()))
+ {
return false;
}
}
String source = "";
private String version = "";
-
+
private String ucversion;
private String accessionId = "";
-
+
int sourceKey = Integer.MIN_VALUE;
String canonicalSourceName;
-
- boolean isCanonicalAccession=false;
+
+ boolean isCanonicalAccession = false;
/*
* maps from associated sequence to the database sequence's coordinate system
/**
*
* @param source
- * may not be null
+ * may not be null
* @param version
- * may be null
+ * may be null
* @param accessionId
- * may be null
+ * may be null
*/
public DBRefEntry(String source, String version, String accessionId)
{
- this(source, version, accessionId, null,false);
+ this(source, version, accessionId, null, false);
}
/**
*
* @param source
- * may not be null
+ * may not be null
* @param version
- * may be null
+ * may be null
* @param accessionId
- * may be null
+ * may be null
*/
- public DBRefEntry(String source, String version, String accessionId, Mapping map)
+ public DBRefEntry(String source, String version, String accessionId,
+ Mapping map)
{
- this(source, version, accessionId, map,false);
+ this(source, version, accessionId, map, false);
}
+
/**
*
* @param source
* numbering or null)
*/
public DBRefEntry(String source, String version, String accessionId,
- Mapping map,boolean isCanonical)
+ Mapping map, boolean isCanonical)
{
-
+
this.source = source.toUpperCase(Locale.ROOT);
setVersion(version);
this.accessionId = accessionId;
this.map = map;
- this.isCanonicalAccession=isCanonical;
+ this.isCanonicalAccession = isCanonical;
}
/**
: new String(entry.getVersion())),
(entry.getAccessionId() == null ? ""
: new String(entry.getAccessionId())),
- (entry.getMap() == null ? null : new Mapping(entry.getMap())),entry.isCanonical());
+ (entry.getMap() == null ? null : new Mapping(entry.getMap())),
+ entry.isCanonical());
}
@Override
{
// TODO should also override hashCode to ensure equal objects have equal
// hashcodes
-
-
-// if (o == null || !(o instanceof DBRefEntry))
-// {
-// return false;
-// }
-// DBRefEntry entry = (DBRefEntry) o;
-// if (entry == this)
-// {
-// return true;
-// }
+
+ // if (o == null || !(o instanceof DBRefEntry))
+ // {
+ // return false;
+ // }
+ // DBRefEntry entry = (DBRefEntry) o;
+ // if (entry == this)
+ // {
+ // return true;
+ // }
Mapping em;
- return (o != null && o instanceof DBRefEntry
- && (o == this
- || equalRef((DBRefEntry) o)
- && (map == null) == ((em = ((DBRefEntry) o).map) == null)
- && (map == null || map.equals(em))));
-//
-// {
-// return true;
-// }
-// return false;
+ return (o != null && o instanceof DBRefEntry && (o == this || equalRef(
+ (DBRefEntry) o)
+ && (map == null) == ((em = ((DBRefEntry) o).map) == null)
+ && (map == null || map.equals(em))));
+ //
+ // {
+ // return true;
+ // }
+ // return false;
}
/**
return true;
}
- boolean improved=false;
+ boolean improved = false;
/*
* source must either match or be both null
*/
{
return true;
}
-
- // BH 2019.01.25/2019.02.04 source cannot/should not be null.
+
+ // BH 2019.01.25/2019.02.04 source cannot/should not be null.
// for example, StructureChooser has dbRef.getSource().equalsIgnoreCase...
-
+
return (entry != null
&& (source != null && entry.getSource() != null
&& source.equalsIgnoreCase(entry.getSource()))
return source;
}
- public int getSourceKey()
+ public int getSourceKey()
{
- return (sourceKey == Integer.MIN_VALUE ? (sourceKey = DBRefSource.getSourceKey(getCanonicalSourceName())) : sourceKey);
+ return (sourceKey == Integer.MIN_VALUE
+ ? (sourceKey = DBRefSource
+ .getSourceKey(getCanonicalSourceName()))
+ : sourceKey);
}
/**
@Override
public void setAccessionId(String accessionId)
{
- this.accessionId = accessionId;
-// this.accessionId = (accessionId == null ? "" : accessionId).toUpperCase(Locale.ROOT);
+ this.accessionId = accessionId;
+ // this.accessionId = (accessionId == null ? "" :
+ // accessionId).toUpperCase(Locale.ROOT);
}
/**
@Override
public void setSource(String source)
{
- this.source = source;
-
-// this.source = (source == null ? "" : source).toUpperCase(Locale.ROOT);
-// this.canonicalSourceName = DBRefUtils.getCanonicalName(this.source);
-// this.sourceKey = DBRefSource.getSourceKey(this.canonicalSourceName);
+ this.source = source;
+
+ // this.source = (source == null ? "" : source).toUpperCase(Locale.ROOT);
+ // this.canonicalSourceName = DBRefUtils.getCanonicalName(this.source);
+ // this.sourceKey = DBRefSource.getSourceKey(this.canonicalSourceName);
}
@Override
public void setVersion(String version)
{
this.version = version;
- this.ucversion = (version == null ? null : version.toUpperCase(Locale.ROOT));
+ this.ucversion = (version == null ? null
+ : version.toUpperCase(Locale.ROOT));
}
@Override
return false;
}
MapList ml = map.getMap();
- if (ml.getFromRatio() != ml.getToRatio()
- || ml.getFromRatio() != 1)
+ if (ml.getFromRatio() != ml.getToRatio() || ml.getFromRatio() != 1)
{
return false;
}
// check map is between identical single contiguous ranges
List<int[]> fromRanges, toRanges;
- if ((fromRanges = ml.getFromRanges()).size() != 1 || (toRanges = ml.getToRanges()).size() != 1)
+ if ((fromRanges = ml.getFromRanges()).size() != 1
+ || (toRanges = ml.getToRanges()).size() != 1)
{
return false;
}
// no version string implies the reference has not been verified at all.
return false;
}
-
+
return DBRefSource.isPrimaryCandidate(ucversion);
}
*
* @return
*/
- public String getCanonicalSourceName() {
- return (canonicalSourceName == null ? (canonicalSourceName = DBRefUtils.getCanonicalName(this.source)) : canonicalSourceName);
+ public String getCanonicalSourceName()
+ {
+ return (canonicalSourceName == null
+ ? (canonicalSourceName = DBRefUtils
+ .getCanonicalName(this.source))
+ : canonicalSourceName);
}
/**
{
isCanonicalAccession = canonical;
}
+
/**
*
- * @return true if this is the primary canonical accession for the database source
+ * @return true if this is the primary canonical accession for the database
+ * source
*/
public boolean isCanonical()
{
public class DBRefSource
{
-
-
-
+
public static final String UNIPROT = "UNIPROT";
- public static final String UP_NAME = "UNIPROT_NAME".toUpperCase(Locale.ROOT);
+
+ public static final String UP_NAME = "UNIPROT_NAME"
+ .toUpperCase(Locale.ROOT);
+
/**
* Uniprot Knowledgebase/TrEMBL as served from EMBL protein products.
*/
- public static final String UNIPROTKB = "UniProtKB/TrEMBL".toUpperCase(Locale.ROOT);
+ public static final String UNIPROTKB = "UniProtKB/TrEMBL"
+ .toUpperCase(Locale.ROOT);
+
+ public static final String ENSEMBL = "ENSEMBL";
- public static final String ENSEMBL = "ENSEMBL";
public static final String ENSEMBLGENOMES = "ENSEMBLGENOMES";
-
- public static final String EMBL = "EMBL";
- public static final String EMBLCDS = "EMBLCDS";
- public static final String EMBLCDSProduct = "EMBLCDSProtein".toUpperCase(Locale.ROOT);
-
- public static final String PDB = "PDB";
- public static final String PFAM = "PFAM";
- public static final String RFAM = "RFAM";
+
+ public static final String EMBL = "EMBL";
+
+ public static final String EMBLCDS = "EMBLCDS";
+
+ public static final String EMBLCDSProduct = "EMBLCDSProtein"
+ .toUpperCase(Locale.ROOT);
+
+ public static final String PDB = "PDB";
+
+ public static final String PFAM = "PFAM";
+
+ public static final String RFAM = "RFAM";
+
public static final String GENEDB = "GeneDB".toUpperCase(Locale.ROOT);
public static final String PDB_CANONICAL_NAME = PDB;
+ public static final String[] allSources = new String[] { UNIPROT, UP_NAME,
+ UNIPROTKB, ENSEMBL, ENSEMBLGENOMES, EMBL, EMBLCDS, EMBLCDSProduct,
+ PDB, PFAM, RFAM, GENEDB };
+
+ public static final int UNIPROT_MASK = 1 << 0;
+
+ public static final int UP_NAME_MASK = 1 << 1;
+
+ public static final int UNIPROT_KB_MASK = 1 << 2;
+
+ public static final int ENSEMBL_MASK = 1 << 3;
+
+ public static final int ENSEMBL_GENOMES_MASK = 1 << 4;
+
+ public static final int EMBL_MASK = 1 << 5;
+
+ public static final int EMBL_CDS_MASK = 1 << 6;
+
+ public static final int EMBL_CDS_PRODUCT_MASK = 1 << 7;
+
+ public static final int PDB_MASK = 1 << 8;
+
+ public static final int PFAM_MASK = 1 << 9;
- public static final String[] allSources = new String[] {
- UNIPROT,
- UP_NAME, UNIPROTKB,
- ENSEMBL, ENSEMBLGENOMES,
- EMBL, EMBLCDS, EMBLCDSProduct,
- PDB, PFAM, RFAM, GENEDB
- };
-
- public static final int UNIPROT_MASK = 1<<0;
- public static final int UP_NAME_MASK = 1<<1;
- public static final int UNIPROT_KB_MASK = 1<<2;
- public static final int ENSEMBL_MASK = 1<<3;
- public static final int ENSEMBL_GENOMES_MASK = 1<<4;
- public static final int EMBL_MASK = 1<<5;
- public static final int EMBL_CDS_MASK = 1<<6;
- public static final int EMBL_CDS_PRODUCT_MASK = 1<<7;
- public static final int PDB_MASK = 1<<8;
- public static final int PFAM_MASK = 1<<9;
- public static final int RFAM_MASK = 1<<10;
- public static final int GENE_DB_MASK = 1<<11;
-
- public static final int MASK_COUNT = 12;
-
- public static final int ALL_MASKS = (1 << MASK_COUNT) - 1;
-
- public static int getSourceKey(String name) {
- for (int i = 0; i < MASK_COUNT; i++) {
- if (name.equals(allSources[i]))
- {
- return 1<<i;
- }
- }
- return 0;
- }
-
- public static final int PRIMARY_MASK = UNIPROT_MASK | ENSEMBL_MASK;
-
- /**
- * List of databases whose sequences might have coding regions annotated
- */
- public static final String[] DNACODINGDBS = {
- ENSEMBL, ENSEMBLGENOMES,
- EMBL, EMBLCDS, GENEDB
- };
-
- public static final int DNA_CODING_MASK =
- ENSEMBL_MASK | ENSEMBL_GENOMES_MASK
- | EMBL_MASK | EMBL_CDS_MASK | GENE_DB_MASK;
-
-
-
- public static final String[] CODINGDBS = { EMBLCDS, GENEDB, ENSEMBL };
-
- public static final int CODING_MASK = EMBL_CDS_MASK | GENE_DB_MASK | ENSEMBL_MASK;
-
-
-
- public static final String[] PROTEINDBS = {
- UNIPROT, UNIPROTKB,
- ENSEMBL, EMBLCDSProduct }; // Ensembl ENSP* entries are protein
-
- public static final int PROTEIN_MASK =
- UNIPROT_MASK | UNIPROT_KB_MASK
- | ENSEMBL_MASK | EMBL_CDS_PRODUCT_MASK ;
-
-
- // for SequenceAnnotationReport only
-
-// public static final String[][] PRIMARY_SOURCES = new String[][] {
-// CODINGDBS, DNACODINGDBS, PROTEINDBS };
-//
- public static final int PRIMARY_SOURCES_MASK = CODING_MASK | DNA_CODING_MASK | PROTEIN_MASK;
-
- public static boolean isPrimarySource(String source)
+ public static final int RFAM_MASK = 1 << 10;
+
+ public static final int GENE_DB_MASK = 1 << 11;
+
+ public static final int MASK_COUNT = 12;
+
+ public static final int ALL_MASKS = (1 << MASK_COUNT) - 1;
+
+ public static int getSourceKey(String name)
+ {
+ for (int i = 0; i < MASK_COUNT; i++)
{
- return ((PRIMARY_SOURCES_MASK & getSourceKey(source)) != 0);
+ if (name.equals(allSources[i]))
+ {
+ return 1 << i;
+ }
}
+ return 0;
+ }
+
+ public static final int PRIMARY_MASK = UNIPROT_MASK | ENSEMBL_MASK;
+
+ /**
+ * List of databases whose sequences might have coding regions annotated
+ */
+ public static final String[] DNACODINGDBS = { ENSEMBL, ENSEMBLGENOMES,
+ EMBL, EMBLCDS, GENEDB };
+
+ public static final int DNA_CODING_MASK = ENSEMBL_MASK
+ | ENSEMBL_GENOMES_MASK | EMBL_MASK | EMBL_CDS_MASK | GENE_DB_MASK;
- public static boolean isPrimaryCandidate(String ucversion) {
+ public static final String[] CODINGDBS = { EMBLCDS, GENEDB, ENSEMBL };
+
+ public static final int CODING_MASK = EMBL_CDS_MASK | GENE_DB_MASK
+ | ENSEMBL_MASK;
+
+ public static final String[] PROTEINDBS = { UNIPROT, UNIPROTKB, ENSEMBL,
+ EMBLCDSProduct }; // Ensembl ENSP* entries are protein
+
+ public static final int PROTEIN_MASK = UNIPROT_MASK | UNIPROT_KB_MASK
+ | ENSEMBL_MASK | EMBL_CDS_PRODUCT_MASK;
+
+ // for SequenceAnnotationReport only
+
+ // public static final String[][] PRIMARY_SOURCES = new String[][] {
+ // CODINGDBS, DNACODINGDBS, PROTEINDBS };
+ //
+ public static final int PRIMARY_SOURCES_MASK = CODING_MASK
+ | DNA_CODING_MASK | PROTEIN_MASK;
+
+ public static boolean isPrimarySource(String source)
+ {
+ return ((PRIMARY_SOURCES_MASK & getSourceKey(source)) != 0);
+ }
+
+ public static boolean isPrimaryCandidate(String ucversion)
+ {
// tricky - this test really needs to search the sequence's set of dbrefs to
// see if there is a primary reference that derived this reference.
for (int i = allSources.length; --i >= 0;)
{
- if (ucversion.startsWith(allSources[i])) // BH 2019.01.25 .toUpperCase(Locale.ROOT) unnecessary here for allSources
+ if (ucversion.startsWith(allSources[i])) // BH 2019.01.25
+ // .toUpperCase(Locale.ROOT)
+ // unnecessary here for
+ // allSources
{
// by convention, many secondary references inherit the primary
// reference's
}
}
return true;
-}
-
-
+ }
-
}
}
/**
- * Answers the species identifier e.g. "human", stored as field <code>source</code> of
- * DBRefEntry
+ * Answers the species identifier e.g. "human", stored as field
+ * <code>source</code> of DBRefEntry
*/
@Override
public String getSpeciesId()
// all overlapping regions and we need contained regions
if (region[0] >= start && region[1] <= end)
{
- hiddenColumns.add(
- new int[]
- { region[0] - offset, region[1] - offset });
+ hiddenColumns
+ .add(new int[]
+ { region[0] - offset, region[1] - offset });
numColumns += region[1] - region[0] + 1;
}
}
if (!hiddenColumns.isEmpty())
{
// set up cursor reset values
- HiddenCursorPosition cursorPos = cursor.findRegionForColumn(start, false);
+ HiddenCursorPosition cursorPos = cursor.findRegionForColumn(start,
+ false);
regionindex = cursorPos.getRegionIndex();
if (regionindex > 0)
int oldstart = region[0];
region[0] = Math.min(region[0], start);
numColumns += oldstart - region[0]; // new columns are between old and
- // adjusted starts
+ // adjusted starts
added = true;
}
else if (start <= region[1] + 1)
if (!hiddenColumns.isEmpty())
{
- result += cursor.findRegionForColumn(column, true)
- .getHiddenSoFar();
+ result += cursor.findRegionForColumn(column, true).getHiddenSoFar();
}
return result;
.findRegionForColumn(hiddenColumn, false);
int index = cursorPos.getRegionIndex();
int hiddenBeforeCol = cursorPos.getHiddenSoFar();
-
+
// just subtract hidden cols count - this works fine if column is
// visible
result = hiddenColumn - hiddenBeforeCol;
-
+
// now check in case column is hidden - it will be in the returned
// hidden region
if (index < hiddenColumns.size())
}
}
-
/**
* Returns a hashCode built from hidden column ranges
*/
for (int firstSet = tohide
.nextSetBit(start), lastSet = start; firstSet >= start
&& lastSet <= end; firstSet = tohide
- .nextSetBit(lastSet))
+ .nextSetBit(lastSet))
{
lastSet = tohide.nextClearBit(firstSet);
if (lastSet <= end)
try
{
LOCK.writeLock().lock();
-
+
if (!hiddenColumns.isEmpty())
{
HiddenCursorPosition pos = cursor.findRegionForColumn(start, false);
HiddenCursorPosition pos = cursor
.findRegionForColumn(absoluteStart - 1, false);
- return new StartRegionIterator(pos, start, end,
- hiddenColumns);
+ return new StartRegionIterator(pos, start, end, hiddenColumns);
} finally
{
LOCK.readLock().unlock();
* if true, start and end are visible column positions, not absolute
* positions*
*/
- public VisibleContigsIterator getVisContigsIterator(int start,
- int end,
+ public VisibleContigsIterator getVisContigsIterator(int start, int end,
boolean useVisibleCoords)
{
int adjstart = start;
if (!hiddenCols.isEmpty())
{
firstColumn = hiddenColumns.get(0)[0];
- cursorPos = new HiddenCursorPosition(index,
- hiddencount);
+ cursorPos = new HiddenCursorPosition(index, hiddencount);
}
}
* determine codon positions and canonical codon
* for a peptide-to-CDS mapping
*/
- int[] codonIntervals = mapping.getMap().locateInFrom(toPosition, toPosition);
+ int[] codonIntervals = mapping.getMap().locateInFrom(toPosition,
+ toPosition);
int[] codonPositions = codonIntervals == null ? null
: MappingUtils.flattenRanges(codonIntervals);
if (codonPositions != null && codonPositions.length == 3)
codonPos = codonPositions;
baseCodon = new char[3];
int cdsStart = featureSequence.getStart();
- baseCodon[0] = Character
- .toUpperCase(featureSequence.getCharAt(codonPos[0] - cdsStart));
- baseCodon[1] = Character
- .toUpperCase(featureSequence.getCharAt(codonPos[1] - cdsStart));
- baseCodon[2] = Character
- .toUpperCase(featureSequence.getCharAt(codonPos[2] - cdsStart));
+ baseCodon[0] = Character.toUpperCase(
+ featureSequence.getCharAt(codonPos[0] - cdsStart));
+ baseCodon[1] = Character.toUpperCase(
+ featureSequence.getCharAt(codonPos[1] - cdsStart));
+ baseCodon[2] = Character.toUpperCase(
+ featureSequence.getCharAt(codonPos[2] - cdsStart));
}
else
{
*/
var.append("c.").append(String.valueOf(cdsPos))
.append(String.valueOf(baseCodon[i])).append(">")
- .append(String.valueOf(variantCodon[i]))
- .append("(p.=)");
+ .append(String.valueOf(variantCodon[i])).append("(p.=)");
}
else
{
private static final int PDB_ID_LENGTH = 4;
/**
- * property set when id is a 'manufactured' identifier from the structure data's filename
+ * property set when id is a 'manufactured' identifier from the structure
+ * data's filename
*/
private static final String FAKED_ID = "faked_pdbid";
+
/**
- * property set when the id is authoritative, and should be used in preference to any identifiers in the structure data
+ * property set when the id is authoritative, and should be used in preference
+ * to any identifiers in the structure data
*/
private static final String AUTHORITATIVE_ID = "authoritative_pdbid";
{
// TODO is FILE needed; if not is this enum needed, or can we
// use FileFormatI for PDB, MMCIF?
- PDB("pdb", "pdb"), MMCIF("mmcif", "cif"), BCIF("bcif","bcif"),FILE("?", "?");
+ PDB("pdb", "pdb"), MMCIF("mmcif", "cif"), BCIF("bcif", "bcif"),
+ FILE("?", "?");
/*
* file extension for cached structure file; must be one that
}
return true;
}
-
+
public void setAuthoritative(boolean isAuthoritative)
{
setProperty(AUTHORITATIVE_ID, Boolean.valueOf(isAuthoritative));
}
-
+
/**
*
* @return true if the identifier should be preferred over any identifiers
{
if (_hasProperty(AUTHORITATIVE_ID))
{
- return ((Boolean)getProperty(AUTHORITATIVE_ID));
+ return ((Boolean) getProperty(AUTHORITATIVE_ID));
}
return false;
}
/**
* set when Jalview has manufactured the ID using a local filename
+ *
* @return
*/
public boolean fakedPDBId()
}
return false;
}
+
public void setFakedPDBId(boolean faked)
{
if (faked)
{
setProperty(FAKED_ID, Boolean.TRUE);
}
- else
+ else
{
- if (properties!=null) {
+ if (properties != null)
+ {
properties.remove(FAKED_ID);
}
}
* @param rangeList
* list of ranges to iterate over
*/
- RangeIterator(int lowerBound, int upperBound,
- List<int[]> rangeList)
+ RangeIterator(int lowerBound, int upperBound, List<int[]> rangeList)
{
init(lowerBound, upperBound, rangeList);
}
* @param upperBound
* upper bound to iterate to
*/
- private void init(int lowerBound, int upperBound,
- List<int[]> rangeList)
+ private void init(int lowerBound, int upperBound, List<int[]> rangeList)
{
int start = lowerBound;
int end = upperBound;
}
}
- if (offset!=GAP_COUNT)
+ if (offset != GAP_COUNT)
{
// update modal residue count
maxCount = Math.max(maxCount, newValue);
{
mfound = true;
matchStart = sequence.findIndex(m.start) - 1;
- matchEnd = m.start == m.end ? matchStart : sequence
- .findIndex(m.end) - 1;
+ matchEnd = m.start == m.end ? matchStart
+ : sequence.findIndex(m.end) - 1;
}
if (mfound)
* a token that may be validated by the sequence to check the cursor
* is not stale
*/
- public SequenceCursor(SequenceI seq, int resPos, int column, int firstResCol,
- int lastResCol, int tok)
+ public SequenceCursor(SequenceI seq, int resPos, int column,
+ int firstResCol, int lastResCol, int tok)
{
sequence = seq;
residuePosition = resPos;
*/
public SequenceFeature(SequenceFeature cpy)
{
- this(cpy, cpy.getBegin(), cpy.getEnd(), cpy.getFeatureGroup(), cpy
- .getScore());
+ this(cpy, cpy.getBegin(), cpy.getEnd(), cpy.getFeatureGroup(),
+ cpy.getScore());
}
/**
/**
* Answers the value of the specified attribute as string, or null if no such
- * value. If more than one attribute name is provided, tries to resolve as keys
- * to nested maps. For example, if attribute "CSQ" holds a map of key-value
- * pairs, then getValueAsString("CSQ", "Allele") returns the value of "Allele"
- * in that map.
+ * value. If more than one attribute name is provided, tries to resolve as
+ * keys to nested maps. For example, if attribute "CSQ" holds a map of
+ * key-value pairs, then getValueAsString("CSQ", "Allele") returns the value
+ * of "Allele" in that map.
*
* @param key
* @return
sb.append("<br>");
sb.append("<table>");
String name = mf == null ? seqName : mf.getLinkedSequenceName();
- sb.append(String.format(ROW_DATA, "Location", name,
- begin == end ? begin
- : begin + (isContactFeature() ? ":" : "-") + end));
+ sb.append(String.format(ROW_DATA, "Location", name, begin == end ? begin
+ : begin + (isContactFeature() ? ":" : "-") + end));
String consequence = "";
if (mf != null)
sm.putAll(values);
for (Entry<?, ?> e : sm.entrySet())
{
- sb.append(String.format(ROW_DATA, key, e.getKey().toString(), e
- .getValue().toString()));
+ sb.append(String.format(ROW_DATA, key, e.getKey().toString(),
+ e.getValue().toString()));
}
}
else
String s = entry.getValue().toString();
if (isValueInteresting(key, s, metadata))
{
- sb.append(String.format(ROW_DATA, key, attDesc == null ? ""
- : attDesc, s));
+ sb.append(String.format(ROW_DATA, key,
+ attDesc == null ? "" : attDesc, s));
}
}
}
}
FeatureAttributeType attType = metadata.getAttributeType(key);
- if (attType != null
- && (attType == FeatureAttributeType.Float || attType
- .equals(FeatureAttributeType.Integer)))
+ if (attType != null && (attType == FeatureAttributeType.Float
+ || attType.equals(FeatureAttributeType.Integer)))
{
try
{
private int startRes = 0;
/**
- * end column (base 0)
+ * end column (base 0)
*/
private int endRes = 0;
displayBoxes = seqsel.displayBoxes;
displayText = seqsel.displayText;
colourText = seqsel.colourText;
-
+
startRes = seqsel.startRes;
endRes = seqsel.endRes;
cs = new ResidueShader((ResidueShader) seqsel.cs);
for (int i = 0, ipos = 0; i < inorder.length; i++)
{
SequenceI seq = inorder[i];
- SequenceI seqipos = seqs[ipos] = seq.getSubSequence(startRes, endRes + 1);
+ SequenceI seqipos = seqs[ipos] = seq.getSubSequence(startRes,
+ endRes + 1);
if (seqipos != null)
{
seqipos.setDescription(seq.getDescription());
public void setStartRes(int newStart)
{
int before = startRes;
- startRes= Math.max(0,newStart); // sanity check for negative start column positions
- changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before, startRes);
-
-
+ startRes = Math.max(0, newStart); // sanity check for negative start column
+ // positions
+ changeSupport.firePropertyChange(SEQ_GROUP_CHANGED, before, startRes);
}
/**
* set the array of Database references for the sequence.
*
- * BH 2019.02.04 changes param to DBModlist
+ * BH 2019.02.04 changes param to DBModlist
*
* @param dbs
* @deprecated - use is discouraged since side-effects may occur if DBRefEntry
* set are not normalised.
- * @throws InvalidArgumentException if the is not one created by Sequence itself
+ * @throws InvalidArgumentException
+ * if the is not one created by Sequence itself
*/
@Deprecated
public void setDBRefs(DBModList<DBRefEntry> dbs);
/**
* Returns a (possibly empty) list of any annotations that match on given
- * calcId (source), label (type) and description (observation instance).
- * Null values do not match.
+ * calcId (source), label (type) and description (observation instance). Null
+ * values do not match.
*
* @param calcId
* @param label
*/
public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
String label, String description);
+
/**
* create a new dataset sequence (if necessary) for this sequence and sets
* this sequence to refer to it. This call will move any features or
* optional feature types to restrict results to
* @return
*/
- List<SequenceFeature> findFeatures(int fromCol, int toCol, String... types);
+ List<SequenceFeature> findFeatures(int fromCol, int toCol,
+ String... types);
/**
* Method to call to indicate that the sequence (characters or alignment/gaps)
* positions to be invalidated.
*/
void sequenceChanged();
-
+
/**
*
* @return BitSet corresponding to index [0,length) where Comparison.isGap()
* @param chromosomeId
* @param map
*/
- void setGeneLoci(String speciesId, String assemblyId,
- String chromosomeId, MapList map);
-
+ void setGeneLoci(String speciesId, String assemblyId, String chromosomeId,
+ MapList map);
/**
* Returns the sequence string constructed from the substrings of a sequence
*/
public int firstResidueOutsideIterator(Iterator<int[]> it);
-
}
-
// navigate to start, keeping count of hidden columns
int i = 0;
int hiddenSoFar = 0;
-
+
if (pos != null)
{
// use the cursor position provided
return result;
}
}
-
private boolean endsAtHidden = false;
- VisibleContigsIterator(int start, int end,
- List<int[]> hiddenColumns)
+ VisibleContigsIterator(int start, int end, List<int[]> hiddenColumns)
{
if (hiddenColumns != null && hiddenColumns.size() > 0)
{
return endsAtHidden;
}
}
-
}
/**
- * Answers the description of the attribute, if recorded and unique, or null if either no, or more than description is recorded
+ * Answers the description of the attribute, if recorded and unique, or null
+ * if either no, or more than description is recorded
+ *
* @return
*/
public String getDescription()
{
return;
}
-
+
Map<String[], AttributeData> atts = attributes.get(featureType);
if (atts == null)
{
byLabel = forLabel;
byScore = forScore;
}
+
@Override
public boolean matches(SequenceFeature feature)
{
}
/**
- * Answers a string description of this matcher, suitable for display, debugging
- * or logging. The format may change in future.
+ * Answers a string description of this matcher, suitable for display,
+ * debugging or logging. The format may change in future.
*/
@Override
public String toString()
sb.append(displayName);
}
}
-
+
Condition condition = matcher.getCondition();
sb.append(SPACE).append(condition.getStableName());
String pattern = matcher.getPattern();
sb.append(SPACE).append(pattern);
}
}
-
+
return sb.toString();
}
}
if (!first)
{
String joiner = andConditions ? AND_18N : OR_I18N;
- sb.append(SPACE).append(joiner.toLowerCase(Locale.ROOT)).append(SPACE);
+ sb.append(SPACE).append(joiner.toLowerCase(Locale.ROOT))
+ .append(SPACE);
}
first = false;
if (multiple)
private String name;
private Map<String, String> attributeNames;
-
+
private Map<String, FeatureAttributeType> attributeTypes;
-
+
/**
* Constructor
*
{
if (feature.isNonPositional())
{
- return nonPositionalFeatures == null ? false : nonPositionalFeatures
- .contains(feature);
+ return nonPositionalFeatures == null ? false
+ : nonPositionalFeatures.contains(feature);
}
if (feature.isContactFeature())
{
- return contactFeatureStarts == null ? false : listContains(
- contactFeatureStarts, feature);
+ return contactFeatureStarts == null ? false
+ : listContains(contactFeatureStarts, feature);
}
- return features == null ? false : features
- .contains(feature);
+ return features == null ? false : features.contains(feature);
}
/**
true, Compare.GE, feature.getBegin());
contactFeatureStarts.add(insertPosition, feature);
-
/*
* insert into list sorted by end (second contact position):
* binary search the sorted list to find the insertion point
*/
- insertPosition = BinarySearcher.findFirst(contactFeatureEnds,
- false, Compare.GE, feature.getEnd());
+ insertPosition = BinarySearcher.findFirst(contactFeatureEnds, false,
+ Compare.GE, feature.getEnd());
contactFeatureEnds.add(insertPosition, feature);
return true;
* find the first contact feature (if any)
* whose end point is not before the target range
*/
- int index = BinarySearcher.findFirst(contactFeatureEnds,
- false, Compare.GE, (int) from);
+ int index = BinarySearcher.findFirst(contactFeatureEnds, false,
+ Compare.GE, (int) from);
while (index < contactFeatureEnds.size())
{
SequenceFeature sf = contactFeatureEnds.get(index);
if (!sf.isContactFeature())
{
- System.err.println("Error! non-contact feature type "
- + sf.getType() + " in contact features list");
+ System.err.println("Error! non-contact feature type " + sf.getType()
+ + " in contact features list");
index++;
continue;
}
protected void findContactStartOverlaps(long from, long to,
List<SequenceFeature> result)
{
- int index = BinarySearcher.findFirst(contactFeatureStarts,
- true, Compare.GE, (int) from);
+ int index = BinarySearcher.findFirst(contactFeatureStarts, true,
+ Compare.GE, (int) from);
while (index < contactFeatureStarts.size())
{
public boolean isEmpty()
{
boolean hasFeatures = (contactFeatureStarts != null
- && !contactFeatureStarts
- .isEmpty())
- || (nonPositionalFeatures != null && !nonPositionalFeatures
- .isEmpty())
+ && !contactFeatureStarts.isEmpty())
+ || (nonPositionalFeatures != null
+ && !nonPositionalFeatures.isEmpty())
|| (features != null && features.size() > 0);
return !hasFeatures;
}
else
{
- return nonPositionalFeatureGroups == null ? Collections
- .<String> emptySet() : Collections
- .unmodifiableSet(nonPositionalFeatureGroups);
+ return nonPositionalFeatureGroups == null
+ ? Collections.<String> emptySet()
+ : Collections.unmodifiableSet(nonPositionalFeatureGroups);
}
}
{
if (!positional)
{
- return nonPositionalFeatures == null ? 0 : nonPositionalFeatures
- .size();
+ return nonPositionalFeatures == null ? 0
+ : nonPositionalFeatures.size();
}
int size = 0;
for (SequenceFeature sf : sfs)
{
String featureGroup = sf.getFeatureGroup();
- if (group == null && featureGroup == null || group != null
- && group.equals(featureGroup))
+ if (group == null && featureGroup == null
+ || group != null && group.equals(featureGroup))
{
result.add(sf);
}
return new ArrayList<>();
}
- return getAllFeatures(featureTypes.toArray(new String[featureTypes
- .size()]));
+ return getAllFeatures(
+ featureTypes.toArray(new String[featureTypes.size()]));
}
/**
for (Entry<String, FeatureStore> featureType : featureStore.entrySet())
{
- Set<String> featureGroups = featureType.getValue().getFeatureGroups(
- positionalFeatures);
+ Set<String> featureGroups = featureType.getValue()
+ .getFeatureGroups(positionalFeatures);
for (String group : groups)
{
if (featureGroups.contains(group))
@Override
public float getMinimumScore(String type, boolean positional)
{
- return featureStore.containsKey(type) ? featureStore.get(type)
- .getMinimumScore(positional) : Float.NaN;
+ return featureStore.containsKey(type)
+ ? featureStore.get(type).getMinimumScore(positional)
+ : Float.NaN;
}
/**
@Override
public float getMaximumScore(String type, boolean positional)
{
- return featureStore.containsKey(type) ? featureStore.get(type)
- .getMaximumScore(positional) : Float.NaN;
+ return featureStore.containsKey(type)
+ ? featureStore.get(type).getMaximumScore(positional)
+ : Float.NaN;
}
/**
final boolean forwardStrand)
{
Collections.sort(features,
- forwardStrand
- ? IntervalI.COMPARE_BEGIN_ASC_END_DESC
+ forwardStrand ? IntervalI.COMPARE_BEGIN_ASC_END_DESC
: IntervalI.COMPARE_END_DESC);
}
* @param type
* @return
*/
- List<SequenceFeature> findFeatures(int from, int to,
- String... type);
+ List<SequenceFeature> findFeatures(int from, int to, String... type);
/**
* Answers a list of all features stored, in no particular guaranteed order.
* @param type
* @return
*/
- List<SequenceFeature> getPositionalFeatures(
- String... type);
+ List<SequenceFeature> getPositionalFeatures(String... type);
/**
* Answers a list of all contact features, optionally restricted to specified
* if no type is specified, all are returned
* @return
*/
- List<SequenceFeature> getNonPositionalFeatures(
- String... type);
+ List<SequenceFeature> getNonPositionalFeatures(String... type);
/**
* Deletes the given feature from the store, returning true if it was found
* @param type
* @return
*/
- Set<String> getFeatureGroups(boolean positionalFeatures,
- String... type);
+ Set<String> getFeatureGroups(boolean positionalFeatures, String... type);
/**
* Answers the set of distinct feature types for which there is at least one
* @param groups
* @return
*/
- Set<String> getFeatureTypesForGroups(
- boolean positionalFeatures, String... groups);
+ Set<String> getFeatureTypesForGroups(boolean positionalFeatures,
+ String... groups);
/**
* Answers a set of the distinct feature types for which a feature is stored.
public void removeAt(int index)
{
System.arraycopy(mKeys, index + 1, mKeys, index, mSize - (index + 1));
- System.arraycopy(mValues, index + 1, mValues, index, mSize
- - (index + 1));
+ System.arraycopy(mValues, index + 1, mValues, index,
+ mSize - (index + 1));
mSize--;
}
public void removeAt(int index)
{
System.arraycopy(mKeys, index + 1, mKeys, index, mSize - (index + 1));
- System.arraycopy(mValues, index + 1, mValues, index, mSize
- - (index + 1));
+ System.arraycopy(mValues, index + 1, mValues, index,
+ mSize - (index + 1));
mSize--;
}
{
if (value > 0 && Integer.MAX_VALUE - value < addend)
{
- throw new ArithmeticException("Integer overflow adding " + addend
- + " to " + value);
+ throw new ArithmeticException(
+ "Integer overflow adding " + addend + " to " + value);
}
}
else if (addend < 0)
{
if (value < 0 && Integer.MIN_VALUE - value > addend)
{
- throw new ArithmeticException("Integer underflow adding " + addend
- + " to " + value);
+ throw new ArithmeticException(
+ "Integer underflow adding " + addend + " to " + value);
}
}
}
public void removeAt(int index)
{
System.arraycopy(mKeys, index + 1, mKeys, index, mSize - (index + 1));
- System.arraycopy(mValues, index + 1, mValues, index, mSize
- - (index + 1));
+ System.arraycopy(mValues, index + 1, mValues, index,
+ mSize - (index + 1));
mSize--;
}
for (SequenceFeature sf : sfs)
{
String parentFeature = (String) sf.getValue(PARENT);
- if ( accId.equals(parentFeature))
+ if (accId.equals(parentFeature))
{
result.add(sf);
}
public AlignmentI getSequenceRecords(String query) throws IOException
{
// TODO: use a vararg String... for getSequenceRecords instead?
-
+
List<String> queries = new ArrayList<>();
queries.add(query);
SequenceI seq = parseFeaturesJson(queries);
if (seq == null)
- return null;
+ return null;
return new Alignment(new SequenceI[] { seq });
}
SequenceI seq = new Sequence("Dummy", "");
try
{
- Iterator<Object> rvals = (Iterator<Object>) getJSON(null, queries, -1, MODE_ITERATOR, null);
+ Iterator<Object> rvals = (Iterator<Object>) getJSON(null, queries, -1,
+ MODE_ITERATOR, null);
if (rvals == null)
{
- return null;
+ return null;
}
while (rvals.hasNext())
- {
+ {
try
{
Map<String, Object> obj = (Map<String, Object>) rvals.next();
Object phase = obj.get("phase");
String alleles = JSONUtils
.arrayToStringList((List<Object>) obj.get("alleles"));
- String clinSig = JSONUtils
- .arrayToStringList(
- (List<Object>) obj.get("clinical_significance"));
+ String clinSig = JSONUtils.arrayToStringList(
+ (List<Object>) obj.get("clinical_significance"));
/*
* convert 'variation' to 'sequence_variant', and 'cds' to 'CDS'
sf.setValue("clinical_significance", clinSig);
seq.addSequenceFeature(sf);
-
+
} catch (Throwable t)
{
// ignore - keep trying other features
}
} catch (ParseException | IOException e)
{
- e.printStackTrace();
+ e.printStackTrace();
// ignore
}
* @param obj
* @param key
*/
- protected void setFeatureAttribute(SequenceFeature sf, Map<String, Object> obj,
- String key)
+ protected void setFeatureAttribute(SequenceFeature sf,
+ Map<String, Object> obj, String key)
{
Object object = obj.get(key);
if (object != null)
{
continue;
}
-
+
if (geneAlignment.getHeight() == 1)
{
// ensure id has 'correct' case for the Ensembl identifier
SequenceOntologyI.NMD_TRANSCRIPT_VARIANT,
SequenceOntologyI.TRANSCRIPT, SequenceOntologyI.EXON,
SequenceOntologyI.CDS };
- List<SequenceFeature> sfs = gene.getFeatures().getFeaturesByOntology(
- soTerms);
+ List<SequenceFeature> sfs = gene.getFeatures()
+ .getFeaturesByOntology(soTerms);
for (SequenceFeature sf : sfs)
{
gene.deleteFeature(sf);
transcriptLoci.add(geneMapping.locateInTo(exon[0], exon[1]));
}
- List<int[]> transcriptRange = Arrays.asList(new int[] {
- transcript.getStart(), transcript.getEnd() });
+ List<int[]> transcriptRange = Arrays
+ .asList(new int[]
+ { transcript.getStart(), transcript.getEnd() });
MapList mapList = new MapList(transcriptRange, transcriptLoci, 1, 1);
transcript.setGeneLoci(loci.getSpeciesId(), loci.getAssemblyId(),
/*
* for convenience, pre-fill ensembl.org as the domain for "ENSEMBL"
*/
- divisions.put(DBRefSource.ENSEMBL.toUpperCase(Locale.ROOT), ensemblDomain);
+ divisions.put(DBRefSource.ENSEMBL.toUpperCase(Locale.ROOT),
+ ensemblDomain);
try
{
@SuppressWarnings("unchecked")
- Iterator<Object> rvals = (Iterator<Object>) getJSON(getDivisionsUrl(ensemblGenomesDomain), null, -1, MODE_ITERATOR, null);
+ Iterator<Object> rvals = (Iterator<Object>) getJSON(
+ getDivisionsUrl(ensemblGenomesDomain), null, -1,
+ MODE_ITERATOR, null);
if (rvals == null)
- return;
+ return;
while (rvals.hasNext())
{
String division = rvals.next().toString();
- divisions.put(division.toUpperCase(Locale.ROOT), ensemblGenomesDomain);
+ divisions.put(division.toUpperCase(Locale.ROOT),
+ ensemblGenomesDomain);
}
} catch (IOException | ParseException | NumberFormatException e)
{
/**
* Constructs the URL for the EnsemblGenomes /info/divisions REST service
- * @param domain TODO
+ *
+ * @param domain
+ * TODO
*
* @return
* @throws MalformedURLException
*/
URL getDivisionsUrl(String domain) throws MalformedURLException
{
- return new URL(domain
- + "/info/divisions?content-type=application/json");
+ return new URL(
+ domain + "/info/divisions?content-type=application/json");
}
/**
*
* @return
*/
- public Set<String> getDivisions() {
+ public Set<String> getDivisions()
+ {
if (divisions == null)
{
fetchDivisions();
}
/**
- * Calls the /lookup/id rest service and returns the response as a Map<String, Object>,
- * or null if any error
+ * Calls the /lookup/id rest service and returns the response as a Map<String,
+ * Object>, or null if any error
*
* @param identifier
* @param objectType
* @return
*/
@SuppressWarnings("unchecked")
- protected Map<String, Object> getResult(String identifier, String objectType)
+ protected Map<String, Object> getResult(String identifier,
+ String objectType)
{
List<String> ids = Arrays.asList(new String[] { identifier });
try
{
- return (Map<String, Object>) getJSON(getUrl(identifier, objectType), ids, -1, MODE_MAP, null);
- }
- catch (IOException | ParseException e)
+ return (Map<String, Object>) getJSON(getUrl(identifier, objectType),
+ ids, -1, MODE_MAP, null);
+ } catch (IOException | ParseException e)
{
System.err.println("Error parsing " + identifier + " lookup response "
+ e.getMessage());
boolean reverseStrand = "-1".equals(strand);
int toStart = reverseStrand ? end : start;
int toEnd = reverseStrand ? start : end;
- List<int[]> fromRange = Collections.singletonList(new int[] { 1,
- fromEnd });
- List<int[]> toRange = Collections.singletonList(new int[] { toStart,
- toEnd });
+ List<int[]> fromRange = Collections
+ .singletonList(new int[]
+ { 1, fromEnd });
+ List<int[]> toRange = Collections
+ .singletonList(new int[]
+ { toStart, toEnd });
final Mapping map = new Mapping(
new MapList(fromRange, toRange, 1, 1));
return new GeneLocus(species == null ? "" : species, assembly,
* @return
* @throws MalformedURLException
*/
- protected URL getAssemblyMapUrl(String species, String chromosome, String fromRef,
- String toRef, int startPos, int endPos)
+ protected URL getAssemblyMapUrl(String species, String chromosome,
+ String fromRef, String toRef, int startPos, int endPos)
throws MalformedURLException
{
/*
URL url = null;
try
{
- url = getAssemblyMapUrl(species, chromosome, fromRef, toRef, queryRange[0],
- queryRange[1]);
+ url = getAssemblyMapUrl(species, chromosome, fromRef, toRef,
+ queryRange[0], queryRange[1]);
return (parseAssemblyMappingResponse(url));
} catch (Throwable t)
{
try
{
- Iterator<Object> rvals = (Iterator<Object>) getJSON(url, null, -1, MODE_ITERATOR, MAPPINGS);
+ Iterator<Object> rvals = (Iterator<Object>) getJSON(url, null, -1,
+ MODE_ITERATOR, MAPPINGS);
if (rvals == null)
{
return null;
URL getIdMapUrl(String domain, String accession, int start, int end,
String cdsOrCdna) throws MalformedURLException
{
- String url = String
- .format("%s/map/%s/%s/%d..%d?include_original_region=1&content-type=application/json",
- domain, cdsOrCdna, accession, start, end);
+ String url = String.format(
+ "%s/map/%s/%s/%d..%d?include_original_region=1&content-type=application/json",
+ domain, cdsOrCdna, accession, start, end);
return new URL(url);
}
* @return
*/
@SuppressWarnings("unchecked")
-GeneLociI parseIdMappingResponse(URL url, String accession,
- String domain)
+ GeneLociI parseIdMappingResponse(URL url, String accession, String domain)
{
try
{
- Iterator<Object> rvals = (Iterator<Object>) getJSON(url, null, -1, MODE_ITERATOR, MAPPINGS);
+ Iterator<Object> rvals = (Iterator<Object>) getJSON(url, null, -1,
+ MODE_ITERATOR, MAPPINGS);
if (rvals == null)
{
return null;
while (rvals.hasNext())
{
Map<String, Object> val = (Map<String, Object>) rvals.next();
- Map<String, Object> original = (Map<String, Object>) val.get("original");
+ Map<String, Object> original = (Map<String, Object>) val
+ .get("original");
fromEnd = Integer.parseInt(original.get("end").toString());
Map<String, Object> mapped = (Map<String, Object>) val.get(MAPPED);
String ass = mapped.get("assembly_name").toString();
if (assembly != null && !assembly.equals(ass))
{
- System.err
- .println("EnsemblMap found multiple assemblies - can't resolve");
+ System.err.println(
+ "EnsemblMap found multiple assemblies - can't resolve");
return null;
}
assembly = ass;
String chr = mapped.get("seq_region_name").toString();
if (chromosome != null && !chromosome.equals(chr))
{
- System.err
- .println("EnsemblMap found multiple chromosomes - can't resolve");
+ System.err.println(
+ "EnsemblMap found multiple chromosomes - can't resolve");
return null;
}
chromosome = chr;
.getSpecies(accession);
final String as = assembly;
final String chr = chromosome;
- List<int[]> fromRange = Collections.singletonList(new int[] { 1,
- fromEnd });
+ List<int[]> fromRange = Collections
+ .singletonList(new int[]
+ { 1, fromEnd });
Mapping mapping = new Mapping(new MapList(fromRange, regions, 1, 1));
return new GeneLocus(species == null ? "" : species, as, chr,
mapping);
* fetch and transfer genomic sequence features,
* fetch protein product and add as cross-reference
*/
- for (int i = 0, n = allIds.size(); i < n; i++)
+ for (int i = 0, n = allIds.size(); i < n; i++)
{
addFeaturesAndProduct(allIds.get(i), alignment);
}
*/
SequenceI genomicSequence = null;
EnsemblFeatures gffFetcher = new EnsemblFeatures(getDomain());
- EnsemblFeatureType[] features = getFeaturesToFetch();
-
+ EnsemblFeatureType[] features = getFeaturesToFetch();
+
// Platform.timeCheck("ESP.getsequencerec1", Platform.TIME_MARK);
-
+
AlignmentI geneFeatures = gffFetcher.getSequenceRecords(accId,
features);
if (geneFeatures != null && geneFeatures.getHeight() > 0)
{
genomicSequence = geneFeatures.getSequenceAt(0);
}
-
+
// Platform.timeCheck("ESP.getsequencerec2", Platform.TIME_MARK);
-
+
if (genomicSequence != null)
{
/*
List<DBRefEntry> uprots = DBRefUtils.selectRefs(ds.getDBRefs(),
new String[]
{ DBRefSource.UNIPROT });
- List<DBRefEntry> upxrefs = DBRefUtils.selectRefs(querySeq.getDBRefs(),
- new String[]
+ List<DBRefEntry> upxrefs = DBRefUtils
+ .selectRefs(querySeq.getDBRefs(), new String[]
{ DBRefSource.UNIPROT });
if (uprots != null)
{
*/
protected void getCrossReferences(SequenceI seq)
{
-
+
// Platform.timeCheck("ESP. getdataseq ", Platform.TIME_MARK);
-
while (seq.getDatasetSequence() != null)
{
seq = seq.getDatasetSequence();
EnsemblXref xrefFetcher = new EnsemblXref(getDomain(), getDbSource(),
getEnsemblDataVersion());
List<DBRefEntry> xrefs = xrefFetcher.getCrossReferences(seq.getName());
-
+
for (int i = 0, n = xrefs.size(); i < n; i++)
{
-// Platform.timeCheck("ESP. getxref + " + (i) + "/" + n, Platform.TIME_MARK);
- // BH 2019.01.25 this next method was taking 174 ms PER addition for a 266-reference example.
- // DBRefUtils.ensurePrimaries(seq)
- // was at the end of seq.addDBRef, so executed after ever addition!
- // This method was moved to seq.getPrimaryDBRefs()
+ // Platform.timeCheck("ESP. getxref + " + (i) + "/" + n,
+ // Platform.TIME_MARK);
+ // BH 2019.01.25 this next method was taking 174 ms PER addition for a
+ // 266-reference example.
+ // DBRefUtils.ensurePrimaries(seq)
+ // was at the end of seq.addDBRef, so executed after ever addition!
+ // This method was moved to seq.getPrimaryDBRefs()
seq.addDBRef(xrefs.get(i));
}
-// System.out.println("primaries are " + seq.getPrimaryDBRefs().toString());
+ // System.out.println("primaries are " + seq.getPrimaryDBRefs().toString());
/*
* and add a reference to itself
*/
-
-// Platform.timeCheck("ESP. getxref self ", Platform.TIME_MARK);
+
+ // Platform.timeCheck("ESP. getxref self ", Platform.TIME_MARK);
DBRefEntry self = new DBRefEntry(getDbSource(), getEnsemblDataVersion(),
- seq.getName());
+ seq.getName());
-// Platform.timeCheck("ESP. getxref self add ", Platform.TIME_MARK);
+ // Platform.timeCheck("ESP. getxref self add ", Platform.TIME_MARK);
seq.addDBRef(self);
-
+
// Platform.timeCheck("ESP. seqprox done ", Platform.TIME_MARK);
}
List<SequenceI> seqs = parseSequenceJson(ids);
if (seqs == null)
- return alignment;
+ return alignment;
if (seqs.isEmpty())
{
* in future to handle a JSONArray with more than one
*/
// Platform.timeCheck("ENS seqproxy", Platform.TIME_MARK);
- Map<String, Object> val = (Map<String, Object>) getJSON(null, ids, -1, MODE_MAP, null);
+ Map<String, Object> val = (Map<String, Object>) getJSON(null, ids, -1,
+ MODE_MAP, null);
if (val == null)
- return null;
+ return null;
Object s = val.get("desc");
String desc = s == null ? null : s.toString();
s = val.get("id");
*/
protected abstract List<SequenceFeature> getIdentifyingFeatures(
SequenceI seq, String accId);
-
+
int bhtest = 0;
-
+
/**
* Transfers the sequence feature to the target sequence, locating its start
* and end range based on the mapping. Features which do not overlap the
if (mappedRange != null)
{
-// Platform.timeCheck(null, Platform.TIME_SET);
+ // Platform.timeCheck(null, Platform.TIME_SET);
String group = sf.getFeatureGroup();
if (".".equals(group))
{
}
int newBegin = Math.min(mappedRange[0], mappedRange[1]);
int newEnd = Math.max(mappedRange[0], mappedRange[1]);
-// Platform.timeCheck(null, Platform.TIME_MARK);
+ // Platform.timeCheck(null, Platform.TIME_MARK);
bhtest++;
// 280 ms/1000 here:
- SequenceFeature copy = new SequenceFeature(sf, newBegin, newEnd, group, sf.getScore());
+ SequenceFeature copy = new SequenceFeature(sf, newBegin, newEnd,
+ group, sf.getScore());
// 0.175 ms here:
targetSequence.addSequenceFeature(copy);
return false;
}
-// long start = System.currentTimeMillis();
+ // long start = System.currentTimeMillis();
List<SequenceFeature> sfs = sourceSequence.getFeatures()
.getPositionalFeatures();
MapList mapping = getGenomicRangesFromFeatures(sourceSequence,
accessionId, targetSequence.getStart());
if (mapping == null)
- {
+ {
return false;
}
boolean result = transferFeatures(sfs, targetSequence, mapping,
accessionId);
-// System.out.println("transferFeatures (" + (sfs.size()) + " --> "
-// + targetSequence.getFeatures().getFeatureCount(true) + ") to "
-// + targetSequence.getName() + " took "
-// + (System.currentTimeMillis() - start) + "ms");
+ // System.out.println("transferFeatures (" + (sfs.size()) + " --> "
+ // + targetSequence.getFeatures().getFeatureCount(true) + ") to "
+ // + targetSequence.getName() + " took "
+ // + (System.currentTimeMillis() - start) + "ms");
return result;
}
SequenceFeatures.sortFeatures(sfs, forwardStrand);
boolean transferred = false;
-
+
for (int i = 0, n = sfs.size(); i < n; i++)
{
-// if ((i%1000) == 0) {
-//// Platform.timeCheck("Feature " + bhtest, Platform.TIME_GET);
-// Platform.timeCheck("ESP. xferFeature + " + (i) + "/" + n, Platform.TIME_MARK);
-// }
+ // if ((i%1000) == 0) {
+ //// Platform.timeCheck("Feature " + bhtest, Platform.TIME_GET);
+ // Platform.timeCheck("ESP. xferFeature + " + (i) + "/" + n,
+ // Platform.TIME_MARK);
+ // }
SequenceFeature sf = sfs.get(i);
if (retainFeature(sf, parentId))
protected boolean featureMayBelong(SequenceFeature sf, String identifier)
{
String parent = (String) sf.getValue(PARENT);
- if (parent != null
- && !parent.equalsIgnoreCase(identifier))
+ if (parent != null && !parent.equalsIgnoreCase(identifier))
{
// this genomic feature belongs to a different transcript
return false;
* the default domain names may be overridden in .jalview_properties;
* this allows an easy change from http to https in future if needed
*/
- ensemblDomain = Cache.getDefault(ENSEMBL_BASEURL,
- DEFAULT_ENSEMBL_BASEURL).trim();
+ ensemblDomain = Cache
+ .getDefault(ENSEMBL_BASEURL, DEFAULT_ENSEMBL_BASEURL).trim();
ensemblGenomesDomain = Cache.getDefault(ENSEMBL_GENOMES_BASEURL,
DEFAULT_ENSEMBL_GENOMES_BASEURL).trim();
domain = ensemblDomain;
public class EnsemblSymbol extends EnsemblXref
{
private static final String GENE = "gene";
+
private static final String TYPE = "type";
+
/**
* Constructor given the target domain to fetch data from
*
super(domain, dbName, dbVersion);
}
-// /**
-// * Returns the first "id" value in gene identifier format from the JSON
-// * response, or null if none found
-// *
-// * @param br
-// * @return
-// * @throws IOException
-// */
-// @SuppressWarnings("unchecked")
-//protected String parseSymbolResponse(BufferedReader br) throws IOException
-// {
-// }
+ // /**
+ // * Returns the first "id" value in gene identifier format from the JSON
+ // * response, or null if none found
+ // *
+ // * @param br
+ // * @return
+ // * @throws IOException
+ // */
+ // @SuppressWarnings("unchecked")
+ // protected String parseSymbolResponse(BufferedReader br) throws IOException
+ // {
+ // }
/**
* Constructs the URL for the REST symbol endpoint
{
for (Species taxon : Species.getModelOrganisms())
{
- String geneId = null;///parseSymbolResponse(br);
+ String geneId = null;/// parseSymbolResponse(br);
try
{
- Iterator<Object> rvals = (Iterator<Object>) getJSON(getUrl(query, taxon, GENE), ids, -1, MODE_ITERATOR, null);
+ Iterator<Object> rvals = (Iterator<Object>) getJSON(
+ getUrl(query, taxon, GENE), ids, -1, MODE_ITERATOR,
+ null);
if (rvals == null)
- continue;
+ continue;
while (rvals.hasNext())
{
Map<String, Object> val = (Map<String, Object>) rvals.next();
{
// ignore
}
-
+
if (geneId != null && !result.contains(geneId))
{
result.add(geneId);
try
{
- Iterator<Object> rvals = (Iterator<Object>) getJSON(getUrl(identifier), ids, -1, MODE_ITERATOR, null);
+ Iterator<Object> rvals = (Iterator<Object>) getJSON(
+ getUrl(identifier), ids, -1, MODE_ITERATOR, null);
while (rvals.hasNext())
{
Map<String, Object> val = (Map<String, Object>) rvals.next();
String db = val.get("dbname").toString();
String id = val.get("primary_id").toString();
- if (db != null && id != null
- && !GO_GENE_ONTOLOGY.equals(db))
+ if (db != null && id != null && !GO_GENE_ONTOLOGY.equals(db))
{
db = DBRefUtils.getCanonicalName(db);
DBRefEntry dbref = new DBRefEntry(db, getXRefVersion(), id);
return result;
}
-// /**
-// * Parses "primary_id" and "dbname" values from the JSON response and
-// * constructs a DBRefEntry. Returns a list of the DBRefEntry created. Note we
-// * don't parse "synonyms" as they appear to be either redirected or obsolete
-// * in Uniprot.
-// *
-// * @param br
-// * @return
-// * @throws IOException
-// */
-// @SuppressWarnings("unchecked")
-//protected List<DBRefEntry> parseResponse(BufferedReader br)
-// throws IOException
-// {
-// return result;
-// }
-//
+ // /**
+ // * Parses "primary_id" and "dbname" values from the JSON response and
+ // * constructs a DBRefEntry. Returns a list of the DBRefEntry created. Note
+ // we
+ // * don't parse "synonyms" as they appear to be either redirected or obsolete
+ // * in Uniprot.
+ // *
+ // * @param br
+ // * @return
+ // * @throws IOException
+ // */
+ // @SuppressWarnings("unchecked")
+ // protected List<DBRefEntry> parseResponse(BufferedReader br)
+ // throws IOException
+ // {
+ // return result;
+ // }
+ //
private String xrefVersion = "ENSEMBL:0";
/**
*/
protected URL getUrl(String identifier)
{
- String url = getDomain() + "/xrefs/id/" + identifier
- + CONTENT_TYPE_JSON + "&all_levels=1";
+ String url = getDomain() + "/xrefs/id/" + identifier + CONTENT_TYPE_JSON
+ + "&all_levels=1";
try
{
return new URL(url);
* valid species parameters to Ensembl REST services where applicable
*/
human(true), mouse(true), s_cerevisiae(true), cow(false), pig(false),
- rattus_norvegicus(true), celegans(true), sheep(false), horse(false), gorilla(false),
- rabbit(false), gibbon(false), dog(false), orangutan(false), xenopus_tropicalis(true),
- chimpanzee(false), cat(false), zebrafish(true), chicken(true),
- drosophila_melanogaster(true);
+ rattus_norvegicus(true), celegans(true), sheep(false), horse(false),
+ gorilla(false), rabbit(false), gibbon(false), dog(false),
+ orangutan(false), xenopus_tropicalis(true), chimpanzee(false), cat(false),
+ zebrafish(true), chicken(true), drosophila_melanogaster(true);
static Set<Species> modelOrganisms = new HashSet<>();
}
}
}
+
boolean modelOrganism;
private Species(boolean model)
// ///// end of hts bits.
/**
- * Reads the contig with the given id and returns as a Jalview SequenceI object.
- * Note the database must be indexed for this operation to succeed.
+ * Reads the contig with the given id and returns as a Jalview SequenceI
+ * object. Note the database must be indexed for this operation to succeed.
*
* @param id
* @return
private VCFFileReader reader;
/**
- * Constructor given a raw or compressed VCF file or a (csi or tabix) index file
+ * Constructor given a raw or compressed VCF file or a (csi or tabix) index
+ * file
* <p>
- * If the file path ends in ".tbi" or ".csi", <em>or</em> appending one of these
- * extensions gives a valid file path, open as indexed, else as unindexed.
+ * If the file path ends in ".tbi" or ".csi", <em>or</em> appending one of
+ * these extensions gives a valid file path, open as indexed, else as
+ * unindexed.
*
* @param f
* @throws IOException
final String chrom, final int start, final int end)
{
final CloseableIterator<VariantContext> it = reader.iterator();
-
+
return new CloseableIterator<VariantContext>()
{
boolean atEnd = false;
private static final StructureCommand SHOW_BACKBONE = new StructureCommand(
"select *; cartoons off; backbone");
- private static final StructureCommand FOCUS_VIEW = new StructureCommand("zoom 0");
+ private static final StructureCommand FOCUS_VIEW = new StructureCommand(
+ "zoom 0");
private static final StructureCommand COLOUR_ALL_WHITE = new StructureCommand(
"select *;color white;");
}
@Override
- public List<StructureCommandI> colourByResidues(Map<String, Color> colours)
+ public List<StructureCommandI> colourByResidues(
+ Map<String, Color> colours)
{
List<StructureCommandI> cmds = super.colourByResidues(colours);
cmds.add(0, COLOUR_ALL_WHITE);
atomSpec.append(" or ");
}
first = false;
- atomSpec.append(":").append(tokens[1]).append(" /").append(tokens[0]);
+ atomSpec.append(":").append(tokens[1]).append(" /")
+ .append(tokens[0]);
}
}
/*
* show residues used for superposition as ribbon
*/
- sb.append("select ").append(getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY)).append("|");
- sb.append(getAtomSpec(refAtoms, AtomSpecType.RESIDUE_ONLY)).append(getCommandSeparator())
- .append("cartoons");
+ sb.append("select ")
+ .append(getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY))
+ .append("|");
+ sb.append(getAtomSpec(refAtoms, AtomSpecType.RESIDUE_ONLY))
+ .append(getCommandSeparator()).append("cartoons");
return Arrays.asList(new StructureCommand(sb.toString()));
}
@Override
protected StructureCommandI colourResidues(String atomSpec, Color colour)
{
- StringBuilder sb = new StringBuilder(atomSpec.length()+20);
+ StringBuilder sb = new StringBuilder(atomSpec.length() + 20);
sb.append("select ").append(atomSpec).append(getCommandSeparator())
.append("color").append(getColourString(colour));
return new StructureCommand(sb.toString());
public StructureCommandI loadFile(String file)
{
// https://chemapps.stolaf.edu/jmol/docs/#loadfiles
- return new StructureCommand("load FILES \"" +
- Platform.escapeBackslashes(file) + "\"");
+ return new StructureCommand(
+ "load FILES \"" + Platform.escapeBackslashes(file) + "\"");
}
/**
* @return
*/
@Deprecated
- private static StringBuilder condenseCommand(
- StringBuilder command,
+ private static StringBuilder condenseCommand(StringBuilder command,
int pos)
{
// }
// ;
// instead, we distinguish .cif from non-.cif by filename
- setStructureFileType(getDataName().toLowerCase(Locale.ROOT).endsWith(".cif")
- ? PDBEntry.Type.MMCIF.toString()
- : "PDB");
+ setStructureFileType(
+ getDataName().toLowerCase(Locale.ROOT).endsWith(".cif")
+ ? PDBEntry.Type.MMCIF.toString()
+ : "PDB");
transformJmolModelToJalview(jmolModel.ms);
}
* params -o (output to sysout) -n (nodisplay) -x (exit when finished)
* see http://wiki.jmol.org/index.php/Jmol_Application
*/
-
+
viewer = JalviewJmolBinding.getJmolData(this);
// ensure the 'new' (DSSP) not 'old' (Ramachandran) SS method is used
viewer.setBooleanProperty("defaultStructureDSSP", true);
}
return viewer;
}
-
+
public static Regex getNewAlphafoldValidator()
{
- Regex validator = new Regex("(AF-[A-Z]+[0-9]+[A-Z0-9]+-F1)");
+ Regex validator = new Regex("(AF-[A-Z]+[0-9]+[A-Z0-9]+-F1)");
validator.setIgnoreCase(true);
return validator;
}
- PDBEntry.Type jmolFiletype=null;
+ PDBEntry.Type jmolFiletype = null;
+
/**
- * resolve a jmol filetype string and update the jmolFiletype field accordingly
+ * resolve a jmol filetype string and update the jmolFiletype field
+ * accordingly
+ *
* @param jmolIdentifiedFileType
* @return true if filetype was identified as MMCIF, PDB
*/
public boolean updateFileType(String jmolIdentifiedFileType)
{
- if (jmolIdentifiedFileType == null
+ if (jmolIdentifiedFileType == null
|| jmolIdentifiedFileType.trim().equals(""))
{
return false;
}
- if ("mmcif".equalsIgnoreCase(jmolIdentifiedFileType)) {
+ if ("mmcif".equalsIgnoreCase(jmolIdentifiedFileType))
+ {
jmolFiletype = PDBEntry.Type.MMCIF;
return true;
}
{
jmolFiletype = PDBEntry.Type.PDB;
return true;
- }
+ }
return false;
}
-
+
public void transformJmolModelToJalview(ModelSet ms) throws IOException
{
try
{
setStructureFileType(jmolFiletype.toString());
}
-
+
isMMCIF = PDBEntry.Type.MMCIF.equals(jmolFiletype);
-
+
if (pdbId == null)
{
setId(safeName(getDataName()));
{
setId(pdbId);
setPDBIdAvailable(true);
- alphaFoldModel = alphaFold.search(pdbId) && isMMCIF;
+ alphaFoldModel = alphaFold.search(pdbId) && isMMCIF;
}
List<Atom> significantAtoms = convertSignificantAtoms(ms);
if (tmpchain != null)
{
tmpchain.atoms.addElement(tmpatom);
- } else
+ }
+ else
{
- String tempFString=null;
+ String tempFString = null;
if (isAlphafoldModel())
{
tempFString = "Alphafold Reliability";
}
- tmpchain = new PDBChain(getId(), tmpatom.chain,tempFString);
+ tmpchain = new PDBChain(getId(), tmpatom.chain, tempFString);
getChains().add(tmpchain);
tmpchain.atoms.addElement(tmpatom);
}
public List<StructureCommandI> superposeStructures(AtomSpecModel refAtoms,
AtomSpecModel atomSpec, AtomSpecType specType)
{
-
+
// https://pymolwiki.org/index.php/Super
List<StructureCommandI> commands = new ArrayList<>();
- String refAtomsAlphaOnly = "("+getAtomSpec(refAtoms, specType)+" and (altloc '' or altloc 'a'))";
- String atomSpec2AlphaOnly = "("+getAtomSpec(atomSpec, specType)+" and (altloc '' or altloc 'a'))";
+ String refAtomsAlphaOnly = "(" + getAtomSpec(refAtoms, specType)
+ + " and (altloc '' or altloc 'a'))";
+ String atomSpec2AlphaOnly = "(" + getAtomSpec(atomSpec, specType)
+ + " and (altloc '' or altloc 'a'))";
// pair_fit mobile -> reference
// crashes when undo is enabled on 2.5.2 (incentive)
commands.add(new StructureCommand("undo_disable"));
- commands.add(new StructureCommand("pair_fit",
- atomSpec2AlphaOnly, refAtomsAlphaOnly));
+ commands.add(new StructureCommand("pair_fit", atomSpec2AlphaOnly,
+ refAtomsAlphaOnly));
commands.add(new StructureCommand("undo_enable"));
-
+
/*
* and show superposed residues as cartoon
*/
protected static List<String> getPymolPaths(String os)
{
List<String> pathList = new ArrayList<>();
-
- String userPath = Cache
- .getDefault(Preferences.PYMOL_PATH, null);
+
+ String userPath = Cache.getDefault(Preferences.PYMOL_PATH, null);
if (userPath != null)
{
pathList.add(userPath);
}
-
+
/*
* add default installation paths
*/
public class ChimeraCommands extends StructureCommandsBase
{
// https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/focus.html
- private static final StructureCommand FOCUS_VIEW = new StructureCommand("focus");
+ private static final StructureCommand FOCUS_VIEW = new StructureCommand(
+ "focus");
// https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/listen.html#listresattr
- private static final StructureCommand LIST_RESIDUE_ATTRIBUTES = new StructureCommand("list resattr");
+ private static final StructureCommand LIST_RESIDUE_ATTRIBUTES = new StructureCommand(
+ "list resattr");
// https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/stop.html
- private static final StructureCommand CLOSE_CHIMERA = new StructureCommand("stop really");
+ private static final StructureCommand CLOSE_CHIMERA = new StructureCommand(
+ "stop really");
// https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/listen.html
- private static final StructureCommand STOP_NOTIFY_SELECTION = new StructureCommand("listen stop selection");
+ private static final StructureCommand STOP_NOTIFY_SELECTION = new StructureCommand(
+ "listen stop selection");
- private static final StructureCommand STOP_NOTIFY_MODELS = new StructureCommand("listen stop models");
+ private static final StructureCommand STOP_NOTIFY_MODELS = new StructureCommand(
+ "listen stop models");
// https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/listen.html#listselection
- private static final StructureCommand GET_SELECTION = new StructureCommand("list selection level residue");
+ private static final StructureCommand GET_SELECTION = new StructureCommand(
+ "list selection level residue");
private static final StructureCommand SHOW_BACKBONE = new StructureCommand(
"~display all;~ribbon;chain @CA|P");
* @return
*/
protected StructureCommandI setAttribute(String attributeName,
- String attributeValue,
- AtomSpecModel atomSpecModel)
+ String attributeValue, AtomSpecModel atomSpecModel)
{
StringBuilder sb = new StringBuilder(128);
sb.append("setattr res ").append(attributeName).append(" '")
StringBuilder cmd = new StringBuilder();
String atomSpecAlphaOnly = getAtomSpec(spec, backbone);
String refSpecAlphaOnly = getAtomSpec(ref, backbone);
- cmd.append("match ").append(atomSpecAlphaOnly).append(" ").append(refSpecAlphaOnly);
+ cmd.append("match ").append(atomSpecAlphaOnly).append(" ")
+ .append(refSpecAlphaOnly);
/*
* show superposed residues as ribbon
// https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/listen.html
List<StructureCommandI> cmds = new ArrayList<>();
cmds.add(new StructureCommand("listen start models url " + uri));
- cmds.add(new StructureCommand("listen start select prefix SelectionChanged url " + uri));
+ cmds.add(new StructureCommand(
+ "listen start select prefix SelectionChanged url " + uri));
return cmds;
}
}
/**
- * Returns a viewer command to set the given residue attribute value on residues
- * specified by the AtomSpecModel, for example
+ * Returns a viewer command to set the given residue attribute value on
+ * residues specified by the AtomSpecModel, for example
*
* <pre>
* setattr #0/A:3-9,14-20,39-43 res jv_strand 'strand' create true
String attributeValue, AtomSpecModel atomSpecModel)
{
StringBuilder sb = new StringBuilder(128);
- sb.append("setattr ").append(getAtomSpec(atomSpecModel, AtomSpecType.RESIDUE_ONLY));
+ sb.append("setattr ")
+ .append(getAtomSpec(atomSpecModel, AtomSpecType.RESIDUE_ONLY));
sb.append(" res ").append(attributeName).append(" '")
.append(attributeValue).append("'");
sb.append(" create true");
*/
cmd.append("; ribbon ");
cmd.append(getAtomSpec(spec, AtomSpecType.RESIDUE_ONLY)).append("|");
- cmd.append(getAtomSpec(ref, AtomSpecType.RESIDUE_ONLY)).append("; view");
+ cmd.append(getAtomSpec(ref, AtomSpecType.RESIDUE_ONLY))
+ .append("; view");
return Arrays.asList(new StructureCommand(cmd.toString()));
}
}
/**
- * Returns "POST" as the HTTP request method to use for REST service calls to ChimeraX
+ * Returns "POST" as the HTTP request method to use for REST service calls to
+ * ChimeraX
+ *
* @return
*/
protected String getHttpRequestMethod()
String lastHighlightCommand;
/**
- * Returns a model of the structure positions described by the Chimera format atomspec
+ * Returns a model of the structure positions described by the Chimera format
+ * atomspec
+ *
* @param atomSpec
* @return
*/
- protected AtomSpec parseAtomSpec(String atomSpec)
+ protected AtomSpec parseAtomSpec(String atomSpec)
{
return AtomSpec.fromChimeraAtomspec(atomSpec);
}
/**
* Open a PDB structure file in Chimera and set up mappings from Jalview.
*
- * We check if the PDB model id is already loaded in Chimera, if so don't reopen
- * it. This is the case if Chimera has opened a saved session file.
+ * We check if the PDB model id is already loaded in Chimera, if so don't
+ * reopen it. This is the case if Chimera has opened a saved session file.
*
* @param pe
* @return
{
super(ssm, pdbentry, sequenceIs, protocol);
boolean chimeraX = ViewerType.CHIMERAX.equals(getViewerType());
- chimeraManager = chimeraX ? new ChimeraXManager(new StructureManager(true)) : new ChimeraManager(new StructureManager(true));
- setStructureCommands(chimeraX ? new ChimeraXCommands() : new ChimeraCommands());
+ chimeraManager = chimeraX
+ ? new ChimeraXManager(new StructureManager(true))
+ : new ChimeraManager(new StructureManager(true));
+ setStructureCommands(
+ chimeraX ? new ChimeraXCommands() : new ChimeraCommands());
}
@Override
}
/**
- * Start a dedicated HttpServer to listen for Chimera notifications, and tell it
- * to start listening
+ * Start a dedicated HttpServer to listen for Chimera notifications, and tell
+ * it to start listening
*/
public void startChimeraListener()
{
chimeraListener.shutdown();
chimeraListener = null;
}
-
+
/*
* the following call is added to avoid a stack trace error in Chimera
* after "stop really" is sent; Chimera > 1.14 will not need it; see also
@Override
public boolean isViewerRunning()
{
- return chimeraManager!=null && chimeraManager.isChimeraLaunched();
+ return chimeraManager != null && chimeraManager.isChimeraLaunched();
}
/**
List<String> reply = null;
// trim command or it may never find a match in the replyLog!!
String cmd = command.getCommand().trim();
- List<String> lastReply = chimeraManager
- .sendChimeraCommand(cmd, getResponse);
+ List<String> lastReply = chimeraManager.sendChimeraCommand(cmd,
+ getResponse);
if (getResponse)
{
reply = lastReply;
- if (Console.isDebugEnabled()) {
+ if (Console.isDebugEnabled())
+ {
Console.debug(
- "Response from command ('" + cmd + "') was:\n" + lastReply);
+ "Response from command ('" + cmd + "') was:\n" + lastReply);
}
}
else
}
/**
- * Construct and send a command to highlight zero, one or more atoms. We do this
- * by sending an "rlabel" command to show the residue label at that position.
+ * Construct and send a command to highlight zero, one or more atoms. We do
+ * this by sending an "rlabel" command to show the residue label at that
+ * position.
*/
@Override
public void highlightAtoms(List<AtomSpec> atoms)
first = false;
if (forChimeraX)
{
- cmd.append(cms.get(0).getModelNumber())
- .append("/").append(chain).append(":").append(pdbResNum);
+ cmd.append(cms.get(0).getModelNumber()).append("/").append(chain)
+ .append(":").append(pdbResNum);
}
else
{
- cmd.append(cms.get(0).getModelNumber())
- .append(":").append(pdbResNum);
+ cmd.append(cms.get(0).getModelNumber()).append(":")
+ .append(pdbResNum);
if (!chain.equals(" ") && !forChimeraX)
{
cmd.append(".").append(chain);
if (lastHighlightCommand != null)
{
cmd.insert(0, ";");
- cmd.insert(0,lastHighlightCommand);
- cmd.insert(0,"~");
-
+ cmd.insert(0, lastHighlightCommand);
+ cmd.insert(0, "~");
+
}
- if (cmd.length()>0) {
- executeCommand(true, null, new StructureCommand(cmd.toString()));
+ if (cmd.length() > 0)
+ {
+ executeCommand(true, null, new StructureCommand(cmd.toString()));
}
-
- if (found) {
+
+ if (found)
+ {
this.lastHighlightCommand = command;
}
}
* Ask Chimera for its current selection
*/
StructureCommandI command = getCommandGenerator().getSelectedResidues();
-
+
Runnable action = new Runnable()
{
@Override
public void run()
{
List<String> chimeraReply = executeCommand(command, true);
-
+
List<String> selectedResidues = new ArrayList<>();
if (chimeraReply != null)
{
* selections)
*/
getSsm().mouseOverStructure(atomSpecs);
-
+
}
};
new Thread(action).start();
}
/**
- * Converts a list of Chimera(X) atomspecs to a list of AtomSpec representing the
- * corresponding residues (if any) in Jalview
+ * Converts a list of Chimera(X) atomspecs to a list of AtomSpec representing
+ * the corresponding residues (if any) in Jalview
*
* @param structureSelection
* @return
}
/**
- * Write commands to a temporary file, and send a command to Chimera to open the
- * file as a commands script. For use when sending a large number of separate
- * commands would overload the REST interface mechanism.
+ * Write commands to a temporary file, and send a command to Chimera to open
+ * the file as a commands script. For use when sending a large number of
+ * separate commands would overload the REST interface mechanism.
*
* @param commands
*/
/**
* Returns the file extension required for a file of commands to be read by
* the structure viewer
+ *
* @return
*/
protected String getCommandFileExtension()
public List<String> getChimeraAttributes()
{
List<String> attributes = new ArrayList<>();
- StructureCommandI command = getCommandGenerator().listResidueAttributes();
+ StructureCommandI command = getCommandGenerator()
+ .listResidueAttributes();
final List<String> reply = executeCommand(command, true);
if (reply != null)
{
}
else
{
- Console.debug("Warning: " + term.getName()
- + " has replaced " + replaced.getName()
- + " for lookup of '" + description + "'");
+ Console.debug("Warning: " + term.getName() + " has replaced "
+ + replaced.getName() + " for lookup of '"
+ + description + "'");
}
}
termsByDescription.put(description, term);
Collection<FTSDataColumnI> wantedFields);
/**
- * Fetch index of the primary key column for the dynamic table
- * TODO: consider removing 'hasRefSeq' - never used in code
+ * Fetch index of the primary key column for the dynamic table TODO: consider
+ * removing 'hasRefSeq' - never used in code
+ *
* @param wantedFields
* the available table columns
* @param hasRefSeq
import javax.swing.table.AbstractTableModel;
import javax.swing.table.TableModel;
import javax.swing.table.TableRowSorter;
+
/**
- * Helps render GUI allowing control of which columns to show for entries returned from an FTS query.
- * TODO: push down FTSClient specific code
+ * Helps render GUI allowing control of which columns to show for entries
+ * returned from an FTS query. TODO: push down FTSClient specific code
*
* @author tcofoegbu
*
int x = 0;
for (FTSDataColumnI field : allFTSDataColumns)
- {
- //System.out.println("allFTSDataColumns==" + allFTSDataColumns);
+ {
+ // System.out.println("allFTSDataColumns==" + allFTSDataColumns);
if (field.getName().equalsIgnoreCase("all"))
{
continue;
data[x++] = new Object[] { ftsRestClient
.getAllDefaultDisplayedFTSDataColumns().contains(field),
field.getName(), field.getGroup() };
- //System.out.println(" PUIS " + field.getName() + " ET AUSSI " + field.getGroup() + "X = " + x);
+ // System.out.println(" PUIS " + field.getName() + " ET AUSSI " +
+ // field.getGroup() + "X = " + x);
break;
case STRUCTURE_CHOOSER:
data[x++] = new Object[] { structSummaryColumns.contains(field),
}
});
sorter.setSortKeys(sortKeys);
- // BH 2018 setSortKeys does a sort sorter.sort();
+ // BH 2018 setSortKeys does a sort sorter.sort();
tbl_FTSDataColumnPrefs
.setAutoResizeMode(JTable.AUTO_RESIZE_NEXT_COLUMN);
private int defaultResponsePageSize = 100;
- protected HashMap<String,String> mockQueries = null;
+ protected HashMap<String, String> mockQueries = null;
protected FTSRestClient()
{
InputStream in = getClass().getResourceAsStream(fileName);
- try (BufferedReader br = new BufferedReader(new InputStreamReader(in)))
+ try (BufferedReader br = new BufferedReader(new InputStreamReader(in)))
{
String line;
while ((line = br.readLine()) != null)
public DataTypeI getDataType()
{
final String[] dataTypeString = lineData[2].split("\\|");
- final String classString = dataTypeString[0].toUpperCase(Locale.ROOT);
+ final String classString = dataTypeString[0]
+ .toUpperCase(Locale.ROOT);
return new DataTypeI()
{
FTSDataColumnI that = (FTSDataColumnI) otherObject;
return otherObject == null ? false
: this.getCode().equals(that.getCode())
- && this.getName().equals(that.getName())
- && this.getGroup().equals(that.getGroup());
+ && this.getName().equals(that.getName())
+ && this.getGroup().equals(that.getGroup());
}
};
/**
*
* @param instance
- * @param mocks {{working query, working response}, ...}
+ * @param mocks
+ * {{working query, working response}, ...}
*/
- public static void createMockFTSRestClient(FTSRestClient instance,String[][] mocks)
+ public static void createMockFTSRestClient(FTSRestClient instance,
+ String[][] mocks)
{
instance.setMock(mocks);
}
public static void unMock(FTSRestClient instance)
{
- instance.mockQueries=null;
+ instance.mockQueries = null;
}
protected String getResourceFile(String fileName)
protected void setMock(String[][] mocks)
{
- if (mocks==null) {
- mockQueries=null;
+ if (mocks == null)
+ {
+ mockQueries = null;
return;
}
- mockQueries=new HashMap<String,String>();
- for (String[] mock:mocks)
+ mockQueries = new HashMap<String, String>();
+ for (String[] mock : mocks)
{
- mockQueries.put(mock[0],mock[1]);
+ mockQueries.put(mock[0], mock[1]);
}
}
protected boolean isMocked()
{
- return mockQueries!=null;
+ return mockQueries != null;
}
@Override
columnNames = new String[] { "", "Display", "Group" };
break;
default:
- // non structure sources don't return any other kind of preferences columns
+ // non structure sources don't return any other kind of preferences
+ // columns
break;
}
return columnNames;
/**
* locate column given field name
- * @param string - field name
+ *
+ * @param string
+ * - field name
* @return -1 if not located
*/
public int getFieldIndex(String string)
{
- int i=associatedSequence!=null ? 1 : 0;
- for (FTSDataColumnI field:wantedFields)
+ int i = associatedSequence != null ? 1 : 0;
+ for (FTSDataColumnI field : wantedFields)
{
if (field.getName().equals(string))
{
- return i;
+ return i;
}
i++;
}
public class FTSRestResponse
{
private int numberOfItemsFound;
-
+
private String responseTime;
private Collection<FTSData> searchSummary;
getFTSFrameTitle());
protected JTabbedPane tabs = new JTabbedPane();
-
+
protected IProgressIndicator progressIndicator;
protected JComboBox<FTSDataColumnI> cmb_searchTarget = new JComboBox<>();
public void focusGained(FocusEvent e)
{
// TODO: make selected tab gain focus in correct widget
- if (tabs != null
- && tabs.getSelectedComponent() == ftsPanel)
+ if (tabs != null && tabs.getSelectedComponent() == ftsPanel)
{
txt_search.getComponent().requestFocusInWindow();
}
txt_search.getComponent().setFont(VERDANA_12);
txt_search.addKeyListener(new KeyAdapter()
- {
- @Override
- public void keyPressed(KeyEvent e)
- {
- if (e.getKeyCode() == KeyEvent.VK_ENTER)
- {
- if (getTypedText() == null || getTypedText().isEmpty())
- {
- return;
- }
- String primaryKeyName = getFTSRestClient()
- .getPrimaryKeyColumn().getName();
- if (primaryKeyName.equalsIgnoreCase(getCmbSearchTarget()
- .getSelectedItem().toString()))
- {
- // TODO: nicer to show the list in the result set before
- // viewing in Jalview perhaps ?
- transferToSequenceFetcher(getTypedText());
- }
- else
- {
- performSearchAction();
- }
- }
- }
- });
+ {
+ @Override
+ public void keyPressed(KeyEvent e)
+ {
+ if (e.getKeyCode() == KeyEvent.VK_ENTER)
+ {
+ if (getTypedText() == null || getTypedText().isEmpty())
+ {
+ return;
+ }
+ String primaryKeyName = getFTSRestClient().getPrimaryKeyColumn()
+ .getName();
+ if (primaryKeyName.equalsIgnoreCase(
+ getCmbSearchTarget().getSelectedItem().toString()))
+ {
+ // TODO: nicer to show the list in the result set before
+ // viewing in Jalview perhaps ?
+ transferToSequenceFetcher(getTypedText());
+ }
+ else
+ {
+ performSearchAction();
+ }
+ }
+ }
+ });
final DeferredTextInputListener listener = new DeferredTextInputListener(
1500, new ActionListener()
{
if (isPaginationEnabled() && resultSetCount > 0)
{
- String f1 = totalNumberformatter.format(Integer.valueOf(offSet + 1));
+ String f1 = totalNumberformatter
+ .format(Integer.valueOf(offSet + 1));
String f2 = totalNumberformatter
.format(Integer.valueOf(offSet + resultSetCount));
String f3 = totalNumberformatter
{
e1.printStackTrace();
}
- }
+ }
}
\ No newline at end of file
/*
* fields in the JSON object
*/
- public static String Uniprot_Id= "id";
- public static String Uniprot_Start= "uniprot_start";
- public static String Uniprot_End= "uniprot_end";
- public static String Provider= "provider";
- public static String Model_id= "model_identifier";
- public static String Model_Category= "model_category";
- public static String Model_Type= "model_type";
- public static String Model_Title="model_title";
- public static String Resolution= "resolution";
- public static String Confidence= "confidence_avg_local_score";
- public static String Confidence_Score_Type= "confidence_type";
- public static String Confidence_Score_Version= "confidence_version";
- public static String Coverage= "coverage";
- public static String Sequence_Identity= "sequence_identity";
- public static String Created_Date= "created";
- public static String UniProt_Accession= "uniprot_accession";
- public static String Url= "model_url";
- public static String Page_URL= "model_page_url";
- public static String Ensemble_Sample_Url= "ensembl_sample_url";
+ public static String Uniprot_Id = "id";
+
+ public static String Uniprot_Start = "uniprot_start";
+
+ public static String Uniprot_End = "uniprot_end";
+
+ public static String Provider = "provider";
+
+ public static String Model_id = "model_identifier";
+
+ public static String Model_Category = "model_category";
+
+ public static String Model_Type = "model_type";
+
+ public static String Model_Title = "model_title";
+
+ public static String Resolution = "resolution";
+
+ public static String Confidence = "confidence_avg_local_score";
+
+ public static String Confidence_Score_Type = "confidence_type";
+
+ public static String Confidence_Score_Version = "confidence_version";
+
+ public static String Coverage = "coverage";
+
+ public static String Sequence_Identity = "sequence_identity";
+
+ public static String Created_Date = "created";
+
+ public static String UniProt_Accession = "uniprot_accession";
+
+ public static String Url = "model_url";
+
+ public static String Page_URL = "model_page_url";
+
+ public static String Ensemble_Sample_Url = "ensembl_sample_url";
/**
* original response from server
AlignmentI tdbAl = fl.readFile(tdbURL, DataSourceType.URL,
FileFormat.MMCif);
- // TODO: pad structure according to its Uniprot Start so all line up w.r.t. the Uniprot reference sequence
- // TODO: give the structure a sensible name (not the giant URL *:o) )
+ // TODO: pad structure according to its Uniprot Start so all line up
+ // w.r.t. the Uniprot reference sequence
+ // TODO: give the structure a sensible name (not the giant URL *:o)
+ // )
if (tdbAl != null)
{
if (allSeqs != null)
}
} catch (Exception x)
{
- Console.warn(
- "Couldn't retrieve 3d-beacons model for uniprot id"
- + searchTerm + " : " + tdbURL,
- x);
+ Console.warn("Couldn't retrieve 3d-beacons model for uniprot id"
+ + searchTerm + " : " + tdbURL, x);
}
}
seqFetcher.parseResult(allSeqs,
/**
* production server URI
*/
- private static String TDB_PROD_API="https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/";
+ private static String TDB_PROD_API = "https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/";
+
/**
* dev server URI
*/
- private static String TDB_DEV_API="https://wwwdev.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/";
- private static String DEFAULT_THREEDBEACONS_DOMAIN = TDB_PROD_API;
+ private static String TDB_DEV_API = "https://wwwdev.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/";
+
+ private static String DEFAULT_THREEDBEACONS_DOMAIN = TDB_PROD_API;
public static FTSRestClientI instance = null;
protected TDBeaconsFTSRestClient()
{
}
+
@SuppressWarnings("unchecked")
@Override
public FTSRestResponse executeRequest(FTSRestRequest tdbRestRequest)
}
WebResource webResource;
- webResource = client.resource(DEFAULT_THREEDBEACONS_DOMAIN+query);
+ webResource = client.resource(DEFAULT_THREEDBEACONS_DOMAIN + query);
URI uri = webResource.getURI();
System.out.println(uri.toString());
// Execute the REST request
ClientResponse clientResponse;
- if (isMocked()) {
+ if (isMocked())
+ {
clientResponse = null;
}
else
String responseString = null;
// Check the response status and report exception if one occurs
- int responseStatus = isMocked() ? (mockQueries.containsKey(query) ? 200 : 404) : clientResponse.getStatus();
+ int responseStatus = isMocked()
+ ? (mockQueries.containsKey(query) ? 200 : 404)
+ : clientResponse.getStatus();
switch (responseStatus)
{
// if success
}
else
{
- responseString = isMocked() ? mockQueries.get(query): clientResponse.getEntity(String.class);
+ responseString = isMocked() ? mockQueries.get(query)
+ : clientResponse.getEntity(String.class);
}
break;
case 400:
}
}
throw e;
-
+
}
}
/**
* returns response for when the 3D-Beacons service doesn't have a record for
- * the given query - in 2.11.2 this triggers a failover to the PDBe FTS
+ * the given query - in 2.11.2 this triggers a failover to the PDBe FTS
*
* @return null
*/
SequenceI associatedSeq = tdbRequest.getAssociatedSequence();
int colCounter = 0;
summaryRowData = new Object[(associatedSeq != null)
- ? displayFields.size() + 1
- : displayFields.size()];
- if (associatedSeq != null)
- {
- associatedSequence = associatedSeq;
- summaryRowData[0] = associatedSequence;
- colCounter = 1;
- }
+ ? displayFields.size() + 1
+ : displayFields.size()];
+ if (associatedSeq != null)
+ {
+ associatedSequence = associatedSeq;
+ summaryRowData[0] = associatedSequence;
+ colCounter = 1;
+ }
for (FTSDataColumnI field : displayFields)
{
columnNames = new String[] { "", "Display", "Group" };
break;
case PREFERENCES:
- columnNames = new String[] { "3DB Beacons Field", "Show in search summary",
- "Show in structure summary" };
+ columnNames = new String[] { "3DB Beacons Field",
+ "Show in search summary", "Show in structure summary" };
break;
default:
break;
{
super();
uniprotSearchEndpoint = Cache.getDefault("UNIPROT_DOMAIN",
- DEFAULT_UNIPROT_DOMAIN) + "/uniprot/";
+ DEFAULT_UNIPROT_DOMAIN) + "/uniprot/";
}
@SuppressWarnings("unchecked")
: MessageManager.getString("label.result");
if (isPaginationEnabled() && resultSetCount > 0)
{
- updateSearchFrameTitle(defaultFTSFrameTitle + " - " + result
- + " "
- + totalNumberformatter
- .format(Integer.valueOf(offSet + 1))
- + " to "
- + totalNumberformatter
- .format(Integer
+ updateSearchFrameTitle(
+ defaultFTSFrameTitle + " - " + result + " "
+ + totalNumberformatter
+ .format(Integer.valueOf(offSet + 1))
+ + " to "
+ + totalNumberformatter.format(Integer
.valueOf(offSet + resultSetCount))
- + " of "
- + totalNumberformatter
- .format(Integer.valueOf(totalResultSetCount))
- + " " + " (" + (endTime - startTime) + " milli secs)");
+ + " of "
+ + totalNumberformatter.format(
+ Integer.valueOf(totalResultSetCount))
+ + " " + " (" + (endTime - startTime)
+ + " milli secs)");
}
else
{
{
private static boolean setAPQHandlers = false;
- public APQHandlers() {
+ public APQHandlers()
+ {
}
- protected static boolean setAPQHandlers(jalview.gui.Desktop jalviewDesktop)
+ protected static boolean setAPQHandlers(
+ jalview.gui.Desktop jalviewDesktop)
{
// flagging this test to avoid unnecessary reflection
if (!setAPQHandlers)
{ PreferencesHandler.class }) != null)
{
- hdesktop.setPreferencesHandler(
- new PreferencesHandler()
+ hdesktop.setPreferencesHandler(new PreferencesHandler()
{
- @Override
- public void handlePreferences(
- PreferencesEvent e)
- {
- jalviewDesktop.preferences_actionPerformed(null);
- }
- });
+ @Override
+ public void handlePreferences(PreferencesEvent e)
+ {
+ jalviewDesktop.preferences_actionPerformed(null);
+ }
+ });
}
hdesktop.setQuitHandler(new QuitHandler()
{
@Override
- public void handleQuitRequestWith(
- QuitEvent e, QuitResponse r)
+ public void handleQuitRequestWith(QuitEvent e,
+ QuitResponse r)
{
- boolean confirmQuit = Cache
- .getDefault(
- jalview.gui.Desktop.CONFIRM_KEYBOARD_QUIT,
- true);
+ boolean confirmQuit = Cache.getDefault(
+ jalview.gui.Desktop.CONFIRM_KEYBOARD_QUIT, true);
int n;
if (confirmQuit)
{
}
}
});
- hdesktop.setQuitStrategy(
- QuitStrategy.CLOSE_ALL_WINDOWS);
+ hdesktop.setQuitStrategy(QuitStrategy.CLOSE_ALL_WINDOWS);
}
}
}
}
-
+
return setAPQHandlers;
}
MessageManager.getString("action.cancel") };
dialog.showInternalDialog(this,
MessageManager.getString("label.export_settings"),
- JvOptionPane.OK_CANCEL_OPTION, JvOptionPane.PLAIN_MESSAGE,
- null, options, MessageManager.getString("action.ok"));
+ JvOptionPane.OK_CANCEL_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
+ options, MessageManager.getString("action.ok"));
}
/**
boolean set = chkHiddenSeqs.isEnabled() && isSelected;
chkHiddenSeqs.setSelected(set);
settings.setExportHiddenSequences(set);
-
+
set = chkHiddenCols.isEnabled() && isSelected;
chkHiddenCols.setSelected(set);
settings.setExportHiddenColumns(set);
-
+
set = isComplexAlignFile && chkExportAnnots.isEnabled() && isSelected;
chkExportAnnots.setSelected(set);
settings.setExportAnnotations(set);
-
+
set = isComplexAlignFile && chkExportFeats.isEnabled() && isSelected;
chkExportFeats.setSelected(set);
settings.setExportFeatures(set);
-
+
set = isComplexAlignFile && chkExportGrps.isEnabled() && isSelected;
chkExportGrps.setSelected(set);
settings.setExportGroups(set);
settings.setExportHiddenSequences(chkHiddenSeqs.isSelected());
}
});
-
+
chkHiddenCols.setText(
MessageManager.getString("action.export_hidden_columns"));
chkHiddenCols.addActionListener(new ActionListener()
settings.setExportHiddenColumns(chkHiddenCols.isSelected());
}
});
-
+
chkExportAnnots
.setText(MessageManager.getString("action.export_annotations"));
chkExportAnnots.addActionListener(new ActionListener()
settings.setExportAnnotations(chkExportAnnots.isSelected());
}
});
-
+
chkExportFeats
.setText(MessageManager.getString("action.export_features"));
chkExportFeats.addActionListener(new ActionListener()
settings.setExportFeatures(chkExportFeats.isSelected());
}
});
-
+
chkExportGrps.setText(MessageManager.getString("action.export_groups"));
chkExportGrps.addActionListener(new ActionListener()
{
settings.setExportGroups(chkExportGrps.isSelected());
}
});
-
+
JCheckBox chkAll = new JCheckBox(
MessageManager.getString("action.select_all"));
-
+
JPanel hiddenRegionConfPanel = new JPanel(new BorderLayout());
JPanel complexExportPanel = new JPanel(new BorderLayout());
this.setLayout(new BorderLayout());
-
+
chkAll.addItemListener(new ItemListener()
{
@Override
checkAllAction(chkAll.isSelected());
}
});
-
+
hiddenRegionConfPanel.add(chkHiddenSeqs, BorderLayout.CENTER);
hiddenRegionConfPanel.add(chkHiddenCols, BorderLayout.SOUTH);
chkHiddenSeqs.setEnabled(hasHiddenSeq);
chkHiddenCols.setEnabled(hasHiddenCols);
-
+
complexExportPanel.add(chkExportAnnots, BorderLayout.NORTH);
complexExportPanel.add(chkExportFeats, BorderLayout.CENTER);
complexExportPanel.add(chkExportGrps, BorderLayout.SOUTH);
-
+
JPanel actionPanel = new JPanel(new FlowLayout(FlowLayout.CENTER));
actionPanel.add(chkAll);
-
+
JPanel optionsPanel = new JPanel();
if (this.isComplexAlignFile)
{
optionsPanel.add(complexExportPanel);
}
-
+
if (hasHiddenSeq || hasHiddenCols)
{
optionsPanel.add(hiddenRegionConfPanel);
}
-
+
add(optionsPanel, BorderLayout.NORTH);
add(actionPanel, BorderLayout.SOUTH);
}
// modifyPID.setEnabled(false);
}
- String sortby = Cache.getDefault("SORT_ALIGNMENT",
- "No sort");
+ String sortby = Cache.getDefault("SORT_ALIGNMENT", "No sort");
if (sortby.equals("Id"))
{
});
if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase(Locale.ROOT)
.indexOf("devel") > -1
- || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase(Locale.ROOT)
- .indexOf("test") > -1)
+ || Cache.getDefault("VERSION", "DEVELOPMENT")
+ .toLowerCase(Locale.ROOT).indexOf("test") > -1)
{
formatMenu.add(vsel);
}
}
if (viewport.cursorMode)
{
- alignPanel.getSeqPanel().moveCursor(0, -1,evt.isShiftDown());
+ alignPanel.getSeqPanel().moveCursor(0, -1, evt.isShiftDown());
}
break;
jws2servs.attachWSMenuEntry(webService, me);
for (Jws2Instance sv : jws2servs.getServices())
{
- if (sv.description.toLowerCase(Locale.ROOT).contains("jpred"))
+ if (sv.description.toLowerCase(Locale.ROOT)
+ .contains("jpred"))
{
for (JMenuItem jmi : legacyItems)
{
al = dna.translateCdna(codeTable);
} catch (Exception ex)
{
- Console.error(
- "Exception during translation. Please report this !", ex);
+ Console.error("Exception during translation. Please report this !",
+ ex);
final String msg = MessageManager.getString(
"label.error_when_translating_sequences_submit_bug_report");
final String errorTitle = MessageManager
schemeName = Cache.getDefault(Preferences.DEFAULT_COLOUR,
ResidueColourScheme.NONE);
}
- ColourSchemeI colourScheme = ColourSchemeProperty
- .getColourScheme(this, alignment, schemeName);
+ ColourSchemeI colourScheme = ColourSchemeProperty.getColourScheme(this,
+ alignment, schemeName);
residueShading = new ResidueShader(colourScheme);
if (colourScheme instanceof UserColourScheme)
final String question = JvSwingUtils.wrapTooltip(true,
MessageManager.getString("label.open_split_window?"));
final AlignViewport us = this;
-
+
/*
* options No, Split Window, New Window correspond to
* dialog responses 0, 1, 2 (even though JOptionPane shows them
@Override
public void run()
{
- addDataToAlignment(al);
+ addDataToAlignment(al);
}
}).setResponseHandler(1, new Runnable()
{
us.openLinkedAlignmentAs(al, title, false);
}
});
- dialog.showDialog(question,
+ dialog.showDialog(question,
MessageManager.getString("label.open_split_window"),
JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
options, options[0]);
protected void openLinkedAlignmentAs(AlignmentI al, String title,
boolean newWindowOrSplitPane)
- {
+ {
/*
* Identify protein and dna alignments. Make a copy of this one if opening
* in a new split pane.
try
{
- newAlignFrame.setMaximum(
- Cache.getDefault("SHOW_FULLSCREEN", false));
+ newAlignFrame.setMaximum(Cache.getDefault("SHOW_FULLSCREEN", false));
} catch (java.beans.PropertyVetoException ex)
{
}
}
/**
- * Applies the supplied feature settings descriptor to currently known features.
- * This supports an 'initial configuration' of feature colouring based on a
- * preset or user favourite. This may then be modified in the usual way using
- * the Feature Settings dialogue.
+ * Applies the supplied feature settings descriptor to currently known
+ * features. This supports an 'initial configuration' of feature colouring
+ * based on a preset or user favourite. This may then be modified in the usual
+ * way using the Feature Settings dialogue.
*
* @param featureSettings
*/
/**
* when mergeOnly is set, then group and feature visibility or feature colours
* are not modified for features and groups already known to the feature
- * renderer. Feature ordering is always adjusted, and transparency is always set
- * regardless.
+ * renderer. Feature ordering is always adjusted, and transparency is always
+ * set regardless.
*
* @param featureSettings
* @param mergeOnly
{
return;
}
-
+
FeatureRenderer fr = getAlignPanel().getSeqPanel().seqCanvas
.getFeatureRenderer();
List<String> origRenderOrder = new ArrayList<>();
List<String> origGroups = new ArrayList<>();
- // preserve original render order - allows differentiation between user configured colours and autogenerated ones
+ // preserve original render order - allows differentiation between user
+ // configured colours and autogenerated ones
origRenderOrder.addAll(fr.getRenderOrder());
origGroups.addAll(fr.getFeatureGroups());
&& origColour.getColour().equals(
ColorUtils.createColourFromName(type)))))
{
- // if we are merging, only update if there wasn't already a colour defined for
+ // if we are merging, only update if there wasn't already a colour
+ // defined for
// this type
if (preferredColour != null)
{
{
if (!mergeOnly || !origGroups.contains(group))
{
- // when merging, display groups only if the aren't already marked as not visible
+ // when merging, display groups only if the aren't already marked as not
+ // visible
fr.setGroupVisibility(group,
featureSettings.isGroupDisplayed(group));
}
*/
public AlignmentPanel(AlignFrame af, final AlignViewport av)
{
-// setBackground(Color.white); // BH 2019
+ // setBackground(Color.white); // BH 2019
alignFrame = af;
this.av = av;
setSeqPanel(new SeqPanel(av, this));
/*
* Scroll down to make end of search results visible
*/
- setScrollValues(ranges.getStartRes(), starts + seqIndex - ends
- + 1);
+ setScrollValues(ranges.getStartRes(), starts + seqIndex - ends + 1);
}
/*
* Else results are already visible - no need to scroll
Dimension e = idPanel.getSize();
alabels.setSize(new Dimension(e.width, annotationHeight));
-
annotationSpaceFillerHolder.setPreferredSize(new Dimension(
annotationSpaceFillerHolder.getWidth(), annotationHeight));
annotationScroller.validate();
* single graphics context), then reset to (0, scale height)
*/
alignmentGraphics.translate(alignmentGraphicsOffset, scaleHeight);
- getSeqPanel().seqCanvas.drawPanelForPrinting(alignmentGraphics, startRes,
- endRes, startSeq, endSeq - 1);
+ getSeqPanel().seqCanvas.drawPanelForPrinting(alignmentGraphics,
+ startRes, endRes, startSeq, endSeq - 1);
alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
if (av.isShowAnnotation() && (endSeq == alignmentHeight))
*
* @throws PrinterException
*/
- public int printWrappedAlignment(int pageWidth, int pageHeight, int pageNumber,
- Graphics g) throws PrinterException
+ public int printWrappedAlignment(int pageWidth, int pageHeight,
+ int pageNumber, Graphics g) throws PrinterException
{
getSeqPanel().seqCanvas.calculateWrappedGeometry(getWidth(),
getHeight());
g.translate(idWidth, 0);
- getSeqPanel().seqCanvas.drawWrappedPanelForPrinting(g, pageWidth - idWidth,
- totalHeight, 0);
+ getSeqPanel().seqCanvas.drawWrappedPanelForPrinting(g,
+ pageWidth - idWidth, totalHeight, 0);
if ((pageNumber * pageHeight) < totalHeight)
{
String triplet = null;
if (av.getAlignment().isNucleotide())
{
- triplet = ResidueProperties.nucleotideName.get(seq
- .getCharAt(column) + "");
+ triplet = ResidueProperties.nucleotideName
+ .get(seq.getCharAt(column) + "");
}
else
{
- triplet = ResidueProperties.aa2Triplet.get(seq.getCharAt(column)
- + "");
+ triplet = ResidueProperties.aa2Triplet
+ .get(seq.getCharAt(column) + "");
}
if (triplet == null)
text.append("<area shape=\"rect\" coords=\"")
.append((idWidth + column * av.getCharWidth()))
.append(",").append(sy).append(",")
- .append((idWidth + (column + 1) * av.getCharWidth()))
+ .append((idWidth
+ + (column + 1) * av.getCharWidth()))
.append(",").append((av.getCharHeight() + sy))
.append("\"").append(" onMouseOver=\"toolTip('")
.append(seqPos).append(" ").append(triplet);
}
if (!Comparison.isGap(seq.getCharAt(column)))
{
- List<SequenceFeature> features = seq.findFeatures(column, column);
+ List<SequenceFeature> features = seq.findFeatures(column,
+ column);
for (SequenceFeature sf : features)
{
if (sf.isContactFeature())
setAlignFrameView();
}
}
+
public void setAlignFrameView()
{
alignFrame.setDisplayedView(this);
}
-
+
@Override
public StructureSelectionManager getStructureSelectionManager()
{
"error.implementation_error_dont_know_about_threshold_setting"));
}
thresholdIsMin.setSelected(acg.isThresholdIsMinMax());
- thresholdValue
- .setText(String.valueOf(acg.getAnnotationThreshold()));
+ thresholdValue.setText(String.valueOf(acg.getAnnotationThreshold()));
}
jbInit();
{
continue;
}
- sg.setColourScheme(
- acg.getInstance(av, sg));
+ sg.setColourScheme(acg.getInstance(av, sg));
}
}
}
private HiddenColumns oldHiddenColumns;
protected static int MIN_WIDTH = (Platform.isJS() ? 370 : 420);
+
protected static int MIN_HEIGHT = (Platform.isJS() ? 370 : 430);
public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap)
frame.setContentPane(this);
frame.setLayer(JLayeredPane.PALETTE_LAYER);
Desktop.addInternalFrame(frame,
- MessageManager.getString("label.select_by_annotation"), 0,
- 0);
- // BH note: MIGLayout ignores this completely,
+ MessageManager.getString("label.select_by_annotation"), 0, 0);
+ // BH note: MIGLayout ignores this completely,
// possibly creating a frame smaller than specified:
frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
MessageManager.getString("label.threshold_filter")));
thresholdPanel.setBackground(Color.white);
thresholdPanel.setFont(JvSwingUtils.getLabelFont());
- thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]") );
+ thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]"));
percentThreshold.setBackground(Color.white);
percentThreshold.setFont(JvSwingUtils.getLabelFont());
if (currentAnnotation.threshold == null)
{
currentAnnotation.setThreshold(new jalview.datamodel.GraphLine(
- (currentAnnotation.graphMax
- - currentAnnotation.graphMin) / 2f,
+ (currentAnnotation.graphMax - currentAnnotation.graphMin)
+ / 2f,
"Threshold", Color.black));
}
adjusting = true;
- setSliderModel(currentAnnotation.graphMin,
- currentAnnotation.graphMax,
+ setSliderModel(currentAnnotation.graphMin, currentAnnotation.graphMax,
currentAnnotation.threshold.value);
setThresholdValueText();
AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
if (currentAnnotation.isQuantitative())
{
- filterParams
- .setThresholdValue(currentAnnotation.threshold.value);
+ filterParams.setThresholdValue(currentAnnotation.threshold.value);
if (selectedThresholdItem == AnnotationColourGradient.ABOVE_THRESHOLD)
{
// filterAnnotations, because showing hidden columns has the side effect of
// adding them to the selection
av.showAllHiddenColumns();
- av.getColumnSelection().filterAnnotations(
- currentAnnotation.annotations, filterParams);
+ av.getColumnSelection().filterAnnotations(currentAnnotation.annotations,
+ filterParams);
boolean hideCols = getActionOption() == ACTION_OPTION_HIDE;
if (hideCols)
CardLayout switchableViewsLayout = (CardLayout) switchableViewsPanel
.getLayout();
- switchableViewsLayout.show(switchableViewsPanel, currentView);
+ switchableViewsLayout.show(switchableViewsPanel, currentView);
updateView();
}
searchBox.getComponent().setToolTipText(
MessageManager.getString("info.enter_search_text_here"));
searchBox.addKeyListener(new java.awt.event.KeyAdapter()
- {
- @Override
- public void keyPressed(KeyEvent e)
- {
- if (e.getKeyCode() == KeyEvent.VK_ENTER)
- {
- e.consume();
- searchStringAction();
- }
- }
- });
+ {
+ @Override
+ public void keyPressed(KeyEvent e)
+ {
+ if (e.getKeyCode() == KeyEvent.VK_ENTER)
+ {
+ e.consume();
+ searchStringAction();
+ }
+ }
+ });
searchBox.addFocusListener(new FocusAdapter()
{
@Override
}
/**
- * Configures the dialog for options to export visible features. If from a split
- * frame panel showing linked features, make the option to include these in the
- * export visible.
+ * Configures the dialog for options to export visible features. If from a
+ * split frame panel showing linked features, make the option to include these
+ * in the export visible.
*/
public void exportFeatures()
{
}
/**
- * Answers the text to output for either Features (in GFF or Jalview format) or
- * Annotations (in CSV or Jalview format)
+ * Answers the text to output for either Features (in GFF or Jalview format)
+ * or Annotations (in CSV or Jalview format)
*
* @return
*/
}
/**
- * Returns the text contents for output of annotations in either CSV or Jalview
- * format
+ * Returns the text contents for output of annotations in either CSV or
+ * Jalview format
*
* @return
*/
}
/**
- * Builds a panel with a checkbox for the option to export linked (CDS/peptide)
- * features. This is hidden by default, and only made visible if exporting
- * features from a split frame panel which is configured to show linked
- * features.
+ * Builds a panel with a checkbox for the option to export linked
+ * (CDS/peptide) features. This is hidden by default, and only made visible if
+ * exporting features from a split frame panel which is configured to show
+ * linked features.
*
* @return
*/
linkedFeaturesPanel.setOpaque(false);
boolean nucleotide = ap.av.isNucleotide();
- String complement = nucleotide
- ? MessageManager.getString("label.protein").toLowerCase(Locale.ROOT)
- : "CDS";
- JLabel label = new JLabel(
- MessageManager.formatMessage("label.include_linked_features",
- complement));
+ String complement = nucleotide ? MessageManager
+ .getString("label.protein").toLowerCase(Locale.ROOT) : "CDS";
+ JLabel label = new JLabel(MessageManager
+ .formatMessage("label.include_linked_features", complement));
label.setHorizontalAlignment(SwingConstants.TRAILING);
String tooltip = MessageManager
.formatMessage("label.include_linked_tooltip", complement);
- label.setToolTipText(
- JvSwingUtils.wrapTooltip(true, tooltip));
+ label.setToolTipText(JvSwingUtils.wrapTooltip(true, tooltip));
includeLinkedFeatures = new JCheckBox();
linkedFeaturesPanel.add(label);
}
/**
- * Builds the panel with options to output in Jalview, GFF or CSV format. GFF is
- * only made visible when exporting features, CSV only when exporting
+ * Builds the panel with options to output in Jalview, GFF or CSV format. GFF
+ * is only made visible when exporting features, CSV only when exporting
* annotation.
*
* @return
*/
public AnnotationLabels(AlignmentPanel ap)
{
-
+
this.ap = ap;
av = ap.av;
ToolTipManager.sharedInstance().registerComponent(this);
EditNameDialog dialog = new EditNameDialog(annotation.label,
annotation.description, name, description);
- dialog.showDialog(ap.alignFrame, title,
- new Runnable()
- {
- @Override
- public void run()
- {
- annotation.label = dialog.getName();
- String text = dialog.getDescription();
- if (text != null && text.length() == 0)
- {
- text = null;
- }
- annotation.description = text;
- if (addNew)
- {
- ap.av.getAlignment().addAnnotation(annotation);
- ap.av.getAlignment().setAnnotationIndex(annotation, 0);
- }
- ap.refresh(true);
- }
- });
+ dialog.showDialog(ap.alignFrame, title, new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ annotation.label = dialog.getName();
+ String text = dialog.getDescription();
+ if (text != null && text.length() == 0)
+ {
+ text = null;
+ }
+ annotation.description = text;
+ if (addNew)
+ {
+ ap.av.getAlignment().addAnnotation(annotation);
+ ap.av.getAlignment().setAnnotationIndex(annotation, 0);
+ }
+ ap.refresh(true);
+ }
+ });
}
@Override
* @param pop
*/
static void addConsensusMenuOptions(AlignmentPanel ap,
- AlignmentAnnotation ann,
- JPopupMenu pop)
+ AlignmentAnnotation ann, JPopupMenu pop)
{
pop.addSeparator();
@Override
public void colourSelected(Color c)
{
- HiddenColumns hiddenColumns = av.getAlignment().getHiddenColumns();
+ HiddenColumns hiddenColumns = av.getAlignment()
+ .getHiddenColumns();
for (int index : av.getColumnSelection().getSelected())
{
if (hiddenColumns.isVisible(index))
}
fAnot[index].colour = c;
}
- }};
+ }
+ };
};
- JalviewColourChooser.showColourChooser(this,
- title, Color.black, listener);
+ JalviewColourChooser.showColourChooser(this, title, Color.black,
+ listener);
}
else
// HELIX, SHEET or STEM
}
private volatile boolean imageFresh = false;
- private Rectangle visibleRect = new Rectangle(), clipBounds = new Rectangle();
+
+ private Rectangle visibleRect = new Rectangle(),
+ clipBounds = new Rectangle();
/**
* DOCUMENT ME!
@Override
public void paintComponent(Graphics g)
{
-
- // BH: note that this method is generally recommended to
- // call super.paintComponent(g). Otherwise, the children of this
- // component will not be rendered. That is not needed here
- // because AnnotationPanel does not have any children. It is
- // just a JPanel contained in a JViewPort.
+
+ // BH: note that this method is generally recommended to
+ // call super.paintComponent(g). Otherwise, the children of this
+ // component will not be rendered. That is not needed here
+ // because AnnotationPanel does not have any children. It is
+ // just a JPanel contained in a JViewPort.
computeVisibleRect(visibleRect);
-
+
g.setColor(Color.white);
g.fillRect(0, 0, visibleRect.width, visibleRect.height);
if (image != null)
{
- // BH 2018 optimizing generation of new Rectangle().
- if (fastPaint || (visibleRect.width != (clipBounds = g.getClipBounds(clipBounds)).width)
- || (visibleRect.height != clipBounds.height))
+ // BH 2018 optimizing generation of new Rectangle().
+ if (fastPaint
+ || (visibleRect.width != (clipBounds = g
+ .getClipBounds(clipBounds)).width)
+ || (visibleRect.height != clipBounds.height))
{
-
- g.drawImage(image, 0, 0, this);
+ g.drawImage(image, 0, 0, this);
fastPaint = false;
return;
}
gg.setColor(Color.white);
gg.fillRect(0, 0, imgWidth, image.getHeight());
imageFresh = true;
- } else {
- gg = (Graphics2D) image.getGraphics();
+ }
+ else
+ {
+ gg = (Graphics2D) image.getGraphics();
}
-
+
drawComponent(gg, av.getRanges().getStartRes(),
av.getRanges().getEndRes() + 1);
gg.dispose();
gg.translate(-transX, 0);
gg.dispose();
-
+
fastPaint = true;
// Call repaint on alignment panel so that repaints from other alignment
ap = null;
image = null;
fadedImage = null;
-// gg = null;
+ // gg = null;
_mwl = null;
/*
{
slider.setSliderValue(value);
}
+
/**
- * Answers the value of the slider position as a percentage between minimum and
- * maximum of its range
+ * Answers the value of the slider position as a percentage between minimum
+ * and maximum of its range
*
* @return
*/
}
private void openNewJmol(AlignmentPanel ap, boolean alignAdded,
- PDBEntry[] pdbentrys,
- SequenceI[][] seqs)
+ PDBEntry[] pdbentrys, SequenceI[][] seqs)
{
setProgressIndicator(ap.alignFrame);
jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(),
openNewJmol(ap, alignAdded, pe, seqs);
}
-
void initJmol(String command)
{
jmb.setFinishedInit(false);
jmb.jmolViewer.renderScreenImage(g, width, height);
}
};
- String view = MessageManager.getString("action.view").toLowerCase(Locale.ROOT);
+ String view = MessageManager.getString("action.view")
+ .toLowerCase(Locale.ROOT);
ImageExporter exporter = new ImageExporter(writer,
getProgressIndicator(), type, getTitle());
exporter.doExport(null, this, width, height, view);
try
{
BrowserLauncher // BH 2018
- .openURL("http://wiki.jmol.org");//http://jmol.sourceforge.net/docs/JmolUserGuide/");
+ .openURL("http://wiki.jmol.org");// http://jmol.sourceforge.net/docs/JmolUserGuide/");
} catch (Exception ex)
{
System.err.println("Show Jmol help failed with: " + ex.getMessage());
}
}
}
- else if (jmb == null || jmb.jmolViewer == null || !jmb.isFinishedInit())
+ else if (jmb == null || jmb.jmolViewer == null
+ || !jmb.isFinishedInit())
{
g.setColor(Color.black);
g.fillRect(0, 0, currentSize.width, currentSize.height);
{
// todo - record which pdbids were successfully imported.
StringBuilder errormsgs = new StringBuilder();
-
+
List<String> files = new ArrayList<>();
String pdbid = "";
try
String[] filesInViewer = getStructureFiles();
// TODO: replace with reference fetching/transfer code (validate PDBentry
// as a DBRef?)
-
+
for (int pi = 0; pi < getPdbCount(); pi++)
{
PDBEntry strucEntry = getPdbEntry(pi);
if (file == null)
{
pdbid = strucEntry.getId();
- try{
+ try
+ {
file = structureViewer.fetchPdbFile(strucEntry);
} catch (OutOfMemoryError oomerror)
{
ex.printStackTrace();
errormsgs.append("'").append(pdbid).append("'");
}
- if (file!=null)
+ if (file != null)
{
// success
files.add(file);
name += " (Model " + mn++ + ")";
}
_rnaList.add(varnaPanel.getConfig().clone(), r, name,
- true);
- // BH 2018 SwingJS clone of varnaPanel or its config will be the object itself, not a clone
+ true);
+ // BH 2018 SwingJS clone of varnaPanel or its config will
+ // be the object itself, not a clone
}
}
}
*/
public void addStructure(RNA rna)
{
- VARNAConfig config = vp.getConfig().clone(); // BH 2018 this will NOT be a clone in SwingJS
+ VARNAConfig config = vp.getConfig().clone(); // BH 2018 this will NOT be a
+ // clone in SwingJS
addStructure(rna, config);
}
_channelModel = new ChannelListModel();
// Construct our jalview news channel
Channel chan = new Channel();
- chan.setURL(
- Cache.getDefault("JALVIEW_NEWS_RSS",
- Cache.getDefault("www.jalview.org",
- "https://www.jalview.org")
- + "/feeds/desktop/rss"));
+ chan.setURL(Cache.getDefault("JALVIEW_NEWS_RSS",
+ Cache.getDefault("www.jalview.org", "https://www.jalview.org")
+ + "/feeds/desktop/rss"));
loadLastM();
_channelModel.addChannel(chan);
updating = true;
pca = new JRadioButton(
MessageManager.getString("label.principal_component_analysis"));
pca.setOpaque(false);
-
+
neighbourJoining = new JRadioButton(
MessageManager.getString("label.tree_calc_nj"));
neighbourJoining.setSelected(true);
private int myHeight = 150;
- private JMenuItem writeFeatures=null;
+ private JMenuItem writeFeatures = null;
- private JMenu fetchAttributes=null;
-/**
+ private JMenu fetchAttributes = null;
+
+ /**
* Initialise menu options.
*/
@Override
writeFeatures = new JMenuItem(
MessageManager.getString("label.create_viewer_attributes"));
- writeFeatures.setToolTipText(MessageManager
- .getString("label.create_viewer_attributes_tip"));
+ writeFeatures.setToolTipText(
+ MessageManager.getString("label.create_viewer_attributes_tip"));
writeFeatures.addActionListener(new ActionListener()
{
@Override
});
viewerActionMenu.add(writeFeatures);
- fetchAttributes = new JMenu(
- MessageManager.formatMessage("label.fetch_viewer_attributes",getViewerName()));
- fetchAttributes.setToolTipText(
- MessageManager.formatMessage("label.fetch_viewer_attributes_tip",getViewerName()));
+ fetchAttributes = new JMenu(MessageManager.formatMessage(
+ "label.fetch_viewer_attributes", getViewerName()));
+ fetchAttributes.setToolTipText(MessageManager.formatMessage(
+ "label.fetch_viewer_attributes_tip", getViewerName()));
fetchAttributes.addMouseListener(new MouseAdapter()
{
});
viewerActionMenu.add(fetchAttributes);
}
+
@Override
protected void buildActionMenu()
{
// add these back in after menu is refreshed
viewerActionMenu.add(writeFeatures);
viewerActionMenu.add(fetchAttributes);
-
+
};
+
/**
* Query the structure viewer for its residue attribute names and add them as
* items off the attributes menu
{
// todo pull up?
int count = jmb.sendFeaturesToViewer(getAlignmentPanel());
- statusBar.setText(
- MessageManager.formatMessage("label.attributes_set", count, getViewerName()));
+ statusBar.setText(MessageManager.formatMessage("label.attributes_set",
+ count, getViewerName()));
}
/**
* @param ap
*/
public ChimeraViewFrame(PDBEntry[] pe, boolean alignAdded,
- SequenceI[][] seqs,
- AlignmentPanel ap)
+ SequenceI[][] seqs, AlignmentPanel ap)
{
this();
setAlignAddedStructures(alignAdded);
* the colour scheme (inspected in setColourSelected())
*/
final String name = scheme.getSchemeName();
- String label = MessageManager.getStringOrReturn(
- "label.colourScheme_", name);
+ String label = MessageManager.getStringOrReturn("label.colourScheme_",
+ name);
final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(
label);
radioItem.setName(name);
{
if (jalview.bin.Console.log != null)
{
- jalview.bin.Console.log.setLevel((LogLevel) logLevelCombo.getSelectedItem());
+ jalview.bin.Console.log
+ .setLevel((LogLevel) logLevelCombo.getSelectedItem());
}
}
JalviewAppender jappender = new JalviewAppender(level);
JalviewAppender.setTextArea(textArea);
jappender.start();
- if (jalview.bin.Console.log != null && jalview.bin.Console.log instanceof JLoggerLog4j)
+ if (jalview.bin.Console.log != null
+ && jalview.bin.Console.log instanceof JLoggerLog4j)
{
JLoggerLog4j.addAppender(jalview.bin.Console.log, jappender);
}
if (dna && AlignmentUtils.looksLikeEnsembl(alignment))
{
- // override default featureColourScheme so products have Ensembl variant colours
+ // override default featureColourScheme so products have Ensembl variant
+ // colours
featureColourScheme = new SequenceFetcher()
.getFeatureColourScheme(DBRefSource.ENSEMBL);
}
* and for JAL-3330 also to original alignFrame view(s)
* this currently trashes any original settings.
*/
- for (AlignmentViewPanel origpanel: alignFrame.getAlignPanels()) {
+ for (AlignmentViewPanel origpanel : alignFrame.getAlignPanels())
+ {
origpanel.getAlignViewport()
.mergeFeaturesStyle(featureColourScheme);
}
{
return;
}
-
+
Set<String> ensemblDivisions = new EnsemblInfo().getDivisions();
-
+
/*
* first look for direct dbrefs from sequence to Ensembl
*/
copyAlignment = AlignmentUtils.makeCopyAlignment(sel,
xrefs.getSequencesArray(), dataset);
}
- copyAlignment
- .setGapCharacter(alignFrame.viewport.getGapCharacter());
+ copyAlignment.setGapCharacter(alignFrame.viewport.getGapCharacter());
StructureSelectionManager ssm = StructureSelectionManager
.getStructureSelectionManager(Desktop.instance);
if (copyAlignment.getHeight() <= 0)
{
- System.err.println(
- "No Sequences generated for xRef type " + source);
+ System.err.println("No Sequences generated for xRef type " + source);
return null;
}
af.getViewport().setShowSequenceFeatures(showSeqFeatures);
af.getViewport().setFeaturesDisplayed(fd);
af.setMenusForViewport();
- ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
- colourSchemeName, al);
+ ColourSchemeI cs = ColourSchemeMapper
+ .getJalviewColourScheme(colourSchemeName, al);
if (cs != null)
{
af.changeColour(cs);
try
{
- af.setMaximum(
- Cache.getDefault("SHOW_FULLSCREEN", false));
+ af.setMaximum(Cache.getDefault("SHOW_FULLSCREEN", false));
} catch (Exception ex)
{
}
* @version $Revision: 1.155 $
*/
public class Desktop extends jalview.jbgui.GDesktop
- implements DropTargetListener, ClipboardOwner, IProgressIndicator, jalview.api.StructureSelectionManagerProvider {
+ implements DropTargetListener, ClipboardOwner, IProgressIndicator,
+ jalview.api.StructureSelectionManagerProvider
+{
private static final String CITATION;
static
{
* @param listener
* @see jalview.gui.JalviewChangeSupport#addJalviewPropertyChangeListener(java.beans.PropertyChangeListener)
*/
- public void addJalviewPropertyChangeListener(PropertyChangeListener listener) {
+ public void addJalviewPropertyChangeListener(
+ PropertyChangeListener listener)
+ {
changeSupport.addJalviewPropertyChangeListener(listener);
}
* @see jalview.gui.JalviewChangeSupport#addJalviewPropertyChangeListener(java.lang.String,
* java.beans.PropertyChangeListener)
*/
- public void addJalviewPropertyChangeListener(String propertyName, PropertyChangeListener listener) {
+ public void addJalviewPropertyChangeListener(String propertyName,
+ PropertyChangeListener listener)
+ {
changeSupport.addJalviewPropertyChangeListener(propertyName, listener);
}
* @see jalview.gui.JalviewChangeSupport#removeJalviewPropertyChangeListener(java.lang.String,
* java.beans.PropertyChangeListener)
*/
- public void removeJalviewPropertyChangeListener(String propertyName, PropertyChangeListener listener) {
- changeSupport.removeJalviewPropertyChangeListener(propertyName, listener);
+ public void removeJalviewPropertyChangeListener(String propertyName,
+ PropertyChangeListener listener)
+ {
+ changeSupport.removeJalviewPropertyChangeListener(propertyName,
+ listener);
}
/** Singleton Desktop instance */
public static MyDesktopPane desktop;
- public static MyDesktopPane getDesktop() {
+ public static MyDesktopPane getDesktop()
+ {
// BH 2018 could use currentThread() here as a reference to a
// Hashtable<Thread, MyDesktopPane> in JavaScript
return desktop;
static int fileLoadingCount = 0;
- class MyDesktopManager implements DesktopManager {
+ class MyDesktopManager implements DesktopManager
+ {
private DesktopManager delegate;
- public MyDesktopManager(DesktopManager delegate) {
+ public MyDesktopManager(DesktopManager delegate)
+ {
this.delegate = delegate;
}
@Override
- public void activateFrame(JInternalFrame f) {
- try {
+ public void activateFrame(JInternalFrame f)
+ {
+ try
+ {
delegate.activateFrame(f);
- } catch (NullPointerException npe) {
+ } catch (NullPointerException npe)
+ {
Point p = getMousePosition();
instance.showPasteMenu(p.x, p.y);
}
}
@Override
- public void beginDraggingFrame(JComponent f) {
+ public void beginDraggingFrame(JComponent f)
+ {
delegate.beginDraggingFrame(f);
}
@Override
- public void beginResizingFrame(JComponent f, int direction) {
+ public void beginResizingFrame(JComponent f, int direction)
+ {
delegate.beginResizingFrame(f, direction);
}
@Override
- public void closeFrame(JInternalFrame f) {
+ public void closeFrame(JInternalFrame f)
+ {
delegate.closeFrame(f);
}
@Override
- public void deactivateFrame(JInternalFrame f) {
+ public void deactivateFrame(JInternalFrame f)
+ {
delegate.deactivateFrame(f);
}
@Override
- public void deiconifyFrame(JInternalFrame f) {
+ public void deiconifyFrame(JInternalFrame f)
+ {
delegate.deiconifyFrame(f);
}
@Override
- public void dragFrame(JComponent f, int newX, int newY) {
- if (newY < 0) {
+ public void dragFrame(JComponent f, int newX, int newY)
+ {
+ if (newY < 0)
+ {
newY = 0;
}
delegate.dragFrame(f, newX, newY);
}
@Override
- public void endDraggingFrame(JComponent f) {
+ public void endDraggingFrame(JComponent f)
+ {
delegate.endDraggingFrame(f);
desktop.repaint();
}
@Override
- public void endResizingFrame(JComponent f) {
+ public void endResizingFrame(JComponent f)
+ {
delegate.endResizingFrame(f);
desktop.repaint();
}
@Override
- public void iconifyFrame(JInternalFrame f) {
+ public void iconifyFrame(JInternalFrame f)
+ {
delegate.iconifyFrame(f);
}
@Override
- public void maximizeFrame(JInternalFrame f) {
+ public void maximizeFrame(JInternalFrame f)
+ {
delegate.maximizeFrame(f);
}
@Override
- public void minimizeFrame(JInternalFrame f) {
+ public void minimizeFrame(JInternalFrame f)
+ {
delegate.minimizeFrame(f);
}
@Override
- public void openFrame(JInternalFrame f) {
+ public void openFrame(JInternalFrame f)
+ {
delegate.openFrame(f);
}
@Override
- public void resizeFrame(JComponent f, int newX, int newY, int newWidth, int newHeight) {
- if (newY < 0) {
+ public void resizeFrame(JComponent f, int newX, int newY, int newWidth,
+ int newHeight)
+ {
+ if (newY < 0)
+ {
newY = 0;
}
delegate.resizeFrame(f, newX, newY, newWidth, newHeight);
}
@Override
- public void setBoundsForFrame(JComponent f, int newX, int newY, int newWidth, int newHeight) {
+ public void setBoundsForFrame(JComponent f, int newX, int newY,
+ int newWidth, int newHeight)
+ {
delegate.setBoundsForFrame(f, newX, newY, newWidth, newHeight);
}
/**
* Creates a new Desktop object.
*/
- public Desktop() {
+ public Desktop()
+ {
super();
/**
- * A note to implementors. It is ESSENTIAL that any activities that might block
- * are spawned off as threads rather than waited for during this constructor.
+ * A note to implementors. It is ESSENTIAL that any activities that might
+ * block are spawned off as threads rather than waited for during this
+ * constructor.
*/
instance = this;
doConfigureStructurePrefs();
- setTitle(ChannelProperties.getProperty("app_name") + " " + Cache.getProperty("VERSION"));
+ setTitle(ChannelProperties.getProperty("app_name") + " "
+ + Cache.getProperty("VERSION"));
/**
* Set taskbar "grouped windows" name for linux desktops (works in GNOME and
- * KDE). This uses sun.awt.X11.XToolkit.awtAppClassName which is not officially
- * documented or guaranteed to exist, so we access it via reflection. There
- * appear to be unfathomable criteria about what this string can contain, and it
- * if doesn't meet those criteria then "java" (KDE) or "jalview-bin-Jalview"
- * (GNOME) is used. "Jalview", "Jalview Develop" and "Jalview Test" seem okay,
- * but "Jalview non-release" does not. The reflection access may generate a
- * warning: WARNING: An illegal reflective access operation has occurred
- * WARNING: Illegal reflective access by jalview.gui.Desktop () to field
+ * KDE). This uses sun.awt.X11.XToolkit.awtAppClassName which is not
+ * officially documented or guaranteed to exist, so we access it via
+ * reflection. There appear to be unfathomable criteria about what this
+ * string can contain, and it if doesn't meet those criteria then "java"
+ * (KDE) or "jalview-bin-Jalview" (GNOME) is used. "Jalview", "Jalview
+ * Develop" and "Jalview Test" seem okay, but "Jalview non-release" does
+ * not. The reflection access may generate a warning: WARNING: An illegal
+ * reflective access operation has occurred WARNING: Illegal reflective
+ * access by jalview.gui.Desktop () to field
* sun.awt.X11.XToolkit.awtAppClassName which I don't think can be avoided.
*/
- if (Platform.isLinux()) {
- try {
+ if (Platform.isLinux())
+ {
+ try
+ {
Toolkit xToolkit = Toolkit.getDefaultToolkit();
Field[] declaredFields = xToolkit.getClass().getDeclaredFields();
Field awtAppClassNameField = null;
- if (Arrays.stream(declaredFields).anyMatch(f -> f.getName().equals("awtAppClassName"))) {
- awtAppClassNameField = xToolkit.getClass().getDeclaredField("awtAppClassName");
+ if (Arrays.stream(declaredFields)
+ .anyMatch(f -> f.getName().equals("awtAppClassName")))
+ {
+ awtAppClassNameField = xToolkit.getClass()
+ .getDeclaredField("awtAppClassName");
}
String title = ChannelProperties.getProperty("app_name");
- if (awtAppClassNameField != null) {
+ if (awtAppClassNameField != null)
+ {
awtAppClassNameField.setAccessible(true);
awtAppClassNameField.set(xToolkit, title);
- } else {
+ }
+ else
+ {
jalview.bin.Console.debug("XToolkit: awtAppClassName not found");
}
- } catch (Exception e) {
+ } catch (Exception e)
+ {
jalview.bin.Console.debug("Error setting awtAppClassName");
jalview.bin.Console.trace(Cache.getStackTraceString(e));
}
}
/**
- * APQHandlers sets handlers for About, Preferences and Quit actions peculiar to
- * macOS's application menu. APQHandlers will check to see if a handler is
- * supported before setting it.
+ * APQHandlers sets handlers for About, Preferences and Quit actions
+ * peculiar to macOS's application menu. APQHandlers will check to see if a
+ * handler is supported before setting it.
*/
- try {
+ try
+ {
APQHandlers.setAPQHandlers(this);
- } catch (Exception e) {
+ } catch (Exception e)
+ {
System.out.println("Cannot set APQHandlers");
// e.printStackTrace();
- } catch (Throwable t) {
- jalview.bin.Console.warn("Error setting APQHandlers: " + t.toString());
+ } catch (Throwable t)
+ {
+ jalview.bin.Console
+ .warn("Error setting APQHandlers: " + t.toString());
jalview.bin.Console.trace(Cache.getStackTraceString(t));
}
setIconImages(ChannelProperties.getIconList());
- addWindowListener(new WindowAdapter() {
+ addWindowListener(new WindowAdapter()
+ {
@Override
- public void windowClosing(WindowEvent ev) {
+ public void windowClosing(WindowEvent ev)
+ {
quit();
}
});
// getContentPane().add(sp, BorderLayout.CENTER);
// BH 2018 - just an experiment to try unclipped JInternalFrames.
- if (Platform.isJS()) {
+ if (Platform.isJS())
+ {
getRootPane().putClientProperty("swingjs.overflow.hidden", "false");
}
// This line prevents Windows Look&Feel resizing all new windows to maximum
// if previous window was maximised
- desktop.setDesktopManager(new MyDesktopManager((Platform.isWindowsAndNotJS() ? new DefaultDesktopManager()
- : Platform.isAMacAndNotJS() ? new AquaInternalFrameManager(desktop.getDesktopManager())
- : desktop.getDesktopManager())));
+ desktop.setDesktopManager(new MyDesktopManager(
+ (Platform.isWindowsAndNotJS() ? new DefaultDesktopManager()
+ : Platform.isAMacAndNotJS()
+ ? new AquaInternalFrameManager(
+ desktop.getDesktopManager())
+ : desktop.getDesktopManager())));
Rectangle dims = getLastKnownDimensions("");
- if (dims != null) {
+ if (dims != null)
+ {
setBounds(dims);
- } else {
+ }
+ else
+ {
Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
int xPos = Math.max(5, (screenSize.width - 900) / 2);
int yPos = Math.max(5, (screenSize.height - 650) / 2);
checkURLLinks();
// Spawn a thread that shows the splashscreen
- if (!nosplash) {
- SwingUtilities.invokeLater(new Runnable() {
+ if (!nosplash)
+ {
+ SwingUtilities.invokeLater(new Runnable()
+ {
@Override
- public void run() {
+ public void run()
+ {
new SplashScreen(true);
}
});
// Thread off a new instance of the file chooser - this reduces the time
// it
// takes to open it later on.
- new Thread(new Runnable() {
+ new Thread(new Runnable()
+ {
@Override
- public void run() {
+ public void run()
+ {
jalview.bin.Console.debug("Filechooser init thread started.");
String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
- JalviewFileChooser.forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
+ JalviewFileChooser.forRead(Cache.getProperty("LAST_DIRECTORY"),
+ fileFormat);
jalview.bin.Console.debug("Filechooser init thread finished.");
}
}).start();
// Add the service change listener
- changeSupport.addJalviewPropertyChangeListener("services", new PropertyChangeListener() {
+ changeSupport.addJalviewPropertyChangeListener("services",
+ new PropertyChangeListener()
+ {
- @Override
- public void propertyChange(PropertyChangeEvent evt) {
- jalview.bin.Console.debug("Firing service changed event for " + evt.getNewValue());
- JalviewServicesChanged(evt);
- }
- });
+ @Override
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ jalview.bin.Console
+ .debug("Firing service changed event for "
+ + evt.getNewValue());
+ JalviewServicesChanged(evt);
+ }
+ });
}
this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));
- this.addWindowListener(new WindowAdapter() {
+ this.addWindowListener(new WindowAdapter()
+ {
@Override
- public void windowClosing(WindowEvent evt) {
+ public void windowClosing(WindowEvent evt)
+ {
quit();
}
});
MouseAdapter ma;
- this.addMouseListener(ma = new MouseAdapter() {
+ this.addMouseListener(ma = new MouseAdapter()
+ {
@Override
- public void mousePressed(MouseEvent evt) {
+ public void mousePressed(MouseEvent evt)
+ {
if (evt.isPopupTrigger()) // Mac
{
showPasteMenu(evt.getX(), evt.getY());
}
@Override
- public void mouseReleased(MouseEvent evt) {
+ public void mouseReleased(MouseEvent evt)
+ {
if (evt.isPopupTrigger()) // Windows
{
showPasteMenu(evt.getX(), evt.getY());
*
* @return
*/
- public boolean showExperimental() {
- String experimental = Cache.getDefault(EXPERIMENTAL_FEATURES, Boolean.FALSE.toString());
+ public boolean showExperimental()
+ {
+ String experimental = Cache.getDefault(EXPERIMENTAL_FEATURES,
+ Boolean.FALSE.toString());
return Boolean.valueOf(experimental).booleanValue();
}
- public void doConfigureStructurePrefs() {
+ public void doConfigureStructurePrefs()
+ {
// configure services
- StructureSelectionManager ssm = StructureSelectionManager.getStructureSelectionManager(this);
- if (Cache.getDefault(Preferences.ADD_SS_ANN, true)) {
- ssm.setAddTempFacAnnot(Cache.getDefault(Preferences.ADD_TEMPFACT_ANN, true));
- ssm.setProcessSecondaryStructure(Cache.getDefault(Preferences.STRUCT_FROM_PDB, true));
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(this);
+ if (Cache.getDefault(Preferences.ADD_SS_ANN, true))
+ {
+ ssm.setAddTempFacAnnot(
+ Cache.getDefault(Preferences.ADD_TEMPFACT_ANN, true));
+ ssm.setProcessSecondaryStructure(
+ Cache.getDefault(Preferences.STRUCT_FROM_PDB, true));
// JAL-3915 - RNAView is no longer an option so this has no effect
- ssm.setSecStructServices(Cache.getDefault(Preferences.USE_RNAVIEW, false));
- } else {
+ ssm.setSecStructServices(
+ Cache.getDefault(Preferences.USE_RNAVIEW, false));
+ }
+ else
+ {
ssm.setAddTempFacAnnot(false);
ssm.setProcessSecondaryStructure(false);
ssm.setSecStructServices(false);
}
}
- public void checkForNews() {
+ public void checkForNews()
+ {
final Desktop me = this;
// Thread off the news reader, in case there are connection problems.
- new Thread(new Runnable() {
+ new Thread(new Runnable()
+ {
@Override
- public void run() {
+ public void run()
+ {
jalview.bin.Console.debug("Starting news thread.");
jvnews = new BlogReader(me);
showNews.setVisible(true);
@Override
public void run()
{
- jalview.bin.Console.debug("Downloading data from identifiers.org");
+ jalview.bin.Console
+ .debug("Downloading data from identifiers.org");
try
{
UrlDownloadClient.download(IdOrgSettings.getUrl(),
IdOrgSettings.getDownloadLocation());
} catch (IOException e)
{
- jalview.bin.Console.debug("Exception downloading identifiers.org data"
- + e.getMessage());
+ jalview.bin.Console
+ .debug("Exception downloading identifiers.org data"
+ + e.getMessage());
}
}
}).start();
}
@Override
- protected void showNews_actionPerformed(ActionEvent e) {
+ protected void showNews_actionPerformed(ActionEvent e)
+ {
showNews(showNews.isSelected());
}
- void showNews(boolean visible) {
+ void showNews(boolean visible)
+ {
jalview.bin.Console.debug((visible ? "Showing" : "Hiding") + " news.");
showNews.setSelected(visible);
- if (visible && !jvnews.isVisible()) {
- new Thread(new Runnable() {
+ if (visible && !jvnews.isVisible())
+ {
+ new Thread(new Runnable()
+ {
@Override
- public void run() {
+ public void run()
+ {
long now = System.currentTimeMillis();
- Desktop.instance.setProgressBar(MessageManager.getString("status.refreshing_news"), now);
+ Desktop.instance.setProgressBar(
+ MessageManager.getString("status.refreshing_news"), now);
jvnews.refreshNews();
Desktop.instance.setProgressBar(null, now);
jvnews.showNews();
/**
* recover the last known dimensions for a jalview window
*
- * @param windowName - empty string is desktop, all other windows have unique
- * prefix
+ * @param windowName
+ * - empty string is desktop, all other windows have unique prefix
* @return null or last known dimensions scaled to current geometry (if last
* window geom was known)
*/
- Rectangle getLastKnownDimensions(String windowName) {
+ Rectangle getLastKnownDimensions(String windowName)
+ {
// TODO: lock aspect ratio for scaling desktop Bug #0058199
Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
String x = Cache.getProperty(windowName + "SCREEN_X");
String y = Cache.getProperty(windowName + "SCREEN_Y");
String width = Cache.getProperty(windowName + "SCREEN_WIDTH");
String height = Cache.getProperty(windowName + "SCREEN_HEIGHT");
- if ((x != null) && (y != null) && (width != null) && (height != null)) {
- int ix = Integer.parseInt(x), iy = Integer.parseInt(y), iw = Integer.parseInt(width),
- ih = Integer.parseInt(height);
- if (Cache.getProperty("SCREENGEOMETRY_WIDTH") != null) {
+ if ((x != null) && (y != null) && (width != null) && (height != null))
+ {
+ int ix = Integer.parseInt(x), iy = Integer.parseInt(y),
+ iw = Integer.parseInt(width), ih = Integer.parseInt(height);
+ if (Cache.getProperty("SCREENGEOMETRY_WIDTH") != null)
+ {
// attempt #1 - try to cope with change in screen geometry - this
// version doesn't preserve original jv aspect ratio.
// take ratio of current screen size vs original screen size.
- double sw = ((1f * screenSize.width) / (1f * Integer.parseInt(Cache.getProperty("SCREENGEOMETRY_WIDTH"))));
- double sh = ((1f * screenSize.height) / (1f * Integer.parseInt(Cache.getProperty("SCREENGEOMETRY_HEIGHT"))));
+ double sw = ((1f * screenSize.width) / (1f * Integer
+ .parseInt(Cache.getProperty("SCREENGEOMETRY_WIDTH"))));
+ double sh = ((1f * screenSize.height) / (1f * Integer
+ .parseInt(Cache.getProperty("SCREENGEOMETRY_HEIGHT"))));
// rescale the bounds depending upon the current screen geometry.
ix = (int) (ix * sw);
iw = (int) (iw * sw);
iy = (int) (iy * sh);
ih = (int) (ih * sh);
- while (ix >= screenSize.width) {
- jalview.bin.Console.debug("Window geometry location recall error: shifting horizontal to within screenbounds.");
+ while (ix >= screenSize.width)
+ {
+ jalview.bin.Console.debug(
+ "Window geometry location recall error: shifting horizontal to within screenbounds.");
ix -= screenSize.width;
}
- while (iy >= screenSize.height) {
- jalview.bin.Console.debug("Window geometry location recall error: shifting vertical to within screenbounds.");
+ while (iy >= screenSize.height)
+ {
+ jalview.bin.Console.debug(
+ "Window geometry location recall error: shifting vertical to within screenbounds.");
iy -= screenSize.height;
}
- jalview.bin.Console.debug("Got last known dimensions for " + windowName + ": x:" + ix + " y:" + iy + " width:" + iw
- + " height:" + ih);
+ jalview.bin.Console.debug(
+ "Got last known dimensions for " + windowName + ": x:" + ix
+ + " y:" + iy + " width:" + iw + " height:" + ih);
}
// return dimensions for new instance
return new Rectangle(ix, iy, iw, ih);
return null;
}
- void showPasteMenu(int x, int y) {
+ void showPasteMenu(int x, int y)
+ {
JPopupMenu popup = new JPopupMenu();
- JMenuItem item = new JMenuItem(MessageManager.getString("label.paste_new_window"));
- item.addActionListener(new ActionListener() {
+ JMenuItem item = new JMenuItem(
+ MessageManager.getString("label.paste_new_window"));
+ item.addActionListener(new ActionListener()
+ {
@Override
- public void actionPerformed(ActionEvent evt) {
+ public void actionPerformed(ActionEvent evt)
+ {
paste();
}
});
popup.show(this, x, y);
}
- public void paste() {
- try {
+ public void paste()
+ {
+ try
+ {
Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
Transferable contents = c.getContents(this);
- if (contents != null) {
- String file = (String) contents.getTransferData(DataFlavor.stringFlavor);
+ if (contents != null)
+ {
+ String file = (String) contents
+ .getTransferData(DataFlavor.stringFlavor);
- FileFormatI format = new IdentifyFile().identify(file, DataSourceType.PASTE);
+ FileFormatI format = new IdentifyFile().identify(file,
+ DataSourceType.PASTE);
new FileLoader().LoadFile(file, DataSourceType.PASTE, format);
}
- } catch (Exception ex) {
- System.out.println("Unable to paste alignment from system clipboard:\n" + ex);
+ } catch (Exception ex)
+ {
+ System.out.println(
+ "Unable to paste alignment from system clipboard:\n" + ex);
}
}
/**
* Adds and opens the given frame to the desktop
*
- * @param frame Frame to show
- * @param title Visible Title
- * @param w width
- * @param h height
- */
- public static synchronized void addInternalFrame(final JInternalFrame frame, String title, int w, int h) {
+ * @param frame
+ * Frame to show
+ * @param title
+ * Visible Title
+ * @param w
+ * width
+ * @param h
+ * height
+ */
+ public static synchronized void addInternalFrame(
+ final JInternalFrame frame, String title, int w, int h)
+ {
addInternalFrame(frame, title, true, w, h, true, false);
}
/**
* Add an internal frame to the Jalview desktop
*
- * @param frame Frame to show
- * @param title Visible Title
- * @param makeVisible When true, display frame immediately, otherwise, caller
- * must call setVisible themselves.
- * @param w width
- * @param h height
- */
- public static synchronized void addInternalFrame(final JInternalFrame frame, String title, boolean makeVisible, int w,
- int h) {
+ * @param frame
+ * Frame to show
+ * @param title
+ * Visible Title
+ * @param makeVisible
+ * When true, display frame immediately, otherwise, caller must call
+ * setVisible themselves.
+ * @param w
+ * width
+ * @param h
+ * height
+ */
+ public static synchronized void addInternalFrame(
+ final JInternalFrame frame, String title, boolean makeVisible,
+ int w, int h)
+ {
addInternalFrame(frame, title, makeVisible, w, h, true, false);
}
/**
* Add an internal frame to the Jalview desktop and make it visible
*
- * @param frame Frame to show
- * @param title Visible Title
- * @param w width
- * @param h height
- * @param resizable Allow resize
- */
- public static synchronized void addInternalFrame(final JInternalFrame frame, String title, int w, int h,
- boolean resizable) {
+ * @param frame
+ * Frame to show
+ * @param title
+ * Visible Title
+ * @param w
+ * width
+ * @param h
+ * height
+ * @param resizable
+ * Allow resize
+ */
+ public static synchronized void addInternalFrame(
+ final JInternalFrame frame, String title, int w, int h,
+ boolean resizable)
+ {
addInternalFrame(frame, title, true, w, h, resizable, false);
}
/**
* Add an internal frame to the Jalview desktop
*
- * @param frame Frame to show
- * @param title Visible Title
- * @param makeVisible When true, display frame immediately, otherwise, caller
- * must call setVisible themselves.
- * @param w width
- * @param h height
- * @param resizable Allow resize
- * @param ignoreMinSize Do not set the default minimum size for frame
- */
- public static synchronized void addInternalFrame(final JInternalFrame frame, String title, boolean makeVisible, int w,
- int h, boolean resizable, boolean ignoreMinSize) {
+ * @param frame
+ * Frame to show
+ * @param title
+ * Visible Title
+ * @param makeVisible
+ * When true, display frame immediately, otherwise, caller must call
+ * setVisible themselves.
+ * @param w
+ * width
+ * @param h
+ * height
+ * @param resizable
+ * Allow resize
+ * @param ignoreMinSize
+ * Do not set the default minimum size for frame
+ */
+ public static synchronized void addInternalFrame(
+ final JInternalFrame frame, String title, boolean makeVisible,
+ int w, int h, boolean resizable, boolean ignoreMinSize)
+ {
// TODO: allow callers to determine X and Y position of frame (eg. via
// bounds object).
// the current window title
frame.setTitle(title);
- if (frame.getWidth() < 1 || frame.getHeight() < 1) {
+ if (frame.getWidth() < 1 || frame.getHeight() < 1)
+ {
frame.setSize(w, h);
}
// THIS IS A PUBLIC STATIC METHOD, SO IT MAY BE CALLED EVEN IN
// IF JALVIEW IS RUNNING HEADLESS
// ///////////////////////////////////////////////
if (instance == null || (System.getProperty("java.awt.headless") != null
- && System.getProperty("java.awt.headless").equals("true"))) {
+ && System.getProperty("java.awt.headless").equals("true")))
+ {
return;
}
openFrameCount++;
- if (!ignoreMinSize) {
- frame.setMinimumSize(new Dimension(DEFAULT_MIN_WIDTH, DEFAULT_MIN_HEIGHT));
+ if (!ignoreMinSize)
+ {
+ frame.setMinimumSize(
+ new Dimension(DEFAULT_MIN_WIDTH, DEFAULT_MIN_HEIGHT));
// Set default dimension for Alignment Frame window.
// The Alignment Frame window could be added from a number of places,
// hence,
// I did this here in order not to miss out on any Alignment frame.
- if (frame instanceof AlignFrame) {
- frame.setMinimumSize(new Dimension(ALIGN_FRAME_DEFAULT_MIN_WIDTH, ALIGN_FRAME_DEFAULT_MIN_HEIGHT));
+ if (frame instanceof AlignFrame)
+ {
+ frame.setMinimumSize(new Dimension(ALIGN_FRAME_DEFAULT_MIN_WIDTH,
+ ALIGN_FRAME_DEFAULT_MIN_HEIGHT));
}
}
frame.setIconifiable(resizable);
frame.setOpaque(Platform.isJS());
- if (frame.getX() < 1 && frame.getY() < 1) {
- frame.setLocation(xOffset * openFrameCount, yOffset * ((openFrameCount - 1) % 10) + yOffset);
+ if (frame.getX() < 1 && frame.getY() < 1)
+ {
+ frame.setLocation(xOffset * openFrameCount,
+ yOffset * ((openFrameCount - 1) % 10) + yOffset);
}
/*
* frame is closed)
*/
final JMenuItem menuItem = new JMenuItem(title);
- frame.addInternalFrameListener(new InternalFrameAdapter() {
+ frame.addInternalFrameListener(new InternalFrameAdapter()
+ {
@Override
- public void internalFrameActivated(InternalFrameEvent evt) {
+ public void internalFrameActivated(InternalFrameEvent evt)
+ {
JInternalFrame itf = desktop.getSelectedFrame();
- if (itf != null) {
- if (itf instanceof AlignFrame) {
+ if (itf != null)
+ {
+ if (itf instanceof AlignFrame)
+ {
Jalview.setCurrentAlignFrame((AlignFrame) itf);
}
itf.requestFocus();
}
@Override
- public void internalFrameClosed(InternalFrameEvent evt) {
+ public void internalFrameClosed(InternalFrameEvent evt)
+ {
PaintRefresher.RemoveComponent(frame);
/*
* defensive check to prevent frames being added half off the window
*/
- if (openFrameCount > 0) {
+ if (openFrameCount > 0)
+ {
openFrameCount--;
}
/*
* ensure no reference to alignFrame retained by menu item listener
*/
- if (menuItem.getActionListeners().length > 0) {
+ if (menuItem.getActionListeners().length > 0)
+ {
menuItem.removeActionListener(menuItem.getActionListeners()[0]);
}
windowMenu.remove(menuItem);
}
});
- menuItem.addActionListener(new ActionListener() {
+ menuItem.addActionListener(new ActionListener()
+ {
@Override
- public void actionPerformed(ActionEvent e) {
- try {
+ public void actionPerformed(ActionEvent e)
+ {
+ try
+ {
frame.setSelected(true);
frame.setIcon(false);
- } catch (java.beans.PropertyVetoException ex) {
+ } catch (java.beans.PropertyVetoException ex)
+ {
}
}
windowMenu.add(menuItem);
frame.toFront();
- try {
+ try
+ {
frame.setSelected(true);
frame.requestFocus();
- } catch (java.beans.PropertyVetoException ve) {
- } catch (java.lang.ClassCastException cex) {
+ } catch (java.beans.PropertyVetoException ve)
+ {
+ } catch (java.lang.ClassCastException cex)
+ {
jalview.bin.Console.warn(
- "Squashed a possible GUI implementation error. If you can recreate this, please look at https://issues.jalview.org/browse/JAL-869",
- cex);
+ "Squashed a possible GUI implementation error. If you can recreate this, please look at https://issues.jalview.org/browse/JAL-869",
+ cex);
}
}
/**
- * Add key bindings to a JInternalFrame so that Ctrl-W and Cmd-W will close the
- * window
+ * Add key bindings to a JInternalFrame so that Ctrl-W and Cmd-W will close
+ * the window
*
* @param frame
*/
- private static void setKeyBindings(JInternalFrame frame) {
+ private static void setKeyBindings(JInternalFrame frame)
+ {
@SuppressWarnings("serial")
- final Action closeAction = new AbstractAction() {
+ final Action closeAction = new AbstractAction()
+ {
@Override
- public void actionPerformed(ActionEvent e) {
+ public void actionPerformed(ActionEvent e)
+ {
frame.dispose();
}
};
/*
* set up key bindings for Ctrl-W and Cmd-W, with the same (Close) action
*/
- KeyStroke ctrlWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W, InputEvent.CTRL_DOWN_MASK);
- KeyStroke cmdWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W, ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx());
+ KeyStroke ctrlWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W,
+ InputEvent.CTRL_DOWN_MASK);
+ KeyStroke cmdWKey = KeyStroke.getKeyStroke(KeyEvent.VK_W,
+ ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx());
- InputMap inputMap = frame.getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW);
+ InputMap inputMap = frame
+ .getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW);
String ctrlW = ctrlWKey.toString();
inputMap.put(ctrlWKey, ctrlW);
inputMap.put(cmdWKey, ctrlW);
}
@Override
- public void lostOwnership(Clipboard clipboard, Transferable contents) {
- if (!internalCopy) {
+ public void lostOwnership(Clipboard clipboard, Transferable contents)
+ {
+ if (!internalCopy)
+ {
Desktop.jalviewClipboard = null;
}
}
@Override
- public void dragEnter(DropTargetDragEvent evt) {
+ public void dragEnter(DropTargetDragEvent evt)
+ {
}
@Override
- public void dragExit(DropTargetEvent evt) {
+ public void dragExit(DropTargetEvent evt)
+ {
}
@Override
- public void dragOver(DropTargetDragEvent evt) {
+ public void dragOver(DropTargetDragEvent evt)
+ {
}
@Override
- public void dropActionChanged(DropTargetDragEvent evt) {
+ public void dropActionChanged(DropTargetDragEvent evt)
+ {
}
/**
* DOCUMENT ME!
*
- * @param evt DOCUMENT ME!
+ * @param evt
+ * DOCUMENT ME!
*/
@Override
- public void drop(DropTargetDropEvent evt) {
+ public void drop(DropTargetDropEvent evt)
+ {
boolean success = true;
// JAL-1552 - acceptDrop required before getTransferable call for
// Java's Transferable for native dnd
List<Object> files = new ArrayList<>();
List<DataSourceType> protocols = new ArrayList<>();
- try {
+ try
+ {
Desktop.transferFromDropTarget(files, protocols, evt, t);
- } catch (Exception e) {
+ } catch (Exception e)
+ {
e.printStackTrace();
success = false;
}
- if (files != null) {
- try {
- for (int i = 0; i < files.size(); i++) {
+ if (files != null)
+ {
+ try
+ {
+ for (int i = 0; i < files.size(); i++)
+ {
// BH 2018 File or String
Object file = files.get(i);
String fileName = file.toString();
- DataSourceType protocol = (protocols == null) ? DataSourceType.FILE : protocols.get(i);
+ DataSourceType protocol = (protocols == null)
+ ? DataSourceType.FILE
+ : protocols.get(i);
FileFormatI format = null;
- if (fileName.endsWith(".jar")) {
+ if (fileName.endsWith(".jar"))
+ {
format = FileFormat.Jalview;
- } else {
+ }
+ else
+ {
format = new IdentifyFile().identify(file, protocol);
}
- if (file instanceof File) {
+ if (file instanceof File)
+ {
Platform.cacheFileData((File) file);
}
new FileLoader().LoadFile(null, file, protocol, format);
}
- } catch (Exception ex) {
+ } catch (Exception ex)
+ {
success = false;
}
}
/**
* DOCUMENT ME!
*
- * @param e DOCUMENT ME!
+ * @param e
+ * DOCUMENT ME!
*/
@Override
- public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport) {
+ public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport)
+ {
String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
- JalviewFileChooser chooser = JalviewFileChooser.forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat,
- BackupFiles.getEnabled());
+ JalviewFileChooser chooser = JalviewFileChooser.forRead(
+ Cache.getProperty("LAST_DIRECTORY"), fileFormat,
+ BackupFiles.getEnabled());
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager.getString("label.open_local_file"));
+ chooser.setDialogTitle(
+ MessageManager.getString("label.open_local_file"));
chooser.setToolTipText(MessageManager.getString("action.open"));
- chooser.setResponseHandler(0, new Runnable() {
+ chooser.setResponseHandler(0, new Runnable()
+ {
@Override
- public void run() {
+ public void run()
+ {
File selectedFile = chooser.getSelectedFile();
Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent());
* Skip this step for dynamically added file formats, because IdentifyFile does
* not know how to recognise them.
*/
- if (FileFormats.getInstance().isIdentifiable(format)) {
- try {
- format = new IdentifyFile().identify(selectedFile, DataSourceType.FILE);
- } catch (FileFormatException e) {
+ if (FileFormats.getInstance().isIdentifiable(format))
+ {
+ try
+ {
+ format = new IdentifyFile().identify(selectedFile,
+ DataSourceType.FILE);
+ } catch (FileFormatException e)
+ {
// format = null; //??
}
}
- new FileLoader().LoadFile(viewport, selectedFile, DataSourceType.FILE, format);
+ new FileLoader().LoadFile(viewport, selectedFile,
+ DataSourceType.FILE, format);
}
});
chooser.showOpenDialog(this);
* @param viewport
*/
@Override
- public void inputURLMenuItem_actionPerformed(AlignViewport viewport) {
+ public void inputURLMenuItem_actionPerformed(AlignViewport viewport)
+ {
// This construct allows us to have a wider textfield
// for viewing
- JLabel label = new JLabel(MessageManager.getString("label.input_file_url"));
+ JLabel label = new JLabel(
+ MessageManager.getString("label.input_file_url"));
JPanel panel = new JPanel(new GridLayout(2, 1));
panel.add(label);
*/
JComponent history;
String urlBase = "https://www.";
- if (Platform.isJS()) {
+ if (Platform.isJS())
+ {
history = new JTextField(urlBase, 35);
- } else
+ }
+ else
/**
* Java only
*
asCombo.setEditable(true);
asCombo.addItem(urlBase);
String historyItems = Cache.getProperty("RECENT_URL");
- if (historyItems != null) {
- for (String token : historyItems.split("\\t")) {
+ if (historyItems != null)
+ {
+ for (String token : historyItems.split("\\t"))
+ {
asCombo.addItem(token);
}
}
Object[] options = new Object[] { MessageManager.getString("action.ok"),
MessageManager.getString("action.cancel") };
- Runnable action = new Runnable() {
+ Runnable action = new Runnable()
+ {
@Override
- public void run() {
+ public void run()
+ {
@SuppressWarnings("unchecked")
- String url = (history instanceof JTextField ? ((JTextField) history).getText()
- : ((JComboBox<String>) history).getEditor().getItem().toString().trim());
-
- if (url.toLowerCase(Locale.ROOT).endsWith(".jar")) {
- if (viewport != null) {
- new FileLoader().LoadFile(viewport, url, DataSourceType.URL, FileFormat.Jalview);
- } else {
- new FileLoader().LoadFile(url, DataSourceType.URL, FileFormat.Jalview);
+ String url = (history instanceof JTextField
+ ? ((JTextField) history).getText()
+ : ((JComboBox<String>) history).getEditor().getItem()
+ .toString().trim());
+
+ if (url.toLowerCase(Locale.ROOT).endsWith(".jar"))
+ {
+ if (viewport != null)
+ {
+ new FileLoader().LoadFile(viewport, url, DataSourceType.URL,
+ FileFormat.Jalview);
}
- } else {
+ else
+ {
+ new FileLoader().LoadFile(url, DataSourceType.URL,
+ FileFormat.Jalview);
+ }
+ }
+ else
+ {
FileFormatI format = null;
- try {
+ try
+ {
format = new IdentifyFile().identify(url, DataSourceType.URL);
- } catch (FileFormatException e) {
+ } catch (FileFormatException e)
+ {
// TODO revise error handling, distinguish between
// URL not found and response not valid
}
- if (format == null) {
- String msg = MessageManager.formatMessage("label.couldnt_locate", url);
+ if (format == null)
+ {
+ String msg = MessageManager
+ .formatMessage("label.couldnt_locate", url);
JvOptionPane.showInternalMessageDialog(Desktop.desktop, msg,
- MessageManager.getString("label.url_not_found"), JvOptionPane.WARNING_MESSAGE);
+ MessageManager.getString("label.url_not_found"),
+ JvOptionPane.WARNING_MESSAGE);
return;
}
- if (viewport != null) {
- new FileLoader().LoadFile(viewport, url, DataSourceType.URL, format);
- } else {
+ if (viewport != null)
+ {
+ new FileLoader().LoadFile(viewport, url, DataSourceType.URL,
+ format);
+ }
+ else
+ {
new FileLoader().LoadFile(url, DataSourceType.URL, format);
}
}
}
};
- String dialogOption = MessageManager.getString("label.input_alignment_from_url");
- JvOptionPane.newOptionDialog(desktop).setResponseHandler(0, action).showInternalDialog(panel, dialogOption,
- JvOptionPane.YES_NO_CANCEL_OPTION, JvOptionPane.PLAIN_MESSAGE, null, options,
- MessageManager.getString("action.ok"));
+ String dialogOption = MessageManager
+ .getString("label.input_alignment_from_url");
+ JvOptionPane.newOptionDialog(desktop).setResponseHandler(0, action)
+ .showInternalDialog(panel, dialogOption,
+ JvOptionPane.YES_NO_CANCEL_OPTION,
+ JvOptionPane.PLAIN_MESSAGE, null, options,
+ MessageManager.getString("action.ok"));
}
/**
* Opens the CutAndPaste window for the user to paste an alignment in to
*
- * @param viewPanel - if not null, the pasted alignment is added to the current
- * alignment; if null, to a new alignment window
+ * @param viewPanel
+ * - if not null, the pasted alignment is added to the current
+ * alignment; if null, to a new alignment window
*/
@Override
- public void inputTextboxMenuItem_actionPerformed(AlignmentViewPanel viewPanel) {
+ public void inputTextboxMenuItem_actionPerformed(
+ AlignmentViewPanel viewPanel)
+ {
CutAndPasteTransfer cap = new CutAndPasteTransfer();
cap.setForInput(viewPanel);
- Desktop.addInternalFrame(cap, MessageManager.getString("label.cut_paste_alignmen_file"), true, 600, 500);
+ Desktop.addInternalFrame(cap,
+ MessageManager.getString("label.cut_paste_alignmen_file"), true,
+ 600, 500);
}
/*
* Exit the program
*/
@Override
- public void quit() {
+ public void quit()
+ {
Dimension screen = Toolkit.getDefaultToolkit().getScreenSize();
Cache.setProperty("SCREENGEOMETRY_WIDTH", screen.width + "");
Cache.setProperty("SCREENGEOMETRY_HEIGHT", screen.height + "");
- storeLastKnownDimensions("", new Rectangle(getBounds().x, getBounds().y, getWidth(), getHeight()));
+ storeLastKnownDimensions("", new Rectangle(getBounds().x, getBounds().y,
+ getWidth(), getHeight()));
- if (jconsole != null) {
+ if (jconsole != null)
+ {
storeLastKnownDimensions("JAVA_CONSOLE_", jconsole.getBounds());
jconsole.stopConsole();
}
- if (jvnews != null) {
+ if (jvnews != null)
+ {
storeLastKnownDimensions("JALVIEW_RSS_WINDOW_", jvnews.getBounds());
}
- if (dialogExecutor != null) {
+ if (dialogExecutor != null)
+ {
dialogExecutor.shutdownNow();
}
closeAll_actionPerformed(null);
- if (groovyConsole != null) {
+ if (groovyConsole != null)
+ {
// suppress a possible repeat prompt to save script
groovyConsole.setDirty(false);
groovyConsole.exit();
System.exit(0);
}
- private void storeLastKnownDimensions(String string, Rectangle jc) {
- jalview.bin.Console.debug("Storing last known dimensions for " + string + ": x:" + jc.x + " y:" + jc.y + " width:" + jc.width
- + " height:" + jc.height);
+ private void storeLastKnownDimensions(String string, Rectangle jc)
+ {
+ jalview.bin.Console.debug("Storing last known dimensions for " + string
+ + ": x:" + jc.x + " y:" + jc.y + " width:" + jc.width
+ + " height:" + jc.height);
Cache.setProperty(string + "SCREEN_X", jc.x + "");
Cache.setProperty(string + "SCREEN_Y", jc.y + "");
/**
* DOCUMENT ME!
*
- * @param e DOCUMENT ME!
+ * @param e
+ * DOCUMENT ME!
*/
@Override
- public void aboutMenuItem_actionPerformed(ActionEvent e) {
- new Thread(new Runnable() {
+ public void aboutMenuItem_actionPerformed(ActionEvent e)
+ {
+ new Thread(new Runnable()
+ {
@Override
- public void run() {
+ public void run()
+ {
new SplashScreen(false);
}
}).start();
/**
* Returns the html text for the About screen, including any available version
- * number, build details, author details and citation reference, but without the
- * enclosing {@code html} tags
+ * number, build details, author details and citation reference, but without
+ * the enclosing {@code html} tags
*
* @return
*/
- public String getAboutMessage() {
+ public String getAboutMessage()
+ {
StringBuilder message = new StringBuilder(1024);
- message.append("<div style=\"font-family: sans-serif;\">").append("<h1><strong>Version: ")
- .append(Cache.getProperty("VERSION")).append("</strong></h1>").append("<strong>Built: <em>")
- .append(Cache.getDefault("BUILD_DATE", "unknown")).append("</em> from ")
- .append(Cache.getBuildDetailsForSplash()).append("</strong>");
+ message.append("<div style=\"font-family: sans-serif;\">")
+ .append("<h1><strong>Version: ")
+ .append(Cache.getProperty("VERSION")).append("</strong></h1>")
+ .append("<strong>Built: <em>")
+ .append(Cache.getDefault("BUILD_DATE", "unknown"))
+ .append("</em> from ").append(Cache.getBuildDetailsForSplash())
+ .append("</strong>");
String latestVersion = Cache.getDefault("LATEST_VERSION", "Checking");
- if (latestVersion.equals("Checking")) {
+ if (latestVersion.equals("Checking"))
+ {
// JBP removed this message for 2.11: May be reinstated in future version
// message.append("<br>...Checking latest version...</br>");
- } else if (!latestVersion.equals(Cache.getProperty("VERSION"))) {
+ }
+ else if (!latestVersion.equals(Cache.getProperty("VERSION")))
+ {
boolean red = false;
- if (Cache.getProperty("VERSION").toLowerCase(Locale.ROOT).indexOf("automated build") == -1) {
+ if (Cache.getProperty("VERSION").toLowerCase(Locale.ROOT)
+ .indexOf("automated build") == -1)
+ {
red = true;
// Displayed when code version and jnlp version do not match and code
// version is not a development build
message.append("<div style=\"color: #FF0000;font-style: bold;\">");
}
- message.append("<br>!! Version ").append(Cache.getDefault("LATEST_VERSION", "..Checking.."))
- .append(" is available for download from ")
- .append(Cache.getDefault("www.jalview.org", "https://www.jalview.org")).append(" !!");
- if (red) {
+ message.append("<br>!! Version ")
+ .append(Cache.getDefault("LATEST_VERSION", "..Checking.."))
+ .append(" is available for download from ")
+ .append(Cache.getDefault("www.jalview.org",
+ "https://www.jalview.org"))
+ .append(" !!");
+ if (red)
+ {
message.append("</div>");
}
}
* Action on requesting Help documentation
*/
@Override
- public void documentationMenuItem_actionPerformed() {
- try {
- if (Platform.isJS()) {
+ public void documentationMenuItem_actionPerformed()
+ {
+ try
+ {
+ if (Platform.isJS())
+ {
BrowserLauncher.openURL("https://www.jalview.org/help.html");
- } else
+ }
+ else
/**
* Java only
*
{
Help.showHelpWindow();
}
- } catch (Exception ex) {
+ } catch (Exception ex)
+ {
System.err.println("Error opening help: " + ex.getMessage());
}
}
@Override
- public void closeAll_actionPerformed(ActionEvent e) {
+ public void closeAll_actionPerformed(ActionEvent e)
+ {
// TODO show a progress bar while closing?
JInternalFrame[] frames = desktop.getAllFrames();
- for (int i = 0; i < frames.length; i++) {
- try {
+ for (int i = 0; i < frames.length; i++)
+ {
+ try
+ {
frames[i].setClosed(true);
- } catch (java.beans.PropertyVetoException ex) {
+ } catch (java.beans.PropertyVetoException ex)
+ {
}
}
Jalview.setCurrentAlignFrame(null);
* reset state of singleton objects as appropriate (clear down session state
* when all windows are closed)
*/
- StructureSelectionManager ssm = StructureSelectionManager.getStructureSelectionManager(this);
- if (ssm != null) {
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(this);
+ if (ssm != null)
+ {
ssm.resetAll();
}
}
@Override
- public void raiseRelated_actionPerformed(ActionEvent e) {
+ public void raiseRelated_actionPerformed(ActionEvent e)
+ {
reorderAssociatedWindows(false, false);
}
@Override
- public void minimizeAssociated_actionPerformed(ActionEvent e) {
+ public void minimizeAssociated_actionPerformed(ActionEvent e)
+ {
reorderAssociatedWindows(true, false);
}
- void closeAssociatedWindows() {
+ void closeAssociatedWindows()
+ {
reorderAssociatedWindows(false, true);
}
* ActionEvent)
*/
@Override
- protected void garbageCollect_actionPerformed(ActionEvent e) {
+ protected void garbageCollect_actionPerformed(ActionEvent e)
+ {
// We simply collect the garbage
jalview.bin.Console.debug("Collecting garbage...");
System.gc();
* ActionEvent )
*/
@Override
- protected void showMemusage_actionPerformed(ActionEvent e) {
+ protected void showMemusage_actionPerformed(ActionEvent e)
+ {
desktop.showMemoryUsage(showMemusage.isSelected());
}
* )
*/
@Override
- protected void showConsole_actionPerformed(ActionEvent e) {
+ protected void showConsole_actionPerformed(ActionEvent e)
+ {
showConsole(showConsole.isSelected());
}
*
* @param selected
*/
- void showConsole(boolean selected) {
+ void showConsole(boolean selected)
+ {
// TODO: decide if we should update properties file
if (jconsole != null) // BH 2018
{
showConsole.setSelected(selected);
- Cache.setProperty("SHOW_JAVA_CONSOLE", Boolean.valueOf(selected).toString());
+ Cache.setProperty("SHOW_JAVA_CONSOLE",
+ Boolean.valueOf(selected).toString());
jconsole.setVisible(selected);
}
}
- void reorderAssociatedWindows(boolean minimize, boolean close) {
+ void reorderAssociatedWindows(boolean minimize, boolean close)
+ {
JInternalFrame[] frames = desktop.getAllFrames();
- if (frames == null || frames.length < 1) {
+ if (frames == null || frames.length < 1)
+ {
return;
}
AlignmentViewport source = null, target = null;
- if (frames[0] instanceof AlignFrame) {
+ if (frames[0] instanceof AlignFrame)
+ {
source = ((AlignFrame) frames[0]).getCurrentView();
- } else if (frames[0] instanceof TreePanel) {
+ }
+ else if (frames[0] instanceof TreePanel)
+ {
source = ((TreePanel) frames[0]).getViewPort();
- } else if (frames[0] instanceof PCAPanel) {
+ }
+ else if (frames[0] instanceof PCAPanel)
+ {
source = ((PCAPanel) frames[0]).av;
- } else if (frames[0].getContentPane() instanceof PairwiseAlignPanel) {
+ }
+ else if (frames[0].getContentPane() instanceof PairwiseAlignPanel)
+ {
source = ((PairwiseAlignPanel) frames[0].getContentPane()).av;
}
- if (source != null) {
- for (int i = 0; i < frames.length; i++) {
+ if (source != null)
+ {
+ for (int i = 0; i < frames.length; i++)
+ {
target = null;
- if (frames[i] == null) {
+ if (frames[i] == null)
+ {
continue;
}
- if (frames[i] instanceof AlignFrame) {
+ if (frames[i] instanceof AlignFrame)
+ {
target = ((AlignFrame) frames[i]).getCurrentView();
- } else if (frames[i] instanceof TreePanel) {
+ }
+ else if (frames[i] instanceof TreePanel)
+ {
target = ((TreePanel) frames[i]).getViewPort();
- } else if (frames[i] instanceof PCAPanel) {
+ }
+ else if (frames[i] instanceof PCAPanel)
+ {
target = ((PCAPanel) frames[i]).av;
- } else if (frames[i].getContentPane() instanceof PairwiseAlignPanel) {
+ }
+ else if (frames[i].getContentPane() instanceof PairwiseAlignPanel)
+ {
target = ((PairwiseAlignPanel) frames[i].getContentPane()).av;
}
- if (source == target) {
- try {
- if (close) {
+ if (source == target)
+ {
+ try
+ {
+ if (close)
+ {
frames[i].setClosed(true);
- } else {
+ }
+ else
+ {
frames[i].setIcon(minimize);
- if (!minimize) {
+ if (!minimize)
+ {
frames[i].toFront();
}
}
- } catch (java.beans.PropertyVetoException ex) {
+ } catch (java.beans.PropertyVetoException ex)
+ {
}
}
}
/**
* DOCUMENT ME!
*
- * @param e DOCUMENT ME!
+ * @param e
+ * DOCUMENT ME!
*/
@Override
- protected void preferences_actionPerformed(ActionEvent e) {
+ protected void preferences_actionPerformed(ActionEvent e)
+ {
Preferences.openPreferences();
}
* Jalview project file
*/
@Override
- public void saveState_actionPerformed() {
+ public void saveState_actionPerformed()
+ {
saveState_actionPerformed(false);
}
- public void saveState_actionPerformed(boolean saveAs) {
+ public void saveState_actionPerformed(boolean saveAs)
+ {
java.io.File projectFile = getProjectFile();
// autoSave indicates we already have a file and don't need to ask
- boolean autoSave = projectFile != null && !saveAs && BackupFiles.getEnabled();
+ boolean autoSave = projectFile != null && !saveAs
+ && BackupFiles.getEnabled();
// System.out.println("autoSave="+autoSave+", projectFile='"+projectFile+"',
// saveAs="+saveAs+", Backups
// "+(BackupFiles.getEnabled()?"enabled":"disabled"));
boolean approveSave = false;
- if (!autoSave) {
- JalviewFileChooser chooser = new JalviewFileChooser("jvp", "Jalview Project");
+ if (!autoSave)
+ {
+ JalviewFileChooser chooser = new JalviewFileChooser("jvp",
+ "Jalview Project");
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager.getString("label.save_state"));
int value = chooser.showSaveDialog(this);
- if (value == JalviewFileChooser.APPROVE_OPTION) {
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
projectFile = chooser.getSelectedFile();
setProjectFile(projectFile);
approveSave = true;
}
}
- if (approveSave || autoSave) {
+ if (approveSave || autoSave)
+ {
final Desktop me = this;
final java.io.File chosenFile = projectFile;
- new Thread(new Runnable() {
+ new Thread(new Runnable()
+ {
@Override
- public void run() {
+ public void run()
+ {
// TODO: refactor to Jalview desktop session controller action.
- setProgressBar(
- MessageManager.formatMessage("label.saving_jalview_project", new Object[] { chosenFile.getName() }),
- chosenFile.hashCode());
+ setProgressBar(MessageManager.formatMessage(
+ "label.saving_jalview_project", new Object[]
+ { chosenFile.getName() }), chosenFile.hashCode());
Cache.setProperty("LAST_DIRECTORY", chosenFile.getParent());
// TODO catch and handle errors for savestate
// TODO prevent user from messing with the Desktop whilst we're saving
- try {
+ try
+ {
boolean doBackup = BackupFiles.getEnabled();
- BackupFiles backupfiles = doBackup ? new BackupFiles(chosenFile) : null;
+ BackupFiles backupfiles = doBackup ? new BackupFiles(chosenFile)
+ : null;
- new Jalview2XML().saveState(doBackup ? backupfiles.getTempFile() : chosenFile);
+ new Jalview2XML().saveState(
+ doBackup ? backupfiles.getTempFile() : chosenFile);
- if (doBackup) {
+ if (doBackup)
+ {
backupfiles.setWriteSuccess(true);
backupfiles.rollBackupsAndRenameTempFile();
}
- } catch (OutOfMemoryError oom) {
- new OOMWarning("Whilst saving current state to " + chosenFile.getName(), oom);
- } catch (Exception ex) {
- jalview.bin.Console.error("Problems whilst trying to save to " + chosenFile.getName(), ex);
+ } catch (OutOfMemoryError oom)
+ {
+ new OOMWarning("Whilst saving current state to "
+ + chosenFile.getName(), oom);
+ } catch (Exception ex)
+ {
+ jalview.bin.Console.error("Problems whilst trying to save to "
+ + chosenFile.getName(), ex);
JvOptionPane.showMessageDialog(me,
- MessageManager.formatMessage("label.error_whilst_saving_current_state_to",
- new Object[] { chosenFile.getName() }),
- MessageManager.getString("label.couldnt_save_project"), JvOptionPane.WARNING_MESSAGE);
+ MessageManager.formatMessage(
+ "label.error_whilst_saving_current_state_to",
+ new Object[]
+ { chosenFile.getName() }),
+ MessageManager.getString("label.couldnt_save_project"),
+ JvOptionPane.WARNING_MESSAGE);
}
setProgressBar(null, chosenFile.hashCode());
}
}
@Override
- public void saveAsState_actionPerformed(ActionEvent e) {
+ public void saveAsState_actionPerformed(ActionEvent e)
+ {
saveState_actionPerformed(true);
}
- private void setProjectFile(File choice) {
+ private void setProjectFile(File choice)
+ {
this.projectFile = choice;
}
- public File getProjectFile() {
+ public File getProjectFile()
+ {
return this.projectFile;
}
* Jalview project
*/
@Override
- public void loadState_actionPerformed() {
+ public void loadState_actionPerformed()
+ {
final String[] suffix = new String[] { "jvp", "jar" };
- final String[] desc = new String[] { "Jalview Project", "Jalview Project (old)" };
- JalviewFileChooser chooser = new JalviewFileChooser(Cache.getProperty("LAST_DIRECTORY"), suffix, desc,
- "Jalview Project", true, BackupFiles.getEnabled()); // last two
- // booleans:
- // allFiles,
+ final String[] desc = new String[] { "Jalview Project",
+ "Jalview Project (old)" };
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ Cache.getProperty("LAST_DIRECTORY"), suffix, desc,
+ "Jalview Project", true, BackupFiles.getEnabled()); // last two
+ // booleans:
+ // allFiles,
// allowBackupFiles
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager.getString("label.restore_state"));
- chooser.setResponseHandler(0, new Runnable() {
+ chooser.setResponseHandler(0, new Runnable()
+ {
@Override
- public void run() {
+ public void run()
+ {
File selectedFile = chooser.getSelectedFile();
setProjectFile(selectedFile);
String choice = selectedFile.getAbsolutePath();
Cache.setProperty("LAST_DIRECTORY", selectedFile.getParent());
- new Thread(new Runnable() {
+ new Thread(new Runnable()
+ {
@Override
- public void run() {
- try {
+ public void run()
+ {
+ try
+ {
new Jalview2XML().loadJalviewAlign(selectedFile);
- } catch (OutOfMemoryError oom) {
+ } catch (OutOfMemoryError oom)
+ {
new OOMWarning("Whilst loading project from " + choice, oom);
- } catch (Exception ex) {
- jalview.bin.Console.error("Problems whilst loading project from " + choice, ex);
+ } catch (Exception ex)
+ {
+ jalview.bin.Console.error(
+ "Problems whilst loading project from " + choice, ex);
JvOptionPane.showMessageDialog(Desktop.desktop,
- MessageManager.formatMessage("label.error_whilst_loading_project_from", new Object[] { choice }),
- MessageManager.getString("label.couldnt_load_project"), JvOptionPane.WARNING_MESSAGE);
+ MessageManager.formatMessage(
+ "label.error_whilst_loading_project_from",
+ new Object[]
+ { choice }),
+ MessageManager
+ .getString("label.couldnt_load_project"),
+ JvOptionPane.WARNING_MESSAGE);
}
}
}, "Project Loader").start();
}
@Override
- public void inputSequence_actionPerformed(ActionEvent e) {
+ public void inputSequence_actionPerformed(ActionEvent e)
+ {
new SequenceFetcher(this);
}
ArrayList<JPanel> fileLoadingPanels = new ArrayList<>();
- public void startLoading(final Object fileName) {
- if (fileLoadingCount == 0) {
- fileLoadingPanels
- .add(addProgressPanel(MessageManager.formatMessage("label.loading_file", new Object[] { fileName })));
+ public void startLoading(final Object fileName)
+ {
+ if (fileLoadingCount == 0)
+ {
+ fileLoadingPanels.add(addProgressPanel(MessageManager
+ .formatMessage("label.loading_file", new Object[]
+ { fileName })));
}
fileLoadingCount++;
}
- private JPanel addProgressPanel(String string) {
- if (progressPanel == null) {
+ private JPanel addProgressPanel(String string)
+ {
+ if (progressPanel == null)
+ {
progressPanel = new JPanel(new GridLayout(1, 1));
totalProgressCount = 0;
instance.getContentPane().add(progressPanel, BorderLayout.SOUTH);
thisprogress.add(progressBar, BorderLayout.CENTER);
progressPanel.add(thisprogress);
- ((GridLayout) progressPanel.getLayout()).setRows(((GridLayout) progressPanel.getLayout()).getRows() + 1);
+ ((GridLayout) progressPanel.getLayout()).setRows(
+ ((GridLayout) progressPanel.getLayout()).getRows() + 1);
++totalProgressCount;
instance.validate();
return thisprogress;
int totalProgressCount = 0;
- private void removeProgressPanel(JPanel progbar) {
- if (progressPanel != null) {
- synchronized (progressPanel) {
+ private void removeProgressPanel(JPanel progbar)
+ {
+ if (progressPanel != null)
+ {
+ synchronized (progressPanel)
+ {
progressPanel.remove(progbar);
GridLayout gl = (GridLayout) progressPanel.getLayout();
gl.setRows(gl.getRows() - 1);
- if (--totalProgressCount < 1) {
+ if (--totalProgressCount < 1)
+ {
this.getContentPane().remove(progressPanel);
progressPanel = null;
}
validate();
}
- public void stopLoading() {
+ public void stopLoading()
+ {
fileLoadingCount--;
- if (fileLoadingCount < 1) {
- while (fileLoadingPanels.size() > 0) {
+ if (fileLoadingCount < 1)
+ {
+ while (fileLoadingPanels.size() > 0)
+ {
removeProgressPanel(fileLoadingPanels.remove(0));
}
fileLoadingPanels.clear();
validate();
}
- public static int getViewCount(String alignmentId) {
+ public static int getViewCount(String alignmentId)
+ {
AlignmentViewport[] aps = getViewports(alignmentId);
return (aps == null) ? 0 : aps.length;
}
/**
*
- * @param alignmentId - if null, all sets are returned
+ * @param alignmentId
+ * - if null, all sets are returned
* @return all AlignmentPanels concerning the alignmentId sequence set
*/
- public static AlignmentPanel[] getAlignmentPanels(String alignmentId) {
- if (Desktop.desktop == null) {
+ public static AlignmentPanel[] getAlignmentPanels(String alignmentId)
+ {
+ if (Desktop.desktop == null)
+ {
// no frames created and in headless mode
// TODO: verify that frames are recoverable when in headless mode
return null;
}
List<AlignmentPanel> aps = new ArrayList<>();
AlignFrame[] frames = getAlignFrames();
- if (frames == null) {
+ if (frames == null)
+ {
return null;
}
- for (AlignFrame af : frames) {
- for (AlignmentPanel ap : af.alignPanels) {
- if (alignmentId == null || alignmentId.equals(ap.av.getSequenceSetId())) {
+ for (AlignFrame af : frames)
+ {
+ for (AlignmentPanel ap : af.alignPanels)
+ {
+ if (alignmentId == null
+ || alignmentId.equals(ap.av.getSequenceSetId()))
+ {
aps.add(ap);
}
}
}
- if (aps.size() == 0) {
+ if (aps.size() == 0)
+ {
return null;
}
AlignmentPanel[] vap = aps.toArray(new AlignmentPanel[aps.size()]);
/**
* get all the viewports on an alignment.
*
- * @param sequenceSetId unique alignment id (may be null - all viewports
- * returned in that case)
+ * @param sequenceSetId
+ * unique alignment id (may be null - all viewports returned in that
+ * case)
* @return all viewports on the alignment bound to sequenceSetId
*/
- public static AlignmentViewport[] getViewports(String sequenceSetId) {
+ public static AlignmentViewport[] getViewports(String sequenceSetId)
+ {
List<AlignmentViewport> viewp = new ArrayList<>();
- if (desktop != null) {
+ if (desktop != null)
+ {
AlignFrame[] frames = Desktop.getAlignFrames();
- for (AlignFrame afr : frames) {
- if (sequenceSetId == null || afr.getViewport().getSequenceSetId().equals(sequenceSetId)) {
- if (afr.alignPanels != null) {
- for (AlignmentPanel ap : afr.alignPanels) {
- if (sequenceSetId == null || sequenceSetId.equals(ap.av.getSequenceSetId())) {
+ for (AlignFrame afr : frames)
+ {
+ if (sequenceSetId == null || afr.getViewport().getSequenceSetId()
+ .equals(sequenceSetId))
+ {
+ if (afr.alignPanels != null)
+ {
+ for (AlignmentPanel ap : afr.alignPanels)
+ {
+ if (sequenceSetId == null
+ || sequenceSetId.equals(ap.av.getSequenceSetId()))
+ {
viewp.add(ap.av);
}
}
- } else {
+ }
+ else
+ {
viewp.add(afr.getViewport());
}
}
}
- if (viewp.size() > 0) {
+ if (viewp.size() > 0)
+ {
return viewp.toArray(new AlignmentViewport[viewp.size()]);
}
}
*
* @param af
*/
- public static void explodeViews(AlignFrame af) {
+ public static void explodeViews(AlignFrame af)
+ {
int size = af.alignPanels.size();
- if (size < 2) {
+ if (size < 2)
+ {
return;
}
// FIXME: ideally should use UI interface API
- FeatureSettings viewFeatureSettings = (af.featureSettings != null && af.featureSettings.isOpen())
- ? af.featureSettings
- : null;
+ FeatureSettings viewFeatureSettings = (af.featureSettings != null
+ && af.featureSettings.isOpen()) ? af.featureSettings : null;
Rectangle fsBounds = af.getFeatureSettingsGeometry();
- for (int i = 0; i < size; i++) {
+ for (int i = 0; i < size; i++)
+ {
AlignmentPanel ap = af.alignPanels.get(i);
AlignFrame newaf = new AlignFrame(ap);
// transfer reference for existing feature settings to new alignFrame
- if (ap == af.alignPanel) {
- if (viewFeatureSettings != null && viewFeatureSettings.fr.ap == ap) {
+ if (ap == af.alignPanel)
+ {
+ if (viewFeatureSettings != null && viewFeatureSettings.fr.ap == ap)
+ {
newaf.featureSettings = viewFeatureSettings;
}
newaf.setFeatureSettingsGeometry(fsBounds);
* one exploded frame share and restore the same (frame) position and size.
*/
Rectangle geometry = ap.av.getExplodedGeometry();
- if (geometry != null) {
+ if (geometry != null)
+ {
newaf.setBounds(geometry);
}
ap.av.setGatherViewsHere(false);
- addInternalFrame(newaf, af.getTitle(), AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ addInternalFrame(newaf, af.getTitle(), AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
// and materialise a new feature settings dialog instance for the new
// alignframe
// (closes the old as if 'OK' was pressed)
- if (ap == af.alignPanel && newaf.featureSettings != null && newaf.featureSettings.isOpen()
- && af.alignPanel.getAlignViewport().isShowSequenceFeatures()) {
+ if (ap == af.alignPanel && newaf.featureSettings != null
+ && newaf.featureSettings.isOpen()
+ && af.alignPanel.getAlignViewport().isShowSequenceFeatures())
+ {
newaf.showFeatureSettingsUI();
}
}
/**
* Gather expanded views (separate AlignFrame's) with the same sequence set
- * identifier back in to this frame as additional views, and close the expanded
- * views. Note the expanded frames may themselves have multiple views. We take
- * the lot.
+ * identifier back in to this frame as additional views, and close the
+ * expanded views. Note the expanded frames may themselves have multiple
+ * views. We take the lot.
*
* @param source
*/
- public void gatherViews(AlignFrame source) {
+ public void gatherViews(AlignFrame source)
+ {
source.viewport.setGatherViewsHere(true);
source.viewport.setExplodedGeometry(source.getBounds());
JInternalFrame[] frames = desktop.getAllFrames();
String viewId = source.viewport.getSequenceSetId();
- for (int t = 0; t < frames.length; t++) {
- if (frames[t] instanceof AlignFrame && frames[t] != source) {
+ for (int t = 0; t < frames.length; t++)
+ {
+ if (frames[t] instanceof AlignFrame && frames[t] != source)
+ {
AlignFrame af = (AlignFrame) frames[t];
boolean gatherThis = false;
- for (int a = 0; a < af.alignPanels.size(); a++) {
+ for (int a = 0; a < af.alignPanels.size(); a++)
+ {
AlignmentPanel ap = af.alignPanels.get(a);
- if (viewId.equals(ap.av.getSequenceSetId())) {
+ if (viewId.equals(ap.av.getSequenceSetId()))
+ {
gatherThis = true;
ap.av.setGatherViewsHere(false);
ap.av.setExplodedGeometry(af.getBounds());
}
}
- if (gatherThis) {
- if (af.featureSettings != null && af.featureSettings.isOpen()) {
- if (source.featureSettings == null) {
+ if (gatherThis)
+ {
+ if (af.featureSettings != null && af.featureSettings.isOpen())
+ {
+ if (source.featureSettings == null)
+ {
// preserve the feature settings geometry for this frame
source.featureSettings = af.featureSettings;
- source.setFeatureSettingsGeometry(af.getFeatureSettingsGeometry());
- } else {
+ source.setFeatureSettingsGeometry(
+ af.getFeatureSettingsGeometry());
+ }
+ else
+ {
// close it and forget
af.featureSettings.close();
}
}
// refresh the feature setting UI for the source frame if it exists
- if (source.featureSettings != null && source.featureSettings.isOpen()) {
+ if (source.featureSettings != null && source.featureSettings.isOpen())
+ {
source.showFeatureSettingsUI();
}
}
- public JInternalFrame[] getAllFrames() {
+ public JInternalFrame[] getAllFrames()
+ {
return desktop.getAllFrames();
}
*
* @param url
*/
- public void checkForQuestionnaire(String url) {
+ public void checkForQuestionnaire(String url)
+ {
UserQuestionnaireCheck jvq = new UserQuestionnaireCheck(url);
// javax.swing.SwingUtilities.invokeLater(jvq);
new Thread(jvq).start();
}
- public void checkURLLinks() {
+ public void checkURLLinks()
+ {
// Thread off the URL link checker
- addDialogThread(new Runnable() {
+ addDialogThread(new Runnable()
+ {
@Override
- public void run() {
- if (Cache.getDefault("CHECKURLLINKS", true)) {
+ public void run()
+ {
+ if (Cache.getDefault("CHECKURLLINKS", true))
+ {
// check what the actual links are - if it's just the default don't
// bother with the warning
- List<String> links = Preferences.sequenceUrlLinks.getLinksForMenu();
+ List<String> links = Preferences.sequenceUrlLinks
+ .getLinksForMenu();
// only need to check links if there is one with a
// SEQUENCE_ID which is not the default EMBL_EBI link
ListIterator<String> li = links.listIterator();
boolean check = false;
List<JLabel> urls = new ArrayList<>();
- while (li.hasNext()) {
+ while (li.hasNext())
+ {
String link = li.next();
- if (link.contains(jalview.util.UrlConstants.SEQUENCE_ID) && !UrlConstants.isDefaultString(link)) {
+ if (link.contains(jalview.util.UrlConstants.SEQUENCE_ID)
+ && !UrlConstants.isDefaultString(link))
+ {
check = true;
int barPos = link.indexOf("|");
- String urlMsg = barPos == -1 ? link : link.substring(0, barPos) + ": " + link.substring(barPos + 1);
+ String urlMsg = barPos == -1 ? link
+ : link.substring(0, barPos) + ": "
+ + link.substring(barPos + 1);
urls.add(new JLabel(urlMsg));
}
}
- if (!check) {
+ if (!check)
+ {
return;
}
JPanel msgPanel = new JPanel();
msgPanel.setLayout(new BoxLayout(msgPanel, BoxLayout.PAGE_AXIS));
msgPanel.add(Box.createVerticalGlue());
- JLabel msg = new JLabel(MessageManager.getString("label.SEQUENCE_ID_for_DB_ACCESSION1"));
- JLabel msg2 = new JLabel(MessageManager.getString("label.SEQUENCE_ID_for_DB_ACCESSION2"));
+ JLabel msg = new JLabel(MessageManager
+ .getString("label.SEQUENCE_ID_for_DB_ACCESSION1"));
+ JLabel msg2 = new JLabel(MessageManager
+ .getString("label.SEQUENCE_ID_for_DB_ACCESSION2"));
msgPanel.add(msg);
- for (JLabel url : urls) {
+ for (JLabel url : urls)
+ {
msgPanel.add(url);
}
msgPanel.add(msg2);
- final JCheckBox jcb = new JCheckBox(MessageManager.getString("label.do_not_display_again"));
- jcb.addActionListener(new ActionListener() {
+ final JCheckBox jcb = new JCheckBox(
+ MessageManager.getString("label.do_not_display_again"));
+ jcb.addActionListener(new ActionListener()
+ {
@Override
- public void actionPerformed(ActionEvent e) {
+ public void actionPerformed(ActionEvent e)
+ {
// update Cache settings for "don't show this again"
boolean showWarningAgain = !jcb.isSelected();
- Cache.setProperty("CHECKURLLINKS", Boolean.valueOf(showWarningAgain).toString());
+ Cache.setProperty("CHECKURLLINKS",
+ Boolean.valueOf(showWarningAgain).toString());
}
});
msgPanel.add(jcb);
JvOptionPane.showMessageDialog(Desktop.desktop, msgPanel,
- MessageManager.getString("label.SEQUENCE_ID_no_longer_used"), JvOptionPane.WARNING_MESSAGE);
+ MessageManager
+ .getString("label.SEQUENCE_ID_no_longer_used"),
+ JvOptionPane.WARNING_MESSAGE);
}
}
});
/**
* Proxy class for JDesktopPane which optionally displays the current memory
- * usage and highlights the desktop area with a red bar if free memory runs low.
+ * usage and highlights the desktop area with a red bar if free memory runs
+ * low.
*
* @author AMW
*/
- public class MyDesktopPane extends JDesktopPane implements Runnable {
+ public class MyDesktopPane extends JDesktopPane implements Runnable
+ {
private static final float ONE_MB = 1048576f;
boolean showMemoryUsage = false;
java.text.NumberFormat df;
- float maxMemory, allocatedMemory, freeMemory, totalFreeMemory, percentUsage;
+ float maxMemory, allocatedMemory, freeMemory, totalFreeMemory,
+ percentUsage;
- public MyDesktopPane(boolean showMemoryUsage) {
+ public MyDesktopPane(boolean showMemoryUsage)
+ {
showMemoryUsage(showMemoryUsage);
}
- public void showMemoryUsage(boolean showMemory) {
+ public void showMemoryUsage(boolean showMemory)
+ {
this.showMemoryUsage = showMemory;
- if (showMemory) {
+ if (showMemory)
+ {
Thread worker = new Thread(this);
worker.start();
}
repaint();
}
- public boolean isShowMemoryUsage() {
+ public boolean isShowMemoryUsage()
+ {
return showMemoryUsage;
}
@Override
- public void run() {
+ public void run()
+ {
df = java.text.NumberFormat.getNumberInstance();
df.setMaximumFractionDigits(2);
runtime = Runtime.getRuntime();
- while (showMemoryUsage) {
- try {
+ while (showMemoryUsage)
+ {
+ try
+ {
maxMemory = runtime.maxMemory() / ONE_MB;
allocatedMemory = runtime.totalMemory() / ONE_MB;
freeMemory = runtime.freeMemory() / ONE_MB;
repaint();
// sleep after showing usage
Thread.sleep(3000);
- } catch (Exception ex) {
+ } catch (Exception ex)
+ {
ex.printStackTrace();
}
}
}
@Override
- public void paintComponent(Graphics g) {
- if (showMemoryUsage && g != null && df != null) {
- if (percentUsage < 20) {
+ public void paintComponent(Graphics g)
+ {
+ if (showMemoryUsage && g != null && df != null)
+ {
+ if (percentUsage < 20)
+ {
g.setColor(Color.red);
}
FontMetrics fm = g.getFontMetrics();
- if (fm != null) {
- g.drawString(
- MessageManager.formatMessage("label.memory_stats",
- new Object[] { df.format(totalFreeMemory), df.format(maxMemory), df.format(percentUsage) }),
- 10, getHeight() - fm.getHeight());
+ if (fm != null)
+ {
+ g.drawString(MessageManager.formatMessage("label.memory_stats",
+ new Object[]
+ { df.format(totalFreeMemory), df.format(maxMemory),
+ df.format(percentUsage) }),
+ 10, getHeight() - fm.getHeight());
}
}
*
* @return an array of AlignFrame, or null if none found
*/
- public static AlignFrame[] getAlignFrames() {
- if (Jalview.isHeadlessMode()) {
+ public static AlignFrame[] getAlignFrames()
+ {
+ if (Jalview.isHeadlessMode())
+ {
// Desktop.desktop is null in headless mode
return new AlignFrame[] { Jalview.currentAlignFrame };
}
JInternalFrame[] frames = Desktop.desktop.getAllFrames();
- if (frames == null) {
+ if (frames == null)
+ {
return null;
}
List<AlignFrame> avp = new ArrayList<>();
// REVERSE ORDER
- for (int i = frames.length - 1; i > -1; i--) {
- if (frames[i] instanceof AlignFrame) {
+ for (int i = frames.length - 1; i > -1; i--)
+ {
+ if (frames[i] instanceof AlignFrame)
+ {
avp.add((AlignFrame) frames[i]);
- } else if (frames[i] instanceof SplitFrame) {
+ }
+ else if (frames[i] instanceof SplitFrame)
+ {
/*
* Also check for a split frame containing an AlignFrame
*/
GSplitFrame sf = (GSplitFrame) frames[i];
- if (sf.getTopFrame() instanceof AlignFrame) {
+ if (sf.getTopFrame() instanceof AlignFrame)
+ {
avp.add((AlignFrame) sf.getTopFrame());
}
- if (sf.getBottomFrame() instanceof AlignFrame) {
+ if (sf.getBottomFrame() instanceof AlignFrame)
+ {
avp.add((AlignFrame) sf.getBottomFrame());
}
}
}
- if (avp.size() == 0) {
+ if (avp.size() == 0)
+ {
return null;
}
AlignFrame afs[] = avp.toArray(new AlignFrame[avp.size()]);
*
* @return
*/
- public GStructureViewer[] getJmols() {
+ public GStructureViewer[] getJmols()
+ {
JInternalFrame[] frames = Desktop.desktop.getAllFrames();
- if (frames == null) {
+ if (frames == null)
+ {
return null;
}
List<GStructureViewer> avp = new ArrayList<>();
// REVERSE ORDER
- for (int i = frames.length - 1; i > -1; i--) {
- if (frames[i] instanceof AppJmol) {
+ for (int i = frames.length - 1; i > -1; i--)
+ {
+ if (frames[i] instanceof AppJmol)
+ {
GStructureViewer af = (GStructureViewer) frames[i];
avp.add(af);
}
}
- if (avp.size() == 0) {
+ if (avp.size() == 0)
+ {
return null;
}
GStructureViewer afs[] = avp.toArray(new GStructureViewer[avp.size()]);
* Add Groovy Support to Jalview
*/
@Override
- public void groovyShell_actionPerformed() {
- try {
+ public void groovyShell_actionPerformed()
+ {
+ try
+ {
openGroovyConsole();
- } catch (Exception ex) {
+ } catch (Exception ex)
+ {
jalview.bin.Console.error("Groovy Shell Creation failed.", ex);
JvOptionPane.showInternalMessageDialog(Desktop.desktop,
- MessageManager.getString("label.couldnt_create_groovy_shell"),
- MessageManager.getString("label.groovy_support_failed"), JvOptionPane.ERROR_MESSAGE);
+ MessageManager.getString("label.couldnt_create_groovy_shell"),
+ MessageManager.getString("label.groovy_support_failed"),
+ JvOptionPane.ERROR_MESSAGE);
}
}
/**
* Open the Groovy console
*/
- void openGroovyConsole() {
- if (groovyConsole == null) {
+ void openGroovyConsole()
+ {
+ if (groovyConsole == null)
+ {
groovyConsole = new groovy.ui.Console();
groovyConsole.setVariable("Jalview", this);
groovyConsole.run();
* closed
*/
Window window = (Window) groovyConsole.getFrame();
- window.addWindowListener(new WindowAdapter() {
+ window.addWindowListener(new WindowAdapter()
+ {
@Override
- public void windowClosed(WindowEvent e) {
+ public void windowClosed(WindowEvent e)
+ {
/*
* rebind CMD-Q from Groovy Console to Jalview Quit
*/
}
/**
- * Bind Ctrl/Cmd-Q to Quit - for reset as Groovy Console takes over this binding
- * when opened
- */
- protected void addQuitHandler() {
- getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW).put(
- KeyStroke.getKeyStroke(KeyEvent.VK_Q, jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()),
- "Quit");
- getRootPane().getActionMap().put("Quit", new AbstractAction() {
+ * Bind Ctrl/Cmd-Q to Quit - for reset as Groovy Console takes over this
+ * binding when opened
+ */
+ protected void addQuitHandler()
+ {
+ getRootPane()
+ .getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW).put(
+ KeyStroke
+ .getKeyStroke(KeyEvent.VK_Q,
+ jalview.util.ShortcutKeyMaskExWrapper
+ .getMenuShortcutKeyMaskEx()),
+ "Quit");
+ getRootPane().getActionMap().put("Quit", new AbstractAction()
+ {
@Override
- public void actionPerformed(ActionEvent e) {
+ public void actionPerformed(ActionEvent e)
+ {
quit();
}
});
/**
* Enable or disable 'Run Groovy script' in AlignFrame calculate menus
*
- * @param enabled true if Groovy console is open
+ * @param enabled
+ * true if Groovy console is open
*/
- public void enableExecuteGroovy(boolean enabled) {
+ public void enableExecuteGroovy(boolean enabled)
+ {
/*
* disable opening a second Groovy console (or re-enable when the console is
* closed)
groovyShell.setEnabled(!enabled);
AlignFrame[] alignFrames = getAlignFrames();
- if (alignFrames != null) {
- for (AlignFrame af : alignFrames) {
+ if (alignFrames != null)
+ {
+ for (AlignFrame af : alignFrames)
+ {
af.setGroovyEnabled(enabled);
}
}
* @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
*/
@Override
- public void setProgressBar(String message, long id) {
- if (progressBars == null) {
+ public void setProgressBar(String message, long id)
+ {
+ if (progressBars == null)
+ {
progressBars = new Hashtable<>();
progressBarHandlers = new Hashtable<>();
}
- if (progressBars.get(Long.valueOf(id)) != null) {
+ if (progressBars.get(Long.valueOf(id)) != null)
+ {
JPanel panel = progressBars.remove(Long.valueOf(id));
- if (progressBarHandlers.contains(Long.valueOf(id))) {
+ if (progressBarHandlers.contains(Long.valueOf(id)))
+ {
progressBarHandlers.remove(Long.valueOf(id));
}
removeProgressPanel(panel);
- } else {
+ }
+ else
+ {
progressBars.put(Long.valueOf(id), addProgressPanel(message));
}
}
* jalview.gui.IProgressIndicatorHandler)
*/
@Override
- public void registerHandler(final long id, final IProgressIndicatorHandler handler) {
- if (progressBarHandlers == null || !progressBars.containsKey(Long.valueOf(id))) {
- throw new Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
+ public void registerHandler(final long id,
+ final IProgressIndicatorHandler handler)
+ {
+ if (progressBarHandlers == null
+ || !progressBars.containsKey(Long.valueOf(id)))
+ {
+ throw new Error(MessageManager.getString(
+ "error.call_setprogressbar_before_registering_handler"));
}
progressBarHandlers.put(Long.valueOf(id), handler);
final JPanel progressPanel = progressBars.get(Long.valueOf(id));
- if (handler.canCancel()) {
- JButton cancel = new JButton(MessageManager.getString("action.cancel"));
+ if (handler.canCancel())
+ {
+ JButton cancel = new JButton(
+ MessageManager.getString("action.cancel"));
final IProgressIndicator us = this;
- cancel.addActionListener(new ActionListener() {
+ cancel.addActionListener(new ActionListener()
+ {
@Override
- public void actionPerformed(ActionEvent e) {
+ public void actionPerformed(ActionEvent e)
+ {
handler.cancelActivity(id);
- us.setProgressBar(MessageManager.formatMessage("label.cancelled_params",
- new Object[] { ((JLabel) progressPanel.getComponent(0)).getText() }), id);
+ us.setProgressBar(MessageManager
+ .formatMessage("label.cancelled_params", new Object[]
+ { ((JLabel) progressPanel.getComponent(0)).getText() }),
+ id);
}
});
progressPanel.add(cancel, BorderLayout.EAST);
* @return true if any progress bars are still active
*/
@Override
- public boolean operationInProgress() {
- if (progressBars != null && progressBars.size() > 0) {
+ public boolean operationInProgress()
+ {
+ if (progressBars != null && progressBars.size() > 0)
+ {
return true;
}
return false;
}
/**
- * This will return the first AlignFrame holding the given viewport instance. It
- * will break if there are more than one AlignFrames viewing a particular av.
+ * This will return the first AlignFrame holding the given viewport instance.
+ * It will break if there are more than one AlignFrames viewing a particular
+ * av.
*
* @param viewport
* @return alignFrame for viewport
*/
- public static AlignFrame getAlignFrameFor(AlignViewportI viewport) {
- if (desktop != null) {
- AlignmentPanel[] aps = getAlignmentPanels(viewport.getSequenceSetId());
- for (int panel = 0; aps != null && panel < aps.length; panel++) {
- if (aps[panel] != null && aps[panel].av == viewport) {
+ public static AlignFrame getAlignFrameFor(AlignViewportI viewport)
+ {
+ if (desktop != null)
+ {
+ AlignmentPanel[] aps = getAlignmentPanels(
+ viewport.getSequenceSetId());
+ for (int panel = 0; aps != null && panel < aps.length; panel++)
+ {
+ if (aps[panel] != null && aps[panel].av == viewport)
+ {
return aps[panel].alignFrame;
}
}
return null;
}
- public VamsasApplication getVamsasApplication() {
+ public VamsasApplication getVamsasApplication()
+ {
// TODO: JAL-3311 remove remaining code from Jalview relating to VAMSAS
return null;
*
* @return inBatchMode
*/
- public boolean isInBatchMode() {
+ public boolean isInBatchMode()
+ {
return inBatchMode;
}
*
* @param inBatchMode
*/
- public void setInBatchMode(boolean inBatchMode) {
+ public void setInBatchMode(boolean inBatchMode)
+ {
this.inBatchMode = inBatchMode;
}
*/
public void startServiceDiscovery(boolean blocking)
{
- startServiceDiscovery(blocking,false);
+ startServiceDiscovery(blocking, false);
}
/**
* start service discovery threads
*
- * @param blocking - false means call returns
- * immediately
- * @param ignore_SHOW_JWS2_SERVICES_preference - when true JABA services are
- * discovered regardless of user's
- * JWS2 discovery preference setting
+ * @param blocking
+ * - false means call returns immediately
+ * @param ignore_SHOW_JWS2_SERVICES_preference
+ * - when true JABA services are discovered regardless of user's JWS2
+ * discovery preference setting
*/
- public void startServiceDiscovery(boolean blocking, boolean ignore_SHOW_JWS2_SERVICES_preference) {
+ public void startServiceDiscovery(boolean blocking,
+ boolean ignore_SHOW_JWS2_SERVICES_preference)
+ {
boolean alive = true;
Thread t0 = null, t1 = null, t2 = null;
// JAL-940 - JALVIEW 1 services are now being EOLed as of JABA 2.1 release
- if (true) {
+ if (true)
+ {
// todo: changesupport handlers need to be transferred
- if (discoverer == null) {
+ if (discoverer == null)
+ {
discoverer = new jalview.ws.jws1.Discoverer();
// register PCS handler for desktop.
discoverer.addPropertyChangeListener(changeSupport);
(t0 = new Thread(discoverer)).start();
}
- if (ignore_SHOW_JWS2_SERVICES_preference || Cache.getDefault("SHOW_JWS2_SERVICES", true)) {
- t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer().startDiscoverer(changeSupport);
+ if (ignore_SHOW_JWS2_SERVICES_preference
+ || Cache.getDefault("SHOW_JWS2_SERVICES", true))
+ {
+ t2 = jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
+ .startDiscoverer(changeSupport);
}
Thread t3 = null;
{
// TODO: do rest service discovery
}
- if (blocking) {
- while (alive) {
- try {
+ if (blocking)
+ {
+ while (alive)
+ {
+ try
+ {
Thread.sleep(15);
- } catch (Exception e) {
+ } catch (Exception e)
+ {
}
- alive = (t1 != null && t1.isAlive()) || (t2 != null && t2.isAlive()) || (t3 != null && t3.isAlive())
- || (t0 != null && t0.isAlive());
+ alive = (t1 != null && t1.isAlive()) || (t2 != null && t2.isAlive())
+ || (t3 != null && t3.isAlive())
+ || (t0 != null && t0.isAlive());
}
}
}
*
* @param evt
*/
- protected void JalviewServicesChanged(PropertyChangeEvent evt) {
- if (evt.getNewValue() == null || evt.getNewValue() instanceof Vector) {
- final String ermsg = jalview.ws.jws2.Jws2Discoverer.getDiscoverer().getErrorMessages();
- if (ermsg != null) {
- if (Cache.getDefault("SHOW_WSDISCOVERY_ERRORS", true)) {
- if (serviceChangedDialog == null) {
+ protected void JalviewServicesChanged(PropertyChangeEvent evt)
+ {
+ if (evt.getNewValue() == null || evt.getNewValue() instanceof Vector)
+ {
+ final String ermsg = jalview.ws.jws2.Jws2Discoverer.getDiscoverer()
+ .getErrorMessages();
+ if (ermsg != null)
+ {
+ if (Cache.getDefault("SHOW_WSDISCOVERY_ERRORS", true))
+ {
+ if (serviceChangedDialog == null)
+ {
// only run if we aren't already displaying one of these.
- addDialogThread(serviceChangedDialog = new Runnable() {
+ addDialogThread(serviceChangedDialog = new Runnable()
+ {
@Override
- public void run() {
+ public void run()
+ {
/*
* JalviewDialog jd =new JalviewDialog() {
* jd.waitForInput();
*/
JvOptionPane.showConfirmDialog(Desktop.desktop,
- new JLabel("<html><table width=\"450\"><tr><td>" + ermsg + "</td></tr></table>"
- + "<p>It may be that you have invalid JABA URLs<br/>in your web service preferences,"
- + "<br>or as a command-line argument, or mis-configured HTTP proxy settings.</p>"
- + "<p>Check the <em>Connections</em> and <em>Web services</em> tab<br/>of the"
- + " Tools->Preferences dialog box to change them.</p></html>"),
- "Web Service Configuration Problem", JvOptionPane.DEFAULT_OPTION, JvOptionPane.ERROR_MESSAGE);
+ new JLabel("<html><table width=\"450\"><tr><td>"
+ + ermsg + "</td></tr></table>"
+ + "<p>It may be that you have invalid JABA URLs<br/>in your web service preferences,"
+ + "<br>or as a command-line argument, or mis-configured HTTP proxy settings.</p>"
+ + "<p>Check the <em>Connections</em> and <em>Web services</em> tab<br/>of the"
+ + " Tools->Preferences dialog box to change them.</p></html>"),
+ "Web Service Configuration Problem",
+ JvOptionPane.DEFAULT_OPTION,
+ JvOptionPane.ERROR_MESSAGE);
serviceChangedDialog = null;
}
});
}
- } else {
- jalview.bin.Console.error("Errors reported by JABA discovery service. Check web services preferences.\n" + ermsg);
+ }
+ else
+ {
+ jalview.bin.Console.error(
+ "Errors reported by JABA discovery service. Check web services preferences.\n"
+ + ermsg);
}
}
}
*
* @param url
*/
- public static void showUrl(final String url) {
+ public static void showUrl(final String url)
+ {
showUrl(url, Desktop.instance);
}
* Like showUrl but allows progress handler to be specified
*
* @param url
- * @param progress (null) or object implementing IProgressIndicator
+ * @param progress
+ * (null) or object implementing IProgressIndicator
*/
- public static void showUrl(final String url, final IProgressIndicator progress) {
- new Thread(new Runnable() {
+ public static void showUrl(final String url,
+ final IProgressIndicator progress)
+ {
+ new Thread(new Runnable()
+ {
@Override
- public void run() {
- try {
- if (progress != null) {
- progress.setProgressBar(MessageManager.formatMessage("status.opening_params", new Object[] { url }),
- this.hashCode());
+ public void run()
+ {
+ try
+ {
+ if (progress != null)
+ {
+ progress.setProgressBar(MessageManager
+ .formatMessage("status.opening_params", new Object[]
+ { url }), this.hashCode());
}
jalview.util.BrowserLauncher.openURL(url);
- } catch (Exception ex) {
+ } catch (Exception ex)
+ {
JvOptionPane.showInternalMessageDialog(Desktop.desktop,
- MessageManager.getString("label.web_browser_not_found_unix"),
- MessageManager.getString("label.web_browser_not_found"), JvOptionPane.WARNING_MESSAGE);
+ MessageManager
+ .getString("label.web_browser_not_found_unix"),
+ MessageManager.getString("label.web_browser_not_found"),
+ JvOptionPane.WARNING_MESSAGE);
ex.printStackTrace();
}
- if (progress != null) {
+ if (progress != null)
+ {
progress.setProgressBar(null, this.hashCode());
}
}
public static WsParamSetManager wsparamManager = null;
- public static ParamManager getUserParameterStore() {
- if (wsparamManager == null) {
+ public static ParamManager getUserParameterStore()
+ {
+ if (wsparamManager == null)
+ {
wsparamManager = new WsParamSetManager();
}
return wsparamManager;
*
* @param e
*/
- public static void hyperlinkUpdate(HyperlinkEvent e) {
- if (e.getEventType() == EventType.ACTIVATED) {
+ public static void hyperlinkUpdate(HyperlinkEvent e)
+ {
+ if (e.getEventType() == EventType.ACTIVATED)
+ {
String url = null;
- try {
+ try
+ {
url = e.getURL().toString();
Desktop.showUrl(url);
- } catch (Exception x) {
- if (url != null) {
- jalview.bin.Console.error("Couldn't handle string " + url + " as a URL.");
+ } catch (Exception x)
+ {
+ if (url != null)
+ {
+ jalview.bin.Console
+ .error("Couldn't handle string " + url + " as a URL.");
}
// ignore any exceptions due to dud links.
}
*
* @param prompter
*/
- public void addDialogThread(final Runnable prompter) {
- dialogExecutor.submit(new Runnable() {
+ public void addDialogThread(final Runnable prompter)
+ {
+ dialogExecutor.submit(new Runnable()
+ {
@Override
- public void run() {
- if (dialogPause) {
- try {
+ public void run()
+ {
+ if (dialogPause)
+ {
+ try
+ {
block.acquire();
- } catch (InterruptedException x) {
+ } catch (InterruptedException x)
+ {
}
}
- if (instance == null) {
+ if (instance == null)
+ {
return;
}
- try {
+ try
+ {
SwingUtilities.invokeAndWait(prompter);
- } catch (Exception q) {
- jalview.bin.Console.warn("Unexpected Exception in dialog thread.", q);
+ } catch (Exception q)
+ {
+ jalview.bin.Console.warn("Unexpected Exception in dialog thread.",
+ q);
}
}
});
}
- public void startDialogQueue() {
+ public void startDialogQueue()
+ {
// set the flag so we don't pause waiting for another permit and semaphore
// the current task to begin
dialogPause = false;
* </pre>
*/
@Override
- protected void snapShotWindow_actionPerformed(ActionEvent e) {
+ protected void snapShotWindow_actionPerformed(ActionEvent e)
+ {
// currently the menu option to do this is not shown
invalidate();
int width = getWidth();
int height = getHeight();
- File of = new File("Jalview_snapshot_" + System.currentTimeMillis() + ".eps");
- ImageWriterI writer = new ImageWriterI() {
+ File of = new File(
+ "Jalview_snapshot_" + System.currentTimeMillis() + ".eps");
+ ImageWriterI writer = new ImageWriterI()
+ {
@Override
- public void exportImage(Graphics g) throws Exception {
+ public void exportImage(Graphics g) throws Exception
+ {
paintAll(g);
- jalview.bin.Console.info("Successfully written snapshot to file " + of.getAbsolutePath());
+ jalview.bin.Console.info("Successfully written snapshot to file "
+ + of.getAbsolutePath());
}
};
String title = "View of desktop";
- ImageExporter exporter = new ImageExporter(writer, null, TYPE.EPS, title);
+ ImageExporter exporter = new ImageExporter(writer, null, TYPE.EPS,
+ title);
exporter.doExport(of, this, width, height, title);
}
/**
* Explode the views in the given SplitFrame into separate SplitFrame windows.
- * This respects (remembers) any previous 'exploded geometry' i.e. the size and
- * location last time the view was expanded (if any). However it does not
+ * This respects (remembers) any previous 'exploded geometry' i.e. the size
+ * and location last time the view was expanded (if any). However it does not
* remember the split pane divider location - this is set to match the
* 'exploding' frame.
*
* @param sf
*/
- public void explodeViews(SplitFrame sf) {
+ public void explodeViews(SplitFrame sf)
+ {
AlignFrame oldTopFrame = (AlignFrame) sf.getTopFrame();
AlignFrame oldBottomFrame = (AlignFrame) sf.getBottomFrame();
- List<? extends AlignmentViewPanel> topPanels = oldTopFrame.getAlignPanels();
- List<? extends AlignmentViewPanel> bottomPanels = oldBottomFrame.getAlignPanels();
+ List<? extends AlignmentViewPanel> topPanels = oldTopFrame
+ .getAlignPanels();
+ List<? extends AlignmentViewPanel> bottomPanels = oldBottomFrame
+ .getAlignPanels();
int viewCount = topPanels.size();
- if (viewCount < 2) {
+ if (viewCount < 2)
+ {
return;
}
* Processing in reverse order works, forwards order leaves the first panels not
* visible. I don't know why!
*/
- for (int i = viewCount - 1; i >= 0; i--) {
+ for (int i = viewCount - 1; i >= 0; i--)
+ {
/*
* Make new top and bottom frames. These take over the respective AlignmentPanel
* objects, including their AlignmentViewports, so the cdna/protein
AlignFrame newTopFrame = new AlignFrame(topPanel);
newTopFrame.setSize(oldTopFrame.getSize());
newTopFrame.setVisible(true);
- Rectangle geometry = ((AlignViewport) topPanel.getAlignViewport()).getExplodedGeometry();
- if (geometry != null) {
+ Rectangle geometry = ((AlignViewport) topPanel.getAlignViewport())
+ .getExplodedGeometry();
+ if (geometry != null)
+ {
newTopFrame.setSize(geometry.getSize());
}
AlignFrame newBottomFrame = new AlignFrame(bottomPanel);
newBottomFrame.setSize(oldBottomFrame.getSize());
newBottomFrame.setVisible(true);
- geometry = ((AlignViewport) bottomPanel.getAlignViewport()).getExplodedGeometry();
- if (geometry != null) {
+ geometry = ((AlignViewport) bottomPanel.getAlignViewport())
+ .getExplodedGeometry();
+ if (geometry != null)
+ {
newBottomFrame.setSize(geometry.getSize());
}
topPanel.av.setGatherViewsHere(false);
bottomPanel.av.setGatherViewsHere(false);
- JInternalFrame splitFrame = new SplitFrame(newTopFrame, newBottomFrame);
- if (geometry != null) {
+ JInternalFrame splitFrame = new SplitFrame(newTopFrame,
+ newBottomFrame);
+ if (geometry != null)
+ {
splitFrame.setLocation(geometry.getLocation());
}
Desktop.addInternalFrame(splitFrame, sf.getTitle(), -1, -1);
*
* @param source
*/
- public void gatherViews(GSplitFrame source) {
+ public void gatherViews(GSplitFrame source)
+ {
/*
* special handling of explodedGeometry for a view within a SplitFrame: - it
* holds the (x, y) position of the enclosing SplitFrame, and the (width,
*/
AlignFrame myTopFrame = (AlignFrame) source.getTopFrame();
AlignFrame myBottomFrame = (AlignFrame) source.getBottomFrame();
- myTopFrame.viewport.setExplodedGeometry(
- new Rectangle(source.getX(), source.getY(), myTopFrame.getWidth(), myTopFrame.getHeight()));
- myBottomFrame.viewport.setExplodedGeometry(
- new Rectangle(source.getX(), source.getY(), myBottomFrame.getWidth(), myBottomFrame.getHeight()));
+ myTopFrame.viewport.setExplodedGeometry(new Rectangle(source.getX(),
+ source.getY(), myTopFrame.getWidth(), myTopFrame.getHeight()));
+ myBottomFrame.viewport
+ .setExplodedGeometry(new Rectangle(source.getX(), source.getY(),
+ myBottomFrame.getWidth(), myBottomFrame.getHeight()));
myTopFrame.viewport.setGatherViewsHere(true);
myBottomFrame.viewport.setGatherViewsHere(true);
String topViewId = myTopFrame.viewport.getSequenceSetId();
String bottomViewId = myBottomFrame.viewport.getSequenceSetId();
JInternalFrame[] frames = desktop.getAllFrames();
- for (JInternalFrame frame : frames) {
- if (frame instanceof SplitFrame && frame != source) {
+ for (JInternalFrame frame : frames)
+ {
+ if (frame instanceof SplitFrame && frame != source)
+ {
SplitFrame sf = (SplitFrame) frame;
AlignFrame topFrame = (AlignFrame) sf.getTopFrame();
AlignFrame bottomFrame = (AlignFrame) sf.getBottomFrame();
boolean gatherThis = false;
- for (int a = 0; a < topFrame.alignPanels.size(); a++) {
+ for (int a = 0; a < topFrame.alignPanels.size(); a++)
+ {
AlignmentPanel topPanel = topFrame.alignPanels.get(a);
AlignmentPanel bottomPanel = bottomFrame.alignPanels.get(a);
if (topViewId.equals(topPanel.av.getSequenceSetId())
- && bottomViewId.equals(bottomPanel.av.getSequenceSetId())) {
+ && bottomViewId.equals(bottomPanel.av.getSequenceSetId()))
+ {
gatherThis = true;
topPanel.av.setGatherViewsHere(false);
bottomPanel.av.setGatherViewsHere(false);
- topPanel.av.setExplodedGeometry(new Rectangle(sf.getLocation(), topFrame.getSize()));
- bottomPanel.av.setExplodedGeometry(new Rectangle(sf.getLocation(), bottomFrame.getSize()));
+ topPanel.av.setExplodedGeometry(
+ new Rectangle(sf.getLocation(), topFrame.getSize()));
+ bottomPanel.av.setExplodedGeometry(
+ new Rectangle(sf.getLocation(), bottomFrame.getSize()));
myTopFrame.addAlignmentPanel(topPanel, false);
myBottomFrame.addAlignmentPanel(bottomPanel, false);
}
}
- if (gatherThis) {
+ if (gatherThis)
+ {
topFrame.getAlignPanels().clear();
bottomFrame.getAlignPanels().clear();
sf.close();
myTopFrame.setDisplayedView(myTopFrame.alignPanel);
}
- public static groovy.ui.Console getGroovyConsole() {
+ public static groovy.ui.Console getGroovyConsole()
+ {
return groovyConsole;
}
*
* TODO refactor to desktop utilities class
*
- * @param files - Data source strings extracted from the drop event
- * @param protocols - protocol for each data source extracted from the drop
- * event
- * @param evt - the drop event
- * @param t - the payload from the drop event
+ * @param files
+ * - Data source strings extracted from the drop event
+ * @param protocols
+ * - protocol for each data source extracted from the drop event
+ * @param evt
+ * - the drop event
+ * @param t
+ * - the payload from the drop event
* @throws Exception
*/
- public static void transferFromDropTarget(List<Object> files, List<DataSourceType> protocols, DropTargetDropEvent evt,
- Transferable t) throws Exception {
+ public static void transferFromDropTarget(List<Object> files,
+ List<DataSourceType> protocols, DropTargetDropEvent evt,
+ Transferable t) throws Exception
+ {
- DataFlavor uriListFlavor = new DataFlavor("text/uri-list;class=java.lang.String"), urlFlavour = null;
- try {
- urlFlavour = new DataFlavor("application/x-java-url; class=java.net.URL");
- } catch (ClassNotFoundException cfe) {
- jalview.bin.Console.debug("Couldn't instantiate the URL dataflavor.", cfe);
+ DataFlavor uriListFlavor = new DataFlavor(
+ "text/uri-list;class=java.lang.String"), urlFlavour = null;
+ try
+ {
+ urlFlavour = new DataFlavor(
+ "application/x-java-url; class=java.net.URL");
+ } catch (ClassNotFoundException cfe)
+ {
+ jalview.bin.Console.debug("Couldn't instantiate the URL dataflavor.",
+ cfe);
}
- if (urlFlavour != null && t.isDataFlavorSupported(urlFlavour)) {
+ if (urlFlavour != null && t.isDataFlavorSupported(urlFlavour))
+ {
- try {
+ try
+ {
java.net.URL url = (URL) t.getTransferData(urlFlavour);
// nb: java 8 osx bug https://bugs.openjdk.java.net/browse/JDK-8156099
// means url may be null.
- if (url != null) {
+ if (url != null)
+ {
protocols.add(DataSourceType.URL);
files.add(url.toString());
- jalview.bin.Console.debug("Drop handled as URL dataflavor " + files.get(files.size() - 1));
+ jalview.bin.Console.debug("Drop handled as URL dataflavor "
+ + files.get(files.size() - 1));
return;
- } else {
- if (Platform.isAMacAndNotJS()) {
- System.err.println("Please ignore plist error - occurs due to problem with java 8 on OSX");
+ }
+ else
+ {
+ if (Platform.isAMacAndNotJS())
+ {
+ System.err.println(
+ "Please ignore plist error - occurs due to problem with java 8 on OSX");
}
}
- } catch (Throwable ex) {
+ } catch (Throwable ex)
+ {
jalview.bin.Console.debug("URL drop handler failed.", ex);
}
}
- if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor)) {
+ if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))
+ {
// Works on Windows and MacOSX
jalview.bin.Console.debug("Drop handled as javaFileListFlavor");
- for (Object file : (List) t.getTransferData(DataFlavor.javaFileListFlavor)) {
+ for (Object file : (List) t
+ .getTransferData(DataFlavor.javaFileListFlavor))
+ {
files.add(file);
protocols.add(DataSourceType.FILE);
}
- } else {
+ }
+ else
+ {
// Unix like behaviour
boolean added = false;
String data = null;
- if (t.isDataFlavorSupported(uriListFlavor)) {
+ if (t.isDataFlavorSupported(uriListFlavor))
+ {
jalview.bin.Console.debug("Drop handled as uriListFlavor");
// This is used by Unix drag system
data = (String) t.getTransferData(uriListFlavor);
}
- if (data == null) {
+ if (data == null)
+ {
// fallback to text: workaround - on OSX where there's a JVM bug
- jalview.bin.Console.debug("standard URIListFlavor failed. Trying text");
+ jalview.bin.Console
+ .debug("standard URIListFlavor failed. Trying text");
// try text fallback
- DataFlavor textDf = new DataFlavor("text/plain;class=java.lang.String");
- if (t.isDataFlavorSupported(textDf)) {
+ DataFlavor textDf = new DataFlavor(
+ "text/plain;class=java.lang.String");
+ if (t.isDataFlavorSupported(textDf))
+ {
data = (String) t.getTransferData(textDf);
}
- jalview.bin.Console.debug("Plain text drop content returned " + (data == null ? "Null - failed" : data));
+ jalview.bin.Console.debug("Plain text drop content returned "
+ + (data == null ? "Null - failed" : data));
}
- if (data != null) {
- while (protocols.size() < files.size()) {
- jalview.bin.Console.debug("Adding missing FILE protocol for " + files.get(protocols.size()));
+ if (data != null)
+ {
+ while (protocols.size() < files.size())
+ {
+ jalview.bin.Console.debug("Adding missing FILE protocol for "
+ + files.get(protocols.size()));
protocols.add(DataSourceType.FILE);
}
- for (java.util.StringTokenizer st = new java.util.StringTokenizer(data, "\r\n"); st.hasMoreTokens();) {
+ for (java.util.StringTokenizer st = new java.util.StringTokenizer(
+ data, "\r\n"); st.hasMoreTokens();)
+ {
added = true;
String s = st.nextToken();
- if (s.startsWith("#")) {
+ if (s.startsWith("#"))
+ {
// the line is a comment (as per the RFC 2483)
continue;
}
java.net.URI uri = new java.net.URI(s);
- if (uri.getScheme().toLowerCase(Locale.ROOT).startsWith("http")) {
+ if (uri.getScheme().toLowerCase(Locale.ROOT).startsWith("http"))
+ {
protocols.add(DataSourceType.URL);
files.add(uri.toString());
- } else {
+ }
+ else
+ {
// otherwise preserve old behaviour: catch all for file objects
java.io.File file = new java.io.File(uri);
protocols.add(DataSourceType.FILE);
}
}
- if (jalview.bin.Console.isDebugEnabled()) {
- if (data == null || !added) {
+ if (jalview.bin.Console.isDebugEnabled())
+ {
+ if (data == null || !added)
+ {
- if (t.getTransferDataFlavors() != null && t.getTransferDataFlavors().length > 0) {
- jalview.bin.Console.debug("Couldn't resolve drop data. Here are the supported flavors:");
- for (DataFlavor fl : t.getTransferDataFlavors()) {
- jalview.bin.Console.debug("Supported transfer dataflavor: " + fl.toString());
+ if (t.getTransferDataFlavors() != null
+ && t.getTransferDataFlavors().length > 0)
+ {
+ jalview.bin.Console.debug(
+ "Couldn't resolve drop data. Here are the supported flavors:");
+ for (DataFlavor fl : t.getTransferDataFlavors())
+ {
+ jalview.bin.Console.debug(
+ "Supported transfer dataflavor: " + fl.toString());
Object df = t.getTransferData(fl);
- if (df != null) {
+ if (df != null)
+ {
jalview.bin.Console.debug("Retrieves: " + df);
- } else {
+ }
+ else
+ {
jalview.bin.Console.debug("Retrieved nothing");
}
}
- } else {
- jalview.bin.Console.debug("Couldn't resolve dataflavor for drop: " + t.toString());
+ }
+ else
+ {
+ jalview.bin.Console
+ .debug("Couldn't resolve dataflavor for drop: "
+ + t.toString());
}
}
}
}
- if (Platform.isWindowsAndNotJS()) {
- jalview.bin.Console.debug("Scanning dropped content for Windows Link Files");
+ if (Platform.isWindowsAndNotJS())
+ {
+ jalview.bin.Console
+ .debug("Scanning dropped content for Windows Link Files");
// resolve any .lnk files in the file drop
- for (int f = 0; f < files.size(); f++) {
+ for (int f = 0; f < files.size(); f++)
+ {
String source = files.get(f).toString().toLowerCase(Locale.ROOT);
if (protocols.get(f).equals(DataSourceType.FILE)
- && (source.endsWith(".lnk") || source.endsWith(".url") || source.endsWith(".site"))) {
- try {
+ && (source.endsWith(".lnk") || source.endsWith(".url")
+ || source.endsWith(".site")))
+ {
+ try
+ {
Object obj = files.get(f);
- File lf = (obj instanceof File ? (File) obj : new File((String) obj));
+ File lf = (obj instanceof File ? (File) obj
+ : new File((String) obj));
// process link file to get a URL
jalview.bin.Console.debug("Found potential link file: " + lf);
WindowsShortcut wscfile = new WindowsShortcut(lf);
String fullname = wscfile.getRealFilename();
protocols.set(f, FormatAdapter.checkProtocol(fullname));
files.set(f, fullname);
- jalview.bin.Console.debug("Parsed real filename " + fullname + " to extract protocol: " + protocols.get(f));
- } catch (Exception ex) {
- jalview.bin.Console.error("Couldn't parse " + files.get(f) + " as a link file.", ex);
+ jalview.bin.Console.debug("Parsed real filename " + fullname
+ + " to extract protocol: " + protocols.get(f));
+ } catch (Exception ex)
+ {
+ jalview.bin.Console.error(
+ "Couldn't parse " + files.get(f) + " as a link file.",
+ ex);
}
}
}
* depending on the state of the controlling menu item
*/
@Override
- protected void showExperimental_actionPerformed(boolean selected) {
+ protected void showExperimental_actionPerformed(boolean selected)
+ {
Cache.setProperty(EXPERIMENTAL_FEATURES, Boolean.toString(selected));
}
/**
- * Answers a (possibly empty) list of any structure viewer frames (currently for
- * either Jmol or Chimera) which are currently open. This may optionally be
- * restricted to viewers of a specified class, or viewers linked to a specified
- * alignment panel.
+ * Answers a (possibly empty) list of any structure viewer frames (currently
+ * for either Jmol or Chimera) which are currently open. This may optionally
+ * be restricted to viewers of a specified class, or viewers linked to a
+ * specified alignment panel.
*
- * @param apanel if not null, only return viewers linked to this
- * panel
- * @param structureViewerClass if not null, only return viewers of this class
+ * @param apanel
+ * if not null, only return viewers linked to this panel
+ * @param structureViewerClass
+ * if not null, only return viewers of this class
* @return
*/
- public List<StructureViewerBase> getStructureViewers(AlignmentPanel apanel,
- Class<? extends StructureViewerBase> structureViewerClass) {
+ public List<StructureViewerBase> getStructureViewers(
+ AlignmentPanel apanel,
+ Class<? extends StructureViewerBase> structureViewerClass)
+ {
List<StructureViewerBase> result = new ArrayList<>();
JInternalFrame[] frames = Desktop.instance.getAllFrames();
- for (JInternalFrame frame : frames) {
- if (frame instanceof StructureViewerBase) {
- if (structureViewerClass == null || structureViewerClass.isInstance(frame)) {
- if (apanel == null || ((StructureViewerBase) frame).isLinkedWith(apanel)) {
+ for (JInternalFrame frame : frames)
+ {
+ if (frame instanceof StructureViewerBase)
+ {
+ if (structureViewerClass == null
+ || structureViewerClass.isInstance(frame))
+ {
+ if (apanel == null
+ || ((StructureViewerBase) frame).isLinkedWith(apanel))
+ {
result.add((StructureViewerBase) frame);
}
}
private static boolean debugScaleMessageDone = false;
- public static void debugScaleMessage(Graphics g) {
- if (debugScaleMessageDone) {
+ public static void debugScaleMessage(Graphics g)
+ {
+ if (debugScaleMessageDone)
+ {
return;
}
// output used by tests to check HiDPI scaling settings in action
- try {
+ try
+ {
Graphics2D gg = (Graphics2D) g;
- if (gg != null) {
+ if (gg != null)
+ {
AffineTransform t = gg.getTransform();
double scaleX = t.getScaleX();
double scaleY = t.getScaleY();
jalview.bin.Console.debug(debugScaleMessage + scaleX + " (X)");
jalview.bin.Console.debug(debugScaleMessage + scaleY + " (Y)");
debugScaleMessageDone = true;
- } else {
+ }
+ else
+ {
jalview.bin.Console.debug("Desktop graphics null");
}
- } catch (Exception e) {
+ } catch (Exception e)
+ {
jalview.bin.Console.debug(Cache.getStackTraceString(e));
}
}
{
private static final Font COURIER_12 = new Font("Courier", Font.PLAIN,
12);
+
JTextField id;
JTextField description;
*
* @param action
*/
- public void showDialog(JComponent parent, String title,
- Runnable action)
+ public void showDialog(JComponent parent, String title, Runnable action)
{
Object[] options = new Object[] { MessageManager.getString("action.ok"),
MessageManager.getString("action.cancel") };
});
description = new JTextArea(3, 25);
-
+
start = new JSpinner();
end = new JSpinner();
start.setPreferredSize(new Dimension(80, 20));
end.setPreferredSize(new Dimension(80, 20));
-
+
/*
* ensure that start can never be more than end
*/
- start.addChangeListener(new ChangeListener()
+ start.addChangeListener(new ChangeListener()
{
@Override
public void stateChanged(ChangeEvent e)
{
- Integer startVal = (Integer) start.getValue();
+ Integer startVal = (Integer) start.getValue();
((SpinnerNumberModel) end.getModel()).setMinimum(startVal);
}
});
- end.addChangeListener(new ChangeListener()
+ end.addChangeListener(new ChangeListener()
{
@Override
public void stateChanged(ChangeEvent e)
{
- Integer endVal = (Integer) end.getValue();
+ Integer endVal = (Integer) end.getValue();
((SpinnerNumberModel) start.getModel()).setMaximum(endVal);
}
});
start.setValue(new Integer(firstFeature.getBegin()));
end.setValue(new Integer(firstFeature.getEnd()));
- ((SpinnerNumberModel) start.getModel()).setMaximum(firstFeature.getEnd());
- ((SpinnerNumberModel) end.getModel()).setMinimum(firstFeature.getBegin());
+ ((SpinnerNumberModel) start.getModel())
+ .setMaximum(firstFeature.getEnd());
+ ((SpinnerNumberModel) end.getModel())
+ .setMinimum(firstFeature.getBegin());
description.setText(firstFeature.getDescription());
featureColour = fr.getFeatureStyle(featureType);
*/
public void showDialog()
{
- Runnable okAction = forCreate ? getCreateAction() : getAmendAction();
- Runnable cancelAction = getCancelAction();
+ Runnable okAction = forCreate ? getCreateAction() : getAmendAction();
+ Runnable cancelAction = getCancelAction();
/*
* set dialog action handlers for OK (create/Amend) and Cancel options
* also for Delete if applicable (when amending features)
*/
JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop)
- .setResponseHandler(0, okAction).setResponseHandler(2, cancelAction);
+ .setResponseHandler(0, okAction)
+ .setResponseHandler(2, cancelAction);
if (!forCreate)
{
dialog.setResponseHandler(1, getDeleteAction());
}
dialog.showInternalDialog(mainPanel, title,
- JvOptionPane.YES_NO_CANCEL_OPTION,
- JvOptionPane.PLAIN_MESSAGE, null, options,
- MessageManager.getString("action.ok"));
+ JvOptionPane.YES_NO_CANCEL_OPTION, JvOptionPane.PLAIN_MESSAGE,
+ null, options, MessageManager.getString("action.ok"));
}
/**
*/
protected Runnable getCancelAction()
{
- Runnable okAction = new Runnable()
+ Runnable okAction = new Runnable()
{
@Override
public void run()
*/
protected Runnable getCreateAction()
{
- Runnable okAction = new Runnable()
+ Runnable okAction = new Runnable()
{
boolean useLastDefaults = features.get(0).getType() == null;
*/
protected Runnable getDeleteAction()
{
- Runnable deleteAction = new Runnable()
+ Runnable deleteAction = new Runnable()
{
public void run()
{
*/
protected Runnable getAmendAction()
{
- Runnable okAction = new Runnable()
+ Runnable okAction = new Runnable()
{
boolean useLastDefaults = features.get(0).getType() == null;
-
+
String featureType = name.getText();
-
+
String featureGroup = group.getText();
-
+
public void run()
{
final String enteredType = name.getText().trim();
transparency.setValue(100 - transparencyAsPercent);
inConstruction = incon;
}
+
/**
* Constructor
*
});
frame.setLayer(JLayeredPane.PALETTE_LAYER);
}
- inConstruction = false;
- }
+ inConstruction = false;
+ }
/**
* Sets the state of buttons to show complement features from viewport
change = null;
}
- /**
- * Constructs and shows a popup menu of possible actions on the selected row and
- * feature type
- *
- * @param rowSelected
- * @param type
- * @param typeCol
- * @param pt
- */
- protected void showPopupMenu(final int rowSelected, final String type, final Object typeCol, final Point pt)
+ /**
+ * Constructs and shows a popup menu of possible actions on the selected row
+ * and feature type
+ *
+ * @param rowSelected
+ * @param type
+ * @param typeCol
+ * @param pt
+ */
+ protected void showPopupMenu(final int rowSelected, final String type,
+ final Object typeCol, final Point pt)
{
JPopupMenu men = new JPopupMenu(MessageManager
.formatMessage("label.settings_for_param", new String[]
}
/**
- * close ourselves but leave any existing UI handlers (e.g a CDS/Protein tabbed
- * feature settings dialog) intact
+ * close ourselves but leave any existing UI handlers (e.g a CDS/Protein
+ * tabbed feature settings dialog) intact
*/
public void closeOldSettings()
{
}
});
- final String byScoreLabel = MessageManager.getString("label.seq_sort_by_score");
+ final String byScoreLabel = MessageManager
+ .getString("label.seq_sort_by_score");
JButton sortByScore = new JButton(byScoreLabel);
sortByScore.setFont(JvSwingUtils.getLabelFont());
sortByScore.addActionListener(new ActionListener()
}
}
});
- final String byDensityLabel = MessageManager.getString("label.sequence_sort_by_density");
+ final String byDensityLabel = MessageManager
+ .getString("label.sequence_sort_by_density");
JButton sortByDens = new JButton(byDensityLabel);
sortByDens.setFont(JvSwingUtils.getLabelFont());
sortByDens.addActionListener(new ActionListener()
}
}
});
- // Cancel for a SplitFrame should just revert changes to the currently displayed
+ // Cancel for a SplitFrame should just revert changes to the currently
+ // displayed
// settings. May want to do this for either or both - so need a splitview
// feature settings cancel/OK.
JButton cancel = new JButton(MessageManager
MessageManager.getString("label.transparency_tip"));
boolean nucleotide = af.getViewport().getAlignment().isNucleotide();
- String text = MessageManager.formatMessage("label.show_linked_features",
- nucleotide
- ? MessageManager.getString("label.protein")
- .toLowerCase(Locale.ROOT)
- : "CDS");
+ String text = MessageManager
+ .formatMessage("label.show_linked_features",
+ nucleotide
+ ? MessageManager.getString("label.protein")
+ .toLowerCase(Locale.ROOT)
+ : "CDS");
showComplement = new JCheckBox(text);
showComplement.addActionListener(new ActionListener()
{
*
* @param fcol
* @param withHint
- * if true include 'click to edit' and similar text
+ * if true include 'click to edit' and similar text
* @return
*/
public static String getColorTooltip(FeatureColourI fcol,
JRadioButton graduatedColour = new JRadioButton();
JPanel coloursPanel;
-
+
JPanel filtersPanel;
JPanel singleColour = new JPanel();
ap = fr.ap;
originalFilter = fr.getFeatureFilter(theType);
originalColour = fr.getFeatureColours().get(theType);
-
+
adjusting = true;
-
+
try
{
initialise();
ex.printStackTrace();
return;
}
-
+
updateColoursPanel();
-
+
updateFiltersPanel();
-
+
adjusting = false;
-
+
colourChanged(false);
-
+
String title = MessageManager
.formatMessage("label.display_settings_for", new String[]
{ theType });
}
/**
- * Configures the widgets on the Colours panel according to the current feature
- * colour scheme
+ * Configures the widgets on the Colours panel according to the current
+ * feature colour scheme
*/
private void updateColoursPanel()
{
{
if (minColour.isEnabled())
{
- String ttl = MessageManager.getString("label.select_colour_minimum_value");
+ String ttl = MessageManager
+ .getString("label.select_colour_minimum_value");
showColourChooser(minColour, ttl);
}
}
{
if (maxColour.isEnabled())
{
- String ttl = MessageManager.getString("label.select_colour_maximum_value");
+ String ttl = MessageManager
+ .getString("label.select_colour_maximum_value");
showColourChooser(maxColour, ttl);
}
}
// }
// else
// {
- singleColour.setBackground(originalColour.getColour());
- singleColour.setForeground(originalColour.getColour());
+ singleColour.setBackground(originalColour.getColour());
+ singleColour.setForeground(originalColour.getColour());
// }
singleColour.addMouseListener(new MouseAdapter()
{
{
if (simpleColour.isSelected())
{
- String ttl = MessageManager.formatMessage("label.select_colour_for", featureType);
+ String ttl = MessageManager
+ .formatMessage("label.select_colour_for", featureType);
showColourChooser(singleColour, ttl);
}
}
colourChanged(true);
}
};
- JalviewColourChooser.showColourChooser(this, title,
- colourPanel.getBackground(), listener);
+ JalviewColourChooser.showColourChooser(this, title,
+ colourPanel.getBackground(), listener);
}
/**
*/
adjusting = true;
float f = Float.parseFloat(thresholdValue.getText());
- f = Float.max(f, this.min);
+ f = Float.max(f, this.min);
f = Float.min(f, this.max);
setThresholdValueText(f);
slider.setSliderValue(f);
}
/**
- * Sets the text field for threshold value, rounded to four significant figures
+ * Sets the text field for threshold value, rounded to four significant
+ * figures
*
* @param f
*/
List<Object> displayAttsObjects = new ArrayList<>(displayAtts);
JComboBox<Object> attCombo = JvSwingUtils
.buildComboWithTooltips(displayAttsObjects, tooltips);
-
+
return attCombo;
}
{
if (idMatch.size() > 0 && searchResults.getCount() > 0)
{
- message.append(" ").append(
- MessageManager.getString("label.and").toLowerCase(Locale.ROOT))
- .append(" ");
+ message.append(" ").append(MessageManager.getString("label.and")
+ .toLowerCase(Locale.ROOT)).append(" ");
}
message.append(MessageManager.formatMessage(
"label.subsequence_matches_found",
BufferedImage image;
-// Graphics2D gg;
+ // Graphics2D gg;
int imgHeight = 0;
this.av = av;
PaintRefresher.Register(this, av.getSequenceSetId());
av.getRanges().addPropertyChangeListener(this);
- }
+ }
/**
* DOCUMENT ME!
gg.translate(0, -transY);
gg.dispose();
-
+
fastPaint = true;
// Call repaint on alignment panel so that repaints from other alignment
{
g.setColor(Color.white);
g.fillRect(0, 0, getWidth(), getHeight());
-
+
if (fastPaint)
{
fastPaint = false;
g.drawImage(image, 0, 0, this);
-
+
return;
}
-
+
int oldHeight = imgHeight;
-
+
imgHeight = getHeight();
imgHeight -= (imgHeight % av.getCharHeight());
-
+
if (imgHeight < 1)
{
return;
}
-
+
if (oldHeight != imgHeight || image.getWidth(this) != getWidth())
{
- image = new BufferedImage(getWidth(), imgHeight,
- BufferedImage.TYPE_INT_RGB);
+ image = new BufferedImage(getWidth(), imgHeight,
+ BufferedImage.TYPE_INT_RGB);
}
-
+
Graphics2D gg = image.createGraphics();
-
+
// Fill in the background
gg.setColor(Color.white);
gg.fillRect(0, 0, getWidth(), imgHeight);
-
- drawIds(gg, av, av.getRanges().getStartSeq(), av.getRanges().getEndSeq(), searchResults);
+
+ drawIds(gg, av, av.getRanges().getStartSeq(),
+ av.getRanges().getEndSeq(), searchResults);
gg.dispose();
-
+
g.drawImage(image, 0, 0, this);
}
* @param endSeq
* @param selection
*/
- void drawIds(Graphics2D g, AlignViewport alignViewport, final int startSeq,
- final int endSeq, List<SequenceI> selection)
+ void drawIds(Graphics2D g, AlignViewport alignViewport,
+ final int startSeq, final int endSeq, List<SequenceI> selection)
{
Font font = alignViewport.getFont();
if (alignViewport.isSeqNameItalics())
{
- setIdfont(new Font(font.getName(), Font.ITALIC,
- font.getSize()));
+ setIdfont(new Font(font.getName(), Font.ITALIC, font.getSize()));
}
else
{
g.setColor(currentColor);
int charHeight = alignViewport.getCharHeight();
- g.fillRect(0, (i - startSeq) * charHeight,
- getWidth(), charHeight);
+ g.fillRect(0, (i - startSeq) * charHeight, getWidth(), charHeight);
g.setColor(currentTextColor);
xPos = panelWidth - fm.stringWidth(string) - 4;
}
- g.drawString(string, xPos, (((i - startSeq) * charHeight) + charHeight)
- - (charHeight / 5));
+ g.drawString(string, xPos,
+ (((i - startSeq) * charHeight) + charHeight)
+ - (charHeight / 5));
if (hasHiddenRows && av.getShowHiddenMarkers())
{
* @param starty
* @param yoffset
*/
- void drawMarker(Graphics2D g, AlignViewport alignViewport, int seqIndex, int starty, int yoffset)
+ void drawMarker(Graphics2D g, AlignViewport alignViewport, int seqIndex,
+ int starty, int yoffset)
{
SequenceI[] hseqs = alignViewport.getAlignment()
.getHiddenSequences().hiddenSequences;
/*
* vertices of the triangle, below or above hidden seqs
*/
- int[] xPoints = new int[]
- { getWidth() - charHeight,
+ int[] xPoints = new int[] { getWidth() - charHeight,
getWidth() - charHeight, getWidth() };
int yShift = seqIndex - starty;
StringBuilder text = new StringBuilder();
text.append("Sequence ").append(String.valueOf(seq + 1))
- .append(" ID: ")
- .append(sequence.getName());
+ .append(" ID: ").append(sequence.getName());
alignPanel.alignFrame.setStatus(text.toString());
}
}
}
MousePos pos = alignPanel.getSeqPanel().findMousePosition(e);
-
+
if (e.isPopupTrigger()) // Mac reports this in mousePressed
{
showPopupMenu(e, pos);
*/
public interface ImageWriterI
{
- void exportImage(Graphics g)
- throws Exception;
+ void exportImage(Graphics g) throws Exception;
}
private IProgressIndicator messageBoard;
String type = imageType.getName();
try
{
-// setStatus(
-// MessageManager.formatMessage(
-// "status.exporting_alignment_as_x_file", type),
-// messageId);
+ // setStatus(
+ // MessageManager.formatMessage(
+ // "status.exporting_alignment_as_x_file", type),
+ // messageId);
ImageMaker im = new ImageMaker(imageType, width, height, chosenFile,
title, asLineart);
imageWriter.exportImage(im.getGraphics());
messageId);
} catch (Exception e)
{
- System.out
- .println(String.format("Error creating %s file: %s", type,
- e.toString()));
+ System.out.println(String.format("Error creating %s file: %s", type,
+ e.toString()));
setStatus(MessageManager.formatMessage("info.error_creating_file",
type), messageId);
}
}
else
{
- names[i] = ((String) child.getUserObject()).toLowerCase(Locale.ROOT);
+ names[i] = ((String) child.getUserObject())
+ .toLowerCase(Locale.ROOT);
sortTreeNodes(child);
}
}
lstners.remove(actionListener);
}
-
@Override
public void keyPressed(KeyEvent arg0)
{
{
return buttonFalse;
}
-
+
@Override
public void addActionListener(ActionListener l)
{
int modelNumber = chimeraMaps.size() + 1;
String command = "setattr #" + modelNumber + " models name "
+ pe.getId();
- executeCommand(new StructureCommand(command), false);
+ executeCommand(new StructureCommand(command), false);
modelsToMap.add(new ChimeraModel(pe.getId(), ModelType.PDB_MODEL,
modelNumber, 0));
}
}
/**
- * Returns a model of the structure positions described by the ChimeraX format atomspec
+ * Returns a model of the structure positions described by the ChimeraX format
+ * atomspec
+ *
* @param atomSpec
* @return
*/
public interface ColourChooserListener
{
void colourSelected(Color c);
-
- default void cancel() {};
+
+ default void cancel()
+ {
+ };
}
/**
{
colorChooser.setColor(initialColour);
}
- ActionListener onChoose = evt -> listener.colourSelected(colorChooser.getColor());
+ ActionListener onChoose = evt -> listener
+ .colourSelected(colorChooser.getColor());
ActionListener onCancel = evt -> listener.cancel();
- JDialog dialog = JColorChooser.createDialog(parent, title, true, colorChooser,
- onChoose, onCancel);
- dialog.setVisible(true);
+ JDialog dialog = JColorChooser.createDialog(parent, title, true,
+ colorChooser, onChoose, onCancel);
+ dialog.setVisible(true);
}
/**
import javax.swing.JOptionPane;
import javax.swing.JPanel;
-public class JvOptionPane extends JOptionPane implements DialogRunnerI,
- PropertyChangeListener
+public class JvOptionPane extends JOptionPane
+ implements DialogRunnerI, PropertyChangeListener
{
private static final long serialVersionUID = -3019167117756785229L;
* option (text); this list allows conversion to index (int)
*/
List<Object> ourOptions;
-
+
public JvOptionPane(final Component parent)
{
this.parentComponent = Platform.isJS() ? this : parent;
switch (optionType)
{
case JvOptionPane.YES_NO_CANCEL_OPTION:
- // FeatureRenderer amendFeatures ?? TODO ??
+ // FeatureRenderer amendFeatures ?? TODO ??
// Chimera close
// PromptUserConfig
// $FALL-THROUGH$
Object message)
{
// JvOptionPaneTest only;
- return isInteractiveMode() ? JOptionPane.showInternalConfirmDialog(
- parentComponent, message) : (int) getMockResponse();
+ return isInteractiveMode()
+ ? JOptionPane.showInternalConfirmDialog(parentComponent,
+ message)
+ : (int) getMockResponse();
}
/**
JOptionPane.showMessageDialog(parentComponent, message);
}
-
/**
* Adds title and messageType
*
return JOptionPane.showInputDialog(message, initialSelectionValue);
}
+
/**
* centered on parent
*
public static String showInputDialog(Component parentComponent,
String message, String initialSelectionValue)
{
-
+
// AnnotationPanel
-
+
return isInteractiveMode()
? JOptionPane.showInputDialog(parentComponent, message,
initialSelectionValue)
: getMockResponse().toString();
}
-
/**
* input with initial selection
public static String showInputDialog(Component parentComponent,
Object message, Object initialSelectionValue)
{
-
+
// AnnotationPanel
-
+
return isInteractiveMode()
? JOptionPane.showInputDialog(parentComponent, message,
initialSelectionValue)
// test only
- return isInteractiveMode() ? JOptionPane
- .showInputDialog(parentComponent, message, title, messageType)
+ return isInteractiveMode()
+ ? JOptionPane.showInputDialog(parentComponent, message, title,
+ messageType)
: getMockResponse().toString();
}
/**
- * Customized input option
+ * Customized input option
*
* @param parentComponent
* @param message
Object[] selectionValues, Object initialSelectionValue)
throws HeadlessException
{
-
+
// test only
-
+
return isInteractiveMode()
? JOptionPane.showInputDialog(parentComponent, message, title,
messageType, icon, selectionValues,
: getMockResponse().toString();
}
-
-
/**
* internal version
*
String message)
{
// test only
-
+
return isInteractiveMode()
? JOptionPane.showInternalInputDialog(parentComponent, message)
: getMockResponse().toString();
}
-
/**
* internal with title and messageType
*
public static String showInternalInputDialog(Component parentComponent,
String message, String title, int messageType)
{
-
+
// AlignFrame tabbedPane_mousePressed
-
+
return isInteractiveMode()
? JOptionPane.showInternalInputDialog(parentComponent,
getPrefix(messageType) + message, title, messageType)
Object[] selectionValues, Object initialSelectionValue)
{
// test only
-
+
return isInteractiveMode()
? JOptionPane.showInternalInputDialog(parentComponent, message,
title, messageType, icon, selectionValues,
: getMockResponse().toString();
}
-
///////////// end of options ///////////////
-
-
+
private static void outputMessage(Object message)
{
System.out.println(">>> JOption Message : " + message.toString());
private static String getPrefix(int messageType)
{
- String prefix = "";
-
+ String prefix = "";
+
// JavaScript only
if (Platform.isJS())
{
return new JvOptionPane(parentComponent);
}
- public void showDialog(
- String message, String title, int optionType, int messageType,
- Icon icon, Object[] options, Object initialValue)
+ public void showDialog(String message, String title, int optionType,
+ int messageType, Icon icon, Object[] options, Object initialValue)
{
if (!isInteractiveMode())
//
// 2) UserDefinedColors warning about saving over a name already defined
//
-
+
ourOptions = Arrays.asList(options);
-
- int response = JOptionPane.showOptionDialog(parentComponent, message, title,
- optionType, messageType, icon, options, initialValue);
-
+
+ int response = JOptionPane.showOptionDialog(parentComponent, message,
+ title, optionType, messageType, icon, options, initialValue);
+
/*
* In Java, the response is returned to this thread and handled here;
* (for Javascript, see propertyChange)
{
handleResponse(getMockResponse());
}
-
+
ourOptions = Arrays.asList(options);
int response;
- if (parentComponent != this)
+ if (parentComponent != this)
{
- response = JOptionPane.showInternalOptionDialog(parentComponent, mainPanel,
- title, yesNoCancelOption, questionMessage, icon, options,
- initresponse);
+ response = JOptionPane.showInternalOptionDialog(parentComponent,
+ mainPanel, title, yesNoCancelOption, questionMessage, icon,
+ options, initresponse);
}
else
{
- response = JOptionPane.showOptionDialog(parentComponent, mainPanel, title,
- yesNoCancelOption, questionMessage, icon, options,
+ response = JOptionPane.showOptionDialog(parentComponent, mainPanel,
+ title, yesNoCancelOption, questionMessage, icon, options,
initresponse);
}
if (!Platform.isJS())
handleResponse(response);
}
}
-
+
@Override
public JvOptionPane setResponseHandler(Object response, Runnable action)
{
- callbacks.put(response, action);
+ callbacks.put(response, action);
return this;
}
/**
- * JalviewJS signals option selection by a property change event
- * for the option e.g. "OK". This methods responds to that by
- * running the response action that corresponds to that option.
+ * JalviewJS signals option selection by a property change event for the
+ * option e.g. "OK". This methods responds to that by running the response
+ * action that corresponds to that option.
*
* @param evt
*/
public void propertyChange(PropertyChangeEvent evt)
{
Object newValue = evt.getNewValue();
- int ourOption = ourOptions.indexOf(newValue);
+ int ourOption = ourOptions.indexOf(newValue);
if (ourOption >= 0)
{
handleResponse(ourOption);
public void handleResponse(Object response)
{
/*
- * this test is for NaN in Chrome
- */
+ * this test is for NaN in Chrome
+ */
if (response != null && !response.equals(response))
{
return;
}
return (enclose ? "<html>" : "")
- // BH 2018
+ // BH 2018
+ "<style> div.ttip {width:350px;white-space:pre-wrap;padding:2px;overflow-wrap:break-word;}</style><div class=\"ttip\">"
-// + "<style> p.ttip {width:350px;margin:-14px 0px -14px 0px;padding:2px;overflow-wrap:break-word;}"
-// + "</style><p class=\"ttip\">"
- + ttext
- + " </div>"
-// + "</p>"
+ // + "<style> p.ttip {width:350px;margin:-14px 0px -14px
+ // 0px;padding:2px;overflow-wrap:break-word;}"
+ // + "</style><p class=\"ttip\">"
+ + ttext + " </div>"
+ // + "</p>"
+ ((enclose ? "</html>" : ""));
}
combo.setToolTipText(tooltips.get(j));
}
}
+
@Override
public void mouseExited(MouseEvent e)
{
desktop = instance;
if (oomex != null)
{
- Console.error("Out of Memory when " + action,
- oomex);
+ Console.error("Out of Memory when " + action, oomex);
}
javax.swing.SwingUtilities.invokeLater(this);
System.gc();
if (!adjusting)
{
float value = slider.getSliderValue();
- valueField.setText(
- integ ? Integer.toString((int) value)
- : Float.toString(value));
+ valueField.setText(integ ? Integer.toString((int) value)
+ : Float.toString(value));
checkIfModified();
}
}
{
}
});
- valueField.addFocusListener(new FocusAdapter() {
+ valueField.addFocusListener(new FocusAdapter()
+ {
@Override
public void focusLost(FocusEvent e)
{
actionPerformed(null);
}
-
+
});
valueField.setPreferredSize(new Dimension(60, 25));
valueField.setText(parm.getValue());
{
valueField.setText(valueField.getText().trim());
iVal = Integer.valueOf(valueField.getText());
- if (minValue != null
- && minValue.intValue() > iVal)
+ if (minValue != null && minValue.intValue() > iVal)
{
iVal = minValue.intValue();
// TODO: provide visual indication that hard limit was reached for
{
valueField.setText(valueField.getText().trim());
fVal = Float.valueOf(valueField.getText());
- if (minValue != null
- && minValue.floatValue() > fVal)
+ if (minValue != null && minValue.floatValue() > fVal)
{
fVal = minValue.floatValue();
// TODO: provide visual indication that hard limit was reached for
// update value field to reflect any bound checking we performed.
valueField.setText("" + fVal);
}
- if (maxValue != null
- && maxValue.floatValue() < fVal)
+ if (maxValue != null && maxValue.floatValue() < fVal)
{
fVal = maxValue.floatValue();
// TODO: provide visual indication that hard limit was reached for
@Override
public void paintComponent(Graphics g)
{
- //super.paintComponent(g);
+ // super.paintComponent(g);
if (restart)
{
{
// if there is annotation, scale the alignment and annotation
// separately
- if (od.getGraphHeight() > 0
- && od.getSequencesHeight() > 0 // BH 2019
- )
+ if (od.getGraphHeight() > 0 && od.getSequencesHeight() > 0 // BH 2019
+ )
{
BufferedImage topImage = lastMiniMe.getSubimage(0, 0,
od.getWidth(), od.getSequencesHeight());
{
g.drawImage(lastMiniMe, 0, 0, getWidth(), getHeight(), this);
}
-
+
// draw the box
g.setColor(Color.red);
od.drawBox(g);
}
-
public void dispose()
{
dispose = true;
if (showHidden)
{
od = new OverviewDimensionsShowHidden(av.getRanges(),
- (av.isShowAnnotation()
- && av.getAlignmentConservationAnnotation() != null));
+ (av.isShowAnnotation()
+ && av.getAlignmentConservationAnnotation() != null));
}
else
{
// without this the overview window does not size to fit the overview canvas
setPreferredSize(new Dimension(od.getWidth(), od.getHeight()));
-
+
addComponentListener(new ComponentAdapter()
{
@Override
@Override
public void mousePressed(MouseEvent evt)
{
-
- if (Platform.isWinRightButton(evt)) {
- showPopupMenu(evt);
- return;
- }
- if (SwingUtilities.isRightMouseButton(evt)) {
- return;
+
+ if (Platform.isWinRightButton(evt))
+ {
+ showPopupMenu(evt);
+ return;
}
- // don't do anything if the mouse press is in the overview's box
- // (wait to see if it's a drag instead)
- // otherwise update the viewport
- if (!od.isPositionInBox(evt.getX(), evt.getY()))
- {
- draggingBox = false;
+ if (SwingUtilities.isRightMouseButton(evt))
+ {
+ return;
+ }
+ // don't do anything if the mouse press is in the overview's box
+ // (wait to see if it's a drag instead)
+ // otherwise update the viewport
+ if (!od.isPositionInBox(evt.getX(), evt.getY()))
+ {
+ draggingBox = false;
- // display drag cursor at mouse position
- setCursor(Cursor.getPredefinedCursor(Cursor.MOVE_CURSOR));
+ // display drag cursor at mouse position
+ setCursor(Cursor.getPredefinedCursor(Cursor.MOVE_CURSOR));
- od.updateViewportFromMouse(evt.getX(), evt.getY(),
- av.getAlignment().getHiddenSequences(),
- av.getAlignment().getHiddenColumns());
- getParent().setCursor(
- Cursor.getPredefinedCursor(Cursor.HAND_CURSOR));
- }
- else
- {
- draggingBox = true;
- od.setDragPoint(evt.getX(), evt.getY(),
- av.getAlignment().getHiddenSequences(),
- av.getAlignment().getHiddenColumns());
- }
+ od.updateViewportFromMouse(evt.getX(), evt.getY(),
+ av.getAlignment().getHiddenSequences(),
+ av.getAlignment().getHiddenColumns());
+ getParent().setCursor(
+ Cursor.getPredefinedCursor(Cursor.HAND_CURSOR));
+ }
+ else
+ {
+ draggingBox = true;
+ od.setDragPoint(evt.getX(), evt.getY(),
+ av.getAlignment().getHiddenSequences(),
+ av.getAlignment().getHiddenColumns());
+ }
}
@Override
od.setWidth(getWidth());
od.setHeight(getHeight() - progressPanel.getHeight());
}
-
+
setPreferredSize(new Dimension(od.getWidth(),
od.getHeight() + progressPanel.getHeight()));
thread.start();
repaint();
-
}
@Override
* close the parent frame (which also removes it from the
* Desktop Windows menu)
*/
- ((JInternalFrame) SwingUtilities.getAncestorOfClass(
- JInternalFrame.class, (this))).setClosed(true);
+ ((JInternalFrame) SwingUtilities
+ .getAncestorOfClass(JInternalFrame.class, (this)))
+ .setClosed(true);
} catch (PropertyVetoException e)
{
// ignore
ScoreModelI scoreModel = ScoreModels.getInstance()
.getScoreModel(modelName, ap);
- setPcaModel(new PCAModel(seqstrings, seqs, nucleotide, scoreModel,
- params));
+ setPcaModel(
+ new PCAModel(seqstrings, seqs, nucleotide, scoreModel, params));
PaintRefresher.Register(this, av.getSequenceSetId());
setRotatableCanvas(new RotatableCanvas(alignPanel));
@Override
public void exportImage(Graphics g) throws Exception
{
- RotatableCanvas canvas = getRotatableCanvas();
- canvas.drawBackground(g);
- canvas.drawScene(g);
+ RotatableCanvas canvas = getRotatableCanvas();
+ canvas.drawBackground(g);
+ canvas.drawScene(g);
if (canvas.drawAxes)
{
canvas.drawAxes(g);
final IProgressIndicatorHandler handler)
{
progressBar.registerHandler(id, handler);
- // if (progressBarHandlers == null || !progressBars.contains(Long.valueOf(id)))
+ // if (progressBarHandlers == null ||
+ // !progressBars.contains(Long.valueOf(id)))
// {
// throw new
// Error(MessageManager.getString("error.call_setprogressbar_before_registering_handler"));
&& selectionGroup.getSize() > 0;
AlignmentView view = viewport.getAlignmentView(isSelection);
// String[] seqStrings = viewport.getViewAsString(true);
- String[] seqStrings = view.getSequenceStrings(viewport
- .getGapCharacter());
+ String[] seqStrings = view
+ .getSequenceStrings(viewport.getGapCharacter());
SequenceI[] seqs;
if (isSelection)
{
- seqs = (SequenceI[]) view.getAlignmentAndHiddenColumns(viewport
- .getGapCharacter())[0];
+ seqs = (SequenceI[]) view
+ .getAlignmentAndHiddenColumns(viewport.getGapCharacter())[0];
}
else
{
}
first = false;
as.printAlignment(System.out);
- scores[i][j] = as.getMaxScore()
- / as.getASeq1().length;
+ scores[i][j] = as.getMaxScore() / as.getASeq1().length;
totscore = totscore + scores[i][j];
textarea.append(as.getOutput());
for (int i = 0; i < seqs.length; i++)
{
- System.out.println(String.format("%3d %s", i + 1,
- seqs[i].getDisplayId(true)));
+ System.out.println(
+ String.format("%3d %s", i + 1, seqs[i].getDisplayId(true)));
}
/*
}
/**
- * Constructor for a PopupMenu for a click in the alignment panel (on a residue)
+ * Constructor for a PopupMenu for a click in the alignment panel (on a
+ * residue)
*
* @param ap
- * the panel in which the mouse is clicked
+ * the panel in which the mouse is clicked
* @param seq
- * the sequence under the mouse
+ * the sequence under the mouse
* @throws NullPointerException
- * if seq is null
+ * if seq is null
*/
public PopupMenu(final AlignmentPanel ap, SequenceI seq, int column)
{
* Constructor for a PopupMenu for a click in the sequence id panel
*
* @param alignPanel
- * the panel in which the mouse is clicked
+ * the panel in which the mouse is clicked
* @param seq
- * the sequence under the mouse click
+ * the sequence under the mouse click
* @param groupLinks
- * templates for sequence external links
+ * templates for sequence external links
* @throws NullPointerException
- * if seq is null
+ * if seq is null
*/
public PopupMenu(final AlignmentPanel alignPanel, final SequenceI seq,
List<String> groupLinks)
* @param alignPanel
* @param seq
* @param column
- * aligned column position (0...)
+ * aligned column position (0...)
* @param groupLinks
*/
- private PopupMenu(boolean fromIdPanel,
- final AlignmentPanel alignPanel,
+ private PopupMenu(boolean fromIdPanel, final AlignmentPanel alignPanel,
final SequenceI seq, final int column, List<String> groupLinks)
{
Objects.requireNonNull(seq);
/*
* And repeat for the current selection group (if there is one):
*/
- final List<SequenceI> selectedGroup = (alignPanel.av.getSelectionGroup() == null
- ? Collections.<SequenceI> emptyList()
- : alignPanel.av.getSelectionGroup().getSequences());
+ final List<SequenceI> selectedGroup = (alignPanel.av
+ .getSelectionGroup() == null
+ ? Collections.<SequenceI> emptyList()
+ : alignPanel.av.getSelectionGroup().getSequences());
buildAnnotationTypesMenus(groupShowAnnotationsMenu,
groupHideAnnotationsMenu, selectedGroup);
configureReferenceAnnotationsMenu(groupAddReferenceAnnotations,
buildGroupURLMenu(sg, groupLinks);
}
// Add a 'show all structures' for the current selection
- Hashtable<String, PDBEntry> pdbe = new Hashtable<>(), reppdb = new Hashtable<>();
+ Hashtable<String, PDBEntry> pdbe = new Hashtable<>(),
+ reppdb = new Hashtable<>();
SequenceI sqass = null;
for (SequenceI sq : alignPanel.av.getSequenceSelection())
{
createGroupMenuItem.setVisible(true);
unGroupMenuItem.setVisible(false);
- editGroupMenu.setText(MessageManager.getString("action.edit_new_group"));
+ editGroupMenu
+ .setText(MessageManager.getString("action.edit_new_group"));
}
else
{
* <li>positional feature links (alignment panel popup menu)</li>
* <li>feature details links (alignment panel popup menu)</li>
* </ul>
- * If this panel is also showed complementary (CDS/protein) features, then links
- * to their feature details are also added.
+ * If this panel is also showed complementary (CDS/protein) features, then
+ * links to their feature details are also added.
*
* @param seq
* @param column
if (((String[]) sarray[1])[sq] == null)
{
- if (!e.hasMap() || (e.getMap()
- .locateMappedRange(start, end) != null))
+ if (!e.hasMap()
+ || (e.getMap().locateMappedRange(start, end) != null))
{
((String[]) sarray[1])[sq] = e.getAccessionId();
((int[]) sarray[0])[0]++;
}
inserts.and(sq.getInsertionsAsBits());
}
- hidden.clearAndHideColumns(inserts, ap.av.getSelectionGroup().getStartRes(),
+ hidden.clearAndHideColumns(inserts,
+ ap.av.getSelectionGroup().getStartRes(),
ap.av.getSelectionGroup().getEndRes());
}
/**
* Shows a dialog where the sequence name and description may be edited. If a
- * name containing spaces is entered, these are converted to underscores, with a
- * warning message.
+ * name containing spaces is entered, these are converted to underscores, with
+ * a warning message.
*/
void sequenceName_actionPerformed()
{
sequence.getDescription(),
MessageManager.getString("label.sequence_name"),
MessageManager.getString("label.sequence_description"));
- dialog.showDialog(ap.alignFrame,
- MessageManager.getString(
- "label.edit_sequence_name_description"),
- new Runnable()
+ dialog.showDialog(ap.alignFrame, MessageManager.getString(
+ "label.edit_sequence_name_description"), new Runnable()
{
@Override
public void run()
*/
protected void outline_actionPerformed()
{
- String title = MessageManager
- .getString("label.select_outline_colour");
+ String title = MessageManager.getString("label.select_outline_colour");
ColourChooserListener listener = new ColourChooserListener()
{
@Override
refresh();
}
};
- JalviewColourChooser.showColourChooser(Desktop.getDesktop(),
- title, Color.BLUE, listener);
+ JalviewColourChooser.showColourChooser(Desktop.getDesktop(), title,
+ Color.BLUE, listener);
}
/**
// changing visibility
labelPanel.setLayout(labelLayout);
barPanel.setLayout(barLayout);
-
+
labelPanel.add(progressLabel, VISIBLE);
labelPanel.add(new JPanel(), INVISIBLE);
barPanel.add(progressBar, VISIBLE);
// verify the property is set for debugging
if (Console.isDebugEnabled())
{
- Console.debug("User set property to "
- + Cache.getProperty(property));
+ Console.debug(
+ "User set property to " + Cache.getProperty(property));
}
} catch (Exception e)
{
{
// todo promote to StructureCommandsI.showLabel()
String modelId = getModelIdForFile(atom.getPdbFile());
- sb.append(String.format(" %s//%s/%d/*", modelId,
- atom.getChain(),
+ sb.append(String.format(" %s//%s/%d/*", modelId, atom.getChain(),
atom.getPdbResNum()));
}
String labelSpec = sb.toString();
@Override
public boolean isViewerRunning()
{
- return pymolManager !=null && pymolManager.isPymolLaunched();
+ return pymolManager != null && pymolManager.isPymolLaunched();
}
@Override
* a second parameter sets the pdbid as the loaded PyMOL object name
*/
String pdbId = pe.getId();
- try {
- String safePDBId = java.net.URLEncoder.encode(pdbId,"UTF-8");
+ try
+ {
+ String safePDBId = java.net.URLEncoder.encode(pdbId, "UTF-8");
pdbId = safePDBId.replace('%', '_');
pdbId = pdbId.replace("-", "__");
char fc = pdbId.charAt(0);
// put an 's' before any numerics
- if (fc>='0' && fc<='9')
+ if (fc >= '0' && fc <= '9')
{
- pdbId = 's'+pdbId;
+ pdbId = 's' + pdbId;
}
-// pdbId.replace('-', 0)
+ // pdbId.replace('-', 0)
} catch (Exception x)
{
- Console.error("Unxpected encoding exception for '"+pdbId+"'",x);
+ Console.error("Unxpected encoding exception for '" + pdbId + "'", x);
}
cmd.addParameter(pdbId);
AlignmentPanel ap)
{
this();
- openNewPymol(ap, new PDBEntry[] { pdb },
- new SequenceI[][]
- { seqs });
+ openNewPymol(ap, new PDBEntry[] { pdb }, new SequenceI[][] { seqs });
}
public PymolViewer(PDBEntry[] pe, boolean alignAdded, SequenceI[][] seqs,
public void run()
{
// todo pull up much of this
-
+
StringBuilder errormsgs = new StringBuilder(128);
List<PDBEntry> filePDB = new ArrayList<>();
List<Integer> filePDBpos = new ArrayList<>();
- String[] curfiles = binding.getStructureFiles(); // files currently in viewer
+ String[] curfiles = binding.getStructureFiles(); // files currently in
+ // viewer
for (int pi = 0; pi < binding.getPdbCount(); pi++)
{
String file = null;
/*
* got file already
*/
- file = new File(thePdbEntry.getFile()).getAbsoluteFile()
- .getPath();
+ file = new File(thePdbEntry.getFile()).getAbsoluteFile().getPath();
// todo - skip if already loaded in PyMOL
}
if (file != null)
filePDBpos.add(Integer.valueOf(pi));
}
}
-
+
if (!filePDB.isEmpty())
{
/*
StructureFile pdb = binding.getSsm().setMapping(
binding.getSequence()[pos], binding.getChains()[pos],
- pe.getFile(), protocol,
- getProgressIndicator());
+ pe.getFile(), protocol, getProgressIndicator());
binding.stashFoundChains(pdb, pe.getFile());
} catch (Exception ex)
{
- Console.error(
- "Couldn't open " + pe.getFile() + " in "+getViewerName()+"!",
- ex);
+ Console.error("Couldn't open " + pe.getFile() + " in "
+ + getViewerName() + "!", ex);
} finally
{
// Cache.debug("File locations are " + files);
boolean opened = binding.openSession(pymolSessionFile);
if (!opened)
{
- Console.error(
- "An error occurred opening PyMOL session file "
+ Console.error("An error occurred opening PyMOL session file "
+ pymolSessionFile);
}
}
{
return "PyMOL";
}
+
JMenuItem writeFeatures = null;
+
@Override
protected void initMenus()
{
writeFeatures = new JMenuItem(
MessageManager.getString("label.create_viewer_attributes"));
- writeFeatures.setToolTipText(MessageManager
- .getString("label.create_viewer_attributes_tip"));
+ writeFeatures.setToolTipText(
+ MessageManager.getString("label.create_viewer_attributes_tip"));
writeFeatures.addActionListener(new ActionListener()
{
@Override
});
viewerActionMenu.add(writeFeatures);
}
-
+
@Override
protected void buildActionMenu()
{
protected void sendFeaturesToPymol()
{
int count = binding.sendFeaturesToViewer(getAlignmentPanel());
- statusBar.setText(
- MessageManager.formatMessage("label.attributes_set", count, getViewerName()));
+ statusBar.setText(MessageManager.formatMessage("label.attributes_set",
+ count, getViewerName()));
}
}
* Models a Panel on which a set of points, and optionally x/y/z axes, can be
* drawn, and rotated or zoomed with the mouse
*/
-public class RotatableCanvas extends JPanel implements MouseListener,
- MouseMotionListener, KeyListener, RotatableCanvasI,
- MouseWheelListener
+public class RotatableCanvas extends JPanel
+ implements MouseListener, MouseMotionListener, KeyListener,
+ RotatableCanvasI, MouseWheelListener
{
private static final float ZOOM_OUT = 0.9f;
{
float[] max = new float[DIMS];
float[] min = new float[DIMS];
-
+
max[0] = -Float.MAX_VALUE;
max[1] = -Float.MAX_VALUE;
max[2] = -Float.MAX_VALUE;
-
+
min[0] = Float.MAX_VALUE;
min[1] = Float.MAX_VALUE;
min[2] = Float.MAX_VALUE;
-
+
for (SequencePoint sp : sequencePoints)
{
max[0] = Math.max(max[0], sp.coord.x);
min[1] = Math.min(min[1], sp.coord.y);
min[2] = Math.min(min[2], sp.coord.z);
}
-
+
seqMin = min;
seqMax = max;
}
// Now translate back again
sp.translate(centre[0], centre[1], centre[2]);
-
+
zMin = Math.min(zMin, sp.coord.z);
zMax = Math.max(zMax, sp.coord.z);
}
if (av != null)
{
SequenceI sequence = sp.getSequence();
- if (!av.getSelectionGroup().getSequences(null)
- .contains(sequence))
+ if (!av.getSelectionGroup().getSequences(null).contains(sequence))
{
av.getSelectionGroup().addSequence(sequence, true);
}
for (int i = 0; i < npoint; i++)
{
SequencePoint sp = sequencePoints.get(i);
- int px = (int) ((sp.coord.x - centre[0]) * scaleBy)
- + halfwidth;
- int py = (int) ((sp.coord.y - centre[1]) * scaleBy)
- + halfheight;
+ int px = (int) ((sp.coord.x - centre[0]) * scaleBy) + halfwidth;
+ int py = (int) ((sp.coord.y - centre[1]) * scaleBy) + halfheight;
if ((Math.abs(px - x) < NEARBY) && (Math.abs(py - y) < NEARBY))
{
});
pop.add(item);
- if (av.getAlignment().getHiddenColumns().hasMultiHiddenColumnRegions())
+ if (av.getAlignment().getHiddenColumns()
+ .hasMultiHiddenColumnRegions())
{
item = new JMenuItem(MessageManager.getString("action.reveal_all"));
item.addActionListener(new ActionListener()
// todo res calculation should be a method on AlignViewport
int xCords = Math.max(0, evt.getX()); // prevent negative X coordinates
ViewportRanges ranges = av.getRanges();
- int res = (xCords / av.getCharWidth())
- + ranges.getStartRes();
+ int res = (xCords / av.getCharWidth()) + ranges.getStartRes();
res = Math.min(res, ranges.getEndRes());
if (av.hasHiddenColumns())
{
@Override
public void paintComponent(Graphics g)
{
- //super.paintComponent(g); // BH 2019
+ // super.paintComponent(g); // BH 2019
/*
* shouldn't get called in wrapped mode as the scale above is
gg.fillPolygon(
new int[]
- { -1 + res * avCharWidth - avCharHeight / 4,
- -1 + res * avCharWidth + avCharHeight / 4,
- -1 + res * avCharWidth }, new int[]
- { y, y, y + 2 * yOf }, 3);
+ { -1 + res * avCharWidth - avCharHeight / 4,
+ -1 + res * avCharWidth + avCharHeight / 4,
+ -1 + res * avCharWidth },
+ new int[]
+ { y, y, y + 2 * yOf }, 3);
}
}
}
|| evt.getPropertyName().equals(ViewportRanges.MOVE_VIEWPORT))
{
// scroll event, repaint panel
-
- // Call repaint on alignment panel so that repaints from other alignment
- // panel components can be aggregated. Otherwise performance of the overview
- // window and others may be adversely affected.
+
+ // Call repaint on alignment panel so that repaints from other alignment
+ // panel components can be aggregated. Otherwise performance of the
+ // overview
+ // window and others may be adversely affected.
av.getAlignPanel().repaint();
}
}
public class SeqCanvas extends JPanel implements ViewportListenerI
{
/**
- * vertical gap in pixels between sequences and annotations when in wrapped mode
+ * vertical gap in pixels between sequences and annotations when in wrapped
+ * mode
*/
static final int SEQS_ANNOTATION_GAP = 3;
private int wrappedVisibleWidths; // number of wrapped widths displayed
// Don't do this! Graphics handles are supposed to be transient
- //private Graphics2D gg;
+ // private Graphics2D gg;
/**
* Creates a new SeqCanvas object.
public SequenceRenderer getSequenceRenderer()
{
- return seqRdr;
+ return seqRdr;
}
public FeatureRenderer getFeatureRenderer()
int yPos = ypos + charHeight;
int startX = startx;
int endX = endx;
-
+
if (av.hasHiddenColumns())
{
HiddenColumns hiddenColumns = av.getAlignment().getHiddenColumns();
}
}
-
/*
* white fill the space for the scale
*/
}
}
-
// System.err.println(">>> FastPaint to " + transX + " " + transY + " "
// + horizontal + " " + vertical + " " + startRes + " " + endRes
// + " " + startSeq + " " + endSeq);
drawCursor(g, startRes, endRes, startSeq, endSeq);
}
}
-
+
/**
* Draw an alignment panel for printing
*
{
drawPanel(g1, startRes, endRes, startSeq, endSeq, 0);
- drawSelectionGroup((Graphics2D) g1, startRes, endRes,
- startSeq, endSeq);
+ drawSelectionGroup((Graphics2D) g1, startRes, endRes, startSeq, endSeq);
}
/**
if (group != null)
{
drawWrappedSelection((Graphics2D) g, group, canvasWidth, canvasHeight,
- startRes);
+ startRes);
}
}
FontMetrics fm = getFontMetrics(av.getFont());
int labelWidth = 0;
-
+
if (av.getScaleRightWrapped() || av.getScaleLeftWrapped())
{
labelWidth = getLabelWidth(fm);
int currentWidth = 0;
while ((currentWidth < wrappedVisibleWidths) && (start < maxWidth))
{
- int endColumn = Math
- .min(maxWidth, start + wrappedWidthInResidues - 1);
+ int endColumn = Math.min(maxWidth,
+ start + wrappedWidthInResidues - 1);
drawWrappedWidth(g, ypos, start, endColumn, canvasHeight);
ypos += wrappedRepeatHeightPx;
start += wrappedWidthInResidues;
* - start with space above plus sequences
*/
wrappedRepeatHeightPx = wrappedSpaceAboveAlignment;
- wrappedRepeatHeightPx += av.getAlignment().getHeight()
- * charHeight;
+ wrappedRepeatHeightPx += av.getAlignment().getHeight() * charHeight;
/*
* add annotations panel height if shown
int charWidth = av.getCharWidth();
int xOffset = labelWidthWest
+ ((startColumn - ranges.getStartRes()) % viewportWidth)
- * charWidth;
+ * charWidth;
g.translate(xOffset, 0);
if (av.getScaleRightWrapped())
{
int x = labelWidthWest + viewportWidth * charWidth;
-
+
g.translate(x, 0);
drawVerticalScale(g, startCol, endColumn, ypos, false);
g.translate(-x, 0);
*/
g.translate(labelWidthWest, 0);
g.setColor(Color.white);
- g.fillRect(0, ypos - wrappedSpaceAboveAlignment, viewportWidth
- * charWidth + labelWidthWest, wrappedSpaceAboveAlignment);
+ g.fillRect(0, ypos - wrappedSpaceAboveAlignment,
+ viewportWidth * charWidth + labelWidthWest,
+ wrappedSpaceAboveAlignment);
g.setColor(Color.black);
g.translate(-labelWidthWest, 0);
* Draw a selection group over a wrapped alignment
*/
private void drawWrappedSelection(Graphics2D g, SequenceGroup group,
- int canvasWidth,
- int canvasHeight, int startRes)
+ int canvasWidth, int canvasHeight, int startRes)
{
// chop the wrapped alignment extent up into panel-sized blocks and treat
// each block as if it were a block from an unwrapped alignment
g.translate(labelWidthWest, 0);
drawUnwrappedSelection(g, group, startx, endx, 0,
- av.getAlignment().getHeight() - 1,
- ypos);
+ av.getAlignment().getHeight() - 1, ypos);
g.translate(-labelWidthWest, 0);
ypos += wrappedRepeatHeightPx;
}
/**
- * Answers zero if annotations are not shown, otherwise recalculates and answers
- * the total height of all annotation rows in pixels
+ * Answers zero if annotations are not shown, otherwise recalculates and
+ * answers the total height of all annotation rows in pixels
*
* @return
*/
* the cursor drawn on it, if any
*/
private void drawCursor(Graphics g, int startRes, int endRes,
- int startSeq,
- int endSeq)
+ int startSeq, int endSeq)
{
// convert the cursorY into a position on the visible alignment
int cursor_ypos = cursorY;
}
}
-
/**
* Draw a selection group over an unwrapped alignment
*
int startRes, int endRes, int startSeq, int endSeq, int offset)
{
int charWidth = av.getCharWidth();
-
+
if (!av.hasHiddenColumns())
{
drawPartialGroupOutline(g, group, startRes, endRes, startSeq, endSeq,
blockStart = region[0];
g.translate(screenY * charWidth, 0);
- drawPartialGroupOutline(g, group,
- blockStart, blockEnd, startSeq, endSeq, offset);
+ drawPartialGroupOutline(g, group, blockStart, blockEnd, startSeq,
+ endSeq, offset);
g.translate(-screenY * charWidth, 0);
screenY += blockEnd - blockStart + 1;
g.drawLine(sx + xwidth, oldY, sx + xwidth, sy);
}
}
-
+
/**
* Highlights search results in the visible region by rendering as white text
* on a black background. Any previous highlighting is removed. Answers true
return highlightSearchResults(results, false);
}
-
+
/**
* Highlights search results in the visible region by rendering as white text
* on a black background. Any previous highlighting is removed. Answers true
{
firstCol = alignment.getHiddenColumns()
.absoluteToVisibleColumn(firstCol);
- lastCol = alignment.getHiddenColumns().absoluteToVisibleColumn(lastCol);
+ lastCol = alignment.getHiddenColumns()
+ .absoluteToVisibleColumn(lastCol);
}
int transX = (firstCol - ranges.getStartRes()) * av.getCharWidth();
int transY = (firstSeq - ranges.getStartSeq()) * av.getCharHeight();
try
{
-
+
Graphics gg = img.getGraphics();
-
+
calculateWrappedGeometry(getWidth(), getHeight());
/*
if (scrollX < 0)
{
int startRes = ranges.getStartRes();
- drawWrappedWidth(gg, wrappedSpaceAboveAlignment, startRes, startRes
- - scrollX - 1, getHeight());
+ drawWrappedWidth(gg, wrappedSpaceAboveAlignment, startRes,
+ startRes - scrollX - 1, getHeight());
}
else
{
drawWrappedDecorators(gg, ranges.getStartRes());
gg.dispose();
-
+
repaint();
} finally
{
}
Graphics gg = img.getGraphics();
-
+
ViewportRanges ranges = av.getRanges();
int viewportWidth = ranges.getViewportWidth();
int charWidth = av.getCharWidth();
*/
int visibleWidths = wrappedVisibleWidths;
int canvasHeight = getHeight();
- boolean lastWidthPartHeight = (wrappedVisibleWidths * wrappedRepeatHeightPx) > canvasHeight;
+ boolean lastWidthPartHeight = (wrappedVisibleWidths
+ * wrappedRepeatHeightPx) > canvasHeight;
if (lastWidthPartHeight)
{
/*
* white fill first to erase annotations
*/
-
-
+
gg.translate(xOffset, 0);
gg.setColor(Color.white);
- gg.fillRect(labelWidthWest, ypos,
- (endRes - startRes + 1) * charWidth, wrappedRepeatHeightPx);
+ gg.fillRect(labelWidthWest, ypos, (endRes - startRes + 1) * charWidth,
+ wrappedRepeatHeightPx);
gg.translate(-xOffset, 0);
drawWrappedWidth(gg, ypos, startRes, endRes, canvasHeight);
-
+
}
/*
gg.fillRect(0, canvasHeight - heightBelow, getWidth(), heightBelow);
}
gg.dispose();
- }
+ }
/**
* Shifts the visible alignment by the specified number of columns - left if
if (y + wrappedRepeatHeightPx < canvasHeight - wrappedRepeatHeightPx
&& (xpos + viewportWidth <= xMax))
{
- gg.copyArea(labelWidthWest, y + wrappedRepeatHeightPx, -positions
- * charWidth, heightToCopy, widthToCopy,
+ gg.copyArea(labelWidthWest, y + wrappedRepeatHeightPx,
+ -positions * charWidth, heightToCopy, widthToCopy,
-wrappedRepeatHeightPx);
}
y += wrappedRepeatHeightPx;
gg.dispose();
}
-
/**
* Redraws any positions in the search results in the visible region of a
* wrapped alignment. Any highlights are drawn depending on the search results
}
int firstVisibleColumn = ranges.getStartRes();
- int lastVisibleColumn = ranges.getStartRes() + repeats
- * ranges.getViewportWidth() - 1;
+ int lastVisibleColumn = ranges.getStartRes()
+ + repeats * ranges.getViewportWidth() - 1;
AlignmentI alignment = av.getAlignment();
if (av.hasHiddenColumns())
int gapHeight = charHeight * (av.getScaleAboveWrapped() ? 2 : 1);
-
Graphics gg = img.getGraphics();
for (int seqNo = ranges.getStartSeq(); seqNo <= ranges
* transX: offset from left edge of canvas to residue position
*/
int transX = labelWidthWest
- + ((displayColumn - ranges.getStartRes()) % wrappedWidth)
- * av.getCharWidth();
+ + ((displayColumn - ranges.getStartRes())
+ % wrappedWidth) * av.getCharWidth();
/*
* transY: offset from top edge of canvas to residue position
}
}
}
-
+
gg.dispose();
return matchFound;
ToolTipManager.sharedInstance().registerComponent(this);
ToolTipManager.sharedInstance().setInitialDelay(0);
ToolTipManager.sharedInstance().setDismissDelay(10000);
-
-
+
this.av = viewport;
setBackground(Color.white);
return new MousePos(col, seqIndex, annIndex);
}
+
/**
* Returns the aligned sequence position (base 0) at the mouse position, or
* the closest visible one
void moveCursor(int dx, int dy)
{
- moveCursor(dx, dy,false);
+ moveCursor(dx, dy, false);
}
+
void moveCursor(int dx, int dy, boolean nextWord)
{
HiddenColumns hidden = av.getAlignment().getHiddenColumns();
if (nextWord)
{
int maxWidth = av.getAlignment().getWidth();
- int maxHeight=av.getAlignment().getHeight();
- SequenceI seqAtRow = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
+ int maxHeight = av.getAlignment().getHeight();
+ SequenceI seqAtRow = av.getAlignment()
+ .getSequenceAt(seqCanvas.cursorY);
// look for next gap or residue
- boolean isGap = Comparison.isGap(seqAtRow.getCharAt(seqCanvas.cursorX));
- int p = seqCanvas.cursorX,lastP,r=seqCanvas.cursorY,lastR;
+ boolean isGap = Comparison
+ .isGap(seqAtRow.getCharAt(seqCanvas.cursorX));
+ int p = seqCanvas.cursorX, lastP, r = seqCanvas.cursorY, lastR;
do
{
lastP = p;
p = nextVisible(hidden, maxWidth, p, dx);
} while ((dx != 0 ? p != lastP : r != lastR)
&& isGap == Comparison.isGap(seqAtRow.getCharAt(p)));
- seqCanvas.cursorX=p;
- seqCanvas.cursorY=r;
- } else {
+ seqCanvas.cursorX = p;
+ seqCanvas.cursorY = r;
+ }
+ else
+ {
int maxWidth = av.getAlignment().getWidth();
- seqCanvas.cursorX = nextVisible(hidden, maxWidth, seqCanvas.cursorX, dx);
+ seqCanvas.cursorX = nextVisible(hidden, maxWidth, seqCanvas.cursorX,
+ dx);
seqCanvas.cursorY += dy;
}
scrollToVisible(false);
}
- private int nextVisible(HiddenColumns hidden,int maxWidth, int original, int dx)
+ private int nextVisible(HiddenColumns hidden, int maxWidth, int original,
+ int dx)
{
- int newCursorX=original+dx;
+ int newCursorX = original + dx;
if (av.hasHiddenColumns() && !hidden.isVisible(newCursorX))
{
int visx = hidden.absoluteToVisibleColumn(newCursorX - dx);
}
}
newCursorX = (newCursorX < 0) ? 0 : newCursorX;
- if (newCursorX >= maxWidth
- || !hidden.isVisible(newCursorX))
+ if (newCursorX >= maxWidth || !hidden.isVisible(newCursorX))
{
newCursorX = original;
}
return newCursorX;
}
+
/**
* Scroll to make the cursor visible in the viewport.
*
if (av.getAlignment().getHiddenColumns().isVisible(seqCanvas.cursorX))
{
setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY),
- seqCanvas.cursorX, seqCanvas.cursorY);
+ seqCanvas.cursorX, seqCanvas.cursorY);
}
if (repaintNeeded)
}
}
-
void setSelectionAreaAtCursor(boolean topLeft)
{
SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
SequenceI seq = match.getSequence();
SequenceI ds = seq.getDatasetSequence() == null ? seq
: seq.getDatasetSequence();
- MappedFeatures mf = fr2
- .findComplementFeaturesAtResidue(ds, pos);
+ MappedFeatures mf = fr2.findComplementFeaturesAtResidue(ds, pos);
if (mf != null)
{
for (SequenceFeature sf : mf.features)
{
List<SequenceFeature> features = ap.getFeatureRenderer()
.findFeaturesAtColumn(sequence, column + 1);
- unshownFeatures = seqARep.appendFeatures(tooltipText, pos,
- features, this.ap.getSeqPanel().seqCanvas.fr,
- MAX_TOOLTIP_LENGTH);
+ unshownFeatures = seqARep.appendFeatures(tooltipText, pos, features,
+ this.ap.getSeqPanel().seqCanvas.fr, MAX_TOOLTIP_LENGTH);
/*
* add features in CDS/protein complement at the corresponding
pos);
if (mf != null)
{
- unshownFeatures += seqARep.appendFeatures(tooltipText,
- pos, mf, fr2, MAX_TOOLTIP_LENGTH);
+ unshownFeatures += seqARep.appendFeatures(tooltipText, pos, mf,
+ fr2, MAX_TOOLTIP_LENGTH);
}
}
}
if (!textString.equals(lastTooltip))
{
lastTooltip = textString;
- lastFormattedTooltip = JvSwingUtils.wrapTooltip(true,
- textString);
+ lastFormattedTooltip = JvSwingUtils.wrapTooltip(true, textString);
setToolTipText(lastFormattedTooltip);
}
}
tempTip.setTipText(lastFormattedTooltip);
int tipWidth = (int) tempTip.getPreferredSize().getWidth();
-
- // was x += (w - x < 200) ? -(w / 2) : 5;
+
+ // was x += (w - x < 200) ? -(w / 2) : 5;
x = (x + tipWidth < w ? x + 10 : w - tipWidth);
Point p = new Point(x, y + av.getCharHeight()); // BH 2018 was - 20?
* changed, so selective redraws can be applied (ie. only structures, only
* overview, etc)
*/
- private boolean updateOverviewAndStructs = false; // TODO: refactor to avcontroller
+ private boolean updateOverviewAndStructs = false; // TODO: refactor to
+ // avcontroller
/**
* set if av.getSelectionGroup() refers to a group that is defined on the
* Sequence number (if known), and sequence name.
*/
String seqno = seqIndex == -1 ? "" : " " + (seqIndex + 1);
- text.append("Sequence").append(seqno).append(" ID: ")
- .append(seqName);
+ text.append("Sequence").append(seqno).append(" ID: ").append(seqName);
String residue = null;
String label = null;
if (groupEditing)
{
- message.append("Edit group:");
+ message.append("Edit group:");
label = MessageManager.getString("action.edit_group");
}
else
{
- message.append("Edit sequence: " + seq.getName());
+ message.append("Edit sequence: " + seq.getName());
label = seq.getName();
if (label.length() > 10)
{
{
for (int j = 0; j < startres - editLastRes; j++)
{
- if (!Comparison
- .isGap(groupSeqs[g].getCharAt(fixedRight - j)))
+ if (!Comparison.isGap(groupSeqs[g].getCharAt(fixedRight - j)))
{
blank = false;
break;
* highlight the first feature at the position on the alignment
*/
SearchResultsI highlight = new SearchResults();
- highlight.addResult(sequence, features.get(0).getBegin(), features
- .get(0).getEnd());
+ highlight.addResult(sequence, features.get(0).getBegin(),
+ features.get(0).getEnd());
seqCanvas.highlightSearchResults(highlight, true);
/*
return;
}
- res = Math.min(res, av.getAlignment().getWidth()-1);
+ res = Math.min(res, av.getAlignment().getWidth() - 1);
if (stretchGroup.getEndRes() == res)
{
{
allGroups = av.getAlignment().findAllGroups(seq);
return resColourFinder.getResidueColour(av.getShowBoxes(),
- av.getResidueShading(),
- allGroups, seq, position,
- finder);
+ av.getResidueShading(), allGroups, seq, position, finder);
}
/**
if (i < length)
{
SequenceGroup currentSequenceGroup = resColourFinder
- .getCurrentSequenceGroup(
- allGroups, i);
+ .getCurrentSequenceGroup(allGroups, i);
if (currentSequenceGroup != null)
{
if (currentSequenceGroup.getDisplayBoxes())
{
resBoxColour = resColourFinder.getBoxColour(
- currentSequenceGroup.getGroupColourScheme(), seq,
- i);
+ currentSequenceGroup.getGroupColourScheme(), seq, i);
}
}
else if (av.getShowBoxes())
}
graphics.setColor(av.getTextColour());
- boolean drawAllText = monospacedFont && av.getShowText() && allGroups.length == 0
- && !av.getColourText() && av.getThresholdTextColour() == 0;
+ boolean drawAllText = monospacedFont && av.getShowText()
+ && allGroups.length == 0 && !av.getColourText()
+ && av.getThresholdTextColour() == 0;
/*
* EPS or SVG misaligns monospaced strings (JAL-3239)
}
SequenceGroup currentSequenceGroup = resColourFinder
- .getCurrentSequenceGroup(
- allGroups, i);
+ .getCurrentSequenceGroup(allGroups, i);
if (currentSequenceGroup != null)
{
if (!currentSequenceGroup.getDisplayText())
{
getboxColour = true;
resBoxColour = resColourFinder.getBoxColour(
- currentSequenceGroup.getGroupColourScheme(), seq,
- i);
+ currentSequenceGroup.getGroupColourScheme(), seq, i);
if (currentSequenceGroup.getColourText())
{
graphics.setColor(currentSequenceGroup.textColour);
}
boolean isgrep = currentSequenceGroup != null
- ? currentSequenceGroup.getSeqrep() == seq : false;
+ ? currentSequenceGroup.getSeqrep() == seq
+ : false;
if (!isarep && !isgrep
&& currentSequenceGroup.getShowNonconserved()) // todo
// optimize
}
/**
- * Answers the value of the slider position as a percentage between minimum and
- * maximum of its range
+ * Answers the value of the slider position as a percentage between minimum
+ * and maximum of its range
*
* @return
*/
* calculate the maximum ratio that leaves at least the height
* of two sequences (after rounding) visible in the bottom panel
*/
- int bottomSequencesHeight = bottomFrame.alignPanel.getSeqPanel().seqCanvas
- .getHeight();
+ int bottomSequencesHeight = bottomFrame.alignPanel
+ .getSeqPanel().seqCanvas.getHeight();
int bottomPanelMinHeight = bottomPanelHeight
- Math.max(0, bottomSequencesHeight - 3 * bottomCharHeight);
double maxRatio = (totalHeight - bottomPanelMinHeight) / totalHeight;
* Ctrl-W / Cmd-W - close view or window
*/
KeyStroke key_cmdW = KeyStroke.getKeyStroke(KeyEvent.VK_W,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ jalview.util.ShortcutKeyMaskExWrapper
+ .getMenuShortcutKeyMaskEx(),
+ false);
action = new AbstractAction()
{
@Override
* Ctrl-T / Cmd-T open new view
*/
KeyStroke key_cmdT = KeyStroke.getKeyStroke(KeyEvent.VK_T,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ jalview.util.ShortcutKeyMaskExWrapper
+ .getMenuShortcutKeyMaskEx(),
+ false);
AbstractAction action = new AbstractAction()
{
@Override
* Ctrl-F / Cmd-F open Finder dialog, 'focused' on the right alignment
*/
KeyStroke key_cmdF = KeyStroke.getKeyStroke(KeyEvent.VK_F,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ jalview.util.ShortcutKeyMaskExWrapper
+ .getMenuShortcutKeyMaskEx(),
+ false);
AbstractAction action = new AbstractAction()
{
@Override
}
/**
- * holds the frame for feature settings, so Protein and DNA tabs can be managed
+ * holds the frame for feature settings, so Protein and DNA tabs can be
+ * managed
*/
JInternalFrame featureSettingsUI;
/**
* raises dialog for Uniprot fetch followed by 3D beacons search
- * @param ignoreGui - when true, don't ask, just fetch
+ *
+ * @param ignoreGui
+ * - when true, don't ask, just fetch
*/
public void promptForTDBFetch(boolean ignoreGui)
{
{
mainFrame.setEnabled(false);
cmb_filterOption.setEnabled(false);
- progressBar.setProgressBar(MessageManager.getString("status.searching_3d_beacons"), progressId);
+ progressBar.setProgressBar(
+ MessageManager.getString("status.searching_3d_beacons"),
+ progressId);
// TODO: warn if no accessions discovered
populateSeqsWithoutSourceDBRef();
// redo initial discovery - this time with 3d beacons
// Executors.
- previousWantedFields=null;
- lastSelected=(FilterOption) cmb_filterOption.getSelectedItem();
+ previousWantedFields = null;
+ lastSelected = (FilterOption) cmb_filterOption.getSelectedItem();
cmb_filterOption.setSelectedItem(null);
- cachedPDBExists=false; // reset to initial
+ cachedPDBExists = false; // reset to initial
initialStructureDiscovery();
if (!isStructuresDiscovered())
{
- progressBar.setProgressBar(MessageManager.getString("status.no_structures_discovered_from_3d_beacons"), progressId);
- btn_queryTDB.setToolTipText(MessageManager.getString("status.no_structures_discovered_from_3d_beacons"));
+ progressBar.setProgressBar(MessageManager.getString(
+ "status.no_structures_discovered_from_3d_beacons"),
+ progressId);
+ btn_queryTDB.setToolTipText(MessageManager.getString(
+ "status.no_structures_discovered_from_3d_beacons"));
btn_queryTDB.setEnabled(false);
- } else {
+ }
+ else
+ {
cmb_filterOption.setSelectedIndex(0); // select 'best'
btn_queryTDB.setVisible(false);
progressBar.setProgressBar(null, progressId);
final FetchFinishedListenerI afterDbRefFetch = new FetchFinishedListenerI()
{
-
+
@Override
public void finished()
{
notQueriedTDBYet = false;
// new thread to discover structures - via 3d beacons
Executors.defaultThreadFactory().newThread(strucDiscovery).start();
-
+
}
};
-
+
// fetch db refs if OK pressed
- final Runnable discoverCanonicalDBrefs = new Runnable()
+ final Runnable discoverCanonicalDBrefs = new Runnable()
{
@Override
public void run()
dbRefFetcher.addListener(afterDbRefFetch);
// ideally this would also gracefully run with callbacks
dbRefFetcher.fetchDBRefs(true);
- } else {
+ }
+ else
+ {
// call finished action directly
afterDbRefFetch.finished();
}
}
};
- final Runnable revertview = new Runnable() {
- public void run() {
- if (lastSelected!=null) {
+ final Runnable revertview = new Runnable()
+ {
+ public void run()
+ {
+ if (lastSelected != null)
+ {
cmb_filterOption.setSelectedItem(lastSelected);
}
};
};
if (ignoreGui)
{
- Executors.defaultThreadFactory().newThread(discoverCanonicalDBrefs).start();
+ Executors.defaultThreadFactory().newThread(discoverCanonicalDBrefs)
+ .start();
return;
}
// need cancel and no to result in the discoverPDB action - mocked is
MessageManager.formatMessage(
"label.fetch_references_for_3dbeacons",
seqsWithoutSourceDBRef.size()),
- MessageManager
- .getString("label.3dbeacons"),
+ MessageManager.getString("label.3dbeacons"),
JvOptionPane.YES_NO_OPTION, JvOptionPane.PLAIN_MESSAGE,
null, new Object[]
{ MessageManager.getString("action.ok"),
{
FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
.getSelectedItem());
-
+
if (lastSelected == selectedFilterOpt)
{
// don't need to do anything, probably
String filterTitle = mainFrame.getTitle();
mainFrame.setTitle(frameTitle);
chk_invertFilter.setVisible(false);
-
+
if (selectedFilterOpt.getView() == VIEWS_FILTER)
{
mainFrame.setTitle(filterTitle);
FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
.getSelectedItem());
String currentView = selectedFilterOpt.getView();
-
- if (currentView == VIEWS_FILTER && data instanceof ThreeDBStructureChooserQuerySource)
+
+ if (currentView == VIEWS_FILTER
+ && data instanceof ThreeDBStructureChooserQuerySource)
{
-
- TDB_FTSData row=((ThreeDBStructureChooserQuerySource)data).getFTSDataFor(getResultTable(), selectedRow, discoveredStructuresSet);
- String pageUrl = row.getModelViewUrl();
+
+ TDB_FTSData row = ((ThreeDBStructureChooserQuerySource) data)
+ .getFTSDataFor(getResultTable(), selectedRow,
+ discoveredStructuresSet);
+ String pageUrl = row.getModelViewUrl();
JPopupMenu popup = new JPopupMenu("3D Beacons");
JMenuItem viewUrl = new JMenuItem("View model web page");
- viewUrl.addActionListener(
- new ActionListener() {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- Desktop.showUrl(pageUrl);
- }
- }
- );
+ viewUrl.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ Desktop.showUrl(pageUrl);
+ }
+ });
popup.add(viewUrl);
- SwingUtilities.invokeLater(new Runnable() {
- public void run() { popup.show(getResultTable(), x, y); }
+ SwingUtilities.invokeLater(new Runnable()
+ {
+ public void run()
+ {
+ popup.show(getResultTable(), x, y);
+ }
});
return true;
}
// event not handled by us
return false;
}
+
/**
* Validates inputs from the Manual PDB entry panel
*/
{
validateSelections();
}
- private FilterOption lastSelected=null;
+
+ private FilterOption lastSelected = null;
+
/**
* Handles the state change event for the 'filter' combo-box and 'invert'
* check-box
if (pdbIdStr.split(":").length > 1)
{
pdbEntry.setId(pdbIdStr.split(":")[0]);
- pdbEntry.setChainCode(pdbIdStr.split(":")[1].toUpperCase(Locale.ROOT));
+ pdbEntry.setChainCode(
+ pdbIdStr.split(":")[1].toUpperCase(Locale.ROOT));
}
else
{
&& mainFrame.isVisible()
&& cmb_filterOption.getSelectedItem() != null;
}
+
/**
*
* @return true if the 3D-Beacons query button will/has been displayed
*/
- public boolean isCanQueryTDB() {
- return canQueryTDB;
+ public boolean isCanQueryTDB()
+ {
+ return canQueryTDB;
}
public boolean isNotQueriedTDBYet()
*
* @param structureSelectionManager
*/
- public StructureViewer(StructureSelectionManager structureSelectionManager)
+ public StructureViewer(
+ StructureSelectionManager structureSelectionManager)
{
ssm = structureSelectionManager;
}
return sv;
}
-
@Override
public String toString()
{
}
return "New View";
}
+
/**
*
- * @return ViewerType for currently configured structure viewer
+ * @return ViewerType for currently configured structure viewer
*/
public static ViewerType getViewerType()
{
Map<PDBEntry, SequenceI[]> seqsForPdbs = getSequencesForPdbs(pdbs,
seqs);
- PDBEntry[] pdbsForFile = seqsForPdbs.keySet().toArray(
- new PDBEntry[seqsForPdbs.size()]);
- SequenceI[][] theSeqs = seqsForPdbs.values().toArray(
- new SequenceI[seqsForPdbs.size()][]);
+ PDBEntry[] pdbsForFile = seqsForPdbs.keySet()
+ .toArray(new PDBEntry[seqsForPdbs.size()]);
+ SequenceI[][] theSeqs = seqsForPdbs.values()
+ .toArray(new SequenceI[seqsForPdbs.size()][]);
if (sview != null)
{
sview.setAlignAddedStructures(superposeAdded);
return viewer;
}
-
public boolean isBusy()
{
if (sview != null)
@Override
public void mousePressed(MouseEvent e)
{
- String ttl = MessageManager.getString("label.select_colour_for_text");
+ String ttl = MessageManager
+ .getString("label.select_colour_for_text");
ColourChooserListener listener = new ColourChooserListener()
{
@Override
@Override
public void mousePressed(MouseEvent e)
{
- String ttl = MessageManager.getString("label.select_colour_for_text");
+ String ttl = MessageManager
+ .getString("label.select_colour_for_text");
ColourChooserListener listener = new ColourChooserListener()
{
@Override
if ((node.left() == null) && (node.right() == null))
{
double height = node.height;
-// double dist = node.dist;
-// int xstart = (int) ((height - dist) * wscale) + offx;
+ // double dist = node.dist;
+ // int xstart = (int) ((height - dist) * wscale) + offx;
int xend = (int) (height * wscale) + offx;
int ypos = (int) (node.ycount * chunk) + offy;
void chooseSubtreeColour()
{
String ttl = MessageManager.getString("label.select_subtree_colour");
- ColourChooserListener listener = new ColourChooserListener() {
+ ColourChooserListener listener = new ColourChooserListener()
+ {
@Override
public void colourSelected(Color c)
{
repaint();
}
};
- JalviewColourChooser.showColourChooser(this, ttl, highlightNode.color, listener);
+ JalviewColourChooser.showColourChooser(this, ttl, highlightNode.color,
+ listener);
}
@Override
if (ob instanceof SequenceI)
{
treeSelectionChanged((Sequence) ob);
- PaintRefresher.Refresh(tp, getAssociatedPanel().av.getSequenceSetId());
+ PaintRefresher.Refresh(tp,
+ getAssociatedPanel().av.getSequenceSetId());
repaint();
av.sendSelection();
return;
}
}
- PaintRefresher.Refresh(tp, getAssociatedPanel().av.getSequenceSetId());
+ PaintRefresher.Refresh(tp,
+ getAssociatedPanel().av.getSequenceSetId());
repaint();
}
}
else
{
- ScoreModelI sm = ScoreModels.getInstance()
- .getScoreModel(scoreModelName,
- treeCanvas.getAssociatedPanel());
+ ScoreModelI sm = ScoreModels.getInstance().getScoreModel(
+ scoreModelName, treeCanvas.getAssociatedPanel());
TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING)
? new NJTree(av, sm, similarityParams)
: new AverageDistanceTree(av, sm, similarityParams);
}
else
{
- treeCanvas.getAssociatedPanel().alignFrame
- .addHistoryItem(
- sortAlignmentIn(treeCanvas.getAssociatedPanel()));
+ treeCanvas.getAssociatedPanel().alignFrame.addHistoryItem(
+ sortAlignmentIn(treeCanvas.getAssociatedPanel()));
}
}
String tree = MessageManager.getString("label.tree");
ImageExporter exporter = new ImageExporter(writer, null, imageFormat,
tree);
- exporter.doExport(null, this, width, height, tree.toLowerCase(Locale.ROOT));
+ exporter.doExport(null, this, width, height,
+ tree.toLowerCase(Locale.ROOT));
}
/**
/*
* i18n description of Neighbour Joining or Average Distance method
*/
- String treecalcnm = MessageManager
- .getString("label.tree_calc_" + treeType.toLowerCase(Locale.ROOT));
+ String treecalcnm = MessageManager.getString(
+ "label.tree_calc_" + treeType.toLowerCase(Locale.ROOT));
/*
* short score model name (long description can be too long)
int width = treeCanvas.getWidth();
int height = treeCanvas.getHeight();
- FileOutputStream out = new FileOutputStream(
- outFile);
+ FileOutputStream out = new FileOutputStream(outFile);
EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
height);
pg.setAccurateTextMode(!textOption);
ex.printStackTrace();
}
}
-
+
public AlignViewport getViewport()
{
return av;
{
int row = i / cols + 1;
int index = (row * cols) + i;
- JButton button = makeButton(ResidueProperties.aa[i].toLowerCase(Locale.ROOT),
- ResidueProperties.aa[i].toLowerCase(Locale.ROOT), lowerCaseButtons, i);
+ JButton button = makeButton(
+ ResidueProperties.aa[i].toLowerCase(Locale.ROOT),
+ ResidueProperties.aa[i].toLowerCase(Locale.ROOT),
+ lowerCaseButtons, i);
buttonPanel.add(button, index);
}
chooser.setDialogTitle(
MessageManager.getString("label.load_colour_scheme"));
chooser.setToolTipText(MessageManager.getString("action.load"));
- chooser.setResponseHandler(0, new Runnable()
- {
- @Override
- public void run()
- {
- File choice = chooser.getSelectedFile();
- Cache.setProperty(LAST_DIRECTORY, choice.getParent());
-
- UserColourScheme ucs = ColourSchemeLoader
- .loadColourScheme(choice.getAbsolutePath());
- Color[] colors = ucs.getColours();
- schemeName.setText(ucs.getSchemeName());
-
- if (ucs.getLowerCaseColours() != null)
- {
- caseSensitive.setSelected(true);
- lcaseColour.setEnabled(true);
- resetButtonPanel(true);
- for (int i = 0; i < lowerCaseButtons.size(); i++)
- {
- JButton button = lowerCaseButtons.get(i);
- button.setBackground(ucs.getLowerCaseColours()[i]);
- }
- }
- else
- {
- caseSensitive.setSelected(false);
- lcaseColour.setEnabled(false);
- resetButtonPanel(false);
- }
-
- for (int i = 0; i < upperCaseButtons.size(); i++)
- {
- JButton button = upperCaseButtons.get(i);
- button.setBackground(colors[i]);
- }
-
- addNewColourScheme(choice.getPath());
- }
- });
-
+ chooser.setResponseHandler(0, new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ File choice = chooser.getSelectedFile();
+ Cache.setProperty(LAST_DIRECTORY, choice.getParent());
+
+ UserColourScheme ucs = ColourSchemeLoader
+ .loadColourScheme(choice.getAbsolutePath());
+ Color[] colors = ucs.getColours();
+ schemeName.setText(ucs.getSchemeName());
+
+ if (ucs.getLowerCaseColours() != null)
+ {
+ caseSensitive.setSelected(true);
+ lcaseColour.setEnabled(true);
+ resetButtonPanel(true);
+ for (int i = 0; i < lowerCaseButtons.size(); i++)
+ {
+ JButton button = lowerCaseButtons.get(i);
+ button.setBackground(ucs.getLowerCaseColours()[i]);
+ }
+ }
+ else
+ {
+ caseSensitive.setSelected(false);
+ lcaseColour.setEnabled(false);
+ resetButtonPanel(false);
+ }
+
+ for (int i = 0; i < upperCaseButtons.size(); i++)
+ {
+ JButton button = upperCaseButtons.get(i);
+ button.setBackground(colors[i]);
+ }
+
+ addNewColourScheme(choice.getPath());
+ }
+ });
+
chooser.showOpenDialog(this);
}
} catch (Exception e)
{
- Console.error("Couldn't instantiate vamsas client !",
- e);
+ Console.error("Couldn't instantiate vamsas client !", e);
return false;
}
return true;
addStoreDocumentHandler();
startSession();
inInitialUpdate = true;
- Console.debug(
- "Jalview loading the Vamsas Session for the first time.");
+ Console.debug("Jalview loading the Vamsas Session for the first time.");
dealWithDocumentUpdate(false); // we don't push an update out to the
inInitialUpdate = false;
// document yet.
} catch (Exception e)
{
errorsDuringUpdate = true;
- Console.error("Exception synchronizing " + af.getTitle()
- + " "
+ Console.error("Exception synchronizing " + af.getTitle() + " "
+ (af.getViewport().getViewName() == null ? ""
: " view " + af.getViewport().getViewName())
+ " to document.", e);
}
}
});
- final ViewSelectionMenu us=this;
+ final ViewSelectionMenu us = this;
checkBox.addMouseListener(new MouseAdapter()
{
@Override
final String setname = (String) setName.getSelectedItem();
if (Console.isDebugEnabled())
{
- Console.debug("Item state changed for " + setname
- + " (handling ? " + !settingDialog + ")");
+ Console.debug("Item state changed for " + setname + " (handling ? "
+ + !settingDialog + ")");
}
if (settingDialog)
{
if (parser != null)
{
WsParamSetI pset = parser.parseServiceParameterFile(
- wspset.getName(), wspset.getDescription(),
- urlArray, wspset.getParameters());
+ wspset.getName(), wspset.getDescription(), urlArray,
+ wspset.getParameters());
if (pset != null)
{
pset.setSourceFile(filename);
}
if (outfile != null)
{
- String paramFiles = Cache.getDefault("WS_PARAM_FILES",
- filename);
+ String paramFiles = Cache.getDefault("WS_PARAM_FILES", filename);
if (paramFiles.indexOf(filename) == -1)
{
if (paramFiles.length() > 0)
}
-
/**
* Builds a query string for a given sequences using its DBRef entries
*
lastPdbRequest = pdbRequest;
return resultList;
}
+
public List<FilterOption> getAvailableFilterOptions(String VIEWS_FILTER)
{
List<FilterOption> filters = new ArrayList<FilterOption>();
- filters.add(new FilterOption("PDBe "+
- MessageManager.getString("label.best_quality"),
- "overall_quality", VIEWS_FILTER, false,this));
- filters.add(new FilterOption("PDBe "+
- MessageManager.getString("label.best_resolution"),
- "resolution", VIEWS_FILTER, false,this));
- filters.add(new FilterOption("PDBe "+
- MessageManager.getString("label.most_protein_chain"),
- "number_of_protein_chains", VIEWS_FILTER, false,this));
- filters.add(new FilterOption("PDBe "+
- MessageManager.getString("label.most_bound_molecules"),
- "number_of_bound_molecules", VIEWS_FILTER, false,this));
- filters.add(new FilterOption("PDBe "+
- MessageManager.getString("label.most_polymer_residues"),
- "number_of_polymer_residues", VIEWS_FILTER, true,this));
-
+ filters.add(new FilterOption(
+ "PDBe " + MessageManager.getString("label.best_quality"),
+ "overall_quality", VIEWS_FILTER, false, this));
+ filters.add(new FilterOption(
+ "PDBe " + MessageManager.getString("label.best_resolution"),
+ "resolution", VIEWS_FILTER, false, this));
+ filters.add(new FilterOption(
+ "PDBe " + MessageManager.getString("label.most_protein_chain"),
+ "number_of_protein_chains", VIEWS_FILTER, false, this));
+ filters.add(new FilterOption(
+ "PDBe " + MessageManager
+ .getString("label.most_bound_molecules"),
+ "number_of_bound_molecules", VIEWS_FILTER, false, this));
+ filters.add(new FilterOption(
+ "PDBe " + MessageManager
+ .getString("label.most_polymer_residues"),
+ "number_of_polymer_residues", VIEWS_FILTER, true, this));
+
return filters;
}
* @return
* @throws Exception
*/
- public FTSRestResponse selectFirstRankedQuery(SequenceI seq, Collection<FTSData> collectedResults,
+ public FTSRestResponse selectFirstRankedQuery(SequenceI seq,
+ Collection<FTSData> collectedResults,
Collection<FTSDataColumnI> wantedFields, String fieldToFilterBy,
boolean b) throws Exception
{
return resultList;
}
-
@Override
public PDBEntry[] collectSelectedRows(JTable restable, int[] selectedRows,
List<SequenceI> selectedSeqsToView)
{
- int refSeqColIndex = restable.getColumn("Ref Sequence")
- .getModelIndex();
+ int refSeqColIndex = restable.getColumn("Ref Sequence").getModelIndex();
- PDBEntry[] pdbEntriesToView=new PDBEntry[selectedRows.length];
+ PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
int count = 0;
- int idColumnIndex=-1;
- boolean fromTDB=true;
+ int idColumnIndex = -1;
+ boolean fromTDB = true;
idColumnIndex = restable.getColumn("PDB Id").getModelIndex();
-
+
for (int row : selectedRows)
{
-
- String pdbIdStr = restable.getValueAt(row,idColumnIndex)
- .toString();
+
+ String pdbIdStr = restable.getValueAt(row, idColumnIndex).toString();
SequenceI selectedSeq = (SequenceI) restable.getValueAt(row,
refSeqColIndex);
selectedSeqsToView.add(selectedSeq);
PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr);
if (pdbEntry == null)
{
- pdbEntry = getFindEntry(pdbIdStr,
- selectedSeq.getAllPDBEntries());
+ pdbEntry = getFindEntry(pdbIdStr, selectedSeq.getAllPDBEntries());
}
if (pdbEntry == null)
return pdbEntriesToView;
}
-
@Override
protected FTSRestRequest getLastFTSRequest()
{
return lastPdbRequest;
}
-
- public FTSRestResponse executePDBFTSRestRequest(FTSRestRequest pdbRequest) throws Exception
+ public FTSRestResponse executePDBFTSRestRequest(FTSRestRequest pdbRequest)
+ throws Exception
{
return pdbRestClient.executeRequest(pdbRequest);
}
if (refsAvailable > -1)
{
hasCanonical = true;
- } else {
+ }
+ else
+ {
protWithoutCanon++;
}
hasUniprot = true;
- } else {
+ }
+ else
+ {
protWithoutUni++;
-
+
}
}
}
// logic: all canonicals - no fetchdb
// some uniprot no canonicals: defer to PDB, user can optionally fetch
//
- if (hasProtein && hasCanonical && !hasNA && protWithoutCanon == 0 && protWithoutUni == 0)
+ if (hasProtein && hasCanonical && !hasNA && protWithoutCanon == 0
+ && protWithoutUni == 0)
{
return tdbSource;
String provider = (String) row.getSummaryData()[idx_mprov];
String mcat = (String) row.getSummaryData()[idx_mcat];
// this makes sure all new categories are in the score array.
- int scorecat = scoreCategory(mcat);
- if (sourceFilter == null || sourceFilter.equals(provider))
+ int scorecat = scoreCategory(mcat);
+ if (sourceFilter == null || sourceFilter.equals(provider))
{
if (seq == row.getSummaryData()[0] && up_e > seq.getStart()
&& up_s < seq.getEnd())
int o1_s = (Integer) o1data[idx_ups];
int o1_e = (Integer) o1data[idx_upe];
int o1_cat = scoreCategory((String) o1data[idx_mcat]);
- String o1_prov= ((String) o1data[idx_mprov]).toUpperCase(Locale.ROOT);
+ String o1_prov = ((String) o1data[idx_mprov])
+ .toUpperCase(Locale.ROOT);
int o2_s = (Integer) o2data[idx_ups];
int o2_e = (Integer) o2data[idx_upe];
int o2_cat = scoreCategory((String) o2data[idx_mcat]);
- String o2_prov= ((String) o2data[idx_mprov]).toUpperCase(Locale.ROOT);
-
+ String o2_prov = ((String) o2data[idx_mprov])
+ .toUpperCase(Locale.ROOT);
if (o1_cat == o2_cat)
{
{
if (o1_cat == scoreCategory(EXP_CATEGORIES.get(0)))
{
- if (o1_prov.equals(o2_prov)) {
- if ("PDBE".equals(o1_prov)) {
- if (eitherNull(idx_resol,o1data,o2data))
+ if (o1_prov.equals(o2_prov))
+ {
+ if ("PDBE".equals(o1_prov))
+ {
+ if (eitherNull(idx_resol, o1data, o2data))
{
- return nonNullFirst(idx_resol,o1data,o2data);
+ return nonNullFirst(idx_resol, o1data, o2data);
}
- // experimental structures, so rank on quality
- double o1_res = (Double) o1data[idx_resol];
- double o2_res = (Double) o2data[idx_resol];
- return (o2_res < o1_res) ? 1 : (o2_res == o1_res) ? 0 : -1;
- } else {
- return 0; // no change in order
+ // experimental structures, so rank on quality
+ double o1_res = (Double) o1data[idx_resol];
+ double o2_res = (Double) o2data[idx_resol];
+ return (o2_res < o1_res) ? 1
+ : (o2_res == o1_res) ? 0 : -1;
+ }
+ else
+ {
+ return 0; // no change in order
+ }
+ }
+ else
+ {
+ // PDBe always ranked above all other experimentally
+ // determined categories
+ return "PDBE".equals(o1_prov) ? -1
+ : "PDBE".equals(o2_prov) ? 1 : 0;
}
- } else {
- // PDBe always ranked above all other experimentally determined categories
- return "PDBE".equals(o1_prov) ? -1 : "PDBE".equals(o2_prov) ? 1 : 0;
- }
}
else
{
- if (eitherNull(idx_mqual,o1data, o2data)) {
+ if (eitherNull(idx_mqual, o1data, o2data))
+ {
return nonNullFirst(idx_mqual, o1data, o2data);
}
// models, so rank on qmean - b
private int nonNullFirst(int idx_resol, Object[] o1data,
Object[] o2data)
{
- return o1data[idx_resol] == o2data[idx_resol] ? 0: o1data[idx_resol] != null ? -1 : 1;
+ return o1data[idx_resol] == o2data[idx_resol] ? 0
+ : o1data[idx_resol] != null ? -1 : 1;
}
private boolean eitherNull(int idx_resol, Object[] o1data,
Object[] o2data)
{
- return (o1data[idx_resol] == null || o2data[idx_resol]==null);
+ return (o1data[idx_resol] == null || o2data[idx_resol] == null);
}
@Override
cover.andNot(scover);
}
}
- if (selected.size()==0)
+ if (selected.size() == 0)
{
return selected;
}
if (rowset != null && rowset.size() > 0)
{
AlignmentAnnotation alan = null;
- for (int elm = 0,
- elmSize = rowset.size(); elm < elmSize; elm++)
+ for (int elm = 0, elmSize = rowset
+ .size(); elm < elmSize; elm++)
{
alan = (AlignmentAnnotation) rowset.elementAt(elm);
alan.groupRef = theGroup;
{
return readFile(null, file, sourceType, fileFormat);
}
-
- public AlignmentI readFile(File selectedFile, String file, DataSourceType sourceType,
- FileFormatI fileFormat) throws IOException
+
+ public AlignmentI readFile(File selectedFile, String file,
+ DataSourceType sourceType, FileFormatI fileFormat)
+ throws IOException
{
this.selectedFile = selectedFile;
if (isParseWithJMOL)
{
// needs a File option
- alignFile = new JmolParser(selectedFile == null ? inFile : selectedFile, sourceType);
+ alignFile = new JmolParser(
+ selectedFile == null ? inFile : selectedFile, sourceType);
}
else
{
((StructureFile) alignFile).setDbRefType(
FileFormat.PDB.equals(fileFormat) ? Type.PDB : Type.MMCIF);
}
- else if (selectedFile != null) {
- alignFile = fileFormat.getReader(new FileParse(selectedFile, sourceType));
- } else
+ else if (selectedFile != null)
+ {
+ alignFile = fileFormat
+ .getReader(new FileParse(selectedFile, sourceType));
+ }
+ else
{
// alignFile = fileFormat.getAlignmentFile(inFile, sourceType);
alignFile = fileFormat.getReader(new FileParse(inFile, sourceType));
return null;
}
-
/**
* Determines the protocol (i.e DataSourceType.{FILE|PASTE|URL}) for the input
* data
*
* BH 2018 allows File or String, and can return RELATIVE_URL
*
- * @param dataObject File or String
+ * @param dataObject
+ * File or String
* @return the protocol for the input data
*/
public static DataSourceType checkProtocol(Object dataObject)
{
- if(dataObject instanceof File)
+ if (dataObject instanceof File)
{
return DataSourceType.FILE;
}
-
+
String data = dataObject.toString();
DataSourceType protocol = DataSourceType.PASTE;
String ft = data.toLowerCase(Locale.ROOT).trim();
}
String savedFilename = "";
- // if extensionOnly is set then reset the filename to the last occurrence of the extension+templateStart and try the match
+ // if extensionOnly is set then reset the filename to the last occurrence of
+ // the extension+templateStart and try the match
if (extensionMatch)
{
// only trying to match from extension onwards
boolean delete = confirmNewerDeleteFile(fileToBeDeleted,
replacementFile, true);
- Console.trace("BACKUPFILES " + (delete ? "confirmed" : "not")
- + " deleting file "
+ Console.trace("BACKUPFILES "
+ + (delete ? "confirmed" : "not") + " deleting file "
+ fileToBeDeleted.getAbsolutePath()
+ " which is newer than "
+ replacementFile.getAbsolutePath());
File fileToBeDeleted = backupFiles[i];
boolean delete = true;
- Console.trace("BACKUPFILES fileToBeDeleted: " + fileToBeDeleted);
+ Console.trace(
+ "BACKUPFILES fileToBeDeleted: " + fileToBeDeleted);
boolean newer = false;
if (replacementFile != null)
// using boolean '&' instead of '&&' as don't want moveFileToFile attempt to
// be conditional (short-circuit)
ret = ret & moveFileToFile(file, new File(latestBackupFilename));
- Console.debug("BACKUPFILES moving " + file + " to " + latestBackupFilename
- + " was " + (ret ? "" : "NOT ") + "successful");
+ Console.debug(
+ "BACKUPFILES moving " + file + " to " + latestBackupFilename
+ + " was " + (ret ? "" : "NOT ") + "successful");
if (tidyUp)
{
Console.debug("BACKUPFILES tidying up files");
// delete destination file - not usually necessary but Just In Case...
Console.trace("BACKUPFILES deleting " + newFile.getAbsolutePath());
newFile.delete();
- Console.trace("BACKUPFILES moving " + oldFile.getAbsolutePath() + " to "
- + newFile.getAbsolutePath());
+ Console.trace("BACKUPFILES moving " + oldFile.getAbsolutePath()
+ + " to " + newFile.getAbsolutePath());
Files.move(oldPath, newPath, StandardCopyOption.REPLACE_EXISTING);
ret = true;
Console.trace("BACKUPFILES move seems to have succeeded");
public static final String BJS_TEMPLATES_LOCAL_DIRECTORY = Cache
.getDefault("biojs_template_directory", DEFAULT_DIR);
- public static final String BJS_TEMPLATE_GIT_REPO = Cache
- .getDefault("biojs_template_git_repo",
- "https://raw.githubusercontent.com/jalview/exporter-templates/master/biojs/package.json");
+ public static final String BJS_TEMPLATE_GIT_REPO = Cache.getDefault(
+ "biojs_template_git_repo",
+ "https://raw.githubusercontent.com/jalview/exporter-templates/master/biojs/package.json");
public BioJsHTMLOutput(AlignmentPanel ap)
{
* when true, interpret the mol_type 'source' feature attribute
* and generate an RNA sequence from the DNA record
*/
- protected boolean produceRna=true;
-
+ protected boolean produceRna = true;
/*
* values parsed from the data file
protected List<DBRefEntry> dbrefs;
- protected boolean sequenceStringIsRNA=false;
+ protected boolean sequenceStringIsRNA = false;
protected String sequenceString;
* using TreeMap gives CDS sequences in alphabetical, so readable, order
*/
cds = new TreeMap<>(String.CASE_INSENSITIVE_ORDER);
-
+
parse();
}
/**
- * process attributes for 'source' until the next FT feature entry
- * only interested in 'mol_type'
+ * process attributes for 'source' until the next FT feature entry only
+ * interested in 'mol_type'
+ *
* @param tokens
* @return
* @throws IOException
int p = line.indexOf("\\mol_type");
int qs = line.indexOf("\"", p);
int qe = line.indexOf("\"", qs + 1);
- String qualifier=line.substring(qs,qe).toLowerCase(Locale.ROOT);
+ String qualifier = line.substring(qs, qe).toLowerCase(Locale.ROOT);
if (qualifier.indexOf("rna") > -1)
{
sequenceStringIsRNA = true;
{
sequenceStringIsRNA = false;
}
- line=parseFeatureQualifier(sb, false);
+ line = parseFeatureQualifier(sb, false);
}
return line;
}
-
/**
* Parses one (GenBank or EMBL format) CDS feature, saves the parsed data, and
* returns the next line
String[] tokens = line.split(WHITESPACE);
if (tokens.length < 2)
{
- Console.error("Ignoring bad EMBL line for " + this.accession
- + ": " + line);
+ Console.error("Ignoring bad EMBL line for " + this.accession + ": "
+ + line);
break;
}
if (tokens[1].startsWith("/"))
protected String parseFeature(String line) throws IOException
{
String[] tokens = line.trim().split(WHITESPACE);
- if (tokens.length < 2 || (!"CDS".equals(tokens[0]) && (!"source".equals(tokens[0]))))
+ if (tokens.length < 2
+ || (!"CDS".equals(tokens[0]) && (!"source".equals(tokens[0]))))
{
return nextLine();
}
/**
* Constructor which does not parse the file immediately
*
- * @param file File or String filename
+ * @param file
+ * File or String filename
* @param paste
* @throws IOException
*/
- public FeaturesFile(Object file, DataSourceType paste)
- throws IOException
+ public FeaturesFile(Object file, DataSourceType paste) throws IOException
{
super(false, file, paste);
}
}
/**
- * Returns contents of a Jalview format features file, for visible features, as
- * filtered by type and group. Features with a null group are displayed if their
- * feature type is visible. Non-positional features may optionally be included
- * (with no check on type or group).
+ * Returns contents of a Jalview format features file, for visible features,
+ * as filtered by type and group. Features with a null group are displayed if
+ * their feature type is visible. Non-positional features may optionally be
+ * included (with no check on type or group).
*
* @param sequences
* @param fr
* @param includeNonPositional
- * if true, include non-positional features
- * (regardless of group or type)
+ * if true, include non-positional features (regardless of group or
+ * type)
* @param includeComplement
- * if true, include visible complementary
- * (CDS/protein) positional features, with
- * locations converted to local sequence
- * coordinates
+ * if true, include visible complementary (CDS/protein) positional
+ * features, with locations converted to local sequence coordinates
* @return
*/
public String printJalviewFormat(SequenceI[] sequences,
.entrySet())
{
FeatureColourI colour = featureColour.getValue();
- out.append(colour.toJalviewFormat(featureColour.getKey())).append(
- newline);
+ out.append(colour.toJalviewFormat(featureColour.getKey()))
+ .append(newline);
}
}
/**
* Outputs any visible complementary (CDS/peptide) positional features as
- * Jalview format, within feature group. The coordinates of the linked features
- * are converted to the corresponding positions of the local sequences.
+ * Jalview format, within feature group. The coordinates of the linked
+ * features are converted to the corresponding positions of the local
+ * sequences.
*
* @param out
* @param fr
/*
* output features by group
*/
- for (Entry<String, Map<String, List<SequenceFeature>>> groupFeatures : map.entrySet())
+ for (Entry<String, Map<String, List<SequenceFeature>>> groupFeatures : map
+ .entrySet())
{
out.append(newline);
String group = groupFeatures.getKey();
}
/**
- * Outputs any feature filters defined for visible feature types, sandwiched by
- * STARTFILTERS and ENDFILTERS lines
+ * Outputs any feature filters defined for visible feature types, sandwiched
+ * by STARTFILTERS and ENDFILTERS lines
*
* @param out
* @param visible
* @param includeNonPositional
* @return
*/
- private int outputFeaturesByGroup(StringBuilder out,
- FeatureRenderer fr, String[] featureTypes,
- SequenceI[] sequences, boolean includeNonPositional)
+ private int outputFeaturesByGroup(StringBuilder out, FeatureRenderer fr,
+ String[] featureTypes, SequenceI[] sequences,
+ boolean includeNonPositional)
{
List<String> featureGroups = fr.getFeatureGroups();
if (featureTypes.length > 0
&& (isNullGroup || visibleGroups.contains(group)))
{
- features.addAll(sequences[i].getFeatures().getFeaturesForGroup(
- true, group, featureTypes));
+ features.addAll(sequences[i].getFeatures()
+ .getFeaturesForGroup(true, group, featureTypes));
}
for (SequenceFeature sf : features)
* @param sequenceName
* @param sequenceFeature
*/
- protected void formatJalviewFeature(
- StringBuilder out, String sequenceName,
- SequenceFeature sequenceFeature)
+ protected void formatJalviewFeature(StringBuilder out,
+ String sequenceName, SequenceFeature sequenceFeature)
{
if (sequenceFeature.description == null
|| sequenceFeature.description.equals(""))
* Returns features output in GFF2 format
*
* @param sequences
- * the sequences whose features are to be
- * output
+ * the sequences whose features are to be output
* @param visible
- * a map whose keys are the type names of
- * visible features
+ * a map whose keys are the type names of visible features
* @param visibleFeatureGroups
* @param includeNonPositionalFeatures
* @param includeComplement
* @return
*/
- public String printGffFormat(SequenceI[] sequences,
- FeatureRenderer fr, boolean includeNonPositionalFeatures,
- boolean includeComplement)
+ public String printGffFormat(SequenceI[] sequences, FeatureRenderer fr,
+ boolean includeNonPositionalFeatures, boolean includeComplement)
{
FeatureRenderer fr2 = null;
if (includeComplement)
fr2 = Desktop.getAlignFrameFor(comp).getFeatureRenderer();
}
- Map<String, FeatureColourI> visibleColours = fr.getDisplayedFeatureCols();
+ Map<String, FeatureColourI> visibleColours = fr
+ .getDisplayedFeatureCols();
StringBuilder out = new StringBuilder(256);
- out.append(String.format("%s %d\n", GFF_VERSION, gffVersion == 0 ? 2 : gffVersion));
+ out.append(String.format("%s %d\n", GFF_VERSION,
+ gffVersion == 0 ? 2 : gffVersion));
String[] types = visibleColours == null ? new String[0]
: visibleColours.keySet()
* AC_Male=0;AF_NFE=0.00000e 00;Hom_FIN=0;GQ_MEDIAN=9
* </pre>
*
- * A map-valued attribute is formatted as a comma-delimited list within braces,
- * for example
+ * A map-valued attribute is formatted as a comma-delimited list within
+ * braces, for example
*
* <pre>
* jvmap_CSQ={ALLELE_NUM=1,UNIPARC=UPI0002841053,Feature=ENST00000585561}
* </pre>
*
- * The {@code jvmap_} prefix designates a values map and is removed if the value
- * is parsed when read in. (The GFF3 specification allows 'semi-structured data'
- * to be represented provided the attribute name begins with a lower case
- * letter.)
+ * The {@code jvmap_} prefix designates a values map and is removed if the
+ * value is parsed when read in. (The GFF3 specification allows
+ * 'semi-structured data' to be represented provided the attribute name begins
+ * with a lower case letter.)
*
* @param sb
* @param map
* format)
*
* @param alignedRegions
- * a list of "Align fromStart toStart fromCount"
+ * a list of "Align fromStart toStart fromCount"
* @param mapIsFromCdna
- * if true, 'from' is dna, else 'from' is protein
+ * if true, 'from' is dna, else 'from' is protein
* @param strand
- * either 1 (forward) or -1 (reverse)
+ * either 1 (forward) or -1 (reverse)
* @return
* @throws IOException
*/
List<SequenceFeature> sfs = seq.getFeatures().getPositionalFeatures();
if (!sfs.isEmpty())
{
- String newName = (String) sfs.get(0).getValue(
- GffHelperI.RENAME_TOKEN);
+ String newName = (String) sfs.get(0)
+ .getValue(GffHelperI.RENAME_TOKEN);
if (newName != null)
{
seq.setName(newName);
* @param shortName
* @param extensions
* comma-separated list of file extensions associated with the format
- * @param isReadable - can be recognised by IdentifyFile and imported with the given reader
- * @param isWritable - can be exported with the returned writer
+ * @param isReadable
+ * - can be recognised by IdentifyFile and imported with the given
+ * reader
+ * @param isWritable
+ * - can be exported with the returned writer
*/
private FileFormat(String shortName, String extensions,
boolean isReadable, boolean isWritable)
*/
public FileFormatI forName(String format)
{
- return format == null ? null : formats.get(format.toUpperCase(Locale.ROOT));
+ return format == null ? null
+ : formats.get(format.toUpperCase(Locale.ROOT));
}
/**
DataSourceType protocol, FileFormatI format)
{
this.viewport = viewport;
- if (file instanceof File) {
+ if (file instanceof File)
+ {
this.selectedFile = (File) file;
file = selectedFile.getPath();
}
format = new IdentifyFile().identify(source, false);
// identify stream and rewind rather than close
}
- else if (selectedFile != null) {
+ else if (selectedFile != null)
+ {
format = new IdentifyFile().identify(selectedFile, protocol);
}
else
// We read the data anyway - it might make sense.
}
// BH 2018 switch to File object here instead of filename
- alignFrame = new Jalview2XML(raiseGUI).loadJalviewAlign(selectedFile == null ? file : selectedFile);
+ alignFrame = new Jalview2XML(raiseGUI).loadJalviewAlign(
+ selectedFile == null ? file : selectedFile);
}
else
{
file.lastIndexOf("."));
String tempStructureFileStr = createNamedJvTempFile(
urlLeafName, structExt);
-
+
// BH - switching to File object here so as to hold
// ._bytes array directly
File tempFile = new File(tempStructureFileStr);
UrlDownloadClient.download(file, tempFile);
-
- al = fa.readFile(tempFile, DataSourceType.FILE,
- format);
+
+ al = fa.readFile(tempFile, DataSourceType.FILE, format);
source = fa.getAlignFile();
}
else
{
- if (selectedFile == null) {
+ if (selectedFile == null)
+ {
al = fa.readFile(file, protocol, format);
-
- } else {
+
+ }
+ else
+ {
al = fa.readFile(selectedFile, protocol, format);
- }
+ }
source = fa.getAlignFile(); // keep reference for later if
-
- // necessary.
+
+ // necessary.
}
}
} catch (java.io.IOException ex)
try
{
- alignFrame.setMaximum(Cache
- .getDefault("SHOW_FULLSCREEN", false));
+ alignFrame.setMaximum(
+ Cache.getDefault("SHOW_FULLSCREEN", false));
} catch (java.beans.PropertyVetoException ex)
{
}
{
if (Cache.getDefault("STRUCT_FROM_PDB", true))
{
- annotFromStructure = Cache.getDefault("ADD_TEMPFACT_ANN",
- true);
- localSecondaryStruct = Cache.getDefault("ADD_SS_ANN",
- true);
- serviceSecondaryStruct = Cache.getDefault("USE_RNAVIEW",
- true);
+ annotFromStructure = Cache.getDefault("ADD_TEMPFACT_ANN", true);
+ localSecondaryStruct = Cache.getDefault("ADD_SS_ANN", true);
+ serviceSecondaryStruct = Cache.getDefault("USE_RNAVIEW", true);
}
else
{
public boolean getCacheSuffixDefault(FileFormatI format)
{
- return Cache.getDefault(format.getName().toUpperCase(Locale.ROOT) + "_JVSUFFIX",
- true);
+ return Cache.getDefault(
+ format.getName().toUpperCase(Locale.ROOT) + "_JVSUFFIX", true);
}
public String formatSequences(FileFormatI format, AlignmentI alignment,
return ap.printWrappedAlignment(pwidth, pheight, pi, pg[0]);
}
- String getHtml(String titleSvg, String alignmentSvg,
- String jsonData, boolean wrapped)
+ String getHtml(String titleSvg, String alignmentSvg, String jsonData,
+ boolean wrapped)
{
StringBuilder htmlSvg = new StringBuilder();
htmlSvg.append("<html>\n");
@Override
public boolean isEmbedData()
{
- return Boolean.valueOf(
- Cache.getDefault("EXPORT_EMBBED_BIOJSON", "true"));
+ return Boolean
+ .valueOf(Cache.getDefault("EXPORT_EMBBED_BIOJSON", "true"));
}
@Override
aDimension.getWidth(), aDimension.getHeight());
if (!textCharacters) // Lineart selected
{
- idPanelGraphics.setRenderingHint(
- SVGHints.KEY_DRAW_STRING_TYPE,
+ idPanelGraphics.setRenderingHint(SVGHints.KEY_DRAW_STRING_TYPE,
SVGHints.VALUE_DRAW_STRING_TYPE_VECTOR);
- alignPanelGraphics.setRenderingHint(
- SVGHints.KEY_DRAW_STRING_TYPE,
+ alignPanelGraphics.setRenderingHint(SVGHints.KEY_DRAW_STRING_TYPE,
SVGHints.VALUE_DRAW_STRING_TYPE_VECTOR);
}
if (ap.av.getWrapAlignment())
}
else
{
- printUnwrapped(aDimension.getWidth(), aDimension.getHeight(),
- 0, idPanelGraphics, alignPanelGraphics);
+ printUnwrapped(aDimension.getWidth(), aDimension.getHeight(), 0,
+ idPanelGraphics, alignPanelGraphics);
}
String idPanelSvgData = idPanelGraphics.getSVGDocument();
String alignPanelSvgData = alignPanelGraphics.getSVGDocument();
String jsonData = getBioJSONData();
- String htmlData = getHtml(idPanelSvgData, alignPanelSvgData,
- jsonData, ap.av.getWrapAlignment());
+ String htmlData = getHtml(idPanelSvgData, alignPanelSvgData, jsonData,
+ ap.av.getWrapAlignment());
FileOutputStream out = new FileOutputStream(generatedFile);
out.write(htmlData.getBytes());
out.flush();
*/
public class IdentifyFile
{
-
- public FileFormatI identify(Object file, DataSourceType protocol) throws FileFormatException
+
+ public FileFormatI identify(Object file, DataSourceType protocol)
+ throws FileFormatException
{
// BH 2018
- return (file instanceof File ? identify((File) file, protocol) : identify((String) file, protocol));
-
+ return (file instanceof File ? identify((File) file, protocol)
+ : identify((String) file, protocol));
+
}
public FileFormatI identify(File file, DataSourceType sourceType)
if (source.inFile != null)
{
String fileStr = source.inFile.getName();
- if (fileStr.contains(".jar")
- || fileStr.contains(".zip") || fileStr.contains(".jvp"))
+ if (fileStr.contains(".jar") || fileStr.contains(".zip")
+ || fileStr.contains(".jvp"))
{
// possibly a Jalview archive (but check further)
reply = FileFormat.Jalview;
}
}
-
}
jsonAlignmentPojo.getSeqGroups().add(seqGrpPojo);
}
}
-
+
jsonOutput = JSONUtils.stringify(jsonAlignmentPojo);
return jsonOutput.replaceAll("xstart", "xStart").replaceAll("xend",
"xEnd");
/*
* get all features currently visible (and any non-positional features)
*/
- List<SequenceFeature> seqFeatures = seq.getFeatures().getAllFeatures(
- visibleFeatureTypes);
+ List<SequenceFeature> seqFeatures = seq.getFeatures()
+ .getAllFeatures(visibleFeatureTypes);
for (SequenceFeature sf : seqFeatures)
{
SequenceFeaturesPojo jsonFeature = new SequenceFeaturesPojo(
String.valueOf(seq.hashCode()));
- String featureColour = (fr == null) ? null : Format
- .getHexString(finder.findFeatureColour(Color.white, seq,
- seq.findIndex(sf.getBegin())));
+ String featureColour = (fr == null) ? null
+ : Format.getHexString(finder.findFeatureColour(Color.white,
+ seq, seq.findIndex(sf.getBegin())));
int xStart = sf.getBegin() == 0 ? 0
: seq.findIndex(sf.getBegin()) - 1;
int xEnd = sf.getEnd() == 0 ? 0 : seq.findIndex(sf.getEnd());
{
try
{
- Map<String, Object> alignmentJsonObj = (Map<String, Object>) JSONUtils.parse(jsonAlignmentString);
- List<Object> seqJsonArray = (List<Object>) alignmentJsonObj.get("seqs");
+ Map<String, Object> alignmentJsonObj = (Map<String, Object>) JSONUtils
+ .parse(jsonAlignmentString);
+ List<Object> seqJsonArray = (List<Object>) alignmentJsonObj
+ .get("seqs");
List<Object> alAnnotJsonArray = (List<Object>) alignmentJsonObj
.get("alignAnnotation");
List<Object> jsonSeqArray = (List<Object>) alignmentJsonObj
hiddenSequences = new ArrayList<>();
seqMap = new Hashtable<>();
- for (Iterator<Object> sequenceIter = seqJsonArray.iterator(); sequenceIter.hasNext();)
+ for (Iterator<Object> sequenceIter = seqJsonArray
+ .iterator(); sequenceIter.hasNext();)
{
- Map<String, Object> sequence = (Map<String, Object>) sequenceIter.next();
+ Map<String, Object> sequence = (Map<String, Object>) sequenceIter
+ .next();
String sequcenceString = sequence.get("seq").toString();
String sequenceName = sequence.get("name").toString();
String seqUniqueId = sequence.get("id").toString();
parseFeatures(jsonSeqArray);
- for (Iterator<Object> seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter.hasNext();)
+ for (Iterator<Object> seqGrpIter = seqGrpJsonArray
+ .iterator(); seqGrpIter.hasNext();)
{
- Map<String, Object> seqGrpObj = (Map<String, Object>)seqGrpIter.next();
+ Map<String, Object> seqGrpObj = (Map<String, Object>) seqGrpIter
+ .next();
String grpName = seqGrpObj.get("groupName").toString();
String colourScheme = seqGrpObj.get("colourScheme").toString();
String description = (seqGrpObj.get("description") == null) ? null
int startRes = Integer
.valueOf(seqGrpObj.get("startRes").toString());
int endRes = Integer.valueOf(seqGrpObj.get("endRes").toString());
- List<Object> sequenceRefs = (List<Object>) seqGrpObj.get("sequenceRefs");
+ List<Object> sequenceRefs = (List<Object>) seqGrpObj
+ .get("sequenceRefs");
ArrayList<SequenceI> grpSeqs = new ArrayList<>();
if (sequenceRefs.size() > 0)
}
- for (Iterator<Object> alAnnotIter = alAnnotJsonArray.iterator(); alAnnotIter.hasNext();)
+ for (Iterator<Object> alAnnotIter = alAnnotJsonArray
+ .iterator(); alAnnotIter.hasNext();)
{
- Map<String, Object> alAnnot = (Map<String, Object>) alAnnotIter.next();
- List<Object> annotJsonArray = (List<Object>) alAnnot.get("annotations");
+ Map<String, Object> alAnnot = (Map<String, Object>) alAnnotIter
+ .next();
+ List<Object> annotJsonArray = (List<Object>) alAnnot
+ .get("annotations");
Annotation[] annotations = new Annotation[annotJsonArray.size()];
int count = 0;
- for (Iterator<Object> annotIter = annotJsonArray.iterator(); annotIter.hasNext();)
+ for (Iterator<Object> annotIter = annotJsonArray
+ .iterator(); annotIter.hasNext();)
{
- Map<String, Object> annot = (Map<String, Object>) annotIter.next();
+ Map<String, Object> annot = (Map<String, Object>) annotIter
+ .next();
if (annot == null)
{
annotations[count] = null;
displayedFeatures = new FeaturesDisplayed();
for (Object o : jsonSeqFeatures)
{
- Map<String, Object> jsonFeature = (Map<String, Object>) o;
+ Map<String, Object> jsonFeature = (Map<String, Object>) o;
Long begin = (Long) jsonFeature.get("xStart");
Long end = (Long) jsonFeature.get("xEnd");
String type = (String) jsonFeature.get("type");
/*
* begin/end of 0 is for a non-positional feature
*/
- int featureBegin = begin.intValue() == 0 ? 0 : seq
- .findPosition(begin.intValue());
- int featureEnd = end.intValue() == 0 ? 0 : seq.findPosition(end
- .intValue()) - 1;
+ int featureBegin = begin.intValue() == 0 ? 0
+ : seq.findPosition(begin.intValue());
+ int featureEnd = end.intValue() == 0 ? 0
+ : seq.findPosition(end.intValue()) - 1;
SequenceFeature sequenceFeature = new SequenceFeature(type,
description, featureBegin, featureEnd, score, featureGrp);
- List<Object> linksJsonArray = (List<Object>) jsonFeature.get("links");
+ List<Object> linksJsonArray = (List<Object>) jsonFeature
+ .get("links");
if (linksJsonArray != null && linksJsonArray.size() > 0)
{
Iterator<Object> linkList = linksJsonArray.iterator();
* @author AMW
*
*/
-public class JalviewFileChooser extends JFileChooser implements DialogRunnerI,
- PropertyChangeListener
+public class JalviewFileChooser extends JFileChooser
+ implements DialogRunnerI, PropertyChangeListener
{
private static final long serialVersionUID = 1L;
private Map<Object, Runnable> callbacks = new HashMap<>();
-
+
File selectedFile = null;
/**
}
/**
- * Overridden for JalviewJS compatibility: only one thread in Javascript,
- * so we can't wait for user choice in another thread and then perform the
+ * Overridden for JalviewJS compatibility: only one thread in Javascript, so
+ * we can't wait for user choice in another thread and then perform the
* desired action
*/
@Override
public int showOpenDialog(Component parent)
{
int value = super.showOpenDialog(this);
-
+
if (!Platform.isJS())
/**
* Java only
multi.setLayout(new BoxLayout(multi, BoxLayout.PAGE_AXIS));
if (backupfilesCheckBox == null)
{
- try {
+ try
+ {
includeBackupFiles = Boolean.parseBoolean(
Cache.getProperty(BackupFiles.NS + "_FC_INCLUDE"));
} catch (Exception e)
}
// fake the OK button changing (to force it to upate)
String s = jfc.getApproveButtonText();
- jfc.firePropertyChange(
- APPROVE_BUTTON_TEXT_CHANGED_PROPERTY, null, s);
+ jfc.firePropertyChange(APPROVE_BUTTON_TEXT_CHANGED_PROPERTY,
+ null, s);
// fake the file filter changing (its behaviour actually has)
jfc.firePropertyChange(FILE_FILTER_CHANGED_PROPERTY, null, f);
class RecentlyOpened extends JPanel
{
private static final long serialVersionUID = 1L;
+
JList<String> list;
RecentlyOpened()
{
- setPreferredSize(new Dimension(300,100));
+ setPreferredSize(new Dimension(300, 100));
String historyItems = Cache.getProperty("RECENT_FILE");
StringTokenizer st;
Vector<String> recent = new Vector<>();
}
list = new JList<>(recent);
-
+
DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
dlcr.setHorizontalAlignment(DefaultListCellRenderer.RIGHT);
list.setCellRenderer(dlcr);
@Override
public DialogRunnerI setResponseHandler(Object response, Runnable action)
{
- callbacks.put(response, action);
- return this;
+ callbacks.put(response, action);
+ return this;
}
@Override
public void handleResponse(Object response)
{
/*
- * this test is for NaN in Chrome
- */
+ * this test is for NaN in Chrome
+ */
if (response != null && !response.equals(response))
{
return;
}
/**
- * JalviewJS signals file selection by a property change event
- * for property "SelectedFile". This methods responds to that by
- * running the response action for 'OK' in the dialog.
+ * JalviewJS signals file selection by a property change event for property
+ * "SelectedFile". This methods responds to that by running the response
+ * action for 'OK' in the dialog.
*
* @param evt
*/
/*
* property name here matches that used in JFileChooser.js
*/
- case "SelectedFile":
+ case "SelectedFile":
handleResponse(APPROVE_OPTION);
break;
}
}
}
}
-
+
return false;
}
for (String ext : exts.split(","))
{
ext = ext.trim().toLowerCase(Locale.ROOT);
- extensions.put(ext,
- desc + ("jar".equals(ext) ? " (old)" : ""));
+ extensions.put(ext, desc + ("jar".equals(ext) ? " (old)" : ""));
}
}
}
public String getTypeDescription(File f)
{
String extension = getExtension(f);
-
+
String type = getDescriptionForExtension(extension);
-
+
if (extension != null)
{
if (extensions.containsKey(extension))
int end = start + 10;
int length = s[j].getLength();
- if ((end < length)
- && (start < length))
+ if ((end < length) && (start < length))
{
out.append(s[j].getSequence(start, end));
private resCode validResidueCode(String field)
{
Integer val = null;
- Regex r = new Regex(
- "\\s*((([-0-9]+).?)|FIRST|LAST|@)");
+ Regex r = new Regex("\\s*((([-0-9]+).?)|FIRST|LAST|@)");
if (!r.search(field))
{
List<DBRefEntry> dbr = seq.getDatasetSequence().getDBRefs();
for (int i = 0, ni = dbr.size(); i < ni; i++)
{
- DBRefEntry dbri = dbr.get(i);
+ DBRefEntry dbri = dbr.get(i);
if (dbri != null)
{
// JBPNote PDB dbRefEntry needs properties to propagate onto
// ModellerField
// JBPNote Need to get info from the user about whether the sequence
// is the one being modelled, or if it is a template.
- if (dbri.getSource()
- .equals(jalview.datamodel.DBRefSource.PDB))
+ if (dbri.getSource().equals(jalview.datamodel.DBRefSource.PDB))
{
fields.put(Fields[LOCALID], dbri.getAccessionId());
t = 2;
boolean ascending = false; // flag indicating that we are leaving the
// current node
- Regex majorsyms = new Regex(
- "[(\\['),;]");
+ Regex majorsyms = new Regex("[(\\['),;]");
int nextcp = 0;
int ncp = cp;
// Deal with quoted fields
case '\'':
- Regex qnodename = new Regex(
- "'([^']|'')+'");
+ Regex qnodename = new Regex("'([^']|'')+'");
if (qnodename.searchFrom(nf, fcp))
{
nodename = new String(
qnodename.stringMatched().substring(1, nl - 1));
// unpack any escaped colons
- Regex xpandquotes = Regex
- .perlCode("s/''/'/");
+ Regex xpandquotes = Regex.perlCode("s/''/'/");
String widernodename = xpandquotes.replaceAll(nodename);
nodename = widernodename;
// jump to after end of quoted nodename
* '"+nf.substring(cp,fcp)+"'"); }
*/
// verify termination.
- Regex comment = new Regex(
- "]");
+ Regex comment = new Regex("]");
if (comment.searchFrom(nf, fcp))
{
// Skip the comment field
+ fstring.substring(cend + 1);
}
- Regex uqnodename = new Regex(
- "\\b([^' :;\\](),]+)");
- Regex nbootstrap = new Regex(
- "\\s*([0-9+]+)\\s*:");
- Regex ndist = new Regex(
- ":([-0-9Ee.+]+)");
+ Regex uqnodename = new Regex("\\b([^' :;\\](),]+)");
+ Regex nbootstrap = new Regex("\\s*([0-9+]+)\\s*:");
+ Regex ndist = new Regex(":([-0-9Ee.+]+)");
if (!parsednodename && uqnodename.search(fstring)
&& ((uqnodename.matchedFrom(1) == 0) || (fstring
StringBuffer sb = new StringBuffer(Integer.toString(sqs.length));
sb.append(" ");
// if there are no sequences, then define the number of characters as 0
- sb.append(
-(sqs.length > 0) ? Integer.toString(sqs[0].getLength())
- : "0")
+ sb.append((sqs.length > 0) ? Integer.toString(sqs[0].getLength()) : "0")
.append(newline);
// Due to how IO is handled, there doesn't appear to be a way to store
i++;
}
- out.append(" MSF: " + s[0].getLength()
- + " Type: P Check: " + bigChecksum % 10000 + " ..");
+ out.append(" MSF: " + s[0].getLength() + " Type: P Check: "
+ + bigChecksum % 10000 + " ..");
out.append(newline);
out.append(newline);
out.append(newline);
private static String linkImageURL;
- // public static final String[][] PRIMARY_SOURCES moved to DBRefSource.java
+ // public static final String[][] PRIMARY_SOURCES moved to DBRefSource.java
/*
* Comparator to order DBRefEntry by Source + accession id (case-insensitive),
{
return 1;
}
- int comp = s1 == null ? -1 : (s2 == null ? 1 : s1
- .compareToIgnoreCase(s2));
+ int comp = s1 == null ? -1
+ : (s2 == null ? 1 : s1.compareToIgnoreCase(s2));
if (comp == 0)
{
String a1 = ref1.getAccessionId();
String a2 = ref2.getAccessionId();
- comp = a1 == null ? -1 : (a2 == null ? 1 : a1
- .compareToIgnoreCase(a2));
+ comp = a1 == null ? -1
+ : (a2 == null ? 1 : a1.compareToIgnoreCase(a2));
}
return comp;
}
-// private boolean isPrimarySource(String source)
-// {
-// for (String[] primary : DBRefSource.PRIMARY_SOURCES)
-// {
-// for (String s : primary)
-// {
-// if (source.equals(s))
-// {
-// return true;
-// }
-// }
-// }
-// return false;
-// }
+ // private boolean isPrimarySource(String source)
+ // {
+ // for (String[] primary : DBRefSource.PRIMARY_SOURCES)
+ // {
+ // for (String s : primary)
+ // {
+ // if (source.equals(s))
+ // {
+ // return true;
+ // }
+ // }
+ // }
+ // return false;
+ // }
};
private boolean forTooltip;
* @param minmax
* @param maxlength
*/
- public int appendFeatures(final StringBuilder sb,
- int residuePos, List<SequenceFeature> features,
- FeatureRendererModel fr, int maxlength)
+ public int appendFeatures(final StringBuilder sb, int residuePos,
+ List<SequenceFeature> features, FeatureRendererModel fr,
+ int maxlength)
{
for (int i = 0; i < features.size(); i++)
{
{
for (List<String> urllink : createLinksFrom(null, urlstring))
{
- sb.append("<br/> <a href=\""
- + urllink.get(3)
- + "\" target=\""
- + urllink.get(0)
- + "\">"
- + (urllink.get(0).toLowerCase(Locale.ROOT)
- .equals(urllink.get(1).toLowerCase(Locale.ROOT)) ? urllink
- .get(0) : (urllink.get(0) + ":" + urllink
- .get(1)))
+ sb.append("<br/> <a href=\"" + urllink.get(3) + "\" target=\""
+ + urllink.get(0) + "\">"
+ + (urllink.get(0).toLowerCase(Locale.ROOT).equals(
+ urllink.get(1).toLowerCase(Locale.ROOT))
+ ? urllink.get(0)
+ : (urllink.get(0) + ":"
+ + urllink.get(1)))
+ "</a><br/>");
}
} catch (Exception x)
{
- System.err.println("problem when creating links from "
- + urlstring);
+ System.err.println(
+ "problem when creating links from " + urlstring);
x.printStackTrace();
}
}
SequenceI sequence, boolean showDbRefs, boolean showNpFeats,
FeatureRendererModel fr)
{
- int maxWidth = createSequenceAnnotationReport(tip, sequence,
- showDbRefs, showNpFeats, fr, true);
+ int maxWidth = createSequenceAnnotationReport(tip, sequence, showDbRefs,
+ showNpFeats, fr, true);
if (maxWidth > 60)
{
}
StructureImportSettings.setShowSeqFeatures(true);
}
-
+
/**
- * Answers the first PDBChain found matching the given id, or null if none
- * is found
+ * Answers the first PDBChain found matching the given id, or null if none is
+ * found
*
* @param id
* @return
String seqsetidobj = av.getSequenceSetId();
views = Desktop.getViewports(seqsetidobj);
Console.debug("Found " + (views == null ? " no " : "" + views.length)
- + " views for '" + av.getSequenceSetId() + "'");
+ + " views for '" + av.getSequenceSetId() + "'");
if (views.length > 1)
{
// we need to close the original document view.
* @return
*/
protected SequenceFeature buildSequenceFeature(String[] gff,
- int typeColumn, String group, Map<String, List<String>> attributes)
+ int typeColumn, String group,
+ Map<String, List<String>> attributes)
{
try
{
/**
* An override that
* <ul>
- * <li>uses Source (column 2) as feature type instead of the default column 3</li>
+ * <li>uses Source (column 2) as feature type instead of the default column
+ * 3</li>
* <li>sets "InterProScan" as the feature group</li>
* <li>extracts "signature_desc" attribute as the feature description</li>
* </ul>
{
modifiedthedoc |= new jalview.io.vamsas.Dbref(datastore,
// dbentry =
- entries.get(db), sq, (Sequence) vobj, dataset).docWasUpdated();
+ entries.get(db), sq, (Sequence) vobj, dataset)
+ .docWasUpdated();
}
if (vobj.getMapCount() > 1)
{
Console.debug("Ignoring additional mappings on DbRef: "
- + jvobj.getSource() + ":" + jvobj.getAccessionId());
+ + jvobj.getSource() + ":" + jvobj.getAccessionId());
}
jalview.datamodel.Mapping mp = new jalview.datamodel.Mapping(
parsemapType(vobj.getMap(0)));
DbRef vobj = (DbRef) this.vobj;
DBRefEntry jvobj = (DBRefEntry) this.jvobj;
Console.debug("Conflict in dbentry update for " + vobj.getAccessionId()
- + vobj.getSource() + " " + vobj.getVorbaId());
+ + vobj.getSource() + " " + vobj.getVorbaId());
// TODO Auto-generated method stub
}
if (vobj.getMapCount() > 1)
{
Console.debug("Ignoring additional mappings on DbRef: "
- + jvobj.getSource() + ":" + jvobj.getAccessionId());
+ + jvobj.getSource() + ":" + jvobj.getAccessionId());
}
jalview.datamodel.Mapping mp = new jalview.datamodel.Mapping(
parsemapType(vobj.getMap(0)));
if (!map.getLocal().hasUnit() || map.getMapped().hasUnit())
{
Console.warn("using default mapping length of 1:1 for map "
- + (map.isRegistered() ? map.getVorbaId().toString()
- : ("<no Id registered> " + map.toString())));
+ + (map.isRegistered() ? map.getVorbaId().toString()
+ : ("<no Id registered> " + map.toString())));
}
return parsemapType(map, 1, 1);
}
private void update(jalview.datamodel.Mapping mjvmapping,
SequenceMapping sequenceMapping)
{
- Console.error(
- "Not implemented: Jalview Update Sequence DBRef Mapping");
+ Console.error("Not implemented: Jalview Update Sequence DBRef Mapping");
}
/**
{
if (Console.isDebugEnabled())
{
- Console.debug("Not matching conjugate refs for "
- + from.getName() + " and " + to.getName());
+ Console.debug("Not matching conjugate refs for " + from.getName()
+ + " and " + to.getName());
}
return;
}
if (Console.isDebugEnabled())
{
- Console.debug("Matching conjugate refs for "
- + from.getName() + " and " + to.getName());
+ Console.debug("Matching conjugate refs for " + from.getName()
+ + " and " + to.getName());
}
List<DBRefEntry> fdb = from.getDBRefs();
List<DBRefEntry> tdb = new ArrayList<DBRefEntry>(to.getDBRefs());
int tdblen = to.getDBRefs().size();
-//
-//
-// YOWSER
-//
-// System.arraycopy(to.getDBRefs(), 0, tdb, 0, tdblen);
-//
-//
-//
-//
+ //
+ //
+ // YOWSER
+ //
+ // System.arraycopy(to.getDBRefs(), 0, tdb, 0, tdblen);
+ //
+ //
+ //
+ //
Vector matched = new Vector();
jalview.util.MapList smapI = smap.getInverse();
for (int f = 0, fn = fdb.size(); f < fn; f++)
if (tp.getTree() == null)
{
- Console.warn(
- "Not updating SequenceTreeMap for " + tree.getVorbaId());
+ Console.warn("Not updating SequenceTreeMap for " + tree.getVorbaId());
return;
}
Vector<SequenceNode> leaves = tp.getTree()
{
if (tp.getEntry(pe).getInputCount() > 1)
{
- Console.warn(
- "Ignoring additional input spec in provenance entry "
- + tp.getEntry(pe).toString());
+ Console.warn("Ignoring additional input spec in provenance entry "
+ + tp.getEntry(pe).toString());
}
// LATER: deal sensibly with multiple inputs
Input vInput = tp.getEntry(pe).getInput(0);
private static final String DEFAULT_SPECIES = "homo_sapiens";
/**
- * A class to model the mapping from sequence to VCF coordinates. Cases include
+ * A class to model the mapping from sequence to VCF coordinates. Cases
+ * include
* <ul>
* <li>a direct 1:1 mapping where the sequence is one of the VCF contigs</li>
- * <li>a mapping of sequence to chromosomal coordinates, where sequence and VCF
- * use the same reference assembly</li>
- * <li>a modified mapping of sequence to chromosomal coordinates, where sequence
- * and VCF use different reference assembles</li>
+ * <li>a mapping of sequence to chromosomal coordinates, where sequence and
+ * VCF use the same reference assembly</li>
+ * <li>a modified mapping of sequence to chromosomal coordinates, where
+ * sequence and VCF use different reference assembles</li>
* </ul>
*/
class VCFMap
private static final String VCF_SPECIES = "VCF_SPECIES"; // default is human
- private static final String DEFAULT_REFERENCE = "grch37"; // fallback default is human GRCh37
+ private static final String DEFAULT_REFERENCE = "grch37"; // fallback default
+ // is human GRCh37
/*
* keys to fields of VEP CSQ consequence data
* see https://www.ensembl.org/info/docs/tools/vep/vep_formats.html
*/
private static final String CSQ_CONSEQUENCE_KEY = "Consequence";
+
private static final String CSQ_ALLELE_KEY = "Allele";
- private static final String CSQ_ALLELE_NUM_KEY = "ALLELE_NUM"; // 0 (ref), 1...
+
+ private static final String CSQ_ALLELE_NUM_KEY = "ALLELE_NUM"; // 0 (ref),
+ // 1...
+
private static final String CSQ_FEATURE_KEY = "Feature"; // Ensembl stable id
/*
* see http://www.ensembl.org/info/docs/tools/vep/vep_formats.html
*/
private int csqConsequenceFieldIndex = -1;
+
private int csqAlleleFieldIndex = -1;
+
private int csqAlleleNumberFieldIndex = -1;
+
private int csqFeatureFieldIndex = -1;
// todo the same fields for SnpEff ANN data if wanted
*/
public SequenceI loadVCFContig(String contig)
{
- VCFHeaderLine headerLine = header.getOtherHeaderLine(VCFHeader.REFERENCE_KEY);
+ VCFHeaderLine headerLine = header
+ .getOtherHeaderLine(VCFHeader.REFERENCE_KEY);
if (headerLine == null)
{
Console.error("VCF reference header not found");
/**
* Attempts to determine and save the species and genome assembly version to
- * which the VCF data applies. This may be done by parsing the {@code reference}
- * header line, configured in a property file, or (potentially) confirmed
- * interactively by the user.
+ * which the VCF data applies. This may be done by parsing the
+ * {@code reference} header line, configured in a property file, or
+ * (potentially) confirmed interactively by the user.
* <p>
* The saved values should be identifiers valid for Ensembl's REST service
* {@code map} endpoint, so they can be used (if necessary) to retrieve the
{
try
{
- patterns.add(Pattern.compile(token.toUpperCase(Locale.ROOT)));
+ patterns.add(Pattern.compile(token.toUpperCase(Locale.ROOT)));
} catch (PatternSyntaxException e)
{
System.err.println("Invalid pattern ignored: " + token);
}
/**
- * Tries to add overlapping variants read from a VCF file to the given sequence,
- * and returns the number of variant features added
+ * Tries to add overlapping variants read from a VCF file to the given
+ * sequence, and returns the number of variant features added
*
* @param seq
* @return
vcfAssembly);
if (newRange == null)
{
- Console.error(
- String.format("Failed to map %s:%s:%s:%d:%d to %s", species,
- chromosome, seqRef, range[0], range[1],
- vcfAssembly));
+ Console.error(String.format("Failed to map %s:%s:%s:%d:%d to %s",
+ species, chromosome, seqRef, range[0], range[1],
+ vcfAssembly));
continue;
}
else
* RuntimeException throwable by htsjdk
*/
String msg = String.format("Error reading VCF for %s:%d-%d: %s ",
- map.chromosome, vcfStart, vcfEnd,e.getLocalizedMessage());
+ map.chromosome, vcfStart, vcfEnd, e.getLocalizedMessage());
Console.error(msg);
}
}
/**
* Inspects one allele and attempts to add a variant feature for it to the
* sequence. The additional data associated with this allele is extracted to
- * store in the feature's key-value map. Answers the number of features added (0
- * or 1).
+ * store in the feature's key-value map. Answers the number of features added
+ * (0 or 1).
*
* @param seq
* @param variant
* pick out the consequence data (if any) that is for the current allele
* and feature (transcript) that matches the current sequence
*/
- String consequence = getConsequenceForAlleleAndFeature(variant, CSQ_FIELD,
- altAlleleIndex, csqAlleleFieldIndex,
- csqAlleleNumberFieldIndex, seq.getName().toLowerCase(Locale.ROOT),
- csqFeatureFieldIndex);
+ String consequence = getConsequenceForAlleleAndFeature(variant,
+ CSQ_FIELD, altAlleleIndex, csqAlleleFieldIndex,
+ csqAlleleNumberFieldIndex,
+ seq.getName().toLowerCase(Locale.ROOT), csqFeatureFieldIndex);
/*
* pick out the ontology term for the consequence type
/**
* Answers the VCF FILTER value for the variant - or an approximation to it.
* This field is either PASS, or a semi-colon separated list of filters not
- * passed. htsjdk saves filters as a HashSet, so the order when reassembled into
- * a list may be different.
+ * passed. htsjdk saves filters as a HashSet, so the order when reassembled
+ * into a list may be different.
*
* @param variant
* @return
}
/**
- * Determines the Sequence Ontology term to use for the variant feature type in
- * Jalview. The default is 'sequence_variant', but a more specific term is used
- * if:
+ * Determines the Sequence Ontology term to use for the variant feature type
+ * in Jalview. The default is 'sequence_variant', but a more specific term is
+ * used if:
* <ul>
* <li>VEP (or SnpEff) Consequence annotation is included in the VCF</li>
* <li>sequence id can be matched to VEP Feature (or SnpEff Feature_ID)</li>
*/
private String getConsequenceForAlleleAndFeature(VariantContext variant,
String vcfInfoId, int altAlleleIndex, int alleleFieldIndex,
- int alleleNumberFieldIndex,
- String seqName, int featureFieldIndex)
+ int alleleNumberFieldIndex, String seqName, int featureFieldIndex)
{
if (alleleFieldIndex == -1 || featureFieldIndex == -1)
{
if (csqFields.length > featureFieldIndex)
{
String featureIdentifier = csqFields[featureFieldIndex];
- if (featureIdentifier.length() > 4
- && seqName.indexOf(featureIdentifier.toLowerCase(Locale.ROOT)) > -1)
+ if (featureIdentifier.length() > 4 && seqName
+ .indexOf(featureIdentifier.toLowerCase(Locale.ROOT)) > -1)
{
/*
* feature (transcript) matched - now check for allele match
}
/**
- * Answers true for '.', null, or an empty value, or if the INFO type is String.
- * If the INFO type is Integer or Float, answers false if the value is not in
- * valid format.
+ * Answers true for '.', null, or an empty value, or if the INFO type is
+ * String. If the INFO type is Integer or Float, answers false if the value is
+ * not in valid format.
*
* @param variant
* @param infoId
* @param toRef
* @return
*/
- protected int[] findSubsumedRangeMapping(int[] queryRange, String chromosome,
- String species, String fromRef, String toRef)
+ protected int[] findSubsumedRangeMapping(int[] queryRange,
+ String chromosome, String species, String fromRef, String toRef)
{
String key = makeRangesKey(chromosome, species, fromRef, toRef);
if (assemblyMappings.containsKey(key))
*/
int offset = queryRange[0] - fromRange[0];
int mappedRangeFrom = toRange[0] + offset;
- int mappedRangeTo = mappedRangeFrom + (queryRange[1] - queryRange[0]);
+ int mappedRangeTo = mappedRangeFrom
+ + (queryRange[1] - queryRange[0]);
return new int[] { mappedRangeFrom, mappedRangeTo };
}
}
SequenceI targetSequence, MapList mapping)
{
int[] mappedRange = mapping.locateInTo(sf.getBegin(), sf.getEnd());
-
+
if (mappedRange != null)
{
String group = sf.getFeatureGroup();
protected static String makeRangesKey(String chromosome, String species,
String fromRef, String toRef)
{
- return species + EXCL + chromosome + EXCL + fromRef + EXCL
- + toRef;
+ return species + EXCL + chromosome + EXCL + fromRef + EXCL + toRef;
}
}
// structure
ArrayList<String[]> ccomands = new ArrayList<>();
ArrayList<String> pdbfn = new ArrayList<>();
- String[] colcommands = new JmolCommands()
- .colourBySequence(ssm, modelSet, sequence, sr,
- (AlignmentViewPanel) source);
+ String[] colcommands = new JmolCommands().colourBySequence(ssm,
+ modelSet, sequence, sr, (AlignmentViewPanel) source);
if (colcommands == null)
{
return;
* @author hansonr Bob Hanson St. Olaf College 1/24/2019
*
*/
-public class JSON {
-
- /**
- * A simple encoding of sequential key/value pairs for a jQuery.ajax call. If
- * the first key is "url" and the second is an object, then the ajax object is
- * attached to that url as well, just for transport purposes within the system.
- *
- * @param keyValues assumed to be simple String,Object pairs. String objects
- * will be surrounded by double quotes.
- */
- @SuppressWarnings("static-access")
- public static Object setAjax(Object... keyValues) {
- return /** @j2sNative swingjs.JSUtil.setAjax$OA(keyValues) || */null;
- }
-
- public static void setAjax(URL url) {
+public class JSON
+{
+
+ /**
+ * A simple encoding of sequential key/value pairs for a jQuery.ajax call. If
+ * the first key is "url" and the second is an object, then the ajax object is
+ * attached to that url as well, just for transport purposes within the
+ * system.
+ *
+ * @param keyValues
+ * assumed to be simple String,Object pairs. String objects will be
+ * surrounded by double quotes.
+ */
+ @SuppressWarnings("static-access")
+ public static Object setAjax(Object... keyValues)
+ {
+ return /** @j2sNative swingjs.JSUtil.setAjax$OA(keyValues) || */
+ null;
+ }
+
+ public static void setAjax(URL url)
+ {
/** @j2sNative swingjs.JSUtil.setAjax$java_net_URL(url); */
- }
+ }
- public static BufferedReader getJSONReader(InputStream is) {
- return /** @j2sNative swingjs.JSUtil.getJSONReader$O(is) || */null;
+ public static BufferedReader getJSONReader(InputStream is)
+ {
+ return /** @j2sNative swingjs.JSUtil.getJSONReader$O(is) || */
+ null;
}
/**
null;
}
- public static String stringify(Object obj) {
- return /** @j2sNative swingjs.JSUtil.stringifyJSON$O(obj) || */null;
- }
+ public static String stringify(Object obj)
+ {
+ return /** @j2sNative swingjs.JSUtil.stringifyJSON$O(obj) || */
+ null;
+ }
}
public class Client
{
- public static Client create(ClientConfig clientConfig)
+ public static Client create(ClientConfig clientConfig)
{
return new Client();
}
}
// https://www.ebi.ac.uk/pdbe/search/pdb/select?wt=json&fl=pdb_id,title,experimental_method,resolution&rows=500&start=0&q=(text:q93xj9_soltu)+AND+molecule_sequence:%5B%27%27+TO+*%5D+AND+status:REL&sort=overall_quality+desc
-
-//{
-//"responseHeader":{
-// "status":0,
-// "QTime":0,
-// "params":{
-// "q":"(text:q93xj9_soltu) AND molecule_sequence:['' TO *] AND status:REL",
-// "fl":"pdb_id,title,experimental_method,resolution",
-// "start":"0",
-// "sort":"overall_quality desc",
-// "rows":"500",
-// "wt":"json"}},
-//"response":{"numFound":1,"start":0,"docs":[
-// {
-// "experimental_method":["X-ray diffraction"],
-// "pdb_id":"4zhp",
-// "resolution":2.46,
-// "title":"The crystal structure of Potato ferredoxin I with 2Fe-2S cluster"}]
-//}}
-//
+
+ // {
+ // "responseHeader":{
+ // "status":0,
+ // "QTime":0,
+ // "params":{
+ // "q":"(text:q93xj9_soltu) AND molecule_sequence:['' TO *] AND status:REL",
+ // "fl":"pdb_id,title,experimental_method,resolution",
+ // "start":"0",
+ // "sort":"overall_quality desc",
+ // "rows":"500",
+ // "wt":"json"}},
+ // "response":{"numFound":1,"start":0,"docs":[
+ // {
+ // "experimental_method":["X-ray diffraction"],
+ // "pdb_id":"4zhp",
+ // "resolution":2.46,
+ // "title":"The crystal structure of Potato ferredoxin I with 2Fe-2S
+ // cluster"}]
+ // }}
+ //
public int getStatus()
{
@Override
public boolean equals(Object obj)
{
- if (obj instanceof FilterOption) {
- FilterOption o=(FilterOption) obj;
- return o.name.equals(name) && o.querySource==querySource && o.value.equals(value) && o.view==view;
- } else {
+ if (obj instanceof FilterOption)
+ {
+ FilterOption o = (FilterOption) obj;
+ return o.name.equals(name) && o.querySource == querySource
+ && o.value.equals(value) && o.view == view;
+ }
+ else
+ {
return super.equals(obj);
}
}
closeMenuItem.setText(MessageManager.getString("action.close"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_W,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ jalview.util.ShortcutKeyMaskExWrapper
+ .getMenuShortcutKeyMaskEx(),
+ false);
al = new ActionListener()
{
@Override
JMenuItem selectAllSequenceMenuItem = new JMenuItem(
MessageManager.getString("action.select_all"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_A,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ jalview.util.ShortcutKeyMaskExWrapper
+ .getMenuShortcutKeyMaskEx(),
+ false);
al = new ActionListener()
{
@Override
JMenuItem invertSequenceMenuItem = new JMenuItem(
MessageManager.getString("action.invert_sequence_selection"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_I,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ jalview.util.ShortcutKeyMaskExWrapper
+ .getMenuShortcutKeyMaskEx(),
+ false);
al = new ActionListener()
{
@Override
JMenuItem remove2LeftMenuItem = new JMenuItem(
MessageManager.getString("action.remove_left"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_L,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ jalview.util.ShortcutKeyMaskExWrapper
+ .getMenuShortcutKeyMaskEx(),
+ false);
al = new ActionListener()
{
@Override
JMenuItem remove2RightMenuItem = new JMenuItem(
MessageManager.getString("action.remove_right"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_R,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ jalview.util.ShortcutKeyMaskExWrapper
+ .getMenuShortcutKeyMaskEx(),
+ false);
al = new ActionListener()
{
@Override
JMenuItem removeGappedColumnMenuItem = new JMenuItem(
MessageManager.getString("action.remove_empty_columns"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_E,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ jalview.util.ShortcutKeyMaskExWrapper
+ .getMenuShortcutKeyMaskEx(),
+ false);
al = new ActionListener()
{
@Override
JMenuItem removeRedundancyMenuItem = new JMenuItem(
MessageManager.getString("action.remove_redundancy"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_D,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ jalview.util.ShortcutKeyMaskExWrapper
+ .getMenuShortcutKeyMaskEx(),
+ false);
al = new ActionListener()
{
@Override
undoMenuItem.setEnabled(false);
undoMenuItem.setText(MessageManager.getString("action.undo"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Z,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ jalview.util.ShortcutKeyMaskExWrapper
+ .getMenuShortcutKeyMaskEx(),
+ false);
al = new ActionListener()
{
@Override
redoMenuItem.setEnabled(false);
redoMenuItem.setText(MessageManager.getString("action.redo"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_Y,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ jalview.util.ShortcutKeyMaskExWrapper
+ .getMenuShortcutKeyMaskEx(),
+ false);
al = new ActionListener()
{
@Override
JMenuItem printMenuItem = new JMenuItem(
MessageManager.getString("action.print"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_P,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ jalview.util.ShortcutKeyMaskExWrapper
+ .getMenuShortcutKeyMaskEx(),
+ false);
al = new ActionListener()
{
@Override
JMenuItem findMenuItem = new JMenuItem(
MessageManager.getString("action.find"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_F,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ jalview.util.ShortcutKeyMaskExWrapper
+ .getMenuShortcutKeyMaskEx(),
+ false);
findMenuItem.setToolTipText(JvSwingUtils.wrapTooltip(true,
MessageManager.getString("label.find_tip")));
al = new ActionListener()
JMenuItem deleteGroups = new JMenuItem(
MessageManager.getString("action.undefine_groups"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_U,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ jalview.util.ShortcutKeyMaskExWrapper
+ .getMenuShortcutKeyMaskEx(),
+ false);
al = new ActionListener()
{
@Override
JMenuItem createGroup = new JMenuItem(
MessageManager.getString("action.create_group"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ jalview.util.ShortcutKeyMaskExWrapper
+ .getMenuShortcutKeyMaskEx(),
+ false);
al = new ActionListener()
{
@Override
copy.setText(MessageManager.getString("action.copy"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ jalview.util.ShortcutKeyMaskExWrapper
+ .getMenuShortcutKeyMaskEx(),
+ false);
al = new ActionListener()
{
cut.setText(MessageManager.getString("action.cut"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_X,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ jalview.util.ShortcutKeyMaskExWrapper
+ .getMenuShortcutKeyMaskEx(),
+ false);
al = new ActionListener()
{
@Override
JMenuItem pasteThis = new JMenuItem(
MessageManager.getString("label.to_this_alignment"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_V,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ jalview.util.ShortcutKeyMaskExWrapper
+ .getMenuShortcutKeyMaskEx(),
+ false);
al = new ActionListener()
{
@Override
.setText(MessageManager.getString("action.calculate_tree_pca"));
padGapsMenuitem.setText(MessageManager.getString("label.pad_gaps"));
- padGapsMenuitem
- .setState(Cache.getDefault("PAD_GAPS", false));
+ padGapsMenuitem.setState(Cache.getDefault("PAD_GAPS", false));
padGapsMenuitem.addActionListener(new ActionListener()
{
@Override
});
autoCalculate.setText(
MessageManager.getString("label.autocalculate_consensus"));
- autoCalculate.setState(
- Cache.getDefault("AUTO_CALC_CONSENSUS", true));
+ autoCalculate.setState(Cache.getDefault("AUTO_CALC_CONSENSUS", true));
autoCalculate.addActionListener(new ActionListener()
{
@Override
MessageManager.getString("label.sort_alignment_new_tree"));
sortByTree.setToolTipText("<html>" + MessageManager.getString(
"label.enable_automatically_sort_alignment_when_open_new_tree"));
- sortByTree
- .setState(Cache.getDefault("SORT_BY_TREE", false));
+ sortByTree.setState(Cache.getDefault("SORT_BY_TREE", false));
sortByTree.addActionListener(new ActionListener()
{
@Override
JMenuItem save = new JMenuItem(MessageManager.getString("action.save"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_S,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ jalview.util.ShortcutKeyMaskExWrapper
+ .getMenuShortcutKeyMaskEx(),
+ false);
al = new ActionListener()
{
@Override
JMenuItem newView = new JMenuItem(
MessageManager.getString("action.new_view"));
keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_T,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
+ jalview.util.ShortcutKeyMaskExWrapper
+ .getMenuShortcutKeyMaskEx(),
+ false);
al = new ActionListener()
{
@Override
@SuppressWarnings("serial")
public class GAlignmentPanel extends JPanel
{
- protected JScrollBar vscroll = new JScrollBar();
+ protected JScrollBar vscroll = new JScrollBar();
- protected JScrollBar hscroll = new JScrollBar();
+ protected JScrollBar hscroll = new JScrollBar();
- BorderLayout borderLayout1 = new BorderLayout();
+ BorderLayout borderLayout1 = new BorderLayout();
- BorderLayout borderLayout3 = new BorderLayout();
+ BorderLayout borderLayout3 = new BorderLayout();
- BorderLayout borderLayout5 = new BorderLayout();
+ BorderLayout borderLayout5 = new BorderLayout();
- BorderLayout borderLayout6 = new BorderLayout();
+ BorderLayout borderLayout6 = new BorderLayout();
- ButtonGroup buttonGroup1 = new ButtonGroup();
+ ButtonGroup buttonGroup1 = new ButtonGroup();
- BorderLayout borderLayout7 = new BorderLayout();
+ BorderLayout borderLayout7 = new BorderLayout();
- BorderLayout borderLayout10 = new BorderLayout();
+ BorderLayout borderLayout10 = new BorderLayout();
- BorderLayout borderLayout11 = new BorderLayout();
+ BorderLayout borderLayout11 = new BorderLayout();
public JScrollPane annotationScroller = new JScrollPane();
- Border border1;
+ Border border1;
- BorderLayout borderLayout4 = new BorderLayout();
+ BorderLayout borderLayout4 = new BorderLayout();
-
- static JPanel newJPanel() { // BH 2019
- JPanel p = new JPanel();
- // leaving this in, as it prevents
- // the checkerboard business, despite how
- // funky that looks. Remove if you want to.
- p.setBackground(Color.white);
- return p;
- }
+ static JPanel newJPanel()
+ { // BH 2019
+ JPanel p = new JPanel();
+ // leaving this in, as it prevents
+ // the checkerboard business, despite how
+ // funky that looks. Remove if you want to.
+ p.setBackground(Color.white);
+ return p;
+ }
protected JPanel sequenceHolderPanel = newJPanel();
+
protected JPanel seqPanelHolder = newJPanel();
+
protected JPanel scalePanelHolder = newJPanel();
+
protected JPanel idPanelHolder = newJPanel();
+
protected JPanel idSpaceFillerPanel1 = newJPanel();
+
public JPanel annotationSpaceFillerHolder = newJPanel();
- protected JPanel hscrollFillerPanel = newJPanel();
- JPanel hscrollHolder = newJPanel();
+ protected JPanel hscrollFillerPanel = newJPanel();
+ JPanel hscrollHolder = newJPanel();
public GAlignmentPanel()
{
private void jbInit() throws Exception
{
- // annotationScroller.setBackground(Color.white); // BH 2019
-
+ // annotationScroller.setBackground(Color.white); // BH 2019
+
border1 = BorderFactory.createLineBorder(Color.gray, 1);
idPanelHolder.setBorder(null);
idPanelHolder.setPreferredSize(new Dimension(70, 10));
cancel_actionPerformed(e);
}
});
- close.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_W,
- jalview.util.ShortcutKeyMaskExWrapper
- .getMenuShortcutKeyMaskEx(),
- false));
+ close.setAccelerator(
+ javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_W,
+ jalview.util.ShortcutKeyMaskExWrapper
+ .getMenuShortcutKeyMaskEx(),
+ false));
selectAll.setText(MessageManager.getString("action.select_all"));
- selectAll.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_A,
- jalview.util.ShortcutKeyMaskExWrapper
- .getMenuShortcutKeyMaskEx(),
- false));
+ selectAll
+ .setAccelerator(
+ javax.swing.KeyStroke
+ .getKeyStroke(java.awt.event.KeyEvent.VK_A,
+ jalview.util.ShortcutKeyMaskExWrapper
+ .getMenuShortcutKeyMaskEx(),
+ false));
selectAll.addActionListener(new ActionListener()
{
@Override
});
jMenu1.setText(MessageManager.getString("action.file"));
save.setText(MessageManager.getString("action.save"));
- save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_S,
- jalview.util.ShortcutKeyMaskExWrapper
- .getMenuShortcutKeyMaskEx(),
- false));
+ save.setAccelerator(
+ javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_S,
+ jalview.util.ShortcutKeyMaskExWrapper
+ .getMenuShortcutKeyMaskEx(),
+ false));
save.addActionListener(new ActionListener()
{
@Override
save_actionPerformed(e);
}
});
- copyItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_C,
- jalview.util.ShortcutKeyMaskExWrapper
- .getMenuShortcutKeyMaskEx(),
- false));
+ copyItem.setAccelerator(
+ javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_C,
+ jalview.util.ShortcutKeyMaskExWrapper
+ .getMenuShortcutKeyMaskEx(),
+ false));
editMenubar.add(jMenu1);
editMenubar.add(editMenu);
textarea.setBorder(null);
selectAll.setText(MessageManager.getString("action.select_all"));
- selectAll.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_A,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false));
+ selectAll
+ .setAccelerator(
+ javax.swing.KeyStroke
+ .getKeyStroke(java.awt.event.KeyEvent.VK_A,
+ jalview.util.ShortcutKeyMaskExWrapper
+ .getMenuShortcutKeyMaskEx(),
+ false));
selectAll.addActionListener(new ActionListener()
{
@Override
});
jMenu1.setText(MessageManager.getString("action.file"));
save.setText(MessageManager.getString("action.save"));
- save.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_S,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false));
+ save.setAccelerator(
+ javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_S,
+ jalview.util.ShortcutKeyMaskExWrapper
+ .getMenuShortcutKeyMaskEx(),
+ false));
save.addActionListener(new ActionListener()
{
@Override
save_actionPerformed(e);
}
});
- copyItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_C,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false));
- pasteMenu.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
- java.awt.event.KeyEvent.VK_V,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false));
+ copyItem.setAccelerator(
+ javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_C,
+ jalview.util.ShortcutKeyMaskExWrapper
+ .getMenuShortcutKeyMaskEx(),
+ false));
+ pasteMenu
+ .setAccelerator(
+ javax.swing.KeyStroke
+ .getKeyStroke(java.awt.event.KeyEvent.VK_V,
+ jalview.util.ShortcutKeyMaskExWrapper
+ .getMenuShortcutKeyMaskEx(),
+ false));
editMenubar.add(jMenu1);
editMenubar.add(editMenu);
textarea.setFont(new java.awt.Font("Monospaced", Font.PLAIN, 12));
e.printStackTrace();
}
- if (Platform.allowMnemonics())
+ if (Platform.allowMnemonics())
{
- //BH was !Platform.isAMacAndNotJS()) i.e. "JS or not Mac"
- // but here we want just not a Mac, period, right?
+ // BH was !Platform.isAMacAndNotJS()) i.e. "JS or not Mac"
+ // but here we want just not a Mac, period, right?
FileMenu.setMnemonic('F');
inputLocalFileMenuItem.setMnemonic('L');
inputURLMenuItem.setMnemonic('U');
HelpMenu.setText(MessageManager.getString("action.help"));
inputLocalFileMenuItem
.setText(MessageManager.getString("label.load_tree_from_file"));
- inputLocalFileMenuItem.setAccelerator(
- javax.swing.KeyStroke.getKeyStroke(java.awt.event.KeyEvent.VK_O,
- jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(),
- false));
+ inputLocalFileMenuItem
+ .setAccelerator(
+ javax.swing.KeyStroke
+ .getKeyStroke(java.awt.event.KeyEvent.VK_O,
+ jalview.util.ShortcutKeyMaskExWrapper
+ .getMenuShortcutKeyMaskEx(),
+ false));
inputLocalFileMenuItem
.addActionListener(new java.awt.event.ActionListener()
{
Float specversion = Platform.isJS() ? Float.valueOf(8)
: Float.parseFloat(
System.getProperty("java.specification.version"));
-
+
desktopMenubar.add(FileMenu);
desktopMenubar.add(toolsMenu);
desktopMenubar.add(HelpMenu);
FileMenu.add(inputMenu);
FileMenu.add(inputSequence);
FileMenu.addSeparator();
- //FileMenu.add(saveState);
+ // FileMenu.add(saveState);
FileMenu.add(saveAsState);
FileMenu.add(loadState);
FileMenu.addSeparator();
*/
protected void quit()
{
- //System.out.println("********** GDesktop.quit()");
+ // System.out.println("********** GDesktop.quit()");
}
/**
searchBox = new JvCacheableInputBox<>(FINDER_CACHE_KEY, 25);
searchBox.getComponent().setFont(VERDANA_12);
searchBox.addCaretListener(new CaretListener()
- {
- @Override
- public void caretUpdate(CaretEvent e)
- {
- textfield_caretUpdate();
- }
- });
+ {
+ @Override
+ public void caretUpdate(CaretEvent e)
+ {
+ textfield_caretUpdate();
+ }
+ });
searchBox.addKeyListener(new KeyAdapter()
- {
- @Override
- public void keyPressed(KeyEvent e)
- {
- textfield_keyPressed(e);
- }
- });
+ {
+ @Override
+ public void keyPressed(KeyEvent e)
+ {
+ textfield_keyPressed(e);
+ }
+ });
centrePanel.add(searchBox.getComponent());
/*
ignoreHidden.setText(MessageManager.getString("label.ignore_hidden"));
ignoreHidden.setToolTipText(
MessageManager.getString("label.ignore_hidden_tooltip"));
-
+
centrePanel.add(caseSensitive);
centrePanel.add(searchDescription);
centrePanel.add(ignoreHidden);
private void jbInit() throws Exception
{
-
+
setName("jalview-rnastructureviewer");
}
*/
public class GSliderPanel extends JPanel
{
- private static final Font VERDANA_11 = new java.awt.Font("Verdana", 0, 11);
+ private static final Font VERDANA_11 = new java.awt.Font("Verdana", 0,
+ 11);
protected static final int FRAME_WIDTH = 420;
}
else
{
- ((BasicInternalFrameUI) topFrame.getUI()).setNorthPane(null);
- ((BasicInternalFrameUI) bottomFrame.getUI()).setNorthPane(null);
+ ((BasicInternalFrameUI) topFrame.getUI()).setNorthPane(null);
+ ((BasicInternalFrameUI) bottomFrame.getUI()).setNorthPane(null);
}
}
protected JButton btn_newView;
protected JButton btn_pdbFromFile = new JButton();
-
+
protected JButton btn_queryTDB = new JButton();
protected JCheckBox chk_superpose = new JCheckBox(
protected ImageIcon warningImage = new ImageIcon(
getClass().getResource("/images/warning.gif"));
- protected ImageIcon tdbImage = new ImageIcon(
- getClass().getResource("/images/3d-beacons-logo-transparent.png"));
+ protected ImageIcon tdbImage = new ImageIcon(getClass()
+ .getResource("/images/3d-beacons-logo-transparent.png"));
protected JLabel lbl_loading = new JLabel(loadingImage);
protected JTabbedPane pnl_filter = new JTabbedPane();
protected abstract FTSDataColumnPreferences getFTSDocFieldPrefs();
- protected abstract void setFTSDocFieldPrefs(FTSDataColumnPreferences newPrefs);
+ protected abstract void setFTSDocFieldPrefs(
+ FTSDataColumnPreferences newPrefs);
protected FTSDataColumnI[] previousWantedFields;
+ "...\"")
: JvSwingUtils.wrapTooltip(true, toolTipText)));
return toolTipText;
- }
+ }
};
public GStructureChooser()
{
}
+
protected void initDialog()
{
e.printStackTrace();
}
}
-
+
// BH SwingJS optimization
// (a) 100-ms interruptable timer for text entry -- BH 1/10/2019
// (b) two-character minimum, at least for JavaScript.
-
- private Timer timer;
-
- protected void txt_search_ActionPerformedDelayed() {
- if (timer != null) {
- timer.stop();
- }
- timer = new Timer(300, new ActionListener() {
-
- @Override
- public void actionPerformed(ActionEvent e) {
- txt_search_ActionPerformed();
- }
- });
- timer.setRepeats(false);
- timer.start();
+
+ private Timer timer;
+
+ protected void txt_search_ActionPerformedDelayed()
+ {
+ if (timer != null)
+ {
+ timer.stop();
+ }
+ timer = new Timer(300, new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ txt_search_ActionPerformed();
+ }
+ });
+ timer.setRepeats(false);
+ timer.start();
}
//
-
+
/**
* Initializes the GUI default properties
*
super.mousePressed(e);
}
}
+
@Override
public void mouseClicked(MouseEvent e)
{
{
if (!popupAction(e))
{
- validateSelections();
+ validateSelections();
}
}
+
boolean popupAction(MouseEvent e)
{
- if (e.isPopupTrigger())
- {
- Point pt = e.getPoint();
- int selectedRow = tbl_summary.rowAtPoint(pt);
- if (showPopupFor(selectedRow,pt.x,pt.y))
- {
- return true;
- }
- }
- return false;
+ if (e.isPopupTrigger())
+ {
+ Point pt = e.getPoint();
+ int selectedRow = tbl_summary.rowAtPoint(pt);
+ if (showPopupFor(selectedRow, pt.x, pt.y))
+ {
+ return true;
+ }
+ }
+ return false;
}
});
tbl_summary.addKeyListener(new KeyAdapter()
}
}
});
-
- // TODO: JAL-3898 - get list of available external programs to view structures with
+
+ // TODO: JAL-3898 - get list of available external programs to view
+ // structures with
btn_add = new JButton(MessageManager.getString("action.add"));
btn_add.setFont(VERDANA_12);
chk_invertFilter.addItemListener(this);
btn_queryTDB.setFont(VERDANA_12);
- //btn_queryTDB.setPreferredSize(new Dimension(200,22));
- btn_queryTDB.setText(MessageManager.getString("label.search_3dbeacons"));
- btn_queryTDB.setToolTipText(MessageManager.getString("label.find_models_from_3dbeacons"));
+ // btn_queryTDB.setPreferredSize(new Dimension(200,22));
+ btn_queryTDB
+ .setText(MessageManager.getString("label.search_3dbeacons"));
+ btn_queryTDB.setToolTipText(
+ MessageManager.getString("label.find_models_from_3dbeacons"));
btn_queryTDB.setIcon(tdbImage);
btn_queryTDB.setVisible(false);
JPanel pnl_main = new JPanel(new BorderLayout());
JPanel pnl_controls = new JPanel();
- pnl_main.add(btn_queryTDB,BorderLayout.NORTH);
+ pnl_main.add(btn_queryTDB, BorderLayout.NORTH);
pnl_controls.add(cmb_filterOption);
pnl_controls.add(lbl_loading);
pnl_controls.add(chk_invertFilter);
- pnl_main.add(pnl_controls,BorderLayout.CENTER);
+ pnl_main.add(pnl_controls, BorderLayout.CENTER);
lbl_loading.setVisible(false);
JPanel pnl_fileChooser = new JPanel(new FlowLayout());
Desktop.addInternalFrame(mainFrame, frameTitle, width, height);
}
+ protected abstract boolean showPopupFor(int selectedRow, int x, int y);
-protected abstract boolean showPopupFor(int selectedRow, int x, int y);
-protected void closeAction(int preferredHeight)
+ protected void closeAction(int preferredHeight)
{
// System.out.println(">>>>>>>>>> closing internal frame!!!");
// System.out.println("width : " + mainFrame.getWidth());
cancel.addActionListener(new java.awt.event.ActionListener()
{
@Override
- public void actionPerformed(ActionEvent e)
+ public void actionPerformed(ActionEvent e)
{
cancel_actionPerformed(e);
}
{
Objects.requireNonNull(jsonString,
"Supplied jsonString must not be null");
- Map<String, Object> JsonObj = (Map<String, Object>) JSONUtils.parse(jsonString);
+ Map<String, Object> JsonObj = (Map<String, Object>) JSONUtils
+ .parse(jsonString);
this.description = (String) JsonObj.get("description");
this.latestReleaseVersion = (String) JsonObj
.get("latestReleaseVersion");
- List<Object> repositoriesJsonArray = (List<Object>) JsonObj.get("releases");
+ List<Object> repositoriesJsonArray = (List<Object>) JsonObj
+ .get("releases");
for (Iterator<Object> repoIter = repositoriesJsonArray
.iterator(); repoIter.hasNext();)
{
void multiply(double d);
/**
- * Answers true if the two matrices have the same dimensions, and corresponding values all differ by no
- * more than delta (which should be a positive value), else false
+ * Answers true if the two matrices have the same dimensions, and
+ * corresponding values all differ by no more than delta (which should be a
+ * positive value), else false
*
* @param m2
* @param delta
{
System.err.println("error writing date: " + e.toString());
}
- object.setVersion(
- Cache.getDefault("VERSION", "Development Build"));
+ object.setVersion(Cache.getDefault("VERSION", "Development Build"));
/**
* rjal is full height alignment, jal is actual alignment with full metadata
.getHiddenColumns();
if (hidden == null)
{
- Console.warn("REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this.");
+ Console.warn(
+ "REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this.");
}
else
{
}
else
{
- Console.warn("Cannot resolve a service for the parameters used in this project. Try configuring a JABAWS server.");
+ Console.warn(
+ "Cannot resolve a service for the parameters used in this project. Try configuring a JABAWS server.");
return false;
}
}
return id.toString();
}
// give up and warn that something has gone wrong
- Console.warn("Cannot find ID for object in external mapping : " + jvobj);
+ Console.warn(
+ "Cannot find ID for object in external mapping : " + jvobj);
}
return altCode;
}
}
else
{
- Console.warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
+ Console.warn(
+ "Couldn't find entry in Jalview Jar for " + jarEntryName);
}
} catch (Exception ex)
{
tp.getTreeCanvas().setApplyToAllViews(tree.isLinkToAllViews());
if (tp == null)
{
- Console.warn("There was a problem recovering stored Newick tree: \n"
- + tree.getNewick());
+ Console.warn(
+ "There was a problem recovering stored Newick tree: \n"
+ + tree.getNewick());
continue;
}
{
if (ds != null && ds != seqSetDS)
{
- Console.warn("JAL-3171 regression: Overwriting a dataset reference for an alignment"
- + " - CDS/Protein crossreference data may be lost");
+ Console.warn(
+ "JAL-3171 regression: Overwriting a dataset reference for an alignment"
+ + " - CDS/Protein crossreference data may be lost");
if (xtant_ds != null)
{
// This can only happen if the unique sequence set ID was bound to a
// dataset that did not contain any of the sequences in the view
// currently being restored.
- Console.warn("JAL-3171 SERIOUS! TOTAL CONFUSION - please consider contacting the Jalview Development team so they can investigate why your project caused this message to be displayed.");
+ Console.warn(
+ "JAL-3171 SERIOUS! TOTAL CONFUSION - please consider contacting the Jalview Development team so they can investigate why your project caused this message to be displayed.");
}
}
ds = seqSetDS;
{
if (dataset.getDataset() != null)
{
- Console.warn("Serious issue! Dataset Object passed to getDatasetIdRef is not a Jalview DATASET alignment...");
+ Console.warn(
+ "Serious issue! Dataset Object passed to getDatasetIdRef is not a Jalview DATASET alignment...");
}
String datasetId = makeHashCode(dataset, null);
if (datasetId == null)
}
else
{
- Console.warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
+ Console.warn(
+ "Couldn't find entry in Jalview Jar for " + jarEntryName);
}
} catch (Exception ex)
{
boolean validRes = false;
boolean validEnd = false;
boolean labelAllCols = false;
-// boolean centreColLabels;
-// boolean centreColLabelsDef = av.isCentreColumnLabels();
+ // boolean centreColLabels;
+ // boolean centreColLabelsDef = av.isCentreColumnLabels();
boolean scaleColLabel = false;
final AlignmentAnnotation consensusAnnot = av
.getAlignmentConsensusAnnotation();
{
continue;
}
-// centreColLabels = row.centreColLabels || centreColLabelsDef;
+ // centreColLabels = row.centreColLabels || centreColLabelsDef;
labelAllCols = row.showAllColLabels;
scaleColLabel = row.scaleColLabel;
lastSS = ' ';
private OverviewResColourFinder resColFinder;
public OverviewRenderer(FeatureRenderer fr, OverviewDimensions od,
- AlignmentI alignment,
- ResidueShaderI resshader, OverviewResColourFinder colFinder)
+ AlignmentI alignment, ResidueShaderI resshader,
+ OverviewResColourFinder colFinder)
{
finder = new FeatureColourFinder(fr);
resColFinder = colFinder;
{
break;
}
-
+
// get details of this alignment row
SequenceI seq = rows.getSequence(alignmentRow);
// calculate where this row extends to in pixels
int endRow = Math.min(Math.round((seqIndex + 1) * pixelsPerSeq) - 1,
miniMe.getHeight() - 1);
-
+
int colIndex = 0;
int pixelCol = 0;
for (int alignmentCol : cols)
{
break;
}
-
+
// calculate where this column extends to in pixels
int endCol = Math.min(Math.round((colIndex + 1) * pixelsPerCol) - 1,
miniMe.getWidth() - 1);
-
+
// don't do expensive colour determination if we're not going to use it
// NB this is important to avoid performance issues in the overview
// panel
{
rgbcolor = getColumnColourFromSequence(allGroups, seq,
alignmentCol);
-
+
// fill in the appropriate number of pixels
for (int row = pixelRow; row <= endRow; ++row)
{
* column position to get colour for
* @return colour of sequence at this position, as RGB
*/
- int getColumnColourFromSequence(SequenceGroup[] allGroups,
- SequenceI seq, int lastcol)
+ int getColumnColourFromSequence(SequenceGroup[] allGroups, SequenceI seq,
+ int lastcol)
{
Color color = resColFinder.GAP_COLOUR;
*/
@Override
protected Color getResidueBoxColour(boolean showBoxes,
- ResidueShaderI shader,
- SequenceGroup[] allGroups, SequenceI seq, int i)
+ ResidueShaderI shader, SequenceGroup[] allGroups, SequenceI seq,
+ int i)
{
ResidueShaderI currentShader;
SequenceGroup currentSequenceGroup = getCurrentSequenceGroup(allGroups,
* @return colour of the residue
*/
public Color getResidueColour(boolean showBoxes, ResidueShaderI shader,
- SequenceGroup[] allGroups,
- final SequenceI seq, int position, FeatureColourFinder finder)
+ SequenceGroup[] allGroups, final SequenceI seq, int position,
+ FeatureColourFinder finder)
{
Color col = getResidueBoxColour(showBoxes, shader, allGroups, seq,
position);
* @return
*/
protected Color getResidueBoxColour(boolean showBoxes,
- ResidueShaderI shader,
- SequenceGroup[] allGroups,
- SequenceI seq, int i)
+ ResidueShaderI shader, SequenceGroup[] allGroups, SequenceI seq,
+ int i)
{
SequenceGroup currentSequenceGroup = getCurrentSequenceGroup(allGroups,
i);
{
return getBoxColour(shader, seq, i);
}
-
+
return Color.white;
}
}
int featureStartCol = seq.findIndex(visibleStart);
- int featureEndCol = sf.begin == sf.end ? featureStartCol : seq
- .findIndex(visibleEnd);
+ int featureEndCol = sf.begin == sf.end ? featureStartCol
+ : seq.findIndex(visibleEnd);
// Color featureColour = getColour(sequenceFeature);
else
{
*/
- boolean drawn = renderFeature(g, seq,
- featureStartCol - 1,
- featureEndCol - 1, featureColour,
- start, end, y1, colourOnly);
- if (drawn)
- {
- drawnColour = featureColour;
- }
+ boolean drawn = renderFeature(g, seq, featureStartCol - 1,
+ featureEndCol - 1, featureColour, start, end, y1,
+ colourOnly);
+ if (drawn)
+ {
+ drawnColour = featureColour;
+ }
/*}*/
}
}
for (int pos = visibleStart; pos <= visibleEnd; pos++)
{
int column = seq.findIndex(pos);
- MappedFeatures mf = fr2
- .findComplementFeaturesAtResidue(seq, pos);
+ MappedFeatures mf = fr2.findComplementFeaturesAtResidue(seq, pos);
if (mf != null)
{
for (SequenceFeature sf : mf.features)
AlignViewportI complement = av.getCodingComplement();
AlignFrame af = Desktop.getAlignFrameFor(complement);
FeatureRendererModel fr2 = af.getFeatureRenderer();
- MappedFeatures mf = fr2.findComplementFeaturesAtResidue(
- seq, seq.findPosition(column - 1));
+ MappedFeatures mf = fr2.findComplementFeaturesAtResidue(seq,
+ seq.findPosition(column - 1));
if (mf == null)
{
return null;
{
range = ann.graphMax == ann.threshold.value ? 1f
: (value - ann.threshold.value)
- / (ann.graphMax - ann.threshold.value);
+ / (ann.graphMax - ann.threshold.value);
}
else if (thresholdIsMinMax && ann.threshold != null
&& aboveAnnotationThreshold == BELOW_THRESHOLD
* @return
*/
public static ColourSchemeI getColourScheme(AlignViewportI view,
- AnnotatedCollectionI forData,
- String name)
+ AnnotatedCollectionI forData, String name)
{
if (ResidueColourScheme.NONE.equalsIgnoreCase(name))
{
* create a new instance of it
*/
ColourSchemeI scheme = ColourSchemes.getInstance().getColourScheme(name,
- view,
- forData, null);
+ view, forData, null);
if (scheme != null)
{
return scheme;
* represent
* @return
*/
- public ColourSchemeI getColourScheme(String name,
- AlignViewportI viewport, AnnotatedCollectionI forData,
+ public ColourSchemeI getColourScheme(String name, AlignViewportI viewport,
+ AnnotatedCollectionI forData,
Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
{
if (name == null)
return null;
}
ColourSchemeI cs = schemes.get(name.toLowerCase(Locale.ROOT));
- return cs == null ? null
- : cs.getInstance(viewport, forData);
+ return cs == null ? null : cs.getInstance(viewport, forData);
}
/**
* <li>the range may be the full value range, or may be limited by the threshold
* value</li>
* </ul>
- * <li>colour by (text) value of a named attribute</li> <li>graduated colour by
- * (numeric) value of a named attribute</li> </ul>
+ * <li>colour by (text) value of a named attribute</li>
+ * <li>graduated colour by (numeric) value of a named attribute</li>
+ * </ul>
*/
public class FeatureColour implements FeatureColourI
{
{
String label = attributeName == null ? feature.getDescription()
: feature.getValueAsString(attributeName);
- return label == null ? noColour : ColorUtils
- .createColourFromName(label);
+ return label == null ? noColour
+ : ColorUtils.createColourFromName(label);
}
if (!isGraduatedColour())
sb.append(BAR).append(Format.getHexString(getMinColour()))
.append(BAR);
sb.append(Format.getHexString(getMaxColour())).append(BAR);
-
+
/*
* 'no value' colour should be null, min or max colour;
* if none of these, coerce to minColour
{
}
+
public IdColourScheme(AlignViewportI view, AnnotatedCollectionI coll)
{
this.view = view;
}
-
@Override
public String getSchemeName()
{
public static String STOP = "STOP";
- public static List<String> STOP_CODONS = Arrays.asList("TGA", "TAA", "TAG");
+ public static List<String> STOP_CODONS = Arrays.asList("TGA", "TAA",
+ "TAG");
public static String START = "ATG";
}
/**
- * Parses a ChimeraX atomspec to construct an AtomSpec model (with
- * null pdb file name)
+ * Parses a ChimeraX atomspec to construct an AtomSpec model (with null pdb
+ * file name)
*
* <pre>
* ChimeraX format:
@Override
public String toString()
{
- if (!hasParameters())
+ if (!hasParameters())
{
return command;
}
}
/**
- * Helper method to add one contiguous range to the AtomSpec model for the given
- * value (creating the model if necessary). As used by Jalview, {@code value} is
+ * Helper method to add one contiguous range to the AtomSpec model for the
+ * given value (creating the model if necessary). As used by Jalview,
+ * {@code value} is
* <ul>
* <li>a colour, when building a 'colour structure by sequence' command</li>
* <li>a feature value, when building a 'set Chimera attributes from features'
atomSpec = new AtomSpecModel();
map.put(value, atomSpec);
}
-
+
atomSpec.addRange(model, startPos, endPos, chain);
}
*
* @param refAtoms
* @param atomSpec
- * @param backbone - superpose based on which kind of atomType
+ * @param backbone
+ * - superpose based on which kind of atomType
* @return
*/
List<StructureCommandI> superposeStructures(AtomSpecModel refAtoms,
*/
StructureCommandI saveSession(String filepath);
- enum AtomSpecType { RESIDUE_ONLY, ALPHA, PHOSPHATE };
+ enum AtomSpecType
+ {
+ RESIDUE_ONLY, ALPHA, PHOSPHATE
+ };
+
/**
* Returns a representation of the atom set represented by the model, in
* viewer syntax format. If {@code alphaOnly} is true, this is restricted to
* @return null or the structure data parsed as a pdb file
*/
synchronized public StructureFile setMapping(SequenceI[] sequence,
- String[] targetChains, String pdbFile, DataSourceType protocol,
+ String[] targetChains, String pdbFile, DataSourceType protocol,
IProgressIndicator progress)
{
return computeMapping(true, sequence, targetChains, pdbFile, protocol,
* mapping operation
* @return null or the structure data parsed as a pdb file
*/
- synchronized public StructureFile computeMapping(
- boolean forStructureView, SequenceI[] sequenceArray,
- String[] targetChainIds, String pdbFile, DataSourceType sourceType,
+ synchronized public StructureFile computeMapping(boolean forStructureView,
+ SequenceI[] sequenceArray, String[] targetChainIds,
+ String pdbFile, DataSourceType sourceType,
IProgressIndicator progress)
{
long progressSessionId = System.currentTimeMillis() * 3;
registerPDBFile(pdb.getId().trim(), pdbFile);
}
// if PDBId is unavailable then skip SIFTS mapping execution path
- // TODO: JAL-3868 need to know if structure is actually from
- // PDB (has valid PDB ID and has provenance suggesting it
+ // TODO: JAL-3868 need to know if structure is actually from
+ // PDB (has valid PDB ID and has provenance suggesting it
// actually came from PDB)
boolean isProtein = false;
- for (SequenceI s:sequenceArray) {
- if (s.isProtein()) {
+ for (SequenceI s : sequenceArray)
+ {
+ if (s.isProtein())
+ {
isProtein = true;
break;
}
}
- isMapUsingSIFTs = isMapUsingSIFTs && pdb.isPPDBIdAvailable() && !pdb.getId().startsWith("AF-") && isProtein;
+ isMapUsingSIFTs = isMapUsingSIFTs && pdb.isPPDBIdAvailable()
+ && !pdb.getId().startsWith("AF-") && isProtein;
} catch (Exception ex)
{
List<StructureMapping> seqToStrucMapping = new ArrayList<>();
if (isMapUsingSIFTs && seq.isProtein())
{
- if (progress!=null) {
- progress.setProgressBar(MessageManager
- .getString("status.obtaining_mapping_with_sifts"),
+ if (progress != null)
+ {
+ progress.setProgressBar(
+ MessageManager
+ .getString("status.obtaining_mapping_with_sifts"),
progressSessionId);
}
jalview.datamodel.Mapping sqmpping = maxAlignseq
pdb, maxChain, sqmpping, maxAlignseq, siftsClient);
seqToStrucMapping.add(siftsMapping);
maxChain.makeExactMapping(siftsMapping, seq);
- maxChain.transferRESNUMFeatures(seq, "IEA: SIFTS",pdb.getId().toLowerCase(Locale.ROOT));
+ maxChain.transferRESNUMFeatures(seq, "IEA: SIFTS",
+ pdb.getId().toLowerCase(Locale.ROOT));
maxChain.transferResidueAnnotation(siftsMapping, null);
ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
targetChainId, maxChain, pdb, maxAlignseq);
seqToStrucMapping.add(nwMapping);
maxChain.makeExactMapping(maxAlignseq, seq);
- maxChain.transferRESNUMFeatures(seq, "IEA:Jalview",pdb.getId().toLowerCase(Locale.ROOT)); // FIXME: is
- // this
- // "IEA:Jalview" ?
+ maxChain.transferRESNUMFeatures(seq, "IEA:Jalview",
+ pdb.getId().toLowerCase(Locale.ROOT)); // FIXME: is
+ // this
+ // "IEA:Jalview" ?
maxChain.transferResidueAnnotation(nwMapping, sqmpping);
ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
}
StructureMapping siftsMapping = null;
try
{
- siftsMapping = getStructureMapping(seq,
- pdbFile, chain.id, pdb, chain, sqmpping, maxAlignseq,
- siftsClient);
+ siftsMapping = getStructureMapping(seq, pdbFile, chain.id,
+ pdb, chain, sqmpping, maxAlignseq, siftsClient);
foundSiftsMappings.add(siftsMapping);
chain.makeExactMapping(siftsMapping, seq);
- chain.transferRESNUMFeatures(seq, "IEA: SIFTS",pdb.getId().toLowerCase(Locale.ROOT));// FIXME: is this
+ chain.transferRESNUMFeatures(seq, "IEA: SIFTS",
+ pdb.getId().toLowerCase(Locale.ROOT));// FIXME: is this
// "IEA:SIFTS" ?
chain.transferResidueAnnotation(siftsMapping, null);
} catch (SiftsException e)
{
System.err.println(e.getMessage());
- }
- catch (Exception e)
+ } catch (Exception e)
{
- System.err
- .println(
- "Unexpected exception during SIFTS mapping - falling back to NW for this sequence/structure pair");
+ System.err.println(
+ "Unexpected exception during SIFTS mapping - falling back to NW for this sequence/structure pair");
System.err.println(e.getMessage());
}
}
StructureMapping nwMapping = getNWMappings(seq, pdbFile,
maxChainId, maxChain, pdb, maxAlignseq);
seqToStrucMapping.add(nwMapping);
- maxChain.transferRESNUMFeatures(seq, null,pdb.getId().toLowerCase(Locale.ROOT)); // FIXME: is this
- // "IEA:Jalview" ?
+ maxChain.transferRESNUMFeatures(seq, null,
+ pdb.getId().toLowerCase(Locale.ROOT)); // FIXME: is this
+ // "IEA:Jalview" ?
maxChain.transferResidueAnnotation(nwMapping, sqmpping);
ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
}
{
if (progress != null)
{
- progress.setProgressBar(MessageManager
- .getString("status.obtaining_mapping_with_nw_alignment"),
+ progress.setProgressBar(
+ MessageManager.getString(
+ "status.obtaining_mapping_with_nw_alignment"),
progressSessionId);
}
StructureMapping nwMapping = getNWMappings(seq, pdbFile, maxChainId,
private StructureMapping getStructureMapping(SequenceI seq,
String pdbFile, String targetChainId, StructureFile pdb,
PDBChain maxChain, jalview.datamodel.Mapping sqmpping,
- AlignSeq maxAlignseq, SiftsClient siftsClient) throws SiftsException
+ AlignSeq maxAlignseq, SiftsClient siftsClient)
+ throws SiftsException
{
StructureMapping curChainMapping = siftsClient
.getSiftsStructureMapping(seq, pdbFile, targetChainId);
maxChain.makeExactMapping(maxAlignseq, seq);
jalview.datamodel.Mapping sqmpping = maxAlignseq
.getMappingFromS1(false);
- maxChain.transferRESNUMFeatures(seq, null, pdb.getId().toLowerCase(Locale.ROOT));
+ maxChain.transferRESNUMFeatures(seq, null,
+ pdb.getId().toLowerCase(Locale.ROOT));
HashMap<Integer, int[]> mapping = new HashMap<>();
int resNum = -10000;
/**
*
- * A base class to hold common function for 3D structure model binding.
- * Initial version created by refactoring JMol and Chimera binding models, but
- * other structure viewers could in principle be accommodated in future.
+ * A base class to hold common function for 3D structure model binding. Initial
+ * version created by refactoring JMol and Chimera binding models, but other
+ * structure viewers could in principle be accommodated in future.
*
* @author gmcarstairs
*
}
}
}
-
@Override
public abstract void highlightAtoms(List<AtomSpec> atoms);
*/
// todo better way to ensure synchronous than setting getReply true!!
executeCommands(commandGenerator.showBackbone(), true, null);
-
- AtomSpecType backbone = structures[refStructure].isRna ? AtomSpecType.PHOSPHATE : AtomSpecType.ALPHA;
+
+ AtomSpecType backbone = structures[refStructure].isRna
+ ? AtomSpecType.PHOSPHATE
+ : AtomSpecType.ALPHA;
/*
* superpose each (other) structure to the reference in turn
*/
for (String reply : replies)
{
// return this error (Chimera only) to the user
- if (reply.toLowerCase(Locale.ROOT).contains("unequal numbers of atoms"))
+ if (reply.toLowerCase(Locale.ROOT)
+ .contains("unequal numbers of atoms"))
{
error += "; " + reply;
}
* @return hashmap of identifiers.org data, keyed by MIRIAM id
*/
@SuppressWarnings("unchecked")
-private HashMap<String, UrlLink> readIdentifiers(String idFileName)
+ private HashMap<String, UrlLink> readIdentifiers(String idFileName)
{
// identifiers.org data
HashMap<String, UrlLink> idData = new HashMap<>();
String errorMessage = null;
try
{
- // NOTE: THIS WILL FAIL IN SWINGJS BECAUSE IT INVOLVES A FILE READER
-
+ // NOTE: THIS WILL FAIL IN SWINGJS BECAUSE IT INVOLVES A FILE READER
+
FileReader reader = new FileReader(idFileName);
String key = "";
- Map<String, Object> obj = (Map<String, Object>) JSONUtils.parse(reader);
+ Map<String, Object> obj = (Map<String, Object>) JSONUtils
+ .parse(reader);
if (obj.containsKey(ID_ORG_KEY))
{
key = ID_ORG_KEY;
} catch (IOException | ParseException e)
{
// unnecessary e.printStackTrace();
- // Note how in JavaScript we can grab the first bytes from any file reader.
+ // Note how in JavaScript we can grab the first bytes from any file
+ // reader.
// Typical report here is "NetworkError" because the file does not exist.
- // "https://." is coming from System.getProperty("user.home"), but this could
+ // "https://." is coming from System.getProperty("user.home"), but this
+ // could
// be set by the page developer to anything, of course.
errorMessage = e.toString();
idData.clear();
// BH 2018 -- added more valuable report
if (errorMessage != null)
{
- System.err.println("IdentifiersUrlProvider: cannot read " + idFileName + ": " + errorMessage);
+ System.err.println("IdentifiersUrlProvider: cannot read " + idFileName
+ + ": " + errorMessage);
}
return idData;
}
public class ColorUtils
{
private static final int MAX_CACHE_SIZE = 1729;
+
/*
* a cache for colours generated from text strings
*/
*/
public static final boolean isNucleotide(SequenceI seq)
{
- if (seq==null)
+ if (seq == null)
{
return false;
}
* Check for nucleotide count > 85% of total count (in a form that evades
* int / float conversion or divide by zero).
*/
- if ((ntCount+nCount) * 100 > EIGHTY_FIVE * (ntCount + aaCount))
+ if ((ntCount + nCount) * 100 > EIGHTY_FIVE * (ntCount + aaCount))
{
- return ntCount>0; // all N is considered protein. Could use a threshold here too
+ return ntCount > 0; // all N is considered protein. Could use a threshold
+ // here too
}
else
{
*/
private static Map<String, String> canonicalSourceNameLookup = new HashMap<>();
- public final static int DB_SOURCE = 1;
- public final static int DB_VERSION = 2;
- public final static int DB_ID = 4;
- public final static int DB_MAP = 8;
-
- public final static int SEARCH_MODE_NO_MAP_NO_VERSION = DB_SOURCE | DB_ID;
- public final static int SEARCH_MODE_FULL = DB_SOURCE | DB_VERSION | DB_ID | DB_MAP;
-
- static
- {
- // TODO load these from a resource file?
- canonicalSourceNameLookup.put("uniprotkb/swiss-prot", DBRefSource.UNIPROT);
- canonicalSourceNameLookup.put("uniprotkb/trembl", DBRefSource.UNIPROT);
-
- // Ensembl values for dbname in xref REST service:
- canonicalSourceNameLookup.put("uniprot/sptrembl", DBRefSource.UNIPROT);
- canonicalSourceNameLookup.put("uniprot/swissprot", DBRefSource.UNIPROT);
-
- canonicalSourceNameLookup.put("pdb", DBRefSource.PDB);
- canonicalSourceNameLookup.put("ensembl", DBRefSource.ENSEMBL);
- // Ensembl Gn and Tr are for Ensembl genomic and transcript IDs as served
- // from ENA.
- canonicalSourceNameLookup.put("ensembl-tr", DBRefSource.ENSEMBL);
- canonicalSourceNameLookup.put("ensembl-gn", DBRefSource.ENSEMBL);
-
- // guarantee we always have lowercase entries for canonical string lookups
- for (String k : canonicalSourceNameLookup.keySet())
- {
- canonicalSourceNameLookup.put(k.toLowerCase(Locale.ROOT),
- canonicalSourceNameLookup.get(k));
- }
- }
+ public final static int DB_SOURCE = 1;
+
+ public final static int DB_VERSION = 2;
+
+ public final static int DB_ID = 4;
+
+ public final static int DB_MAP = 8;
+
+ public final static int SEARCH_MODE_NO_MAP_NO_VERSION = DB_SOURCE | DB_ID;
+
+ public final static int SEARCH_MODE_FULL = DB_SOURCE | DB_VERSION | DB_ID
+ | DB_MAP;
+
+ static
+ {
+ // TODO load these from a resource file?
+ canonicalSourceNameLookup.put("uniprotkb/swiss-prot",
+ DBRefSource.UNIPROT);
+ canonicalSourceNameLookup.put("uniprotkb/trembl", DBRefSource.UNIPROT);
+
+ // Ensembl values for dbname in xref REST service:
+ canonicalSourceNameLookup.put("uniprot/sptrembl", DBRefSource.UNIPROT);
+ canonicalSourceNameLookup.put("uniprot/swissprot", DBRefSource.UNIPROT);
+
+ canonicalSourceNameLookup.put("pdb", DBRefSource.PDB);
+ canonicalSourceNameLookup.put("ensembl", DBRefSource.ENSEMBL);
+ // Ensembl Gn and Tr are for Ensembl genomic and transcript IDs as served
+ // from ENA.
+ canonicalSourceNameLookup.put("ensembl-tr", DBRefSource.ENSEMBL);
+ canonicalSourceNameLookup.put("ensembl-gn", DBRefSource.ENSEMBL);
+
+ // guarantee we always have lowercase entries for canonical string lookups
+ for (String k : canonicalSourceNameLookup.keySet())
+ {
+ canonicalSourceNameLookup.put(k.toLowerCase(Locale.ROOT),
+ canonicalSourceNameLookup.get(k));
+ }
+ }
/**
* Returns those DBRefEntry objects whose source identifier (once converted to
* Jalview's canonical form) is in the list of sources to search for. Returns
* null if no matches found.
*
- * @param dbrefs DBRefEntry objects to search
- * @param sources array of sources to select
+ * @param dbrefs
+ * DBRefEntry objects to search
+ * @param sources
+ * array of sources to select
* @return
*/
- public static List<DBRefEntry> selectRefs(List<DBRefEntry> dbrefs, String[] sources)
+ public static List<DBRefEntry> selectRefs(List<DBRefEntry> dbrefs,
+ String[] sources)
{
- if (dbrefs == null || sources == null)
- {
- return dbrefs;
- }
-
- // BH TODO (what?)
- HashSet<String> srcs = new HashSet<String>();
- for (String src : sources)
- {
- srcs.add(src.toUpperCase(Locale.ROOT));
- }
-
- int nrefs = dbrefs.size();
- List<DBRefEntry> res = new ArrayList<DBRefEntry>();
- for (int ib = 0; ib < nrefs; ib++)
- {
- DBRefEntry dbr = dbrefs.get(ib);
- String source = getCanonicalName(dbr.getSource());
- if (srcs.contains(source.toUpperCase(Locale.ROOT)))
- {
- res.add(dbr);
- }
- }
- if (res.size() > 0)
- {
- // List<DBRefEntry> reply = new DBRefEntry[res.size()];
- return res;// .toArray(reply);
- }
- return null;
+ if (dbrefs == null || sources == null)
+ {
+ return dbrefs;
+ }
+
+ // BH TODO (what?)
+ HashSet<String> srcs = new HashSet<String>();
+ for (String src : sources)
+ {
+ srcs.add(src.toUpperCase(Locale.ROOT));
+ }
+
+ int nrefs = dbrefs.size();
+ List<DBRefEntry> res = new ArrayList<DBRefEntry>();
+ for (int ib = 0; ib < nrefs; ib++)
+ {
+ DBRefEntry dbr = dbrefs.get(ib);
+ String source = getCanonicalName(dbr.getSource());
+ if (srcs.contains(source.toUpperCase(Locale.ROOT)))
+ {
+ res.add(dbr);
+ }
+ }
+ if (res.size() > 0)
+ {
+ // List<DBRefEntry> reply = new DBRefEntry[res.size()];
+ return res;// .toArray(reply);
+ }
+ return null;
}
- private static boolean selectRefsBS(List<DBRefEntry> dbrefs, int sourceKeys, BitSet bsSelect)
+ private static boolean selectRefsBS(List<DBRefEntry> dbrefs,
+ int sourceKeys, BitSet bsSelect)
{
- if (dbrefs == null || sourceKeys == 0)
- {
- return false;
- }
- for (int i = 0, n = dbrefs.size(); i < n; i++)
- {
- DBRefEntry dbr = dbrefs.get(i);
- if ((dbr.getSourceKey() & sourceKeys) != 0)
- {
- bsSelect.clear(i);
- }
- }
- return !bsSelect.isEmpty();
+ if (dbrefs == null || sourceKeys == 0)
+ {
+ return false;
+ }
+ for (int i = 0, n = dbrefs.size(); i < n; i++)
+ {
+ DBRefEntry dbr = dbrefs.get(i);
+ if ((dbr.getSourceKey() & sourceKeys) != 0)
+ {
+ bsSelect.clear(i);
+ }
+ }
+ return !bsSelect.isEmpty();
}
/**
return rfs;
}
- /**
- * look up source in an internal list of database reference sources and return
- * the canonical jalview name for the source, or the original string if it has
- * no canonical form.
- *
- * @param source
- * @return canonical jalview source (one of jalview.datamodel.DBRefSource.*) or
- * original source
- */
- public static String getCanonicalName(String source)
- {
- if (source == null)
- {
- return null;
- }
- String canonical = canonicalSourceNameLookup.get(source.toLowerCase(Locale.ROOT));
- return canonical == null ? source : canonical;
- }
-
- /**
- * Returns a (possibly empty) list of those references that match the given
- * entry. Currently uses a comparator which matches if
- * <ul>
- * <li>database sources are the same</li>
- * <li>accession ids are the same</li>
- * <li>both have no mapping, or the mappings are the same</li>
- * </ul>
- *
- * @param ref Set of references to search
- * @param entry pattern to match
- * @param mode SEARCH_MODE_FULL for all; SEARCH_MODE_NO_MAP_NO_VERSION optional
- * @return
- */
- public static List<DBRefEntry> searchRefs(List<DBRefEntry> ref, DBRefEntry entry, int mode) {
- return searchRefs(ref, entry, matchDbAndIdAndEitherMapOrEquivalentMapList, mode);
- }
-
- /**
- * Returns a list of those references that match the given accession id
- * <ul>
- * <li>database sources are the same</li>
- * <li>accession ids are the same</li>
- * <li>both have no mapping, or the mappings are the same</li>
- * </ul>
- *
- * @param refs Set of references to search
- * @param accId accession id to match
- * @return
- */
- public static List<DBRefEntry> searchRefs(List<DBRefEntry> refs, String accId) {
- List<DBRefEntry> rfs = new ArrayList<DBRefEntry>();
- if (refs == null || accId == null) {
- return rfs;
- }
- for (int i = 0, n = refs.size(); i < n; i++) {
- DBRefEntry e = refs.get(i);
- if (accId.equals(e.getAccessionId())) {
- rfs.add(e);
- }
- }
- return rfs;
-// return searchRefs(refs, new DBRefEntry("", "", accId), matchId, SEARCH_MODE_FULL);
- }
-
- /**
- * Returns a (possibly empty) list of those references that match the given
- * entry, according to the given comparator.
- *
- * @param refs an array of database references to search
- * @param entry an entry to compare against
- * @param comparator
- * @param mode SEARCH_MODE_FULL for all; SEARCH_MODE_NO_MAP_NO_VERSION
- * optional
- * @return
- */
- static List<DBRefEntry> searchRefs(List<DBRefEntry> refs, DBRefEntry entry, DbRefComp comparator, int mode) {
- List<DBRefEntry> rfs = new ArrayList<DBRefEntry>();
- if (refs == null || entry == null) {
- return rfs;
- }
- for (int i = 0, n = refs.size(); i < n; i++) {
- DBRefEntry e = refs.get(i);
- if (comparator.matches(entry, e, SEARCH_MODE_FULL)) {
- rfs.add(e);
- }
- }
- return rfs;
- }
-
- interface DbRefComp {
- default public boolean matches(DBRefEntry refa, DBRefEntry refb) {
- return matches(refa, refb, SEARCH_MODE_FULL);
- };
-
- public boolean matches(DBRefEntry refa, DBRefEntry refb, int mode);
- }
-
- /**
- * match on all non-null fields in refa
- */
- // TODO unused - remove? would be broken by equating "" with null
- public static DbRefComp matchNonNullonA = new DbRefComp() {
- @Override
- public boolean matches(DBRefEntry refa, DBRefEntry refb, int mode) {
- if ((mode & DB_SOURCE) != 0 &&
- (refa.getSource() == null || DBRefUtils.getCanonicalName(refb.getSource())
- .equals(DBRefUtils.getCanonicalName(refa.getSource())))) {
- if ((mode & DB_VERSION) != 0 &&
- (refa.getVersion() == null || refb.getVersion().equals(refa.getVersion()))) {
- if ((mode & DB_ID) != 0 &&
- (refa.getAccessionId() == null || refb.getAccessionId().equals(refa.getAccessionId()))) {
- if ((mode & DB_MAP) != 0 &&
- (refa.getMap() == null || (refb.getMap() != null && refb.getMap().equals(refa.getMap())))) {
- return true;
- }
- }
- }
- }
- return false;
- }
- };
-
- /**
- * either field is null or field matches for all of source, version, accession
- * id and map.
- */
- // TODO unused - remove?
- public static DbRefComp matchEitherNonNull = new DbRefComp() {
- @Override
- public boolean matches(DBRefEntry refa, DBRefEntry refb, int mode) {
- if (nullOrEqualSource(refa.getSource(), refb.getSource())
- && nullOrEqual(refa.getVersion(), refb.getVersion())
- && nullOrEqual(refa.getAccessionId(), refb.getAccessionId())
- && nullOrEqual(refa.getMap(), refb.getMap())) {
- return true;
- }
- return false;
- }
-
- };
+ /**
+ * look up source in an internal list of database reference sources and return
+ * the canonical jalview name for the source, or the original string if it has
+ * no canonical form.
+ *
+ * @param source
+ * @return canonical jalview source (one of jalview.datamodel.DBRefSource.*)
+ * or original source
+ */
+ public static String getCanonicalName(String source)
+ {
+ if (source == null)
+ {
+ return null;
+ }
+ String canonical = canonicalSourceNameLookup
+ .get(source.toLowerCase(Locale.ROOT));
+ return canonical == null ? source : canonical;
+ }
+
+ /**
+ * Returns a (possibly empty) list of those references that match the given
+ * entry. Currently uses a comparator which matches if
+ * <ul>
+ * <li>database sources are the same</li>
+ * <li>accession ids are the same</li>
+ * <li>both have no mapping, or the mappings are the same</li>
+ * </ul>
+ *
+ * @param ref
+ * Set of references to search
+ * @param entry
+ * pattern to match
+ * @param mode
+ * SEARCH_MODE_FULL for all; SEARCH_MODE_NO_MAP_NO_VERSION optional
+ * @return
+ */
+ public static List<DBRefEntry> searchRefs(List<DBRefEntry> ref,
+ DBRefEntry entry, int mode)
+ {
+ return searchRefs(ref, entry,
+ matchDbAndIdAndEitherMapOrEquivalentMapList, mode);
+ }
+
+ /**
+ * Returns a list of those references that match the given accession id
+ * <ul>
+ * <li>database sources are the same</li>
+ * <li>accession ids are the same</li>
+ * <li>both have no mapping, or the mappings are the same</li>
+ * </ul>
+ *
+ * @param refs
+ * Set of references to search
+ * @param accId
+ * accession id to match
+ * @return
+ */
+ public static List<DBRefEntry> searchRefs(List<DBRefEntry> refs,
+ String accId)
+ {
+ List<DBRefEntry> rfs = new ArrayList<DBRefEntry>();
+ if (refs == null || accId == null)
+ {
+ return rfs;
+ }
+ for (int i = 0, n = refs.size(); i < n; i++)
+ {
+ DBRefEntry e = refs.get(i);
+ if (accId.equals(e.getAccessionId()))
+ {
+ rfs.add(e);
+ }
+ }
+ return rfs;
+ // return searchRefs(refs, new DBRefEntry("", "", accId), matchId,
+ // SEARCH_MODE_FULL);
+ }
+
+ /**
+ * Returns a (possibly empty) list of those references that match the given
+ * entry, according to the given comparator.
+ *
+ * @param refs
+ * an array of database references to search
+ * @param entry
+ * an entry to compare against
+ * @param comparator
+ * @param mode
+ * SEARCH_MODE_FULL for all; SEARCH_MODE_NO_MAP_NO_VERSION optional
+ * @return
+ */
+ static List<DBRefEntry> searchRefs(List<DBRefEntry> refs,
+ DBRefEntry entry, DbRefComp comparator, int mode)
+ {
+ List<DBRefEntry> rfs = new ArrayList<DBRefEntry>();
+ if (refs == null || entry == null)
+ {
+ return rfs;
+ }
+ for (int i = 0, n = refs.size(); i < n; i++)
+ {
+ DBRefEntry e = refs.get(i);
+ if (comparator.matches(entry, e, SEARCH_MODE_FULL))
+ {
+ rfs.add(e);
+ }
+ }
+ return rfs;
+ }
+
+ interface DbRefComp
+ {
+ default public boolean matches(DBRefEntry refa, DBRefEntry refb)
+ {
+ return matches(refa, refb, SEARCH_MODE_FULL);
+ };
+
+ public boolean matches(DBRefEntry refa, DBRefEntry refb, int mode);
+ }
+
+ /**
+ * match on all non-null fields in refa
+ */
+ // TODO unused - remove? would be broken by equating "" with null
+ public static DbRefComp matchNonNullonA = new DbRefComp()
+ {
+ @Override
+ public boolean matches(DBRefEntry refa, DBRefEntry refb, int mode)
+ {
+ if ((mode & DB_SOURCE) != 0 && (refa.getSource() == null
+ || DBRefUtils.getCanonicalName(refb.getSource()).equals(
+ DBRefUtils.getCanonicalName(refa.getSource()))))
+ {
+ if ((mode & DB_VERSION) != 0 && (refa.getVersion() == null
+ || refb.getVersion().equals(refa.getVersion())))
+ {
+ if ((mode & DB_ID) != 0 && (refa.getAccessionId() == null
+ || refb.getAccessionId().equals(refa.getAccessionId())))
+ {
+ if ((mode & DB_MAP) != 0
+ && (refa.getMap() == null || (refb.getMap() != null
+ && refb.getMap().equals(refa.getMap()))))
+ {
+ return true;
+ }
+ }
+ }
+ }
+ return false;
+ }
+ };
+
+ /**
+ * either field is null or field matches for all of source, version, accession
+ * id and map.
+ */
+ // TODO unused - remove?
+ public static DbRefComp matchEitherNonNull = new DbRefComp()
+ {
+ @Override
+ public boolean matches(DBRefEntry refa, DBRefEntry refb, int mode)
+ {
+ if (nullOrEqualSource(refa.getSource(), refb.getSource())
+ && nullOrEqual(refa.getVersion(), refb.getVersion())
+ && nullOrEqual(refa.getAccessionId(), refb.getAccessionId())
+ && nullOrEqual(refa.getMap(), refb.getMap()))
+ {
+ return true;
+ }
+ return false;
+ }
+
+ };
/**
* Parses a DBRefEntry and adds it to the sequence, also a PDBEntry if the
return ref;
}
- /**
- * accession ID and DB must be identical. Version is ignored. Map is either not
- * defined or is a match (or is compatible?)
- */
- // TODO unused - remove?
- public static DbRefComp matchDbAndIdAndEitherMap = new DbRefComp() {
- @Override
- public boolean matches(DBRefEntry refa, DBRefEntry refb, int mode) {
- if (refa.getSource() != null && refb.getSource() != null && DBRefUtils.getCanonicalName(refb.getSource())
- .equals(DBRefUtils.getCanonicalName(refa.getSource()))) {
- // We dont care about version
- if (refa.getAccessionId() != null && refb.getAccessionId() != null
- // FIXME should be && not || here?
- || refb.getAccessionId().equals(refa.getAccessionId())) {
- if ((refa.getMap() == null || refb.getMap() == null) || (refa.getMap() != null
- && refb.getMap() != null && refb.getMap().equals(refa.getMap()))) {
- return true;
- }
- }
- }
- return false;
- }
- };
-
- /**
- * accession ID and DB must be identical. Version is ignored. No map on either
- * or map but no maplist on either or maplist of map on a is the complement of
- * maplist of map on b.
- */
- // TODO unused - remove?
- public static DbRefComp matchDbAndIdAndComplementaryMapList = new DbRefComp() {
- @Override
- public boolean matches(DBRefEntry refa, DBRefEntry refb, int mode) {
- if (refa.getSource() != null && refb.getSource() != null && DBRefUtils.getCanonicalName(refb.getSource())
- .equals(DBRefUtils.getCanonicalName(refa.getSource()))) {
- // We dont care about version
- if (refa.getAccessionId() != null && refb.getAccessionId() != null
- || refb.getAccessionId().equals(refa.getAccessionId())) {
- if ((refa.getMap() == null && refb.getMap() == null)
- || (refa.getMap() != null && refb.getMap() != null)) {
- if ((refb.getMap().getMap() == null && refa.getMap().getMap() == null)
- || (refb.getMap().getMap() != null && refa.getMap().getMap() != null
- && refb.getMap().getMap().getInverse().equals(refa.getMap().getMap()))) {
- return true;
- }
- }
- }
- }
- return false;
- }
- };
-
- /**
- * accession ID and DB must be identical. Version is ignored. No map on both or
- * or map but no maplist on either or maplist of map on a is equivalent to the
- * maplist of map on b.
- */
- // TODO unused - remove?
- public static DbRefComp matchDbAndIdAndEquivalentMapList = new DbRefComp() {
- @Override
- public boolean matches(DBRefEntry refa, DBRefEntry refb, int mode) {
- if (refa.getSource() != null && refb.getSource() != null && DBRefUtils.getCanonicalName(refb.getSource())
- .equals(DBRefUtils.getCanonicalName(refa.getSource()))) {
- // We dont care about version
- // if ((refa.getVersion()==null || refb.getVersion()==null)
- // || refb.getVersion().equals(refa.getVersion()))
- // {
- if (refa.getAccessionId() != null && refb.getAccessionId() != null
- || refb.getAccessionId().equals(refa.getAccessionId())) {
- if (refa.getMap() == null && refb.getMap() == null) {
- return true;
- }
- if (refa.getMap() != null && refb.getMap() != null
- && ((refb.getMap().getMap() == null && refa.getMap().getMap() == null)
- || (refb.getMap().getMap() != null && refa.getMap().getMap() != null
- && refb.getMap().getMap().equals(refa.getMap().getMap())))) {
- return true;
- }
- }
- }
- return false;
- }
- };
-
- /**
- * accession ID and DB must be identical, or null on a. Version is ignored. No
- * map on either or map but no maplist on either or maplist of map on a is
- * equivalent to the maplist of map on b.
- */
- public static DbRefComp matchDbAndIdAndEitherMapOrEquivalentMapList = new DbRefComp()
- {
- @Override
- public boolean matches(DBRefEntry refa, DBRefEntry refb, int mode)
- {
- if (refa.getSource() != null && refb.getSource() != null && DBRefUtils.getCanonicalName(refb.getSource())
- .equals(DBRefUtils.getCanonicalName(refa.getSource())))
- {
- // We dont care about version
- if (refa.getAccessionId() == null || refa.getAccessionId().equals(refb.getAccessionId()))
- {
- if (refa.getMap() == null || refb.getMap() == null)
- {
- return true;
- }
- if ((refa.getMap() != null && refb.getMap() != null)
- && (refb.getMap().getMap() == null && refa.getMap().getMap() == null)
- || (refb.getMap().getMap() != null && refa.getMap().getMap() != null
- && (refb.getMap().getMap().equals(refa.getMap().getMap()))))
- {
- return true;
- }
- }
- }
- return false;
- }
- };
-
- /**
+ /**
+ * accession ID and DB must be identical. Version is ignored. Map is either
+ * not defined or is a match (or is compatible?)
+ */
+ // TODO unused - remove?
+ public static DbRefComp matchDbAndIdAndEitherMap = new DbRefComp()
+ {
+ @Override
+ public boolean matches(DBRefEntry refa, DBRefEntry refb, int mode)
+ {
+ if (refa.getSource() != null && refb.getSource() != null
+ && DBRefUtils.getCanonicalName(refb.getSource()).equals(
+ DBRefUtils.getCanonicalName(refa.getSource())))
+ {
+ // We dont care about version
+ if (refa.getAccessionId() != null && refb.getAccessionId() != null
+ // FIXME should be && not || here?
+ || refb.getAccessionId().equals(refa.getAccessionId()))
+ {
+ if ((refa.getMap() == null || refb.getMap() == null)
+ || (refa.getMap() != null && refb.getMap() != null
+ && refb.getMap().equals(refa.getMap())))
+ {
+ return true;
+ }
+ }
+ }
+ return false;
+ }
+ };
+
+ /**
+ * accession ID and DB must be identical. Version is ignored. No map on either
+ * or map but no maplist on either or maplist of map on a is the complement of
+ * maplist of map on b.
+ */
+ // TODO unused - remove?
+ public static DbRefComp matchDbAndIdAndComplementaryMapList = new DbRefComp()
+ {
+ @Override
+ public boolean matches(DBRefEntry refa, DBRefEntry refb, int mode)
+ {
+ if (refa.getSource() != null && refb.getSource() != null
+ && DBRefUtils.getCanonicalName(refb.getSource()).equals(
+ DBRefUtils.getCanonicalName(refa.getSource())))
+ {
+ // We dont care about version
+ if (refa.getAccessionId() != null && refb.getAccessionId() != null
+ || refb.getAccessionId().equals(refa.getAccessionId()))
+ {
+ if ((refa.getMap() == null && refb.getMap() == null)
+ || (refa.getMap() != null && refb.getMap() != null))
+ {
+ if ((refb.getMap().getMap() == null
+ && refa.getMap().getMap() == null)
+ || (refb.getMap().getMap() != null
+ && refa.getMap().getMap() != null
+ && refb.getMap().getMap().getInverse()
+ .equals(refa.getMap().getMap())))
+ {
+ return true;
+ }
+ }
+ }
+ }
+ return false;
+ }
+ };
+
+ /**
+ * accession ID and DB must be identical. Version is ignored. No map on both
+ * or or map but no maplist on either or maplist of map on a is equivalent to
+ * the maplist of map on b.
+ */
+ // TODO unused - remove?
+ public static DbRefComp matchDbAndIdAndEquivalentMapList = new DbRefComp()
+ {
+ @Override
+ public boolean matches(DBRefEntry refa, DBRefEntry refb, int mode)
+ {
+ if (refa.getSource() != null && refb.getSource() != null
+ && DBRefUtils.getCanonicalName(refb.getSource()).equals(
+ DBRefUtils.getCanonicalName(refa.getSource())))
+ {
+ // We dont care about version
+ // if ((refa.getVersion()==null || refb.getVersion()==null)
+ // || refb.getVersion().equals(refa.getVersion()))
+ // {
+ if (refa.getAccessionId() != null && refb.getAccessionId() != null
+ || refb.getAccessionId().equals(refa.getAccessionId()))
+ {
+ if (refa.getMap() == null && refb.getMap() == null)
+ {
+ return true;
+ }
+ if (refa.getMap() != null && refb.getMap() != null
+ && ((refb.getMap().getMap() == null
+ && refa.getMap().getMap() == null)
+ || (refb.getMap().getMap() != null
+ && refa.getMap().getMap() != null
+ && refb.getMap().getMap()
+ .equals(refa.getMap().getMap()))))
+ {
+ return true;
+ }
+ }
+ }
+ return false;
+ }
+ };
+
+ /**
+ * accession ID and DB must be identical, or null on a. Version is ignored. No
+ * map on either or map but no maplist on either or maplist of map on a is
+ * equivalent to the maplist of map on b.
+ */
+ public static DbRefComp matchDbAndIdAndEitherMapOrEquivalentMapList = new DbRefComp()
+ {
+ @Override
+ public boolean matches(DBRefEntry refa, DBRefEntry refb, int mode)
+ {
+ if (refa.getSource() != null && refb.getSource() != null
+ && DBRefUtils.getCanonicalName(refb.getSource()).equals(
+ DBRefUtils.getCanonicalName(refa.getSource())))
+ {
+ // We dont care about version
+ if (refa.getAccessionId() == null
+ || refa.getAccessionId().equals(refb.getAccessionId()))
+ {
+ if (refa.getMap() == null || refb.getMap() == null)
+ {
+ return true;
+ }
+ if ((refa.getMap() != null && refb.getMap() != null)
+ && (refb.getMap().getMap() == null
+ && refa.getMap().getMap() == null)
+ || (refb.getMap().getMap() != null
+ && refa.getMap().getMap() != null
+ && (refb.getMap().getMap()
+ .equals(refa.getMap().getMap()))))
+ {
+ return true;
+ }
+ }
+ }
+ return false;
+ }
+ };
+
+ /**
* Returns the (possibly empty) list of those supplied dbrefs which have the
* specified source database, with a case-insensitive match of source name
*
return matches;
}
- /**
- * Returns true if either object is null, or they are equal
- *
- * @param o1
- * @param o2
- * @return
- */
- public static boolean nullOrEqual(Object o1, Object o2) {
- if (o1 == null || o2 == null) {
- return true;
- }
- return o1.equals(o2);
- }
-
- /**
- * canonicalise source string before comparing. null is always wildcard
- *
- * @param o1 - null or source string to compare
- * @param o2 - null or source string to compare
- * @return true if either o1 or o2 are null, or o1 equals o2 under
- * DBRefUtils.getCanonicalName
- * (o1).equals(DBRefUtils.getCanonicalName(o2))
- */
- public static boolean nullOrEqualSource(String o1, String o2) {
- if (o1 == null || o2 == null) {
- return true;
- }
- return DBRefUtils.getCanonicalName(o1).equals(DBRefUtils.getCanonicalName(o2));
- }
-
- /**
- * Selects just the DNA or protein references from a set of references
- *
- * @param selectDna if true, select references to 'standard' DNA databases, else
- * to 'standard' peptide databases
- * @param refs a set of references to select from
- * @return
- */
- public static List<DBRefEntry> selectDbRefs(boolean selectDna, List<DBRefEntry> refs) {
- return selectRefs(refs, selectDna ? DBRefSource.DNACODINGDBS : DBRefSource.PROTEINDBS);
- // could attempt to find other cross
- // refs here - ie PDB xrefs
- // (not dna, not protein seq)
- }
-
- /**
- * Returns the (possibly empty) list of those supplied dbrefs which have the
- * specified source database, with a case-insensitive match of source name
- *
- * @param dbRefs
- * @param source
- * @return
- */
- public static List<DBRefEntry> searchRefsForSource(List<DBRefEntry> dbRefs, String source) {
- List<DBRefEntry> matches = new ArrayList<DBRefEntry>();
- if (dbRefs != null && source != null) {
- for (DBRefEntry dbref : dbRefs) {
- if (source.equalsIgnoreCase(dbref.getSource())) {
- matches.add(dbref);
- }
- }
- }
- return matches;
- }
-
- /**
- * promote direct database references to primary for nucleotide or protein
- * sequences if they have an appropriate primary ref
- * <table>
- * <tr>
- * <th>Seq Type</th>
- * <th>Primary DB</th>
- * <th>Direct which will be promoted</th>
- * </tr>
- * <tr align=center>
- * <td>peptides</td>
- * <td>Ensembl</td>
- * <td>Uniprot</td>
- * </tr>
- * <tr align=center>
- * <td>peptides</td>
- * <td>Ensembl</td>
- * <td>Uniprot</td>
- * </tr>
- * <tr align=center>
- * <td>dna</td>
- * <td>Ensembl</td>
- * <td>ENA</td>
- * </tr>
- * </table>
- *
- * @param sequence
- */
- public static void ensurePrimaries(SequenceI sequence, List<DBRefEntry> pr) {
- if (pr.size() == 0) {
- // nothing to do
- return;
- }
- int sstart = sequence.getStart();
- int send = sequence.getEnd();
- boolean isProtein = sequence.isProtein();
- BitSet bsSelect = new BitSet();
-
-// List<DBRefEntry> selfs = new ArrayList<DBRefEntry>();
-// {
-
-// List<DBRefEntry> selddfs = selectDbRefs(!isprot, sequence.getDBRefs());
-// if (selfs == null || selfs.size() == 0)
-// {
-// // nothing to do
-// return;
-// }
-
- List<DBRefEntry> dbrefs = sequence.getDBRefs();
- bsSelect.set(0, dbrefs.size());
-
- if (!selectRefsBS(dbrefs, isProtein ? DBRefSource.PROTEIN_MASK : DBRefSource.DNA_CODING_MASK, bsSelect))
- return;
-
-// selfs.addAll(selfArray);
-// }
-
- // filter non-primary refs
- for (int ip = pr.size(); --ip >= 0;) {
- DBRefEntry p = pr.get(ip);
- for (int i = bsSelect.nextSetBit(0); i >= 0; i = bsSelect.nextSetBit(i + 1)) {
- if (dbrefs.get(i) == p)
- bsSelect.clear(i);
- }
-// while (selfs.contains(p))
-// {
-// selfs.remove(p);
-// }
- }
-// List<DBRefEntry> toPromote = new ArrayList<DBRefEntry>();
-
- for (int ip = pr.size(), keys = 0; --ip >= 0 && keys != DBRefSource.PRIMARY_MASK;) {
- DBRefEntry p = pr.get(ip);
- if (isProtein) {
- switch (getCanonicalName(p.getSource())) {
- case DBRefSource.UNIPROT:
- keys |= DBRefSource.UNIPROT_MASK;
- break;
- case DBRefSource.ENSEMBL:
- keys |= DBRefSource.ENSEMBL_MASK;
- break;
- }
- } else {
- // TODO: promote transcript refs ??
- }
- if (keys == 0 || !selectRefsBS(dbrefs, keys, bsSelect))
- return;
-// if (candidates != null)
- {
- for (int ic = bsSelect.nextSetBit(0); ic >= 0; ic = bsSelect.nextSetBit(ic + 1))
-// for (int ic = 0, n = candidates.size(); ic < n; ic++)
- {
- DBRefEntry cand = dbrefs.get(ic);// candidates.get(ic);
- if (cand.hasMap()) {
- Mapping map = cand.getMap();
- SequenceI cto = map.getTo();
- if (cto != null && cto != sequence) {
- // can't promote refs with mappings to other sequences
- continue;
- }
- MapList mlist = map.getMap();
- if (mlist.getFromLowest() != sstart && mlist.getFromHighest() != send) {
- // can't promote refs with mappings from a region of this sequence
- // - eg CDS
- continue;
- }
- }
- // and promote - not that version must be non-null here,
- // as p must have passed isPrimaryCandidate()
- cand.setVersion(p.getVersion() + " (promoted)");
- bsSelect.clear(ic);
- // selfs.remove(cand);
-// toPromote.add(cand);
- if (!cand.isPrimaryCandidate()) {
- System.out.println("Warning: Couldn't promote dbref " + cand.toString() + " for sequence "
- + sequence.toString());
- }
- }
- }
- }
- }
+ /**
+ * Returns true if either object is null, or they are equal
+ *
+ * @param o1
+ * @param o2
+ * @return
+ */
+ public static boolean nullOrEqual(Object o1, Object o2)
+ {
+ if (o1 == null || o2 == null)
+ {
+ return true;
+ }
+ return o1.equals(o2);
+ }
+
+ /**
+ * canonicalise source string before comparing. null is always wildcard
+ *
+ * @param o1
+ * - null or source string to compare
+ * @param o2
+ * - null or source string to compare
+ * @return true if either o1 or o2 are null, or o1 equals o2 under
+ * DBRefUtils.getCanonicalName
+ * (o1).equals(DBRefUtils.getCanonicalName(o2))
+ */
+ public static boolean nullOrEqualSource(String o1, String o2)
+ {
+ if (o1 == null || o2 == null)
+ {
+ return true;
+ }
+ return DBRefUtils.getCanonicalName(o1)
+ .equals(DBRefUtils.getCanonicalName(o2));
+ }
+
+ /**
+ * Selects just the DNA or protein references from a set of references
+ *
+ * @param selectDna
+ * if true, select references to 'standard' DNA databases, else to
+ * 'standard' peptide databases
+ * @param refs
+ * a set of references to select from
+ * @return
+ */
+ public static List<DBRefEntry> selectDbRefs(boolean selectDna,
+ List<DBRefEntry> refs)
+ {
+ return selectRefs(refs,
+ selectDna ? DBRefSource.DNACODINGDBS : DBRefSource.PROTEINDBS);
+ // could attempt to find other cross
+ // refs here - ie PDB xrefs
+ // (not dna, not protein seq)
+ }
+
+ /**
+ * Returns the (possibly empty) list of those supplied dbrefs which have the
+ * specified source database, with a case-insensitive match of source name
+ *
+ * @param dbRefs
+ * @param source
+ * @return
+ */
+ public static List<DBRefEntry> searchRefsForSource(
+ List<DBRefEntry> dbRefs, String source)
+ {
+ List<DBRefEntry> matches = new ArrayList<DBRefEntry>();
+ if (dbRefs != null && source != null)
+ {
+ for (DBRefEntry dbref : dbRefs)
+ {
+ if (source.equalsIgnoreCase(dbref.getSource()))
+ {
+ matches.add(dbref);
+ }
+ }
+ }
+ return matches;
+ }
+
+ /**
+ * promote direct database references to primary for nucleotide or protein
+ * sequences if they have an appropriate primary ref
+ * <table>
+ * <tr>
+ * <th>Seq Type</th>
+ * <th>Primary DB</th>
+ * <th>Direct which will be promoted</th>
+ * </tr>
+ * <tr align=center>
+ * <td>peptides</td>
+ * <td>Ensembl</td>
+ * <td>Uniprot</td>
+ * </tr>
+ * <tr align=center>
+ * <td>peptides</td>
+ * <td>Ensembl</td>
+ * <td>Uniprot</td>
+ * </tr>
+ * <tr align=center>
+ * <td>dna</td>
+ * <td>Ensembl</td>
+ * <td>ENA</td>
+ * </tr>
+ * </table>
+ *
+ * @param sequence
+ */
+ public static void ensurePrimaries(SequenceI sequence,
+ List<DBRefEntry> pr)
+ {
+ if (pr.size() == 0)
+ {
+ // nothing to do
+ return;
+ }
+ int sstart = sequence.getStart();
+ int send = sequence.getEnd();
+ boolean isProtein = sequence.isProtein();
+ BitSet bsSelect = new BitSet();
+
+ // List<DBRefEntry> selfs = new ArrayList<DBRefEntry>();
+ // {
+
+ // List<DBRefEntry> selddfs = selectDbRefs(!isprot, sequence.getDBRefs());
+ // if (selfs == null || selfs.size() == 0)
+ // {
+ // // nothing to do
+ // return;
+ // }
+
+ List<DBRefEntry> dbrefs = sequence.getDBRefs();
+ bsSelect.set(0, dbrefs.size());
+
+ if (!selectRefsBS(dbrefs, isProtein ? DBRefSource.PROTEIN_MASK
+ : DBRefSource.DNA_CODING_MASK, bsSelect))
+ return;
+
+ // selfs.addAll(selfArray);
+ // }
+
+ // filter non-primary refs
+ for (int ip = pr.size(); --ip >= 0;)
+ {
+ DBRefEntry p = pr.get(ip);
+ for (int i = bsSelect.nextSetBit(0); i >= 0; i = bsSelect
+ .nextSetBit(i + 1))
+ {
+ if (dbrefs.get(i) == p)
+ bsSelect.clear(i);
+ }
+ // while (selfs.contains(p))
+ // {
+ // selfs.remove(p);
+ // }
+ }
+ // List<DBRefEntry> toPromote = new ArrayList<DBRefEntry>();
+
+ for (int ip = pr.size(), keys = 0; --ip >= 0
+ && keys != DBRefSource.PRIMARY_MASK;)
+ {
+ DBRefEntry p = pr.get(ip);
+ if (isProtein)
+ {
+ switch (getCanonicalName(p.getSource()))
+ {
+ case DBRefSource.UNIPROT:
+ keys |= DBRefSource.UNIPROT_MASK;
+ break;
+ case DBRefSource.ENSEMBL:
+ keys |= DBRefSource.ENSEMBL_MASK;
+ break;
+ }
+ }
+ else
+ {
+ // TODO: promote transcript refs ??
+ }
+ if (keys == 0 || !selectRefsBS(dbrefs, keys, bsSelect))
+ return;
+ // if (candidates != null)
+ {
+ for (int ic = bsSelect.nextSetBit(0); ic >= 0; ic = bsSelect
+ .nextSetBit(ic + 1))
+ // for (int ic = 0, n = candidates.size(); ic < n; ic++)
+ {
+ DBRefEntry cand = dbrefs.get(ic);// candidates.get(ic);
+ if (cand.hasMap())
+ {
+ Mapping map = cand.getMap();
+ SequenceI cto = map.getTo();
+ if (cto != null && cto != sequence)
+ {
+ // can't promote refs with mappings to other sequences
+ continue;
+ }
+ MapList mlist = map.getMap();
+ if (mlist.getFromLowest() != sstart
+ && mlist.getFromHighest() != send)
+ {
+ // can't promote refs with mappings from a region of this sequence
+ // - eg CDS
+ continue;
+ }
+ }
+ // and promote - not that version must be non-null here,
+ // as p must have passed isPrimaryCandidate()
+ cand.setVersion(p.getVersion() + " (promoted)");
+ bsSelect.clear(ic);
+ // selfs.remove(cand);
+ // toPromote.add(cand);
+ if (!cand.isPrimaryCandidate())
+ {
+ System.out.println(
+ "Warning: Couldn't promote dbref " + cand.toString()
+ + " for sequence " + sequence.toString());
+ }
+ }
+ }
+ }
+ }
}
{
return file.startsWith("http://") || file.startsWith("https://");
}
-
/**
* wrapper to get/post to a URL or check headers
+ *
* @param url
* @param ids
* @param readTimeout
* @throws IOException
* @throws ProtocolException
*/
- public static boolean checkUrlAvailable(URL url,
- int readTimeout) throws IOException, ProtocolException
+ public static boolean checkUrlAvailable(URL url, int readTimeout)
+ throws IOException, ProtocolException
{
// System.out.println(System.currentTimeMillis() + " " + url);
* @param useLineart
* @throws IOException
*/
- public ImageMaker(TYPE imageType, int width, int height,
- File file, String fileTitle, boolean useLineart)
- throws IOException
+ public ImageMaker(TYPE imageType, int width, int height, File file,
+ String fileTitle, boolean useLineart) throws IOException
{
this.type = imageType;
if (range.length != 2)
{
// throw new IllegalArgumentException(range);
- Console.error("Invalid format for toRange "
- + Arrays.toString(range) + " may cause errors");
+ Console.error("Invalid format for toRange " + Arrays.toString(range)
+ + " may cause errors");
}
toLowest = Math.min(toLowest, Math.min(range[0], range[1]));
toHighest = Math.max(toHighest, Math.max(range[0], range[1]));
{
// rather than use acf.getCoveringMapping() we iterate through all
// mappings to make sure all CDS are selected for a protein
- for (SequenceToSequenceMapping map: acf.getMappings())
+ for (SequenceToSequenceMapping map : acf.getMappings())
{
- if (map.covers(selected) && map.covers(seq))
- {
- /*
- * Found a sequence mapping. Locate the start/end mapped residues.
- */
- List<AlignedCodonFrame> mapping = Arrays
- .asList(new AlignedCodonFrame[]
- { acf });
- // locate start
- SearchResultsI sr = buildSearchResults(selected,
- startResiduePos, mapping);
- for (SearchResultMatchI m : sr.getResults())
+ if (map.covers(selected) && map.covers(seq))
{
- mappedStartResidue = m.getStart();
- mappedEndResidue = m.getEnd();
- }
- // locate end - allowing for adjustment of start range
- sr = buildSearchResults(selected, endResiduePos, mapping);
- for (SearchResultMatchI m : sr.getResults())
- {
- mappedStartResidue = Math.min(mappedStartResidue,
- m.getStart());
- mappedEndResidue = Math.max(mappedEndResidue, m.getEnd());
- }
+ /*
+ * Found a sequence mapping. Locate the start/end mapped residues.
+ */
+ List<AlignedCodonFrame> mapping = Arrays
+ .asList(new AlignedCodonFrame[]
+ { acf });
+ // locate start
+ SearchResultsI sr = buildSearchResults(selected,
+ startResiduePos, mapping);
+ for (SearchResultMatchI m : sr.getResults())
+ {
+ mappedStartResidue = m.getStart();
+ mappedEndResidue = m.getEnd();
+ }
+ // locate end - allowing for adjustment of start range
+ sr = buildSearchResults(selected, endResiduePos, mapping);
+ for (SearchResultMatchI m : sr.getResults())
+ {
+ mappedStartResidue = Math.min(mappedStartResidue,
+ m.getStart());
+ mappedEndResidue = Math.max(mappedEndResidue, m.getEnd());
+ }
- /*
- * Find the mapped aligned columns, save the range. Note findIndex
- * returns a base 1 position, SequenceGroup uses base 0
- */
- int mappedStartCol = seq.findIndex(mappedStartResidue) - 1;
- minStartCol = minStartCol == -1 ? mappedStartCol
- : Math.min(minStartCol, mappedStartCol);
- int mappedEndCol = seq.findIndex(mappedEndResidue) - 1;
- maxEndCol = maxEndCol == -1 ? mappedEndCol
- : Math.max(maxEndCol, mappedEndCol);
- mappedGroup.addSequence(seq, false);
- break;
+ /*
+ * Find the mapped aligned columns, save the range. Note findIndex
+ * returns a base 1 position, SequenceGroup uses base 0
+ */
+ int mappedStartCol = seq.findIndex(mappedStartResidue) - 1;
+ minStartCol = minStartCol == -1 ? mappedStartCol
+ : Math.min(minStartCol, mappedStartCol);
+ int mappedEndCol = seq.findIndex(mappedEndResidue) - 1;
+ maxEndCol = maxEndCol == -1 ? mappedEndCol
+ : Math.max(maxEndCol, mappedEndCol);
+ mappedGroup.addSequence(seq, false);
+ break;
+ }
}
- }}
+ }
}
}
mappedGroup.setStartRes(minStartCol < 0 ? 0 : minStartCol);
{
for (AlignedCodonFrame acf : mappings)
{
- for (SequenceI seq2 : mapTo.getSequences())
+ for (SequenceI seq2 : mapTo.getSequences())
+ {
+ /*
+ * the corresponding peptide / CDS is the one for which there is
+ * a complete ('covering') mapping to 'seq'
+ */
+ SequenceI peptide = mappingToNucleotide ? seq2 : seq;
+ SequenceI cds = mappingToNucleotide ? seq : seq2;
+ SequenceToSequenceMapping s2s = acf.getCoveringMapping(cds,
+ peptide);
+ if (s2s != null)
{
- /*
- * the corresponding peptide / CDS is the one for which there is
- * a complete ('covering') mapping to 'seq'
- */
- SequenceI peptide = mappingToNucleotide ? seq2 : seq;
- SequenceI cds = mappingToNucleotide ? seq : seq2;
- SequenceToSequenceMapping s2s = acf.getCoveringMapping(cds,
- peptide);
- if (s2s != null)
- {
- mappedOrder.add(seq2);
- j++;
- break;
- }
+ mappedOrder.add(seq2);
+ j++;
+ break;
}
+ }
}
}
if (colsel == null)
{
- return;
+ return;
}
char fromGapChar = mapFrom.getAlignment().getGapCharacter();
mapHiddenColumns(regions.next(), codonFrames, newHidden,
fromSequences, toSequences, fromGapChar);
}
- return;
+ return;
}
/**
public static boolean isLinux()
{
return (isLinux == null
- ? (isLinux = (System.getProperty("os.name").indexOf("Linux") >= 0))
+ ? (isLinux = (System.getProperty("os.name")
+ .indexOf("Linux") >= 0))
: isLinux);
}
public static Object parseJSON(String json) throws ParseException
{
- return (isJS() ? JSON.parse(json)
- : new JSONParser().parse(json));
+ return (isJS() ? JSON.parse(json) : new JSONParser().parse(json));
}
public static Object parseJSON(Reader r)
* @param is
* @param outFile
* @throws IOException
- * if the file cannot be created or there is a problem
- * reading the input stream.
+ * if the file cannot be created or there is a problem reading the
+ * input stream.
*/
public static void streamToFile(InputStream is, File outFile)
throws IOException
if (isJS())
{
System.out.println(
- "Platform adding known access-control-allow-origin * for domain "
- + domain);
+ "Platform adding known access-control-allow-origin * for domain "
+ + domain);
/**
* @j2sNative
*
public static void getURLCommandArguments()
{
- try {
+ try
+ {
/**
* Retrieve the first query field as command arguments to Jalview. Include
* only if prior to "?j2s" or "&j2s" or "#". Assign the applet's
*
* @j2sNative var a =
* decodeURI((document.location.href.replace("&","?").split("?j2s")[0]
- * + "?").split("?")[1].split("#")[0]); a && (System.out.println("URL arguments detected were "+a)) &&
- * (J2S.thisApplet.__Info.urlargs = a.split(" "));
- * (!J2S.thisApplet.__Info.args || J2S.thisApplet.__Info.args == "" || J2S.thisApplet.__Info.args == "??") && (J2S.thisApplet.__Info.args = a) && (System.out.println("URL arguments were passed to J2S main."));
+ * + "?").split("?")[1].split("#")[0]); a &&
+ * (System.out.println("URL arguments detected were "+a)) &&
+ * (J2S.thisApplet.__Info.urlargs = a.split(" "));
+ * (!J2S.thisApplet.__Info.args || J2S.thisApplet.__Info.args
+ * == "" || J2S.thisApplet.__Info.args == "??") &&
+ * (J2S.thisApplet.__Info.args = a) && (System.out.println("URL
+ * arguments were passed to J2S main."));
*/
} catch (Throwable t)
{
}
/**
- * A (case sensitive) file path comparator that ignores the difference between /
- * and \
+ * A (case sensitive) file path comparator that ignores the difference between
+ * / and \
*
* @param path1
* @param path2
return e.getModifiersEx();
}
-
}
{
return s.toUpperCase(Locale.ROOT);
}
- return s.substring(0, 1).toUpperCase(Locale.ROOT) + s.substring(1).toLowerCase(Locale.ROOT);
+ return s.substring(0, 1).toUpperCase(Locale.ROOT)
+ + s.substring(1).toLowerCase(Locale.ROOT);
}
/**
* @author jprocter
*
*/
-public interface DialogRunnerI {
+public interface DialogRunnerI
+{
- /**
- * Sets the action to be performed when the dialog returns the given response.
- * Note this also handles <code>int</code>-valued responses, which will be
- * converted to <code>Integer</code> when this method is invoked.
- *
- * @param response
- * @param action
- * @return
- */
- DialogRunnerI setResponseHandler(Object response, Runnable action);
+ /**
+ * Sets the action to be performed when the dialog returns the given response.
+ * Note this also handles <code>int</code>-valued responses, which will be
+ * converted to <code>Integer</code> when this method is invoked.
+ *
+ * @param response
+ * @param action
+ * @return
+ */
+ DialogRunnerI setResponseHandler(Object response, Runnable action);
- /**
- * Runs the registered handler (if any) for the given response. The default
- * action is to do nothing. Typically an action will be need on 'OK' or other
- * positive selection in the dialog. An action might in some cases also be
- * needed for a 'Cancel' response.
- *
- * @param response
- * @return
- */
- default void handleResponse(Object response) {
- }
+ /**
+ * Runs the registered handler (if any) for the given response. The default
+ * action is to do nothing. Typically an action will be need on 'OK' or other
+ * positive selection in the dialog. An action might in some cases also be
+ * needed for a 'Cancel' response.
+ *
+ * @param response
+ * @return
+ */
+ default void handleResponse(Object response)
+ {
+ }
}
patternType = PatternType.String;
}
- uppercasePattern = pattern == null ? null : pattern.toUpperCase(Locale.ROOT);
+ uppercasePattern = pattern == null ? null
+ : pattern.toUpperCase(Locale.ROOT);
// if we add regex conditions (e.g. matchesPattern), then
// pattern should hold the raw regex, and
{
boolean matched = false;
String upper = compareTo.toUpperCase(Locale.ROOT).trim();
- switch(condition) {
+ switch (condition)
+ {
case Matches:
matched = upper.equals(uppercasePattern);
break;
{
return false;
}
-
+
boolean matched = false;
- switch (condition) {
+ switch (condition)
+ {
case LT:
matched = f < compareTo;
break;
*/
return matchesFloat(compareTo, longValue);
}
-
+
boolean matched = false;
- switch (condition) {
+ switch (condition)
+ {
case LT:
matched = val < longValue;
break;
default:
break;
}
-
+
return matched;
}
* retain any colour thresholds per group while
* changing choice of colour scheme (JAL-2386)
*/
- sg.setColourScheme(
- cs == null ? null : cs.getInstance(this, sg));
+ sg.setColourScheme(cs == null ? null : cs.getInstance(this, sg));
if (cs != null)
{
sg.getGroupColourScheme().alignmentChanged(sg,
AlignmentAnnotation clone = new AlignmentAnnotation(annot);
if (selectedOnly && selectionGroup != null)
{
- clone.makeVisibleAnnotation(
- selectionGroup.getStartRes(), selectionGroup.getEndRes(),
- alignment.getHiddenColumns());
+ clone.makeVisibleAnnotation(selectionGroup.getStartRes(),
+ selectionGroup.getEndRes(), alignment.getHiddenColumns());
}
else
{
}
@Override
- public AlignmentExportData getAlignExportData(AlignExportSettingsI options)
+ public AlignmentExportData getAlignExportData(
+ AlignExportSettingsI options)
{
AlignmentI alignmentToExport = null;
String[] omitHidden = null;
omitHidden, alignmentStartEnd);
return ed;
}
-
+
/**
* flag set to indicate if structure views might be out of sync with sequences
* in the alignment
heightRatio = (float) alheight / sequencesHeight;
}
-
/**
* {@inheritDoc} Callers should have already called resetAlignmentDims to
* refresh widthRatio
}
int residuesToScroll = width * widthsToScroll;
- int newStartRes = up ? oldStartRes - residuesToScroll : oldStartRes
- + residuesToScroll;
+ int newStartRes = up ? oldStartRes - residuesToScroll
+ : oldStartRes + residuesToScroll;
if (newStartRes < 0)
{
newStartRes = 0;
{
scrollUp(false);
}
-
+
HiddenColumns hidden = al.getHiddenColumns();
while (x < hidden.visibleToAbsoluteColumn(startRes))
{
}
@Override
- public List<SequenceFeature> findFeaturesAtColumn(SequenceI sequence, int column)
+ public List<SequenceFeature> findFeaturesAtColumn(SequenceI sequence,
+ int column)
{
/*
* include features at the position provided their feature type is
}
if (groupDisplayed)
{
- Set<String> types = asq.getFeatures().getFeatureTypesForGroups(
- true, group);
+ Set<String> types = asq.getFeatures()
+ .getFeatureTypesForGroups(true, group);
for (String type : types)
{
if (!allfeatures.contains(type)) // or use HashSet and no test?
}
}
}
+
protected Boolean firing = Boolean.FALSE;
/**
*/
public boolean showFeatureOfType(String type)
{
- return type == null ? false : (av.getFeaturesDisplayed() == null ? true
- : av.getFeaturesDisplayed().isVisible(type));
+ return type == null ? false
+ : (av.getFeaturesDisplayed() == null ? true
+ : av.getFeaturesDisplayed().isVisible(type));
}
@Override
}
/**
- * Sets the priority order for features, with the highest priority (displayed on
- * top) at the start of the data array
+ * Sets the priority order for features, with the highest priority (displayed
+ * on top) at the start of the data array
*
* @param data
* an array of { Type, Colour, Filter, Boolean }
* @param visibleNew
* when true current featureDisplay list will be cleared
- * @return true if any visible features have been reordered or recoloured, else
- * false (i.e. no need to repaint)
+ * @return true if any visible features have been reordered or recoloured,
+ * else false (i.e. no need to repaint)
*/
public boolean setFeaturePriority(FeatureSettingsBean[] data,
boolean visibleNew)
*/
public boolean featureGroupNotShown(final SequenceFeature sequenceFeature)
{
- return featureGroups != null
- && sequenceFeature.featureGroup != null
+ return featureGroups != null && sequenceFeature.featureGroup != null
&& sequenceFeature.featureGroup.length() != 0
&& featureGroups.containsKey(sequenceFeature.featureGroup)
&& !featureGroups.get(sequenceFeature.featureGroup)
List<String> visibleFeatures = getDisplayedFeatureTypes();
String[] visibleTypes = visibleFeatures
.toArray(new String[visibleFeatures.size()]);
- List<SequenceFeature> features = sequence.getFeatures().findFeatures(
- fromResNo, toResNo, visibleTypes);
-
+ List<SequenceFeature> features = sequence.getFeatures()
+ .findFeatures(fromResNo, toResNo, visibleTypes);
+
for (SequenceFeature sf : features)
{
if (!featureGroupNotShown(sf) && getColour(sf) != null)
* (checking type and isContactFeature as a fail-safe here, although
* currently they are guaranteed to match in this context)
*/
- if (lastFeature != null
- && sf.getBegin() == lastFeature.getBegin()
+ if (lastFeature != null && sf.getBegin() == lastFeature.getBegin()
&& sf.getEnd() == lastFeature.getEnd()
&& sf.isContactFeature() == lastFeature.isContactFeature()
&& sf.getType().equals(lastFeature.getType()))
}
@Override
- public void setFeatureFilter(String featureType, FeatureMatcherSetI filter)
+ public void setFeatureFilter(String featureType,
+ FeatureMatcherSetI filter)
{
if (filter == null || filter.isEmpty())
{
{
return null;
}
-
+
return fc.getColor(sf);
}
int fromRes = match.getStart();
int toRes = match.getEnd();
mapFrom = match.getSequence();
- List<SequenceFeature> fs = findFeaturesAtResidue(
- mapFrom, fromRes, toRes);
+ List<SequenceFeature> fs = findFeaturesAtResidue(mapFrom, fromRes,
+ toRes);
for (SequenceFeature sf : fs)
{
if (!found.contains(sf))
}
}
}
-
- return new MappedFeatures(mapping.getMapping(), mapFrom, pos, residue, result);
+
+ return new MappedFeatures(mapping.getMapping(), mapFrom, pos, residue,
+ result);
}
@Override
throw (new Exception(
"Timed out when communicating with server\nTry again later.\n"));
}
- Console.debug("Job " + j + " Result state "
- + jobs[j].getState() + "(ServerError="
- + jobs[j].isServerError() + ")");
+ Console.debug("Job " + j + " Result state " + jobs[j].getState()
+ + "(ServerError=" + jobs[j].isServerError() + ")");
} catch (Exception ex)
{
// Deal with Transaction exceptions
jobs[j].clearResponse(); // may contain out of date result data
wsInfo.setStatus(jobs[j].jobnum,
WebserviceInfo.STATE_STOPPED_ERROR);
- Console.error("Out of memory when retrieving Job " + j
- + " id:" + WsUrl + "/" + jobs[j].jobId, er);
+ Console.error("Out of memory when retrieving Job " + j + " id:"
+ + WsUrl + "/" + jobs[j].jobId, er);
new jalview.gui.OOMWarning(
"retrieving result for " + WebServiceName, er);
System.gc();
Thread.sleep(5000);
} catch (InterruptedException e)
{
- Console.debug("Interrupted sleep waiting for next job poll.",
- e);
+ Console.debug("Interrupted sleep waiting for next job poll.", e);
}
// System.out.println("I'm alive "+alTitle);
}
e.printStackTrace();
}
- Vector<SequenceI> sdataset = new Vector<>(
- Arrays.asList(dataset));
+ Vector<SequenceI> sdataset = new Vector<>(Arrays.asList(dataset));
List<String> warningMessages = new ArrayList<>();
// clear any old feature display settings recorded from past sessions
{
if (Console.isDebugEnabled())
{
- Console.debug("Querying " + dbsource.getDbName()
- + " with : '" + queryString.toString() + "'");
+ Console.debug("Querying " + dbsource.getDbName() + " with : '"
+ + queryString.toString() + "'");
}
retrieved = dbsource.getSequenceRecords(queryString.toString());
} catch (Exception ex)
}
if (retrieved != null)
{
- transferReferences(sdataset, dbsource, retrieved,
- trimDsSeqs, warningMessages);
+ transferReferences(sdataset, dbsource, retrieved, trimDsSeqs,
+ warningMessages);
}
}
else
{
for (int j = 0, n = uprefs.size(); j < n; j++)
{
- DBRefEntry upref = uprefs.get(j);
+ DBRefEntry upref = uprefs.get(j);
addSeqId(sequence, upref.getAccessionId());
queries.addElement(
upref.getAccessionId().toUpperCase(Locale.ROOT));
}
else
{
- Pattern possibleIds = Pattern.compile("[A-Za-z0-9_]+");
+ Pattern possibleIds = Pattern.compile("[A-Za-z0-9_]+");
// generate queries from sequence ID string
Matcher tokens = possibleIds.matcher(sequence.getName());
- int p=0;
+ int p = 0;
while (tokens.find(p))
{
String token = tokens.group();
* a list of messages to add to
*/
boolean transferReferences(Vector<SequenceI> sdataset,
- DbSourceProxy dbSourceProxy,
- AlignmentI retrievedAl, boolean trimDatasetSeqs,
- List<String> warningMessages)
+ DbSourceProxy dbSourceProxy, AlignmentI retrievedAl,
+ boolean trimDatasetSeqs, List<String> warningMessages)
{
// System.out.println("trimming ? " + trimDatasetSeqs);
if (retrievedAl == null || retrievedAl.getHeight() == 0)
}
for (int j = 0, n = entryRefs.size(); j < n; j++)
{
- DBRefEntry ref = entryRefs.get(j);
+ DBRefEntry ref = entryRefs.get(j);
String accessionId = ref.getAccessionId();
// match up on accessionId
if (seqRefs.containsKey(accessionId.toUpperCase(Locale.ROOT)))
.toUpperCase(Locale.ROOT);
int oldstrt = alseqs[alsq].getStart();
alseqs[alsq].setStart(sequence.getSequenceAsString()
- .toUpperCase(Locale.ROOT).indexOf(ngAlsq) + sequence.getStart());
+ .toUpperCase(Locale.ROOT).indexOf(ngAlsq)
+ + sequence.getStart());
if (oldstrt != alseqs[alsq].getStart())
{
alseqs[alsq].setEnd(
/**
*
- * @return any feature settings associated with sources that have provided sequences
+ * @return any feature settings associated with sources that have provided
+ * sequences
*/
- public List<FeatureSettingsModelI>getFeatureSettingsModels()
+ public List<FeatureSettingsModelI> getFeatureSettingsModels()
{
return featureDisplaySettings == null
? Arrays.asList(new FeatureSettingsModelI[0])
: Arrays.asList(featureDisplaySettings.values()
.toArray(new FeatureSettingsModelI[1]));
}
+
/**
* Adds the message to the list unless it already contains it
*
*/
private SequenceI[] recoverDbSequences(SequenceI[] sequencesArray)
{
- int n;
- if (sequencesArray == null || (n = sequencesArray.length) == 0)
- return sequencesArray;
+ int n;
+ if (sequencesArray == null || (n = sequencesArray.length) == 0)
+ return sequencesArray;
ArrayList<SequenceI> nseq = new ArrayList<>();
- for (int i = 0;i < n; i++)
+ for (int i = 0; i < n; i++)
{
nseq.add(sequencesArray[i]);
List<DBRefEntry> dbr = sequencesArray[i].getDBRefs();
{
nseq.add(map.getTo());
}
- }
+ }
}
}
}
- // BH 2019.01.25 question here if this is the right logic. Return the original if nothing found?
+ // BH 2019.01.25 question here if this is the right logic. Return the
+ // original if nothing found?
if (nseq.size() > 0)
{
return nseq.toArray(new SequenceI[nseq.size()]);
// httpGet.setEntity(ue);
HttpResponse response = httpclient.execute(httpGet);
HttpEntity resEntity = response.getEntity();
-
+
if (resEntity != null)
{
BufferedReader r = new BufferedReader(
}
/**
- * return an ordered list of database sources excluding alignment only databases
+ * return an ordered list of database sources excluding alignment only
+ * databases
*/
public String[] getNonAlignmentSources()
{
@Override
public Regex getAccessionValidator()
{
- Regex validator = new Regex("(AF-[A-Z]+[0-9]+[A-Z0-9]+-F1)");
+ Regex validator = new Regex("(AF-[A-Z]+[0-9]+[A-Z0-9]+-F1)");
validator.setIgnoreCase(true);
return validator;
}
{
return getSequenceRecords(queries, null);
}
- public AlignmentI getSequenceRecords(String queries, String retrievalUrl) throws Exception
+
+ public AlignmentI getSequenceRecords(String queries, String retrievalUrl)
+ throws Exception
{
AlignmentI pdbAlignment = null;
String chain = null;
{
File tmpFile = File.createTempFile(id, ".cif");
UrlDownloadClient.download(alphaFoldCif, tmpFile);
-
+
// may not need this check ?
file = tmpFile.getAbsolutePath();
if (file == null)
return null;
}
- pdbAlignment = importDownloadedStructureFromUrl(alphaFoldCif, tmpFile, id, chain, getDbSource(),getDbVersion());
-
+ pdbAlignment = importDownloadedStructureFromUrl(alphaFoldCif, tmpFile,
+ id, chain, getDbSource(), getDbVersion());
if (pdbAlignment == null || pdbAlignment.getHeight() < 1)
{
}
/**
- * general purpose structure importer - designed to yield alignment useful for transfer of annotation to associated sequences
+ * general purpose structure importer - designed to yield alignment useful for
+ * transfer of annotation to associated sequences
+ *
* @param alphaFoldCif
* @param tmpFile
* @param id
* @return
* @throws Exception
*/
- public static AlignmentI importDownloadedStructureFromUrl(String alphaFoldCif,
- File tmpFile, String id, String chain, String dbSource, String dbVersion) throws Exception
+ public static AlignmentI importDownloadedStructureFromUrl(
+ String alphaFoldCif, File tmpFile, String id, String chain,
+ String dbSource, String dbVersion) throws Exception
{
String file = tmpFile.getAbsolutePath();
// todo get rid of Type and use FileFormatI instead?
// dbentry.setMap()
pdbcs.addDBRef(dbentry);
// update any feature groups
- List<SequenceFeature> allsf = pdbcs.getFeatures().getAllFeatures();
+ List<SequenceFeature> allsf = pdbcs.getFeatures()
+ .getAllFeatures();
List<SequenceFeature> newsf = new ArrayList<SequenceFeature>();
- if (allsf!=null && allsf.size()>0)
+ if (allsf != null && allsf.size() > 0)
{
- for (SequenceFeature f:allsf)
+ for (SequenceFeature f : allsf)
{
if (file.equals(f.getFeatureGroup()))
{
- f = new SequenceFeature(f, f.type, f.begin, f.end, id, f.score);
+ f = new SequenceFeature(f, f.type, f.begin, f.end, id,
+ f.score);
}
newsf.add(f);
}
try
{
reply = dbFetch.fetchDataAsFile(
- dbName.toLowerCase(Locale.ROOT) + ":" + query.trim(), null, "gz");
+ dbName.toLowerCase(Locale.ROOT) + ":" + query.trim(), null,
+ "gz");
} catch (Exception e)
{
stopQuery();
if (al == null)
{
- Console.error(
- "No record found for '" + dbName + ":" + query + "'");
+ Console.error("No record found for '" + dbName + ":" + query + "'");
}
}
// todo get rid of Type and use FileFormatI instead?
FileFormatI fileFormat = (pdbFileFormat == Type.PDB) ? FileFormat.PDB
: FileFormat.MMCif;
- pdbAlignment = new FormatAdapter().readFile(tmpFile, DataSourceType.FILE,
- fileFormat);
+ pdbAlignment = new FormatAdapter().readFile(tmpFile,
+ DataSourceType.FILE, fileFormat);
if (pdbAlignment != null)
{
List<SequenceI> toremove = new ArrayList<SequenceI>();
static final String PFAM_BASEURL_KEY = "PFAM_BASEURL";
private static final String DEFAULT_PFAM_BASEURL = "https://pfam.xfam.org";
- static {
+ static
+ {
Platform.addJ2SDirectDatabaseCall(DEFAULT_PFAM_BASEURL);
}
private static final String DEFAULT_RFAM_BASEURL = "https://rfam.xfam.org";
- static {
+ static
+ {
Platform.addJ2SDirectDatabaseCall(DEFAULT_RFAM_BASEURL);
}
+
/*
* append to URLs to retrieve as a gzipped file
*/
private static final String DEFAULT_UNIPROT_DOMAIN = "https://www.uniprot.org";
private static final String BAR_DELIMITER = "|";
-
+
private static final String DEFAULT_THREEDBEACONS_DOMAIN = "https://wwwdev.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons-hub-api/uniprot/summary/";
/**
private String getDomain()
{
return Cache.getDefault("UNIPROT_DOMAIN", DEFAULT_UNIPROT_DOMAIN);
- //return Cache.getDefault("3DB_DOMAIN", DEFAULT_THREEDBEACONS_DOMAIN );
+ // return Cache.getDefault("3DB_DOMAIN", DEFAULT_THREEDBEACONS_DOMAIN );
}
/*
"(UNIPROT\\|?|UNIPROT_|UNIREF\\d+_|UNIREF\\d+\\|?)", "");
AlignmentI al = null;
- String downloadstring = getDomain() + "/uniprot/" + queries
- + ".xml";
-// String downloadstring = getDomain() + queries + ".json";
+ String downloadstring = getDomain() + "/uniprot/" + queries + ".xml";
+ // String downloadstring = getDomain() + queries + ".json";
URL url = new URL(downloadstring);
URLConnection urlconn = url.openConnection();
String seqString = entry.getSequence().getValue().replaceAll("\\s*",
"");
- SequenceI sequence = new Sequence(id,
- seqString);
+ SequenceI sequence = new Sequence(id, seqString);
sequence.setDescription(getUniprotEntryDescription(entry));
/*
XMLStreamReader streamReader = XMLInputFactory.newInstance()
.createXMLStreamReader(is);
javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
- JAXBElement<jalview.xml.binding.uniprot.Uniprot> uniprotElement =
- um.unmarshal(streamReader, jalview.xml.binding.uniprot.Uniprot.class);
- jalview.xml.binding.uniprot.Uniprot uniprot = uniprotElement.getValue();
-
+ JAXBElement<jalview.xml.binding.uniprot.Uniprot> uniprotElement = um
+ .unmarshal(streamReader,
+ jalview.xml.binding.uniprot.Uniprot.class);
+ jalview.xml.binding.uniprot.Uniprot uniprot = uniprotElement
+ .getValue();
+
if (uniprot != null && !uniprot.getEntry().isEmpty())
{
entries = uniprot.getEntry();
"(UNIPROT\\|?|UNIPROT_|UNIREF\\d+_|UNIREF\\d+\\|?)", "");
AlignmentI al = null;
- String downloadstring = getDomain() + "/uniprot/" + queries
- + ".xml";
+ String downloadstring = getDomain() + "/uniprot/" + queries + ".xml";
URL url = new URL(downloadstring);
- HttpURLConnection urlconn = (HttpURLConnection)url.openConnection();
+ HttpURLConnection urlconn = (HttpURLConnection) url.openConnection();
// anything other than 200 means we don't have data
- // TODO: JAL-3882 reuse the EnsemblRestClient's fair
+ // TODO: JAL-3882 reuse the EnsemblRestClient's fair
// use/backoff logic to retry when the server tells us to go away
if (urlconn.getResponseCode() == 200)
{
}
stopQuery();
return al;
-
+
} catch (Exception e)
{
throw (e);
String seqString = entry.getSequence().getValue().replaceAll("\\s*",
"");
- SequenceI sequence = new Sequence(id,
- seqString);
+ SequenceI sequence = new Sequence(id, seqString);
sequence.setDescription(getUniprotEntryDescription(entry));
/*
*/
final String dbVersion = getDbVersion();
List<DBRefEntry> dbRefs = new ArrayList<>();
- boolean canonical=true;
+ boolean canonical = true;
for (String accessionId : entry.getAccession())
{
DBRefEntry dbRef = new DBRefEntry(DBRefSource.UNIPROT, dbVersion,
- accessionId,null,canonical);
- canonical=false;
+ accessionId, null, canonical);
+ canonical = false;
dbRefs.add(dbRef);
}
XMLStreamReader streamReader = XMLInputFactory.newInstance()
.createXMLStreamReader(is);
javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
- JAXBElement<jalview.xml.binding.uniprot.Uniprot> uniprotElement =
- um.unmarshal(streamReader, jalview.xml.binding.uniprot.Uniprot.class);
- jalview.xml.binding.uniprot.Uniprot uniprot = uniprotElement.getValue();
-
+ JAXBElement<jalview.xml.binding.uniprot.Uniprot> uniprotElement = um
+ .unmarshal(streamReader,
+ jalview.xml.binding.uniprot.Uniprot.class);
+ jalview.xml.binding.uniprot.Uniprot uniprot = uniprotElement
+ .getValue();
+
if (uniprot != null && !uniprot.getEntry().isEmpty())
{
entries = uniprot.getEntry();
} catch (JAXBException | XMLStreamException
| FactoryConfigurationError e)
{
- if (e instanceof javax.xml.bind.UnmarshalException && e.getCause()!=null && e.getCause() instanceof XMLStreamException && e.getCause().getMessage().contains("[row,col]:[1,1]"))
+ if (e instanceof javax.xml.bind.UnmarshalException
+ && e.getCause() != null
+ && e.getCause() instanceof XMLStreamException
+ && e.getCause().getMessage().contains("[row,col]:[1,1]"))
{
// trying to parse an empty stream
return null;
String getURL(String queries)
{
- return getURLPrefix() + "/family/" + queries.trim().toUpperCase(Locale.ROOT)
- + getURLSuffix();
+ return getURLPrefix() + "/family/"
+ + queries.trim().toUpperCase(Locale.ROOT) + getURLSuffix();
}
/**
}
return null;
}
- static {
+
+ static
+ {
Platform.addJ2SDirectDatabaseCall("https://www.ebi.ac.uk/");
}
+
/**
* Constructs the URL to fetch from
*
else
{
url = "https://www.ebi.ac.uk/Tools/dbfetch/dbfetch/"
- + database.toLowerCase(Locale.ROOT) + "/" + ids.toLowerCase(Locale.ROOT)
+ + database.toLowerCase(Locale.ROOT) + "/"
+ + ids.toLowerCase(Locale.ROOT)
+ (format != null ? "/" + format : "");
}
return url;
} catch (Exception ex)
{
Console.warn("Problem whilst trying to make a URL from '"
- + ((url != null) ? url : "<null>") + "'");
+ + ((url != null) ? url : "<null>") + "'");
Console.warn(
"This was probably due to a malformed comma separated list"
+ " in the DISCOVERY_URLS entry of $(HOME)/.jalview_properties)");
Console.debug("(Re)-Initialising the discovery URL list.");
try
{
- reallyDiscoverServices = Cache
- .getDefault("DISCOVERY_START", false);
+ reallyDiscoverServices = Cache.getDefault("DISCOVERY_START", false);
if (reallyDiscoverServices)
{
ServiceURLList = getDiscoveryURLS();
{
if (!cat.contains(sh[i]))
{
- Console.debug("A " + sh[i].getAbstractName()
- + " service called " + sh[i].getName() + " exists at "
- + sh[i].getEndpointURL() + "\n");
+ Console.debug("A " + sh[i].getAbstractName() + " service called "
+ + sh[i].getName() + " exists at " + sh[i].getEndpointURL()
+ + "\n");
if (!sscat.containsKey(sh[i].getAbstractName()))
{
sscat.put(sh[i].getAbstractName(), cat = new Vector<>());
} catch (Exception e)
{
Console.debug("Ignoring bad discovery service URL "
- + sh[i].getEndpointURL(), e);
+ + sh[i].getEndpointURL(), e);
}
}
}
}
while (s_url < ServiceURLList.size())
{
- if ((sh = getServices(
- ServiceURLList.get(s_url))) != null)
+ if ((sh = getServices(ServiceURLList.get(s_url))) != null)
{
buildServiceLists(sh, cat, sscat);
}
else
{
- Console.warn("No services at "
- + (ServiceURLList.get(s_url))
+ Console.warn("No services at " + (ServiceURLList.get(s_url))
+ " - check DISCOVERY_URLS property in .jalview_properties");
}
s_url++;
serviceClientBindings.put("SecStrPred", new JPredClient());
serviceClientBindings.put("SeqSearch", new SeqSearchWSClient());
}
- WS1Client instance = serviceClientBindings
- .get(sh.getAbstractName());
+ WS1Client instance = serviceClientBindings.get(sh.getAbstractName());
if (instance == null)
{
System.err.println(
} catch (Exception q)
{
Console.info("Couldn't recover disorder prediction for sequence "
- + seq.getName() + "(Prediction name was " + seqId
- + ")"
- + "\nSee http://issues.jalview.org/browse/JAL-1319 for one possible reason why disorder predictions might fail.");
+ + seq.getName() + "(Prediction name was " + seqId + ")"
+ + "\nSee http://issues.jalview.org/browse/JAL-1319 for one possible reason why disorder predictions might fail.");
}
float last = Float.NaN, val = Float.NaN;
int lastAnnot = ourAnnot.size();
if (vals.hasNext())
{
val = vals.next().floatValue();
- sf = new SequenceFeature(type[0], type[1],
- base + rn.from, base + rn.to, val, methodName);
+ sf = new SequenceFeature(type[0], type[1], base + rn.from,
+ base + rn.to, val, methodName);
}
else
{
- sf = new SequenceFeature(type[0], type[1],
- base + rn.from, base + rn.to, methodName);
+ sf = new SequenceFeature(type[0], type[1], base + rn.from,
+ base + rn.to, methodName);
}
dseq.addSequenceFeature(sf);
if (last != val && !Float.isNaN(last))
}
if (collectAnnotationResultsFor(rslt))
{
- Console.debug("Updating result annotation from Job "
- + rslt + " at " + service.getUri());
+ Console.debug("Updating result annotation from Job " + rslt
+ + " at " + service.getUri());
updateResultAnnotation(true);
ap.adjustAnnotationHeight();
}
ArrayList<Jws2Instance> hostservices = hosts.get(service.getHost());
if (hostservices == null)
{
- hosts.put(service.getHost(),
- hostservices = new ArrayList<>());
+ hosts.put(service.getHost(), hostservices = new ArrayList<>());
hostlist.add(service.getHost());
}
hostservices.add(service);
public Vector<Jws2Instance> getServices()
{
- return (services == null) ? new Vector<>()
- : new Vector<>(services);
+ return (services == null) ? new Vector<>() : new Vector<>(services);
}
/**
if (msa != null)
{
- new MsaWSClient(service, af.getTitle(), msa, withGaps,
- true,
- af.getViewport().getAlignment().getDataset(),
- af);
+ new MsaWSClient(service, af.getTitle(), msa, withGaps, true,
+ af.getViewport().getAlignment().getDataset(), af);
}
}
@Override
public void actionPerformed(ActionEvent e)
{
- AlignmentView msa = af
- .gatherSequencesForAlignment();
+ AlignmentView msa = af.gatherSequencesForAlignment();
if (msa != null)
{
MsaWSClient msac = new MsaWSClient(service, preSet,
af.getTitle(), msa, false, true,
- af.getViewport().getAlignment()
- .getDataset(),
- af);
+ af.getViewport().getAlignment().getDataset(), af);
}
}
protected void startJob(final Jws2Instance service, final AlignFrame af,
final boolean withGaps, AlignmentView msa)
{
- try {
- new MsaWSClient(service, null, null, true,
- af.getTitle(), msa, withGaps, true,
- af.getViewport().getAlignment().getDataset(),
- af);
- } catch (Exception e) {
+ try
+ {
+ new MsaWSClient(service, null, null, true, af.getTitle(), msa,
+ withGaps, true, af.getViewport().getAlignment().getDataset(),
+ af);
+ } catch (Exception e)
+ {
JvOptionPane.showMessageDialog(alignFrame, e.getMessage(),
MessageManager.getString("label.state_job_error"),
JvOptionPane.WARNING_MESSAGE);
{
valid = false;
warnings.append("Invalid value for parameter "
- + mtch.group(1).toLowerCase(Locale.ROOT) + " '" + mtch.group(2)
- + "' (expected an integer)\n");
+ + mtch.group(1).toLowerCase(Locale.ROOT) + " '"
+ + mtch.group(2) + "' (expected an integer)\n");
}
if (!configureProperty(mtch.group(1), mtch.group(2), warnings))
try
{
for (RestServiceDescription descr : RestServiceDescription
- .parseDescriptions(
- Cache.getDefault(RSBS_SERVICES,
- makeShmmrRestClient().service.toString())))
+ .parseDescriptions(Cache.getDefault(RSBS_SERVICES,
+ makeShmmrRestClient().service.toString())))
{
services.add(descr.toString());
}
+ "</a><br/>Filtered response content below:<br/>");
} catch (IOException e)
{
- Console.debug("IOException when consuming unhandled response",
- e);
+ Console.debug("IOException when consuming unhandled response", e);
}
;
}
// BH 2015.01.25 check about version/accessid being null here
List<DBRefEntry> frefs = DBRefUtils.searchRefs(
seqs[is].getDBRefs(),
- new DBRefEntry(db, null, null), DBRefUtils.SEARCH_MODE_FULL);
+ new DBRefEntry(db, null, null),
+ DBRefUtils.SEARCH_MODE_FULL);
for (DBRefEntry dbr : frefs)
{
queriesFound.add(dbr.getAccessionId());
.get(proxy.getDbSource());
if (slist == null)
{
- fetchableDbs.put(proxy.getDbSource(),
- slist = new Hashtable<>());
+ fetchableDbs.put(proxy.getDbSource(), slist = new Hashtable<>());
}
slist.put(proxy.getDbName(), proxy);
}
.getMapRegion();
for (MapRegion mapRegion : mapRegions)
{
- accessions
- .add(mapRegion.getDb().getDbAccessionId().toLowerCase(Locale.ROOT));
+ accessions.add(mapRegion.getDb().getDbAccessionId()
+ .toLowerCase(Locale.ROOT));
}
}
}
HashSet<String> dbRefAccessionIdsString = new HashSet<String>();
for (DBRefEntry dbref : seq.getDBRefs())
{
- dbRefAccessionIdsString.add(dbref.getAccessionId().toLowerCase(Locale.ROOT));
+ dbRefAccessionIdsString
+ .add(dbref.getAccessionId().toLowerCase(Locale.ROOT));
}
- dbRefAccessionIdsString.add(sourceDBRef.getAccessionId().toLowerCase(Locale.ROOT));
+ dbRefAccessionIdsString
+ .add(sourceDBRef.getAccessionId().toLowerCase(Locale.ROOT));
curDBRefAccessionIdsString = dbRefAccessionIdsString;
curSourceDBRef = sourceDBRef.getAccessionId();
{
boolean isStrictMatch = true;
return isStrictMatch ? curSourceDBRef.equalsIgnoreCase(accession)
- : curDBRefAccessionIdsString.contains(accession.toLowerCase(Locale.ROOT));
+ : curDBRefAccessionIdsString
+ .contains(accession.toLowerCase(Locale.ROOT));
}
private boolean isFoundInSiftsEntry(String accessionId)
throws IOException
{
- FileOutputStream fos = null;
- ReadableByteChannel rbc = null;
- Path temp = null;
- try
- {
- temp = Files.createTempFile(".jalview_", ".tmp");
+ FileOutputStream fos = null;
+ ReadableByteChannel rbc = null;
+ Path temp = null;
+ try
+ {
+ temp = Files.createTempFile(".jalview_", ".tmp");
- URL url = new URL(urlstring);
- rbc = Channels.newChannel(url.openStream());
- fos = new FileOutputStream(temp.toString());
- fos.getChannel().transferFrom(rbc, 0, Long.MAX_VALUE);
+ URL url = new URL(urlstring);
+ rbc = Channels.newChannel(url.openStream());
+ fos = new FileOutputStream(temp.toString());
+ fos.getChannel().transferFrom(rbc, 0, Long.MAX_VALUE);
- // copy tempfile to outfile once our download completes
- // incase something goes wrong
- Files.copy(temp, Paths.get(outfile),
- StandardCopyOption.REPLACE_EXISTING);
- } catch (IOException e)
- {
- throw e;
- } finally
+ // copy tempfile to outfile once our download completes
+ // incase something goes wrong
+ Files.copy(temp, Paths.get(outfile),
+ StandardCopyOption.REPLACE_EXISTING);
+ } catch (IOException e)
+ {
+ throw e;
+ } finally
+ {
+ try
{
- try
- {
- if (fos != null)
- {
- fos.close();
- }
- } catch (IOException e)
+ if (fos != null)
{
- System.out.println(
- "Exception while closing download file output stream: "
- + e.getMessage());
+ fos.close();
}
- try
- {
- if (rbc != null)
- {
- rbc.close();
- }
- } catch (IOException e)
+ } catch (IOException e)
+ {
+ System.out.println(
+ "Exception while closing download file output stream: "
+ + e.getMessage());
+ }
+ try
+ {
+ if (rbc != null)
{
- System.out.println("Exception while closing download channel: "
- + e.getMessage());
+ rbc.close();
}
- try
- {
- if (temp != null)
- {
- Files.deleteIfExists(temp);
- }
- } catch (IOException e)
+ } catch (IOException e)
+ {
+ System.out.println("Exception while closing download channel: "
+ + e.getMessage());
+ }
+ try
+ {
+ if (temp != null)
{
- System.out.println("Exception while deleting download temp file: "
- + e.getMessage());
+ Files.deleteIfExists(temp);
}
+ } catch (IOException e)
+ {
+ System.out.println("Exception while deleting download temp file: "
+ + e.getMessage());
}
+ }
}
- public static void download(String urlstring, File tempFile) throws IOException
+ public static void download(String urlstring, File tempFile)
+ throws IOException
{
if (!Platform.setFileBytes(tempFile, urlstring))
{
// Generated on: 2018.09.14 at 02:46:00 PM BST
//
-
package jalview.xml.binding.embl;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
-
/**
- * <p>Java class for EntrySetType complex type.
+ * <p>
+ * Java class for EntrySetType complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
*
* <pre>
* <complexType name="EntrySetType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "EntrySetType", propOrder = {
- "entry"
-})
-public class EntrySetType {
+@XmlType(name = "EntrySetType", propOrder = { "entry" })
+public class EntrySetType
+{
- @XmlElement(required = true)
- protected List<EntryType> entry;
+ @XmlElement(required = true)
+ protected List<EntryType> entry;
- /**
- * Gets the value of the entry property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the entry property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getEntry().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EntryType }
- *
- *
- */
- public List<EntryType> getEntry() {
- if (entry == null) {
- entry = new ArrayList<EntryType>();
- }
- return this.entry;
+ /**
+ * Gets the value of the entry property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the entry property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getEntry().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link EntryType }
+ *
+ *
+ */
+ public List<EntryType> getEntry()
+ {
+ if (entry == null)
+ {
+ entry = new ArrayList<EntryType>();
}
+ return this.entry;
+ }
}
// Generated on: 2018.09.14 at 02:46:00 PM BST
//
-
package jalview.xml.binding.embl;
import java.math.BigInteger;
import javax.xml.bind.annotation.XmlType;
import javax.xml.datatype.XMLGregorianCalendar;
-
/**
- * <p>Java class for EntryType complex type.
+ * <p>
+ * Java class for EntryType complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
*
* <pre>
* <complexType name="EntryType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "EntryType", propOrder = {
- "secondaryAccession",
- "projectAccession",
- "description",
- "comment",
- "keyword",
- "reference",
- "xref",
- "feature",
- "assembly",
- "contig",
- "sequence"
-})
-public class EntryType {
-
- protected List<String> secondaryAccession;
- protected List<String> projectAccession;
+@XmlType(
+ name = "EntryType",
+ propOrder =
+ { "secondaryAccession", "projectAccession", "description", "comment",
+ "keyword", "reference", "xref", "feature", "assembly", "contig",
+ "sequence" })
+public class EntryType
+{
+
+ protected List<String> secondaryAccession;
+
+ protected List<String> projectAccession;
+
+ @XmlElement(required = true)
+ protected String description;
+
+ protected String comment;
+
+ protected List<String> keyword;
+
+ protected List<EntryType.Reference> reference;
+
+ protected List<XrefType> xref;
+
+ protected List<EntryType.Feature> feature;
+
+ protected EntryType.Assembly assembly;
+
+ protected EntryType.Contig contig;
+
+ protected String sequence;
+
+ @XmlAttribute(name = "accession", required = true)
+ protected String accession;
+
+ @XmlAttribute(name = "version", required = true)
+ protected BigInteger version;
+
+ @XmlAttribute(name = "entryVersion")
+ protected BigInteger entryVersion;
+
+ @XmlAttribute(name = "dataClass", required = true)
+ protected String dataClass;
+
+ @XmlAttribute(name = "taxonomicDivision", required = true)
+ protected String taxonomicDivision;
+
+ @XmlAttribute(name = "moleculeType", required = true)
+ protected String moleculeType;
+
+ @XmlAttribute(name = "sequenceLength", required = true)
+ protected BigInteger sequenceLength;
+
+ @XmlAttribute(name = "topology", required = true)
+ protected String topology;
+
+ @XmlAttribute(name = "firstPublic")
+ @XmlSchemaType(name = "date")
+ protected XMLGregorianCalendar firstPublic;
+
+ @XmlAttribute(name = "firstPublicRelease")
+ protected BigInteger firstPublicRelease;
+
+ @XmlAttribute(name = "lastUpdated")
+ @XmlSchemaType(name = "date")
+ protected XMLGregorianCalendar lastUpdated;
+
+ @XmlAttribute(name = "lastUpdatedRelease")
+ protected BigInteger lastUpdatedRelease;
+
+ /**
+ * Gets the value of the secondaryAccession property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the secondaryAccession property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getSecondaryAccession().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link String }
+ *
+ *
+ */
+ public List<String> getSecondaryAccession()
+ {
+ if (secondaryAccession == null)
+ {
+ secondaryAccession = new ArrayList<String>();
+ }
+ return this.secondaryAccession;
+ }
+
+ /**
+ * Gets the value of the projectAccession property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the projectAccession property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getProjectAccession().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link String }
+ *
+ *
+ */
+ public List<String> getProjectAccession()
+ {
+ if (projectAccession == null)
+ {
+ projectAccession = new ArrayList<String>();
+ }
+ return this.projectAccession;
+ }
+
+ /**
+ * Gets the value of the description property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDescription()
+ {
+ return description;
+ }
+
+ /**
+ * Sets the value of the description property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setDescription(String value)
+ {
+ this.description = value;
+ }
+
+ /**
+ * Gets the value of the comment property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getComment()
+ {
+ return comment;
+ }
+
+ /**
+ * Sets the value of the comment property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setComment(String value)
+ {
+ this.comment = value;
+ }
+
+ /**
+ * Gets the value of the keyword property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the keyword property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getKeyword().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link String }
+ *
+ *
+ */
+ public List<String> getKeyword()
+ {
+ if (keyword == null)
+ {
+ keyword = new ArrayList<String>();
+ }
+ return this.keyword;
+ }
+
+ /**
+ * Gets the value of the reference property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the reference property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getReference().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EntryType.Reference }
+ *
+ *
+ */
+ public List<EntryType.Reference> getReference()
+ {
+ if (reference == null)
+ {
+ reference = new ArrayList<EntryType.Reference>();
+ }
+ return this.reference;
+ }
+
+ /**
+ * Gets the value of the xref property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the xref property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getXref().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link XrefType }
+ *
+ *
+ */
+ public List<XrefType> getXref()
+ {
+ if (xref == null)
+ {
+ xref = new ArrayList<XrefType>();
+ }
+ return this.xref;
+ }
+
+ /**
+ * Gets the value of the feature property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the feature property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getFeature().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EntryType.Feature }
+ *
+ *
+ */
+ public List<EntryType.Feature> getFeature()
+ {
+ if (feature == null)
+ {
+ feature = new ArrayList<EntryType.Feature>();
+ }
+ return this.feature;
+ }
+
+ /**
+ * Gets the value of the assembly property.
+ *
+ * @return possible object is {@link EntryType.Assembly }
+ *
+ */
+ public EntryType.Assembly getAssembly()
+ {
+ return assembly;
+ }
+
+ /**
+ * Sets the value of the assembly property.
+ *
+ * @param value
+ * allowed object is {@link EntryType.Assembly }
+ *
+ */
+ public void setAssembly(EntryType.Assembly value)
+ {
+ this.assembly = value;
+ }
+
+ /**
+ * Gets the value of the contig property.
+ *
+ * @return possible object is {@link EntryType.Contig }
+ *
+ */
+ public EntryType.Contig getContig()
+ {
+ return contig;
+ }
+
+ /**
+ * Sets the value of the contig property.
+ *
+ * @param value
+ * allowed object is {@link EntryType.Contig }
+ *
+ */
+ public void setContig(EntryType.Contig value)
+ {
+ this.contig = value;
+ }
+
+ /**
+ * Gets the value of the sequence property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getSequence()
+ {
+ return sequence;
+ }
+
+ /**
+ * Sets the value of the sequence property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setSequence(String value)
+ {
+ this.sequence = value;
+ }
+
+ /**
+ * Gets the value of the accession property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getAccession()
+ {
+ return accession;
+ }
+
+ /**
+ * Sets the value of the accession property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setAccession(String value)
+ {
+ this.accession = value;
+ }
+
+ /**
+ * Gets the value of the version property.
+ *
+ * @return possible object is {@link BigInteger }
+ *
+ */
+ public BigInteger getVersion()
+ {
+ return version;
+ }
+
+ /**
+ * Sets the value of the version property.
+ *
+ * @param value
+ * allowed object is {@link BigInteger }
+ *
+ */
+ public void setVersion(BigInteger value)
+ {
+ this.version = value;
+ }
+
+ /**
+ * Gets the value of the entryVersion property.
+ *
+ * @return possible object is {@link BigInteger }
+ *
+ */
+ public BigInteger getEntryVersion()
+ {
+ return entryVersion;
+ }
+
+ /**
+ * Sets the value of the entryVersion property.
+ *
+ * @param value
+ * allowed object is {@link BigInteger }
+ *
+ */
+ public void setEntryVersion(BigInteger value)
+ {
+ this.entryVersion = value;
+ }
+
+ /**
+ * Gets the value of the dataClass property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDataClass()
+ {
+ return dataClass;
+ }
+
+ /**
+ * Sets the value of the dataClass property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setDataClass(String value)
+ {
+ this.dataClass = value;
+ }
+
+ /**
+ * Gets the value of the taxonomicDivision property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getTaxonomicDivision()
+ {
+ return taxonomicDivision;
+ }
+
+ /**
+ * Sets the value of the taxonomicDivision property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setTaxonomicDivision(String value)
+ {
+ this.taxonomicDivision = value;
+ }
+
+ /**
+ * Gets the value of the moleculeType property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getMoleculeType()
+ {
+ return moleculeType;
+ }
+
+ /**
+ * Sets the value of the moleculeType property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setMoleculeType(String value)
+ {
+ this.moleculeType = value;
+ }
+
+ /**
+ * Gets the value of the sequenceLength property.
+ *
+ * @return possible object is {@link BigInteger }
+ *
+ */
+ public BigInteger getSequenceLength()
+ {
+ return sequenceLength;
+ }
+
+ /**
+ * Sets the value of the sequenceLength property.
+ *
+ * @param value
+ * allowed object is {@link BigInteger }
+ *
+ */
+ public void setSequenceLength(BigInteger value)
+ {
+ this.sequenceLength = value;
+ }
+
+ /**
+ * Gets the value of the topology property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getTopology()
+ {
+ return topology;
+ }
+
+ /**
+ * Sets the value of the topology property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setTopology(String value)
+ {
+ this.topology = value;
+ }
+
+ /**
+ * Gets the value of the firstPublic property.
+ *
+ * @return possible object is {@link XMLGregorianCalendar }
+ *
+ */
+ public XMLGregorianCalendar getFirstPublic()
+ {
+ return firstPublic;
+ }
+
+ /**
+ * Sets the value of the firstPublic property.
+ *
+ * @param value
+ * allowed object is {@link XMLGregorianCalendar }
+ *
+ */
+ public void setFirstPublic(XMLGregorianCalendar value)
+ {
+ this.firstPublic = value;
+ }
+
+ /**
+ * Gets the value of the firstPublicRelease property.
+ *
+ * @return possible object is {@link BigInteger }
+ *
+ */
+ public BigInteger getFirstPublicRelease()
+ {
+ return firstPublicRelease;
+ }
+
+ /**
+ * Sets the value of the firstPublicRelease property.
+ *
+ * @param value
+ * allowed object is {@link BigInteger }
+ *
+ */
+ public void setFirstPublicRelease(BigInteger value)
+ {
+ this.firstPublicRelease = value;
+ }
+
+ /**
+ * Gets the value of the lastUpdated property.
+ *
+ * @return possible object is {@link XMLGregorianCalendar }
+ *
+ */
+ public XMLGregorianCalendar getLastUpdated()
+ {
+ return lastUpdated;
+ }
+
+ /**
+ * Sets the value of the lastUpdated property.
+ *
+ * @param value
+ * allowed object is {@link XMLGregorianCalendar }
+ *
+ */
+ public void setLastUpdated(XMLGregorianCalendar value)
+ {
+ this.lastUpdated = value;
+ }
+
+ /**
+ * Gets the value of the lastUpdatedRelease property.
+ *
+ * @return possible object is {@link BigInteger }
+ *
+ */
+ public BigInteger getLastUpdatedRelease()
+ {
+ return lastUpdatedRelease;
+ }
+
+ /**
+ * Sets the value of the lastUpdatedRelease property.
+ *
+ * @param value
+ * allowed object is {@link BigInteger }
+ *
+ */
+ public void setLastUpdatedRelease(BigInteger value)
+ {
+ this.lastUpdatedRelease = value;
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="range" maxOccurs="unbounded">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "range" })
+ public static class Assembly
+ {
+
@XmlElement(required = true)
- protected String description;
- protected String comment;
- protected List<String> keyword;
- protected List<EntryType.Reference> reference;
- protected List<XrefType> xref;
- protected List<EntryType.Feature> feature;
- protected EntryType.Assembly assembly;
- protected EntryType.Contig contig;
- protected String sequence;
- @XmlAttribute(name = "accession", required = true)
- protected String accession;
- @XmlAttribute(name = "version", required = true)
- protected BigInteger version;
- @XmlAttribute(name = "entryVersion")
- protected BigInteger entryVersion;
- @XmlAttribute(name = "dataClass", required = true)
- protected String dataClass;
- @XmlAttribute(name = "taxonomicDivision", required = true)
- protected String taxonomicDivision;
- @XmlAttribute(name = "moleculeType", required = true)
- protected String moleculeType;
- @XmlAttribute(name = "sequenceLength", required = true)
- protected BigInteger sequenceLength;
- @XmlAttribute(name = "topology", required = true)
- protected String topology;
- @XmlAttribute(name = "firstPublic")
- @XmlSchemaType(name = "date")
- protected XMLGregorianCalendar firstPublic;
- @XmlAttribute(name = "firstPublicRelease")
- protected BigInteger firstPublicRelease;
- @XmlAttribute(name = "lastUpdated")
- @XmlSchemaType(name = "date")
- protected XMLGregorianCalendar lastUpdated;
- @XmlAttribute(name = "lastUpdatedRelease")
- protected BigInteger lastUpdatedRelease;
+ protected List<EntryType.Assembly.Range> range;
/**
- * Gets the value of the secondaryAccession property.
+ * Gets the value of the range property.
*
* <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the secondaryAccession property.
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the range property.
*
* <p>
* For example, to add a new item, do as follows:
+ *
* <pre>
- * getSecondaryAccession().add(newItem);
+ * getRange().add(newItem);
* </pre>
*
*
* <p>
* Objects of the following type(s) are allowed in the list
- * {@link String }
+ * {@link EntryType.Assembly.Range }
*
*
*/
- public List<String> getSecondaryAccession() {
- if (secondaryAccession == null) {
- secondaryAccession = new ArrayList<String>();
- }
- return this.secondaryAccession;
+ public List<EntryType.Assembly.Range> getRange()
+ {
+ if (range == null)
+ {
+ range = new ArrayList<EntryType.Assembly.Range>();
+ }
+ return this.range;
}
/**
- * Gets the value of the projectAccession property.
- *
* <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the projectAccession property.
+ * Java class for anonymous complex type.
*
* <p>
- * For example, to add a new item, do as follows:
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
* <pre>
- * getProjectAccession().add(newItem);
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
* </pre>
*
*
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link String }
- *
- *
*/
- public List<String> getProjectAccession() {
- if (projectAccession == null) {
- projectAccession = new ArrayList<String>();
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Range
+ {
+
+ @XmlAttribute(name = "begin", required = true)
+ protected BigInteger begin;
+
+ @XmlAttribute(name = "end", required = true)
+ protected BigInteger end;
+
+ @XmlAttribute(name = "primaryBegin")
+ protected BigInteger primaryBegin;
+
+ @XmlAttribute(name = "primaryEnd")
+ protected BigInteger primaryEnd;
+
+ @XmlAttribute(name = "accession", required = true)
+ protected String accession;
+
+ @XmlAttribute(name = "version", required = true)
+ protected BigInteger version;
+
+ @XmlAttribute(name = "complement")
+ protected Boolean complement;
+
+ /**
+ * Gets the value of the begin property.
+ *
+ * @return possible object is {@link BigInteger }
+ *
+ */
+ public BigInteger getBegin()
+ {
+ return begin;
+ }
+
+ /**
+ * Sets the value of the begin property.
+ *
+ * @param value
+ * allowed object is {@link BigInteger }
+ *
+ */
+ public void setBegin(BigInteger value)
+ {
+ this.begin = value;
+ }
+
+ /**
+ * Gets the value of the end property.
+ *
+ * @return possible object is {@link BigInteger }
+ *
+ */
+ public BigInteger getEnd()
+ {
+ return end;
+ }
+
+ /**
+ * Sets the value of the end property.
+ *
+ * @param value
+ * allowed object is {@link BigInteger }
+ *
+ */
+ public void setEnd(BigInteger value)
+ {
+ this.end = value;
+ }
+
+ /**
+ * Gets the value of the primaryBegin property.
+ *
+ * @return possible object is {@link BigInteger }
+ *
+ */
+ public BigInteger getPrimaryBegin()
+ {
+ return primaryBegin;
+ }
+
+ /**
+ * Sets the value of the primaryBegin property.
+ *
+ * @param value
+ * allowed object is {@link BigInteger }
+ *
+ */
+ public void setPrimaryBegin(BigInteger value)
+ {
+ this.primaryBegin = value;
+ }
+
+ /**
+ * Gets the value of the primaryEnd property.
+ *
+ * @return possible object is {@link BigInteger }
+ *
+ */
+ public BigInteger getPrimaryEnd()
+ {
+ return primaryEnd;
+ }
+
+ /**
+ * Sets the value of the primaryEnd property.
+ *
+ * @param value
+ * allowed object is {@link BigInteger }
+ *
+ */
+ public void setPrimaryEnd(BigInteger value)
+ {
+ this.primaryEnd = value;
+ }
+
+ /**
+ * Gets the value of the accession property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getAccession()
+ {
+ return accession;
+ }
+
+ /**
+ * Sets the value of the accession property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setAccession(String value)
+ {
+ this.accession = value;
+ }
+
+ /**
+ * Gets the value of the version property.
+ *
+ * @return possible object is {@link BigInteger }
+ *
+ */
+ public BigInteger getVersion()
+ {
+ return version;
+ }
+
+ /**
+ * Sets the value of the version property.
+ *
+ * @param value
+ * allowed object is {@link BigInteger }
+ *
+ */
+ public void setVersion(BigInteger value)
+ {
+ this.version = value;
+ }
+
+ /**
+ * Gets the value of the complement property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isComplement()
+ {
+ if (complement == null)
+ {
+ return false;
}
- return this.projectAccession;
- }
-
- /**
- * Gets the value of the description property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDescription() {
- return description;
- }
-
- /**
- * Sets the value of the description property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDescription(String value) {
- this.description = value;
- }
+ else
+ {
+ return complement;
+ }
+ }
+
+ /**
+ * Sets the value of the complement property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setComplement(Boolean value)
+ {
+ this.complement = value;
+ }
- /**
- * Gets the value of the comment property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getComment() {
- return comment;
}
- /**
- * Sets the value of the comment property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setComment(String value) {
- this.comment = value;
- }
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <choice maxOccurs="unbounded" minOccurs="0">
+ * <element name="range">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="gap">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="length" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="unknownLength" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </choice>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "rangeOrGap" })
+ public static class Contig
+ {
+
+ @XmlElements({
+ @XmlElement(name = "range", type = EntryType.Contig.Range.class),
+ @XmlElement(name = "gap", type = EntryType.Contig.Gap.class) })
+ protected List<Object> rangeOrGap;
/**
- * Gets the value of the keyword property.
+ * Gets the value of the rangeOrGap property.
*
* <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the keyword property.
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the rangeOrGap property.
*
* <p>
* For example, to add a new item, do as follows:
- * <pre>
- * getKeyword().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link String }
- *
- *
- */
- public List<String> getKeyword() {
- if (keyword == null) {
- keyword = new ArrayList<String>();
- }
- return this.keyword;
- }
-
- /**
- * Gets the value of the reference property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the reference property.
*
- * <p>
- * For example, to add a new item, do as follows:
* <pre>
- * getReference().add(newItem);
+ * getRangeOrGap().add(newItem);
* </pre>
*
*
* <p>
* Objects of the following type(s) are allowed in the list
- * {@link EntryType.Reference }
+ * {@link EntryType.Contig.Range } {@link EntryType.Contig.Gap }
*
*
*/
- public List<EntryType.Reference> getReference() {
- if (reference == null) {
- reference = new ArrayList<EntryType.Reference>();
- }
- return this.reference;
+ public List<Object> getRangeOrGap()
+ {
+ if (rangeOrGap == null)
+ {
+ rangeOrGap = new ArrayList<Object>();
+ }
+ return this.rangeOrGap;
}
/**
- * Gets the value of the xref property.
- *
* <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the xref property.
+ * Java class for anonymous complex type.
*
* <p>
- * For example, to add a new item, do as follows:
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
* <pre>
- * getXref().add(newItem);
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="length" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="unknownLength" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
* </pre>
*
*
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link XrefType }
- *
- *
*/
- public List<XrefType> getXref() {
- if (xref == null) {
- xref = new ArrayList<XrefType>();
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Gap
+ {
+
+ @XmlAttribute(name = "begin", required = true)
+ protected BigInteger begin;
+
+ @XmlAttribute(name = "end", required = true)
+ protected BigInteger end;
+
+ @XmlAttribute(name = "length", required = true)
+ protected BigInteger length;
+
+ @XmlAttribute(name = "unknownLength")
+ protected Boolean unknownLength;
+
+ /**
+ * Gets the value of the begin property.
+ *
+ * @return possible object is {@link BigInteger }
+ *
+ */
+ public BigInteger getBegin()
+ {
+ return begin;
+ }
+
+ /**
+ * Sets the value of the begin property.
+ *
+ * @param value
+ * allowed object is {@link BigInteger }
+ *
+ */
+ public void setBegin(BigInteger value)
+ {
+ this.begin = value;
+ }
+
+ /**
+ * Gets the value of the end property.
+ *
+ * @return possible object is {@link BigInteger }
+ *
+ */
+ public BigInteger getEnd()
+ {
+ return end;
+ }
+
+ /**
+ * Sets the value of the end property.
+ *
+ * @param value
+ * allowed object is {@link BigInteger }
+ *
+ */
+ public void setEnd(BigInteger value)
+ {
+ this.end = value;
+ }
+
+ /**
+ * Gets the value of the length property.
+ *
+ * @return possible object is {@link BigInteger }
+ *
+ */
+ public BigInteger getLength()
+ {
+ return length;
+ }
+
+ /**
+ * Sets the value of the length property.
+ *
+ * @param value
+ * allowed object is {@link BigInteger }
+ *
+ */
+ public void setLength(BigInteger value)
+ {
+ this.length = value;
+ }
+
+ /**
+ * Gets the value of the unknownLength property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isUnknownLength()
+ {
+ if (unknownLength == null)
+ {
+ return false;
+ }
+ else
+ {
+ return unknownLength;
}
- return this.xref;
+ }
+
+ /**
+ * Sets the value of the unknownLength property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setUnknownLength(Boolean value)
+ {
+ this.unknownLength = value;
+ }
+
}
/**
- * Gets the value of the feature property.
- *
* <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the feature property.
+ * Java class for anonymous complex type.
*
* <p>
- * For example, to add a new item, do as follows:
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
* <pre>
- * getFeature().add(newItem);
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
* </pre>
*
*
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EntryType.Feature }
- *
- *
*/
- public List<EntryType.Feature> getFeature() {
- if (feature == null) {
- feature = new ArrayList<EntryType.Feature>();
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Range
+ {
+
+ @XmlAttribute(name = "begin", required = true)
+ protected BigInteger begin;
+
+ @XmlAttribute(name = "end", required = true)
+ protected BigInteger end;
+
+ @XmlAttribute(name = "primaryBegin")
+ protected BigInteger primaryBegin;
+
+ @XmlAttribute(name = "primaryEnd")
+ protected BigInteger primaryEnd;
+
+ @XmlAttribute(name = "accession", required = true)
+ protected String accession;
+
+ @XmlAttribute(name = "version", required = true)
+ protected BigInteger version;
+
+ @XmlAttribute(name = "complement")
+ protected Boolean complement;
+
+ /**
+ * Gets the value of the begin property.
+ *
+ * @return possible object is {@link BigInteger }
+ *
+ */
+ public BigInteger getBegin()
+ {
+ return begin;
+ }
+
+ /**
+ * Sets the value of the begin property.
+ *
+ * @param value
+ * allowed object is {@link BigInteger }
+ *
+ */
+ public void setBegin(BigInteger value)
+ {
+ this.begin = value;
+ }
+
+ /**
+ * Gets the value of the end property.
+ *
+ * @return possible object is {@link BigInteger }
+ *
+ */
+ public BigInteger getEnd()
+ {
+ return end;
+ }
+
+ /**
+ * Sets the value of the end property.
+ *
+ * @param value
+ * allowed object is {@link BigInteger }
+ *
+ */
+ public void setEnd(BigInteger value)
+ {
+ this.end = value;
+ }
+
+ /**
+ * Gets the value of the primaryBegin property.
+ *
+ * @return possible object is {@link BigInteger }
+ *
+ */
+ public BigInteger getPrimaryBegin()
+ {
+ return primaryBegin;
+ }
+
+ /**
+ * Sets the value of the primaryBegin property.
+ *
+ * @param value
+ * allowed object is {@link BigInteger }
+ *
+ */
+ public void setPrimaryBegin(BigInteger value)
+ {
+ this.primaryBegin = value;
+ }
+
+ /**
+ * Gets the value of the primaryEnd property.
+ *
+ * @return possible object is {@link BigInteger }
+ *
+ */
+ public BigInteger getPrimaryEnd()
+ {
+ return primaryEnd;
+ }
+
+ /**
+ * Sets the value of the primaryEnd property.
+ *
+ * @param value
+ * allowed object is {@link BigInteger }
+ *
+ */
+ public void setPrimaryEnd(BigInteger value)
+ {
+ this.primaryEnd = value;
+ }
+
+ /**
+ * Gets the value of the accession property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getAccession()
+ {
+ return accession;
+ }
+
+ /**
+ * Sets the value of the accession property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setAccession(String value)
+ {
+ this.accession = value;
+ }
+
+ /**
+ * Gets the value of the version property.
+ *
+ * @return possible object is {@link BigInteger }
+ *
+ */
+ public BigInteger getVersion()
+ {
+ return version;
+ }
+
+ /**
+ * Sets the value of the version property.
+ *
+ * @param value
+ * allowed object is {@link BigInteger }
+ *
+ */
+ public void setVersion(BigInteger value)
+ {
+ this.version = value;
+ }
+
+ /**
+ * Gets the value of the complement property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isComplement()
+ {
+ if (complement == null)
+ {
+ return false;
}
- return this.feature;
- }
+ else
+ {
+ return complement;
+ }
+ }
+
+ /**
+ * Sets the value of the complement property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setComplement(Boolean value)
+ {
+ this.complement = value;
+ }
- /**
- * Gets the value of the assembly property.
- *
- * @return
- * possible object is
- * {@link EntryType.Assembly }
- *
- */
- public EntryType.Assembly getAssembly() {
- return assembly;
}
- /**
- * Sets the value of the assembly property.
- *
- * @param value
- * allowed object is
- * {@link EntryType.Assembly }
- *
- */
- public void setAssembly(EntryType.Assembly value) {
- this.assembly = value;
- }
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="taxon" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="lineage" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="taxon" maxOccurs="unbounded">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="commonName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="taxId" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="xref" type="{}XrefType" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="qualifier" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="value" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="location" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "taxon", "xref", "qualifier" })
+ public static class Feature
+ {
+
+ protected EntryType.Feature.FeatureTaxon taxon;
- /**
- * Gets the value of the contig property.
- *
- * @return
- * possible object is
- * {@link EntryType.Contig }
- *
- */
- public EntryType.Contig getContig() {
- return contig;
- }
+ protected List<XrefType> xref;
- /**
- * Sets the value of the contig property.
- *
- * @param value
- * allowed object is
- * {@link EntryType.Contig }
- *
- */
- public void setContig(EntryType.Contig value) {
- this.contig = value;
- }
+ protected List<EntryType.Feature.Qualifier> qualifier;
- /**
- * Gets the value of the sequence property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getSequence() {
- return sequence;
- }
+ @XmlAttribute(name = "name", required = true)
+ protected String name;
- /**
- * Sets the value of the sequence property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setSequence(String value) {
- this.sequence = value;
- }
+ @XmlAttribute(name = "location", required = true)
+ protected String location;
/**
- * Gets the value of the accession property.
+ * Gets the value of the taxon property.
+ *
+ * @return possible object is {@link EntryType.Feature.FeatureTaxon }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getAccession() {
- return accession;
+ public EntryType.Feature.FeatureTaxon getTaxon()
+ {
+ return taxon;
}
/**
- * Sets the value of the accession property.
+ * Sets the value of the taxon property.
*
* @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setAccession(String value) {
- this.accession = value;
- }
-
- /**
- * Gets the value of the version property.
+ * allowed object is {@link EntryType.Feature.FeatureTaxon }
*
- * @return
- * possible object is
- * {@link BigInteger }
- *
*/
- public BigInteger getVersion() {
- return version;
+ public void setTaxon(EntryType.Feature.FeatureTaxon value)
+ {
+ this.taxon = value;
}
/**
- * Sets the value of the version property.
+ * Gets the value of the xref property.
*
- * @param value
- * allowed object is
- * {@link BigInteger }
- *
- */
- public void setVersion(BigInteger value) {
- this.version = value;
- }
-
- /**
- * Gets the value of the entryVersion property.
+ * <p>
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the xref property.
*
- * @return
- * possible object is
- * {@link BigInteger }
- *
- */
- public BigInteger getEntryVersion() {
- return entryVersion;
- }
-
- /**
- * Sets the value of the entryVersion property.
+ * <p>
+ * For example, to add a new item, do as follows:
*
- * @param value
- * allowed object is
- * {@link BigInteger }
- *
- */
- public void setEntryVersion(BigInteger value) {
- this.entryVersion = value;
- }
-
- /**
- * Gets the value of the dataClass property.
+ * <pre>
+ * getXref().add(newItem);
+ * </pre>
*
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDataClass() {
- return dataClass;
- }
-
- /**
- * Sets the value of the dataClass property.
*
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDataClass(String value) {
- this.dataClass = value;
- }
-
- /**
- * Gets the value of the taxonomicDivision property.
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link XrefType
+ * }
*
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getTaxonomicDivision() {
- return taxonomicDivision;
- }
-
- /**
- * Sets the value of the taxonomicDivision property.
*
- * @param value
- * allowed object is
- * {@link String }
- *
*/
- public void setTaxonomicDivision(String value) {
- this.taxonomicDivision = value;
+ public List<XrefType> getXref()
+ {
+ if (xref == null)
+ {
+ xref = new ArrayList<XrefType>();
+ }
+ return this.xref;
}
/**
- * Gets the value of the moleculeType property.
+ * Gets the value of the qualifier property.
*
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getMoleculeType() {
- return moleculeType;
- }
-
- /**
- * Sets the value of the moleculeType property.
+ * <p>
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the qualifier property.
*
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setMoleculeType(String value) {
- this.moleculeType = value;
- }
-
- /**
- * Gets the value of the sequenceLength property.
+ * <p>
+ * For example, to add a new item, do as follows:
*
- * @return
- * possible object is
- * {@link BigInteger }
- *
- */
- public BigInteger getSequenceLength() {
- return sequenceLength;
- }
-
- /**
- * Sets the value of the sequenceLength property.
+ * <pre>
+ * getQualifier().add(newItem);
+ * </pre>
*
- * @param value
- * allowed object is
- * {@link BigInteger }
- *
- */
- public void setSequenceLength(BigInteger value) {
- this.sequenceLength = value;
- }
-
- /**
- * Gets the value of the topology property.
*
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getTopology() {
- return topology;
- }
-
- /**
- * Sets the value of the topology property.
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EntryType.Feature.Qualifier }
*
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setTopology(String value) {
- this.topology = value;
- }
-
- /**
- * Gets the value of the firstPublic property.
*
- * @return
- * possible object is
- * {@link XMLGregorianCalendar }
- *
*/
- public XMLGregorianCalendar getFirstPublic() {
- return firstPublic;
+ public List<EntryType.Feature.Qualifier> getQualifier()
+ {
+ if (qualifier == null)
+ {
+ qualifier = new ArrayList<EntryType.Feature.Qualifier>();
+ }
+ return this.qualifier;
}
/**
- * Sets the value of the firstPublic property.
+ * Gets the value of the name property.
*
- * @param value
- * allowed object is
- * {@link XMLGregorianCalendar }
- *
- */
- public void setFirstPublic(XMLGregorianCalendar value) {
- this.firstPublic = value;
- }
-
- /**
- * Gets the value of the firstPublicRelease property.
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link BigInteger }
- *
*/
- public BigInteger getFirstPublicRelease() {
- return firstPublicRelease;
+ public String getName()
+ {
+ return name;
}
/**
- * Sets the value of the firstPublicRelease property.
+ * Sets the value of the name property.
*
* @param value
- * allowed object is
- * {@link BigInteger }
- *
- */
- public void setFirstPublicRelease(BigInteger value) {
- this.firstPublicRelease = value;
- }
-
- /**
- * Gets the value of the lastUpdated property.
+ * allowed object is {@link String }
*
- * @return
- * possible object is
- * {@link XMLGregorianCalendar }
- *
*/
- public XMLGregorianCalendar getLastUpdated() {
- return lastUpdated;
+ public void setName(String value)
+ {
+ this.name = value;
}
/**
- * Sets the value of the lastUpdated property.
+ * Gets the value of the location property.
*
- * @param value
- * allowed object is
- * {@link XMLGregorianCalendar }
- *
- */
- public void setLastUpdated(XMLGregorianCalendar value) {
- this.lastUpdated = value;
- }
-
- /**
- * Gets the value of the lastUpdatedRelease property.
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link BigInteger }
- *
*/
- public BigInteger getLastUpdatedRelease() {
- return lastUpdatedRelease;
+ public String getLocation()
+ {
+ return location;
}
/**
- * Sets the value of the lastUpdatedRelease property.
+ * Sets the value of the location property.
*
* @param value
- * allowed object is
- * {@link BigInteger }
- *
+ * allowed object is {@link String }
+ *
*/
- public void setLastUpdatedRelease(BigInteger value) {
- this.lastUpdatedRelease = value;
+ public void setLocation(String value)
+ {
+ this.location = value;
}
-
/**
- * <p>Java class for anonymous complex type.
+ * <p>
+ * Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
*
* <pre>
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
* <sequence>
- * <element name="range" maxOccurs="unbounded">
+ * <element name="lineage" minOccurs="0">
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <sequence>
+ * <element name="taxon" maxOccurs="unbounded">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
* </restriction>
* </complexContent>
* </complexType>
* </element>
* </sequence>
+ * <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="commonName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="taxId" type="{http://www.w3.org/2001/XMLSchema}integer" />
* </restriction>
* </complexContent>
* </complexType>
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "range"
- })
- public static class Assembly {
+ @XmlType(name = "", propOrder = { "lineage" })
+ public static class FeatureTaxon
+ {
+
+ protected EntryType.Feature.FeatureTaxon.Lineage lineage;
+
+ @XmlAttribute(name = "scientificName", required = true)
+ protected String scientificName;
+
+ @XmlAttribute(name = "commonName")
+ protected String commonName;
+
+ @XmlAttribute(name = "taxId")
+ protected BigInteger taxId;
+
+ /**
+ * Gets the value of the lineage property.
+ *
+ * @return possible object is
+ * {@link EntryType.Feature.FeatureTaxon.Lineage }
+ *
+ */
+ public EntryType.Feature.FeatureTaxon.Lineage getLineage()
+ {
+ return lineage;
+ }
+
+ /**
+ * Sets the value of the lineage property.
+ *
+ * @param value
+ * allowed object is
+ * {@link EntryType.Feature.FeatureTaxon.Lineage }
+ *
+ */
+ public void setLineage(EntryType.Feature.FeatureTaxon.Lineage value)
+ {
+ this.lineage = value;
+ }
+
+ /**
+ * Gets the value of the scientificName property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getScientificName()
+ {
+ return scientificName;
+ }
+
+ /**
+ * Sets the value of the scientificName property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setScientificName(String value)
+ {
+ this.scientificName = value;
+ }
+
+ /**
+ * Gets the value of the commonName property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getCommonName()
+ {
+ return commonName;
+ }
+
+ /**
+ * Sets the value of the commonName property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setCommonName(String value)
+ {
+ this.commonName = value;
+ }
+
+ /**
+ * Gets the value of the taxId property.
+ *
+ * @return possible object is {@link BigInteger }
+ *
+ */
+ public BigInteger getTaxId()
+ {
+ return taxId;
+ }
+
+ /**
+ * Sets the value of the taxId property.
+ *
+ * @param value
+ * allowed object is {@link BigInteger }
+ *
+ */
+ public void setTaxId(BigInteger value)
+ {
+ this.taxId = value;
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="taxon" maxOccurs="unbounded">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "taxon" })
+ public static class Lineage
+ {
@XmlElement(required = true)
- protected List<EntryType.Assembly.Range> range;
+ protected List<EntryType.Feature.FeatureTaxon.Lineage.Taxon> taxon;
/**
- * Gets the value of the range property.
+ * Gets the value of the taxon property.
*
* <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the range property.
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list
+ * will be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the taxon property.
*
* <p>
* For example, to add a new item, do as follows:
+ *
* <pre>
- * getRange().add(newItem);
+ * getTaxon().add(newItem);
* </pre>
*
*
* <p>
* Objects of the following type(s) are allowed in the list
- * {@link EntryType.Assembly.Range }
- *
- *
- */
- public List<EntryType.Assembly.Range> getRange() {
- if (range == null) {
- range = new ArrayList<EntryType.Assembly.Range>();
- }
- return this.range;
- }
-
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * {@link EntryType.Feature.FeatureTaxon.Lineage.Taxon }
*
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class Range {
-
- @XmlAttribute(name = "begin", required = true)
- protected BigInteger begin;
- @XmlAttribute(name = "end", required = true)
- protected BigInteger end;
- @XmlAttribute(name = "primaryBegin")
- protected BigInteger primaryBegin;
- @XmlAttribute(name = "primaryEnd")
- protected BigInteger primaryEnd;
- @XmlAttribute(name = "accession", required = true)
- protected String accession;
- @XmlAttribute(name = "version", required = true)
- protected BigInteger version;
- @XmlAttribute(name = "complement")
- protected Boolean complement;
-
- /**
- * Gets the value of the begin property.
- *
- * @return
- * possible object is
- * {@link BigInteger }
- *
- */
- public BigInteger getBegin() {
- return begin;
- }
-
- /**
- * Sets the value of the begin property.
- *
- * @param value
- * allowed object is
- * {@link BigInteger }
- *
- */
- public void setBegin(BigInteger value) {
- this.begin = value;
- }
-
- /**
- * Gets the value of the end property.
- *
- * @return
- * possible object is
- * {@link BigInteger }
- *
- */
- public BigInteger getEnd() {
- return end;
- }
-
- /**
- * Sets the value of the end property.
- *
- * @param value
- * allowed object is
- * {@link BigInteger }
- *
- */
- public void setEnd(BigInteger value) {
- this.end = value;
- }
-
- /**
- * Gets the value of the primaryBegin property.
- *
- * @return
- * possible object is
- * {@link BigInteger }
- *
- */
- public BigInteger getPrimaryBegin() {
- return primaryBegin;
- }
-
- /**
- * Sets the value of the primaryBegin property.
- *
- * @param value
- * allowed object is
- * {@link BigInteger }
- *
- */
- public void setPrimaryBegin(BigInteger value) {
- this.primaryBegin = value;
- }
-
- /**
- * Gets the value of the primaryEnd property.
- *
- * @return
- * possible object is
- * {@link BigInteger }
- *
- */
- public BigInteger getPrimaryEnd() {
- return primaryEnd;
- }
-
- /**
- * Sets the value of the primaryEnd property.
- *
- * @param value
- * allowed object is
- * {@link BigInteger }
- *
- */
- public void setPrimaryEnd(BigInteger value) {
- this.primaryEnd = value;
- }
-
- /**
- * Gets the value of the accession property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getAccession() {
- return accession;
- }
-
- /**
- * Sets the value of the accession property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setAccession(String value) {
- this.accession = value;
- }
-
- /**
- * Gets the value of the version property.
- *
- * @return
- * possible object is
- * {@link BigInteger }
- *
- */
- public BigInteger getVersion() {
- return version;
- }
-
- /**
- * Sets the value of the version property.
- *
- * @param value
- * allowed object is
- * {@link BigInteger }
- *
- */
- public void setVersion(BigInteger value) {
- this.version = value;
- }
-
- /**
- * Gets the value of the complement property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isComplement() {
- if (complement == null) {
- return false;
- } else {
- return complement;
- }
- }
-
- /**
- * Sets the value of the complement property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setComplement(Boolean value) {
- this.complement = value;
- }
-
+ public List<EntryType.Feature.FeatureTaxon.Lineage.Taxon> getTaxon()
+ {
+ if (taxon == null)
+ {
+ taxon = new ArrayList<EntryType.Feature.FeatureTaxon.Lineage.Taxon>();
+ }
+ return this.taxon;
}
- }
-
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <choice maxOccurs="unbounded" minOccurs="0">
- * <element name="range">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="gap">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="length" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="unknownLength" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </choice>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "rangeOrGap"
- })
- public static class Contig {
-
- @XmlElements({
- @XmlElement(name = "range", type = EntryType.Contig.Range.class),
- @XmlElement(name = "gap", type = EntryType.Contig.Gap.class)
- })
- protected List<Object> rangeOrGap;
-
/**
- * Gets the value of the rangeOrGap property.
- *
* <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the rangeOrGap property.
+ * Java class for anonymous complex type.
*
* <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getRangeOrGap().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EntryType.Contig.Range }
- * {@link EntryType.Contig.Gap }
- *
- *
- */
- public List<Object> getRangeOrGap() {
- if (rangeOrGap == null) {
- rangeOrGap = new ArrayList<Object>();
- }
- return this.rangeOrGap;
- }
-
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * The following schema fragment specifies the expected content
+ * contained within this class.
*
* <pre>
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="length" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="unknownLength" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
* </restriction>
* </complexContent>
* </complexType>
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "")
- public static class Gap {
-
- @XmlAttribute(name = "begin", required = true)
- protected BigInteger begin;
- @XmlAttribute(name = "end", required = true)
- protected BigInteger end;
- @XmlAttribute(name = "length", required = true)
- protected BigInteger length;
- @XmlAttribute(name = "unknownLength")
- protected Boolean unknownLength;
-
- /**
- * Gets the value of the begin property.
- *
- * @return
- * possible object is
- * {@link BigInteger }
- *
- */
- public BigInteger getBegin() {
- return begin;
- }
-
- /**
- * Sets the value of the begin property.
- *
- * @param value
- * allowed object is
- * {@link BigInteger }
- *
- */
- public void setBegin(BigInteger value) {
- this.begin = value;
- }
-
- /**
- * Gets the value of the end property.
- *
- * @return
- * possible object is
- * {@link BigInteger }
- *
- */
- public BigInteger getEnd() {
- return end;
- }
-
- /**
- * Sets the value of the end property.
- *
- * @param value
- * allowed object is
- * {@link BigInteger }
- *
- */
- public void setEnd(BigInteger value) {
- this.end = value;
- }
-
- /**
- * Gets the value of the length property.
- *
- * @return
- * possible object is
- * {@link BigInteger }
- *
- */
- public BigInteger getLength() {
- return length;
- }
-
- /**
- * Sets the value of the length property.
- *
- * @param value
- * allowed object is
- * {@link BigInteger }
- *
- */
- public void setLength(BigInteger value) {
- this.length = value;
- }
-
- /**
- * Gets the value of the unknownLength property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isUnknownLength() {
- if (unknownLength == null) {
- return false;
- } else {
- return unknownLength;
- }
- }
-
- /**
- * Sets the value of the unknownLength property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setUnknownLength(Boolean value) {
- this.unknownLength = value;
- }
+ public static class Taxon
+ {
+
+ @XmlAttribute(name = "scientificName", required = true)
+ protected String scientificName;
+
+ /**
+ * Gets the value of the scientificName property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getScientificName()
+ {
+ return scientificName;
+ }
+
+ /**
+ * Sets the value of the scientificName property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setScientificName(String value)
+ {
+ this.scientificName = value;
+ }
}
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class Range {
-
- @XmlAttribute(name = "begin", required = true)
- protected BigInteger begin;
- @XmlAttribute(name = "end", required = true)
- protected BigInteger end;
- @XmlAttribute(name = "primaryBegin")
- protected BigInteger primaryBegin;
- @XmlAttribute(name = "primaryEnd")
- protected BigInteger primaryEnd;
- @XmlAttribute(name = "accession", required = true)
- protected String accession;
- @XmlAttribute(name = "version", required = true)
- protected BigInteger version;
- @XmlAttribute(name = "complement")
- protected Boolean complement;
-
- /**
- * Gets the value of the begin property.
- *
- * @return
- * possible object is
- * {@link BigInteger }
- *
- */
- public BigInteger getBegin() {
- return begin;
- }
-
- /**
- * Sets the value of the begin property.
- *
- * @param value
- * allowed object is
- * {@link BigInteger }
- *
- */
- public void setBegin(BigInteger value) {
- this.begin = value;
- }
-
- /**
- * Gets the value of the end property.
- *
- * @return
- * possible object is
- * {@link BigInteger }
- *
- */
- public BigInteger getEnd() {
- return end;
- }
-
- /**
- * Sets the value of the end property.
- *
- * @param value
- * allowed object is
- * {@link BigInteger }
- *
- */
- public void setEnd(BigInteger value) {
- this.end = value;
- }
-
- /**
- * Gets the value of the primaryBegin property.
- *
- * @return
- * possible object is
- * {@link BigInteger }
- *
- */
- public BigInteger getPrimaryBegin() {
- return primaryBegin;
- }
-
- /**
- * Sets the value of the primaryBegin property.
- *
- * @param value
- * allowed object is
- * {@link BigInteger }
- *
- */
- public void setPrimaryBegin(BigInteger value) {
- this.primaryBegin = value;
- }
-
- /**
- * Gets the value of the primaryEnd property.
- *
- * @return
- * possible object is
- * {@link BigInteger }
- *
- */
- public BigInteger getPrimaryEnd() {
- return primaryEnd;
- }
-
- /**
- * Sets the value of the primaryEnd property.
- *
- * @param value
- * allowed object is
- * {@link BigInteger }
- *
- */
- public void setPrimaryEnd(BigInteger value) {
- this.primaryEnd = value;
- }
-
- /**
- * Gets the value of the accession property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getAccession() {
- return accession;
- }
-
- /**
- * Sets the value of the accession property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setAccession(String value) {
- this.accession = value;
- }
-
- /**
- * Gets the value of the version property.
- *
- * @return
- * possible object is
- * {@link BigInteger }
- *
- */
- public BigInteger getVersion() {
- return version;
- }
-
- /**
- * Sets the value of the version property.
- *
- * @param value
- * allowed object is
- * {@link BigInteger }
- *
- */
- public void setVersion(BigInteger value) {
- this.version = value;
- }
-
- /**
- * Gets the value of the complement property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isComplement() {
- if (complement == null) {
- return false;
- } else {
- return complement;
- }
- }
-
- /**
- * Sets the value of the complement property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setComplement(Boolean value) {
- this.complement = value;
- }
-
- }
+ }
}
-
/**
- * <p>Java class for anonymous complex type.
+ * <p>
+ * Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
*
* <pre>
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
* <sequence>
- * <element name="taxon" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="lineage" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="taxon" maxOccurs="unbounded">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="commonName" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="taxId" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="xref" type="{}XrefType" maxOccurs="unbounded" minOccurs="0"/>
- * <element name="qualifier" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="value" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- * </sequence>
- * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
+ * <element name="value" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
* </sequence>
* <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="location" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
* </restriction>
* </complexContent>
* </complexType>
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "taxon",
- "xref",
- "qualifier"
- })
- public static class Feature {
-
- protected EntryType.Feature.FeatureTaxon taxon;
- protected List<XrefType> xref;
- protected List<EntryType.Feature.Qualifier> qualifier;
- @XmlAttribute(name = "name", required = true)
- protected String name;
- @XmlAttribute(name = "location", required = true)
- protected String location;
+ @XmlType(name = "", propOrder = { "value" })
+ public static class Qualifier
+ {
+
+ protected String value;
+
+ @XmlAttribute(name = "name", required = true)
+ protected String name;
+
+ /**
+ * Gets the value of the value property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getValue()
+ {
+ return value;
+ }
+
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setValue(String value)
+ {
+ this.value = value;
+ }
+
+ /**
+ * Gets the value of the name property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getName()
+ {
+ return name;
+ }
+
+ /**
+ * Sets the value of the name property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setName(String value)
+ {
+ this.name = value;
+ }
- /**
- * Gets the value of the taxon property.
- *
- * @return
- * possible object is
- * {@link EntryType.Feature.FeatureTaxon }
- *
- */
- public EntryType.Feature.FeatureTaxon getTaxon() {
- return taxon;
- }
+ }
- /**
- * Sets the value of the taxon property.
- *
- * @param value
- * allowed object is
- * {@link EntryType.Feature.FeatureTaxon }
- *
- */
- public void setTaxon(EntryType.Feature.FeatureTaxon value) {
- this.taxon = value;
- }
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="title" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="author" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="applicant" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="consortium" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="submissionDate" type="{http://www.w3.org/2001/XMLSchema}date" minOccurs="0"/>
+ * <element name="journal" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="year" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="volume" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="issue" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="firstPage" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="lastPage" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="comment" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="referenceLocation" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ * <element name="xref" type="{}XrefType" maxOccurs="unbounded" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="type" use="required">
+ * <simpleType>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ * <enumeration value="submission"/>
+ * <enumeration value="book"/>
+ * <enumeration value="article"/>
+ * <enumeration value="patent"/>
+ * <enumeration value="thesis"/>
+ * <enumeration value="unpublished"/>
+ * </restriction>
+ * </simpleType>
+ * </attribute>
+ * <attribute name="number" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="location" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(
+ name = "",
+ propOrder =
+ { "title", "author", "applicant", "consortium", "submissionDate",
+ "journal", "year", "volume", "issue", "firstPage", "lastPage",
+ "comment", "referenceLocation", "xref" })
+ public static class Reference
+ {
+
+ protected String title;
+
+ protected List<String> author;
+
+ protected List<String> applicant;
+
+ protected String consortium;
- /**
- * Gets the value of the xref property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the xref property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getXref().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link XrefType }
- *
- *
- */
- public List<XrefType> getXref() {
- if (xref == null) {
- xref = new ArrayList<XrefType>();
- }
- return this.xref;
- }
+ @XmlSchemaType(name = "date")
+ protected XMLGregorianCalendar submissionDate;
- /**
- * Gets the value of the qualifier property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the qualifier property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getQualifier().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EntryType.Feature.Qualifier }
- *
- *
- */
- public List<EntryType.Feature.Qualifier> getQualifier() {
- if (qualifier == null) {
- qualifier = new ArrayList<EntryType.Feature.Qualifier>();
- }
- return this.qualifier;
- }
+ protected String journal;
- /**
- * Gets the value of the name property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getName() {
- return name;
- }
+ protected String year;
- /**
- * Sets the value of the name property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setName(String value) {
- this.name = value;
- }
+ protected String volume;
- /**
- * Gets the value of the location property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getLocation() {
- return location;
- }
+ protected String issue;
- /**
- * Sets the value of the location property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setLocation(String value) {
- this.location = value;
- }
+ protected String firstPage;
+ protected String lastPage;
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="lineage" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="taxon" maxOccurs="unbounded">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="commonName" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="taxId" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "lineage"
- })
- public static class FeatureTaxon {
-
- protected EntryType.Feature.FeatureTaxon.Lineage lineage;
- @XmlAttribute(name = "scientificName", required = true)
- protected String scientificName;
- @XmlAttribute(name = "commonName")
- protected String commonName;
- @XmlAttribute(name = "taxId")
- protected BigInteger taxId;
-
- /**
- * Gets the value of the lineage property.
- *
- * @return
- * possible object is
- * {@link EntryType.Feature.FeatureTaxon.Lineage }
- *
- */
- public EntryType.Feature.FeatureTaxon.Lineage getLineage() {
- return lineage;
- }
-
- /**
- * Sets the value of the lineage property.
- *
- * @param value
- * allowed object is
- * {@link EntryType.Feature.FeatureTaxon.Lineage }
- *
- */
- public void setLineage(EntryType.Feature.FeatureTaxon.Lineage value) {
- this.lineage = value;
- }
-
- /**
- * Gets the value of the scientificName property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getScientificName() {
- return scientificName;
- }
-
- /**
- * Sets the value of the scientificName property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setScientificName(String value) {
- this.scientificName = value;
- }
-
- /**
- * Gets the value of the commonName property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getCommonName() {
- return commonName;
- }
-
- /**
- * Sets the value of the commonName property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setCommonName(String value) {
- this.commonName = value;
- }
-
- /**
- * Gets the value of the taxId property.
- *
- * @return
- * possible object is
- * {@link BigInteger }
- *
- */
- public BigInteger getTaxId() {
- return taxId;
- }
-
- /**
- * Sets the value of the taxId property.
- *
- * @param value
- * allowed object is
- * {@link BigInteger }
- *
- */
- public void setTaxId(BigInteger value) {
- this.taxId = value;
- }
-
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="taxon" maxOccurs="unbounded">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "taxon"
- })
- public static class Lineage {
-
- @XmlElement(required = true)
- protected List<EntryType.Feature.FeatureTaxon.Lineage.Taxon> taxon;
-
- /**
- * Gets the value of the taxon property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the taxon property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getTaxon().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EntryType.Feature.FeatureTaxon.Lineage.Taxon }
- *
- *
- */
- public List<EntryType.Feature.FeatureTaxon.Lineage.Taxon> getTaxon() {
- if (taxon == null) {
- taxon = new ArrayList<EntryType.Feature.FeatureTaxon.Lineage.Taxon>();
- }
- return this.taxon;
- }
-
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class Taxon {
-
- @XmlAttribute(name = "scientificName", required = true)
- protected String scientificName;
-
- /**
- * Gets the value of the scientificName property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getScientificName() {
- return scientificName;
- }
-
- /**
- * Sets the value of the scientificName property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setScientificName(String value) {
- this.scientificName = value;
- }
-
- }
-
- }
+ protected String comment;
- }
+ protected String referenceLocation;
+ protected List<XrefType> xref;
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="value" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- * </sequence>
- * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "value"
- })
- public static class Qualifier {
-
- protected String value;
- @XmlAttribute(name = "name", required = true)
- protected String name;
-
- /**
- * Gets the value of the value property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getValue() {
- return value;
- }
-
- /**
- * Sets the value of the value property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setValue(String value) {
- this.value = value;
- }
-
- /**
- * Gets the value of the name property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getName() {
- return name;
- }
-
- /**
- * Sets the value of the name property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setName(String value) {
- this.name = value;
- }
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
- }
+ @XmlAttribute(name = "number", required = true)
+ protected BigInteger number;
+
+ @XmlAttribute(name = "location")
+ protected String location;
+ /**
+ * Gets the value of the title property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getTitle()
+ {
+ return title;
}
+ /**
+ * Sets the value of the title property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setTitle(String value)
+ {
+ this.title = value;
+ }
/**
- * <p>Java class for anonymous complex type.
+ * Gets the value of the author property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the author property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
*
* <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="title" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- * <element name="author" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
- * <element name="applicant" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
- * <element name="consortium" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- * <element name="submissionDate" type="{http://www.w3.org/2001/XMLSchema}date" minOccurs="0"/>
- * <element name="journal" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- * <element name="year" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- * <element name="volume" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- * <element name="issue" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- * <element name="firstPage" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- * <element name="lastPage" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- * <element name="comment" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- * <element name="referenceLocation" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- * <element name="xref" type="{}XrefType" maxOccurs="unbounded" minOccurs="0"/>
- * </sequence>
- * <attribute name="type" use="required">
- * <simpleType>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
- * <enumeration value="submission"/>
- * <enumeration value="book"/>
- * <enumeration value="article"/>
- * <enumeration value="patent"/>
- * <enumeration value="thesis"/>
- * <enumeration value="unpublished"/>
- * </restriction>
- * </simpleType>
- * </attribute>
- * <attribute name="number" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="location" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
+ * getAuthor().add(newItem);
* </pre>
*
*
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link String }
+ *
+ *
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "title",
- "author",
- "applicant",
- "consortium",
- "submissionDate",
- "journal",
- "year",
- "volume",
- "issue",
- "firstPage",
- "lastPage",
- "comment",
- "referenceLocation",
- "xref"
- })
- public static class Reference {
-
- protected String title;
- protected List<String> author;
- protected List<String> applicant;
- protected String consortium;
- @XmlSchemaType(name = "date")
- protected XMLGregorianCalendar submissionDate;
- protected String journal;
- protected String year;
- protected String volume;
- protected String issue;
- protected String firstPage;
- protected String lastPage;
- protected String comment;
- protected String referenceLocation;
- protected List<XrefType> xref;
- @XmlAttribute(name = "type", required = true)
- protected String type;
- @XmlAttribute(name = "number", required = true)
- protected BigInteger number;
- @XmlAttribute(name = "location")
- protected String location;
-
- /**
- * Gets the value of the title property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getTitle() {
- return title;
- }
-
- /**
- * Sets the value of the title property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setTitle(String value) {
- this.title = value;
- }
+ public List<String> getAuthor()
+ {
+ if (author == null)
+ {
+ author = new ArrayList<String>();
+ }
+ return this.author;
+ }
- /**
- * Gets the value of the author property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the author property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getAuthor().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link String }
- *
- *
- */
- public List<String> getAuthor() {
- if (author == null) {
- author = new ArrayList<String>();
- }
- return this.author;
- }
-
- /**
- * Gets the value of the applicant property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the applicant property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getApplicant().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link String }
- *
- *
- */
- public List<String> getApplicant() {
- if (applicant == null) {
- applicant = new ArrayList<String>();
- }
- return this.applicant;
- }
-
- /**
- * Gets the value of the consortium property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getConsortium() {
- return consortium;
- }
+ /**
+ * Gets the value of the applicant property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the applicant property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getApplicant().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link String }
+ *
+ *
+ */
+ public List<String> getApplicant()
+ {
+ if (applicant == null)
+ {
+ applicant = new ArrayList<String>();
+ }
+ return this.applicant;
+ }
- /**
- * Sets the value of the consortium property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setConsortium(String value) {
- this.consortium = value;
- }
+ /**
+ * Gets the value of the consortium property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getConsortium()
+ {
+ return consortium;
+ }
- /**
- * Gets the value of the submissionDate property.
- *
- * @return
- * possible object is
- * {@link XMLGregorianCalendar }
- *
- */
- public XMLGregorianCalendar getSubmissionDate() {
- return submissionDate;
- }
+ /**
+ * Sets the value of the consortium property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setConsortium(String value)
+ {
+ this.consortium = value;
+ }
- /**
- * Sets the value of the submissionDate property.
- *
- * @param value
- * allowed object is
- * {@link XMLGregorianCalendar }
- *
- */
- public void setSubmissionDate(XMLGregorianCalendar value) {
- this.submissionDate = value;
- }
+ /**
+ * Gets the value of the submissionDate property.
+ *
+ * @return possible object is {@link XMLGregorianCalendar }
+ *
+ */
+ public XMLGregorianCalendar getSubmissionDate()
+ {
+ return submissionDate;
+ }
- /**
- * Gets the value of the journal property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getJournal() {
- return journal;
- }
+ /**
+ * Sets the value of the submissionDate property.
+ *
+ * @param value
+ * allowed object is {@link XMLGregorianCalendar }
+ *
+ */
+ public void setSubmissionDate(XMLGregorianCalendar value)
+ {
+ this.submissionDate = value;
+ }
- /**
- * Sets the value of the journal property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setJournal(String value) {
- this.journal = value;
- }
+ /**
+ * Gets the value of the journal property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getJournal()
+ {
+ return journal;
+ }
- /**
- * Gets the value of the year property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getYear() {
- return year;
- }
+ /**
+ * Sets the value of the journal property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setJournal(String value)
+ {
+ this.journal = value;
+ }
- /**
- * Sets the value of the year property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setYear(String value) {
- this.year = value;
- }
+ /**
+ * Gets the value of the year property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getYear()
+ {
+ return year;
+ }
- /**
- * Gets the value of the volume property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getVolume() {
- return volume;
- }
+ /**
+ * Sets the value of the year property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setYear(String value)
+ {
+ this.year = value;
+ }
- /**
- * Sets the value of the volume property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setVolume(String value) {
- this.volume = value;
- }
+ /**
+ * Gets the value of the volume property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getVolume()
+ {
+ return volume;
+ }
- /**
- * Gets the value of the issue property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getIssue() {
- return issue;
- }
+ /**
+ * Sets the value of the volume property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setVolume(String value)
+ {
+ this.volume = value;
+ }
- /**
- * Sets the value of the issue property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setIssue(String value) {
- this.issue = value;
- }
+ /**
+ * Gets the value of the issue property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getIssue()
+ {
+ return issue;
+ }
- /**
- * Gets the value of the firstPage property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getFirstPage() {
- return firstPage;
- }
+ /**
+ * Sets the value of the issue property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setIssue(String value)
+ {
+ this.issue = value;
+ }
- /**
- * Sets the value of the firstPage property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setFirstPage(String value) {
- this.firstPage = value;
- }
+ /**
+ * Gets the value of the firstPage property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getFirstPage()
+ {
+ return firstPage;
+ }
- /**
- * Gets the value of the lastPage property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getLastPage() {
- return lastPage;
- }
+ /**
+ * Sets the value of the firstPage property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setFirstPage(String value)
+ {
+ this.firstPage = value;
+ }
- /**
- * Sets the value of the lastPage property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setLastPage(String value) {
- this.lastPage = value;
- }
+ /**
+ * Gets the value of the lastPage property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getLastPage()
+ {
+ return lastPage;
+ }
- /**
- * Gets the value of the comment property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getComment() {
- return comment;
- }
+ /**
+ * Sets the value of the lastPage property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setLastPage(String value)
+ {
+ this.lastPage = value;
+ }
- /**
- * Sets the value of the comment property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setComment(String value) {
- this.comment = value;
- }
+ /**
+ * Gets the value of the comment property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getComment()
+ {
+ return comment;
+ }
- /**
- * Gets the value of the referenceLocation property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getReferenceLocation() {
- return referenceLocation;
- }
+ /**
+ * Sets the value of the comment property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setComment(String value)
+ {
+ this.comment = value;
+ }
- /**
- * Sets the value of the referenceLocation property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setReferenceLocation(String value) {
- this.referenceLocation = value;
- }
+ /**
+ * Gets the value of the referenceLocation property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getReferenceLocation()
+ {
+ return referenceLocation;
+ }
- /**
- * Gets the value of the xref property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the xref property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getXref().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link XrefType }
- *
- *
- */
- public List<XrefType> getXref() {
- if (xref == null) {
- xref = new ArrayList<XrefType>();
- }
- return this.xref;
- }
+ /**
+ * Sets the value of the referenceLocation property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setReferenceLocation(String value)
+ {
+ this.referenceLocation = value;
+ }
- /**
- * Gets the value of the type property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getType() {
- return type;
- }
+ /**
+ * Gets the value of the xref property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the xref property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getXref().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link XrefType
+ * }
+ *
+ *
+ */
+ public List<XrefType> getXref()
+ {
+ if (xref == null)
+ {
+ xref = new ArrayList<XrefType>();
+ }
+ return this.xref;
+ }
- /**
- * Sets the value of the type property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setType(String value) {
- this.type = value;
- }
+ /**
+ * Gets the value of the type property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getType()
+ {
+ return type;
+ }
- /**
- * Gets the value of the number property.
- *
- * @return
- * possible object is
- * {@link BigInteger }
- *
- */
- public BigInteger getNumber() {
- return number;
- }
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setType(String value)
+ {
+ this.type = value;
+ }
- /**
- * Sets the value of the number property.
- *
- * @param value
- * allowed object is
- * {@link BigInteger }
- *
- */
- public void setNumber(BigInteger value) {
- this.number = value;
- }
+ /**
+ * Gets the value of the number property.
+ *
+ * @return possible object is {@link BigInteger }
+ *
+ */
+ public BigInteger getNumber()
+ {
+ return number;
+ }
- /**
- * Gets the value of the location property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getLocation() {
- return location;
- }
+ /**
+ * Sets the value of the number property.
+ *
+ * @param value
+ * allowed object is {@link BigInteger }
+ *
+ */
+ public void setNumber(BigInteger value)
+ {
+ this.number = value;
+ }
- /**
- * Sets the value of the location property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setLocation(String value) {
- this.location = value;
- }
+ /**
+ * Gets the value of the location property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getLocation()
+ {
+ return location;
+ }
+ /**
+ * Sets the value of the location property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setLocation(String value)
+ {
+ this.location = value;
}
+ }
+
}
// Generated on: 2018.09.14 at 02:46:00 PM BST
//
-
package jalview.xml.binding.embl;
import javax.xml.bind.annotation.XmlRegistry;
-
/**
- * This object contains factory methods for each
- * Java content interface and Java element interface
- * generated in the jalview.xml.binding.embl package.
- * <p>An ObjectFactory allows you to programatically
- * construct new instances of the Java representation
- * for XML content. The Java representation of XML
- * content can consist of schema derived interfaces
- * and classes representing the binding of schema
- * type definitions, element declarations and model
- * groups. Factory methods for each of these are
- * provided in this class.
+ * This object contains factory methods for each Java content interface and Java
+ * element interface generated in the jalview.xml.binding.embl package.
+ * <p>
+ * An ObjectFactory allows you to programatically construct new instances of the
+ * Java representation for XML content. The Java representation of XML content
+ * can consist of schema derived interfaces and classes representing the binding
+ * of schema type definitions, element declarations and model groups. Factory
+ * methods for each of these are provided in this class.
*
*/
@XmlRegistry
-public class ObjectFactory {
-
-
- /**
- * Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: jalview.xml.binding.embl
- *
- */
- public ObjectFactory() {
- }
-
- /**
- * Create an instance of {@link EntryType }
- *
- */
- public EntryType createEntryType() {
- return new EntryType();
- }
-
- /**
- * Create an instance of {@link EntryType.Contig }
- *
- */
- public EntryType.Contig createEntryTypeContig() {
- return new EntryType.Contig();
- }
-
- /**
- * Create an instance of {@link EntryType.Assembly }
- *
- */
- public EntryType.Assembly createEntryTypeAssembly() {
- return new EntryType.Assembly();
- }
-
- /**
- * Create an instance of {@link EntryType.Feature }
- *
- */
- public EntryType.Feature createEntryTypeFeature() {
- return new EntryType.Feature();
- }
-
- /**
- * Create an instance of {@link EntryType.Feature.FeatureTaxon }
- *
- */
- public EntryType.Feature.FeatureTaxon createEntryTypeFeatureFeatureTaxon() {
- return new EntryType.Feature.FeatureTaxon();
- }
-
- /**
- * Create an instance of {@link EntryType.Feature.FeatureTaxon.Lineage }
- *
- */
- public EntryType.Feature.FeatureTaxon.Lineage createEntryTypeFeatureFeatureTaxonLineage() {
- return new EntryType.Feature.FeatureTaxon.Lineage();
- }
-
- /**
- * Create an instance of {@link ROOT }
- *
- */
- public ROOT createROOT() {
- return new ROOT();
- }
-
- /**
- * Create an instance of {@link EntrySetType }
- *
- */
- public EntrySetType createEntrySetType() {
- return new EntrySetType();
- }
-
- /**
- * Create an instance of {@link XrefType }
- *
- */
- public XrefType createXrefType() {
- return new XrefType();
- }
-
- /**
- * Create an instance of {@link EntryType.Reference }
- *
- */
- public EntryType.Reference createEntryTypeReference() {
- return new EntryType.Reference();
- }
-
- /**
- * Create an instance of {@link EntryType.Contig.Range }
- *
- */
- public EntryType.Contig.Range createEntryTypeContigRange() {
- return new EntryType.Contig.Range();
- }
-
- /**
- * Create an instance of {@link EntryType.Contig.Gap }
- *
- */
- public EntryType.Contig.Gap createEntryTypeContigGap() {
- return new EntryType.Contig.Gap();
- }
-
- /**
- * Create an instance of {@link EntryType.Assembly.Range }
- *
- */
- public EntryType.Assembly.Range createEntryTypeAssemblyRange() {
- return new EntryType.Assembly.Range();
- }
-
- /**
- * Create an instance of {@link EntryType.Feature.Qualifier }
- *
- */
- public EntryType.Feature.Qualifier createEntryTypeFeatureQualifier() {
- return new EntryType.Feature.Qualifier();
- }
-
- /**
- * Create an instance of {@link EntryType.Feature.FeatureTaxon.Lineage.Taxon }
- *
- */
- public EntryType.Feature.FeatureTaxon.Lineage.Taxon createEntryTypeFeatureFeatureTaxonLineageTaxon() {
- return new EntryType.Feature.FeatureTaxon.Lineage.Taxon();
- }
+public class ObjectFactory
+{
+
+ /**
+ * Create a new ObjectFactory that can be used to create new instances of
+ * schema derived classes for package: jalview.xml.binding.embl
+ *
+ */
+ public ObjectFactory()
+ {
+ }
+
+ /**
+ * Create an instance of {@link EntryType }
+ *
+ */
+ public EntryType createEntryType()
+ {
+ return new EntryType();
+ }
+
+ /**
+ * Create an instance of {@link EntryType.Contig }
+ *
+ */
+ public EntryType.Contig createEntryTypeContig()
+ {
+ return new EntryType.Contig();
+ }
+
+ /**
+ * Create an instance of {@link EntryType.Assembly }
+ *
+ */
+ public EntryType.Assembly createEntryTypeAssembly()
+ {
+ return new EntryType.Assembly();
+ }
+
+ /**
+ * Create an instance of {@link EntryType.Feature }
+ *
+ */
+ public EntryType.Feature createEntryTypeFeature()
+ {
+ return new EntryType.Feature();
+ }
+
+ /**
+ * Create an instance of {@link EntryType.Feature.FeatureTaxon }
+ *
+ */
+ public EntryType.Feature.FeatureTaxon createEntryTypeFeatureFeatureTaxon()
+ {
+ return new EntryType.Feature.FeatureTaxon();
+ }
+
+ /**
+ * Create an instance of {@link EntryType.Feature.FeatureTaxon.Lineage }
+ *
+ */
+ public EntryType.Feature.FeatureTaxon.Lineage createEntryTypeFeatureFeatureTaxonLineage()
+ {
+ return new EntryType.Feature.FeatureTaxon.Lineage();
+ }
+
+ /**
+ * Create an instance of {@link ROOT }
+ *
+ */
+ public ROOT createROOT()
+ {
+ return new ROOT();
+ }
+
+ /**
+ * Create an instance of {@link EntrySetType }
+ *
+ */
+ public EntrySetType createEntrySetType()
+ {
+ return new EntrySetType();
+ }
+
+ /**
+ * Create an instance of {@link XrefType }
+ *
+ */
+ public XrefType createXrefType()
+ {
+ return new XrefType();
+ }
+
+ /**
+ * Create an instance of {@link EntryType.Reference }
+ *
+ */
+ public EntryType.Reference createEntryTypeReference()
+ {
+ return new EntryType.Reference();
+ }
+
+ /**
+ * Create an instance of {@link EntryType.Contig.Range }
+ *
+ */
+ public EntryType.Contig.Range createEntryTypeContigRange()
+ {
+ return new EntryType.Contig.Range();
+ }
+
+ /**
+ * Create an instance of {@link EntryType.Contig.Gap }
+ *
+ */
+ public EntryType.Contig.Gap createEntryTypeContigGap()
+ {
+ return new EntryType.Contig.Gap();
+ }
+
+ /**
+ * Create an instance of {@link EntryType.Assembly.Range }
+ *
+ */
+ public EntryType.Assembly.Range createEntryTypeAssemblyRange()
+ {
+ return new EntryType.Assembly.Range();
+ }
+
+ /**
+ * Create an instance of {@link EntryType.Feature.Qualifier }
+ *
+ */
+ public EntryType.Feature.Qualifier createEntryTypeFeatureQualifier()
+ {
+ return new EntryType.Feature.Qualifier();
+ }
+
+ /**
+ * Create an instance of {@link EntryType.Feature.FeatureTaxon.Lineage.Taxon }
+ *
+ */
+ public EntryType.Feature.FeatureTaxon.Lineage.Taxon createEntryTypeFeatureFeatureTaxonLineageTaxon()
+ {
+ return new EntryType.Feature.FeatureTaxon.Lineage.Taxon();
+ }
}
// Generated on: 2018.09.14 at 02:46:00 PM BST
//
-
package jalview.xml.binding.embl;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlRootElement;
import javax.xml.bind.annotation.XmlType;
-
/**
- * <p>Java class for anonymous complex type.
+ * <p>
+ * Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
*
* <pre>
* <complexType>
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = {
- "entrySet",
- "entry"
-})
+@XmlType(name = "", propOrder = { "entrySet", "entry" })
@XmlRootElement(name = "ROOT")
-public class ROOT {
+public class ROOT
+{
+
+ protected EntrySetType entrySet;
- protected EntrySetType entrySet;
- protected EntryType entry;
+ protected EntryType entry;
- /**
- * Gets the value of the entrySet property.
- *
- * @return
- * possible object is
- * {@link EntrySetType }
- *
- */
- public EntrySetType getEntrySet() {
- return entrySet;
- }
+ /**
+ * Gets the value of the entrySet property.
+ *
+ * @return possible object is {@link EntrySetType }
+ *
+ */
+ public EntrySetType getEntrySet()
+ {
+ return entrySet;
+ }
- /**
- * Sets the value of the entrySet property.
- *
- * @param value
- * allowed object is
- * {@link EntrySetType }
- *
- */
- public void setEntrySet(EntrySetType value) {
- this.entrySet = value;
- }
+ /**
+ * Sets the value of the entrySet property.
+ *
+ * @param value
+ * allowed object is {@link EntrySetType }
+ *
+ */
+ public void setEntrySet(EntrySetType value)
+ {
+ this.entrySet = value;
+ }
- /**
- * Gets the value of the entry property.
- *
- * @return
- * possible object is
- * {@link EntryType }
- *
- */
- public EntryType getEntry() {
- return entry;
- }
+ /**
+ * Gets the value of the entry property.
+ *
+ * @return possible object is {@link EntryType }
+ *
+ */
+ public EntryType getEntry()
+ {
+ return entry;
+ }
- /**
- * Sets the value of the entry property.
- *
- * @param value
- * allowed object is
- * {@link EntryType }
- *
- */
- public void setEntry(EntryType value) {
- this.entry = value;
- }
+ /**
+ * Sets the value of the entry property.
+ *
+ * @param value
+ * allowed object is {@link EntryType }
+ *
+ */
+ public void setEntry(EntryType value)
+ {
+ this.entry = value;
+ }
}
// Generated on: 2018.09.14 at 02:46:00 PM BST
//
-
package jalview.xml.binding.embl;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlType;
-
/**
* Database cross-reference.
*
- * <p>Java class for XrefType complex type.
+ * <p>
+ * Java class for XrefType complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
*
* <pre>
* <complexType name="XrefType">
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "XrefType")
-public class XrefType {
+public class XrefType
+{
+
+ @XmlAttribute(name = "db", required = true)
+ protected String db;
+
+ @XmlAttribute(name = "id", required = true)
+ protected String id;
- @XmlAttribute(name = "db", required = true)
- protected String db;
- @XmlAttribute(name = "id", required = true)
- protected String id;
- @XmlAttribute(name = "secondaryId")
- protected String secondaryId;
+ @XmlAttribute(name = "secondaryId")
+ protected String secondaryId;
- /**
- * Gets the value of the db property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDb() {
- return db;
- }
+ /**
+ * Gets the value of the db property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDb()
+ {
+ return db;
+ }
- /**
- * Sets the value of the db property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDb(String value) {
- this.db = value;
- }
+ /**
+ * Sets the value of the db property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setDb(String value)
+ {
+ this.db = value;
+ }
- /**
- * Gets the value of the id property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getId() {
- return id;
- }
+ /**
+ * Gets the value of the id property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getId()
+ {
+ return id;
+ }
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setId(String value) {
- this.id = value;
- }
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setId(String value)
+ {
+ this.id = value;
+ }
- /**
- * Gets the value of the secondaryId property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getSecondaryId() {
- return secondaryId;
- }
+ /**
+ * Gets the value of the secondaryId property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getSecondaryId()
+ {
+ return secondaryId;
+ }
- /**
- * Sets the value of the secondaryId property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setSecondaryId(String value) {
- this.secondaryId = value;
- }
+ /**
+ * Sets the value of the secondaryId property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setSecondaryId(String value)
+ {
+ this.secondaryId = value;
+ }
}
// Generated on: 2021.08.30 at 11:05:22 AM BST
//
-
package jalview.xml.binding.jalview;
import java.math.BigInteger;
import javax.xml.bind.annotation.XmlRootElement;
import javax.xml.bind.annotation.XmlType;
-
/**
* <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
*
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="alcodon" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
- * &lt;attribute name="pos2" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
- * &lt;attribute name="pos3" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="alcodMap" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Mapping"/&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="dnasq" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;/sequence&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="alcodon" maxOccurs="unbounded"
+ * minOccurs="0"&gt; &lt;complexType&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
+ * name="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
+ * &lt;attribute name="pos2"
+ * type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; &lt;attribute
+ * name="pos3" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt; &lt;element
+ * name="alcodMap" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element
+ * ref="{www.vamsas.ac.uk/jalview/version2}Mapping"/&gt;
+ * &lt;/sequence&gt; &lt;attribute name="dnasq" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt;
+ * &lt;/sequence&gt; &lt;/restriction&gt;
+ * &lt;/complexContent&gt; &lt;/complexType&gt; </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = {
- "alcodon",
- "alcodMap"
-})
+@XmlType(name = "", propOrder = { "alcodon", "alcodMap" })
@XmlRootElement(name = "AlcodonFrame")
-public class AlcodonFrame {
+public class AlcodonFrame
+{
+
+ protected List<AlcodonFrame.Alcodon> alcodon;
+
+ protected List<AlcodonFrame.AlcodMap> alcodMap;
- protected List<AlcodonFrame.Alcodon> alcodon;
- protected List<AlcodonFrame.AlcodMap> alcodMap;
+ /**
+ * Gets the value of the alcodon property.
+ *
+ * <p> This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will be
+ * present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the alcodon property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getAlcodon().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link AlcodonFrame.Alcodon }
+ *
+ *
+ */
+ public List<AlcodonFrame.Alcodon> getAlcodon()
+ {
+ if (alcodon == null)
+ {
+ alcodon = new ArrayList<AlcodonFrame.Alcodon>();
+ }
+ return this.alcodon;
+ }
+
+ /**
+ * Gets the value of the alcodMap property.
+ *
+ * <p> This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will be
+ * present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the alcodMap property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getAlcodMap().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link AlcodonFrame.AlcodMap }
+ *
+ *
+ */
+ public List<AlcodonFrame.AlcodMap> getAlcodMap()
+ {
+ if (alcodMap == null)
+ {
+ alcodMap = new ArrayList<AlcodonFrame.AlcodMap>();
+ }
+ return this.alcodMap;
+ }
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
+ *
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element
+ * ref="{www.vamsas.ac.uk/jalview/version2}Mapping"/&gt;
+ * &lt;/sequence&gt; &lt;attribute name="dnasq" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "mapping" })
+ public static class AlcodMap
+ {
+
+ @XmlElement(name = "Mapping", required = true)
+ protected Mapping mapping;
+
+ @XmlAttribute(name = "dnasq", required = true)
+ protected String dnasq;
/**
- * Gets the value of the alcodon property.
*
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the alcodon property.
+ * a Mapping entry and an associated protein sequence
*
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getAlcodon().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link AlcodonFrame.Alcodon }
*
+ * @return possible object is {@link Mapping }
*
*/
- public List<AlcodonFrame.Alcodon> getAlcodon() {
- if (alcodon == null) {
- alcodon = new ArrayList<AlcodonFrame.Alcodon>();
- }
- return this.alcodon;
+ public Mapping getMapping()
+ {
+ return mapping;
}
/**
- * Gets the value of the alcodMap property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the alcodMap property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getAlcodMap().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link AlcodonFrame.AlcodMap }
+ * Sets the value of the mapping property.
*
+ * @param value
+ * allowed object is {@link Mapping }
*
*/
- public List<AlcodonFrame.AlcodMap> getAlcodMap() {
- if (alcodMap == null) {
- alcodMap = new ArrayList<AlcodonFrame.AlcodMap>();
- }
- return this.alcodMap;
+ public void setMapping(Mapping value)
+ {
+ this.mapping = value;
}
-
/**
- * <p>Java class for anonymous complex type.
+ * Gets the value of the dnasq property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * @return possible object is {@link String }
*
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Mapping"/&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="dnasq" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ */
+ public String getDnasq()
+ {
+ return dnasq;
+ }
+
+ /**
+ * Sets the value of the dnasq property.
*
+ * @param value
+ * allowed object is {@link String }
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "mapping"
- })
- public static class AlcodMap {
+ public void setDnasq(String value)
+ {
+ this.dnasq = value;
+ }
- @XmlElement(name = "Mapping", required = true)
- protected Mapping mapping;
- @XmlAttribute(name = "dnasq", required = true)
- protected String dnasq;
+ }
- /**
- *
- * a Mapping entry and an associated protein sequence
- *
- *
- * @return
- * possible object is
- * {@link Mapping }
- *
- */
- public Mapping getMapping() {
- return mapping;
- }
+ /**
+ *
+ * specifies a series of aligned codons from an associated DNA sequence
+ * alignment that when translated correspond to columns of a peptide
+ * alignment. Element may have either all pos1,2,3 attributes specified, or
+ * none at all (indicating a gapped column with no translated peptide).
+ *
+ *
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
+ *
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
+ * name="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
+ * &lt;attribute name="pos2"
+ * type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
+ * &lt;attribute name="pos3"
+ * type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Alcodon
+ {
- /**
- * Sets the value of the mapping property.
- *
- * @param value
- * allowed object is
- * {@link Mapping }
- *
- */
- public void setMapping(Mapping value) {
- this.mapping = value;
- }
+ @XmlAttribute(name = "pos1")
+ protected BigInteger pos1;
- /**
- * Gets the value of the dnasq property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDnasq() {
- return dnasq;
- }
+ @XmlAttribute(name = "pos2")
+ protected BigInteger pos2;
- /**
- * Sets the value of the dnasq property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDnasq(String value) {
- this.dnasq = value;
- }
+ @XmlAttribute(name = "pos3")
+ protected BigInteger pos3;
+ /**
+ * Gets the value of the pos1 property.
+ *
+ * @return possible object is {@link BigInteger }
+ *
+ */
+ public BigInteger getPos1()
+ {
+ return pos1;
}
-
/**
+ * Sets the value of the pos1 property.
*
- * specifies a series of aligned codons from an associated DNA sequence alignment that when translated correspond to columns of a peptide alignment.
- * Element may have either all pos1,2,3 attributes specified, or none at all (indicating a gapped column with no translated peptide).
- *
+ * @param value
+ * allowed object is {@link BigInteger }
*
- * <p>Java class for anonymous complex type.
+ */
+ public void setPos1(BigInteger value)
+ {
+ this.pos1 = value;
+ }
+
+ /**
+ * Gets the value of the pos2 property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * @return possible object is {@link BigInteger }
*
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
- * &lt;attribute name="pos2" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
- * &lt;attribute name="pos3" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ */
+ public BigInteger getPos2()
+ {
+ return pos2;
+ }
+
+ /**
+ * Sets the value of the pos2 property.
*
+ * @param value
+ * allowed object is {@link BigInteger }
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class Alcodon {
-
- @XmlAttribute(name = "pos1")
- protected BigInteger pos1;
- @XmlAttribute(name = "pos2")
- protected BigInteger pos2;
- @XmlAttribute(name = "pos3")
- protected BigInteger pos3;
-
- /**
- * Gets the value of the pos1 property.
- *
- * @return
- * possible object is
- * {@link BigInteger }
- *
- */
- public BigInteger getPos1() {
- return pos1;
- }
-
- /**
- * Sets the value of the pos1 property.
- *
- * @param value
- * allowed object is
- * {@link BigInteger }
- *
- */
- public void setPos1(BigInteger value) {
- this.pos1 = value;
- }
-
- /**
- * Gets the value of the pos2 property.
- *
- * @return
- * possible object is
- * {@link BigInteger }
- *
- */
- public BigInteger getPos2() {
- return pos2;
- }
-
- /**
- * Sets the value of the pos2 property.
- *
- * @param value
- * allowed object is
- * {@link BigInteger }
- *
- */
- public void setPos2(BigInteger value) {
- this.pos2 = value;
- }
-
- /**
- * Gets the value of the pos3 property.
- *
- * @return
- * possible object is
- * {@link BigInteger }
- *
- */
- public BigInteger getPos3() {
- return pos3;
- }
+ public void setPos2(BigInteger value)
+ {
+ this.pos2 = value;
+ }
- /**
- * Sets the value of the pos3 property.
- *
- * @param value
- * allowed object is
- * {@link BigInteger }
- *
- */
- public void setPos3(BigInteger value) {
- this.pos3 = value;
- }
+ /**
+ * Gets the value of the pos3 property.
+ *
+ * @return possible object is {@link BigInteger }
+ *
+ */
+ public BigInteger getPos3()
+ {
+ return pos3;
+ }
+ /**
+ * Sets the value of the pos3 property.
+ *
+ * @param value
+ * allowed object is {@link BigInteger }
+ *
+ */
+ public void setPos3(BigInteger value)
+ {
+ this.pos3 = value;
}
+ }
+
}
// Generated on: 2021.08.30 at 11:05:22 AM BST
//
-
package jalview.xml.binding.jalview;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlRootElement;
import javax.xml.bind.annotation.XmlType;
-
/**
* <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
*
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}annotationElement" maxOccurs="unbounded" minOccurs="0"/&gt;
- * &lt;element name="label" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
- * &lt;element name="description" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
- * &lt;element name="thresholdLine" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="label" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="property" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="graph" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="graphType" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="groupRef" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="graphColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="graphGroup" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="graphHeight" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="scoreOnly" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="score" type="{http://www.w3.org/2001/XMLSchema}double" /&gt;
- * &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="centreColLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="scaleColLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="showAllColLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="autoCalculated" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="belowAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="calcId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element
+ * ref="{www.vamsas.ac.uk/jalview/version2}annotationElement"
+ * maxOccurs="unbounded" minOccurs="0"/&gt; &lt;element name="label"
+ * type="{http://www.w3.org/2001/XMLSchema}string"/&gt; &lt;element
+ * name="description" type="{http://www.w3.org/2001/XMLSchema}string"
+ * minOccurs="0"/&gt; &lt;element name="thresholdLine"
+ * minOccurs="0"&gt; &lt;complexType&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
+ * name="label" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}float"
+ * /&gt; &lt;attribute name="colour"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt; &lt;element
+ * name="property" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string"
+ * /&gt; &lt;attribute name="value"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt;
+ * &lt;/sequence&gt; &lt;attribute name="graph" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
+ * name="graphType" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="sequenceRef"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="groupRef" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="graphColour"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="graphGroup" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="graphHeight"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="scoreOnly"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="score"
+ * type="{http://www.w3.org/2001/XMLSchema}double" /&gt; &lt;attribute
+ * name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="centreColLabels"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
+ * name="scaleColLabels" type="{http://www.w3.org/2001/XMLSchema}boolean"
+ * /&gt; &lt;attribute name="showAllColLabels"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
+ * name="autoCalculated" type="{http://www.w3.org/2001/XMLSchema}boolean"
+ * default="false" /&gt; &lt;attribute name="belowAlignment"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="calcId"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = {
- "annotationElement",
- "label",
- "description",
- "thresholdLine",
- "property"
-})
+@XmlType(
+ name = "",
+ propOrder =
+ { "annotationElement", "label", "description", "thresholdLine",
+ "property" })
@XmlRootElement(name = "Annotation")
-public class Annotation {
+public class Annotation
+{
- protected List<AnnotationElement> annotationElement;
- @XmlElement(required = true)
- protected String label;
- protected String description;
- protected Annotation.ThresholdLine thresholdLine;
- protected List<Annotation.Property> property;
- @XmlAttribute(name = "graph", required = true)
- protected boolean graph;
- @XmlAttribute(name = "graphType")
- protected Integer graphType;
- @XmlAttribute(name = "sequenceRef")
- protected String sequenceRef;
- @XmlAttribute(name = "groupRef")
- protected String groupRef;
- @XmlAttribute(name = "graphColour")
- protected Integer graphColour;
- @XmlAttribute(name = "graphGroup")
- protected Integer graphGroup;
- @XmlAttribute(name = "graphHeight")
- protected Integer graphHeight;
- @XmlAttribute(name = "id")
- protected String id;
- @XmlAttribute(name = "scoreOnly")
- protected Boolean scoreOnly;
- @XmlAttribute(name = "score")
- protected Double score;
- @XmlAttribute(name = "visible")
- protected Boolean visible;
- @XmlAttribute(name = "centreColLabels")
- protected Boolean centreColLabels;
- @XmlAttribute(name = "scaleColLabels")
- protected Boolean scaleColLabels;
- @XmlAttribute(name = "showAllColLabels")
- protected Boolean showAllColLabels;
- @XmlAttribute(name = "autoCalculated")
- protected Boolean autoCalculated;
- @XmlAttribute(name = "belowAlignment")
- protected Boolean belowAlignment;
- @XmlAttribute(name = "calcId")
- protected String calcId;
+ protected List<AnnotationElement> annotationElement;
- /**
- * Gets the value of the annotationElement property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the annotationElement property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getAnnotationElement().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link AnnotationElement }
- *
- *
- */
- public List<AnnotationElement> getAnnotationElement() {
- if (annotationElement == null) {
- annotationElement = new ArrayList<AnnotationElement>();
- }
- return this.annotationElement;
- }
-
- /**
- * Gets the value of the label property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getLabel() {
- return label;
- }
-
- /**
- * Sets the value of the label property.
+ @XmlElement(required = true)
+ protected String label;
+
+ protected String description;
+
+ protected Annotation.ThresholdLine thresholdLine;
+
+ protected List<Annotation.Property> property;
+
+ @XmlAttribute(name = "graph", required = true)
+ protected boolean graph;
+
+ @XmlAttribute(name = "graphType")
+ protected Integer graphType;
+
+ @XmlAttribute(name = "sequenceRef")
+ protected String sequenceRef;
+
+ @XmlAttribute(name = "groupRef")
+ protected String groupRef;
+
+ @XmlAttribute(name = "graphColour")
+ protected Integer graphColour;
+
+ @XmlAttribute(name = "graphGroup")
+ protected Integer graphGroup;
+
+ @XmlAttribute(name = "graphHeight")
+ protected Integer graphHeight;
+
+ @XmlAttribute(name = "id")
+ protected String id;
+
+ @XmlAttribute(name = "scoreOnly")
+ protected Boolean scoreOnly;
+
+ @XmlAttribute(name = "score")
+ protected Double score;
+
+ @XmlAttribute(name = "visible")
+ protected Boolean visible;
+
+ @XmlAttribute(name = "centreColLabels")
+ protected Boolean centreColLabels;
+
+ @XmlAttribute(name = "scaleColLabels")
+ protected Boolean scaleColLabels;
+
+ @XmlAttribute(name = "showAllColLabels")
+ protected Boolean showAllColLabels;
+
+ @XmlAttribute(name = "autoCalculated")
+ protected Boolean autoCalculated;
+
+ @XmlAttribute(name = "belowAlignment")
+ protected Boolean belowAlignment;
+
+ @XmlAttribute(name = "calcId")
+ protected String calcId;
+
+ /**
+ * Gets the value of the annotationElement property.
+ *
+ * <p> This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will be
+ * present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the annotationElement property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getAnnotationElement().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link AnnotationElement }
+ *
+ *
+ */
+ public List<AnnotationElement> getAnnotationElement()
+ {
+ if (annotationElement == null)
+ {
+ annotationElement = new ArrayList<AnnotationElement>();
+ }
+ return this.annotationElement;
+ }
+
+ /**
+ * Gets the value of the label property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getLabel()
+ {
+ return label;
+ }
+
+ /**
+ * Sets the value of the label property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setLabel(String value)
+ {
+ this.label = value;
+ }
+
+ /**
+ * Gets the value of the description property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDescription()
+ {
+ return description;
+ }
+
+ /**
+ * Sets the value of the description property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setDescription(String value)
+ {
+ this.description = value;
+ }
+
+ /**
+ * Gets the value of the thresholdLine property.
+ *
+ * @return possible object is {@link Annotation.ThresholdLine }
+ *
+ */
+ public Annotation.ThresholdLine getThresholdLine()
+ {
+ return thresholdLine;
+ }
+
+ /**
+ * Sets the value of the thresholdLine property.
+ *
+ * @param value
+ * allowed object is {@link Annotation.ThresholdLine }
+ *
+ */
+ public void setThresholdLine(Annotation.ThresholdLine value)
+ {
+ this.thresholdLine = value;
+ }
+
+ /**
+ * Gets the value of the property property.
+ *
+ * <p> This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will be
+ * present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the property property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getProperty().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link Annotation.Property }
+ *
+ *
+ */
+ public List<Annotation.Property> getProperty()
+ {
+ if (property == null)
+ {
+ property = new ArrayList<Annotation.Property>();
+ }
+ return this.property;
+ }
+
+ /**
+ * Gets the value of the graph property.
+ *
+ */
+ public boolean isGraph()
+ {
+ return graph;
+ }
+
+ /**
+ * Sets the value of the graph property.
+ *
+ */
+ public void setGraph(boolean value)
+ {
+ this.graph = value;
+ }
+
+ /**
+ * Gets the value of the graphType property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getGraphType()
+ {
+ return graphType;
+ }
+
+ /**
+ * Sets the value of the graphType property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setGraphType(Integer value)
+ {
+ this.graphType = value;
+ }
+
+ /**
+ * Gets the value of the sequenceRef property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getSequenceRef()
+ {
+ return sequenceRef;
+ }
+
+ /**
+ * Sets the value of the sequenceRef property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setSequenceRef(String value)
+ {
+ this.sequenceRef = value;
+ }
+
+ /**
+ * Gets the value of the groupRef property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getGroupRef()
+ {
+ return groupRef;
+ }
+
+ /**
+ * Sets the value of the groupRef property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setGroupRef(String value)
+ {
+ this.groupRef = value;
+ }
+
+ /**
+ * Gets the value of the graphColour property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getGraphColour()
+ {
+ return graphColour;
+ }
+
+ /**
+ * Sets the value of the graphColour property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setGraphColour(Integer value)
+ {
+ this.graphColour = value;
+ }
+
+ /**
+ * Gets the value of the graphGroup property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getGraphGroup()
+ {
+ return graphGroup;
+ }
+
+ /**
+ * Sets the value of the graphGroup property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setGraphGroup(Integer value)
+ {
+ this.graphGroup = value;
+ }
+
+ /**
+ * Gets the value of the graphHeight property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getGraphHeight()
+ {
+ return graphHeight;
+ }
+
+ /**
+ * Sets the value of the graphHeight property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setGraphHeight(Integer value)
+ {
+ this.graphHeight = value;
+ }
+
+ /**
+ * Gets the value of the id property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getId()
+ {
+ return id;
+ }
+
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setId(String value)
+ {
+ this.id = value;
+ }
+
+ /**
+ * Gets the value of the scoreOnly property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isScoreOnly()
+ {
+ if (scoreOnly == null)
+ {
+ return false;
+ }
+ else
+ {
+ return scoreOnly;
+ }
+ }
+
+ /**
+ * Sets the value of the scoreOnly property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setScoreOnly(Boolean value)
+ {
+ this.scoreOnly = value;
+ }
+
+ /**
+ * Gets the value of the score property.
+ *
+ * @return possible object is {@link Double }
+ *
+ */
+ public Double getScore()
+ {
+ return score;
+ }
+
+ /**
+ * Sets the value of the score property.
+ *
+ * @param value
+ * allowed object is {@link Double }
+ *
+ */
+ public void setScore(Double value)
+ {
+ this.score = value;
+ }
+
+ /**
+ * Gets the value of the visible property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isVisible()
+ {
+ return visible;
+ }
+
+ /**
+ * Sets the value of the visible property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setVisible(Boolean value)
+ {
+ this.visible = value;
+ }
+
+ /**
+ * Gets the value of the centreColLabels property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isCentreColLabels()
+ {
+ return centreColLabels;
+ }
+
+ /**
+ * Sets the value of the centreColLabels property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setCentreColLabels(Boolean value)
+ {
+ this.centreColLabels = value;
+ }
+
+ /**
+ * Gets the value of the scaleColLabels property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isScaleColLabels()
+ {
+ return scaleColLabels;
+ }
+
+ /**
+ * Sets the value of the scaleColLabels property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setScaleColLabels(Boolean value)
+ {
+ this.scaleColLabels = value;
+ }
+
+ /**
+ * Gets the value of the showAllColLabels property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowAllColLabels()
+ {
+ return showAllColLabels;
+ }
+
+ /**
+ * Sets the value of the showAllColLabels property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowAllColLabels(Boolean value)
+ {
+ this.showAllColLabels = value;
+ }
+
+ /**
+ * Gets the value of the autoCalculated property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isAutoCalculated()
+ {
+ if (autoCalculated == null)
+ {
+ return false;
+ }
+ else
+ {
+ return autoCalculated;
+ }
+ }
+
+ /**
+ * Sets the value of the autoCalculated property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setAutoCalculated(Boolean value)
+ {
+ this.autoCalculated = value;
+ }
+
+ /**
+ * Gets the value of the belowAlignment property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isBelowAlignment()
+ {
+ if (belowAlignment == null)
+ {
+ return true;
+ }
+ else
+ {
+ return belowAlignment;
+ }
+ }
+
+ /**
+ * Sets the value of the belowAlignment property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setBelowAlignment(Boolean value)
+ {
+ this.belowAlignment = value;
+ }
+
+ /**
+ * Gets the value of the calcId property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getCalcId()
+ {
+ return calcId;
+ }
+
+ /**
+ * Sets the value of the calcId property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setCalcId(String value)
+ {
+ this.calcId = value;
+ }
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
+ *
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
+ * name="name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="value"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Property
+ {
+
+ @XmlAttribute(name = "name")
+ protected String name;
+
+ @XmlAttribute(name = "value")
+ protected String value;
+
+ /**
+ * Gets the value of the name property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getName()
+ {
+ return name;
+ }
+
+ /**
+ * Sets the value of the name property.
*
* @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setLabel(String value) {
- this.label = value;
- }
-
- /**
- * Gets the value of the description property.
+ * allowed object is {@link String }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getDescription() {
- return description;
+ public void setName(String value)
+ {
+ this.name = value;
}
/**
- * Sets the value of the description property.
+ * Gets the value of the value property.
*
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDescription(String value) {
- this.description = value;
- }
-
- /**
- * Gets the value of the thresholdLine property.
- *
- * @return
- * possible object is
- * {@link Annotation.ThresholdLine }
- *
- */
- public Annotation.ThresholdLine getThresholdLine() {
- return thresholdLine;
- }
-
- /**
- * Sets the value of the thresholdLine property.
- *
- * @param value
- * allowed object is
- * {@link Annotation.ThresholdLine }
- *
- */
- public void setThresholdLine(Annotation.ThresholdLine value) {
- this.thresholdLine = value;
- }
-
- /**
- * Gets the value of the property property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the property property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getProperty().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Annotation.Property }
- *
- *
- */
- public List<Annotation.Property> getProperty() {
- if (property == null) {
- property = new ArrayList<Annotation.Property>();
- }
- return this.property;
- }
-
- /**
- * Gets the value of the graph property.
- *
- */
- public boolean isGraph() {
- return graph;
- }
-
- /**
- * Sets the value of the graph property.
- *
- */
- public void setGraph(boolean value) {
- this.graph = value;
- }
-
- /**
- * Gets the value of the graphType property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getGraphType() {
- return graphType;
- }
-
- /**
- * Sets the value of the graphType property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setGraphType(Integer value) {
- this.graphType = value;
- }
-
- /**
- * Gets the value of the sequenceRef property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getSequenceRef() {
- return sequenceRef;
- }
-
- /**
- * Sets the value of the sequenceRef property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setSequenceRef(String value) {
- this.sequenceRef = value;
- }
-
- /**
- * Gets the value of the groupRef property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getGroupRef() {
- return groupRef;
- }
-
- /**
- * Sets the value of the groupRef property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setGroupRef(String value) {
- this.groupRef = value;
- }
-
- /**
- * Gets the value of the graphColour property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getGraphColour() {
- return graphColour;
- }
-
- /**
- * Sets the value of the graphColour property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setGraphColour(Integer value) {
- this.graphColour = value;
- }
-
- /**
- * Gets the value of the graphGroup property.
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link Integer }
- *
*/
- public Integer getGraphGroup() {
- return graphGroup;
+ public String getValue()
+ {
+ return value;
}
/**
- * Sets the value of the graphGroup property.
+ * Sets the value of the value property.
*
* @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setGraphGroup(Integer value) {
- this.graphGroup = value;
- }
-
- /**
- * Gets the value of the graphHeight property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getGraphHeight() {
- return graphHeight;
- }
-
- /**
- * Sets the value of the graphHeight property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setGraphHeight(Integer value) {
- this.graphHeight = value;
- }
-
- /**
- * Gets the value of the id property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getId() {
- return id;
- }
-
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setId(String value) {
- this.id = value;
- }
-
- /**
- * Gets the value of the scoreOnly property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isScoreOnly() {
- if (scoreOnly == null) {
- return false;
- } else {
- return scoreOnly;
- }
- }
-
- /**
- * Sets the value of the scoreOnly property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setScoreOnly(Boolean value) {
- this.scoreOnly = value;
- }
-
- /**
- * Gets the value of the score property.
- *
- * @return
- * possible object is
- * {@link Double }
- *
- */
- public Double getScore() {
- return score;
- }
-
- /**
- * Sets the value of the score property.
- *
- * @param value
- * allowed object is
- * {@link Double }
- *
- */
- public void setScore(Double value) {
- this.score = value;
- }
-
- /**
- * Gets the value of the visible property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isVisible() {
- return visible;
- }
+ * allowed object is {@link String }
+ *
+ */
+ public void setValue(String value)
+ {
+ this.value = value;
+ }
+
+ }
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
+ *
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
+ * name="label" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="value"
+ * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute
+ * name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class ThresholdLine
+ {
+
+ @XmlAttribute(name = "label")
+ protected String label;
- /**
- * Sets the value of the visible property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setVisible(Boolean value) {
- this.visible = value;
- }
+ @XmlAttribute(name = "value")
+ protected Float value;
- /**
- * Gets the value of the centreColLabels property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isCentreColLabels() {
- return centreColLabels;
- }
+ @XmlAttribute(name = "colour")
+ protected Integer colour;
/**
- * Sets the value of the centreColLabels property.
+ * Gets the value of the label property.
*
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setCentreColLabels(Boolean value) {
- this.centreColLabels = value;
- }
-
- /**
- * Gets the value of the scaleColLabels property.
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link Boolean }
- *
*/
- public Boolean isScaleColLabels() {
- return scaleColLabels;
+ public String getLabel()
+ {
+ return label;
}
/**
- * Sets the value of the scaleColLabels property.
+ * Sets the value of the label property.
*
* @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setScaleColLabels(Boolean value) {
- this.scaleColLabels = value;
- }
-
- /**
- * Gets the value of the showAllColLabels property.
+ * allowed object is {@link String }
*
- * @return
- * possible object is
- * {@link Boolean }
- *
*/
- public Boolean isShowAllColLabels() {
- return showAllColLabels;
+ public void setLabel(String value)
+ {
+ this.label = value;
}
/**
- * Sets the value of the showAllColLabels property.
+ * Gets the value of the value property.
*
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowAllColLabels(Boolean value) {
- this.showAllColLabels = value;
- }
-
- /**
- * Gets the value of the autoCalculated property.
+ * @return possible object is {@link Float }
*
- * @return
- * possible object is
- * {@link Boolean }
- *
*/
- public boolean isAutoCalculated() {
- if (autoCalculated == null) {
- return false;
- } else {
- return autoCalculated;
- }
+ public Float getValue()
+ {
+ return value;
}
/**
- * Sets the value of the autoCalculated property.
+ * Sets the value of the value property.
*
* @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setAutoCalculated(Boolean value) {
- this.autoCalculated = value;
- }
-
- /**
- * Gets the value of the belowAlignment property.
+ * allowed object is {@link Float }
*
- * @return
- * possible object is
- * {@link Boolean }
- *
*/
- public boolean isBelowAlignment() {
- if (belowAlignment == null) {
- return true;
- } else {
- return belowAlignment;
- }
+ public void setValue(Float value)
+ {
+ this.value = value;
}
/**
- * Sets the value of the belowAlignment property.
+ * Gets the value of the colour property.
*
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setBelowAlignment(Boolean value) {
- this.belowAlignment = value;
- }
-
- /**
- * Gets the value of the calcId property.
+ * @return possible object is {@link Integer }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getCalcId() {
- return calcId;
+ public Integer getColour()
+ {
+ return colour;
}
/**
- * Sets the value of the calcId property.
+ * Sets the value of the colour property.
*
* @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setCalcId(String value) {
- this.calcId = value;
- }
-
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
- *
+ * allowed object is {@link Integer }
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class Property {
-
- @XmlAttribute(name = "name")
- protected String name;
- @XmlAttribute(name = "value")
- protected String value;
-
- /**
- * Gets the value of the name property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getName() {
- return name;
- }
-
- /**
- * Sets the value of the name property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setName(String value) {
- this.name = value;
- }
-
- /**
- * Gets the value of the value property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getValue() {
- return value;
- }
-
- /**
- * Sets the value of the value property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setValue(String value) {
- this.value = value;
- }
-
+ public void setColour(Integer value)
+ {
+ this.colour = value;
}
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="label" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class ThresholdLine {
-
- @XmlAttribute(name = "label")
- protected String label;
- @XmlAttribute(name = "value")
- protected Float value;
- @XmlAttribute(name = "colour")
- protected Integer colour;
-
- /**
- * Gets the value of the label property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getLabel() {
- return label;
- }
-
- /**
- * Sets the value of the label property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setLabel(String value) {
- this.label = value;
- }
-
- /**
- * Gets the value of the value property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getValue() {
- return value;
- }
-
- /**
- * Sets the value of the value property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setValue(Float value) {
- this.value = value;
- }
-
- /**
- * Gets the value of the colour property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getColour() {
- return colour;
- }
-
- /**
- * Sets the value of the colour property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setColour(Integer value) {
- this.colour = value;
- }
-
- }
+ }
}
// Generated on: 2021.08.30 at 11:05:22 AM BST
//
-
package jalview.xml.binding.jalview;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlType;
-
/**
* <p>Java class for AnnotationColourScheme complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
*
- * <pre>
- * &lt;complexType name="AnnotationColourScheme"&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="aboveThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="annotation" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="minColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="maxColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="colourScheme" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="perSequence" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="predefinedColours" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre> &lt;complexType name="AnnotationColourScheme"&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
+ * name="aboveThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="annotation"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="minColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="maxColour"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="colourScheme" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="threshold"
+ * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute
+ * name="perSequence" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="predefinedColours"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "AnnotationColourScheme", namespace = "www.jalview.org")
-public class AnnotationColourScheme {
-
- @XmlAttribute(name = "aboveThreshold")
- protected Integer aboveThreshold;
- @XmlAttribute(name = "annotation")
- protected String annotation;
- @XmlAttribute(name = "minColour")
- protected Integer minColour;
- @XmlAttribute(name = "maxColour")
- protected Integer maxColour;
- @XmlAttribute(name = "colourScheme")
- protected String colourScheme;
- @XmlAttribute(name = "threshold")
- protected Float threshold;
- @XmlAttribute(name = "perSequence")
- protected Boolean perSequence;
- @XmlAttribute(name = "predefinedColours")
- protected Boolean predefinedColours;
-
- /**
- * Gets the value of the aboveThreshold property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getAboveThreshold() {
- return aboveThreshold;
- }
-
- /**
- * Sets the value of the aboveThreshold property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setAboveThreshold(Integer value) {
- this.aboveThreshold = value;
- }
-
- /**
- * Gets the value of the annotation property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getAnnotation() {
- return annotation;
- }
-
- /**
- * Sets the value of the annotation property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setAnnotation(String value) {
- this.annotation = value;
- }
-
- /**
- * Gets the value of the minColour property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getMinColour() {
- return minColour;
- }
-
- /**
- * Sets the value of the minColour property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setMinColour(Integer value) {
- this.minColour = value;
- }
-
- /**
- * Gets the value of the maxColour property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getMaxColour() {
- return maxColour;
- }
-
- /**
- * Sets the value of the maxColour property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setMaxColour(Integer value) {
- this.maxColour = value;
- }
-
- /**
- * Gets the value of the colourScheme property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getColourScheme() {
- return colourScheme;
- }
-
- /**
- * Sets the value of the colourScheme property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setColourScheme(String value) {
- this.colourScheme = value;
- }
-
- /**
- * Gets the value of the threshold property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getThreshold() {
- return threshold;
- }
-
- /**
- * Sets the value of the threshold property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setThreshold(Float value) {
- this.threshold = value;
- }
-
- /**
- * Gets the value of the perSequence property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isPerSequence() {
- return perSequence;
- }
-
- /**
- * Sets the value of the perSequence property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setPerSequence(Boolean value) {
- this.perSequence = value;
- }
-
- /**
- * Gets the value of the predefinedColours property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isPredefinedColours() {
- return predefinedColours;
- }
-
- /**
- * Sets the value of the predefinedColours property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setPredefinedColours(Boolean value) {
- this.predefinedColours = value;
- }
+public class AnnotationColourScheme
+{
+
+ @XmlAttribute(name = "aboveThreshold")
+ protected Integer aboveThreshold;
+
+ @XmlAttribute(name = "annotation")
+ protected String annotation;
+
+ @XmlAttribute(name = "minColour")
+ protected Integer minColour;
+
+ @XmlAttribute(name = "maxColour")
+ protected Integer maxColour;
+
+ @XmlAttribute(name = "colourScheme")
+ protected String colourScheme;
+
+ @XmlAttribute(name = "threshold")
+ protected Float threshold;
+
+ @XmlAttribute(name = "perSequence")
+ protected Boolean perSequence;
+
+ @XmlAttribute(name = "predefinedColours")
+ protected Boolean predefinedColours;
+
+ /**
+ * Gets the value of the aboveThreshold property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getAboveThreshold()
+ {
+ return aboveThreshold;
+ }
+
+ /**
+ * Sets the value of the aboveThreshold property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setAboveThreshold(Integer value)
+ {
+ this.aboveThreshold = value;
+ }
+
+ /**
+ * Gets the value of the annotation property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getAnnotation()
+ {
+ return annotation;
+ }
+
+ /**
+ * Sets the value of the annotation property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setAnnotation(String value)
+ {
+ this.annotation = value;
+ }
+
+ /**
+ * Gets the value of the minColour property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getMinColour()
+ {
+ return minColour;
+ }
+
+ /**
+ * Sets the value of the minColour property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setMinColour(Integer value)
+ {
+ this.minColour = value;
+ }
+
+ /**
+ * Gets the value of the maxColour property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getMaxColour()
+ {
+ return maxColour;
+ }
+
+ /**
+ * Sets the value of the maxColour property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setMaxColour(Integer value)
+ {
+ this.maxColour = value;
+ }
+
+ /**
+ * Gets the value of the colourScheme property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getColourScheme()
+ {
+ return colourScheme;
+ }
+
+ /**
+ * Sets the value of the colourScheme property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setColourScheme(String value)
+ {
+ this.colourScheme = value;
+ }
+
+ /**
+ * Gets the value of the threshold property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getThreshold()
+ {
+ return threshold;
+ }
+
+ /**
+ * Sets the value of the threshold property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setThreshold(Float value)
+ {
+ this.threshold = value;
+ }
+
+ /**
+ * Gets the value of the perSequence property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isPerSequence()
+ {
+ return perSequence;
+ }
+
+ /**
+ * Sets the value of the perSequence property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setPerSequence(Boolean value)
+ {
+ this.perSequence = value;
+ }
+
+ /**
+ * Gets the value of the predefinedColours property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isPredefinedColours()
+ {
+ return predefinedColours;
+ }
+
+ /**
+ * Sets the value of the predefinedColours property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setPredefinedColours(Boolean value)
+ {
+ this.predefinedColours = value;
+ }
}
// Generated on: 2021.08.30 at 11:05:22 AM BST
//
-
package jalview.xml.binding.jalview;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlRootElement;
import javax.xml.bind.annotation.XmlType;
-
/**
* <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
*
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="displayCharacter" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
- * &lt;element name="description" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
- * &lt;element name="secondaryStructure" minOccurs="0"&gt;
- * &lt;simpleType&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt;
- * &lt;length value="1"/&gt;
- * &lt;/restriction&gt;
- * &lt;/simpleType&gt;
- * &lt;/element&gt;
- * &lt;element name="value" type="{http://www.w3.org/2001/XMLSchema}float" minOccurs="0"/&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="position" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="displayCharacter"
+ * type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
+ * &lt;element name="description"
+ * type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
+ * &lt;element name="secondaryStructure" minOccurs="0"&gt;
+ * &lt;simpleType&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}string"&gt; &lt;length
+ * value="1"/&gt; &lt;/restriction&gt; &lt;/simpleType&gt;
+ * &lt;/element&gt; &lt;element name="value"
+ * type="{http://www.w3.org/2001/XMLSchema}float" minOccurs="0"/&gt;
+ * &lt;/sequence&gt; &lt;attribute name="position" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = {
- "displayCharacter",
- "description",
- "secondaryStructure",
- "value"
-})
+@XmlType(
+ name = "",
+ propOrder =
+ { "displayCharacter", "description", "secondaryStructure", "value" })
@XmlRootElement(name = "annotationElement")
-public class AnnotationElement {
-
- protected String displayCharacter;
- protected String description;
- protected String secondaryStructure;
- protected Float value;
- @XmlAttribute(name = "position", required = true)
- protected int position;
- @XmlAttribute(name = "colour")
- protected Integer colour;
-
- /**
- * Gets the value of the displayCharacter property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDisplayCharacter() {
- return displayCharacter;
- }
-
- /**
- * Sets the value of the displayCharacter property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDisplayCharacter(String value) {
- this.displayCharacter = value;
- }
-
- /**
- * Gets the value of the description property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDescription() {
- return description;
- }
-
- /**
- * Sets the value of the description property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDescription(String value) {
- this.description = value;
- }
-
- /**
- * Gets the value of the secondaryStructure property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getSecondaryStructure() {
- return secondaryStructure;
- }
-
- /**
- * Sets the value of the secondaryStructure property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setSecondaryStructure(String value) {
- this.secondaryStructure = value;
- }
-
- /**
- * Gets the value of the value property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getValue() {
- return value;
- }
-
- /**
- * Sets the value of the value property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setValue(Float value) {
- this.value = value;
- }
-
- /**
- * Gets the value of the position property.
- *
- */
- public int getPosition() {
- return position;
- }
-
- /**
- * Sets the value of the position property.
- *
- */
- public void setPosition(int value) {
- this.position = value;
- }
-
- /**
- * Gets the value of the colour property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getColour() {
- return colour;
- }
-
- /**
- * Sets the value of the colour property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setColour(Integer value) {
- this.colour = value;
- }
+public class AnnotationElement
+{
+
+ protected String displayCharacter;
+
+ protected String description;
+
+ protected String secondaryStructure;
+
+ protected Float value;
+
+ @XmlAttribute(name = "position", required = true)
+ protected int position;
+
+ @XmlAttribute(name = "colour")
+ protected Integer colour;
+
+ /**
+ * Gets the value of the displayCharacter property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDisplayCharacter()
+ {
+ return displayCharacter;
+ }
+
+ /**
+ * Sets the value of the displayCharacter property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setDisplayCharacter(String value)
+ {
+ this.displayCharacter = value;
+ }
+
+ /**
+ * Gets the value of the description property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDescription()
+ {
+ return description;
+ }
+
+ /**
+ * Sets the value of the description property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setDescription(String value)
+ {
+ this.description = value;
+ }
+
+ /**
+ * Gets the value of the secondaryStructure property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getSecondaryStructure()
+ {
+ return secondaryStructure;
+ }
+
+ /**
+ * Sets the value of the secondaryStructure property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setSecondaryStructure(String value)
+ {
+ this.secondaryStructure = value;
+ }
+
+ /**
+ * Gets the value of the value property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getValue()
+ {
+ return value;
+ }
+
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setValue(Float value)
+ {
+ this.value = value;
+ }
+
+ /**
+ * Gets the value of the position property.
+ *
+ */
+ public int getPosition()
+ {
+ return position;
+ }
+
+ /**
+ * Sets the value of the position property.
+ *
+ */
+ public void setPosition(int value)
+ {
+ this.position = value;
+ }
+
+ /**
+ * Gets the value of the colour property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getColour()
+ {
+ return colour;
+ }
+
+ /**
+ * Sets the value of the colour property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setColour(Integer value)
+ {
+ this.colour = value;
+ }
}
// Generated on: 2021.08.30 at 11:05:22 AM BST
//
-
package jalview.xml.binding.jalview;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
-
/**
* <p>Java class for DoubleMatrix complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
*
- * <pre>
- * &lt;complexType name="DoubleMatrix"&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="row" type="{www.jalview.org}DoubleVector" maxOccurs="unbounded" minOccurs="0"/&gt;
- * &lt;element name="D" type="{www.jalview.org}DoubleVector" minOccurs="0"/&gt;
- * &lt;element name="E" type="{www.jalview.org}DoubleVector" minOccurs="0"/&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="rows" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="columns" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre> &lt;complexType name="DoubleMatrix"&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="row"
+ * type="{www.jalview.org}DoubleVector" maxOccurs="unbounded"
+ * minOccurs="0"/&gt; &lt;element name="D"
+ * type="{www.jalview.org}DoubleVector" minOccurs="0"/&gt; &lt;element
+ * name="E" type="{www.jalview.org}DoubleVector" minOccurs="0"/&gt;
+ * &lt;/sequence&gt; &lt;attribute name="rows"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="columns" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "DoubleMatrix", namespace = "www.jalview.org", propOrder = {
- "row",
- "d",
- "e"
-})
-public class DoubleMatrix {
-
- protected List<DoubleVector> row;
- @XmlElement(name = "D")
- protected DoubleVector d;
- @XmlElement(name = "E")
- protected DoubleVector e;
- @XmlAttribute(name = "rows")
- protected Integer rows;
- @XmlAttribute(name = "columns")
- protected Integer columns;
-
- /**
- * Gets the value of the row property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the row property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getRow().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link DoubleVector }
- *
- *
- */
- public List<DoubleVector> getRow() {
- if (row == null) {
- row = new ArrayList<DoubleVector>();
- }
- return this.row;
- }
-
- /**
- * Gets the value of the d property.
- *
- * @return
- * possible object is
- * {@link DoubleVector }
- *
- */
- public DoubleVector getD() {
- return d;
- }
-
- /**
- * Sets the value of the d property.
- *
- * @param value
- * allowed object is
- * {@link DoubleVector }
- *
- */
- public void setD(DoubleVector value) {
- this.d = value;
- }
-
- /**
- * Gets the value of the e property.
- *
- * @return
- * possible object is
- * {@link DoubleVector }
- *
- */
- public DoubleVector getE() {
- return e;
- }
-
- /**
- * Sets the value of the e property.
- *
- * @param value
- * allowed object is
- * {@link DoubleVector }
- *
- */
- public void setE(DoubleVector value) {
- this.e = value;
- }
-
- /**
- * Gets the value of the rows property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getRows() {
- return rows;
- }
-
- /**
- * Sets the value of the rows property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setRows(Integer value) {
- this.rows = value;
- }
-
- /**
- * Gets the value of the columns property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getColumns() {
- return columns;
- }
-
- /**
- * Sets the value of the columns property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setColumns(Integer value) {
- this.columns = value;
+@XmlType(
+ name = "DoubleMatrix",
+ namespace = "www.jalview.org",
+ propOrder =
+ { "row", "d", "e" })
+public class DoubleMatrix
+{
+
+ protected List<DoubleVector> row;
+
+ @XmlElement(name = "D")
+ protected DoubleVector d;
+
+ @XmlElement(name = "E")
+ protected DoubleVector e;
+
+ @XmlAttribute(name = "rows")
+ protected Integer rows;
+
+ @XmlAttribute(name = "columns")
+ protected Integer columns;
+
+ /**
+ * Gets the value of the row property.
+ *
+ * <p> This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will be
+ * present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the row property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getRow().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link DoubleVector }
+ *
+ *
+ */
+ public List<DoubleVector> getRow()
+ {
+ if (row == null)
+ {
+ row = new ArrayList<DoubleVector>();
}
+ return this.row;
+ }
+
+ /**
+ * Gets the value of the d property.
+ *
+ * @return possible object is {@link DoubleVector }
+ *
+ */
+ public DoubleVector getD()
+ {
+ return d;
+ }
+
+ /**
+ * Sets the value of the d property.
+ *
+ * @param value
+ * allowed object is {@link DoubleVector }
+ *
+ */
+ public void setD(DoubleVector value)
+ {
+ this.d = value;
+ }
+
+ /**
+ * Gets the value of the e property.
+ *
+ * @return possible object is {@link DoubleVector }
+ *
+ */
+ public DoubleVector getE()
+ {
+ return e;
+ }
+
+ /**
+ * Sets the value of the e property.
+ *
+ * @param value
+ * allowed object is {@link DoubleVector }
+ *
+ */
+ public void setE(DoubleVector value)
+ {
+ this.e = value;
+ }
+
+ /**
+ * Gets the value of the rows property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getRows()
+ {
+ return rows;
+ }
+
+ /**
+ * Sets the value of the rows property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setRows(Integer value)
+ {
+ this.rows = value;
+ }
+
+ /**
+ * Gets the value of the columns property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getColumns()
+ {
+ return columns;
+ }
+
+ /**
+ * Sets the value of the columns property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setColumns(Integer value)
+ {
+ this.columns = value;
+ }
}
// Generated on: 2021.08.30 at 11:05:22 AM BST
//
-
package jalview.xml.binding.jalview;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
-
/**
* <p>Java class for DoubleVector complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
*
- * <pre>
- * &lt;complexType name="DoubleVector"&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="v" type="{http://www.w3.org/2001/XMLSchema}double" maxOccurs="unbounded" minOccurs="0"/&gt;
- * &lt;/sequence&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre> &lt;complexType name="DoubleVector"&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="v"
+ * type="{http://www.w3.org/2001/XMLSchema}double" maxOccurs="unbounded"
+ * minOccurs="0"/&gt; &lt;/sequence&gt; &lt;/restriction&gt;
+ * &lt;/complexContent&gt; &lt;/complexType&gt; </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "DoubleVector", namespace = "www.jalview.org", propOrder = {
- "v"
-})
-public class DoubleVector {
+@XmlType(
+ name = "DoubleVector",
+ namespace = "www.jalview.org",
+ propOrder =
+ { "v" })
+public class DoubleVector
+{
- @XmlElement(type = Double.class)
- protected List<Double> v;
+ @XmlElement(type = Double.class)
+ protected List<Double> v;
- /**
- * Gets the value of the v property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the v property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getV().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Double }
- *
- *
- */
- public List<Double> getV() {
- if (v == null) {
- v = new ArrayList<Double>();
- }
- return this.v;
+ /**
+ * Gets the value of the v property.
+ *
+ * <p> This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will be
+ * present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the v property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getV().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link Double }
+ *
+ *
+ */
+ public List<Double> getV()
+ {
+ if (v == null)
+ {
+ v = new ArrayList<Double>();
}
+ return this.v;
+ }
}
// Generated on: 2021.08.30 at 11:05:22 AM BST
//
-
package jalview.xml.binding.jalview;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlType;
-
/**
* <p>Java class for feature complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
*
- * <pre>
- * &lt;complexType name="feature"&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="otherData" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="key" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="key2" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="description" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="status" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="featureGroup" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="score" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre> &lt;complexType name="feature"&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="otherData"
+ * maxOccurs="unbounded" minOccurs="0"&gt; &lt;complexType&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
+ * name="key" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
+ * /&gt; &lt;attribute name="key2"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
+ * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt;
+ * &lt;/sequence&gt; &lt;attribute name="begin" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
+ * /&gt; &lt;attribute name="type" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="description" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="status"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="featureGroup" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="score" type="{http://www.w3.org/2001/XMLSchema}float"
+ * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "feature", namespace = "www.jalview.org", propOrder = {
- "otherData"
-})
-public class Feature {
-
- protected List<Feature.OtherData> otherData;
- @XmlAttribute(name = "begin", required = true)
- protected int begin;
- @XmlAttribute(name = "end", required = true)
- protected int end;
- @XmlAttribute(name = "type", required = true)
- protected String type;
- @XmlAttribute(name = "description")
- protected String description;
- @XmlAttribute(name = "status")
- protected String status;
- @XmlAttribute(name = "featureGroup")
- protected String featureGroup;
- @XmlAttribute(name = "score")
- protected Float score;
-
- /**
- * Gets the value of the otherData property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the otherData property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getOtherData().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Feature.OtherData }
- *
- *
- */
- public List<Feature.OtherData> getOtherData() {
- if (otherData == null) {
- otherData = new ArrayList<Feature.OtherData>();
- }
- return this.otherData;
+@XmlType(
+ name = "feature",
+ namespace = "www.jalview.org",
+ propOrder =
+ { "otherData" })
+public class Feature
+{
+
+ protected List<Feature.OtherData> otherData;
+
+ @XmlAttribute(name = "begin", required = true)
+ protected int begin;
+
+ @XmlAttribute(name = "end", required = true)
+ protected int end;
+
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
+
+ @XmlAttribute(name = "description")
+ protected String description;
+
+ @XmlAttribute(name = "status")
+ protected String status;
+
+ @XmlAttribute(name = "featureGroup")
+ protected String featureGroup;
+
+ @XmlAttribute(name = "score")
+ protected Float score;
+
+ /**
+ * Gets the value of the otherData property.
+ *
+ * <p> This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will be
+ * present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the otherData property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getOtherData().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link Feature.OtherData }
+ *
+ *
+ */
+ public List<Feature.OtherData> getOtherData()
+ {
+ if (otherData == null)
+ {
+ otherData = new ArrayList<Feature.OtherData>();
}
+ return this.otherData;
+ }
+
+ /**
+ * Gets the value of the begin property.
+ *
+ */
+ public int getBegin()
+ {
+ return begin;
+ }
+
+ /**
+ * Sets the value of the begin property.
+ *
+ */
+ public void setBegin(int value)
+ {
+ this.begin = value;
+ }
+
+ /**
+ * Gets the value of the end property.
+ *
+ */
+ public int getEnd()
+ {
+ return end;
+ }
+
+ /**
+ * Sets the value of the end property.
+ *
+ */
+ public void setEnd(int value)
+ {
+ this.end = value;
+ }
+
+ /**
+ * Gets the value of the type property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getType()
+ {
+ return type;
+ }
+
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setType(String value)
+ {
+ this.type = value;
+ }
+
+ /**
+ * Gets the value of the description property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDescription()
+ {
+ return description;
+ }
+
+ /**
+ * Sets the value of the description property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setDescription(String value)
+ {
+ this.description = value;
+ }
+
+ /**
+ * Gets the value of the status property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getStatus()
+ {
+ return status;
+ }
+
+ /**
+ * Sets the value of the status property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setStatus(String value)
+ {
+ this.status = value;
+ }
+
+ /**
+ * Gets the value of the featureGroup property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getFeatureGroup()
+ {
+ return featureGroup;
+ }
+
+ /**
+ * Sets the value of the featureGroup property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setFeatureGroup(String value)
+ {
+ this.featureGroup = value;
+ }
+
+ /**
+ * Gets the value of the score property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getScore()
+ {
+ return score;
+ }
+
+ /**
+ * Sets the value of the score property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setScore(Float value)
+ {
+ this.score = value;
+ }
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
+ *
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
+ * name="key" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
+ * /&gt; &lt;attribute name="key2"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
+ * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class OtherData
+ {
+
+ @XmlAttribute(name = "key", required = true)
+ protected String key;
+
+ @XmlAttribute(name = "key2")
+ protected String key2;
+
+ @XmlAttribute(name = "value", required = true)
+ protected String value;
/**
- * Gets the value of the begin property.
+ * Gets the value of the key property.
*
- */
- public int getBegin() {
- return begin;
- }
-
- /**
- * Sets the value of the begin property.
- *
- */
- public void setBegin(int value) {
- this.begin = value;
- }
-
- /**
- * Gets the value of the end property.
- *
- */
- public int getEnd() {
- return end;
- }
-
- /**
- * Sets the value of the end property.
- *
- */
- public void setEnd(int value) {
- this.end = value;
- }
-
- /**
- * Gets the value of the type property.
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getType() {
- return type;
+ public String getKey()
+ {
+ return key;
}
/**
- * Sets the value of the type property.
+ * Sets the value of the key property.
*
* @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setType(String value) {
- this.type = value;
- }
-
- /**
- * Gets the value of the description property.
+ * allowed object is {@link String }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getDescription() {
- return description;
+ public void setKey(String value)
+ {
+ this.key = value;
}
/**
- * Sets the value of the description property.
+ * Gets the value of the key2 property.
*
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDescription(String value) {
- this.description = value;
- }
-
- /**
- * Gets the value of the status property.
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getStatus() {
- return status;
+ public String getKey2()
+ {
+ return key2;
}
/**
- * Sets the value of the status property.
+ * Sets the value of the key2 property.
*
* @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setStatus(String value) {
- this.status = value;
- }
-
- /**
- * Gets the value of the featureGroup property.
+ * allowed object is {@link String }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getFeatureGroup() {
- return featureGroup;
+ public void setKey2(String value)
+ {
+ this.key2 = value;
}
/**
- * Sets the value of the featureGroup property.
+ * Gets the value of the value property.
*
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setFeatureGroup(String value) {
- this.featureGroup = value;
- }
-
- /**
- * Gets the value of the score property.
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link Float }
- *
*/
- public Float getScore() {
- return score;
+ public String getValue()
+ {
+ return value;
}
/**
- * Sets the value of the score property.
+ * Sets the value of the value property.
*
* @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setScore(Float value) {
- this.score = value;
- }
-
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="key" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="key2" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
- *
+ * allowed object is {@link String }
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class OtherData {
-
- @XmlAttribute(name = "key", required = true)
- protected String key;
- @XmlAttribute(name = "key2")
- protected String key2;
- @XmlAttribute(name = "value", required = true)
- protected String value;
-
- /**
- * Gets the value of the key property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getKey() {
- return key;
- }
-
- /**
- * Sets the value of the key property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setKey(String value) {
- this.key = value;
- }
-
- /**
- * Gets the value of the key2 property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getKey2() {
- return key2;
- }
-
- /**
- * Sets the value of the key2 property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setKey2(String value) {
- this.key2 = value;
- }
-
- /**
- * Gets the value of the value property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getValue() {
- return value;
- }
-
- /**
- * Sets the value of the value property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setValue(String value) {
- this.value = value;
- }
-
+ public void setValue(String value)
+ {
+ this.value = value;
}
+ }
+
}
// Generated on: 2021.08.30 at 11:05:22 AM BST
//
-
package jalview.xml.binding.jalview;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
-
/**
* <p>Java class for FeatureMatcher complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
*
- * <pre>
- * &lt;complexType name="FeatureMatcher"&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&gt;
- * &lt;element name="condition" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
- * &lt;element name="value" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="by" type="{www.jalview.org/colours}FilterBy" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre> &lt;complexType name="FeatureMatcher"&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="attributeName"
+ * type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2"
+ * minOccurs="0"/&gt; &lt;element name="condition"
+ * type="{http://www.w3.org/2001/XMLSchema}string"/&gt; &lt;element
+ * name="value" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
+ * &lt;/sequence&gt; &lt;attribute name="by"
+ * type="{www.jalview.org/colours}FilterBy" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "FeatureMatcher", namespace = "www.jalview.org/colours", propOrder = {
- "attributeName",
- "condition",
- "value"
-})
-public class FeatureMatcher {
+@XmlType(
+ name = "FeatureMatcher",
+ namespace = "www.jalview.org/colours",
+ propOrder =
+ { "attributeName", "condition", "value" })
+public class FeatureMatcher
+{
- @XmlElement(namespace = "")
- protected List<String> attributeName;
- @XmlElement(namespace = "", required = true)
- protected String condition;
- @XmlElement(namespace = "", required = true)
- protected String value;
- @XmlAttribute(name = "by")
- protected FilterBy by;
+ @XmlElement(namespace = "")
+ protected List<String> attributeName;
- /**
- * Gets the value of the attributeName property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the attributeName property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getAttributeName().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link String }
- *
- *
- */
- public List<String> getAttributeName() {
- if (attributeName == null) {
- attributeName = new ArrayList<String>();
- }
- return this.attributeName;
- }
+ @XmlElement(namespace = "", required = true)
+ protected String condition;
- /**
- * Gets the value of the condition property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getCondition() {
- return condition;
- }
+ @XmlElement(namespace = "", required = true)
+ protected String value;
- /**
- * Sets the value of the condition property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setCondition(String value) {
- this.condition = value;
- }
+ @XmlAttribute(name = "by")
+ protected FilterBy by;
- /**
- * Gets the value of the value property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getValue() {
- return value;
+ /**
+ * Gets the value of the attributeName property.
+ *
+ * <p> This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will be
+ * present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the attributeName property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getAttributeName().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link String }
+ *
+ *
+ */
+ public List<String> getAttributeName()
+ {
+ if (attributeName == null)
+ {
+ attributeName = new ArrayList<String>();
}
+ return this.attributeName;
+ }
- /**
- * Sets the value of the value property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setValue(String value) {
- this.value = value;
- }
+ /**
+ * Gets the value of the condition property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getCondition()
+ {
+ return condition;
+ }
- /**
- * Gets the value of the by property.
- *
- * @return
- * possible object is
- * {@link FilterBy }
- *
- */
- public FilterBy getBy() {
- return by;
- }
+ /**
+ * Sets the value of the condition property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setCondition(String value)
+ {
+ this.condition = value;
+ }
- /**
- * Sets the value of the by property.
- *
- * @param value
- * allowed object is
- * {@link FilterBy }
- *
- */
- public void setBy(FilterBy value) {
- this.by = value;
- }
+ /**
+ * Gets the value of the value property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getValue()
+ {
+ return value;
+ }
+
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setValue(String value)
+ {
+ this.value = value;
+ }
+
+ /**
+ * Gets the value of the by property.
+ *
+ * @return possible object is {@link FilterBy }
+ *
+ */
+ public FilterBy getBy()
+ {
+ return by;
+ }
+
+ /**
+ * Sets the value of the by property.
+ *
+ * @param value
+ * allowed object is {@link FilterBy }
+ *
+ */
+ public void setBy(FilterBy value)
+ {
+ this.by = value;
+ }
}
// Generated on: 2021.08.30 at 11:05:22 AM BST
//
-
package jalview.xml.binding.jalview;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
-
/**
* A feature match condition, which may be simple or compound
*
* <p>Java class for FeatureMatcherSet complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
*
- * <pre>
- * &lt;complexType name="FeatureMatcherSet"&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;choice&gt;
- * &lt;element name="matchCondition" type="{www.jalview.org/colours}FeatureMatcher"/&gt;
- * &lt;element name="compoundMatcher"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" maxOccurs="2" minOccurs="2"/&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="and" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;/choice&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre> &lt;complexType name="FeatureMatcherSet"&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;choice&gt; &lt;element name="matchCondition"
+ * type="{www.jalview.org/colours}FeatureMatcher"/&gt; &lt;element
+ * name="compoundMatcher"&gt; &lt;complexType&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="matcherSet"
+ * type="{www.jalview.org/colours}FeatureMatcherSet" maxOccurs="2"
+ * minOccurs="2"/&gt; &lt;/sequence&gt; &lt;attribute name="and"
+ * use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt; &lt;/choice&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "FeatureMatcherSet", namespace = "www.jalview.org/colours", propOrder = {
- "matchCondition",
- "compoundMatcher"
-})
-public class FeatureMatcherSet {
-
- @XmlElement(namespace = "")
- protected FeatureMatcher matchCondition;
- @XmlElement(namespace = "")
- protected FeatureMatcherSet.CompoundMatcher compoundMatcher;
+@XmlType(
+ name = "FeatureMatcherSet",
+ namespace = "www.jalview.org/colours",
+ propOrder =
+ { "matchCondition", "compoundMatcher" })
+public class FeatureMatcherSet
+{
+
+ @XmlElement(namespace = "")
+ protected FeatureMatcher matchCondition;
+
+ @XmlElement(namespace = "")
+ protected FeatureMatcherSet.CompoundMatcher compoundMatcher;
+
+ /**
+ * Gets the value of the matchCondition property.
+ *
+ * @return possible object is {@link FeatureMatcher }
+ *
+ */
+ public FeatureMatcher getMatchCondition()
+ {
+ return matchCondition;
+ }
+
+ /**
+ * Sets the value of the matchCondition property.
+ *
+ * @param value
+ * allowed object is {@link FeatureMatcher }
+ *
+ */
+ public void setMatchCondition(FeatureMatcher value)
+ {
+ this.matchCondition = value;
+ }
+
+ /**
+ * Gets the value of the compoundMatcher property.
+ *
+ * @return possible object is {@link FeatureMatcherSet.CompoundMatcher }
+ *
+ */
+ public FeatureMatcherSet.CompoundMatcher getCompoundMatcher()
+ {
+ return compoundMatcher;
+ }
+
+ /**
+ * Sets the value of the compoundMatcher property.
+ *
+ * @param value
+ * allowed object is {@link FeatureMatcherSet.CompoundMatcher }
+ *
+ */
+ public void setCompoundMatcher(FeatureMatcherSet.CompoundMatcher value)
+ {
+ this.compoundMatcher = value;
+ }
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
+ *
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="matcherSet"
+ * type="{www.jalview.org/colours}FeatureMatcherSet" maxOccurs="2"
+ * minOccurs="2"/&gt; &lt;/sequence&gt; &lt;attribute
+ * name="and" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean"
+ * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "matcherSet" })
+ public static class CompoundMatcher
+ {
+
+ @XmlElement(namespace = "", required = true)
+ protected List<FeatureMatcherSet> matcherSet;
+
+ @XmlAttribute(name = "and", required = true)
+ protected boolean and;
/**
- * Gets the value of the matchCondition property.
+ * Gets the value of the matcherSet property.
*
- * @return
- * possible object is
- * {@link FeatureMatcher }
- *
- */
- public FeatureMatcher getMatchCondition() {
- return matchCondition;
- }
-
- /**
- * Sets the value of the matchCondition property.
+ * <p> This accessor method returns a reference to the live list, not
+ * a snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the matcherSet property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getMatcherSet().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link FeatureMatcherSet }
*
- * @param value
- * allowed object is
- * {@link FeatureMatcher }
- *
- */
- public void setMatchCondition(FeatureMatcher value) {
- this.matchCondition = value;
- }
-
- /**
- * Gets the value of the compoundMatcher property.
*
- * @return
- * possible object is
- * {@link FeatureMatcherSet.CompoundMatcher }
- *
*/
- public FeatureMatcherSet.CompoundMatcher getCompoundMatcher() {
- return compoundMatcher;
+ public List<FeatureMatcherSet> getMatcherSet()
+ {
+ if (matcherSet == null)
+ {
+ matcherSet = new ArrayList<FeatureMatcherSet>();
+ }
+ return this.matcherSet;
}
/**
- * Sets the value of the compoundMatcher property.
+ * Gets the value of the and property.
*
- * @param value
- * allowed object is
- * {@link FeatureMatcherSet.CompoundMatcher }
- *
*/
- public void setCompoundMatcher(FeatureMatcherSet.CompoundMatcher value) {
- this.compoundMatcher = value;
+ public boolean isAnd()
+ {
+ return and;
}
-
/**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" maxOccurs="2" minOccurs="2"/&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="and" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
- *
+ * Sets the value of the and property.
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "matcherSet"
- })
- public static class CompoundMatcher {
-
- @XmlElement(namespace = "", required = true)
- protected List<FeatureMatcherSet> matcherSet;
- @XmlAttribute(name = "and", required = true)
- protected boolean and;
-
- /**
- * Gets the value of the matcherSet property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the matcherSet property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getMatcherSet().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link FeatureMatcherSet }
- *
- *
- */
- public List<FeatureMatcherSet> getMatcherSet() {
- if (matcherSet == null) {
- matcherSet = new ArrayList<FeatureMatcherSet>();
- }
- return this.matcherSet;
- }
-
- /**
- * Gets the value of the and property.
- *
- */
- public boolean isAnd() {
- return and;
- }
-
- /**
- * Sets the value of the and property.
- *
- */
- public void setAnd(boolean value) {
- this.and = value;
- }
-
+ public void setAnd(boolean value)
+ {
+ this.and = value;
}
+ }
+
}
// Generated on: 2021.08.30 at 11:05:22 AM BST
//
-
package jalview.xml.binding.jalview;
import javax.xml.bind.annotation.XmlEnum;
import javax.xml.bind.annotation.XmlEnumValue;
import javax.xml.bind.annotation.XmlType;
-
/**
* <p>Java class for FilterBy.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
- * <pre>
- * &lt;simpleType name="FilterBy"&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt;
- * &lt;enumeration value="byLabel"/&gt;
- * &lt;enumeration value="byScore"/&gt;
- * &lt;enumeration value="byAttribute"/&gt;
- * &lt;/restriction&gt;
- * &lt;/simpleType&gt;
- * </pre>
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class. <pre> &lt;simpleType
+ * name="FilterBy"&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}string"&gt; &lt;enumeration
+ * value="byLabel"/&gt; &lt;enumeration value="byScore"/&gt;
+ * &lt;enumeration value="byAttribute"/&gt; &lt;/restriction&gt;
+ * &lt;/simpleType&gt; </pre>
*
*/
@XmlType(name = "FilterBy", namespace = "www.jalview.org/colours")
@XmlEnum
-public enum FilterBy {
-
- @XmlEnumValue("byLabel")
- BY_LABEL("byLabel"),
- @XmlEnumValue("byScore")
- BY_SCORE("byScore"),
- @XmlEnumValue("byAttribute")
- BY_ATTRIBUTE("byAttribute");
- private final String value;
-
- FilterBy(String v) {
- value = v;
- }
-
- public String value() {
- return value;
- }
-
- public static FilterBy fromValue(String v) {
- for (FilterBy c: FilterBy.values()) {
- if (c.value.equals(v)) {
- return c;
- }
- }
- throw new IllegalArgumentException(v);
+public enum FilterBy
+{
+
+ @XmlEnumValue("byLabel")
+ BY_LABEL("byLabel"), @XmlEnumValue("byScore")
+ BY_SCORE("byScore"), @XmlEnumValue("byAttribute")
+ BY_ATTRIBUTE("byAttribute");
+
+ private final String value;
+
+ FilterBy(String v)
+ {
+ value = v;
+ }
+
+ public String value()
+ {
+ return value;
+ }
+
+ public static FilterBy fromValue(String v)
+ {
+ for (FilterBy c : FilterBy.values())
+ {
+ if (c.value.equals(v))
+ {
+ return c;
+ }
}
+ throw new IllegalArgumentException(v);
+ }
}
// Generated on: 2021.08.30 at 11:05:22 AM BST
//
-
package jalview.xml.binding.jalview;
import java.util.ArrayList;
import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
import javax.xml.datatype.XMLGregorianCalendar;
-
/**
* <p>Java class for JalviewModel complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
*
- * <pre>
- * &lt;complexType name="JalviewModel"&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="creationDate" type="{http://www.w3.org/2001/XMLSchema}dateTime"/&gt;
- * &lt;element name="version" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
- * &lt;element name="vamsasModel" type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/&gt;
- * &lt;sequence&gt;
- * &lt;element name="JSeq" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/&gt;
- * &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;extension base="{www.jalview.org}pdbentry"&gt;
- * &lt;sequence&gt;
- * &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;simpleContent&gt;
- * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
- * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
- * &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/extension&gt;
- * &lt;/simpleContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;/sequence&gt;
- * &lt;/extension&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/&gt;
- * &lt;element name="rnaViewer" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="secondaryStructure" maxOccurs="unbounded"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;/sequence&gt;
- * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
- * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="JGroup" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/&gt;
- * &lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="Viewport" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
- * &lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&gt;
- * &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/extension&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;/sequence&gt;
- * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
- * &lt;attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
- * &lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="UserColours" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="tree" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence minOccurs="0"&gt;
- * &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
- * &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
- * &lt;/sequence&gt;
- * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
- * &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
- * &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="PcaViewer" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="sequencePoint" maxOccurs="unbounded"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attGroup ref="{www.jalview.org}position"/&gt;
- * &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="axis" maxOccurs="3" minOccurs="3"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attGroup ref="{www.jalview.org}position"/&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="seqPointMin"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attGroup ref="{www.jalview.org}position"/&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="seqPointMax"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attGroup ref="{www.jalview.org}position"/&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="pcaData" type="{www.jalview.org}PcaDataType"/&gt;
- * &lt;/sequence&gt;
- * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
- * &lt;attGroup ref="{www.jalview.org}SimilarityParams"/&gt;
- * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="FeatureSettings" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="setting" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&gt;
- * &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
- * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="group" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;/sequence&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;/sequence&gt;
- * &lt;/sequence&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre> &lt;complexType name="JalviewModel"&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="creationDate"
+ * type="{http://www.w3.org/2001/XMLSchema}dateTime"/&gt; &lt;element
+ * name="version" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
+ * &lt;element name="vamsasModel"
+ * type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/&gt;
+ * &lt;sequence&gt; &lt;element name="JSeq" maxOccurs="unbounded"
+ * minOccurs="0"&gt; &lt;complexType&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="features"
+ * type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/&gt;
+ * &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt; &lt;complexContent&gt; &lt;extension
+ * base="{www.jalview.org}pdbentry"&gt; &lt;sequence&gt;
+ * &lt;element name="structureState" maxOccurs="unbounded"
+ * minOccurs="0"&gt; &lt;complexType&gt;
+ * &lt;simpleContent&gt; &lt;extension
+ * base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
+ * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
+ * &lt;attribute name="visible"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
+ * name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="alignwithAlignPanel"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="colourwithAlignPanel"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="colourByJmol"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string"
+ * /&gt; &lt;/extension&gt; &lt;/simpleContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt;
+ * &lt;/sequence&gt; &lt;/extension&gt;
+ * &lt;/complexContent&gt; &lt;/complexType&gt;
+ * &lt;/element&gt; &lt;element name="hiddenSequences"
+ * type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded"
+ * minOccurs="0"/&gt; &lt;element name="rnaViewer" maxOccurs="unbounded"
+ * minOccurs="0"&gt; &lt;complexType&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="secondaryStructure"
+ * maxOccurs="unbounded"&gt; &lt;complexType&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
+ * name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="annotationId" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="viewerState"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt;
+ * &lt;/sequence&gt; &lt;attGroup
+ * ref="{www.jalview.org}swingwindow"/&gt; &lt;attribute name="title"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="dividerLocation"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt;
+ * &lt;/sequence&gt; &lt;attribute name="colour"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
+ * /&gt; &lt;attribute name="end" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
+ * /&gt; &lt;attribute name="hidden"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
+ * name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean"
+ * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt; &lt;element
+ * name="JGroup" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="seq"
+ * type="{http://www.w3.org/2001/XMLSchema}string"
+ * maxOccurs="unbounded"/&gt; &lt;element name="annotationColours"
+ * type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
+ * &lt;/sequence&gt; &lt;attribute name="start"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string"
+ * /&gt; &lt;attribute name="colour"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="pidThreshold"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="displayBoxes"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
+ * name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="colourText"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
+ * name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="textCol2"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int"
+ * /&gt; &lt;attribute name="showUnconserved"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
+ * name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean"
+ * default="true" /&gt; &lt;attribute name="showConsensusHistogram"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="showSequenceLogo"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="normaliseSequenceLogo"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string"
+ * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt; &lt;element
+ * name="Viewport" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="AnnotationColours"
+ * type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
+ * &lt;element name="hiddenColumns" maxOccurs="unbounded"
+ * minOccurs="0"&gt; &lt;complexType&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
+ * name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int"
+ * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt; &lt;element
+ * name="calcIdParam" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt; &lt;complexContent&gt; &lt;extension
+ * base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&gt;
+ * &lt;attribute name="calcId" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean"
+ * default="false" /&gt; &lt;attribute name="autoUpdate" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/extension&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt;
+ * &lt;/sequence&gt; &lt;attGroup
+ * ref="{www.jalview.org}swingwindow"/&gt; &lt;attribute
+ * name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean"
+ * /&gt; &lt;attribute name="pidSelected"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
+ * name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="consThreshold"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="title"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="rightAlignIds"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
+ * name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="showColourText"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
+ * name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean"
+ * default="false" /&gt; &lt;attribute name="showBoxes"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
+ * name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean"
+ * /&gt; &lt;attribute name="renderGaps"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
+ * name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean"
+ * /&gt; &lt;attribute name="showNPfeatureTooltip"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
+ * name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean"
+ * /&gt; &lt;attribute name="followHighlight"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="followSelection"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="showAnnotation"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
+ * name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean"
+ * default="false" /&gt; &lt;attribute name="showGroupConservation"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="showGroupConsensus"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="showConsensusHistogram"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="showSequenceLogo"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="normaliseSequenceLogo"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="ignoreGapsinConsensus"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="startRes"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="fontName"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="fontStyle"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean"
+ * default="true" /&gt; &lt;attribute name="viewName"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string"
+ * /&gt; &lt;attribute name="gatheredViews"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
+ * name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="textCol2"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int"
+ * /&gt; &lt;attribute name="id"
+ * type="{http://www.w3.org/2001/XMLSchema}ID" /&gt; &lt;attribute
+ * name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="showComplementFeatures"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="showComplementFeaturesOnTop"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt; &lt;element
+ * name="UserColours" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="UserColourScheme"
+ * type="{www.jalview.org/colours}JalviewUserColours"/&gt;
+ * &lt;/sequence&gt; &lt;attribute name="id"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt; &lt;element
+ * name="tree" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence minOccurs="0"&gt; &lt;element name="title"
+ * type="{http://www.w3.org/2001/XMLSchema}string"/&gt; &lt;element
+ * name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
+ * &lt;/sequence&gt; &lt;attGroup
+ * ref="{www.jalview.org}swingwindow"/&gt; &lt;attribute name="fontName"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="fontStyle"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="showBootstrap"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
+ * name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean"
+ * /&gt; &lt;attribute name="markUnlinked"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
+ * name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="currentTree"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
+ * name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
+ * &lt;attribute name="linkToAllViews"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt; &lt;element
+ * name="PcaViewer" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="sequencePoint"
+ * maxOccurs="unbounded"&gt; &lt;complexType&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
+ * ref="{www.jalview.org}position"/&gt; &lt;attribute name="sequenceRef"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt; &lt;element
+ * name="axis" maxOccurs="3" minOccurs="3"&gt; &lt;complexType&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
+ * ref="{www.jalview.org}position"/&gt; &lt;/restriction&gt;
+ * &lt;/complexContent&gt; &lt;/complexType&gt;
+ * &lt;/element&gt; &lt;element name="seqPointMin"&gt;
+ * &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attGroup ref="{www.jalview.org}position"/&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt; &lt;element
+ * name="seqPointMax"&gt; &lt;complexType&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
+ * ref="{www.jalview.org}position"/&gt; &lt;/restriction&gt;
+ * &lt;/complexContent&gt; &lt;/complexType&gt;
+ * &lt;/element&gt; &lt;element name="pcaData"
+ * type="{www.jalview.org}PcaDataType"/&gt; &lt;/sequence&gt;
+ * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt; &lt;attGroup
+ * ref="{www.jalview.org}SimilarityParams"/&gt; &lt;attribute
+ * name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="scoreModelName"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int"
+ * /&gt; &lt;attribute name="zDim"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="scaleFactor"
+ * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute
+ * name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="linkToAllViews"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt; &lt;element
+ * name="FeatureSettings" minOccurs="0"&gt; &lt;complexType&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="setting" maxOccurs="unbounded"
+ * minOccurs="0"&gt; &lt;complexType&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="attributeName"
+ * type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2"
+ * minOccurs="0"/&gt; &lt;element name="matcherSet"
+ * type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&gt;
+ * &lt;/sequence&gt; &lt;attribute name="type" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
+ * /&gt; &lt;attribute name="display" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
+ * name="order" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="mincolour"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="noValueColour" type="{www.jalview.org/colours}NoValueColour"
+ * default="Min" /&gt; &lt;attribute name="threshold"
+ * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute
+ * name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float"
+ * /&gt; &lt;attribute name="min"
+ * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute
+ * name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean"
+ * /&gt; &lt;attribute name="autoScale"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt; &lt;element
+ * name="group" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="name" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="display" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt;
+ * &lt;/sequence&gt; &lt;/restriction&gt;
+ * &lt;/complexContent&gt; &lt;/complexType&gt;
+ * &lt;/element&gt; &lt;/sequence&gt; &lt;/sequence&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "JalviewModel", namespace = "www.jalview.org", propOrder = {
- "creationDate",
- "version",
- "vamsasModel",
- "jSeq",
- "jGroup",
- "viewport",
- "userColours",
- "tree",
- "pcaViewer",
- "featureSettings"
-})
-public class JalviewModel {
-
- @XmlElement(required = true)
- @XmlSchemaType(name = "dateTime")
- protected XMLGregorianCalendar creationDate;
- @XmlElement(required = true)
- protected String version;
- @XmlElement(required = true)
- protected VAMSAS vamsasModel;
- @XmlElement(name = "JSeq")
- protected List<JalviewModel.JSeq> jSeq;
- @XmlElement(name = "JGroup")
- protected List<JalviewModel.JGroup> jGroup;
- @XmlElement(name = "Viewport")
- protected List<JalviewModel.Viewport> viewport;
- @XmlElement(name = "UserColours")
- protected List<JalviewModel.UserColours> userColours;
- protected List<JalviewModel.Tree> tree;
- @XmlElement(name = "PcaViewer")
- protected List<JalviewModel.PcaViewer> pcaViewer;
- @XmlElement(name = "FeatureSettings")
- protected JalviewModel.FeatureSettings featureSettings;
-
- /**
- * Gets the value of the creationDate property.
- *
- * @return
- * possible object is
- * {@link XMLGregorianCalendar }
- *
- */
- public XMLGregorianCalendar getCreationDate() {
- return creationDate;
- }
-
- /**
- * Sets the value of the creationDate property.
+@XmlType(
+ name = "JalviewModel",
+ namespace = "www.jalview.org",
+ propOrder =
+ { "creationDate", "version", "vamsasModel", "jSeq", "jGroup", "viewport",
+ "userColours", "tree", "pcaViewer", "featureSettings" })
+public class JalviewModel
+{
+
+ @XmlElement(required = true)
+ @XmlSchemaType(name = "dateTime")
+ protected XMLGregorianCalendar creationDate;
+
+ @XmlElement(required = true)
+ protected String version;
+
+ @XmlElement(required = true)
+ protected VAMSAS vamsasModel;
+
+ @XmlElement(name = "JSeq")
+ protected List<JalviewModel.JSeq> jSeq;
+
+ @XmlElement(name = "JGroup")
+ protected List<JalviewModel.JGroup> jGroup;
+
+ @XmlElement(name = "Viewport")
+ protected List<JalviewModel.Viewport> viewport;
+
+ @XmlElement(name = "UserColours")
+ protected List<JalviewModel.UserColours> userColours;
+
+ protected List<JalviewModel.Tree> tree;
+
+ @XmlElement(name = "PcaViewer")
+ protected List<JalviewModel.PcaViewer> pcaViewer;
+
+ @XmlElement(name = "FeatureSettings")
+ protected JalviewModel.FeatureSettings featureSettings;
+
+ /**
+ * Gets the value of the creationDate property.
+ *
+ * @return possible object is {@link XMLGregorianCalendar }
+ *
+ */
+ public XMLGregorianCalendar getCreationDate()
+ {
+ return creationDate;
+ }
+
+ /**
+ * Sets the value of the creationDate property.
+ *
+ * @param value
+ * allowed object is {@link XMLGregorianCalendar }
+ *
+ */
+ public void setCreationDate(XMLGregorianCalendar value)
+ {
+ this.creationDate = value;
+ }
+
+ /**
+ * Gets the value of the version property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getVersion()
+ {
+ return version;
+ }
+
+ /**
+ * Sets the value of the version property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setVersion(String value)
+ {
+ this.version = value;
+ }
+
+ /**
+ * Gets the value of the vamsasModel property.
+ *
+ * @return possible object is {@link VAMSAS }
+ *
+ */
+ public VAMSAS getVamsasModel()
+ {
+ return vamsasModel;
+ }
+
+ /**
+ * Sets the value of the vamsasModel property.
+ *
+ * @param value
+ * allowed object is {@link VAMSAS }
+ *
+ */
+ public void setVamsasModel(VAMSAS value)
+ {
+ this.vamsasModel = value;
+ }
+
+ /**
+ * Gets the value of the jSeq property.
+ *
+ * <p> This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will be
+ * present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the jSeq property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getJSeq().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.JSeq }
+ *
+ *
+ */
+ public List<JalviewModel.JSeq> getJSeq()
+ {
+ if (jSeq == null)
+ {
+ jSeq = new ArrayList<JalviewModel.JSeq>();
+ }
+ return this.jSeq;
+ }
+
+ /**
+ * Gets the value of the jGroup property.
+ *
+ * <p> This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will be
+ * present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the jGroup property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getJGroup().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.JGroup }
+ *
+ *
+ */
+ public List<JalviewModel.JGroup> getJGroup()
+ {
+ if (jGroup == null)
+ {
+ jGroup = new ArrayList<JalviewModel.JGroup>();
+ }
+ return this.jGroup;
+ }
+
+ /**
+ * Gets the value of the viewport property.
+ *
+ * <p> This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will be
+ * present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the viewport property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getViewport().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.Viewport }
+ *
+ *
+ */
+ public List<JalviewModel.Viewport> getViewport()
+ {
+ if (viewport == null)
+ {
+ viewport = new ArrayList<JalviewModel.Viewport>();
+ }
+ return this.viewport;
+ }
+
+ /**
+ * Gets the value of the userColours property.
+ *
+ * <p> This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will be
+ * present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the userColours property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getUserColours().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.UserColours }
+ *
+ *
+ */
+ public List<JalviewModel.UserColours> getUserColours()
+ {
+ if (userColours == null)
+ {
+ userColours = new ArrayList<JalviewModel.UserColours>();
+ }
+ return this.userColours;
+ }
+
+ /**
+ * Gets the value of the tree property.
+ *
+ * <p> This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will be
+ * present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the tree property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getTree().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.Tree }
+ *
+ *
+ */
+ public List<JalviewModel.Tree> getTree()
+ {
+ if (tree == null)
+ {
+ tree = new ArrayList<JalviewModel.Tree>();
+ }
+ return this.tree;
+ }
+
+ /**
+ * Gets the value of the pcaViewer property.
+ *
+ * <p> This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will be
+ * present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the pcaViewer property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getPcaViewer().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.PcaViewer }
+ *
+ *
+ */
+ public List<JalviewModel.PcaViewer> getPcaViewer()
+ {
+ if (pcaViewer == null)
+ {
+ pcaViewer = new ArrayList<JalviewModel.PcaViewer>();
+ }
+ return this.pcaViewer;
+ }
+
+ /**
+ * Gets the value of the featureSettings property.
+ *
+ * @return possible object is {@link JalviewModel.FeatureSettings }
+ *
+ */
+ public JalviewModel.FeatureSettings getFeatureSettings()
+ {
+ return featureSettings;
+ }
+
+ /**
+ * Sets the value of the featureSettings property.
+ *
+ * @param value
+ * allowed object is {@link JalviewModel.FeatureSettings }
+ *
+ */
+ public void setFeatureSettings(JalviewModel.FeatureSettings value)
+ {
+ this.featureSettings = value;
+ }
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
+ *
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="setting"
+ * maxOccurs="unbounded" minOccurs="0"&gt; &lt;complexType&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="attributeName"
+ * type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2"
+ * minOccurs="0"/&gt; &lt;element name="matcherSet"
+ * type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&gt;
+ * &lt;/sequence&gt; &lt;attribute name="type" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
+ * /&gt; &lt;attribute name="display" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="order"
+ * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute
+ * name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="noValueColour"
+ * type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
+ * &lt;attribute name="threshold"
+ * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute
+ * name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float"
+ * /&gt; &lt;attribute name="min"
+ * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute
+ * name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean"
+ * /&gt; &lt;attribute name="autoScale"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt; &lt;element
+ * name="group" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
+ * name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
+ * /&gt; &lt;attribute name="display" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt;
+ * &lt;/sequence&gt; &lt;/restriction&gt;
+ * &lt;/complexContent&gt; &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "setting", "group" })
+ public static class FeatureSettings
+ {
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<JalviewModel.FeatureSettings.Setting> setting;
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<JalviewModel.FeatureSettings.Group> group;
+
+ /**
+ * Gets the value of the setting property.
+ *
+ * <p> This accessor method returns a reference to the live list, not
+ * a snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the setting property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getSetting().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.FeatureSettings.Setting }
+ *
+ *
+ */
+ public List<JalviewModel.FeatureSettings.Setting> getSetting()
+ {
+ if (setting == null)
+ {
+ setting = new ArrayList<JalviewModel.FeatureSettings.Setting>();
+ }
+ return this.setting;
+ }
+
+ /**
+ * Gets the value of the group property.
+ *
+ * <p> This accessor method returns a reference to the live list, not
+ * a snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the group property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getGroup().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.FeatureSettings.Group }
+ *
+ *
+ */
+ public List<JalviewModel.FeatureSettings.Group> getGroup()
+ {
+ if (group == null)
+ {
+ group = new ArrayList<JalviewModel.FeatureSettings.Group>();
+ }
+ return this.group;
+ }
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
+ *
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="name" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="display" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Group
+ {
+
+ @XmlAttribute(name = "name", required = true)
+ protected String name;
+
+ @XmlAttribute(name = "display", required = true)
+ protected boolean display;
+
+ /**
+ * Gets the value of the name property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getName()
+ {
+ return name;
+ }
+
+ /**
+ * Sets the value of the name property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setName(String value)
+ {
+ this.name = value;
+ }
+
+ /**
+ * Gets the value of the display property.
+ *
+ */
+ public boolean isDisplay()
+ {
+ return display;
+ }
+
+ /**
+ * Sets the value of the display property.
+ *
+ */
+ public void setDisplay(boolean value)
+ {
+ this.display = value;
+ }
+
+ }
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
+ *
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="attributeName"
+ * type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2"
+ * minOccurs="0"/&gt; &lt;element name="matcherSet"
+ * type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&gt;
+ * &lt;/sequence&gt; &lt;attribute name="type" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="colour" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="display" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="order"
+ * type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="mincolour"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="noValueColour" type="{www.jalview.org/colours}NoValueColour"
+ * default="Min" /&gt; &lt;attribute name="threshold"
+ * type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="threshstate"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="min"
+ * type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="colourByLabel"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="autoScale"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "attributeName", "matcherSet" })
+ public static class Setting
+ {
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<String> attributeName;
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected FeatureMatcherSet matcherSet;
+
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
+
+ @XmlAttribute(name = "colour", required = true)
+ protected int colour;
+
+ @XmlAttribute(name = "display", required = true)
+ protected boolean display;
+
+ @XmlAttribute(name = "order")
+ protected Float order;
+
+ @XmlAttribute(name = "mincolour")
+ protected Integer mincolour;
+
+ @XmlAttribute(name = "noValueColour")
+ protected NoValueColour noValueColour;
+
+ @XmlAttribute(name = "threshold")
+ protected Float threshold;
+
+ @XmlAttribute(name = "threshstate")
+ protected Integer threshstate;
+
+ @XmlAttribute(name = "max")
+ protected Float max;
+
+ @XmlAttribute(name = "min")
+ protected Float min;
+
+ @XmlAttribute(name = "colourByLabel")
+ protected Boolean colourByLabel;
+
+ @XmlAttribute(name = "autoScale")
+ protected Boolean autoScale;
+
+ /**
+ * Gets the value of the attributeName property.
+ *
+ * <p> This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the returned
+ * list will be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the attributeName property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getAttributeName().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link String }
+ *
+ *
+ */
+ public List<String> getAttributeName()
+ {
+ if (attributeName == null)
+ {
+ attributeName = new ArrayList<String>();
+ }
+ return this.attributeName;
+ }
+
+ /**
+ * Gets the value of the matcherSet property.
+ *
+ * @return possible object is {@link FeatureMatcherSet }
+ *
+ */
+ public FeatureMatcherSet getMatcherSet()
+ {
+ return matcherSet;
+ }
+
+ /**
+ * Sets the value of the matcherSet property.
+ *
+ * @param value
+ * allowed object is {@link FeatureMatcherSet }
+ *
+ */
+ public void setMatcherSet(FeatureMatcherSet value)
+ {
+ this.matcherSet = value;
+ }
+
+ /**
+ * Gets the value of the type property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getType()
+ {
+ return type;
+ }
+
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setType(String value)
+ {
+ this.type = value;
+ }
+
+ /**
+ * Gets the value of the colour property.
+ *
+ */
+ public int getColour()
+ {
+ return colour;
+ }
+
+ /**
+ * Sets the value of the colour property.
+ *
+ */
+ public void setColour(int value)
+ {
+ this.colour = value;
+ }
+
+ /**
+ * Gets the value of the display property.
+ *
+ */
+ public boolean isDisplay()
+ {
+ return display;
+ }
+
+ /**
+ * Sets the value of the display property.
+ *
+ */
+ public void setDisplay(boolean value)
+ {
+ this.display = value;
+ }
+
+ /**
+ * Gets the value of the order property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getOrder()
+ {
+ return order;
+ }
+
+ /**
+ * Sets the value of the order property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setOrder(Float value)
+ {
+ this.order = value;
+ }
+
+ /**
+ * Gets the value of the mincolour property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getMincolour()
+ {
+ return mincolour;
+ }
+
+ /**
+ * Sets the value of the mincolour property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setMincolour(Integer value)
+ {
+ this.mincolour = value;
+ }
+
+ /**
+ * Gets the value of the noValueColour property.
+ *
+ * @return possible object is {@link NoValueColour }
+ *
+ */
+ public NoValueColour getNoValueColour()
+ {
+ if (noValueColour == null)
+ {
+ return NoValueColour.MIN;
+ }
+ else
+ {
+ return noValueColour;
+ }
+ }
+
+ /**
+ * Sets the value of the noValueColour property.
+ *
+ * @param value
+ * allowed object is {@link NoValueColour }
+ *
+ */
+ public void setNoValueColour(NoValueColour value)
+ {
+ this.noValueColour = value;
+ }
+
+ /**
+ * Gets the value of the threshold property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getThreshold()
+ {
+ return threshold;
+ }
+
+ /**
+ * Sets the value of the threshold property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setThreshold(Float value)
+ {
+ this.threshold = value;
+ }
+
+ /**
+ * Gets the value of the threshstate property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getThreshstate()
+ {
+ return threshstate;
+ }
+
+ /**
+ * Sets the value of the threshstate property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setThreshstate(Integer value)
+ {
+ this.threshstate = value;
+ }
+
+ /**
+ * Gets the value of the max property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getMax()
+ {
+ return max;
+ }
+
+ /**
+ * Sets the value of the max property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setMax(Float value)
+ {
+ this.max = value;
+ }
+
+ /**
+ * Gets the value of the min property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getMin()
+ {
+ return min;
+ }
+
+ /**
+ * Sets the value of the min property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setMin(Float value)
+ {
+ this.min = value;
+ }
+
+ /**
+ * Gets the value of the colourByLabel property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isColourByLabel()
+ {
+ return colourByLabel;
+ }
+
+ /**
+ * Sets the value of the colourByLabel property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setColourByLabel(Boolean value)
+ {
+ this.colourByLabel = value;
+ }
+
+ /**
+ * Gets the value of the autoScale property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isAutoScale()
+ {
+ return autoScale;
+ }
+
+ /**
+ * Sets the value of the autoScale property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setAutoScale(Boolean value)
+ {
+ this.autoScale = value;
+ }
+
+ }
+
+ }
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
+ *
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="seq"
+ * type="{http://www.w3.org/2001/XMLSchema}string"
+ * maxOccurs="unbounded"/&gt; &lt;element name="annotationColours"
+ * type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
+ * &lt;/sequence&gt; &lt;attribute name="start"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="name"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="colour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="consThreshold"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="outlineColour"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean"
+ * /&gt; &lt;attribute name="displayText"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="colourText"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="textCol1"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="textColThreshold"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean"
+ * /&gt; &lt;attribute name="ignoreGapsinConsensus"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="showConsensusHistogram"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="showSequenceLogo"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="normaliseSequenceLogo"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string"
+ * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "seq", "annotationColours" })
+ public static class JGroup
+ {
+
+ @XmlElement(namespace = "www.jalview.org", required = true)
+ protected List<String> seq;
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected AnnotationColourScheme annotationColours;
+
+ @XmlAttribute(name = "start")
+ protected Integer start;
+
+ @XmlAttribute(name = "end")
+ protected Integer end;
+
+ @XmlAttribute(name = "name")
+ protected String name;
+
+ @XmlAttribute(name = "colour")
+ protected String colour;
+
+ @XmlAttribute(name = "consThreshold")
+ protected Integer consThreshold;
+
+ @XmlAttribute(name = "pidThreshold")
+ protected Integer pidThreshold;
+
+ @XmlAttribute(name = "outlineColour")
+ protected Integer outlineColour;
+
+ @XmlAttribute(name = "displayBoxes")
+ protected Boolean displayBoxes;
+
+ @XmlAttribute(name = "displayText")
+ protected Boolean displayText;
+
+ @XmlAttribute(name = "colourText")
+ protected Boolean colourText;
+
+ @XmlAttribute(name = "textCol1")
+ protected Integer textCol1;
+
+ @XmlAttribute(name = "textCol2")
+ protected Integer textCol2;
+
+ @XmlAttribute(name = "textColThreshold")
+ protected Integer textColThreshold;
+
+ @XmlAttribute(name = "showUnconserved")
+ protected Boolean showUnconserved;
+
+ @XmlAttribute(name = "ignoreGapsinConsensus")
+ protected Boolean ignoreGapsinConsensus;
+
+ @XmlAttribute(name = "showConsensusHistogram")
+ protected Boolean showConsensusHistogram;
+
+ @XmlAttribute(name = "showSequenceLogo")
+ protected Boolean showSequenceLogo;
+
+ @XmlAttribute(name = "normaliseSequenceLogo")
+ protected Boolean normaliseSequenceLogo;
+
+ @XmlAttribute(name = "id")
+ protected String id;
+
+ /**
+ * Gets the value of the seq property.
+ *
+ * <p> This accessor method returns a reference to the live list, not
+ * a snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the seq property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getSeq().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link String }
+ *
*
- * @param value
- * allowed object is
- * {@link XMLGregorianCalendar }
- *
*/
- public void setCreationDate(XMLGregorianCalendar value) {
- this.creationDate = value;
+ public List<String> getSeq()
+ {
+ if (seq == null)
+ {
+ seq = new ArrayList<String>();
+ }
+ return this.seq;
}
/**
- * Gets the value of the version property.
+ * Gets the value of the annotationColours property.
+ *
+ * @return possible object is {@link AnnotationColourScheme }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getVersion() {
- return version;
+ public AnnotationColourScheme getAnnotationColours()
+ {
+ return annotationColours;
}
/**
- * Sets the value of the version property.
+ * Sets the value of the annotationColours property.
*
* @param value
- * allowed object is
- * {@link String }
- *
+ * allowed object is {@link AnnotationColourScheme }
+ *
*/
- public void setVersion(String value) {
- this.version = value;
+ public void setAnnotationColours(AnnotationColourScheme value)
+ {
+ this.annotationColours = value;
}
/**
- * Gets the value of the vamsasModel property.
+ * Gets the value of the start property.
+ *
+ * @return possible object is {@link Integer }
*
- * @return
- * possible object is
- * {@link VAMSAS }
- *
*/
- public VAMSAS getVamsasModel() {
- return vamsasModel;
+ public Integer getStart()
+ {
+ return start;
}
/**
- * Sets the value of the vamsasModel property.
+ * Sets the value of the start property.
*
* @param value
- * allowed object is
- * {@link VAMSAS }
- *
+ * allowed object is {@link Integer }
+ *
*/
- public void setVamsasModel(VAMSAS value) {
- this.vamsasModel = value;
+ public void setStart(Integer value)
+ {
+ this.start = value;
}
/**
- * Gets the value of the jSeq property.
+ * Gets the value of the end property.
*
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the jSeq property.
+ * @return possible object is {@link Integer }
*
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getJSeq().add(newItem);
- * </pre>
+ */
+ public Integer getEnd()
+ {
+ return end;
+ }
+
+ /**
+ * Sets the value of the end property.
*
+ * @param value
+ * allowed object is {@link Integer }
*
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.JSeq }
+ */
+ public void setEnd(Integer value)
+ {
+ this.end = value;
+ }
+
+ /**
+ * Gets the value of the name property.
*
+ * @return possible object is {@link String }
*
*/
- public List<JalviewModel.JSeq> getJSeq() {
- if (jSeq == null) {
- jSeq = new ArrayList<JalviewModel.JSeq>();
- }
- return this.jSeq;
+ public String getName()
+ {
+ return name;
}
/**
- * Gets the value of the jGroup property.
+ * Sets the value of the name property.
*
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the jGroup property.
+ * @param value
+ * allowed object is {@link String }
*
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getJGroup().add(newItem);
- * </pre>
+ */
+ public void setName(String value)
+ {
+ this.name = value;
+ }
+
+ /**
+ * Gets the value of the colour property.
*
+ * @return possible object is {@link String }
*
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.JGroup }
+ */
+ public String getColour()
+ {
+ return colour;
+ }
+
+ /**
+ * Sets the value of the colour property.
*
+ * @param value
+ * allowed object is {@link String }
*
*/
- public List<JalviewModel.JGroup> getJGroup() {
- if (jGroup == null) {
- jGroup = new ArrayList<JalviewModel.JGroup>();
- }
- return this.jGroup;
+ public void setColour(String value)
+ {
+ this.colour = value;
}
/**
- * Gets the value of the viewport property.
+ * Gets the value of the consThreshold property.
*
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the viewport property.
+ * @return possible object is {@link Integer }
*
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getViewport().add(newItem);
- * </pre>
+ */
+ public Integer getConsThreshold()
+ {
+ return consThreshold;
+ }
+
+ /**
+ * Sets the value of the consThreshold property.
*
+ * @param value
+ * allowed object is {@link Integer }
*
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.Viewport }
+ */
+ public void setConsThreshold(Integer value)
+ {
+ this.consThreshold = value;
+ }
+
+ /**
+ * Gets the value of the pidThreshold property.
*
+ * @return possible object is {@link Integer }
*
*/
- public List<JalviewModel.Viewport> getViewport() {
- if (viewport == null) {
- viewport = new ArrayList<JalviewModel.Viewport>();
- }
- return this.viewport;
+ public Integer getPidThreshold()
+ {
+ return pidThreshold;
}
/**
- * Gets the value of the userColours property.
+ * Sets the value of the pidThreshold property.
*
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the userColours property.
+ * @param value
+ * allowed object is {@link Integer }
*
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getUserColours().add(newItem);
- * </pre>
+ */
+ public void setPidThreshold(Integer value)
+ {
+ this.pidThreshold = value;
+ }
+
+ /**
+ * Gets the value of the outlineColour property.
*
+ * @return possible object is {@link Integer }
*
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.UserColours }
+ */
+ public Integer getOutlineColour()
+ {
+ return outlineColour;
+ }
+
+ /**
+ * Sets the value of the outlineColour property.
*
+ * @param value
+ * allowed object is {@link Integer }
*
*/
- public List<JalviewModel.UserColours> getUserColours() {
- if (userColours == null) {
- userColours = new ArrayList<JalviewModel.UserColours>();
- }
- return this.userColours;
+ public void setOutlineColour(Integer value)
+ {
+ this.outlineColour = value;
}
/**
- * Gets the value of the tree property.
+ * Gets the value of the displayBoxes property.
*
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the tree property.
+ * @return possible object is {@link Boolean }
*
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getTree().add(newItem);
- * </pre>
+ */
+ public Boolean isDisplayBoxes()
+ {
+ return displayBoxes;
+ }
+
+ /**
+ * Sets the value of the displayBoxes property.
*
+ * @param value
+ * allowed object is {@link Boolean }
*
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.Tree }
+ */
+ public void setDisplayBoxes(Boolean value)
+ {
+ this.displayBoxes = value;
+ }
+
+ /**
+ * Gets the value of the displayText property.
*
+ * @return possible object is {@link Boolean }
*
*/
- public List<JalviewModel.Tree> getTree() {
- if (tree == null) {
- tree = new ArrayList<JalviewModel.Tree>();
- }
- return this.tree;
+ public Boolean isDisplayText()
+ {
+ return displayText;
}
/**
- * Gets the value of the pcaViewer property.
+ * Sets the value of the displayText property.
*
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the pcaViewer property.
+ * @param value
+ * allowed object is {@link Boolean }
*
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getPcaViewer().add(newItem);
- * </pre>
+ */
+ public void setDisplayText(Boolean value)
+ {
+ this.displayText = value;
+ }
+
+ /**
+ * Gets the value of the colourText property.
*
+ * @return possible object is {@link Boolean }
*
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.PcaViewer }
+ */
+ public Boolean isColourText()
+ {
+ return colourText;
+ }
+
+ /**
+ * Sets the value of the colourText property.
*
+ * @param value
+ * allowed object is {@link Boolean }
*
*/
- public List<JalviewModel.PcaViewer> getPcaViewer() {
- if (pcaViewer == null) {
- pcaViewer = new ArrayList<JalviewModel.PcaViewer>();
- }
- return this.pcaViewer;
+ public void setColourText(Boolean value)
+ {
+ this.colourText = value;
}
/**
- * Gets the value of the featureSettings property.
+ * Gets the value of the textCol1 property.
+ *
+ * @return possible object is {@link Integer }
*
- * @return
- * possible object is
- * {@link JalviewModel.FeatureSettings }
- *
*/
- public JalviewModel.FeatureSettings getFeatureSettings() {
- return featureSettings;
+ public Integer getTextCol1()
+ {
+ return textCol1;
}
/**
- * Sets the value of the featureSettings property.
+ * Sets the value of the textCol1 property.
*
* @param value
- * allowed object is
- * {@link JalviewModel.FeatureSettings }
- *
+ * allowed object is {@link Integer }
+ *
*/
- public void setFeatureSettings(JalviewModel.FeatureSettings value) {
- this.featureSettings = value;
+ public void setTextCol1(Integer value)
+ {
+ this.textCol1 = value;
}
+ /**
+ * Gets the value of the textCol2 property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getTextCol2()
+ {
+ return textCol2;
+ }
/**
- * <p>Java class for anonymous complex type.
+ * Sets the value of the textCol2 property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
*
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="setting" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&gt;
- * &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
- * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="group" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;/sequence&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ */
+ public void setTextCol2(Integer value)
+ {
+ this.textCol2 = value;
+ }
+
+ /**
+ * Gets the value of the textColThreshold property.
*
+ * @return possible object is {@link Integer }
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "setting",
- "group"
- })
- public static class FeatureSettings {
+ public Integer getTextColThreshold()
+ {
+ return textColThreshold;
+ }
- @XmlElement(namespace = "www.jalview.org")
- protected List<JalviewModel.FeatureSettings.Setting> setting;
- @XmlElement(namespace = "www.jalview.org")
- protected List<JalviewModel.FeatureSettings.Group> group;
+ /**
+ * Sets the value of the textColThreshold property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setTextColThreshold(Integer value)
+ {
+ this.textColThreshold = value;
+ }
- /**
- * Gets the value of the setting property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the setting property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getSetting().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.FeatureSettings.Setting }
- *
- *
- */
- public List<JalviewModel.FeatureSettings.Setting> getSetting() {
- if (setting == null) {
- setting = new ArrayList<JalviewModel.FeatureSettings.Setting>();
- }
- return this.setting;
- }
+ /**
+ * Gets the value of the showUnconserved property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowUnconserved()
+ {
+ return showUnconserved;
+ }
- /**
- * Gets the value of the group property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the group property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getGroup().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.FeatureSettings.Group }
- *
- *
- */
- public List<JalviewModel.FeatureSettings.Group> getGroup() {
- if (group == null) {
- group = new ArrayList<JalviewModel.FeatureSettings.Group>();
- }
- return this.group;
- }
+ /**
+ * Sets the value of the showUnconserved property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowUnconserved(Boolean value)
+ {
+ this.showUnconserved = value;
+ }
+ /**
+ * Gets the value of the ignoreGapsinConsensus property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isIgnoreGapsinConsensus()
+ {
+ if (ignoreGapsinConsensus == null)
+ {
+ return true;
+ }
+ else
+ {
+ return ignoreGapsinConsensus;
+ }
+ }
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class Group {
-
- @XmlAttribute(name = "name", required = true)
- protected String name;
- @XmlAttribute(name = "display", required = true)
- protected boolean display;
-
- /**
- * Gets the value of the name property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getName() {
- return name;
- }
-
- /**
- * Sets the value of the name property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setName(String value) {
- this.name = value;
- }
-
- /**
- * Gets the value of the display property.
- *
- */
- public boolean isDisplay() {
- return display;
- }
-
- /**
- * Sets the value of the display property.
- *
- */
- public void setDisplay(boolean value) {
- this.display = value;
- }
+ /**
+ * Sets the value of the ignoreGapsinConsensus property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setIgnoreGapsinConsensus(Boolean value)
+ {
+ this.ignoreGapsinConsensus = value;
+ }
- }
+ /**
+ * Gets the value of the showConsensusHistogram property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isShowConsensusHistogram()
+ {
+ if (showConsensusHistogram == null)
+ {
+ return true;
+ }
+ else
+ {
+ return showConsensusHistogram;
+ }
+ }
+ /**
+ * Sets the value of the showConsensusHistogram property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowConsensusHistogram(Boolean value)
+ {
+ this.showConsensusHistogram = value;
+ }
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&gt;
- * &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
- * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "attributeName",
- "matcherSet"
- })
- public static class Setting {
-
- @XmlElement(namespace = "www.jalview.org")
- protected List<String> attributeName;
- @XmlElement(namespace = "www.jalview.org")
- protected FeatureMatcherSet matcherSet;
- @XmlAttribute(name = "type", required = true)
- protected String type;
- @XmlAttribute(name = "colour", required = true)
- protected int colour;
- @XmlAttribute(name = "display", required = true)
- protected boolean display;
- @XmlAttribute(name = "order")
- protected Float order;
- @XmlAttribute(name = "mincolour")
- protected Integer mincolour;
- @XmlAttribute(name = "noValueColour")
- protected NoValueColour noValueColour;
- @XmlAttribute(name = "threshold")
- protected Float threshold;
- @XmlAttribute(name = "threshstate")
- protected Integer threshstate;
- @XmlAttribute(name = "max")
- protected Float max;
- @XmlAttribute(name = "min")
- protected Float min;
- @XmlAttribute(name = "colourByLabel")
- protected Boolean colourByLabel;
- @XmlAttribute(name = "autoScale")
- protected Boolean autoScale;
-
- /**
- * Gets the value of the attributeName property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the attributeName property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getAttributeName().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link String }
- *
- *
- */
- public List<String> getAttributeName() {
- if (attributeName == null) {
- attributeName = new ArrayList<String>();
- }
- return this.attributeName;
- }
-
- /**
- * Gets the value of the matcherSet property.
- *
- * @return
- * possible object is
- * {@link FeatureMatcherSet }
- *
- */
- public FeatureMatcherSet getMatcherSet() {
- return matcherSet;
- }
-
- /**
- * Sets the value of the matcherSet property.
- *
- * @param value
- * allowed object is
- * {@link FeatureMatcherSet }
- *
- */
- public void setMatcherSet(FeatureMatcherSet value) {
- this.matcherSet = value;
- }
-
- /**
- * Gets the value of the type property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getType() {
- return type;
- }
-
- /**
- * Sets the value of the type property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setType(String value) {
- this.type = value;
- }
-
- /**
- * Gets the value of the colour property.
- *
- */
- public int getColour() {
- return colour;
- }
-
- /**
- * Sets the value of the colour property.
- *
- */
- public void setColour(int value) {
- this.colour = value;
- }
-
- /**
- * Gets the value of the display property.
- *
- */
- public boolean isDisplay() {
- return display;
- }
-
- /**
- * Sets the value of the display property.
- *
- */
- public void setDisplay(boolean value) {
- this.display = value;
- }
-
- /**
- * Gets the value of the order property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getOrder() {
- return order;
- }
-
- /**
- * Sets the value of the order property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setOrder(Float value) {
- this.order = value;
- }
-
- /**
- * Gets the value of the mincolour property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getMincolour() {
- return mincolour;
- }
-
- /**
- * Sets the value of the mincolour property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setMincolour(Integer value) {
- this.mincolour = value;
- }
-
- /**
- * Gets the value of the noValueColour property.
- *
- * @return
- * possible object is
- * {@link NoValueColour }
- *
- */
- public NoValueColour getNoValueColour() {
- if (noValueColour == null) {
- return NoValueColour.MIN;
- } else {
- return noValueColour;
- }
- }
-
- /**
- * Sets the value of the noValueColour property.
- *
- * @param value
- * allowed object is
- * {@link NoValueColour }
- *
- */
- public void setNoValueColour(NoValueColour value) {
- this.noValueColour = value;
- }
-
- /**
- * Gets the value of the threshold property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getThreshold() {
- return threshold;
- }
-
- /**
- * Sets the value of the threshold property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setThreshold(Float value) {
- this.threshold = value;
- }
-
- /**
- * Gets the value of the threshstate property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getThreshstate() {
- return threshstate;
- }
-
- /**
- * Sets the value of the threshstate property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setThreshstate(Integer value) {
- this.threshstate = value;
- }
-
- /**
- * Gets the value of the max property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getMax() {
- return max;
- }
-
- /**
- * Sets the value of the max property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setMax(Float value) {
- this.max = value;
- }
-
- /**
- * Gets the value of the min property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getMin() {
- return min;
- }
-
- /**
- * Sets the value of the min property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setMin(Float value) {
- this.min = value;
- }
-
- /**
- * Gets the value of the colourByLabel property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isColourByLabel() {
- return colourByLabel;
- }
-
- /**
- * Sets the value of the colourByLabel property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setColourByLabel(Boolean value) {
- this.colourByLabel = value;
- }
-
- /**
- * Gets the value of the autoScale property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isAutoScale() {
- return autoScale;
- }
-
- /**
- * Sets the value of the autoScale property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setAutoScale(Boolean value) {
- this.autoScale = value;
- }
+ /**
+ * Gets the value of the showSequenceLogo property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isShowSequenceLogo()
+ {
+ if (showSequenceLogo == null)
+ {
+ return false;
+ }
+ else
+ {
+ return showSequenceLogo;
+ }
+ }
- }
+ /**
+ * Sets the value of the showSequenceLogo property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowSequenceLogo(Boolean value)
+ {
+ this.showSequenceLogo = value;
+ }
+ /**
+ * Gets the value of the normaliseSequenceLogo property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isNormaliseSequenceLogo()
+ {
+ if (normaliseSequenceLogo == null)
+ {
+ return false;
+ }
+ else
+ {
+ return normaliseSequenceLogo;
+ }
}
+ /**
+ * Sets the value of the normaliseSequenceLogo property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setNormaliseSequenceLogo(Boolean value)
+ {
+ this.normaliseSequenceLogo = value;
+ }
/**
- * <p>Java class for anonymous complex type.
+ * Gets the value of the id property.
+ *
+ * @return possible object is {@link String }
*
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/&gt;
- * &lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ */
+ public String getId()
+ {
+ return id;
+ }
+
+ /**
+ * Sets the value of the id property.
*
+ * @param value
+ * allowed object is {@link String }
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "seq",
- "annotationColours"
- })
- public static class JGroup {
-
- @XmlElement(namespace = "www.jalview.org", required = true)
- protected List<String> seq;
- @XmlElement(namespace = "www.jalview.org")
- protected AnnotationColourScheme annotationColours;
- @XmlAttribute(name = "start")
- protected Integer start;
- @XmlAttribute(name = "end")
- protected Integer end;
- @XmlAttribute(name = "name")
- protected String name;
- @XmlAttribute(name = "colour")
- protected String colour;
- @XmlAttribute(name = "consThreshold")
- protected Integer consThreshold;
- @XmlAttribute(name = "pidThreshold")
- protected Integer pidThreshold;
- @XmlAttribute(name = "outlineColour")
- protected Integer outlineColour;
- @XmlAttribute(name = "displayBoxes")
- protected Boolean displayBoxes;
- @XmlAttribute(name = "displayText")
- protected Boolean displayText;
- @XmlAttribute(name = "colourText")
- protected Boolean colourText;
- @XmlAttribute(name = "textCol1")
- protected Integer textCol1;
- @XmlAttribute(name = "textCol2")
- protected Integer textCol2;
- @XmlAttribute(name = "textColThreshold")
- protected Integer textColThreshold;
- @XmlAttribute(name = "showUnconserved")
- protected Boolean showUnconserved;
- @XmlAttribute(name = "ignoreGapsinConsensus")
- protected Boolean ignoreGapsinConsensus;
- @XmlAttribute(name = "showConsensusHistogram")
- protected Boolean showConsensusHistogram;
- @XmlAttribute(name = "showSequenceLogo")
- protected Boolean showSequenceLogo;
- @XmlAttribute(name = "normaliseSequenceLogo")
- protected Boolean normaliseSequenceLogo;
- @XmlAttribute(name = "id")
- protected String id;
+ public void setId(String value)
+ {
+ this.id = value;
+ }
- /**
- * Gets the value of the seq property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the seq property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getSeq().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link String }
- *
- *
- */
- public List<String> getSeq() {
- if (seq == null) {
- seq = new ArrayList<String>();
- }
- return this.seq;
- }
+ }
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
+ *
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="features"
+ * type="{www.jalview.org}feature" maxOccurs="unbounded"
+ * minOccurs="0"/&gt; &lt;element name="pdbids" maxOccurs="unbounded"
+ * minOccurs="0"&gt; &lt;complexType&gt;
+ * &lt;complexContent&gt; &lt;extension
+ * base="{www.jalview.org}pdbentry"&gt; &lt;sequence&gt;
+ * &lt;element name="structureState" maxOccurs="unbounded"
+ * minOccurs="0"&gt; &lt;complexType&gt;
+ * &lt;simpleContent&gt; &lt;extension
+ * base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
+ * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
+ * &lt;attribute name="visible"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="viewId"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean"
+ * default="true" /&gt; &lt;attribute name="colourwithAlignPanel"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="colourByJmol"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="type"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/extension&gt; &lt;/simpleContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt;
+ * &lt;/sequence&gt; &lt;/extension&gt;
+ * &lt;/complexContent&gt; &lt;/complexType&gt;
+ * &lt;/element&gt; &lt;element name="hiddenSequences"
+ * type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded"
+ * minOccurs="0"/&gt; &lt;element name="rnaViewer"
+ * maxOccurs="unbounded" minOccurs="0"&gt; &lt;complexType&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="secondaryStructure"
+ * maxOccurs="unbounded"&gt; &lt;complexType&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
+ * name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="annotationId" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="viewerState"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt;
+ * &lt;/sequence&gt; &lt;attGroup
+ * ref="{www.jalview.org}swingwindow"/&gt; &lt;attribute name="title"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="dividerLocation"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt;
+ * &lt;/sequence&gt; &lt;attribute name="colour"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
+ * /&gt; &lt;attribute name="end" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
+ * /&gt; &lt;attribute name="hidden"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="viewreference"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(
+ name = "",
+ propOrder =
+ { "features", "pdbids", "hiddenSequences", "rnaViewer" })
+ public static class JSeq
+ {
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<Feature> features;
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<JalviewModel.JSeq.Pdbids> pdbids;
+
+ @XmlElement(namespace = "www.jalview.org", type = Integer.class)
+ protected List<Integer> hiddenSequences;
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<JalviewModel.JSeq.RnaViewer> rnaViewer;
+
+ @XmlAttribute(name = "colour")
+ protected Integer colour;
+
+ @XmlAttribute(name = "start", required = true)
+ protected int start;
+
+ @XmlAttribute(name = "end", required = true)
+ protected int end;
+
+ @XmlAttribute(name = "id", required = true)
+ protected String id;
+
+ @XmlAttribute(name = "hidden")
+ protected Boolean hidden;
+
+ @XmlAttribute(name = "viewreference")
+ protected Boolean viewreference;
- /**
- * Gets the value of the annotationColours property.
- *
- * @return
- * possible object is
- * {@link AnnotationColourScheme }
- *
- */
- public AnnotationColourScheme getAnnotationColours() {
- return annotationColours;
- }
+ /**
+ * Gets the value of the features property.
+ *
+ * <p> This accessor method returns a reference to the live list, not
+ * a snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the features property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getFeatures().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link Feature }
+ *
+ *
+ */
+ public List<Feature> getFeatures()
+ {
+ if (features == null)
+ {
+ features = new ArrayList<Feature>();
+ }
+ return this.features;
+ }
- /**
- * Sets the value of the annotationColours property.
- *
- * @param value
- * allowed object is
- * {@link AnnotationColourScheme }
- *
- */
- public void setAnnotationColours(AnnotationColourScheme value) {
- this.annotationColours = value;
- }
+ /**
+ * Gets the value of the pdbids property.
+ *
+ * <p> This accessor method returns a reference to the live list, not
+ * a snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the pdbids property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getPdbids().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.JSeq.Pdbids }
+ *
+ *
+ */
+ public List<JalviewModel.JSeq.Pdbids> getPdbids()
+ {
+ if (pdbids == null)
+ {
+ pdbids = new ArrayList<JalviewModel.JSeq.Pdbids>();
+ }
+ return this.pdbids;
+ }
- /**
- * Gets the value of the start property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getStart() {
- return start;
- }
+ /**
+ * Gets the value of the hiddenSequences property.
+ *
+ * <p> This accessor method returns a reference to the live list, not
+ * a snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the hiddenSequences property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getHiddenSequences().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getHiddenSequences()
+ {
+ if (hiddenSequences == null)
+ {
+ hiddenSequences = new ArrayList<Integer>();
+ }
+ return this.hiddenSequences;
+ }
- /**
- * Sets the value of the start property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setStart(Integer value) {
- this.start = value;
- }
+ /**
+ * Gets the value of the rnaViewer property.
+ *
+ * <p> This accessor method returns a reference to the live list, not
+ * a snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the rnaViewer property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getRnaViewer().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.JSeq.RnaViewer }
+ *
+ *
+ */
+ public List<JalviewModel.JSeq.RnaViewer> getRnaViewer()
+ {
+ if (rnaViewer == null)
+ {
+ rnaViewer = new ArrayList<JalviewModel.JSeq.RnaViewer>();
+ }
+ return this.rnaViewer;
+ }
- /**
- * Gets the value of the end property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getEnd() {
- return end;
- }
+ /**
+ * Gets the value of the colour property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getColour()
+ {
+ return colour;
+ }
- /**
- * Sets the value of the end property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setEnd(Integer value) {
- this.end = value;
- }
+ /**
+ * Sets the value of the colour property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setColour(Integer value)
+ {
+ this.colour = value;
+ }
- /**
- * Gets the value of the name property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getName() {
- return name;
- }
+ /**
+ * Gets the value of the start property.
+ *
+ */
+ public int getStart()
+ {
+ return start;
+ }
- /**
- * Sets the value of the name property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setName(String value) {
- this.name = value;
- }
+ /**
+ * Sets the value of the start property.
+ *
+ */
+ public void setStart(int value)
+ {
+ this.start = value;
+ }
+
+ /**
+ * Gets the value of the end property.
+ *
+ */
+ public int getEnd()
+ {
+ return end;
+ }
+
+ /**
+ * Sets the value of the end property.
+ *
+ */
+ public void setEnd(int value)
+ {
+ this.end = value;
+ }
+
+ /**
+ * Gets the value of the id property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getId()
+ {
+ return id;
+ }
+
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setId(String value)
+ {
+ this.id = value;
+ }
+
+ /**
+ * Gets the value of the hidden property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isHidden()
+ {
+ return hidden;
+ }
+
+ /**
+ * Sets the value of the hidden property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setHidden(Boolean value)
+ {
+ this.hidden = value;
+ }
+
+ /**
+ * Gets the value of the viewreference property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isViewreference()
+ {
+ return viewreference;
+ }
+
+ /**
+ * Sets the value of the viewreference property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setViewreference(Boolean value)
+ {
+ this.viewreference = value;
+ }
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
+ *
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;extension base="{www.jalview.org}pdbentry"&gt;
+ * &lt;sequence&gt; &lt;element name="structureState"
+ * maxOccurs="unbounded" minOccurs="0"&gt; &lt;complexType&gt;
+ * &lt;simpleContent&gt; &lt;extension
+ * base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
+ * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
+ * &lt;attribute name="visible"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="viewId"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="alignwithAlignPanel"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="colourwithAlignPanel"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false"
+ * /&gt; &lt;attribute name="colourByJmol"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="type"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/extension&gt; &lt;/simpleContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt;
+ * &lt;/sequence&gt; &lt;/extension&gt;
+ * &lt;/complexContent&gt; &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "structureState" })
+ public static class Pdbids extends Pdbentry
+ {
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<JalviewModel.JSeq.Pdbids.StructureState> structureState;
+
+ /**
+ * Gets the value of the structureState property.
+ *
+ * <p> This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the returned
+ * list will be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the structureState property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getStructureState().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.JSeq.Pdbids.StructureState }
+ *
+ *
+ */
+ public List<JalviewModel.JSeq.Pdbids.StructureState> getStructureState()
+ {
+ if (structureState == null)
+ {
+ structureState = new ArrayList<JalviewModel.JSeq.Pdbids.StructureState>();
+ }
+ return this.structureState;
+ }
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
+ *
+ * <pre> &lt;complexType&gt; &lt;simpleContent&gt;
+ * &lt;extension
+ * base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
+ * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
+ * &lt;attribute name="visible"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="viewId"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="alignwithAlignPanel"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true"
+ * /&gt; &lt;attribute name="colourwithAlignPanel"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false"
+ * /&gt; &lt;attribute name="colourByJmol"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true"
+ * /&gt; &lt;attribute name="type"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/extension&gt; &lt;/simpleContent&gt;
+ * &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "value" })
+ public static class StructureState
+ {
+
+ @XmlValue
+ protected String value;
+
+ @XmlAttribute(name = "visible")
+ protected Boolean visible;
+
+ @XmlAttribute(name = "viewId")
+ protected String viewId;
+
+ @XmlAttribute(name = "alignwithAlignPanel")
+ protected Boolean alignwithAlignPanel;
+
+ @XmlAttribute(name = "colourwithAlignPanel")
+ protected Boolean colourwithAlignPanel;
+
+ @XmlAttribute(name = "colourByJmol")
+ protected Boolean colourByJmol;
+
+ @XmlAttribute(name = "type")
+ protected String type;
+
+ @XmlAttribute(name = "width")
+ protected Integer width;
+
+ @XmlAttribute(name = "height")
+ protected Integer height;
+
+ @XmlAttribute(name = "xpos")
+ protected Integer xpos;
+
+ @XmlAttribute(name = "ypos")
+ protected Integer ypos;
/**
- * Gets the value of the colour property.
+ * Gets the value of the value property.
+ *
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getColour() {
- return colour;
+ public String getValue()
+ {
+ return value;
}
/**
- * Sets the value of the colour property.
+ * Sets the value of the value property.
*
* @param value
- * allowed object is
- * {@link String }
- *
+ * allowed object is {@link String }
+ *
*/
- public void setColour(String value) {
- this.colour = value;
+ public void setValue(String value)
+ {
+ this.value = value;
}
/**
- * Gets the value of the consThreshold property.
+ * Gets the value of the visible property.
+ *
+ * @return possible object is {@link Boolean }
*
- * @return
- * possible object is
- * {@link Integer }
- *
*/
- public Integer getConsThreshold() {
- return consThreshold;
+ public Boolean isVisible()
+ {
+ return visible;
}
/**
- * Sets the value of the consThreshold property.
+ * Sets the value of the visible property.
*
* @param value
- * allowed object is
- * {@link Integer }
- *
+ * allowed object is {@link Boolean }
+ *
*/
- public void setConsThreshold(Integer value) {
- this.consThreshold = value;
+ public void setVisible(Boolean value)
+ {
+ this.visible = value;
}
/**
- * Gets the value of the pidThreshold property.
+ * Gets the value of the viewId property.
+ *
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link Integer }
- *
*/
- public Integer getPidThreshold() {
- return pidThreshold;
+ public String getViewId()
+ {
+ return viewId;
}
/**
- * Sets the value of the pidThreshold property.
+ * Sets the value of the viewId property.
*
* @param value
- * allowed object is
- * {@link Integer }
- *
+ * allowed object is {@link String }
+ *
*/
- public void setPidThreshold(Integer value) {
- this.pidThreshold = value;
+ public void setViewId(String value)
+ {
+ this.viewId = value;
}
/**
- * Gets the value of the outlineColour property.
+ * Gets the value of the alignwithAlignPanel property.
+ *
+ * @return possible object is {@link Boolean }
*
- * @return
- * possible object is
- * {@link Integer }
- *
*/
- public Integer getOutlineColour() {
- return outlineColour;
+ public boolean isAlignwithAlignPanel()
+ {
+ if (alignwithAlignPanel == null)
+ {
+ return true;
+ }
+ else
+ {
+ return alignwithAlignPanel;
+ }
}
/**
- * Sets the value of the outlineColour property.
+ * Sets the value of the alignwithAlignPanel property.
*
* @param value
- * allowed object is
- * {@link Integer }
- *
+ * allowed object is {@link Boolean }
+ *
*/
- public void setOutlineColour(Integer value) {
- this.outlineColour = value;
+ public void setAlignwithAlignPanel(Boolean value)
+ {
+ this.alignwithAlignPanel = value;
}
/**
- * Gets the value of the displayBoxes property.
+ * Gets the value of the colourwithAlignPanel property.
+ *
+ * @return possible object is {@link Boolean }
*
- * @return
- * possible object is
- * {@link Boolean }
- *
*/
- public Boolean isDisplayBoxes() {
- return displayBoxes;
+ public boolean isColourwithAlignPanel()
+ {
+ if (colourwithAlignPanel == null)
+ {
+ return false;
+ }
+ else
+ {
+ return colourwithAlignPanel;
+ }
}
/**
- * Sets the value of the displayBoxes property.
+ * Sets the value of the colourwithAlignPanel property.
*
* @param value
- * allowed object is
- * {@link Boolean }
- *
+ * allowed object is {@link Boolean }
+ *
*/
- public void setDisplayBoxes(Boolean value) {
- this.displayBoxes = value;
+ public void setColourwithAlignPanel(Boolean value)
+ {
+ this.colourwithAlignPanel = value;
}
/**
- * Gets the value of the displayText property.
+ * Gets the value of the colourByJmol property.
+ *
+ * @return possible object is {@link Boolean }
*
- * @return
- * possible object is
- * {@link Boolean }
- *
*/
- public Boolean isDisplayText() {
- return displayText;
+ public boolean isColourByJmol()
+ {
+ if (colourByJmol == null)
+ {
+ return true;
+ }
+ else
+ {
+ return colourByJmol;
+ }
}
/**
- * Sets the value of the displayText property.
+ * Sets the value of the colourByJmol property.
*
* @param value
- * allowed object is
- * {@link Boolean }
- *
+ * allowed object is {@link Boolean }
+ *
*/
- public void setDisplayText(Boolean value) {
- this.displayText = value;
+ public void setColourByJmol(Boolean value)
+ {
+ this.colourByJmol = value;
}
/**
- * Gets the value of the colourText property.
+ * Gets the value of the type property.
+ *
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link Boolean }
- *
*/
- public Boolean isColourText() {
- return colourText;
+ public String getType()
+ {
+ return type;
}
/**
- * Sets the value of the colourText property.
+ * Sets the value of the type property.
*
* @param value
- * allowed object is
- * {@link Boolean }
- *
+ * allowed object is {@link String }
+ *
*/
- public void setColourText(Boolean value) {
- this.colourText = value;
+ public void setType(String value)
+ {
+ this.type = value;
}
/**
- * Gets the value of the textCol1 property.
+ * Gets the value of the width property.
+ *
+ * @return possible object is {@link Integer }
*
- * @return
- * possible object is
- * {@link Integer }
- *
*/
- public Integer getTextCol1() {
- return textCol1;
+ public Integer getWidth()
+ {
+ return width;
}
/**
- * Sets the value of the textCol1 property.
+ * Sets the value of the width property.
*
* @param value
- * allowed object is
- * {@link Integer }
- *
+ * allowed object is {@link Integer }
+ *
*/
- public void setTextCol1(Integer value) {
- this.textCol1 = value;
+ public void setWidth(Integer value)
+ {
+ this.width = value;
}
/**
- * Gets the value of the textCol2 property.
+ * Gets the value of the height property.
+ *
+ * @return possible object is {@link Integer }
*
- * @return
- * possible object is
- * {@link Integer }
- *
*/
- public Integer getTextCol2() {
- return textCol2;
+ public Integer getHeight()
+ {
+ return height;
}
/**
- * Sets the value of the textCol2 property.
+ * Sets the value of the height property.
*
* @param value
- * allowed object is
- * {@link Integer }
- *
+ * allowed object is {@link Integer }
+ *
*/
- public void setTextCol2(Integer value) {
- this.textCol2 = value;
+ public void setHeight(Integer value)
+ {
+ this.height = value;
}
/**
- * Gets the value of the textColThreshold property.
+ * Gets the value of the xpos property.
+ *
+ * @return possible object is {@link Integer }
*
- * @return
- * possible object is
- * {@link Integer }
- *
*/
- public Integer getTextColThreshold() {
- return textColThreshold;
+ public Integer getXpos()
+ {
+ return xpos;
}
/**
- * Sets the value of the textColThreshold property.
+ * Sets the value of the xpos property.
*
* @param value
- * allowed object is
- * {@link Integer }
- *
+ * allowed object is {@link Integer }
+ *
*/
- public void setTextColThreshold(Integer value) {
- this.textColThreshold = value;
+ public void setXpos(Integer value)
+ {
+ this.xpos = value;
}
/**
- * Gets the value of the showUnconserved property.
+ * Gets the value of the ypos property.
+ *
+ * @return possible object is {@link Integer }
*
- * @return
- * possible object is
- * {@link Boolean }
- *
*/
- public Boolean isShowUnconserved() {
- return showUnconserved;
+ public Integer getYpos()
+ {
+ return ypos;
}
/**
- * Sets the value of the showUnconserved property.
+ * Sets the value of the ypos property.
*
* @param value
- * allowed object is
- * {@link Boolean }
- *
+ * allowed object is {@link Integer }
+ *
*/
- public void setShowUnconserved(Boolean value) {
- this.showUnconserved = value;
+ public void setYpos(Integer value)
+ {
+ this.ypos = value;
}
+ }
+
+ }
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
+ *
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="secondaryStructure"
+ * maxOccurs="unbounded"&gt; &lt;complexType&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="title"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="annotationId" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="gapped"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="viewerState"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt;
+ * &lt;/sequence&gt; &lt;attGroup
+ * ref="{www.jalview.org}swingwindow"/&gt; &lt;attribute
+ * name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="viewId"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="dividerLocation"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "secondaryStructure" })
+ public static class RnaViewer
+ {
+
+ @XmlElement(namespace = "www.jalview.org", required = true)
+ protected List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> secondaryStructure;
+
+ @XmlAttribute(name = "title")
+ protected String title;
+
+ @XmlAttribute(name = "viewId")
+ protected String viewId;
+
+ @XmlAttribute(name = "dividerLocation")
+ protected Integer dividerLocation;
+
+ @XmlAttribute(name = "selectedRna")
+ protected Integer selectedRna;
+
+ @XmlAttribute(name = "width")
+ protected Integer width;
+
+ @XmlAttribute(name = "height")
+ protected Integer height;
+
+ @XmlAttribute(name = "xpos")
+ protected Integer xpos;
+
+ @XmlAttribute(name = "ypos")
+ protected Integer ypos;
+
+ /**
+ * Gets the value of the secondaryStructure property.
+ *
+ * <p> This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the returned
+ * list will be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the secondaryStructure
+ * property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getSecondaryStructure().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
+ *
+ *
+ */
+ public List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> getSecondaryStructure()
+ {
+ if (secondaryStructure == null)
+ {
+ secondaryStructure = new ArrayList<JalviewModel.JSeq.RnaViewer.SecondaryStructure>();
+ }
+ return this.secondaryStructure;
+ }
+
+ /**
+ * Gets the value of the title property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getTitle()
+ {
+ return title;
+ }
+
+ /**
+ * Sets the value of the title property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setTitle(String value)
+ {
+ this.title = value;
+ }
+
+ /**
+ * Gets the value of the viewId property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getViewId()
+ {
+ return viewId;
+ }
+
+ /**
+ * Sets the value of the viewId property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setViewId(String value)
+ {
+ this.viewId = value;
+ }
+
+ /**
+ * Gets the value of the dividerLocation property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getDividerLocation()
+ {
+ return dividerLocation;
+ }
+
+ /**
+ * Sets the value of the dividerLocation property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setDividerLocation(Integer value)
+ {
+ this.dividerLocation = value;
+ }
+
+ /**
+ * Gets the value of the selectedRna property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getSelectedRna()
+ {
+ return selectedRna;
+ }
+
+ /**
+ * Sets the value of the selectedRna property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setSelectedRna(Integer value)
+ {
+ this.selectedRna = value;
+ }
+
+ /**
+ * Gets the value of the width property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getWidth()
+ {
+ return width;
+ }
+
+ /**
+ * Sets the value of the width property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setWidth(Integer value)
+ {
+ this.width = value;
+ }
+
+ /**
+ * Gets the value of the height property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getHeight()
+ {
+ return height;
+ }
+
+ /**
+ * Sets the value of the height property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setHeight(Integer value)
+ {
+ this.height = value;
+ }
+
+ /**
+ * Gets the value of the xpos property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getXpos()
+ {
+ return xpos;
+ }
+
+ /**
+ * Sets the value of the xpos property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setXpos(Integer value)
+ {
+ this.xpos = value;
+ }
+
+ /**
+ * Gets the value of the ypos property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getYpos()
+ {
+ return ypos;
+ }
+
+ /**
+ * Sets the value of the ypos property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setYpos(Integer value)
+ {
+ this.ypos = value;
+ }
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
+ *
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="title"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="annotationId" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="gapped"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="viewerState"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class SecondaryStructure
+ {
+
+ @XmlAttribute(name = "title")
+ protected String title;
+
+ @XmlAttribute(name = "annotationId", required = true)
+ protected String annotationId;
+
+ @XmlAttribute(name = "gapped")
+ protected Boolean gapped;
+
+ @XmlAttribute(name = "viewerState")
+ protected String viewerState;
+
/**
- * Gets the value of the ignoreGapsinConsensus property.
+ * Gets the value of the title property.
+ *
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link Boolean }
- *
*/
- public boolean isIgnoreGapsinConsensus() {
- if (ignoreGapsinConsensus == null) {
- return true;
- } else {
- return ignoreGapsinConsensus;
- }
+ public String getTitle()
+ {
+ return title;
}
/**
- * Sets the value of the ignoreGapsinConsensus property.
+ * Sets the value of the title property.
*
* @param value
- * allowed object is
- * {@link Boolean }
- *
+ * allowed object is {@link String }
+ *
*/
- public void setIgnoreGapsinConsensus(Boolean value) {
- this.ignoreGapsinConsensus = value;
+ public void setTitle(String value)
+ {
+ this.title = value;
}
/**
- * Gets the value of the showConsensusHistogram property.
+ * Gets the value of the annotationId property.
+ *
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link Boolean }
- *
*/
- public boolean isShowConsensusHistogram() {
- if (showConsensusHistogram == null) {
- return true;
- } else {
- return showConsensusHistogram;
- }
+ public String getAnnotationId()
+ {
+ return annotationId;
}
/**
- * Sets the value of the showConsensusHistogram property.
+ * Sets the value of the annotationId property.
*
* @param value
- * allowed object is
- * {@link Boolean }
- *
+ * allowed object is {@link String }
+ *
*/
- public void setShowConsensusHistogram(Boolean value) {
- this.showConsensusHistogram = value;
+ public void setAnnotationId(String value)
+ {
+ this.annotationId = value;
}
/**
- * Gets the value of the showSequenceLogo property.
+ * Gets the value of the gapped property.
+ *
+ * @return possible object is {@link Boolean }
*
- * @return
- * possible object is
- * {@link Boolean }
- *
*/
- public boolean isShowSequenceLogo() {
- if (showSequenceLogo == null) {
- return false;
- } else {
- return showSequenceLogo;
- }
+ public Boolean isGapped()
+ {
+ return gapped;
}
/**
- * Sets the value of the showSequenceLogo property.
+ * Sets the value of the gapped property.
*
* @param value
- * allowed object is
- * {@link Boolean }
- *
+ * allowed object is {@link Boolean }
+ *
*/
- public void setShowSequenceLogo(Boolean value) {
- this.showSequenceLogo = value;
+ public void setGapped(Boolean value)
+ {
+ this.gapped = value;
}
/**
- * Gets the value of the normaliseSequenceLogo property.
+ * Gets the value of the viewerState property.
+ *
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link Boolean }
- *
*/
- public boolean isNormaliseSequenceLogo() {
- if (normaliseSequenceLogo == null) {
- return false;
- } else {
- return normaliseSequenceLogo;
- }
+ public String getViewerState()
+ {
+ return viewerState;
}
/**
- * Sets the value of the normaliseSequenceLogo property.
+ * Sets the value of the viewerState property.
*
* @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setNormaliseSequenceLogo(Boolean value) {
- this.normaliseSequenceLogo = value;
- }
-
- /**
- * Gets the value of the id property.
+ * allowed object is {@link String }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getId() {
- return id;
+ public void setViewerState(String value)
+ {
+ this.viewerState = value;
}
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setId(String value) {
- this.id = value;
- }
+ }
}
+ }
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
+ *
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="sequencePoint"
+ * maxOccurs="unbounded"&gt; &lt;complexType&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
+ * ref="{www.jalview.org}position"/&gt; &lt;attribute
+ * name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string"
+ * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt; &lt;element
+ * name="axis" maxOccurs="3" minOccurs="3"&gt; &lt;complexType&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
+ * ref="{www.jalview.org}position"/&gt; &lt;/restriction&gt;
+ * &lt;/complexContent&gt; &lt;/complexType&gt;
+ * &lt;/element&gt; &lt;element name="seqPointMin"&gt;
+ * &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
+ * ref="{www.jalview.org}position"/&gt; &lt;/restriction&gt;
+ * &lt;/complexContent&gt; &lt;/complexType&gt;
+ * &lt;/element&gt; &lt;element name="seqPointMax"&gt;
+ * &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
+ * ref="{www.jalview.org}position"/&gt; &lt;/restriction&gt;
+ * &lt;/complexContent&gt; &lt;/complexType&gt;
+ * &lt;/element&gt; &lt;element name="pcaData"
+ * type="{www.jalview.org}PcaDataType"/&gt; &lt;/sequence&gt;
+ * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
+ * &lt;attGroup ref="{www.jalview.org}SimilarityParams"/&gt;
+ * &lt;attribute name="title"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string"
+ * /&gt; &lt;attribute name="xDim"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int"
+ * /&gt; &lt;attribute name="bgColour"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="showLabels"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="linkToAllViews"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(
+ name = "",
+ propOrder =
+ { "sequencePoint", "axis", "seqPointMin", "seqPointMax", "pcaData" })
+ public static class PcaViewer
+ {
+
+ @XmlElement(namespace = "www.jalview.org", required = true)
+ protected List<JalviewModel.PcaViewer.SequencePoint> sequencePoint;
+
+ @XmlElement(namespace = "www.jalview.org", required = true)
+ protected List<JalviewModel.PcaViewer.Axis> axis;
+
+ @XmlElement(namespace = "www.jalview.org", required = true)
+ protected JalviewModel.PcaViewer.SeqPointMin seqPointMin;
+
+ @XmlElement(namespace = "www.jalview.org", required = true)
+ protected JalviewModel.PcaViewer.SeqPointMax seqPointMax;
+
+ @XmlElement(namespace = "www.jalview.org", required = true)
+ protected PcaDataType pcaData;
+
+ @XmlAttribute(name = "title")
+ protected String title;
+
+ @XmlAttribute(name = "scoreModelName")
+ protected String scoreModelName;
+
+ @XmlAttribute(name = "xDim")
+ protected Integer xDim;
+
+ @XmlAttribute(name = "yDim")
+ protected Integer yDim;
+
+ @XmlAttribute(name = "zDim")
+ protected Integer zDim;
+
+ @XmlAttribute(name = "bgColour")
+ protected Integer bgColour;
+
+ @XmlAttribute(name = "scaleFactor")
+ protected Float scaleFactor;
+
+ @XmlAttribute(name = "showLabels")
+ protected Boolean showLabels;
+
+ @XmlAttribute(name = "linkToAllViews")
+ protected Boolean linkToAllViews;
+
+ @XmlAttribute(name = "width")
+ protected Integer width;
+
+ @XmlAttribute(name = "height")
+ protected Integer height;
+
+ @XmlAttribute(name = "xpos")
+ protected Integer xpos;
+
+ @XmlAttribute(name = "ypos")
+ protected Integer ypos;
+
+ @XmlAttribute(name = "includeGaps")
+ protected Boolean includeGaps;
+
+ @XmlAttribute(name = "matchGaps")
+ protected Boolean matchGaps;
+
+ @XmlAttribute(name = "includeGappedColumns")
+ protected Boolean includeGappedColumns;
+
+ @XmlAttribute(name = "denominateByShortestLength")
+ protected Boolean denominateByShortestLength;
/**
- * <p>Java class for anonymous complex type.
+ * Gets the value of the sequencePoint property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/&gt;
- * &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;extension base="{www.jalview.org}pdbentry"&gt;
- * &lt;sequence&gt;
- * &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;simpleContent&gt;
- * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
- * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
- * &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/extension&gt;
- * &lt;/simpleContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;/sequence&gt;
- * &lt;/extension&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/&gt;
- * &lt;element name="rnaViewer" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="secondaryStructure" maxOccurs="unbounded"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;/sequence&gt;
- * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
- * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <p> This accessor method returns a reference to the live list, not
+ * a snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the sequencePoint property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getSequencePoint().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.PcaViewer.SequencePoint }
*
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "features",
- "pdbids",
- "hiddenSequences",
- "rnaViewer"
- })
- public static class JSeq {
-
- @XmlElement(namespace = "www.jalview.org")
- protected List<Feature> features;
- @XmlElement(namespace = "www.jalview.org")
- protected List<JalviewModel.JSeq.Pdbids> pdbids;
- @XmlElement(namespace = "www.jalview.org", type = Integer.class)
- protected List<Integer> hiddenSequences;
- @XmlElement(namespace = "www.jalview.org")
- protected List<JalviewModel.JSeq.RnaViewer> rnaViewer;
- @XmlAttribute(name = "colour")
- protected Integer colour;
- @XmlAttribute(name = "start", required = true)
- protected int start;
- @XmlAttribute(name = "end", required = true)
- protected int end;
- @XmlAttribute(name = "id", required = true)
- protected String id;
- @XmlAttribute(name = "hidden")
- protected Boolean hidden;
- @XmlAttribute(name = "viewreference")
- protected Boolean viewreference;
-
- /**
- * Gets the value of the features property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the features property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getFeatures().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Feature }
- *
- *
- */
- public List<Feature> getFeatures() {
- if (features == null) {
- features = new ArrayList<Feature>();
- }
- return this.features;
- }
+ public List<JalviewModel.PcaViewer.SequencePoint> getSequencePoint()
+ {
+ if (sequencePoint == null)
+ {
+ sequencePoint = new ArrayList<JalviewModel.PcaViewer.SequencePoint>();
+ }
+ return this.sequencePoint;
+ }
- /**
- * Gets the value of the pdbids property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the pdbids property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getPdbids().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.JSeq.Pdbids }
- *
- *
- */
- public List<JalviewModel.JSeq.Pdbids> getPdbids() {
- if (pdbids == null) {
- pdbids = new ArrayList<JalviewModel.JSeq.Pdbids>();
- }
- return this.pdbids;
- }
+ /**
+ * Gets the value of the axis property.
+ *
+ * <p> This accessor method returns a reference to the live list, not
+ * a snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the axis property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getAxis().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.PcaViewer.Axis }
+ *
+ *
+ */
+ public List<JalviewModel.PcaViewer.Axis> getAxis()
+ {
+ if (axis == null)
+ {
+ axis = new ArrayList<JalviewModel.PcaViewer.Axis>();
+ }
+ return this.axis;
+ }
- /**
- * Gets the value of the hiddenSequences property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the hiddenSequences property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getHiddenSequences().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Integer }
- *
- *
- */
- public List<Integer> getHiddenSequences() {
- if (hiddenSequences == null) {
- hiddenSequences = new ArrayList<Integer>();
- }
- return this.hiddenSequences;
- }
+ /**
+ * Gets the value of the seqPointMin property.
+ *
+ * @return possible object is {@link JalviewModel.PcaViewer.SeqPointMin }
+ *
+ */
+ public JalviewModel.PcaViewer.SeqPointMin getSeqPointMin()
+ {
+ return seqPointMin;
+ }
- /**
- * Gets the value of the rnaViewer property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the rnaViewer property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getRnaViewer().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.JSeq.RnaViewer }
- *
- *
- */
- public List<JalviewModel.JSeq.RnaViewer> getRnaViewer() {
- if (rnaViewer == null) {
- rnaViewer = new ArrayList<JalviewModel.JSeq.RnaViewer>();
- }
- return this.rnaViewer;
- }
+ /**
+ * Sets the value of the seqPointMin property.
+ *
+ * @param value
+ * allowed object is {@link JalviewModel.PcaViewer.SeqPointMin }
+ *
+ */
+ public void setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin value)
+ {
+ this.seqPointMin = value;
+ }
- /**
- * Gets the value of the colour property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getColour() {
- return colour;
- }
+ /**
+ * Gets the value of the seqPointMax property.
+ *
+ * @return possible object is {@link JalviewModel.PcaViewer.SeqPointMax }
+ *
+ */
+ public JalviewModel.PcaViewer.SeqPointMax getSeqPointMax()
+ {
+ return seqPointMax;
+ }
- /**
- * Sets the value of the colour property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setColour(Integer value) {
- this.colour = value;
- }
+ /**
+ * Sets the value of the seqPointMax property.
+ *
+ * @param value
+ * allowed object is {@link JalviewModel.PcaViewer.SeqPointMax }
+ *
+ */
+ public void setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax value)
+ {
+ this.seqPointMax = value;
+ }
- /**
- * Gets the value of the start property.
- *
- */
- public int getStart() {
- return start;
- }
+ /**
+ * Gets the value of the pcaData property.
+ *
+ * @return possible object is {@link PcaDataType }
+ *
+ */
+ public PcaDataType getPcaData()
+ {
+ return pcaData;
+ }
- /**
- * Sets the value of the start property.
- *
- */
- public void setStart(int value) {
- this.start = value;
- }
+ /**
+ * Sets the value of the pcaData property.
+ *
+ * @param value
+ * allowed object is {@link PcaDataType }
+ *
+ */
+ public void setPcaData(PcaDataType value)
+ {
+ this.pcaData = value;
+ }
- /**
- * Gets the value of the end property.
- *
- */
- public int getEnd() {
- return end;
- }
+ /**
+ * Gets the value of the title property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getTitle()
+ {
+ return title;
+ }
- /**
- * Sets the value of the end property.
- *
- */
- public void setEnd(int value) {
- this.end = value;
- }
+ /**
+ * Sets the value of the title property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setTitle(String value)
+ {
+ this.title = value;
+ }
- /**
- * Gets the value of the id property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getId() {
- return id;
- }
+ /**
+ * Gets the value of the scoreModelName property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getScoreModelName()
+ {
+ return scoreModelName;
+ }
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setId(String value) {
- this.id = value;
- }
+ /**
+ * Sets the value of the scoreModelName property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setScoreModelName(String value)
+ {
+ this.scoreModelName = value;
+ }
- /**
- * Gets the value of the hidden property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isHidden() {
- return hidden;
- }
+ /**
+ * Gets the value of the xDim property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getXDim()
+ {
+ return xDim;
+ }
- /**
- * Sets the value of the hidden property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setHidden(Boolean value) {
- this.hidden = value;
- }
+ /**
+ * Sets the value of the xDim property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setXDim(Integer value)
+ {
+ this.xDim = value;
+ }
- /**
- * Gets the value of the viewreference property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isViewreference() {
- return viewreference;
- }
+ /**
+ * Gets the value of the yDim property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getYDim()
+ {
+ return yDim;
+ }
- /**
- * Sets the value of the viewreference property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setViewreference(Boolean value) {
- this.viewreference = value;
- }
+ /**
+ * Sets the value of the yDim property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setYDim(Integer value)
+ {
+ this.yDim = value;
+ }
+ /**
+ * Gets the value of the zDim property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getZDim()
+ {
+ return zDim;
+ }
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;extension base="{www.jalview.org}pdbentry"&gt;
- * &lt;sequence&gt;
- * &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;simpleContent&gt;
- * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
- * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
- * &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/extension&gt;
- * &lt;/simpleContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;/sequence&gt;
- * &lt;/extension&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "structureState"
- })
- public static class Pdbids
- extends Pdbentry
- {
+ /**
+ * Sets the value of the zDim property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setZDim(Integer value)
+ {
+ this.zDim = value;
+ }
- @XmlElement(namespace = "www.jalview.org")
- protected List<JalviewModel.JSeq.Pdbids.StructureState> structureState;
-
- /**
- * Gets the value of the structureState property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the structureState property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getStructureState().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.JSeq.Pdbids.StructureState }
- *
- *
- */
- public List<JalviewModel.JSeq.Pdbids.StructureState> getStructureState() {
- if (structureState == null) {
- structureState = new ArrayList<JalviewModel.JSeq.Pdbids.StructureState>();
- }
- return this.structureState;
- }
-
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * &lt;complexType&gt;
- * &lt;simpleContent&gt;
- * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
- * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
- * &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/extension&gt;
- * &lt;/simpleContent&gt;
- * &lt;/complexType&gt;
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "value"
- })
- public static class StructureState {
-
- @XmlValue
- protected String value;
- @XmlAttribute(name = "visible")
- protected Boolean visible;
- @XmlAttribute(name = "viewId")
- protected String viewId;
- @XmlAttribute(name = "alignwithAlignPanel")
- protected Boolean alignwithAlignPanel;
- @XmlAttribute(name = "colourwithAlignPanel")
- protected Boolean colourwithAlignPanel;
- @XmlAttribute(name = "colourByJmol")
- protected Boolean colourByJmol;
- @XmlAttribute(name = "type")
- protected String type;
- @XmlAttribute(name = "width")
- protected Integer width;
- @XmlAttribute(name = "height")
- protected Integer height;
- @XmlAttribute(name = "xpos")
- protected Integer xpos;
- @XmlAttribute(name = "ypos")
- protected Integer ypos;
-
- /**
- * Gets the value of the value property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getValue() {
- return value;
- }
-
- /**
- * Sets the value of the value property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setValue(String value) {
- this.value = value;
- }
-
- /**
- * Gets the value of the visible property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isVisible() {
- return visible;
- }
-
- /**
- * Sets the value of the visible property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setVisible(Boolean value) {
- this.visible = value;
- }
-
- /**
- * Gets the value of the viewId property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getViewId() {
- return viewId;
- }
-
- /**
- * Sets the value of the viewId property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setViewId(String value) {
- this.viewId = value;
- }
-
- /**
- * Gets the value of the alignwithAlignPanel property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isAlignwithAlignPanel() {
- if (alignwithAlignPanel == null) {
- return true;
- } else {
- return alignwithAlignPanel;
- }
- }
-
- /**
- * Sets the value of the alignwithAlignPanel property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setAlignwithAlignPanel(Boolean value) {
- this.alignwithAlignPanel = value;
- }
-
- /**
- * Gets the value of the colourwithAlignPanel property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isColourwithAlignPanel() {
- if (colourwithAlignPanel == null) {
- return false;
- } else {
- return colourwithAlignPanel;
- }
- }
-
- /**
- * Sets the value of the colourwithAlignPanel property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setColourwithAlignPanel(Boolean value) {
- this.colourwithAlignPanel = value;
- }
-
- /**
- * Gets the value of the colourByJmol property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isColourByJmol() {
- if (colourByJmol == null) {
- return true;
- } else {
- return colourByJmol;
- }
- }
-
- /**
- * Sets the value of the colourByJmol property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setColourByJmol(Boolean value) {
- this.colourByJmol = value;
- }
-
- /**
- * Gets the value of the type property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getType() {
- return type;
- }
-
- /**
- * Sets the value of the type property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setType(String value) {
- this.type = value;
- }
-
- /**
- * Gets the value of the width property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getWidth() {
- return width;
- }
-
- /**
- * Sets the value of the width property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setWidth(Integer value) {
- this.width = value;
- }
-
- /**
- * Gets the value of the height property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getHeight() {
- return height;
- }
-
- /**
- * Sets the value of the height property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setHeight(Integer value) {
- this.height = value;
- }
-
- /**
- * Gets the value of the xpos property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getXpos() {
- return xpos;
- }
-
- /**
- * Sets the value of the xpos property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setXpos(Integer value) {
- this.xpos = value;
- }
-
- /**
- * Gets the value of the ypos property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getYpos() {
- return ypos;
- }
-
- /**
- * Sets the value of the ypos property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setYpos(Integer value) {
- this.ypos = value;
- }
-
- }
+ /**
+ * Gets the value of the bgColour property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getBgColour()
+ {
+ return bgColour;
+ }
- }
+ /**
+ * Sets the value of the bgColour property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setBgColour(Integer value)
+ {
+ this.bgColour = value;
+ }
+ /**
+ * Gets the value of the scaleFactor property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getScaleFactor()
+ {
+ return scaleFactor;
+ }
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="secondaryStructure" maxOccurs="unbounded"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;/sequence&gt;
- * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
- * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "secondaryStructure"
- })
- public static class RnaViewer {
-
- @XmlElement(namespace = "www.jalview.org", required = true)
- protected List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> secondaryStructure;
- @XmlAttribute(name = "title")
- protected String title;
- @XmlAttribute(name = "viewId")
- protected String viewId;
- @XmlAttribute(name = "dividerLocation")
- protected Integer dividerLocation;
- @XmlAttribute(name = "selectedRna")
- protected Integer selectedRna;
- @XmlAttribute(name = "width")
- protected Integer width;
- @XmlAttribute(name = "height")
- protected Integer height;
- @XmlAttribute(name = "xpos")
- protected Integer xpos;
- @XmlAttribute(name = "ypos")
- protected Integer ypos;
-
- /**
- * Gets the value of the secondaryStructure property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the secondaryStructure property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getSecondaryStructure().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
- *
- *
- */
- public List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> getSecondaryStructure() {
- if (secondaryStructure == null) {
- secondaryStructure = new ArrayList<JalviewModel.JSeq.RnaViewer.SecondaryStructure>();
- }
- return this.secondaryStructure;
- }
-
- /**
- * Gets the value of the title property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getTitle() {
- return title;
- }
-
- /**
- * Sets the value of the title property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setTitle(String value) {
- this.title = value;
- }
-
- /**
- * Gets the value of the viewId property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getViewId() {
- return viewId;
- }
-
- /**
- * Sets the value of the viewId property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setViewId(String value) {
- this.viewId = value;
- }
-
- /**
- * Gets the value of the dividerLocation property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getDividerLocation() {
- return dividerLocation;
- }
-
- /**
- * Sets the value of the dividerLocation property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setDividerLocation(Integer value) {
- this.dividerLocation = value;
- }
-
- /**
- * Gets the value of the selectedRna property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getSelectedRna() {
- return selectedRna;
- }
-
- /**
- * Sets the value of the selectedRna property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setSelectedRna(Integer value) {
- this.selectedRna = value;
- }
-
- /**
- * Gets the value of the width property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getWidth() {
- return width;
- }
-
- /**
- * Sets the value of the width property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setWidth(Integer value) {
- this.width = value;
- }
-
- /**
- * Gets the value of the height property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getHeight() {
- return height;
- }
-
- /**
- * Sets the value of the height property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setHeight(Integer value) {
- this.height = value;
- }
-
- /**
- * Gets the value of the xpos property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getXpos() {
- return xpos;
- }
-
- /**
- * Sets the value of the xpos property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setXpos(Integer value) {
- this.xpos = value;
- }
-
- /**
- * Gets the value of the ypos property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getYpos() {
- return ypos;
- }
-
- /**
- * Sets the value of the ypos property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setYpos(Integer value) {
- this.ypos = value;
- }
-
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class SecondaryStructure {
-
- @XmlAttribute(name = "title")
- protected String title;
- @XmlAttribute(name = "annotationId", required = true)
- protected String annotationId;
- @XmlAttribute(name = "gapped")
- protected Boolean gapped;
- @XmlAttribute(name = "viewerState")
- protected String viewerState;
-
- /**
- * Gets the value of the title property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getTitle() {
- return title;
- }
-
- /**
- * Sets the value of the title property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setTitle(String value) {
- this.title = value;
- }
-
- /**
- * Gets the value of the annotationId property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getAnnotationId() {
- return annotationId;
- }
-
- /**
- * Sets the value of the annotationId property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setAnnotationId(String value) {
- this.annotationId = value;
- }
-
- /**
- * Gets the value of the gapped property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isGapped() {
- return gapped;
- }
-
- /**
- * Sets the value of the gapped property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setGapped(Boolean value) {
- this.gapped = value;
- }
-
- /**
- * Gets the value of the viewerState property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getViewerState() {
- return viewerState;
- }
-
- /**
- * Sets the value of the viewerState property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setViewerState(String value) {
- this.viewerState = value;
- }
-
- }
+ /**
+ * Sets the value of the scaleFactor property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setScaleFactor(Float value)
+ {
+ this.scaleFactor = value;
+ }
- }
+ /**
+ * Gets the value of the showLabels property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowLabels()
+ {
+ return showLabels;
+ }
+ /**
+ * Sets the value of the showLabels property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowLabels(Boolean value)
+ {
+ this.showLabels = value;
}
+ /**
+ * Gets the value of the linkToAllViews property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isLinkToAllViews()
+ {
+ return linkToAllViews;
+ }
/**
- * <p>Java class for anonymous complex type.
+ * Sets the value of the linkToAllViews property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="sequencePoint" maxOccurs="unbounded"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attGroup ref="{www.jalview.org}position"/&gt;
- * &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="axis" maxOccurs="3" minOccurs="3"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attGroup ref="{www.jalview.org}position"/&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="seqPointMin"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attGroup ref="{www.jalview.org}position"/&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="seqPointMax"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attGroup ref="{www.jalview.org}position"/&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="pcaData" type="{www.jalview.org}PcaDataType"/&gt;
- * &lt;/sequence&gt;
- * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
- * &lt;attGroup ref="{www.jalview.org}SimilarityParams"/&gt;
- * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setLinkToAllViews(Boolean value)
+ {
+ this.linkToAllViews = value;
+ }
+
+ /**
+ * Gets the value of the width property.
*
+ * @return possible object is {@link Integer }
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "sequencePoint",
- "axis",
- "seqPointMin",
- "seqPointMax",
- "pcaData"
- })
- public static class PcaViewer {
-
- @XmlElement(namespace = "www.jalview.org", required = true)
- protected List<JalviewModel.PcaViewer.SequencePoint> sequencePoint;
- @XmlElement(namespace = "www.jalview.org", required = true)
- protected List<JalviewModel.PcaViewer.Axis> axis;
- @XmlElement(namespace = "www.jalview.org", required = true)
- protected JalviewModel.PcaViewer.SeqPointMin seqPointMin;
- @XmlElement(namespace = "www.jalview.org", required = true)
- protected JalviewModel.PcaViewer.SeqPointMax seqPointMax;
- @XmlElement(namespace = "www.jalview.org", required = true)
- protected PcaDataType pcaData;
- @XmlAttribute(name = "title")
- protected String title;
- @XmlAttribute(name = "scoreModelName")
- protected String scoreModelName;
- @XmlAttribute(name = "xDim")
- protected Integer xDim;
- @XmlAttribute(name = "yDim")
- protected Integer yDim;
- @XmlAttribute(name = "zDim")
- protected Integer zDim;
- @XmlAttribute(name = "bgColour")
- protected Integer bgColour;
- @XmlAttribute(name = "scaleFactor")
- protected Float scaleFactor;
- @XmlAttribute(name = "showLabels")
- protected Boolean showLabels;
- @XmlAttribute(name = "linkToAllViews")
- protected Boolean linkToAllViews;
- @XmlAttribute(name = "width")
- protected Integer width;
- @XmlAttribute(name = "height")
- protected Integer height;
- @XmlAttribute(name = "xpos")
- protected Integer xpos;
- @XmlAttribute(name = "ypos")
- protected Integer ypos;
- @XmlAttribute(name = "includeGaps")
- protected Boolean includeGaps;
- @XmlAttribute(name = "matchGaps")
- protected Boolean matchGaps;
- @XmlAttribute(name = "includeGappedColumns")
- protected Boolean includeGappedColumns;
- @XmlAttribute(name = "denominateByShortestLength")
- protected Boolean denominateByShortestLength;
-
- /**
- * Gets the value of the sequencePoint property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the sequencePoint property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getSequencePoint().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.PcaViewer.SequencePoint }
- *
- *
- */
- public List<JalviewModel.PcaViewer.SequencePoint> getSequencePoint() {
- if (sequencePoint == null) {
- sequencePoint = new ArrayList<JalviewModel.PcaViewer.SequencePoint>();
- }
- return this.sequencePoint;
- }
-
- /**
- * Gets the value of the axis property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the axis property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getAxis().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.PcaViewer.Axis }
- *
- *
- */
- public List<JalviewModel.PcaViewer.Axis> getAxis() {
- if (axis == null) {
- axis = new ArrayList<JalviewModel.PcaViewer.Axis>();
- }
- return this.axis;
- }
-
- /**
- * Gets the value of the seqPointMin property.
- *
- * @return
- * possible object is
- * {@link JalviewModel.PcaViewer.SeqPointMin }
- *
- */
- public JalviewModel.PcaViewer.SeqPointMin getSeqPointMin() {
- return seqPointMin;
- }
-
- /**
- * Sets the value of the seqPointMin property.
- *
- * @param value
- * allowed object is
- * {@link JalviewModel.PcaViewer.SeqPointMin }
- *
- */
- public void setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin value) {
- this.seqPointMin = value;
- }
-
- /**
- * Gets the value of the seqPointMax property.
- *
- * @return
- * possible object is
- * {@link JalviewModel.PcaViewer.SeqPointMax }
- *
- */
- public JalviewModel.PcaViewer.SeqPointMax getSeqPointMax() {
- return seqPointMax;
- }
-
- /**
- * Sets the value of the seqPointMax property.
- *
- * @param value
- * allowed object is
- * {@link JalviewModel.PcaViewer.SeqPointMax }
- *
- */
- public void setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax value) {
- this.seqPointMax = value;
- }
-
- /**
- * Gets the value of the pcaData property.
- *
- * @return
- * possible object is
- * {@link PcaDataType }
- *
- */
- public PcaDataType getPcaData() {
- return pcaData;
- }
-
- /**
- * Sets the value of the pcaData property.
- *
- * @param value
- * allowed object is
- * {@link PcaDataType }
- *
- */
- public void setPcaData(PcaDataType value) {
- this.pcaData = value;
- }
-
- /**
- * Gets the value of the title property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getTitle() {
- return title;
- }
-
- /**
- * Sets the value of the title property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setTitle(String value) {
- this.title = value;
- }
-
- /**
- * Gets the value of the scoreModelName property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getScoreModelName() {
- return scoreModelName;
- }
+ public Integer getWidth()
+ {
+ return width;
+ }
- /**
- * Sets the value of the scoreModelName property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setScoreModelName(String value) {
- this.scoreModelName = value;
- }
+ /**
+ * Sets the value of the width property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setWidth(Integer value)
+ {
+ this.width = value;
+ }
- /**
- * Gets the value of the xDim property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getXDim() {
- return xDim;
- }
+ /**
+ * Gets the value of the height property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getHeight()
+ {
+ return height;
+ }
- /**
- * Sets the value of the xDim property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setXDim(Integer value) {
- this.xDim = value;
- }
+ /**
+ * Sets the value of the height property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setHeight(Integer value)
+ {
+ this.height = value;
+ }
- /**
- * Gets the value of the yDim property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getYDim() {
- return yDim;
- }
+ /**
+ * Gets the value of the xpos property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getXpos()
+ {
+ return xpos;
+ }
- /**
- * Sets the value of the yDim property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setYDim(Integer value) {
- this.yDim = value;
- }
+ /**
+ * Sets the value of the xpos property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setXpos(Integer value)
+ {
+ this.xpos = value;
+ }
- /**
- * Gets the value of the zDim property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getZDim() {
- return zDim;
- }
+ /**
+ * Gets the value of the ypos property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getYpos()
+ {
+ return ypos;
+ }
- /**
- * Sets the value of the zDim property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setZDim(Integer value) {
- this.zDim = value;
- }
+ /**
+ * Sets the value of the ypos property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setYpos(Integer value)
+ {
+ this.ypos = value;
+ }
- /**
- * Gets the value of the bgColour property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getBgColour() {
- return bgColour;
- }
+ /**
+ * Gets the value of the includeGaps property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isIncludeGaps()
+ {
+ return includeGaps;
+ }
- /**
- * Sets the value of the bgColour property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setBgColour(Integer value) {
- this.bgColour = value;
- }
+ /**
+ * Sets the value of the includeGaps property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setIncludeGaps(Boolean value)
+ {
+ this.includeGaps = value;
+ }
- /**
- * Gets the value of the scaleFactor property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getScaleFactor() {
- return scaleFactor;
- }
+ /**
+ * Gets the value of the matchGaps property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isMatchGaps()
+ {
+ return matchGaps;
+ }
- /**
- * Sets the value of the scaleFactor property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setScaleFactor(Float value) {
- this.scaleFactor = value;
- }
+ /**
+ * Sets the value of the matchGaps property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setMatchGaps(Boolean value)
+ {
+ this.matchGaps = value;
+ }
- /**
- * Gets the value of the showLabels property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowLabels() {
- return showLabels;
- }
+ /**
+ * Gets the value of the includeGappedColumns property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isIncludeGappedColumns()
+ {
+ return includeGappedColumns;
+ }
- /**
- * Sets the value of the showLabels property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowLabels(Boolean value) {
- this.showLabels = value;
- }
+ /**
+ * Sets the value of the includeGappedColumns property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setIncludeGappedColumns(Boolean value)
+ {
+ this.includeGappedColumns = value;
+ }
- /**
- * Gets the value of the linkToAllViews property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isLinkToAllViews() {
- return linkToAllViews;
- }
+ /**
+ * Gets the value of the denominateByShortestLength property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isDenominateByShortestLength()
+ {
+ return denominateByShortestLength;
+ }
- /**
- * Sets the value of the linkToAllViews property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setLinkToAllViews(Boolean value) {
- this.linkToAllViews = value;
- }
+ /**
+ * Sets the value of the denominateByShortestLength property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setDenominateByShortestLength(Boolean value)
+ {
+ this.denominateByShortestLength = value;
+ }
- /**
- * Gets the value of the width property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getWidth() {
- return width;
- }
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
+ *
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
+ * ref="{www.jalview.org}position"/&gt; &lt;/restriction&gt;
+ * &lt;/complexContent&gt; &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Axis
+ {
+
+ @XmlAttribute(name = "xPos")
+ protected Float xPos;
+
+ @XmlAttribute(name = "yPos")
+ protected Float yPos;
+
+ @XmlAttribute(name = "zPos")
+ protected Float zPos;
+
+ /**
+ * Gets the value of the xPos property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getXPos()
+ {
+ return xPos;
+ }
+
+ /**
+ * Sets the value of the xPos property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setXPos(Float value)
+ {
+ this.xPos = value;
+ }
+
+ /**
+ * Gets the value of the yPos property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getYPos()
+ {
+ return yPos;
+ }
+
+ /**
+ * Sets the value of the yPos property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setYPos(Float value)
+ {
+ this.yPos = value;
+ }
+
+ /**
+ * Gets the value of the zPos property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getZPos()
+ {
+ return zPos;
+ }
+
+ /**
+ * Sets the value of the zPos property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setZPos(Float value)
+ {
+ this.zPos = value;
+ }
- /**
- * Sets the value of the width property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setWidth(Integer value) {
- this.width = value;
- }
+ }
- /**
- * Gets the value of the height property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getHeight() {
- return height;
- }
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
+ *
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
+ * ref="{www.jalview.org}position"/&gt; &lt;/restriction&gt;
+ * &lt;/complexContent&gt; &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class SeqPointMax
+ {
+
+ @XmlAttribute(name = "xPos")
+ protected Float xPos;
+
+ @XmlAttribute(name = "yPos")
+ protected Float yPos;
+
+ @XmlAttribute(name = "zPos")
+ protected Float zPos;
+
+ /**
+ * Gets the value of the xPos property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getXPos()
+ {
+ return xPos;
+ }
+
+ /**
+ * Sets the value of the xPos property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setXPos(Float value)
+ {
+ this.xPos = value;
+ }
+
+ /**
+ * Gets the value of the yPos property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getYPos()
+ {
+ return yPos;
+ }
+
+ /**
+ * Sets the value of the yPos property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setYPos(Float value)
+ {
+ this.yPos = value;
+ }
+
+ /**
+ * Gets the value of the zPos property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getZPos()
+ {
+ return zPos;
+ }
+
+ /**
+ * Sets the value of the zPos property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setZPos(Float value)
+ {
+ this.zPos = value;
+ }
- /**
- * Sets the value of the height property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setHeight(Integer value) {
- this.height = value;
- }
+ }
- /**
- * Gets the value of the xpos property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getXpos() {
- return xpos;
- }
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
+ *
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
+ * ref="{www.jalview.org}position"/&gt; &lt;/restriction&gt;
+ * &lt;/complexContent&gt; &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class SeqPointMin
+ {
+
+ @XmlAttribute(name = "xPos")
+ protected Float xPos;
+
+ @XmlAttribute(name = "yPos")
+ protected Float yPos;
+
+ @XmlAttribute(name = "zPos")
+ protected Float zPos;
+
+ /**
+ * Gets the value of the xPos property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getXPos()
+ {
+ return xPos;
+ }
+
+ /**
+ * Sets the value of the xPos property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setXPos(Float value)
+ {
+ this.xPos = value;
+ }
+
+ /**
+ * Gets the value of the yPos property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getYPos()
+ {
+ return yPos;
+ }
+
+ /**
+ * Sets the value of the yPos property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setYPos(Float value)
+ {
+ this.yPos = value;
+ }
+
+ /**
+ * Gets the value of the zPos property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getZPos()
+ {
+ return zPos;
+ }
+
+ /**
+ * Sets the value of the zPos property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setZPos(Float value)
+ {
+ this.zPos = value;
+ }
- /**
- * Sets the value of the xpos property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setXpos(Integer value) {
- this.xpos = value;
- }
+ }
- /**
- * Gets the value of the ypos property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getYpos() {
- return ypos;
- }
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
+ *
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
+ * ref="{www.jalview.org}position"/&gt; &lt;attribute
+ * name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string"
+ * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class SequencePoint
+ {
+
+ @XmlAttribute(name = "sequenceRef")
+ protected String sequenceRef;
+
+ @XmlAttribute(name = "xPos")
+ protected Float xPos;
+
+ @XmlAttribute(name = "yPos")
+ protected Float yPos;
+
+ @XmlAttribute(name = "zPos")
+ protected Float zPos;
+
+ /**
+ * Gets the value of the sequenceRef property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getSequenceRef()
+ {
+ return sequenceRef;
+ }
+
+ /**
+ * Sets the value of the sequenceRef property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setSequenceRef(String value)
+ {
+ this.sequenceRef = value;
+ }
+
+ /**
+ * Gets the value of the xPos property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getXPos()
+ {
+ return xPos;
+ }
+
+ /**
+ * Sets the value of the xPos property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setXPos(Float value)
+ {
+ this.xPos = value;
+ }
+
+ /**
+ * Gets the value of the yPos property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getYPos()
+ {
+ return yPos;
+ }
+
+ /**
+ * Sets the value of the yPos property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setYPos(Float value)
+ {
+ this.yPos = value;
+ }
+
+ /**
+ * Gets the value of the zPos property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getZPos()
+ {
+ return zPos;
+ }
+
+ /**
+ * Sets the value of the zPos property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setZPos(Float value)
+ {
+ this.zPos = value;
+ }
- /**
- * Sets the value of the ypos property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setYpos(Integer value) {
- this.ypos = value;
- }
+ }
- /**
- * Gets the value of the includeGaps property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isIncludeGaps() {
- return includeGaps;
- }
+ }
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
+ *
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;sequence
+ * minOccurs="0"&gt; &lt;element name="title"
+ * type="{http://www.w3.org/2001/XMLSchema}string"/&gt; &lt;element
+ * name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
+ * &lt;/sequence&gt; &lt;attGroup
+ * ref="{www.jalview.org}swingwindow"/&gt; &lt;attribute
+ * name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="fontSize"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="threshold"
+ * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute
+ * name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean"
+ * /&gt; &lt;attribute name="showDistances"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="markUnlinked"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="fitToWindow"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="currentTree"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID"
+ * /&gt; &lt;attribute name="linkToAllViews"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "title", "newick" })
+ public static class Tree
+ {
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected String title;
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected String newick;
+
+ @XmlAttribute(name = "fontName")
+ protected String fontName;
+
+ @XmlAttribute(name = "fontSize")
+ protected Integer fontSize;
+
+ @XmlAttribute(name = "fontStyle")
+ protected Integer fontStyle;
+
+ @XmlAttribute(name = "threshold")
+ protected Float threshold;
+
+ @XmlAttribute(name = "showBootstrap")
+ protected Boolean showBootstrap;
+
+ @XmlAttribute(name = "showDistances")
+ protected Boolean showDistances;
+
+ @XmlAttribute(name = "markUnlinked")
+ protected Boolean markUnlinked;
+
+ @XmlAttribute(name = "fitToWindow")
+ protected Boolean fitToWindow;
+
+ @XmlAttribute(name = "currentTree")
+ protected Boolean currentTree;
+
+ @XmlAttribute(name = "id")
+ @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
+ @XmlID
+ @XmlSchemaType(name = "ID")
+ protected String id;
+
+ @XmlAttribute(name = "linkToAllViews")
+ protected Boolean linkToAllViews;
+
+ @XmlAttribute(name = "width")
+ protected Integer width;
+
+ @XmlAttribute(name = "height")
+ protected Integer height;
+
+ @XmlAttribute(name = "xpos")
+ protected Integer xpos;
+
+ @XmlAttribute(name = "ypos")
+ protected Integer ypos;
- /**
- * Sets the value of the includeGaps property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setIncludeGaps(Boolean value) {
- this.includeGaps = value;
- }
+ /**
+ * Gets the value of the title property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getTitle()
+ {
+ return title;
+ }
- /**
- * Gets the value of the matchGaps property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isMatchGaps() {
- return matchGaps;
- }
+ /**
+ * Sets the value of the title property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setTitle(String value)
+ {
+ this.title = value;
+ }
- /**
- * Sets the value of the matchGaps property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setMatchGaps(Boolean value) {
- this.matchGaps = value;
- }
+ /**
+ * Gets the value of the newick property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getNewick()
+ {
+ return newick;
+ }
- /**
- * Gets the value of the includeGappedColumns property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isIncludeGappedColumns() {
- return includeGappedColumns;
- }
+ /**
+ * Sets the value of the newick property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setNewick(String value)
+ {
+ this.newick = value;
+ }
- /**
- * Sets the value of the includeGappedColumns property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setIncludeGappedColumns(Boolean value) {
- this.includeGappedColumns = value;
- }
+ /**
+ * Gets the value of the fontName property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getFontName()
+ {
+ return fontName;
+ }
- /**
- * Gets the value of the denominateByShortestLength property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isDenominateByShortestLength() {
- return denominateByShortestLength;
- }
+ /**
+ * Sets the value of the fontName property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setFontName(String value)
+ {
+ this.fontName = value;
+ }
- /**
- * Sets the value of the denominateByShortestLength property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setDenominateByShortestLength(Boolean value) {
- this.denominateByShortestLength = value;
- }
+ /**
+ * Gets the value of the fontSize property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getFontSize()
+ {
+ return fontSize;
+ }
+ /**
+ * Sets the value of the fontSize property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setFontSize(Integer value)
+ {
+ this.fontSize = value;
+ }
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attGroup ref="{www.jalview.org}position"/&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class Axis {
-
- @XmlAttribute(name = "xPos")
- protected Float xPos;
- @XmlAttribute(name = "yPos")
- protected Float yPos;
- @XmlAttribute(name = "zPos")
- protected Float zPos;
-
- /**
- * Gets the value of the xPos property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getXPos() {
- return xPos;
- }
-
- /**
- * Sets the value of the xPos property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setXPos(Float value) {
- this.xPos = value;
- }
-
- /**
- * Gets the value of the yPos property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getYPos() {
- return yPos;
- }
-
- /**
- * Sets the value of the yPos property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setYPos(Float value) {
- this.yPos = value;
- }
-
- /**
- * Gets the value of the zPos property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getZPos() {
- return zPos;
- }
-
- /**
- * Sets the value of the zPos property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setZPos(Float value) {
- this.zPos = value;
- }
+ /**
+ * Gets the value of the fontStyle property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getFontStyle()
+ {
+ return fontStyle;
+ }
- }
+ /**
+ * Sets the value of the fontStyle property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setFontStyle(Integer value)
+ {
+ this.fontStyle = value;
+ }
+ /**
+ * Gets the value of the threshold property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getThreshold()
+ {
+ return threshold;
+ }
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attGroup ref="{www.jalview.org}position"/&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class SeqPointMax {
-
- @XmlAttribute(name = "xPos")
- protected Float xPos;
- @XmlAttribute(name = "yPos")
- protected Float yPos;
- @XmlAttribute(name = "zPos")
- protected Float zPos;
-
- /**
- * Gets the value of the xPos property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getXPos() {
- return xPos;
- }
-
- /**
- * Sets the value of the xPos property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setXPos(Float value) {
- this.xPos = value;
- }
-
- /**
- * Gets the value of the yPos property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getYPos() {
- return yPos;
- }
-
- /**
- * Sets the value of the yPos property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setYPos(Float value) {
- this.yPos = value;
- }
-
- /**
- * Gets the value of the zPos property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getZPos() {
- return zPos;
- }
-
- /**
- * Sets the value of the zPos property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setZPos(Float value) {
- this.zPos = value;
- }
+ /**
+ * Sets the value of the threshold property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setThreshold(Float value)
+ {
+ this.threshold = value;
+ }
- }
+ /**
+ * Gets the value of the showBootstrap property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowBootstrap()
+ {
+ return showBootstrap;
+ }
+ /**
+ * Sets the value of the showBootstrap property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowBootstrap(Boolean value)
+ {
+ this.showBootstrap = value;
+ }
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attGroup ref="{www.jalview.org}position"/&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class SeqPointMin {
-
- @XmlAttribute(name = "xPos")
- protected Float xPos;
- @XmlAttribute(name = "yPos")
- protected Float yPos;
- @XmlAttribute(name = "zPos")
- protected Float zPos;
-
- /**
- * Gets the value of the xPos property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getXPos() {
- return xPos;
- }
-
- /**
- * Sets the value of the xPos property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setXPos(Float value) {
- this.xPos = value;
- }
-
- /**
- * Gets the value of the yPos property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getYPos() {
- return yPos;
- }
-
- /**
- * Sets the value of the yPos property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setYPos(Float value) {
- this.yPos = value;
- }
-
- /**
- * Gets the value of the zPos property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getZPos() {
- return zPos;
- }
-
- /**
- * Sets the value of the zPos property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setZPos(Float value) {
- this.zPos = value;
- }
+ /**
+ * Gets the value of the showDistances property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowDistances()
+ {
+ return showDistances;
+ }
- }
+ /**
+ * Sets the value of the showDistances property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowDistances(Boolean value)
+ {
+ this.showDistances = value;
+ }
+ /**
+ * Gets the value of the markUnlinked property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isMarkUnlinked()
+ {
+ return markUnlinked;
+ }
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attGroup ref="{www.jalview.org}position"/&gt;
- * &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class SequencePoint {
-
- @XmlAttribute(name = "sequenceRef")
- protected String sequenceRef;
- @XmlAttribute(name = "xPos")
- protected Float xPos;
- @XmlAttribute(name = "yPos")
- protected Float yPos;
- @XmlAttribute(name = "zPos")
- protected Float zPos;
-
- /**
- * Gets the value of the sequenceRef property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getSequenceRef() {
- return sequenceRef;
- }
-
- /**
- * Sets the value of the sequenceRef property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setSequenceRef(String value) {
- this.sequenceRef = value;
- }
-
- /**
- * Gets the value of the xPos property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getXPos() {
- return xPos;
- }
-
- /**
- * Sets the value of the xPos property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setXPos(Float value) {
- this.xPos = value;
- }
-
- /**
- * Gets the value of the yPos property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getYPos() {
- return yPos;
- }
-
- /**
- * Sets the value of the yPos property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setYPos(Float value) {
- this.yPos = value;
- }
-
- /**
- * Gets the value of the zPos property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getZPos() {
- return zPos;
- }
-
- /**
- * Sets the value of the zPos property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setZPos(Float value) {
- this.zPos = value;
- }
+ /**
+ * Sets the value of the markUnlinked property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setMarkUnlinked(Boolean value)
+ {
+ this.markUnlinked = value;
+ }
- }
+ /**
+ * Gets the value of the fitToWindow property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isFitToWindow()
+ {
+ return fitToWindow;
+ }
+ /**
+ * Sets the value of the fitToWindow property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setFitToWindow(Boolean value)
+ {
+ this.fitToWindow = value;
}
+ /**
+ * Gets the value of the currentTree property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isCurrentTree()
+ {
+ return currentTree;
+ }
/**
- * <p>Java class for anonymous complex type.
+ * Sets the value of the currentTree property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
*
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence minOccurs="0"&gt;
- * &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
- * &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
- * &lt;/sequence&gt;
- * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
- * &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
- * &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ */
+ public void setCurrentTree(Boolean value)
+ {
+ this.currentTree = value;
+ }
+
+ /**
+ * Gets the value of the id property.
*
+ * @return possible object is {@link String }
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "title",
- "newick"
- })
- public static class Tree {
+ public String getId()
+ {
+ return id;
+ }
- @XmlElement(namespace = "www.jalview.org")
- protected String title;
- @XmlElement(namespace = "www.jalview.org")
- protected String newick;
- @XmlAttribute(name = "fontName")
- protected String fontName;
- @XmlAttribute(name = "fontSize")
- protected Integer fontSize;
- @XmlAttribute(name = "fontStyle")
- protected Integer fontStyle;
- @XmlAttribute(name = "threshold")
- protected Float threshold;
- @XmlAttribute(name = "showBootstrap")
- protected Boolean showBootstrap;
- @XmlAttribute(name = "showDistances")
- protected Boolean showDistances;
- @XmlAttribute(name = "markUnlinked")
- protected Boolean markUnlinked;
- @XmlAttribute(name = "fitToWindow")
- protected Boolean fitToWindow;
- @XmlAttribute(name = "currentTree")
- protected Boolean currentTree;
- @XmlAttribute(name = "id")
- @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
- @XmlID
- @XmlSchemaType(name = "ID")
- protected String id;
- @XmlAttribute(name = "linkToAllViews")
- protected Boolean linkToAllViews;
- @XmlAttribute(name = "width")
- protected Integer width;
- @XmlAttribute(name = "height")
- protected Integer height;
- @XmlAttribute(name = "xpos")
- protected Integer xpos;
- @XmlAttribute(name = "ypos")
- protected Integer ypos;
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setId(String value)
+ {
+ this.id = value;
+ }
- /**
- * Gets the value of the title property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getTitle() {
- return title;
- }
+ /**
+ * Gets the value of the linkToAllViews property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isLinkToAllViews()
+ {
+ if (linkToAllViews == null)
+ {
+ return false;
+ }
+ else
+ {
+ return linkToAllViews;
+ }
+ }
- /**
- * Sets the value of the title property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setTitle(String value) {
- this.title = value;
- }
+ /**
+ * Sets the value of the linkToAllViews property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setLinkToAllViews(Boolean value)
+ {
+ this.linkToAllViews = value;
+ }
- /**
- * Gets the value of the newick property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getNewick() {
- return newick;
- }
+ /**
+ * Gets the value of the width property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getWidth()
+ {
+ return width;
+ }
- /**
- * Sets the value of the newick property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setNewick(String value) {
- this.newick = value;
- }
+ /**
+ * Sets the value of the width property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setWidth(Integer value)
+ {
+ this.width = value;
+ }
- /**
- * Gets the value of the fontName property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getFontName() {
- return fontName;
- }
+ /**
+ * Gets the value of the height property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getHeight()
+ {
+ return height;
+ }
- /**
- * Sets the value of the fontName property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setFontName(String value) {
- this.fontName = value;
- }
+ /**
+ * Sets the value of the height property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setHeight(Integer value)
+ {
+ this.height = value;
+ }
- /**
- * Gets the value of the fontSize property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getFontSize() {
- return fontSize;
- }
+ /**
+ * Gets the value of the xpos property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getXpos()
+ {
+ return xpos;
+ }
- /**
- * Sets the value of the fontSize property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setFontSize(Integer value) {
- this.fontSize = value;
- }
+ /**
+ * Sets the value of the xpos property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setXpos(Integer value)
+ {
+ this.xpos = value;
+ }
- /**
- * Gets the value of the fontStyle property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getFontStyle() {
- return fontStyle;
- }
+ /**
+ * Gets the value of the ypos property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getYpos()
+ {
+ return ypos;
+ }
- /**
- * Sets the value of the fontStyle property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setFontStyle(Integer value) {
- this.fontStyle = value;
- }
+ /**
+ * Sets the value of the ypos property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setYpos(Integer value)
+ {
+ this.ypos = value;
+ }
- /**
- * Gets the value of the threshold property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getThreshold() {
- return threshold;
- }
+ }
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
+ *
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="UserColourScheme"
+ * type="{www.jalview.org/colours}JalviewUserColours"/&gt;
+ * &lt;/sequence&gt; &lt;attribute name="id"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "userColourScheme" })
+ public static class UserColours
+ {
+
+ @XmlElement(
+ name = "UserColourScheme",
+ namespace = "www.jalview.org",
+ required = true)
+ protected JalviewUserColours userColourScheme;
+
+ @XmlAttribute(name = "id")
+ protected String id;
- /**
- * Sets the value of the threshold property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setThreshold(Float value) {
- this.threshold = value;
- }
+ /**
+ * Gets the value of the userColourScheme property.
+ *
+ * @return possible object is {@link JalviewUserColours }
+ *
+ */
+ public JalviewUserColours getUserColourScheme()
+ {
+ return userColourScheme;
+ }
- /**
- * Gets the value of the showBootstrap property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowBootstrap() {
- return showBootstrap;
- }
+ /**
+ * Sets the value of the userColourScheme property.
+ *
+ * @param value
+ * allowed object is {@link JalviewUserColours }
+ *
+ */
+ public void setUserColourScheme(JalviewUserColours value)
+ {
+ this.userColourScheme = value;
+ }
- /**
- * Sets the value of the showBootstrap property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowBootstrap(Boolean value) {
- this.showBootstrap = value;
- }
+ /**
+ * Gets the value of the id property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getId()
+ {
+ return id;
+ }
- /**
- * Gets the value of the showDistances property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowDistances() {
- return showDistances;
- }
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setId(String value)
+ {
+ this.id = value;
+ }
- /**
- * Sets the value of the showDistances property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowDistances(Boolean value) {
- this.showDistances = value;
- }
+ }
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
+ *
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="AnnotationColours"
+ * type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
+ * &lt;element name="hiddenColumns" maxOccurs="unbounded"
+ * minOccurs="0"&gt; &lt;complexType&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
+ * name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int"
+ * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt; &lt;element
+ * name="calcIdParam" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;extension
+ * base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&gt;
+ * &lt;attribute name="calcId" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean"
+ * default="false" /&gt; &lt;attribute name="autoUpdate"
+ * use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/extension&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt;
+ * &lt;/sequence&gt; &lt;attGroup
+ * ref="{www.jalview.org}swingwindow"/&gt; &lt;attribute
+ * name="conservationSelected"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="pidSelected"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="bgColour"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="pidThreshold"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="showFullId"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="rightAlignIds"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="showText"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="showColourText"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="showUnconserved"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="showBoxes"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="wrapAlignment"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="renderGaps"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="showSequenceFeatures"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="showNPfeatureTooltip"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="showDbRefTooltip"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="followHighlight"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="followSelection"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="showAnnotation"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="centreColumnLabels"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="showGroupConservation"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="showGroupConsensus"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="showConsensusHistogram"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="showSequenceLogo"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="normaliseSequenceLogo"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="ignoreGapsinConsensus"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="startRes"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="fontName"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="fontStyle"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean"
+ * default="true" /&gt; &lt;attribute name="viewName"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string"
+ * /&gt; &lt;attribute name="gatheredViews"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="textCol1"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="textColThreshold"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
+ * &lt;attribute name="complementId"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="showComplementFeatures"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="showComplementFeaturesOnTop"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(
+ name = "",
+ propOrder =
+ { "annotationColours", "hiddenColumns", "calcIdParam" })
+ public static class Viewport
+ {
+
+ @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
+ protected AnnotationColourScheme annotationColours;
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<JalviewModel.Viewport.HiddenColumns> hiddenColumns;
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<JalviewModel.Viewport.CalcIdParam> calcIdParam;
+
+ @XmlAttribute(name = "conservationSelected")
+ protected Boolean conservationSelected;
+
+ @XmlAttribute(name = "pidSelected")
+ protected Boolean pidSelected;
+
+ @XmlAttribute(name = "bgColour")
+ protected String bgColour;
+
+ @XmlAttribute(name = "consThreshold")
+ protected Integer consThreshold;
+
+ @XmlAttribute(name = "pidThreshold")
+ protected Integer pidThreshold;
+
+ @XmlAttribute(name = "title")
+ protected String title;
+
+ @XmlAttribute(name = "showFullId")
+ protected Boolean showFullId;
+
+ @XmlAttribute(name = "rightAlignIds")
+ protected Boolean rightAlignIds;
+
+ @XmlAttribute(name = "showText")
+ protected Boolean showText;
+
+ @XmlAttribute(name = "showColourText")
+ protected Boolean showColourText;
+
+ @XmlAttribute(name = "showUnconserved")
+ protected Boolean showUnconserved;
+
+ @XmlAttribute(name = "showBoxes")
+ protected Boolean showBoxes;
+
+ @XmlAttribute(name = "wrapAlignment")
+ protected Boolean wrapAlignment;
+
+ @XmlAttribute(name = "renderGaps")
+ protected Boolean renderGaps;
- /**
- * Gets the value of the markUnlinked property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isMarkUnlinked() {
- return markUnlinked;
- }
+ @XmlAttribute(name = "showSequenceFeatures")
+ protected Boolean showSequenceFeatures;
- /**
- * Sets the value of the markUnlinked property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setMarkUnlinked(Boolean value) {
- this.markUnlinked = value;
- }
+ @XmlAttribute(name = "showNPfeatureTooltip")
+ protected Boolean showNPfeatureTooltip;
- /**
- * Gets the value of the fitToWindow property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isFitToWindow() {
- return fitToWindow;
- }
+ @XmlAttribute(name = "showDbRefTooltip")
+ protected Boolean showDbRefTooltip;
- /**
- * Sets the value of the fitToWindow property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setFitToWindow(Boolean value) {
- this.fitToWindow = value;
- }
+ @XmlAttribute(name = "followHighlight")
+ protected Boolean followHighlight;
- /**
- * Gets the value of the currentTree property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isCurrentTree() {
- return currentTree;
- }
+ @XmlAttribute(name = "followSelection")
+ protected Boolean followSelection;
- /**
- * Sets the value of the currentTree property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setCurrentTree(Boolean value) {
- this.currentTree = value;
- }
+ @XmlAttribute(name = "showAnnotation")
+ protected Boolean showAnnotation;
- /**
- * Gets the value of the id property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getId() {
- return id;
- }
+ @XmlAttribute(name = "centreColumnLabels")
+ protected Boolean centreColumnLabels;
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setId(String value) {
- this.id = value;
- }
+ @XmlAttribute(name = "showGroupConservation")
+ protected Boolean showGroupConservation;
- /**
- * Gets the value of the linkToAllViews property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isLinkToAllViews() {
- if (linkToAllViews == null) {
- return false;
- } else {
- return linkToAllViews;
- }
- }
+ @XmlAttribute(name = "showGroupConsensus")
+ protected Boolean showGroupConsensus;
- /**
- * Sets the value of the linkToAllViews property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setLinkToAllViews(Boolean value) {
- this.linkToAllViews = value;
- }
+ @XmlAttribute(name = "showConsensusHistogram")
+ protected Boolean showConsensusHistogram;
- /**
- * Gets the value of the width property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getWidth() {
- return width;
- }
+ @XmlAttribute(name = "showSequenceLogo")
+ protected Boolean showSequenceLogo;
- /**
- * Sets the value of the width property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setWidth(Integer value) {
- this.width = value;
- }
+ @XmlAttribute(name = "normaliseSequenceLogo")
+ protected Boolean normaliseSequenceLogo;
- /**
- * Gets the value of the height property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getHeight() {
- return height;
- }
+ @XmlAttribute(name = "ignoreGapsinConsensus")
+ protected Boolean ignoreGapsinConsensus;
- /**
- * Sets the value of the height property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setHeight(Integer value) {
- this.height = value;
- }
+ @XmlAttribute(name = "startRes")
+ protected Integer startRes;
- /**
- * Gets the value of the xpos property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getXpos() {
- return xpos;
- }
+ @XmlAttribute(name = "startSeq")
+ protected Integer startSeq;
- /**
- * Sets the value of the xpos property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setXpos(Integer value) {
- this.xpos = value;
- }
+ @XmlAttribute(name = "fontName")
+ protected String fontName;
- /**
- * Gets the value of the ypos property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getYpos() {
- return ypos;
- }
+ @XmlAttribute(name = "fontSize")
+ protected Integer fontSize;
- /**
- * Sets the value of the ypos property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setYpos(Integer value) {
- this.ypos = value;
- }
+ @XmlAttribute(name = "fontStyle")
+ protected Integer fontStyle;
- }
+ @XmlAttribute(name = "scaleProteinAsCdna")
+ protected Boolean scaleProteinAsCdna;
+ @XmlAttribute(name = "viewName")
+ protected String viewName;
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "userColourScheme"
- })
- public static class UserColours {
+ @XmlAttribute(name = "sequenceSetId")
+ protected String sequenceSetId;
- @XmlElement(name = "UserColourScheme", namespace = "www.jalview.org", required = true)
- protected JalviewUserColours userColourScheme;
- @XmlAttribute(name = "id")
- protected String id;
+ @XmlAttribute(name = "gatheredViews")
+ protected Boolean gatheredViews;
- /**
- * Gets the value of the userColourScheme property.
- *
- * @return
- * possible object is
- * {@link JalviewUserColours }
- *
- */
- public JalviewUserColours getUserColourScheme() {
- return userColourScheme;
- }
+ @XmlAttribute(name = "textCol1")
+ protected Integer textCol1;
- /**
- * Sets the value of the userColourScheme property.
- *
- * @param value
- * allowed object is
- * {@link JalviewUserColours }
- *
- */
- public void setUserColourScheme(JalviewUserColours value) {
- this.userColourScheme = value;
- }
+ @XmlAttribute(name = "textCol2")
+ protected Integer textCol2;
- /**
- * Gets the value of the id property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getId() {
- return id;
- }
+ @XmlAttribute(name = "textColThreshold")
+ protected Integer textColThreshold;
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setId(String value) {
- this.id = value;
- }
+ @XmlAttribute(name = "id")
+ @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
+ @XmlID
+ @XmlSchemaType(name = "ID")
+ protected String id;
- }
+ @XmlAttribute(name = "complementId")
+ protected String complementId;
+ @XmlAttribute(name = "showComplementFeatures")
+ protected Boolean showComplementFeatures;
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
- * &lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&gt;
- * &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/extension&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;/sequence&gt;
- * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
- * &lt;attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
- * &lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "annotationColours",
- "hiddenColumns",
- "calcIdParam"
- })
- public static class Viewport {
-
- @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
- protected AnnotationColourScheme annotationColours;
- @XmlElement(namespace = "www.jalview.org")
- protected List<JalviewModel.Viewport.HiddenColumns> hiddenColumns;
- @XmlElement(namespace = "www.jalview.org")
- protected List<JalviewModel.Viewport.CalcIdParam> calcIdParam;
- @XmlAttribute(name = "conservationSelected")
- protected Boolean conservationSelected;
- @XmlAttribute(name = "pidSelected")
- protected Boolean pidSelected;
- @XmlAttribute(name = "bgColour")
- protected String bgColour;
- @XmlAttribute(name = "consThreshold")
- protected Integer consThreshold;
- @XmlAttribute(name = "pidThreshold")
- protected Integer pidThreshold;
- @XmlAttribute(name = "title")
- protected String title;
- @XmlAttribute(name = "showFullId")
- protected Boolean showFullId;
- @XmlAttribute(name = "rightAlignIds")
- protected Boolean rightAlignIds;
- @XmlAttribute(name = "showText")
- protected Boolean showText;
- @XmlAttribute(name = "showColourText")
- protected Boolean showColourText;
- @XmlAttribute(name = "showUnconserved")
- protected Boolean showUnconserved;
- @XmlAttribute(name = "showBoxes")
- protected Boolean showBoxes;
- @XmlAttribute(name = "wrapAlignment")
- protected Boolean wrapAlignment;
- @XmlAttribute(name = "renderGaps")
- protected Boolean renderGaps;
- @XmlAttribute(name = "showSequenceFeatures")
- protected Boolean showSequenceFeatures;
- @XmlAttribute(name = "showNPfeatureTooltip")
- protected Boolean showNPfeatureTooltip;
- @XmlAttribute(name = "showDbRefTooltip")
- protected Boolean showDbRefTooltip;
- @XmlAttribute(name = "followHighlight")
- protected Boolean followHighlight;
- @XmlAttribute(name = "followSelection")
- protected Boolean followSelection;
- @XmlAttribute(name = "showAnnotation")
- protected Boolean showAnnotation;
- @XmlAttribute(name = "centreColumnLabels")
- protected Boolean centreColumnLabels;
- @XmlAttribute(name = "showGroupConservation")
- protected Boolean showGroupConservation;
- @XmlAttribute(name = "showGroupConsensus")
- protected Boolean showGroupConsensus;
- @XmlAttribute(name = "showConsensusHistogram")
- protected Boolean showConsensusHistogram;
- @XmlAttribute(name = "showSequenceLogo")
- protected Boolean showSequenceLogo;
- @XmlAttribute(name = "normaliseSequenceLogo")
- protected Boolean normaliseSequenceLogo;
- @XmlAttribute(name = "ignoreGapsinConsensus")
- protected Boolean ignoreGapsinConsensus;
- @XmlAttribute(name = "startRes")
- protected Integer startRes;
- @XmlAttribute(name = "startSeq")
- protected Integer startSeq;
- @XmlAttribute(name = "fontName")
- protected String fontName;
- @XmlAttribute(name = "fontSize")
- protected Integer fontSize;
- @XmlAttribute(name = "fontStyle")
- protected Integer fontStyle;
- @XmlAttribute(name = "scaleProteinAsCdna")
- protected Boolean scaleProteinAsCdna;
- @XmlAttribute(name = "viewName")
- protected String viewName;
- @XmlAttribute(name = "sequenceSetId")
- protected String sequenceSetId;
- @XmlAttribute(name = "gatheredViews")
- protected Boolean gatheredViews;
- @XmlAttribute(name = "textCol1")
- protected Integer textCol1;
- @XmlAttribute(name = "textCol2")
- protected Integer textCol2;
- @XmlAttribute(name = "textColThreshold")
- protected Integer textColThreshold;
- @XmlAttribute(name = "id")
- @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
- @XmlID
- @XmlSchemaType(name = "ID")
- protected String id;
- @XmlAttribute(name = "complementId")
- protected String complementId;
- @XmlAttribute(name = "showComplementFeatures")
- protected Boolean showComplementFeatures;
- @XmlAttribute(name = "showComplementFeaturesOnTop")
- protected Boolean showComplementFeaturesOnTop;
- @XmlAttribute(name = "width")
- protected Integer width;
- @XmlAttribute(name = "height")
- protected Integer height;
- @XmlAttribute(name = "xpos")
- protected Integer xpos;
- @XmlAttribute(name = "ypos")
- protected Integer ypos;
+ @XmlAttribute(name = "showComplementFeaturesOnTop")
+ protected Boolean showComplementFeaturesOnTop;
- /**
- * Gets the value of the annotationColours property.
- *
- * @return
- * possible object is
- * {@link AnnotationColourScheme }
- *
- */
- public AnnotationColourScheme getAnnotationColours() {
- return annotationColours;
- }
+ @XmlAttribute(name = "width")
+ protected Integer width;
- /**
- * Sets the value of the annotationColours property.
- *
- * @param value
- * allowed object is
- * {@link AnnotationColourScheme }
- *
- */
- public void setAnnotationColours(AnnotationColourScheme value) {
- this.annotationColours = value;
- }
+ @XmlAttribute(name = "height")
+ protected Integer height;
- /**
- * Gets the value of the hiddenColumns property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the hiddenColumns property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getHiddenColumns().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.Viewport.HiddenColumns }
- *
- *
- */
- public List<JalviewModel.Viewport.HiddenColumns> getHiddenColumns() {
- if (hiddenColumns == null) {
- hiddenColumns = new ArrayList<JalviewModel.Viewport.HiddenColumns>();
- }
- return this.hiddenColumns;
- }
+ @XmlAttribute(name = "xpos")
+ protected Integer xpos;
- /**
- * Gets the value of the calcIdParam property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the calcIdParam property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getCalcIdParam().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.Viewport.CalcIdParam }
- *
- *
- */
- public List<JalviewModel.Viewport.CalcIdParam> getCalcIdParam() {
- if (calcIdParam == null) {
- calcIdParam = new ArrayList<JalviewModel.Viewport.CalcIdParam>();
- }
- return this.calcIdParam;
- }
+ @XmlAttribute(name = "ypos")
+ protected Integer ypos;
- /**
- * Gets the value of the conservationSelected property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isConservationSelected() {
- return conservationSelected;
- }
+ /**
+ * Gets the value of the annotationColours property.
+ *
+ * @return possible object is {@link AnnotationColourScheme }
+ *
+ */
+ public AnnotationColourScheme getAnnotationColours()
+ {
+ return annotationColours;
+ }
- /**
- * Sets the value of the conservationSelected property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setConservationSelected(Boolean value) {
- this.conservationSelected = value;
- }
+ /**
+ * Sets the value of the annotationColours property.
+ *
+ * @param value
+ * allowed object is {@link AnnotationColourScheme }
+ *
+ */
+ public void setAnnotationColours(AnnotationColourScheme value)
+ {
+ this.annotationColours = value;
+ }
- /**
- * Gets the value of the pidSelected property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isPidSelected() {
- return pidSelected;
- }
+ /**
+ * Gets the value of the hiddenColumns property.
+ *
+ * <p> This accessor method returns a reference to the live list, not
+ * a snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the hiddenColumns property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getHiddenColumns().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.Viewport.HiddenColumns }
+ *
+ *
+ */
+ public List<JalviewModel.Viewport.HiddenColumns> getHiddenColumns()
+ {
+ if (hiddenColumns == null)
+ {
+ hiddenColumns = new ArrayList<JalviewModel.Viewport.HiddenColumns>();
+ }
+ return this.hiddenColumns;
+ }
- /**
- * Sets the value of the pidSelected property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setPidSelected(Boolean value) {
- this.pidSelected = value;
- }
+ /**
+ * Gets the value of the calcIdParam property.
+ *
+ * <p> This accessor method returns a reference to the live list, not
+ * a snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the calcIdParam property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getCalcIdParam().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.Viewport.CalcIdParam }
+ *
+ *
+ */
+ public List<JalviewModel.Viewport.CalcIdParam> getCalcIdParam()
+ {
+ if (calcIdParam == null)
+ {
+ calcIdParam = new ArrayList<JalviewModel.Viewport.CalcIdParam>();
+ }
+ return this.calcIdParam;
+ }
- /**
- * Gets the value of the bgColour property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getBgColour() {
- return bgColour;
- }
+ /**
+ * Gets the value of the conservationSelected property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isConservationSelected()
+ {
+ return conservationSelected;
+ }
- /**
- * Sets the value of the bgColour property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setBgColour(String value) {
- this.bgColour = value;
- }
+ /**
+ * Sets the value of the conservationSelected property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setConservationSelected(Boolean value)
+ {
+ this.conservationSelected = value;
+ }
- /**
- * Gets the value of the consThreshold property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getConsThreshold() {
- return consThreshold;
- }
+ /**
+ * Gets the value of the pidSelected property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isPidSelected()
+ {
+ return pidSelected;
+ }
- /**
- * Sets the value of the consThreshold property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setConsThreshold(Integer value) {
- this.consThreshold = value;
- }
+ /**
+ * Sets the value of the pidSelected property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setPidSelected(Boolean value)
+ {
+ this.pidSelected = value;
+ }
- /**
- * Gets the value of the pidThreshold property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getPidThreshold() {
- return pidThreshold;
- }
+ /**
+ * Gets the value of the bgColour property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getBgColour()
+ {
+ return bgColour;
+ }
- /**
- * Sets the value of the pidThreshold property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setPidThreshold(Integer value) {
- this.pidThreshold = value;
- }
+ /**
+ * Sets the value of the bgColour property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setBgColour(String value)
+ {
+ this.bgColour = value;
+ }
- /**
- * Gets the value of the title property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getTitle() {
- return title;
- }
+ /**
+ * Gets the value of the consThreshold property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getConsThreshold()
+ {
+ return consThreshold;
+ }
- /**
- * Sets the value of the title property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setTitle(String value) {
- this.title = value;
- }
+ /**
+ * Sets the value of the consThreshold property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setConsThreshold(Integer value)
+ {
+ this.consThreshold = value;
+ }
- /**
- * Gets the value of the showFullId property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowFullId() {
- return showFullId;
- }
+ /**
+ * Gets the value of the pidThreshold property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getPidThreshold()
+ {
+ return pidThreshold;
+ }
- /**
- * Sets the value of the showFullId property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowFullId(Boolean value) {
- this.showFullId = value;
- }
+ /**
+ * Sets the value of the pidThreshold property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setPidThreshold(Integer value)
+ {
+ this.pidThreshold = value;
+ }
- /**
- * Gets the value of the rightAlignIds property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isRightAlignIds() {
- return rightAlignIds;
- }
+ /**
+ * Gets the value of the title property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getTitle()
+ {
+ return title;
+ }
- /**
- * Sets the value of the rightAlignIds property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setRightAlignIds(Boolean value) {
- this.rightAlignIds = value;
- }
+ /**
+ * Sets the value of the title property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setTitle(String value)
+ {
+ this.title = value;
+ }
- /**
- * Gets the value of the showText property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowText() {
- return showText;
- }
+ /**
+ * Gets the value of the showFullId property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowFullId()
+ {
+ return showFullId;
+ }
- /**
- * Sets the value of the showText property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowText(Boolean value) {
- this.showText = value;
- }
+ /**
+ * Sets the value of the showFullId property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowFullId(Boolean value)
+ {
+ this.showFullId = value;
+ }
- /**
- * Gets the value of the showColourText property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowColourText() {
- return showColourText;
- }
+ /**
+ * Gets the value of the rightAlignIds property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isRightAlignIds()
+ {
+ return rightAlignIds;
+ }
- /**
- * Sets the value of the showColourText property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowColourText(Boolean value) {
- this.showColourText = value;
- }
+ /**
+ * Sets the value of the rightAlignIds property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setRightAlignIds(Boolean value)
+ {
+ this.rightAlignIds = value;
+ }
- /**
- * Gets the value of the showUnconserved property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isShowUnconserved() {
- if (showUnconserved == null) {
- return false;
- } else {
- return showUnconserved;
- }
- }
+ /**
+ * Gets the value of the showText property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowText()
+ {
+ return showText;
+ }
- /**
- * Sets the value of the showUnconserved property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowUnconserved(Boolean value) {
- this.showUnconserved = value;
- }
+ /**
+ * Sets the value of the showText property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowText(Boolean value)
+ {
+ this.showText = value;
+ }
- /**
- * Gets the value of the showBoxes property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowBoxes() {
- return showBoxes;
- }
+ /**
+ * Gets the value of the showColourText property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowColourText()
+ {
+ return showColourText;
+ }
- /**
- * Sets the value of the showBoxes property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowBoxes(Boolean value) {
- this.showBoxes = value;
- }
+ /**
+ * Sets the value of the showColourText property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowColourText(Boolean value)
+ {
+ this.showColourText = value;
+ }
- /**
- * Gets the value of the wrapAlignment property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isWrapAlignment() {
- return wrapAlignment;
- }
+ /**
+ * Gets the value of the showUnconserved property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isShowUnconserved()
+ {
+ if (showUnconserved == null)
+ {
+ return false;
+ }
+ else
+ {
+ return showUnconserved;
+ }
+ }
- /**
- * Sets the value of the wrapAlignment property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setWrapAlignment(Boolean value) {
- this.wrapAlignment = value;
- }
+ /**
+ * Sets the value of the showUnconserved property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowUnconserved(Boolean value)
+ {
+ this.showUnconserved = value;
+ }
- /**
- * Gets the value of the renderGaps property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isRenderGaps() {
- return renderGaps;
- }
+ /**
+ * Gets the value of the showBoxes property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowBoxes()
+ {
+ return showBoxes;
+ }
- /**
- * Sets the value of the renderGaps property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setRenderGaps(Boolean value) {
- this.renderGaps = value;
- }
+ /**
+ * Sets the value of the showBoxes property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowBoxes(Boolean value)
+ {
+ this.showBoxes = value;
+ }
- /**
- * Gets the value of the showSequenceFeatures property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowSequenceFeatures() {
- return showSequenceFeatures;
- }
+ /**
+ * Gets the value of the wrapAlignment property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isWrapAlignment()
+ {
+ return wrapAlignment;
+ }
- /**
- * Sets the value of the showSequenceFeatures property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowSequenceFeatures(Boolean value) {
- this.showSequenceFeatures = value;
- }
+ /**
+ * Sets the value of the wrapAlignment property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setWrapAlignment(Boolean value)
+ {
+ this.wrapAlignment = value;
+ }
- /**
- * Gets the value of the showNPfeatureTooltip property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowNPfeatureTooltip() {
- return showNPfeatureTooltip;
- }
+ /**
+ * Gets the value of the renderGaps property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isRenderGaps()
+ {
+ return renderGaps;
+ }
- /**
- * Sets the value of the showNPfeatureTooltip property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowNPfeatureTooltip(Boolean value) {
- this.showNPfeatureTooltip = value;
- }
+ /**
+ * Sets the value of the renderGaps property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setRenderGaps(Boolean value)
+ {
+ this.renderGaps = value;
+ }
- /**
- * Gets the value of the showDbRefTooltip property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowDbRefTooltip() {
- return showDbRefTooltip;
- }
+ /**
+ * Gets the value of the showSequenceFeatures property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowSequenceFeatures()
+ {
+ return showSequenceFeatures;
+ }
- /**
- * Sets the value of the showDbRefTooltip property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowDbRefTooltip(Boolean value) {
- this.showDbRefTooltip = value;
- }
+ /**
+ * Sets the value of the showSequenceFeatures property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowSequenceFeatures(Boolean value)
+ {
+ this.showSequenceFeatures = value;
+ }
- /**
- * Gets the value of the followHighlight property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isFollowHighlight() {
- if (followHighlight == null) {
- return true;
- } else {
- return followHighlight;
- }
- }
+ /**
+ * Gets the value of the showNPfeatureTooltip property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowNPfeatureTooltip()
+ {
+ return showNPfeatureTooltip;
+ }
- /**
- * Sets the value of the followHighlight property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setFollowHighlight(Boolean value) {
- this.followHighlight = value;
- }
+ /**
+ * Sets the value of the showNPfeatureTooltip property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowNPfeatureTooltip(Boolean value)
+ {
+ this.showNPfeatureTooltip = value;
+ }
- /**
- * Gets the value of the followSelection property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isFollowSelection() {
- if (followSelection == null) {
- return true;
- } else {
- return followSelection;
- }
- }
+ /**
+ * Gets the value of the showDbRefTooltip property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowDbRefTooltip()
+ {
+ return showDbRefTooltip;
+ }
- /**
- * Sets the value of the followSelection property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setFollowSelection(Boolean value) {
- this.followSelection = value;
- }
+ /**
+ * Sets the value of the showDbRefTooltip property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowDbRefTooltip(Boolean value)
+ {
+ this.showDbRefTooltip = value;
+ }
- /**
- * Gets the value of the showAnnotation property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowAnnotation() {
- return showAnnotation;
- }
+ /**
+ * Gets the value of the followHighlight property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isFollowHighlight()
+ {
+ if (followHighlight == null)
+ {
+ return true;
+ }
+ else
+ {
+ return followHighlight;
+ }
+ }
- /**
- * Sets the value of the showAnnotation property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowAnnotation(Boolean value) {
- this.showAnnotation = value;
- }
+ /**
+ * Sets the value of the followHighlight property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setFollowHighlight(Boolean value)
+ {
+ this.followHighlight = value;
+ }
- /**
- * Gets the value of the centreColumnLabels property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isCentreColumnLabels() {
- if (centreColumnLabels == null) {
- return false;
- } else {
- return centreColumnLabels;
- }
- }
+ /**
+ * Gets the value of the followSelection property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isFollowSelection()
+ {
+ if (followSelection == null)
+ {
+ return true;
+ }
+ else
+ {
+ return followSelection;
+ }
+ }
- /**
- * Sets the value of the centreColumnLabels property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setCentreColumnLabels(Boolean value) {
- this.centreColumnLabels = value;
- }
+ /**
+ * Sets the value of the followSelection property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setFollowSelection(Boolean value)
+ {
+ this.followSelection = value;
+ }
- /**
- * Gets the value of the showGroupConservation property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isShowGroupConservation() {
- if (showGroupConservation == null) {
- return false;
- } else {
- return showGroupConservation;
- }
- }
+ /**
+ * Gets the value of the showAnnotation property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowAnnotation()
+ {
+ return showAnnotation;
+ }
- /**
- * Sets the value of the showGroupConservation property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowGroupConservation(Boolean value) {
- this.showGroupConservation = value;
- }
+ /**
+ * Sets the value of the showAnnotation property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowAnnotation(Boolean value)
+ {
+ this.showAnnotation = value;
+ }
- /**
- * Gets the value of the showGroupConsensus property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isShowGroupConsensus() {
- if (showGroupConsensus == null) {
- return false;
- } else {
- return showGroupConsensus;
- }
- }
+ /**
+ * Gets the value of the centreColumnLabels property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isCentreColumnLabels()
+ {
+ if (centreColumnLabels == null)
+ {
+ return false;
+ }
+ else
+ {
+ return centreColumnLabels;
+ }
+ }
- /**
- * Sets the value of the showGroupConsensus property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowGroupConsensus(Boolean value) {
- this.showGroupConsensus = value;
- }
+ /**
+ * Sets the value of the centreColumnLabels property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setCentreColumnLabels(Boolean value)
+ {
+ this.centreColumnLabels = value;
+ }
- /**
- * Gets the value of the showConsensusHistogram property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isShowConsensusHistogram() {
- if (showConsensusHistogram == null) {
- return true;
- } else {
- return showConsensusHistogram;
- }
- }
+ /**
+ * Gets the value of the showGroupConservation property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isShowGroupConservation()
+ {
+ if (showGroupConservation == null)
+ {
+ return false;
+ }
+ else
+ {
+ return showGroupConservation;
+ }
+ }
- /**
- * Sets the value of the showConsensusHistogram property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowConsensusHistogram(Boolean value) {
- this.showConsensusHistogram = value;
- }
+ /**
+ * Sets the value of the showGroupConservation property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowGroupConservation(Boolean value)
+ {
+ this.showGroupConservation = value;
+ }
- /**
- * Gets the value of the showSequenceLogo property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isShowSequenceLogo() {
- if (showSequenceLogo == null) {
- return false;
- } else {
- return showSequenceLogo;
- }
- }
+ /**
+ * Gets the value of the showGroupConsensus property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isShowGroupConsensus()
+ {
+ if (showGroupConsensus == null)
+ {
+ return false;
+ }
+ else
+ {
+ return showGroupConsensus;
+ }
+ }
+
+ /**
+ * Sets the value of the showGroupConsensus property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowGroupConsensus(Boolean value)
+ {
+ this.showGroupConsensus = value;
+ }
- /**
- * Sets the value of the showSequenceLogo property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowSequenceLogo(Boolean value) {
- this.showSequenceLogo = value;
- }
+ /**
+ * Gets the value of the showConsensusHistogram property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isShowConsensusHistogram()
+ {
+ if (showConsensusHistogram == null)
+ {
+ return true;
+ }
+ else
+ {
+ return showConsensusHistogram;
+ }
+ }
- /**
- * Gets the value of the normaliseSequenceLogo property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isNormaliseSequenceLogo() {
- if (normaliseSequenceLogo == null) {
- return false;
- } else {
- return normaliseSequenceLogo;
- }
- }
+ /**
+ * Sets the value of the showConsensusHistogram property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowConsensusHistogram(Boolean value)
+ {
+ this.showConsensusHistogram = value;
+ }
- /**
- * Sets the value of the normaliseSequenceLogo property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setNormaliseSequenceLogo(Boolean value) {
- this.normaliseSequenceLogo = value;
- }
+ /**
+ * Gets the value of the showSequenceLogo property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isShowSequenceLogo()
+ {
+ if (showSequenceLogo == null)
+ {
+ return false;
+ }
+ else
+ {
+ return showSequenceLogo;
+ }
+ }
- /**
- * Gets the value of the ignoreGapsinConsensus property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isIgnoreGapsinConsensus() {
- if (ignoreGapsinConsensus == null) {
- return true;
- } else {
- return ignoreGapsinConsensus;
- }
- }
+ /**
+ * Sets the value of the showSequenceLogo property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowSequenceLogo(Boolean value)
+ {
+ this.showSequenceLogo = value;
+ }
- /**
- * Sets the value of the ignoreGapsinConsensus property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setIgnoreGapsinConsensus(Boolean value) {
- this.ignoreGapsinConsensus = value;
- }
+ /**
+ * Gets the value of the normaliseSequenceLogo property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isNormaliseSequenceLogo()
+ {
+ if (normaliseSequenceLogo == null)
+ {
+ return false;
+ }
+ else
+ {
+ return normaliseSequenceLogo;
+ }
+ }
- /**
- * Gets the value of the startRes property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getStartRes() {
- return startRes;
- }
+ /**
+ * Sets the value of the normaliseSequenceLogo property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setNormaliseSequenceLogo(Boolean value)
+ {
+ this.normaliseSequenceLogo = value;
+ }
- /**
- * Sets the value of the startRes property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setStartRes(Integer value) {
- this.startRes = value;
- }
+ /**
+ * Gets the value of the ignoreGapsinConsensus property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isIgnoreGapsinConsensus()
+ {
+ if (ignoreGapsinConsensus == null)
+ {
+ return true;
+ }
+ else
+ {
+ return ignoreGapsinConsensus;
+ }
+ }
- /**
- * Gets the value of the startSeq property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getStartSeq() {
- return startSeq;
- }
+ /**
+ * Sets the value of the ignoreGapsinConsensus property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setIgnoreGapsinConsensus(Boolean value)
+ {
+ this.ignoreGapsinConsensus = value;
+ }
- /**
- * Sets the value of the startSeq property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setStartSeq(Integer value) {
- this.startSeq = value;
- }
+ /**
+ * Gets the value of the startRes property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getStartRes()
+ {
+ return startRes;
+ }
- /**
- * Gets the value of the fontName property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getFontName() {
- return fontName;
- }
+ /**
+ * Sets the value of the startRes property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setStartRes(Integer value)
+ {
+ this.startRes = value;
+ }
- /**
- * Sets the value of the fontName property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setFontName(String value) {
- this.fontName = value;
- }
+ /**
+ * Gets the value of the startSeq property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getStartSeq()
+ {
+ return startSeq;
+ }
- /**
- * Gets the value of the fontSize property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getFontSize() {
- return fontSize;
- }
+ /**
+ * Sets the value of the startSeq property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setStartSeq(Integer value)
+ {
+ this.startSeq = value;
+ }
- /**
- * Sets the value of the fontSize property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setFontSize(Integer value) {
- this.fontSize = value;
- }
+ /**
+ * Gets the value of the fontName property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getFontName()
+ {
+ return fontName;
+ }
- /**
- * Gets the value of the fontStyle property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getFontStyle() {
- return fontStyle;
- }
+ /**
+ * Sets the value of the fontName property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setFontName(String value)
+ {
+ this.fontName = value;
+ }
- /**
- * Sets the value of the fontStyle property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setFontStyle(Integer value) {
- this.fontStyle = value;
- }
+ /**
+ * Gets the value of the fontSize property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getFontSize()
+ {
+ return fontSize;
+ }
- /**
- * Gets the value of the scaleProteinAsCdna property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isScaleProteinAsCdna() {
- if (scaleProteinAsCdna == null) {
- return true;
- } else {
- return scaleProteinAsCdna;
- }
- }
+ /**
+ * Sets the value of the fontSize property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setFontSize(Integer value)
+ {
+ this.fontSize = value;
+ }
- /**
- * Sets the value of the scaleProteinAsCdna property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setScaleProteinAsCdna(Boolean value) {
- this.scaleProteinAsCdna = value;
- }
+ /**
+ * Gets the value of the fontStyle property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getFontStyle()
+ {
+ return fontStyle;
+ }
- /**
- * Gets the value of the viewName property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getViewName() {
- return viewName;
- }
+ /**
+ * Sets the value of the fontStyle property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setFontStyle(Integer value)
+ {
+ this.fontStyle = value;
+ }
- /**
- * Sets the value of the viewName property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setViewName(String value) {
- this.viewName = value;
- }
+ /**
+ * Gets the value of the scaleProteinAsCdna property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isScaleProteinAsCdna()
+ {
+ if (scaleProteinAsCdna == null)
+ {
+ return true;
+ }
+ else
+ {
+ return scaleProteinAsCdna;
+ }
+ }
- /**
- * Gets the value of the sequenceSetId property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getSequenceSetId() {
- return sequenceSetId;
- }
+ /**
+ * Sets the value of the scaleProteinAsCdna property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setScaleProteinAsCdna(Boolean value)
+ {
+ this.scaleProteinAsCdna = value;
+ }
- /**
- * Sets the value of the sequenceSetId property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setSequenceSetId(String value) {
- this.sequenceSetId = value;
- }
+ /**
+ * Gets the value of the viewName property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getViewName()
+ {
+ return viewName;
+ }
- /**
- * Gets the value of the gatheredViews property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isGatheredViews() {
- return gatheredViews;
- }
+ /**
+ * Sets the value of the viewName property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setViewName(String value)
+ {
+ this.viewName = value;
+ }
- /**
- * Sets the value of the gatheredViews property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setGatheredViews(Boolean value) {
- this.gatheredViews = value;
- }
+ /**
+ * Gets the value of the sequenceSetId property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getSequenceSetId()
+ {
+ return sequenceSetId;
+ }
- /**
- * Gets the value of the textCol1 property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getTextCol1() {
- return textCol1;
- }
+ /**
+ * Sets the value of the sequenceSetId property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setSequenceSetId(String value)
+ {
+ this.sequenceSetId = value;
+ }
- /**
- * Sets the value of the textCol1 property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setTextCol1(Integer value) {
- this.textCol1 = value;
- }
+ /**
+ * Gets the value of the gatheredViews property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isGatheredViews()
+ {
+ return gatheredViews;
+ }
- /**
- * Gets the value of the textCol2 property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getTextCol2() {
- return textCol2;
- }
+ /**
+ * Sets the value of the gatheredViews property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setGatheredViews(Boolean value)
+ {
+ this.gatheredViews = value;
+ }
- /**
- * Sets the value of the textCol2 property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setTextCol2(Integer value) {
- this.textCol2 = value;
- }
+ /**
+ * Gets the value of the textCol1 property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getTextCol1()
+ {
+ return textCol1;
+ }
- /**
- * Gets the value of the textColThreshold property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getTextColThreshold() {
- return textColThreshold;
- }
+ /**
+ * Sets the value of the textCol1 property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setTextCol1(Integer value)
+ {
+ this.textCol1 = value;
+ }
- /**
- * Sets the value of the textColThreshold property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setTextColThreshold(Integer value) {
- this.textColThreshold = value;
- }
+ /**
+ * Gets the value of the textCol2 property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getTextCol2()
+ {
+ return textCol2;
+ }
- /**
- * Gets the value of the id property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getId() {
- return id;
- }
+ /**
+ * Sets the value of the textCol2 property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setTextCol2(Integer value)
+ {
+ this.textCol2 = value;
+ }
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setId(String value) {
- this.id = value;
- }
+ /**
+ * Gets the value of the textColThreshold property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getTextColThreshold()
+ {
+ return textColThreshold;
+ }
- /**
- * Gets the value of the complementId property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getComplementId() {
- return complementId;
- }
+ /**
+ * Sets the value of the textColThreshold property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setTextColThreshold(Integer value)
+ {
+ this.textColThreshold = value;
+ }
- /**
- * Sets the value of the complementId property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setComplementId(String value) {
- this.complementId = value;
- }
+ /**
+ * Gets the value of the id property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getId()
+ {
+ return id;
+ }
- /**
- * Gets the value of the showComplementFeatures property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isShowComplementFeatures() {
- if (showComplementFeatures == null) {
- return false;
- } else {
- return showComplementFeatures;
- }
- }
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setId(String value)
+ {
+ this.id = value;
+ }
- /**
- * Sets the value of the showComplementFeatures property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowComplementFeatures(Boolean value) {
- this.showComplementFeatures = value;
- }
+ /**
+ * Gets the value of the complementId property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getComplementId()
+ {
+ return complementId;
+ }
- /**
- * Gets the value of the showComplementFeaturesOnTop property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isShowComplementFeaturesOnTop() {
- if (showComplementFeaturesOnTop == null) {
- return false;
- } else {
- return showComplementFeaturesOnTop;
- }
- }
+ /**
+ * Sets the value of the complementId property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setComplementId(String value)
+ {
+ this.complementId = value;
+ }
- /**
- * Sets the value of the showComplementFeaturesOnTop property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowComplementFeaturesOnTop(Boolean value) {
- this.showComplementFeaturesOnTop = value;
- }
+ /**
+ * Gets the value of the showComplementFeatures property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isShowComplementFeatures()
+ {
+ if (showComplementFeatures == null)
+ {
+ return false;
+ }
+ else
+ {
+ return showComplementFeatures;
+ }
+ }
- /**
- * Gets the value of the width property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getWidth() {
- return width;
- }
+ /**
+ * Sets the value of the showComplementFeatures property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowComplementFeatures(Boolean value)
+ {
+ this.showComplementFeatures = value;
+ }
- /**
- * Sets the value of the width property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setWidth(Integer value) {
- this.width = value;
- }
+ /**
+ * Gets the value of the showComplementFeaturesOnTop property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isShowComplementFeaturesOnTop()
+ {
+ if (showComplementFeaturesOnTop == null)
+ {
+ return false;
+ }
+ else
+ {
+ return showComplementFeaturesOnTop;
+ }
+ }
- /**
- * Gets the value of the height property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getHeight() {
- return height;
- }
+ /**
+ * Sets the value of the showComplementFeaturesOnTop property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowComplementFeaturesOnTop(Boolean value)
+ {
+ this.showComplementFeaturesOnTop = value;
+ }
- /**
- * Sets the value of the height property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setHeight(Integer value) {
- this.height = value;
- }
+ /**
+ * Gets the value of the width property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getWidth()
+ {
+ return width;
+ }
- /**
- * Gets the value of the xpos property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getXpos() {
- return xpos;
- }
+ /**
+ * Sets the value of the width property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setWidth(Integer value)
+ {
+ this.width = value;
+ }
- /**
- * Sets the value of the xpos property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setXpos(Integer value) {
- this.xpos = value;
- }
+ /**
+ * Gets the value of the height property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getHeight()
+ {
+ return height;
+ }
- /**
- * Gets the value of the ypos property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getYpos() {
- return ypos;
- }
+ /**
+ * Sets the value of the height property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setHeight(Integer value)
+ {
+ this.height = value;
+ }
- /**
- * Sets the value of the ypos property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setYpos(Integer value) {
- this.ypos = value;
- }
+ /**
+ * Gets the value of the xpos property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getXpos()
+ {
+ return xpos;
+ }
+ /**
+ * Sets the value of the xpos property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setXpos(Integer value)
+ {
+ this.xpos = value;
+ }
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&gt;
- * &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/extension&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class CalcIdParam
- extends WebServiceParameterSet
- {
+ /**
+ * Gets the value of the ypos property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getYpos()
+ {
+ return ypos;
+ }
- @XmlAttribute(name = "calcId", required = true)
- protected String calcId;
- @XmlAttribute(name = "needsUpdate")
- protected Boolean needsUpdate;
- @XmlAttribute(name = "autoUpdate", required = true)
- protected boolean autoUpdate;
-
- /**
- * Gets the value of the calcId property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getCalcId() {
- return calcId;
- }
-
- /**
- * Sets the value of the calcId property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setCalcId(String value) {
- this.calcId = value;
- }
-
- /**
- * Gets the value of the needsUpdate property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isNeedsUpdate() {
- if (needsUpdate == null) {
- return false;
- } else {
- return needsUpdate;
- }
- }
-
- /**
- * Sets the value of the needsUpdate property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setNeedsUpdate(Boolean value) {
- this.needsUpdate = value;
- }
-
- /**
- * Gets the value of the autoUpdate property.
- *
- */
- public boolean isAutoUpdate() {
- return autoUpdate;
- }
-
- /**
- * Sets the value of the autoUpdate property.
- *
- */
- public void setAutoUpdate(boolean value) {
- this.autoUpdate = value;
- }
+ /**
+ * Sets the value of the ypos property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setYpos(Integer value)
+ {
+ this.ypos = value;
+ }
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
+ *
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;extension
+ * base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&gt;
+ * &lt;attribute name="calcId" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="needsUpdate"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false"
+ * /&gt; &lt;attribute name="autoUpdate" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/extension&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class CalcIdParam extends WebServiceParameterSet
+ {
+
+ @XmlAttribute(name = "calcId", required = true)
+ protected String calcId;
+
+ @XmlAttribute(name = "needsUpdate")
+ protected Boolean needsUpdate;
+
+ @XmlAttribute(name = "autoUpdate", required = true)
+ protected boolean autoUpdate;
+
+ /**
+ * Gets the value of the calcId property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getCalcId()
+ {
+ return calcId;
+ }
+
+ /**
+ * Sets the value of the calcId property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setCalcId(String value)
+ {
+ this.calcId = value;
+ }
+
+ /**
+ * Gets the value of the needsUpdate property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isNeedsUpdate()
+ {
+ if (needsUpdate == null)
+ {
+ return false;
}
+ else
+ {
+ return needsUpdate;
+ }
+ }
+
+ /**
+ * Sets the value of the needsUpdate property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setNeedsUpdate(Boolean value)
+ {
+ this.needsUpdate = value;
+ }
+
+ /**
+ * Gets the value of the autoUpdate property.
+ *
+ */
+ public boolean isAutoUpdate()
+ {
+ return autoUpdate;
+ }
+
+ /**
+ * Sets the value of the autoUpdate property.
+ *
+ */
+ public void setAutoUpdate(boolean value)
+ {
+ this.autoUpdate = value;
+ }
+ }
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class HiddenColumns {
-
- @XmlAttribute(name = "start")
- protected Integer start;
- @XmlAttribute(name = "end")
- protected Integer end;
-
- /**
- * Gets the value of the start property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getStart() {
- return start;
- }
-
- /**
- * Sets the value of the start property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setStart(Integer value) {
- this.start = value;
- }
-
- /**
- * Gets the value of the end property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getEnd() {
- return end;
- }
-
- /**
- * Sets the value of the end property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setEnd(Integer value) {
- this.end = value;
- }
-
- }
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
+ *
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="start"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class HiddenColumns
+ {
+
+ @XmlAttribute(name = "start")
+ protected Integer start;
+
+ @XmlAttribute(name = "end")
+ protected Integer end;
+
+ /**
+ * Gets the value of the start property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getStart()
+ {
+ return start;
+ }
+
+ /**
+ * Sets the value of the start property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setStart(Integer value)
+ {
+ this.start = value;
+ }
+
+ /**
+ * Gets the value of the end property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getEnd()
+ {
+ return end;
+ }
+
+ /**
+ * Sets the value of the end property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setEnd(Integer value)
+ {
+ this.end = value;
+ }
}
+ }
+
}
// Generated on: 2018.09.18 at 01:33:02 PM BST
//
-
package jalview.xml.binding.jalview;
import java.util.ArrayList;
import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
import javax.xml.datatype.XMLGregorianCalendar;
-
/**
- * <p>Java class for JalviewModelType complex type.
+ * <p>
+ * Java class for JalviewModelType complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
*
* <pre>
* <complexType name="JalviewModelType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "JalviewModelType", namespace = "www.jalview.org", propOrder = {
- "creationDate",
- "version",
- "vamsasModel",
- "jSeq",
- "jGroup",
- "viewport",
- "userColours",
- "tree",
- "featureSettings"
-})
-public class JalviewModelType {
-
- @XmlElement(required = true)
- @XmlSchemaType(name = "dateTime")
- protected XMLGregorianCalendar creationDate;
- @XmlElement(required = true)
- protected String version;
- @XmlElement(required = true)
- protected VAMSAS vamsasModel;
- @XmlElement(name = "JSeq")
- protected List<JalviewModelType.JSeq> jSeq;
- @XmlElement(name = "JGroup")
- protected List<JalviewModelType.JGroup> jGroup;
- @XmlElement(name = "Viewport")
- protected List<JalviewModelType.Viewport> viewport;
- @XmlElement(name = "UserColours")
- protected List<JalviewModelType.UserColours> userColours;
- protected List<JalviewModelType.Tree> tree;
- @XmlElement(name = "FeatureSettings")
- protected JalviewModelType.FeatureSettings featureSettings;
-
- /**
- * Gets the value of the creationDate property.
- *
- * @return
- * possible object is
- * {@link XMLGregorianCalendar }
- *
- */
- public XMLGregorianCalendar getCreationDate() {
- return creationDate;
- }
-
- /**
- * Sets the value of the creationDate property.
- *
- * @param value
- * allowed object is
- * {@link XMLGregorianCalendar }
- *
- */
- public void setCreationDate(XMLGregorianCalendar value) {
- this.creationDate = value;
+@XmlType(
+ name = "JalviewModelType",
+ namespace = "www.jalview.org",
+ propOrder =
+ { "creationDate", "version", "vamsasModel", "jSeq", "jGroup", "viewport",
+ "userColours", "tree", "featureSettings" })
+public class JalviewModelType
+{
+
+ @XmlElement(required = true)
+ @XmlSchemaType(name = "dateTime")
+ protected XMLGregorianCalendar creationDate;
+
+ @XmlElement(required = true)
+ protected String version;
+
+ @XmlElement(required = true)
+ protected VAMSAS vamsasModel;
+
+ @XmlElement(name = "JSeq")
+ protected List<JalviewModelType.JSeq> jSeq;
+
+ @XmlElement(name = "JGroup")
+ protected List<JalviewModelType.JGroup> jGroup;
+
+ @XmlElement(name = "Viewport")
+ protected List<JalviewModelType.Viewport> viewport;
+
+ @XmlElement(name = "UserColours")
+ protected List<JalviewModelType.UserColours> userColours;
+
+ protected List<JalviewModelType.Tree> tree;
+
+ @XmlElement(name = "FeatureSettings")
+ protected JalviewModelType.FeatureSettings featureSettings;
+
+ /**
+ * Gets the value of the creationDate property.
+ *
+ * @return possible object is {@link XMLGregorianCalendar }
+ *
+ */
+ public XMLGregorianCalendar getCreationDate()
+ {
+ return creationDate;
+ }
+
+ /**
+ * Sets the value of the creationDate property.
+ *
+ * @param value
+ * allowed object is {@link XMLGregorianCalendar }
+ *
+ */
+ public void setCreationDate(XMLGregorianCalendar value)
+ {
+ this.creationDate = value;
+ }
+
+ /**
+ * Gets the value of the version property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getVersion()
+ {
+ return version;
+ }
+
+ /**
+ * Sets the value of the version property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setVersion(String value)
+ {
+ this.version = value;
+ }
+
+ /**
+ * Gets the value of the vamsasModel property.
+ *
+ * @return possible object is {@link VAMSAS }
+ *
+ */
+ public VAMSAS getVamsasModel()
+ {
+ return vamsasModel;
+ }
+
+ /**
+ * Sets the value of the vamsasModel property.
+ *
+ * @param value
+ * allowed object is {@link VAMSAS }
+ *
+ */
+ public void setVamsasModel(VAMSAS value)
+ {
+ this.vamsasModel = value;
+ }
+
+ /**
+ * Gets the value of the jSeq property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the jSeq property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getJSeq().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModelType.JSeq }
+ *
+ *
+ */
+ public List<JalviewModelType.JSeq> getJSeq()
+ {
+ if (jSeq == null)
+ {
+ jSeq = new ArrayList<JalviewModelType.JSeq>();
}
-
- /**
- * Gets the value of the version property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getVersion() {
- return version;
+ return this.jSeq;
+ }
+
+ /**
+ * Gets the value of the jGroup property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the jGroup property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getJGroup().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModelType.JGroup }
+ *
+ *
+ */
+ public List<JalviewModelType.JGroup> getJGroup()
+ {
+ if (jGroup == null)
+ {
+ jGroup = new ArrayList<JalviewModelType.JGroup>();
}
-
- /**
- * Sets the value of the version property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setVersion(String value) {
- this.version = value;
+ return this.jGroup;
+ }
+
+ /**
+ * Gets the value of the viewport property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the viewport property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getViewport().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModelType.Viewport }
+ *
+ *
+ */
+ public List<JalviewModelType.Viewport> getViewport()
+ {
+ if (viewport == null)
+ {
+ viewport = new ArrayList<JalviewModelType.Viewport>();
}
-
- /**
- * Gets the value of the vamsasModel property.
- *
- * @return
- * possible object is
- * {@link VAMSAS }
- *
- */
- public VAMSAS getVamsasModel() {
- return vamsasModel;
+ return this.viewport;
+ }
+
+ /**
+ * Gets the value of the userColours property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the userColours property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getUserColours().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModelType.UserColours }
+ *
+ *
+ */
+ public List<JalviewModelType.UserColours> getUserColours()
+ {
+ if (userColours == null)
+ {
+ userColours = new ArrayList<JalviewModelType.UserColours>();
}
-
- /**
- * Sets the value of the vamsasModel property.
- *
- * @param value
- * allowed object is
- * {@link VAMSAS }
- *
- */
- public void setVamsasModel(VAMSAS value) {
- this.vamsasModel = value;
+ return this.userColours;
+ }
+
+ /**
+ * Gets the value of the tree property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the tree property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getTree().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModelType.Tree }
+ *
+ *
+ */
+ public List<JalviewModelType.Tree> getTree()
+ {
+ if (tree == null)
+ {
+ tree = new ArrayList<JalviewModelType.Tree>();
}
+ return this.tree;
+ }
+
+ /**
+ * Gets the value of the featureSettings property.
+ *
+ * @return possible object is {@link JalviewModelType.FeatureSettings }
+ *
+ */
+ public JalviewModelType.FeatureSettings getFeatureSettings()
+ {
+ return featureSettings;
+ }
+
+ /**
+ * Sets the value of the featureSettings property.
+ *
+ * @param value
+ * allowed object is {@link JalviewModelType.FeatureSettings }
+ *
+ */
+ public void setFeatureSettings(JalviewModelType.FeatureSettings value)
+ {
+ this.featureSettings = value;
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="setting" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+ * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+ * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="group" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "setting", "group" })
+ public static class FeatureSettings
+ {
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<JalviewModelType.FeatureSettings.Setting> setting;
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<JalviewModelType.FeatureSettings.Group> group;
/**
- * Gets the value of the jSeq property.
+ * Gets the value of the setting property.
*
* <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the jSeq property.
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the setting property.
*
* <p>
* For example, to add a new item, do as follows:
+ *
* <pre>
- * getJSeq().add(newItem);
+ * getSetting().add(newItem);
* </pre>
*
*
* <p>
* Objects of the following type(s) are allowed in the list
- * {@link JalviewModelType.JSeq }
+ * {@link JalviewModelType.FeatureSettings.Setting }
*
*
*/
- public List<JalviewModelType.JSeq> getJSeq() {
- if (jSeq == null) {
- jSeq = new ArrayList<JalviewModelType.JSeq>();
- }
- return this.jSeq;
+ public List<JalviewModelType.FeatureSettings.Setting> getSetting()
+ {
+ if (setting == null)
+ {
+ setting = new ArrayList<JalviewModelType.FeatureSettings.Setting>();
+ }
+ return this.setting;
}
/**
- * Gets the value of the jGroup property.
+ * Gets the value of the group property.
*
* <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the jGroup property.
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the group property.
*
* <p>
* For example, to add a new item, do as follows:
+ *
* <pre>
- * getJGroup().add(newItem);
+ * getGroup().add(newItem);
* </pre>
*
*
* <p>
* Objects of the following type(s) are allowed in the list
- * {@link JalviewModelType.JGroup }
+ * {@link JalviewModelType.FeatureSettings.Group }
*
*
*/
- public List<JalviewModelType.JGroup> getJGroup() {
- if (jGroup == null) {
- jGroup = new ArrayList<JalviewModelType.JGroup>();
- }
- return this.jGroup;
+ public List<JalviewModelType.FeatureSettings.Group> getGroup()
+ {
+ if (group == null)
+ {
+ group = new ArrayList<JalviewModelType.FeatureSettings.Group>();
+ }
+ return this.group;
}
/**
- * Gets the value of the viewport property.
- *
* <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the viewport property.
+ * Java class for anonymous complex type.
*
* <p>
- * For example, to add a new item, do as follows:
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
* <pre>
- * getViewport().add(newItem);
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
* </pre>
*
*
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModelType.Viewport }
- *
- *
*/
- public List<JalviewModelType.Viewport> getViewport() {
- if (viewport == null) {
- viewport = new ArrayList<JalviewModelType.Viewport>();
- }
- return this.viewport;
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Group
+ {
+
+ @XmlAttribute(name = "name", required = true)
+ protected String name;
+
+ @XmlAttribute(name = "display", required = true)
+ protected boolean display;
+
+ /**
+ * Gets the value of the name property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getName()
+ {
+ return name;
+ }
+
+ /**
+ * Sets the value of the name property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setName(String value)
+ {
+ this.name = value;
+ }
+
+ /**
+ * Gets the value of the display property.
+ *
+ */
+ public boolean isDisplay()
+ {
+ return display;
+ }
+
+ /**
+ * Sets the value of the display property.
+ *
+ */
+ public void setDisplay(boolean value)
+ {
+ this.display = value;
+ }
+
}
/**
- * Gets the value of the userColours property.
- *
* <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the userColours property.
+ * Java class for anonymous complex type.
*
* <p>
- * For example, to add a new item, do as follows:
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
* <pre>
- * getUserColours().add(newItem);
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+ * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+ * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
* </pre>
*
*
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModelType.UserColours }
- *
- *
*/
- public List<JalviewModelType.UserColours> getUserColours() {
- if (userColours == null) {
- userColours = new ArrayList<JalviewModelType.UserColours>();
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "attributeName", "matcherSet" })
+ public static class Setting
+ {
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<String> attributeName;
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected FeatureMatcherSet matcherSet;
+
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
+
+ @XmlAttribute(name = "colour", required = true)
+ protected int colour;
+
+ @XmlAttribute(name = "display", required = true)
+ protected boolean display;
+
+ @XmlAttribute(name = "order")
+ protected Float order;
+
+ @XmlAttribute(name = "mincolour")
+ protected Integer mincolour;
+
+ @XmlAttribute(name = "noValueColour")
+ protected NoValueColour noValueColour;
+
+ @XmlAttribute(name = "threshold")
+ protected Float threshold;
+
+ @XmlAttribute(name = "threshstate")
+ protected Integer threshstate;
+
+ @XmlAttribute(name = "max")
+ protected Float max;
+
+ @XmlAttribute(name = "min")
+ protected Float min;
+
+ @XmlAttribute(name = "colourByLabel")
+ protected Boolean colourByLabel;
+
+ @XmlAttribute(name = "autoScale")
+ protected Boolean autoScale;
+
+ /**
+ * Gets the value of the attributeName property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the attributeName property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getAttributeName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link String
+ * }
+ *
+ *
+ */
+ public List<String> getAttributeName()
+ {
+ if (attributeName == null)
+ {
+ attributeName = new ArrayList<String>();
+ }
+ return this.attributeName;
+ }
+
+ /**
+ * Gets the value of the matcherSet property.
+ *
+ * @return possible object is {@link FeatureMatcherSet }
+ *
+ */
+ public FeatureMatcherSet getMatcherSet()
+ {
+ return matcherSet;
+ }
+
+ /**
+ * Sets the value of the matcherSet property.
+ *
+ * @param value
+ * allowed object is {@link FeatureMatcherSet }
+ *
+ */
+ public void setMatcherSet(FeatureMatcherSet value)
+ {
+ this.matcherSet = value;
+ }
+
+ /**
+ * Gets the value of the type property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getType()
+ {
+ return type;
+ }
+
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setType(String value)
+ {
+ this.type = value;
+ }
+
+ /**
+ * Gets the value of the colour property.
+ *
+ */
+ public int getColour()
+ {
+ return colour;
+ }
+
+ /**
+ * Sets the value of the colour property.
+ *
+ */
+ public void setColour(int value)
+ {
+ this.colour = value;
+ }
+
+ /**
+ * Gets the value of the display property.
+ *
+ */
+ public boolean isDisplay()
+ {
+ return display;
+ }
+
+ /**
+ * Sets the value of the display property.
+ *
+ */
+ public void setDisplay(boolean value)
+ {
+ this.display = value;
+ }
+
+ /**
+ * Gets the value of the order property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getOrder()
+ {
+ return order;
+ }
+
+ /**
+ * Sets the value of the order property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setOrder(Float value)
+ {
+ this.order = value;
+ }
+
+ /**
+ * Gets the value of the mincolour property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getMincolour()
+ {
+ return mincolour;
+ }
+
+ /**
+ * Sets the value of the mincolour property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setMincolour(Integer value)
+ {
+ this.mincolour = value;
+ }
+
+ /**
+ * Gets the value of the noValueColour property.
+ *
+ * @return possible object is {@link NoValueColour }
+ *
+ */
+ public NoValueColour getNoValueColour()
+ {
+ if (noValueColour == null)
+ {
+ return NoValueColour.MIN;
}
- return this.userColours;
+ else
+ {
+ return noValueColour;
+ }
+ }
+
+ /**
+ * Sets the value of the noValueColour property.
+ *
+ * @param value
+ * allowed object is {@link NoValueColour }
+ *
+ */
+ public void setNoValueColour(NoValueColour value)
+ {
+ this.noValueColour = value;
+ }
+
+ /**
+ * Gets the value of the threshold property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getThreshold()
+ {
+ return threshold;
+ }
+
+ /**
+ * Sets the value of the threshold property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setThreshold(Float value)
+ {
+ this.threshold = value;
+ }
+
+ /**
+ * Gets the value of the threshstate property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getThreshstate()
+ {
+ return threshstate;
+ }
+
+ /**
+ * Sets the value of the threshstate property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setThreshstate(Integer value)
+ {
+ this.threshstate = value;
+ }
+
+ /**
+ * Gets the value of the max property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getMax()
+ {
+ return max;
+ }
+
+ /**
+ * Sets the value of the max property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setMax(Float value)
+ {
+ this.max = value;
+ }
+
+ /**
+ * Gets the value of the min property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getMin()
+ {
+ return min;
+ }
+
+ /**
+ * Sets the value of the min property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setMin(Float value)
+ {
+ this.min = value;
+ }
+
+ /**
+ * Gets the value of the colourByLabel property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isColourByLabel()
+ {
+ return colourByLabel;
+ }
+
+ /**
+ * Sets the value of the colourByLabel property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setColourByLabel(Boolean value)
+ {
+ this.colourByLabel = value;
+ }
+
+ /**
+ * Gets the value of the autoScale property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isAutoScale()
+ {
+ return autoScale;
+ }
+
+ /**
+ * Sets the value of the autoScale property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setAutoScale(Boolean value)
+ {
+ this.autoScale = value;
+ }
+
}
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
+ * <element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "seq", "annotationColours" })
+ public static class JGroup
+ {
+
+ @XmlElement(namespace = "www.jalview.org", required = true)
+ protected List<String> seq;
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected AnnotationColourScheme annotationColours;
+
+ @XmlAttribute(name = "start")
+ protected Integer start;
+
+ @XmlAttribute(name = "end")
+ protected Integer end;
+
+ @XmlAttribute(name = "name")
+ protected String name;
+
+ @XmlAttribute(name = "colour")
+ protected String colour;
+
+ @XmlAttribute(name = "consThreshold")
+ protected Integer consThreshold;
+
+ @XmlAttribute(name = "pidThreshold")
+ protected Integer pidThreshold;
+
+ @XmlAttribute(name = "outlineColour")
+ protected Integer outlineColour;
+
+ @XmlAttribute(name = "displayBoxes")
+ protected Boolean displayBoxes;
+
+ @XmlAttribute(name = "displayText")
+ protected Boolean displayText;
+
+ @XmlAttribute(name = "colourText")
+ protected Boolean colourText;
+
+ @XmlAttribute(name = "textCol1")
+ protected Integer textCol1;
+
+ @XmlAttribute(name = "textCol2")
+ protected Integer textCol2;
+
+ @XmlAttribute(name = "textColThreshold")
+ protected Integer textColThreshold;
+
+ @XmlAttribute(name = "showUnconserved")
+ protected Boolean showUnconserved;
+
+ @XmlAttribute(name = "ignoreGapsinConsensus")
+ protected Boolean ignoreGapsinConsensus;
+
+ @XmlAttribute(name = "showConsensusHistogram")
+ protected Boolean showConsensusHistogram;
+
+ @XmlAttribute(name = "showSequenceLogo")
+ protected Boolean showSequenceLogo;
+
+ @XmlAttribute(name = "normaliseSequenceLogo")
+ protected Boolean normaliseSequenceLogo;
+
+ @XmlAttribute(name = "id")
+ protected String id;
+
/**
- * Gets the value of the tree property.
+ * Gets the value of the seq property.
*
* <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the tree property.
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the seq property.
*
* <p>
* For example, to add a new item, do as follows:
+ *
* <pre>
- * getTree().add(newItem);
+ * getSeq().add(newItem);
* </pre>
*
*
* <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModelType.Tree }
+ * Objects of the following type(s) are allowed in the list {@link String }
*
*
*/
- public List<JalviewModelType.Tree> getTree() {
- if (tree == null) {
- tree = new ArrayList<JalviewModelType.Tree>();
- }
- return this.tree;
+ public List<String> getSeq()
+ {
+ if (seq == null)
+ {
+ seq = new ArrayList<String>();
+ }
+ return this.seq;
}
/**
- * Gets the value of the featureSettings property.
+ * Gets the value of the annotationColours property.
+ *
+ * @return possible object is {@link AnnotationColourScheme }
*
- * @return
- * possible object is
- * {@link JalviewModelType.FeatureSettings }
- *
*/
- public JalviewModelType.FeatureSettings getFeatureSettings() {
- return featureSettings;
+ public AnnotationColourScheme getAnnotationColours()
+ {
+ return annotationColours;
}
/**
- * Sets the value of the featureSettings property.
+ * Sets the value of the annotationColours property.
*
* @param value
- * allowed object is
- * {@link JalviewModelType.FeatureSettings }
- *
+ * allowed object is {@link AnnotationColourScheme }
+ *
*/
- public void setFeatureSettings(JalviewModelType.FeatureSettings value) {
- this.featureSettings = value;
+ public void setAnnotationColours(AnnotationColourScheme value)
+ {
+ this.annotationColours = value;
}
-
/**
- * <p>Java class for anonymous complex type.
+ * Gets the value of the start property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * @return possible object is {@link Integer }
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="setting" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
- * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
- * </sequence>
- * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
- * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="group" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ */
+ public Integer getStart()
+ {
+ return start;
+ }
+
+ /**
+ * Sets the value of the start property.
*
+ * @param value
+ * allowed object is {@link Integer }
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "setting",
- "group"
- })
- public static class FeatureSettings {
+ public void setStart(Integer value)
+ {
+ this.start = value;
+ }
- @XmlElement(namespace = "www.jalview.org")
- protected List<JalviewModelType.FeatureSettings.Setting> setting;
- @XmlElement(namespace = "www.jalview.org")
- protected List<JalviewModelType.FeatureSettings.Group> group;
+ /**
+ * Gets the value of the end property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getEnd()
+ {
+ return end;
+ }
- /**
- * Gets the value of the setting property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the setting property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getSetting().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModelType.FeatureSettings.Setting }
- *
- *
- */
- public List<JalviewModelType.FeatureSettings.Setting> getSetting() {
- if (setting == null) {
- setting = new ArrayList<JalviewModelType.FeatureSettings.Setting>();
- }
- return this.setting;
- }
+ /**
+ * Sets the value of the end property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setEnd(Integer value)
+ {
+ this.end = value;
+ }
- /**
- * Gets the value of the group property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the group property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getGroup().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModelType.FeatureSettings.Group }
- *
- *
- */
- public List<JalviewModelType.FeatureSettings.Group> getGroup() {
- if (group == null) {
- group = new ArrayList<JalviewModelType.FeatureSettings.Group>();
- }
- return this.group;
- }
+ /**
+ * Gets the value of the name property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getName()
+ {
+ return name;
+ }
+ /**
+ * Sets the value of the name property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setName(String value)
+ {
+ this.name = value;
+ }
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class Group {
-
- @XmlAttribute(name = "name", required = true)
- protected String name;
- @XmlAttribute(name = "display", required = true)
- protected boolean display;
-
- /**
- * Gets the value of the name property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getName() {
- return name;
- }
-
- /**
- * Sets the value of the name property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setName(String value) {
- this.name = value;
- }
-
- /**
- * Gets the value of the display property.
- *
- */
- public boolean isDisplay() {
- return display;
- }
-
- /**
- * Sets the value of the display property.
- *
- */
- public void setDisplay(boolean value) {
- this.display = value;
- }
+ /**
+ * Gets the value of the colour property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getColour()
+ {
+ return colour;
+ }
- }
+ /**
+ * Sets the value of the colour property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setColour(String value)
+ {
+ this.colour = value;
+ }
+ /**
+ * Gets the value of the consThreshold property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getConsThreshold()
+ {
+ return consThreshold;
+ }
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
- * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
- * </sequence>
- * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
- * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "attributeName",
- "matcherSet"
- })
- public static class Setting {
-
- @XmlElement(namespace = "www.jalview.org")
- protected List<String> attributeName;
- @XmlElement(namespace = "www.jalview.org")
- protected FeatureMatcherSet matcherSet;
- @XmlAttribute(name = "type", required = true)
- protected String type;
- @XmlAttribute(name = "colour", required = true)
- protected int colour;
- @XmlAttribute(name = "display", required = true)
- protected boolean display;
- @XmlAttribute(name = "order")
- protected Float order;
- @XmlAttribute(name = "mincolour")
- protected Integer mincolour;
- @XmlAttribute(name = "noValueColour")
- protected NoValueColour noValueColour;
- @XmlAttribute(name = "threshold")
- protected Float threshold;
- @XmlAttribute(name = "threshstate")
- protected Integer threshstate;
- @XmlAttribute(name = "max")
- protected Float max;
- @XmlAttribute(name = "min")
- protected Float min;
- @XmlAttribute(name = "colourByLabel")
- protected Boolean colourByLabel;
- @XmlAttribute(name = "autoScale")
- protected Boolean autoScale;
-
- /**
- * Gets the value of the attributeName property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the attributeName property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getAttributeName().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link String }
- *
- *
- */
- public List<String> getAttributeName() {
- if (attributeName == null) {
- attributeName = new ArrayList<String>();
- }
- return this.attributeName;
- }
-
- /**
- * Gets the value of the matcherSet property.
- *
- * @return
- * possible object is
- * {@link FeatureMatcherSet }
- *
- */
- public FeatureMatcherSet getMatcherSet() {
- return matcherSet;
- }
-
- /**
- * Sets the value of the matcherSet property.
- *
- * @param value
- * allowed object is
- * {@link FeatureMatcherSet }
- *
- */
- public void setMatcherSet(FeatureMatcherSet value) {
- this.matcherSet = value;
- }
-
- /**
- * Gets the value of the type property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getType() {
- return type;
- }
-
- /**
- * Sets the value of the type property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setType(String value) {
- this.type = value;
- }
-
- /**
- * Gets the value of the colour property.
- *
- */
- public int getColour() {
- return colour;
- }
-
- /**
- * Sets the value of the colour property.
- *
- */
- public void setColour(int value) {
- this.colour = value;
- }
-
- /**
- * Gets the value of the display property.
- *
- */
- public boolean isDisplay() {
- return display;
- }
-
- /**
- * Sets the value of the display property.
- *
- */
- public void setDisplay(boolean value) {
- this.display = value;
- }
-
- /**
- * Gets the value of the order property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getOrder() {
- return order;
- }
-
- /**
- * Sets the value of the order property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setOrder(Float value) {
- this.order = value;
- }
-
- /**
- * Gets the value of the mincolour property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getMincolour() {
- return mincolour;
- }
-
- /**
- * Sets the value of the mincolour property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setMincolour(Integer value) {
- this.mincolour = value;
- }
-
- /**
- * Gets the value of the noValueColour property.
- *
- * @return
- * possible object is
- * {@link NoValueColour }
- *
- */
- public NoValueColour getNoValueColour() {
- if (noValueColour == null) {
- return NoValueColour.MIN;
- } else {
- return noValueColour;
- }
- }
-
- /**
- * Sets the value of the noValueColour property.
- *
- * @param value
- * allowed object is
- * {@link NoValueColour }
- *
- */
- public void setNoValueColour(NoValueColour value) {
- this.noValueColour = value;
- }
-
- /**
- * Gets the value of the threshold property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getThreshold() {
- return threshold;
- }
-
- /**
- * Sets the value of the threshold property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setThreshold(Float value) {
- this.threshold = value;
- }
-
- /**
- * Gets the value of the threshstate property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getThreshstate() {
- return threshstate;
- }
-
- /**
- * Sets the value of the threshstate property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setThreshstate(Integer value) {
- this.threshstate = value;
- }
-
- /**
- * Gets the value of the max property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getMax() {
- return max;
- }
-
- /**
- * Sets the value of the max property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setMax(Float value) {
- this.max = value;
- }
-
- /**
- * Gets the value of the min property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getMin() {
- return min;
- }
-
- /**
- * Sets the value of the min property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setMin(Float value) {
- this.min = value;
- }
-
- /**
- * Gets the value of the colourByLabel property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isColourByLabel() {
- return colourByLabel;
- }
-
- /**
- * Sets the value of the colourByLabel property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setColourByLabel(Boolean value) {
- this.colourByLabel = value;
- }
-
- /**
- * Gets the value of the autoScale property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isAutoScale() {
- return autoScale;
- }
-
- /**
- * Sets the value of the autoScale property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setAutoScale(Boolean value) {
- this.autoScale = value;
- }
+ /**
+ * Sets the value of the consThreshold property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setConsThreshold(Integer value)
+ {
+ this.consThreshold = value;
+ }
- }
+ /**
+ * Gets the value of the pidThreshold property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getPidThreshold()
+ {
+ return pidThreshold;
+ }
+ /**
+ * Sets the value of the pidThreshold property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setPidThreshold(Integer value)
+ {
+ this.pidThreshold = value;
}
+ /**
+ * Gets the value of the outlineColour property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getOutlineColour()
+ {
+ return outlineColour;
+ }
/**
- * <p>Java class for anonymous complex type.
+ * Sets the value of the outlineColour property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * @param value
+ * allowed object is {@link Integer }
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
- * <element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
- * </sequence>
- * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ */
+ public void setOutlineColour(Integer value)
+ {
+ this.outlineColour = value;
+ }
+
+ /**
+ * Gets the value of the displayBoxes property.
*
+ * @return possible object is {@link Boolean }
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "seq",
- "annotationColours"
- })
- public static class JGroup {
-
- @XmlElement(namespace = "www.jalview.org", required = true)
- protected List<String> seq;
- @XmlElement(namespace = "www.jalview.org")
- protected AnnotationColourScheme annotationColours;
- @XmlAttribute(name = "start")
- protected Integer start;
- @XmlAttribute(name = "end")
- protected Integer end;
- @XmlAttribute(name = "name")
- protected String name;
- @XmlAttribute(name = "colour")
- protected String colour;
- @XmlAttribute(name = "consThreshold")
- protected Integer consThreshold;
- @XmlAttribute(name = "pidThreshold")
- protected Integer pidThreshold;
- @XmlAttribute(name = "outlineColour")
- protected Integer outlineColour;
- @XmlAttribute(name = "displayBoxes")
- protected Boolean displayBoxes;
- @XmlAttribute(name = "displayText")
- protected Boolean displayText;
- @XmlAttribute(name = "colourText")
- protected Boolean colourText;
- @XmlAttribute(name = "textCol1")
- protected Integer textCol1;
- @XmlAttribute(name = "textCol2")
- protected Integer textCol2;
- @XmlAttribute(name = "textColThreshold")
- protected Integer textColThreshold;
- @XmlAttribute(name = "showUnconserved")
- protected Boolean showUnconserved;
- @XmlAttribute(name = "ignoreGapsinConsensus")
- protected Boolean ignoreGapsinConsensus;
- @XmlAttribute(name = "showConsensusHistogram")
- protected Boolean showConsensusHistogram;
- @XmlAttribute(name = "showSequenceLogo")
- protected Boolean showSequenceLogo;
- @XmlAttribute(name = "normaliseSequenceLogo")
- protected Boolean normaliseSequenceLogo;
- @XmlAttribute(name = "id")
- protected String id;
+ public Boolean isDisplayBoxes()
+ {
+ return displayBoxes;
+ }
- /**
- * Gets the value of the seq property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the seq property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getSeq().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link String }
- *
- *
- */
- public List<String> getSeq() {
- if (seq == null) {
- seq = new ArrayList<String>();
- }
- return this.seq;
- }
+ /**
+ * Sets the value of the displayBoxes property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setDisplayBoxes(Boolean value)
+ {
+ this.displayBoxes = value;
+ }
- /**
- * Gets the value of the annotationColours property.
- *
- * @return
- * possible object is
- * {@link AnnotationColourScheme }
- *
- */
- public AnnotationColourScheme getAnnotationColours() {
- return annotationColours;
- }
+ /**
+ * Gets the value of the displayText property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isDisplayText()
+ {
+ return displayText;
+ }
- /**
- * Sets the value of the annotationColours property.
- *
- * @param value
- * allowed object is
- * {@link AnnotationColourScheme }
- *
- */
- public void setAnnotationColours(AnnotationColourScheme value) {
- this.annotationColours = value;
- }
+ /**
+ * Sets the value of the displayText property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setDisplayText(Boolean value)
+ {
+ this.displayText = value;
+ }
- /**
- * Gets the value of the start property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getStart() {
- return start;
- }
+ /**
+ * Gets the value of the colourText property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isColourText()
+ {
+ return colourText;
+ }
- /**
- * Sets the value of the start property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setStart(Integer value) {
- this.start = value;
- }
-
- /**
- * Gets the value of the end property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getEnd() {
- return end;
- }
-
- /**
- * Sets the value of the end property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setEnd(Integer value) {
- this.end = value;
- }
-
- /**
- * Gets the value of the name property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getName() {
- return name;
- }
+ /**
+ * Sets the value of the colourText property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setColourText(Boolean value)
+ {
+ this.colourText = value;
+ }
- /**
- * Sets the value of the name property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setName(String value) {
- this.name = value;
- }
+ /**
+ * Gets the value of the textCol1 property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getTextCol1()
+ {
+ return textCol1;
+ }
- /**
- * Gets the value of the colour property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getColour() {
- return colour;
- }
+ /**
+ * Sets the value of the textCol1 property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setTextCol1(Integer value)
+ {
+ this.textCol1 = value;
+ }
- /**
- * Sets the value of the colour property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setColour(String value) {
- this.colour = value;
- }
+ /**
+ * Gets the value of the textCol2 property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getTextCol2()
+ {
+ return textCol2;
+ }
- /**
- * Gets the value of the consThreshold property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getConsThreshold() {
- return consThreshold;
- }
+ /**
+ * Sets the value of the textCol2 property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setTextCol2(Integer value)
+ {
+ this.textCol2 = value;
+ }
- /**
- * Sets the value of the consThreshold property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setConsThreshold(Integer value) {
- this.consThreshold = value;
- }
+ /**
+ * Gets the value of the textColThreshold property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getTextColThreshold()
+ {
+ return textColThreshold;
+ }
- /**
- * Gets the value of the pidThreshold property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getPidThreshold() {
- return pidThreshold;
- }
+ /**
+ * Sets the value of the textColThreshold property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setTextColThreshold(Integer value)
+ {
+ this.textColThreshold = value;
+ }
- /**
- * Sets the value of the pidThreshold property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setPidThreshold(Integer value) {
- this.pidThreshold = value;
- }
+ /**
+ * Gets the value of the showUnconserved property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowUnconserved()
+ {
+ return showUnconserved;
+ }
- /**
- * Gets the value of the outlineColour property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getOutlineColour() {
- return outlineColour;
- }
+ /**
+ * Sets the value of the showUnconserved property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowUnconserved(Boolean value)
+ {
+ this.showUnconserved = value;
+ }
- /**
- * Sets the value of the outlineColour property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setOutlineColour(Integer value) {
- this.outlineColour = value;
- }
+ /**
+ * Gets the value of the ignoreGapsinConsensus property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isIgnoreGapsinConsensus()
+ {
+ if (ignoreGapsinConsensus == null)
+ {
+ return true;
+ }
+ else
+ {
+ return ignoreGapsinConsensus;
+ }
+ }
- /**
- * Gets the value of the displayBoxes property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isDisplayBoxes() {
- return displayBoxes;
- }
+ /**
+ * Sets the value of the ignoreGapsinConsensus property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setIgnoreGapsinConsensus(Boolean value)
+ {
+ this.ignoreGapsinConsensus = value;
+ }
- /**
- * Sets the value of the displayBoxes property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setDisplayBoxes(Boolean value) {
- this.displayBoxes = value;
- }
+ /**
+ * Gets the value of the showConsensusHistogram property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isShowConsensusHistogram()
+ {
+ if (showConsensusHistogram == null)
+ {
+ return true;
+ }
+ else
+ {
+ return showConsensusHistogram;
+ }
+ }
- /**
- * Gets the value of the displayText property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isDisplayText() {
- return displayText;
- }
+ /**
+ * Sets the value of the showConsensusHistogram property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowConsensusHistogram(Boolean value)
+ {
+ this.showConsensusHistogram = value;
+ }
- /**
- * Sets the value of the displayText property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setDisplayText(Boolean value) {
- this.displayText = value;
- }
+ /**
+ * Gets the value of the showSequenceLogo property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isShowSequenceLogo()
+ {
+ if (showSequenceLogo == null)
+ {
+ return false;
+ }
+ else
+ {
+ return showSequenceLogo;
+ }
+ }
- /**
- * Gets the value of the colourText property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isColourText() {
- return colourText;
- }
+ /**
+ * Sets the value of the showSequenceLogo property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowSequenceLogo(Boolean value)
+ {
+ this.showSequenceLogo = value;
+ }
- /**
- * Sets the value of the colourText property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setColourText(Boolean value) {
- this.colourText = value;
- }
+ /**
+ * Gets the value of the normaliseSequenceLogo property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isNormaliseSequenceLogo()
+ {
+ if (normaliseSequenceLogo == null)
+ {
+ return false;
+ }
+ else
+ {
+ return normaliseSequenceLogo;
+ }
+ }
- /**
- * Gets the value of the textCol1 property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getTextCol1() {
- return textCol1;
- }
+ /**
+ * Sets the value of the normaliseSequenceLogo property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setNormaliseSequenceLogo(Boolean value)
+ {
+ this.normaliseSequenceLogo = value;
+ }
- /**
- * Sets the value of the textCol1 property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setTextCol1(Integer value) {
- this.textCol1 = value;
- }
+ /**
+ * Gets the value of the id property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getId()
+ {
+ return id;
+ }
- /**
- * Gets the value of the textCol2 property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getTextCol2() {
- return textCol2;
- }
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setId(String value)
+ {
+ this.id = value;
+ }
- /**
- * Sets the value of the textCol2 property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setTextCol2(Integer value) {
- this.textCol2 = value;
- }
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="pdbids" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <extension base="{www.jalview.org}pdbentry">
+ * <sequence>
+ * <element name="structureState" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <simpleContent>
+ * <extension base="<http://www.w3.org/2001/XMLSchema>string">
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </extension>
+ * </simpleContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </extension>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="secondaryStructure" maxOccurs="unbounded">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(
+ name = "",
+ propOrder =
+ { "features", "pdbids", "hiddenSequences", "rnaViewer" })
+ public static class JSeq
+ {
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<Feature> features;
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<JalviewModelType.JSeq.Pdbids> pdbids;
+
+ @XmlElement(namespace = "www.jalview.org", type = Integer.class)
+ protected List<Integer> hiddenSequences;
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<JalviewModelType.JSeq.RnaViewer> rnaViewer;
+
+ @XmlAttribute(name = "colour")
+ protected Integer colour;
+
+ @XmlAttribute(name = "start", required = true)
+ protected int start;
+
+ @XmlAttribute(name = "end", required = true)
+ protected int end;
+
+ @XmlAttribute(name = "id", required = true)
+ protected String id;
+
+ @XmlAttribute(name = "hidden")
+ protected Boolean hidden;
+
+ @XmlAttribute(name = "viewreference")
+ protected Boolean viewreference;
- /**
- * Gets the value of the textColThreshold property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getTextColThreshold() {
- return textColThreshold;
- }
+ /**
+ * Gets the value of the features property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the features property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getFeatures().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link Feature }
+ *
+ *
+ */
+ public List<Feature> getFeatures()
+ {
+ if (features == null)
+ {
+ features = new ArrayList<Feature>();
+ }
+ return this.features;
+ }
- /**
- * Sets the value of the textColThreshold property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setTextColThreshold(Integer value) {
- this.textColThreshold = value;
- }
+ /**
+ * Gets the value of the pdbids property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the pdbids property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getPdbids().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModelType.JSeq.Pdbids }
+ *
+ *
+ */
+ public List<JalviewModelType.JSeq.Pdbids> getPdbids()
+ {
+ if (pdbids == null)
+ {
+ pdbids = new ArrayList<JalviewModelType.JSeq.Pdbids>();
+ }
+ return this.pdbids;
+ }
- /**
- * Gets the value of the showUnconserved property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowUnconserved() {
- return showUnconserved;
- }
+ /**
+ * Gets the value of the hiddenSequences property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the hiddenSequences property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getHiddenSequences().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getHiddenSequences()
+ {
+ if (hiddenSequences == null)
+ {
+ hiddenSequences = new ArrayList<Integer>();
+ }
+ return this.hiddenSequences;
+ }
- /**
- * Sets the value of the showUnconserved property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowUnconserved(Boolean value) {
- this.showUnconserved = value;
- }
+ /**
+ * Gets the value of the rnaViewer property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the rnaViewer property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getRnaViewer().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModelType.JSeq.RnaViewer }
+ *
+ *
+ */
+ public List<JalviewModelType.JSeq.RnaViewer> getRnaViewer()
+ {
+ if (rnaViewer == null)
+ {
+ rnaViewer = new ArrayList<JalviewModelType.JSeq.RnaViewer>();
+ }
+ return this.rnaViewer;
+ }
- /**
- * Gets the value of the ignoreGapsinConsensus property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isIgnoreGapsinConsensus() {
- if (ignoreGapsinConsensus == null) {
- return true;
- } else {
- return ignoreGapsinConsensus;
- }
- }
+ /**
+ * Gets the value of the colour property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getColour()
+ {
+ return colour;
+ }
- /**
- * Sets the value of the ignoreGapsinConsensus property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setIgnoreGapsinConsensus(Boolean value) {
- this.ignoreGapsinConsensus = value;
- }
+ /**
+ * Sets the value of the colour property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setColour(Integer value)
+ {
+ this.colour = value;
+ }
- /**
- * Gets the value of the showConsensusHistogram property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isShowConsensusHistogram() {
- if (showConsensusHistogram == null) {
- return true;
- } else {
- return showConsensusHistogram;
- }
- }
+ /**
+ * Gets the value of the start property.
+ *
+ */
+ public int getStart()
+ {
+ return start;
+ }
- /**
- * Sets the value of the showConsensusHistogram property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowConsensusHistogram(Boolean value) {
- this.showConsensusHistogram = value;
- }
+ /**
+ * Sets the value of the start property.
+ *
+ */
+ public void setStart(int value)
+ {
+ this.start = value;
+ }
- /**
- * Gets the value of the showSequenceLogo property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isShowSequenceLogo() {
- if (showSequenceLogo == null) {
- return false;
- } else {
- return showSequenceLogo;
- }
- }
+ /**
+ * Gets the value of the end property.
+ *
+ */
+ public int getEnd()
+ {
+ return end;
+ }
- /**
- * Sets the value of the showSequenceLogo property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowSequenceLogo(Boolean value) {
- this.showSequenceLogo = value;
- }
+ /**
+ * Sets the value of the end property.
+ *
+ */
+ public void setEnd(int value)
+ {
+ this.end = value;
+ }
- /**
- * Gets the value of the normaliseSequenceLogo property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isNormaliseSequenceLogo() {
- if (normaliseSequenceLogo == null) {
- return false;
- } else {
- return normaliseSequenceLogo;
- }
- }
+ /**
+ * Gets the value of the id property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getId()
+ {
+ return id;
+ }
- /**
- * Sets the value of the normaliseSequenceLogo property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setNormaliseSequenceLogo(Boolean value) {
- this.normaliseSequenceLogo = value;
- }
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setId(String value)
+ {
+ this.id = value;
+ }
- /**
- * Gets the value of the id property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getId() {
- return id;
- }
+ /**
+ * Gets the value of the hidden property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isHidden()
+ {
+ return hidden;
+ }
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setId(String value) {
- this.id = value;
- }
+ /**
+ * Sets the value of the hidden property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setHidden(Boolean value)
+ {
+ this.hidden = value;
+ }
+ /**
+ * Gets the value of the viewreference property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isViewreference()
+ {
+ return viewreference;
}
+ /**
+ * Sets the value of the viewreference property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setViewreference(Boolean value)
+ {
+ this.viewreference = value;
+ }
/**
- * <p>Java class for anonymous complex type.
+ * <p>
+ * Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
*
* <pre>
* <complexType>
* <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <extension base="{www.jalview.org}pdbentry">
* <sequence>
- * <element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
- * <element name="pdbids" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <extension base="{www.jalview.org}pdbentry">
- * <sequence>
- * <element name="structureState" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <simpleContent>
- * <extension base="<http://www.w3.org/2001/XMLSchema>string">
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </extension>
- * </simpleContent>
- * </complexType>
- * </element>
- * </sequence>
- * </extension>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
- * <element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
+ * <element name="structureState" maxOccurs="unbounded" minOccurs="0">
* <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="secondaryStructure" maxOccurs="unbounded">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
+ * <simpleContent>
+ * <extension base="<http://www.w3.org/2001/XMLSchema>string">
* <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
* <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
- * </restriction>
- * </complexContent>
+ * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </extension>
+ * </simpleContent>
* </complexType>
* </element>
* </sequence>
- * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </restriction>
+ * </extension>
* </complexContent>
* </complexType>
* </pre>
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "features",
- "pdbids",
- "hiddenSequences",
- "rnaViewer"
- })
- public static class JSeq {
-
- @XmlElement(namespace = "www.jalview.org")
- protected List<Feature> features;
- @XmlElement(namespace = "www.jalview.org")
- protected List<JalviewModelType.JSeq.Pdbids> pdbids;
- @XmlElement(namespace = "www.jalview.org", type = Integer.class)
- protected List<Integer> hiddenSequences;
- @XmlElement(namespace = "www.jalview.org")
- protected List<JalviewModelType.JSeq.RnaViewer> rnaViewer;
- @XmlAttribute(name = "colour")
- protected Integer colour;
- @XmlAttribute(name = "start", required = true)
- protected int start;
- @XmlAttribute(name = "end", required = true)
- protected int end;
- @XmlAttribute(name = "id", required = true)
- protected String id;
- @XmlAttribute(name = "hidden")
- protected Boolean hidden;
- @XmlAttribute(name = "viewreference")
- protected Boolean viewreference;
+ @XmlType(name = "", propOrder = { "structureState" })
+ public static class Pdbids extends Pdbentry
+ {
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<JalviewModelType.JSeq.Pdbids.StructureState> structureState;
+
+ /**
+ * Gets the value of the structureState property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the structureState property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getStructureState().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModelType.JSeq.Pdbids.StructureState }
+ *
+ *
+ */
+ public List<JalviewModelType.JSeq.Pdbids.StructureState> getStructureState()
+ {
+ if (structureState == null)
+ {
+ structureState = new ArrayList<JalviewModelType.JSeq.Pdbids.StructureState>();
+ }
+ return this.structureState;
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <simpleContent>
+ * <extension base="<http://www.w3.org/2001/XMLSchema>string">
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </extension>
+ * </simpleContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "value" })
+ public static class StructureState
+ {
+
+ @XmlValue
+ protected String value;
+
+ @XmlAttribute(name = "visible")
+ protected Boolean visible;
+
+ @XmlAttribute(name = "viewId")
+ protected String viewId;
+
+ @XmlAttribute(name = "alignwithAlignPanel")
+ protected Boolean alignwithAlignPanel;
+
+ @XmlAttribute(name = "colourwithAlignPanel")
+ protected Boolean colourwithAlignPanel;
+
+ @XmlAttribute(name = "colourByJmol")
+ protected Boolean colourByJmol;
+
+ @XmlAttribute(name = "type")
+ protected String type;
+
+ @XmlAttribute(name = "width")
+ protected Integer width;
+
+ @XmlAttribute(name = "height")
+ protected Integer height;
+
+ @XmlAttribute(name = "xpos")
+ protected Integer xpos;
+
+ @XmlAttribute(name = "ypos")
+ protected Integer ypos;
/**
- * Gets the value of the features property.
+ * Gets the value of the value property.
*
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the features property.
+ * @return possible object is {@link String }
*
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getFeatures().add(newItem);
- * </pre>
+ */
+ public String getValue()
+ {
+ return value;
+ }
+
+ /**
+ * Sets the value of the value property.
*
+ * @param value
+ * allowed object is {@link String }
*
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Feature }
+ */
+ public void setValue(String value)
+ {
+ this.value = value;
+ }
+
+ /**
+ * Gets the value of the visible property.
*
+ * @return possible object is {@link Boolean }
*
*/
- public List<Feature> getFeatures() {
- if (features == null) {
- features = new ArrayList<Feature>();
- }
- return this.features;
+ public Boolean isVisible()
+ {
+ return visible;
}
/**
- * Gets the value of the pdbids property.
+ * Sets the value of the visible property.
*
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the pdbids property.
+ * @param value
+ * allowed object is {@link Boolean }
*
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getPdbids().add(newItem);
- * </pre>
+ */
+ public void setVisible(Boolean value)
+ {
+ this.visible = value;
+ }
+
+ /**
+ * Gets the value of the viewId property.
*
+ * @return possible object is {@link String }
*
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModelType.JSeq.Pdbids }
+ */
+ public String getViewId()
+ {
+ return viewId;
+ }
+
+ /**
+ * Sets the value of the viewId property.
*
+ * @param value
+ * allowed object is {@link String }
*
*/
- public List<JalviewModelType.JSeq.Pdbids> getPdbids() {
- if (pdbids == null) {
- pdbids = new ArrayList<JalviewModelType.JSeq.Pdbids>();
- }
- return this.pdbids;
+ public void setViewId(String value)
+ {
+ this.viewId = value;
}
/**
- * Gets the value of the hiddenSequences property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the hiddenSequences property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getHiddenSequences().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Integer }
+ * Gets the value of the alignwithAlignPanel property.
*
+ * @return possible object is {@link Boolean }
*
*/
- public List<Integer> getHiddenSequences() {
- if (hiddenSequences == null) {
- hiddenSequences = new ArrayList<Integer>();
- }
- return this.hiddenSequences;
+ public boolean isAlignwithAlignPanel()
+ {
+ if (alignwithAlignPanel == null)
+ {
+ return true;
+ }
+ else
+ {
+ return alignwithAlignPanel;
+ }
}
/**
- * Gets the value of the rnaViewer property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the rnaViewer property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getRnaViewer().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModelType.JSeq.RnaViewer }
+ * Sets the value of the alignwithAlignPanel property.
*
+ * @param value
+ * allowed object is {@link Boolean }
*
*/
- public List<JalviewModelType.JSeq.RnaViewer> getRnaViewer() {
- if (rnaViewer == null) {
- rnaViewer = new ArrayList<JalviewModelType.JSeq.RnaViewer>();
- }
- return this.rnaViewer;
+ public void setAlignwithAlignPanel(Boolean value)
+ {
+ this.alignwithAlignPanel = value;
}
/**
- * Gets the value of the colour property.
+ * Gets the value of the colourwithAlignPanel property.
+ *
+ * @return possible object is {@link Boolean }
*
- * @return
- * possible object is
- * {@link Integer }
- *
*/
- public Integer getColour() {
- return colour;
+ public boolean isColourwithAlignPanel()
+ {
+ if (colourwithAlignPanel == null)
+ {
+ return false;
+ }
+ else
+ {
+ return colourwithAlignPanel;
+ }
}
/**
- * Sets the value of the colour property.
+ * Sets the value of the colourwithAlignPanel property.
*
* @param value
- * allowed object is
- * {@link Integer }
- *
+ * allowed object is {@link Boolean }
+ *
*/
- public void setColour(Integer value) {
- this.colour = value;
+ public void setColourwithAlignPanel(Boolean value)
+ {
+ this.colourwithAlignPanel = value;
}
/**
- * Gets the value of the start property.
+ * Gets the value of the colourByJmol property.
+ *
+ * @return possible object is {@link Boolean }
*
*/
- public int getStart() {
- return start;
+ public boolean isColourByJmol()
+ {
+ if (colourByJmol == null)
+ {
+ return true;
+ }
+ else
+ {
+ return colourByJmol;
+ }
}
/**
- * Sets the value of the start property.
+ * Sets the value of the colourByJmol property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
*
*/
- public void setStart(int value) {
- this.start = value;
+ public void setColourByJmol(Boolean value)
+ {
+ this.colourByJmol = value;
}
/**
- * Gets the value of the end property.
+ * Gets the value of the type property.
+ *
+ * @return possible object is {@link String }
*
*/
- public int getEnd() {
- return end;
+ public String getType()
+ {
+ return type;
}
/**
- * Sets the value of the end property.
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is {@link String }
*
*/
- public void setEnd(int value) {
- this.end = value;
+ public void setType(String value)
+ {
+ this.type = value;
}
/**
- * Gets the value of the id property.
+ * Gets the value of the width property.
+ *
+ * @return possible object is {@link Integer }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getId() {
- return id;
+ public Integer getWidth()
+ {
+ return width;
}
/**
- * Sets the value of the id property.
+ * Sets the value of the width property.
*
* @param value
- * allowed object is
- * {@link String }
- *
+ * allowed object is {@link Integer }
+ *
*/
- public void setId(String value) {
- this.id = value;
+ public void setWidth(Integer value)
+ {
+ this.width = value;
}
/**
- * Gets the value of the hidden property.
+ * Gets the value of the height property.
+ *
+ * @return possible object is {@link Integer }
*
- * @return
- * possible object is
- * {@link Boolean }
- *
*/
- public Boolean isHidden() {
- return hidden;
+ public Integer getHeight()
+ {
+ return height;
}
/**
- * Sets the value of the hidden property.
+ * Sets the value of the height property.
*
* @param value
- * allowed object is
- * {@link Boolean }
- *
+ * allowed object is {@link Integer }
+ *
*/
- public void setHidden(Boolean value) {
- this.hidden = value;
+ public void setHeight(Integer value)
+ {
+ this.height = value;
}
/**
- * Gets the value of the viewreference property.
+ * Gets the value of the xpos property.
+ *
+ * @return possible object is {@link Integer }
*
- * @return
- * possible object is
- * {@link Boolean }
- *
*/
- public Boolean isViewreference() {
- return viewreference;
+ public Integer getXpos()
+ {
+ return xpos;
}
/**
- * Sets the value of the viewreference property.
+ * Sets the value of the xpos property.
*
* @param value
- * allowed object is
- * {@link Boolean }
- *
+ * allowed object is {@link Integer }
+ *
*/
- public void setViewreference(Boolean value) {
- this.viewreference = value;
+ public void setXpos(Integer value)
+ {
+ this.xpos = value;
}
-
/**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <extension base="{www.jalview.org}pdbentry">
- * <sequence>
- * <element name="structureState" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <simpleContent>
- * <extension base="<http://www.w3.org/2001/XMLSchema>string">
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </extension>
- * </simpleContent>
- * </complexType>
- * </element>
- * </sequence>
- * </extension>
- * </complexContent>
- * </complexType>
- * </pre>
+ * Gets the value of the ypos property.
*
+ * @return possible object is {@link Integer }
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "structureState"
- })
- public static class Pdbids
- extends Pdbentry
+ public Integer getYpos()
{
-
- @XmlElement(namespace = "www.jalview.org")
- protected List<JalviewModelType.JSeq.Pdbids.StructureState> structureState;
-
- /**
- * Gets the value of the structureState property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the structureState property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getStructureState().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModelType.JSeq.Pdbids.StructureState }
- *
- *
- */
- public List<JalviewModelType.JSeq.Pdbids.StructureState> getStructureState() {
- if (structureState == null) {
- structureState = new ArrayList<JalviewModelType.JSeq.Pdbids.StructureState>();
- }
- return this.structureState;
- }
-
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * <complexType>
- * <simpleContent>
- * <extension base="<http://www.w3.org/2001/XMLSchema>string">
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </extension>
- * </simpleContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "value"
- })
- public static class StructureState {
-
- @XmlValue
- protected String value;
- @XmlAttribute(name = "visible")
- protected Boolean visible;
- @XmlAttribute(name = "viewId")
- protected String viewId;
- @XmlAttribute(name = "alignwithAlignPanel")
- protected Boolean alignwithAlignPanel;
- @XmlAttribute(name = "colourwithAlignPanel")
- protected Boolean colourwithAlignPanel;
- @XmlAttribute(name = "colourByJmol")
- protected Boolean colourByJmol;
- @XmlAttribute(name = "type")
- protected String type;
- @XmlAttribute(name = "width")
- protected Integer width;
- @XmlAttribute(name = "height")
- protected Integer height;
- @XmlAttribute(name = "xpos")
- protected Integer xpos;
- @XmlAttribute(name = "ypos")
- protected Integer ypos;
-
- /**
- * Gets the value of the value property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getValue() {
- return value;
- }
-
- /**
- * Sets the value of the value property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setValue(String value) {
- this.value = value;
- }
-
- /**
- * Gets the value of the visible property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isVisible() {
- return visible;
- }
-
- /**
- * Sets the value of the visible property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setVisible(Boolean value) {
- this.visible = value;
- }
-
- /**
- * Gets the value of the viewId property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getViewId() {
- return viewId;
- }
-
- /**
- * Sets the value of the viewId property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setViewId(String value) {
- this.viewId = value;
- }
-
- /**
- * Gets the value of the alignwithAlignPanel property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isAlignwithAlignPanel() {
- if (alignwithAlignPanel == null) {
- return true;
- } else {
- return alignwithAlignPanel;
- }
- }
-
- /**
- * Sets the value of the alignwithAlignPanel property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setAlignwithAlignPanel(Boolean value) {
- this.alignwithAlignPanel = value;
- }
-
- /**
- * Gets the value of the colourwithAlignPanel property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isColourwithAlignPanel() {
- if (colourwithAlignPanel == null) {
- return false;
- } else {
- return colourwithAlignPanel;
- }
- }
-
- /**
- * Sets the value of the colourwithAlignPanel property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setColourwithAlignPanel(Boolean value) {
- this.colourwithAlignPanel = value;
- }
-
- /**
- * Gets the value of the colourByJmol property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isColourByJmol() {
- if (colourByJmol == null) {
- return true;
- } else {
- return colourByJmol;
- }
- }
-
- /**
- * Sets the value of the colourByJmol property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setColourByJmol(Boolean value) {
- this.colourByJmol = value;
- }
-
- /**
- * Gets the value of the type property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getType() {
- return type;
- }
-
- /**
- * Sets the value of the type property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setType(String value) {
- this.type = value;
- }
-
- /**
- * Gets the value of the width property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getWidth() {
- return width;
- }
-
- /**
- * Sets the value of the width property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setWidth(Integer value) {
- this.width = value;
- }
-
- /**
- * Gets the value of the height property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getHeight() {
- return height;
- }
-
- /**
- * Sets the value of the height property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setHeight(Integer value) {
- this.height = value;
- }
-
- /**
- * Gets the value of the xpos property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getXpos() {
- return xpos;
- }
-
- /**
- * Sets the value of the xpos property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setXpos(Integer value) {
- this.xpos = value;
- }
-
- /**
- * Gets the value of the ypos property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getYpos() {
- return ypos;
- }
-
- /**
- * Sets the value of the ypos property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setYpos(Integer value) {
- this.ypos = value;
- }
-
- }
-
+ return ypos;
}
-
/**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="secondaryStructure" maxOccurs="unbounded">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * Sets the value of the ypos property.
*
+ * @param value
+ * allowed object is {@link Integer }
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "secondaryStructure"
- })
- public static class RnaViewer {
-
- @XmlElement(namespace = "www.jalview.org", required = true)
- protected List<JalviewModelType.JSeq.RnaViewer.SecondaryStructure> secondaryStructure;
- @XmlAttribute(name = "title")
- protected String title;
- @XmlAttribute(name = "viewId")
- protected String viewId;
- @XmlAttribute(name = "dividerLocation")
- protected Integer dividerLocation;
- @XmlAttribute(name = "selectedRna")
- protected Integer selectedRna;
- @XmlAttribute(name = "width")
- protected Integer width;
- @XmlAttribute(name = "height")
- protected Integer height;
- @XmlAttribute(name = "xpos")
- protected Integer xpos;
- @XmlAttribute(name = "ypos")
- protected Integer ypos;
-
- /**
- * Gets the value of the secondaryStructure property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the secondaryStructure property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getSecondaryStructure().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModelType.JSeq.RnaViewer.SecondaryStructure }
- *
- *
- */
- public List<JalviewModelType.JSeq.RnaViewer.SecondaryStructure> getSecondaryStructure() {
- if (secondaryStructure == null) {
- secondaryStructure = new ArrayList<JalviewModelType.JSeq.RnaViewer.SecondaryStructure>();
- }
- return this.secondaryStructure;
- }
-
- /**
- * Gets the value of the title property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getTitle() {
- return title;
- }
-
- /**
- * Sets the value of the title property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setTitle(String value) {
- this.title = value;
- }
-
- /**
- * Gets the value of the viewId property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getViewId() {
- return viewId;
- }
-
- /**
- * Sets the value of the viewId property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setViewId(String value) {
- this.viewId = value;
- }
-
- /**
- * Gets the value of the dividerLocation property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getDividerLocation() {
- return dividerLocation;
- }
-
- /**
- * Sets the value of the dividerLocation property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setDividerLocation(Integer value) {
- this.dividerLocation = value;
- }
-
- /**
- * Gets the value of the selectedRna property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getSelectedRna() {
- return selectedRna;
- }
-
- /**
- * Sets the value of the selectedRna property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setSelectedRna(Integer value) {
- this.selectedRna = value;
- }
-
- /**
- * Gets the value of the width property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getWidth() {
- return width;
- }
-
- /**
- * Sets the value of the width property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setWidth(Integer value) {
- this.width = value;
- }
-
- /**
- * Gets the value of the height property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getHeight() {
- return height;
- }
-
- /**
- * Sets the value of the height property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setHeight(Integer value) {
- this.height = value;
- }
-
- /**
- * Gets the value of the xpos property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getXpos() {
- return xpos;
- }
-
- /**
- * Sets the value of the xpos property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setXpos(Integer value) {
- this.xpos = value;
- }
-
- /**
- * Gets the value of the ypos property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getYpos() {
- return ypos;
- }
-
- /**
- * Sets the value of the ypos property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setYpos(Integer value) {
- this.ypos = value;
- }
-
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class SecondaryStructure {
-
- @XmlAttribute(name = "title")
- protected String title;
- @XmlAttribute(name = "annotationId", required = true)
- protected String annotationId;
- @XmlAttribute(name = "gapped")
- protected Boolean gapped;
- @XmlAttribute(name = "viewerState")
- protected String viewerState;
-
- /**
- * Gets the value of the title property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getTitle() {
- return title;
- }
-
- /**
- * Sets the value of the title property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setTitle(String value) {
- this.title = value;
- }
-
- /**
- * Gets the value of the annotationId property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getAnnotationId() {
- return annotationId;
- }
-
- /**
- * Sets the value of the annotationId property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setAnnotationId(String value) {
- this.annotationId = value;
- }
-
- /**
- * Gets the value of the gapped property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isGapped() {
- return gapped;
- }
-
- /**
- * Sets the value of the gapped property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setGapped(Boolean value) {
- this.gapped = value;
- }
-
- /**
- * Gets the value of the viewerState property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getViewerState() {
- return viewerState;
- }
-
- /**
- * Sets the value of the viewerState property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setViewerState(String value) {
- this.viewerState = value;
- }
-
- }
-
+ public void setYpos(Integer value)
+ {
+ this.ypos = value;
}
- }
+ }
+ }
/**
- * <p>Java class for anonymous complex type.
+ * <p>
+ * Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
*
* <pre>
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence minOccurs="0">
- * <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
- * <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * <sequence>
+ * <element name="secondaryStructure" maxOccurs="unbounded">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
* </sequence>
* <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
* </restriction>
* </complexContent>
* </complexType>
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "title",
- "newick"
- })
- public static class Tree {
+ @XmlType(name = "", propOrder = { "secondaryStructure" })
+ public static class RnaViewer
+ {
+
+ @XmlElement(namespace = "www.jalview.org", required = true)
+ protected List<JalviewModelType.JSeq.RnaViewer.SecondaryStructure> secondaryStructure;
+
+ @XmlAttribute(name = "title")
+ protected String title;
+
+ @XmlAttribute(name = "viewId")
+ protected String viewId;
+
+ @XmlAttribute(name = "dividerLocation")
+ protected Integer dividerLocation;
+
+ @XmlAttribute(name = "selectedRna")
+ protected Integer selectedRna;
+
+ @XmlAttribute(name = "width")
+ protected Integer width;
+
+ @XmlAttribute(name = "height")
+ protected Integer height;
+
+ @XmlAttribute(name = "xpos")
+ protected Integer xpos;
+
+ @XmlAttribute(name = "ypos")
+ protected Integer ypos;
+
+ /**
+ * Gets the value of the secondaryStructure property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the secondaryStructure property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getSecondaryStructure().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModelType.JSeq.RnaViewer.SecondaryStructure }
+ *
+ *
+ */
+ public List<JalviewModelType.JSeq.RnaViewer.SecondaryStructure> getSecondaryStructure()
+ {
+ if (secondaryStructure == null)
+ {
+ secondaryStructure = new ArrayList<JalviewModelType.JSeq.RnaViewer.SecondaryStructure>();
+ }
+ return this.secondaryStructure;
+ }
+
+ /**
+ * Gets the value of the title property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getTitle()
+ {
+ return title;
+ }
+
+ /**
+ * Sets the value of the title property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setTitle(String value)
+ {
+ this.title = value;
+ }
+
+ /**
+ * Gets the value of the viewId property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getViewId()
+ {
+ return viewId;
+ }
+
+ /**
+ * Sets the value of the viewId property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setViewId(String value)
+ {
+ this.viewId = value;
+ }
+
+ /**
+ * Gets the value of the dividerLocation property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getDividerLocation()
+ {
+ return dividerLocation;
+ }
+
+ /**
+ * Sets the value of the dividerLocation property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setDividerLocation(Integer value)
+ {
+ this.dividerLocation = value;
+ }
+
+ /**
+ * Gets the value of the selectedRna property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getSelectedRna()
+ {
+ return selectedRna;
+ }
+
+ /**
+ * Sets the value of the selectedRna property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setSelectedRna(Integer value)
+ {
+ this.selectedRna = value;
+ }
+
+ /**
+ * Gets the value of the width property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getWidth()
+ {
+ return width;
+ }
+
+ /**
+ * Sets the value of the width property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setWidth(Integer value)
+ {
+ this.width = value;
+ }
+
+ /**
+ * Gets the value of the height property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getHeight()
+ {
+ return height;
+ }
+
+ /**
+ * Sets the value of the height property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setHeight(Integer value)
+ {
+ this.height = value;
+ }
+
+ /**
+ * Gets the value of the xpos property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getXpos()
+ {
+ return xpos;
+ }
+
+ /**
+ * Sets the value of the xpos property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setXpos(Integer value)
+ {
+ this.xpos = value;
+ }
+
+ /**
+ * Gets the value of the ypos property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getYpos()
+ {
+ return ypos;
+ }
+
+ /**
+ * Sets the value of the ypos property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setYpos(Integer value)
+ {
+ this.ypos = value;
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class SecondaryStructure
+ {
- @XmlElement(namespace = "www.jalview.org")
+ @XmlAttribute(name = "title")
protected String title;
- @XmlElement(namespace = "www.jalview.org")
- protected String newick;
- @XmlAttribute(name = "fontName")
- protected String fontName;
- @XmlAttribute(name = "fontSize")
- protected Integer fontSize;
- @XmlAttribute(name = "fontStyle")
- protected Integer fontStyle;
- @XmlAttribute(name = "threshold")
- protected Float threshold;
- @XmlAttribute(name = "showBootstrap")
- protected Boolean showBootstrap;
- @XmlAttribute(name = "showDistances")
- protected Boolean showDistances;
- @XmlAttribute(name = "markUnlinked")
- protected Boolean markUnlinked;
- @XmlAttribute(name = "fitToWindow")
- protected Boolean fitToWindow;
- @XmlAttribute(name = "currentTree")
- protected Boolean currentTree;
- @XmlAttribute(name = "id")
- @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
- @XmlID
- @XmlSchemaType(name = "ID")
- protected String id;
- @XmlAttribute(name = "width")
- protected Integer width;
- @XmlAttribute(name = "height")
- protected Integer height;
- @XmlAttribute(name = "xpos")
- protected Integer xpos;
- @XmlAttribute(name = "ypos")
- protected Integer ypos;
+
+ @XmlAttribute(name = "annotationId", required = true)
+ protected String annotationId;
+
+ @XmlAttribute(name = "gapped")
+ protected Boolean gapped;
+
+ @XmlAttribute(name = "viewerState")
+ protected String viewerState;
/**
* Gets the value of the title property.
*
- * @return
- * possible object is
- * {@link String }
- *
+ * @return possible object is {@link String }
+ *
*/
- public String getTitle() {
- return title;
+ public String getTitle()
+ {
+ return title;
}
/**
* Sets the value of the title property.
*
* @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setTitle(String value) {
- this.title = value;
- }
-
- /**
- * Gets the value of the newick property.
+ * allowed object is {@link String }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getNewick() {
- return newick;
+ public void setTitle(String value)
+ {
+ this.title = value;
}
/**
- * Sets the value of the newick property.
+ * Gets the value of the annotationId property.
*
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setNewick(String value) {
- this.newick = value;
- }
-
- /**
- * Gets the value of the fontName property.
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getFontName() {
- return fontName;
+ public String getAnnotationId()
+ {
+ return annotationId;
}
/**
- * Sets the value of the fontName property.
+ * Sets the value of the annotationId property.
*
* @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setFontName(String value) {
- this.fontName = value;
- }
-
- /**
- * Gets the value of the fontSize property.
+ * allowed object is {@link String }
*
- * @return
- * possible object is
- * {@link Integer }
- *
*/
- public Integer getFontSize() {
- return fontSize;
+ public void setAnnotationId(String value)
+ {
+ this.annotationId = value;
}
/**
- * Sets the value of the fontSize property.
+ * Gets the value of the gapped property.
*
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setFontSize(Integer value) {
- this.fontSize = value;
- }
-
- /**
- * Gets the value of the fontStyle property.
+ * @return possible object is {@link Boolean }
*
- * @return
- * possible object is
- * {@link Integer }
- *
*/
- public Integer getFontStyle() {
- return fontStyle;
+ public Boolean isGapped()
+ {
+ return gapped;
}
/**
- * Sets the value of the fontStyle property.
+ * Sets the value of the gapped property.
*
* @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setFontStyle(Integer value) {
- this.fontStyle = value;
- }
-
- /**
- * Gets the value of the threshold property.
+ * allowed object is {@link Boolean }
*
- * @return
- * possible object is
- * {@link Float }
- *
*/
- public Float getThreshold() {
- return threshold;
+ public void setGapped(Boolean value)
+ {
+ this.gapped = value;
}
/**
- * Sets the value of the threshold property.
+ * Gets the value of the viewerState property.
*
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setThreshold(Float value) {
- this.threshold = value;
- }
-
- /**
- * Gets the value of the showBootstrap property.
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link Boolean }
- *
*/
- public Boolean isShowBootstrap() {
- return showBootstrap;
+ public String getViewerState()
+ {
+ return viewerState;
}
/**
- * Sets the value of the showBootstrap property.
+ * Sets the value of the viewerState property.
*
* @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowBootstrap(Boolean value) {
- this.showBootstrap = value;
- }
-
- /**
- * Gets the value of the showDistances property.
+ * allowed object is {@link String }
*
- * @return
- * possible object is
- * {@link Boolean }
- *
*/
- public Boolean isShowDistances() {
- return showDistances;
+ public void setViewerState(String value)
+ {
+ this.viewerState = value;
}
- /**
- * Sets the value of the showDistances property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowDistances(Boolean value) {
- this.showDistances = value;
- }
+ }
- /**
- * Gets the value of the markUnlinked property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isMarkUnlinked() {
- return markUnlinked;
- }
+ }
- /**
- * Sets the value of the markUnlinked property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setMarkUnlinked(Boolean value) {
- this.markUnlinked = value;
- }
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence minOccurs="0">
+ * <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * </sequence>
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "title", "newick" })
+ public static class Tree
+ {
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected String title;
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected String newick;
+
+ @XmlAttribute(name = "fontName")
+ protected String fontName;
+
+ @XmlAttribute(name = "fontSize")
+ protected Integer fontSize;
+
+ @XmlAttribute(name = "fontStyle")
+ protected Integer fontStyle;
+
+ @XmlAttribute(name = "threshold")
+ protected Float threshold;
+
+ @XmlAttribute(name = "showBootstrap")
+ protected Boolean showBootstrap;
+
+ @XmlAttribute(name = "showDistances")
+ protected Boolean showDistances;
+
+ @XmlAttribute(name = "markUnlinked")
+ protected Boolean markUnlinked;
+
+ @XmlAttribute(name = "fitToWindow")
+ protected Boolean fitToWindow;
+
+ @XmlAttribute(name = "currentTree")
+ protected Boolean currentTree;
+
+ @XmlAttribute(name = "id")
+ @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
+ @XmlID
+ @XmlSchemaType(name = "ID")
+ protected String id;
+
+ @XmlAttribute(name = "width")
+ protected Integer width;
+
+ @XmlAttribute(name = "height")
+ protected Integer height;
+
+ @XmlAttribute(name = "xpos")
+ protected Integer xpos;
+
+ @XmlAttribute(name = "ypos")
+ protected Integer ypos;
- /**
- * Gets the value of the fitToWindow property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isFitToWindow() {
- return fitToWindow;
- }
+ /**
+ * Gets the value of the title property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getTitle()
+ {
+ return title;
+ }
- /**
- * Sets the value of the fitToWindow property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setFitToWindow(Boolean value) {
- this.fitToWindow = value;
- }
+ /**
+ * Sets the value of the title property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setTitle(String value)
+ {
+ this.title = value;
+ }
- /**
- * Gets the value of the currentTree property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isCurrentTree() {
- return currentTree;
- }
+ /**
+ * Gets the value of the newick property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getNewick()
+ {
+ return newick;
+ }
- /**
- * Sets the value of the currentTree property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setCurrentTree(Boolean value) {
- this.currentTree = value;
- }
+ /**
+ * Sets the value of the newick property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setNewick(String value)
+ {
+ this.newick = value;
+ }
- /**
- * Gets the value of the id property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getId() {
- return id;
- }
+ /**
+ * Gets the value of the fontName property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getFontName()
+ {
+ return fontName;
+ }
+
+ /**
+ * Sets the value of the fontName property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setFontName(String value)
+ {
+ this.fontName = value;
+ }
+
+ /**
+ * Gets the value of the fontSize property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getFontSize()
+ {
+ return fontSize;
+ }
+
+ /**
+ * Sets the value of the fontSize property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setFontSize(Integer value)
+ {
+ this.fontSize = value;
+ }
+
+ /**
+ * Gets the value of the fontStyle property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getFontStyle()
+ {
+ return fontStyle;
+ }
+
+ /**
+ * Sets the value of the fontStyle property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setFontStyle(Integer value)
+ {
+ this.fontStyle = value;
+ }
+
+ /**
+ * Gets the value of the threshold property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getThreshold()
+ {
+ return threshold;
+ }
+
+ /**
+ * Sets the value of the threshold property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setThreshold(Float value)
+ {
+ this.threshold = value;
+ }
+
+ /**
+ * Gets the value of the showBootstrap property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowBootstrap()
+ {
+ return showBootstrap;
+ }
+
+ /**
+ * Sets the value of the showBootstrap property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowBootstrap(Boolean value)
+ {
+ this.showBootstrap = value;
+ }
+
+ /**
+ * Gets the value of the showDistances property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowDistances()
+ {
+ return showDistances;
+ }
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setId(String value) {
- this.id = value;
- }
+ /**
+ * Sets the value of the showDistances property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowDistances(Boolean value)
+ {
+ this.showDistances = value;
+ }
- /**
- * Gets the value of the width property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getWidth() {
- return width;
- }
+ /**
+ * Gets the value of the markUnlinked property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isMarkUnlinked()
+ {
+ return markUnlinked;
+ }
- /**
- * Sets the value of the width property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setWidth(Integer value) {
- this.width = value;
- }
+ /**
+ * Sets the value of the markUnlinked property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setMarkUnlinked(Boolean value)
+ {
+ this.markUnlinked = value;
+ }
- /**
- * Gets the value of the height property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getHeight() {
- return height;
- }
+ /**
+ * Gets the value of the fitToWindow property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isFitToWindow()
+ {
+ return fitToWindow;
+ }
- /**
- * Sets the value of the height property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setHeight(Integer value) {
- this.height = value;
- }
+ /**
+ * Sets the value of the fitToWindow property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setFitToWindow(Boolean value)
+ {
+ this.fitToWindow = value;
+ }
- /**
- * Gets the value of the xpos property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getXpos() {
- return xpos;
- }
+ /**
+ * Gets the value of the currentTree property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isCurrentTree()
+ {
+ return currentTree;
+ }
- /**
- * Sets the value of the xpos property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setXpos(Integer value) {
- this.xpos = value;
- }
+ /**
+ * Sets the value of the currentTree property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setCurrentTree(Boolean value)
+ {
+ this.currentTree = value;
+ }
- /**
- * Gets the value of the ypos property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getYpos() {
- return ypos;
- }
+ /**
+ * Gets the value of the id property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getId()
+ {
+ return id;
+ }
- /**
- * Sets the value of the ypos property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setYpos(Integer value) {
- this.ypos = value;
- }
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setId(String value)
+ {
+ this.id = value;
+ }
+ /**
+ * Gets the value of the width property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getWidth()
+ {
+ return width;
}
+ /**
+ * Sets the value of the width property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setWidth(Integer value)
+ {
+ this.width = value;
+ }
/**
- * <p>Java class for anonymous complex type.
+ * Gets the value of the height property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * @return possible object is {@link Integer }
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
- * </sequence>
- * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ */
+ public Integer getHeight()
+ {
+ return height;
+ }
+
+ /**
+ * Sets the value of the height property.
*
+ * @param value
+ * allowed object is {@link Integer }
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "userColourScheme"
- })
- public static class UserColours {
+ public void setHeight(Integer value)
+ {
+ this.height = value;
+ }
- @XmlElement(name = "UserColourScheme", namespace = "www.jalview.org", required = true)
- protected JalviewUserColours userColourScheme;
- @XmlAttribute(name = "id")
- protected String id;
+ /**
+ * Gets the value of the xpos property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getXpos()
+ {
+ return xpos;
+ }
- /**
- * Gets the value of the userColourScheme property.
- *
- * @return
- * possible object is
- * {@link JalviewUserColours }
- *
- */
- public JalviewUserColours getUserColourScheme() {
- return userColourScheme;
- }
+ /**
+ * Sets the value of the xpos property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setXpos(Integer value)
+ {
+ this.xpos = value;
+ }
- /**
- * Sets the value of the userColourScheme property.
- *
- * @param value
- * allowed object is
- * {@link JalviewUserColours }
- *
- */
- public void setUserColourScheme(JalviewUserColours value) {
- this.userColourScheme = value;
- }
+ /**
+ * Gets the value of the ypos property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getYpos()
+ {
+ return ypos;
+ }
- /**
- * Gets the value of the id property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getId() {
- return id;
- }
+ /**
+ * Sets the value of the ypos property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setYpos(Integer value)
+ {
+ this.ypos = value;
+ }
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setId(String value) {
- this.id = value;
- }
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
+ * </sequence>
+ * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "userColourScheme" })
+ public static class UserColours
+ {
+
+ @XmlElement(
+ name = "UserColourScheme",
+ namespace = "www.jalview.org",
+ required = true)
+ protected JalviewUserColours userColourScheme;
+
+ @XmlAttribute(name = "id")
+ protected String id;
+ /**
+ * Gets the value of the userColourScheme property.
+ *
+ * @return possible object is {@link JalviewUserColours }
+ *
+ */
+ public JalviewUserColours getUserColourScheme()
+ {
+ return userColourScheme;
}
+ /**
+ * Sets the value of the userColourScheme property.
+ *
+ * @param value
+ * allowed object is {@link JalviewUserColours }
+ *
+ */
+ public void setUserColourScheme(JalviewUserColours value)
+ {
+ this.userColourScheme = value;
+ }
/**
- * <p>Java class for anonymous complex type.
+ * Gets the value of the id property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * @return possible object is {@link String }
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
- * <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
- * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </extension>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
- * <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ */
+ public String getId()
+ {
+ return id;
+ }
+
+ /**
+ * Sets the value of the id property.
*
+ * @param value
+ * allowed object is {@link String }
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "annotationColours",
- "hiddenColumns",
- "calcIdParam"
- })
- public static class Viewport {
-
- @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
- protected AnnotationColourScheme annotationColours;
- @XmlElement(namespace = "www.jalview.org")
- protected List<JalviewModelType.Viewport.HiddenColumns> hiddenColumns;
- @XmlElement(namespace = "www.jalview.org")
- protected List<JalviewModelType.Viewport.CalcIdParam> calcIdParam;
- @XmlAttribute(name = "conservationSelected")
- protected Boolean conservationSelected;
- @XmlAttribute(name = "pidSelected")
- protected Boolean pidSelected;
- @XmlAttribute(name = "bgColour")
- protected String bgColour;
- @XmlAttribute(name = "consThreshold")
- protected Integer consThreshold;
- @XmlAttribute(name = "pidThreshold")
- protected Integer pidThreshold;
- @XmlAttribute(name = "title")
- protected String title;
- @XmlAttribute(name = "showFullId")
- protected Boolean showFullId;
- @XmlAttribute(name = "rightAlignIds")
- protected Boolean rightAlignIds;
- @XmlAttribute(name = "showText")
- protected Boolean showText;
- @XmlAttribute(name = "showColourText")
- protected Boolean showColourText;
- @XmlAttribute(name = "showUnconserved")
- protected Boolean showUnconserved;
- @XmlAttribute(name = "showBoxes")
- protected Boolean showBoxes;
- @XmlAttribute(name = "wrapAlignment")
- protected Boolean wrapAlignment;
- @XmlAttribute(name = "renderGaps")
- protected Boolean renderGaps;
- @XmlAttribute(name = "showSequenceFeatures")
- protected Boolean showSequenceFeatures;
- @XmlAttribute(name = "showNPfeatureTooltip")
- protected Boolean showNPfeatureTooltip;
- @XmlAttribute(name = "showDbRefTooltip")
- protected Boolean showDbRefTooltip;
- @XmlAttribute(name = "followHighlight")
- protected Boolean followHighlight;
- @XmlAttribute(name = "followSelection")
- protected Boolean followSelection;
- @XmlAttribute(name = "showAnnotation")
- protected Boolean showAnnotation;
- @XmlAttribute(name = "centreColumnLabels")
- protected Boolean centreColumnLabels;
- @XmlAttribute(name = "showGroupConservation")
- protected Boolean showGroupConservation;
- @XmlAttribute(name = "showGroupConsensus")
- protected Boolean showGroupConsensus;
- @XmlAttribute(name = "showConsensusHistogram")
- protected Boolean showConsensusHistogram;
- @XmlAttribute(name = "showSequenceLogo")
- protected Boolean showSequenceLogo;
- @XmlAttribute(name = "normaliseSequenceLogo")
- protected Boolean normaliseSequenceLogo;
- @XmlAttribute(name = "ignoreGapsinConsensus")
- protected Boolean ignoreGapsinConsensus;
- @XmlAttribute(name = "startRes")
- protected Integer startRes;
- @XmlAttribute(name = "startSeq")
- protected Integer startSeq;
- @XmlAttribute(name = "fontName")
- protected String fontName;
- @XmlAttribute(name = "fontSize")
- protected Integer fontSize;
- @XmlAttribute(name = "fontStyle")
- protected Integer fontStyle;
- @XmlAttribute(name = "scaleProteinAsCdna")
- protected Boolean scaleProteinAsCdna;
- @XmlAttribute(name = "viewName")
- protected String viewName;
- @XmlAttribute(name = "sequenceSetId")
- protected String sequenceSetId;
- @XmlAttribute(name = "gatheredViews")
- protected Boolean gatheredViews;
- @XmlAttribute(name = "textCol1")
- protected Integer textCol1;
- @XmlAttribute(name = "textCol2")
- protected Integer textCol2;
- @XmlAttribute(name = "textColThreshold")
- protected Integer textColThreshold;
- @XmlAttribute(name = "id")
- @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
- @XmlID
- @XmlSchemaType(name = "ID")
- protected String id;
- @XmlAttribute(name = "complementId")
- protected String complementId;
- @XmlAttribute(name = "width")
- protected Integer width;
- @XmlAttribute(name = "height")
- protected Integer height;
- @XmlAttribute(name = "xpos")
- protected Integer xpos;
- @XmlAttribute(name = "ypos")
- protected Integer ypos;
+ public void setId(String value)
+ {
+ this.id = value;
+ }
- /**
- * Gets the value of the annotationColours property.
- *
- * @return
- * possible object is
- * {@link AnnotationColourScheme }
- *
- */
- public AnnotationColourScheme getAnnotationColours() {
- return annotationColours;
- }
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+ * <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
+ * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </extension>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+ * <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(
+ name = "",
+ propOrder =
+ { "annotationColours", "hiddenColumns", "calcIdParam" })
+ public static class Viewport
+ {
+
+ @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
+ protected AnnotationColourScheme annotationColours;
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<JalviewModelType.Viewport.HiddenColumns> hiddenColumns;
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected List<JalviewModelType.Viewport.CalcIdParam> calcIdParam;
+
+ @XmlAttribute(name = "conservationSelected")
+ protected Boolean conservationSelected;
+
+ @XmlAttribute(name = "pidSelected")
+ protected Boolean pidSelected;
+
+ @XmlAttribute(name = "bgColour")
+ protected String bgColour;
+
+ @XmlAttribute(name = "consThreshold")
+ protected Integer consThreshold;
+
+ @XmlAttribute(name = "pidThreshold")
+ protected Integer pidThreshold;
+
+ @XmlAttribute(name = "title")
+ protected String title;
+
+ @XmlAttribute(name = "showFullId")
+ protected Boolean showFullId;
+
+ @XmlAttribute(name = "rightAlignIds")
+ protected Boolean rightAlignIds;
+
+ @XmlAttribute(name = "showText")
+ protected Boolean showText;
+
+ @XmlAttribute(name = "showColourText")
+ protected Boolean showColourText;
+
+ @XmlAttribute(name = "showUnconserved")
+ protected Boolean showUnconserved;
+
+ @XmlAttribute(name = "showBoxes")
+ protected Boolean showBoxes;
+
+ @XmlAttribute(name = "wrapAlignment")
+ protected Boolean wrapAlignment;
+
+ @XmlAttribute(name = "renderGaps")
+ protected Boolean renderGaps;
- /**
- * Sets the value of the annotationColours property.
- *
- * @param value
- * allowed object is
- * {@link AnnotationColourScheme }
- *
- */
- public void setAnnotationColours(AnnotationColourScheme value) {
- this.annotationColours = value;
- }
+ @XmlAttribute(name = "showSequenceFeatures")
+ protected Boolean showSequenceFeatures;
- /**
- * Gets the value of the hiddenColumns property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the hiddenColumns property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getHiddenColumns().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModelType.Viewport.HiddenColumns }
- *
- *
- */
- public List<JalviewModelType.Viewport.HiddenColumns> getHiddenColumns() {
- if (hiddenColumns == null) {
- hiddenColumns = new ArrayList<JalviewModelType.Viewport.HiddenColumns>();
- }
- return this.hiddenColumns;
- }
+ @XmlAttribute(name = "showNPfeatureTooltip")
+ protected Boolean showNPfeatureTooltip;
+
+ @XmlAttribute(name = "showDbRefTooltip")
+ protected Boolean showDbRefTooltip;
+
+ @XmlAttribute(name = "followHighlight")
+ protected Boolean followHighlight;
+
+ @XmlAttribute(name = "followSelection")
+ protected Boolean followSelection;
+
+ @XmlAttribute(name = "showAnnotation")
+ protected Boolean showAnnotation;
+
+ @XmlAttribute(name = "centreColumnLabels")
+ protected Boolean centreColumnLabels;
+
+ @XmlAttribute(name = "showGroupConservation")
+ protected Boolean showGroupConservation;
+
+ @XmlAttribute(name = "showGroupConsensus")
+ protected Boolean showGroupConsensus;
+
+ @XmlAttribute(name = "showConsensusHistogram")
+ protected Boolean showConsensusHistogram;
+
+ @XmlAttribute(name = "showSequenceLogo")
+ protected Boolean showSequenceLogo;
+
+ @XmlAttribute(name = "normaliseSequenceLogo")
+ protected Boolean normaliseSequenceLogo;
+
+ @XmlAttribute(name = "ignoreGapsinConsensus")
+ protected Boolean ignoreGapsinConsensus;
+
+ @XmlAttribute(name = "startRes")
+ protected Integer startRes;
+
+ @XmlAttribute(name = "startSeq")
+ protected Integer startSeq;
+
+ @XmlAttribute(name = "fontName")
+ protected String fontName;
+
+ @XmlAttribute(name = "fontSize")
+ protected Integer fontSize;
+
+ @XmlAttribute(name = "fontStyle")
+ protected Integer fontStyle;
+
+ @XmlAttribute(name = "scaleProteinAsCdna")
+ protected Boolean scaleProteinAsCdna;
+
+ @XmlAttribute(name = "viewName")
+ protected String viewName;
+
+ @XmlAttribute(name = "sequenceSetId")
+ protected String sequenceSetId;
+
+ @XmlAttribute(name = "gatheredViews")
+ protected Boolean gatheredViews;
- /**
- * Gets the value of the calcIdParam property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the calcIdParam property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getCalcIdParam().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModelType.Viewport.CalcIdParam }
- *
- *
- */
- public List<JalviewModelType.Viewport.CalcIdParam> getCalcIdParam() {
- if (calcIdParam == null) {
- calcIdParam = new ArrayList<JalviewModelType.Viewport.CalcIdParam>();
- }
- return this.calcIdParam;
- }
+ @XmlAttribute(name = "textCol1")
+ protected Integer textCol1;
- /**
- * Gets the value of the conservationSelected property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isConservationSelected() {
- return conservationSelected;
- }
+ @XmlAttribute(name = "textCol2")
+ protected Integer textCol2;
- /**
- * Sets the value of the conservationSelected property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setConservationSelected(Boolean value) {
- this.conservationSelected = value;
- }
+ @XmlAttribute(name = "textColThreshold")
+ protected Integer textColThreshold;
- /**
- * Gets the value of the pidSelected property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isPidSelected() {
- return pidSelected;
- }
+ @XmlAttribute(name = "id")
+ @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
+ @XmlID
+ @XmlSchemaType(name = "ID")
+ protected String id;
- /**
- * Sets the value of the pidSelected property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setPidSelected(Boolean value) {
- this.pidSelected = value;
- }
+ @XmlAttribute(name = "complementId")
+ protected String complementId;
- /**
- * Gets the value of the bgColour property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getBgColour() {
- return bgColour;
- }
+ @XmlAttribute(name = "width")
+ protected Integer width;
- /**
- * Sets the value of the bgColour property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setBgColour(String value) {
- this.bgColour = value;
- }
+ @XmlAttribute(name = "height")
+ protected Integer height;
- /**
- * Gets the value of the consThreshold property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getConsThreshold() {
- return consThreshold;
- }
+ @XmlAttribute(name = "xpos")
+ protected Integer xpos;
- /**
- * Sets the value of the consThreshold property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setConsThreshold(Integer value) {
- this.consThreshold = value;
- }
+ @XmlAttribute(name = "ypos")
+ protected Integer ypos;
- /**
- * Gets the value of the pidThreshold property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getPidThreshold() {
- return pidThreshold;
- }
+ /**
+ * Gets the value of the annotationColours property.
+ *
+ * @return possible object is {@link AnnotationColourScheme }
+ *
+ */
+ public AnnotationColourScheme getAnnotationColours()
+ {
+ return annotationColours;
+ }
- /**
- * Sets the value of the pidThreshold property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setPidThreshold(Integer value) {
- this.pidThreshold = value;
- }
+ /**
+ * Sets the value of the annotationColours property.
+ *
+ * @param value
+ * allowed object is {@link AnnotationColourScheme }
+ *
+ */
+ public void setAnnotationColours(AnnotationColourScheme value)
+ {
+ this.annotationColours = value;
+ }
- /**
- * Gets the value of the title property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getTitle() {
- return title;
- }
+ /**
+ * Gets the value of the hiddenColumns property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the hiddenColumns property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getHiddenColumns().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModelType.Viewport.HiddenColumns }
+ *
+ *
+ */
+ public List<JalviewModelType.Viewport.HiddenColumns> getHiddenColumns()
+ {
+ if (hiddenColumns == null)
+ {
+ hiddenColumns = new ArrayList<JalviewModelType.Viewport.HiddenColumns>();
+ }
+ return this.hiddenColumns;
+ }
- /**
- * Sets the value of the title property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setTitle(String value) {
- this.title = value;
- }
+ /**
+ * Gets the value of the calcIdParam property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the calcIdParam property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getCalcIdParam().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModelType.Viewport.CalcIdParam }
+ *
+ *
+ */
+ public List<JalviewModelType.Viewport.CalcIdParam> getCalcIdParam()
+ {
+ if (calcIdParam == null)
+ {
+ calcIdParam = new ArrayList<JalviewModelType.Viewport.CalcIdParam>();
+ }
+ return this.calcIdParam;
+ }
- /**
- * Gets the value of the showFullId property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowFullId() {
- return showFullId;
- }
+ /**
+ * Gets the value of the conservationSelected property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isConservationSelected()
+ {
+ return conservationSelected;
+ }
- /**
- * Sets the value of the showFullId property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowFullId(Boolean value) {
- this.showFullId = value;
- }
+ /**
+ * Sets the value of the conservationSelected property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setConservationSelected(Boolean value)
+ {
+ this.conservationSelected = value;
+ }
- /**
- * Gets the value of the rightAlignIds property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isRightAlignIds() {
- return rightAlignIds;
- }
+ /**
+ * Gets the value of the pidSelected property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isPidSelected()
+ {
+ return pidSelected;
+ }
- /**
- * Sets the value of the rightAlignIds property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setRightAlignIds(Boolean value) {
- this.rightAlignIds = value;
- }
+ /**
+ * Sets the value of the pidSelected property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setPidSelected(Boolean value)
+ {
+ this.pidSelected = value;
+ }
- /**
- * Gets the value of the showText property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowText() {
- return showText;
- }
+ /**
+ * Gets the value of the bgColour property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getBgColour()
+ {
+ return bgColour;
+ }
- /**
- * Sets the value of the showText property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowText(Boolean value) {
- this.showText = value;
- }
+ /**
+ * Sets the value of the bgColour property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setBgColour(String value)
+ {
+ this.bgColour = value;
+ }
- /**
- * Gets the value of the showColourText property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowColourText() {
- return showColourText;
- }
+ /**
+ * Gets the value of the consThreshold property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getConsThreshold()
+ {
+ return consThreshold;
+ }
- /**
- * Sets the value of the showColourText property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowColourText(Boolean value) {
- this.showColourText = value;
- }
+ /**
+ * Sets the value of the consThreshold property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setConsThreshold(Integer value)
+ {
+ this.consThreshold = value;
+ }
- /**
- * Gets the value of the showUnconserved property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isShowUnconserved() {
- if (showUnconserved == null) {
- return false;
- } else {
- return showUnconserved;
- }
- }
+ /**
+ * Gets the value of the pidThreshold property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getPidThreshold()
+ {
+ return pidThreshold;
+ }
- /**
- * Sets the value of the showUnconserved property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowUnconserved(Boolean value) {
- this.showUnconserved = value;
- }
+ /**
+ * Sets the value of the pidThreshold property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setPidThreshold(Integer value)
+ {
+ this.pidThreshold = value;
+ }
- /**
- * Gets the value of the showBoxes property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowBoxes() {
- return showBoxes;
- }
+ /**
+ * Gets the value of the title property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getTitle()
+ {
+ return title;
+ }
- /**
- * Sets the value of the showBoxes property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowBoxes(Boolean value) {
- this.showBoxes = value;
- }
+ /**
+ * Sets the value of the title property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setTitle(String value)
+ {
+ this.title = value;
+ }
+
+ /**
+ * Gets the value of the showFullId property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowFullId()
+ {
+ return showFullId;
+ }
+
+ /**
+ * Sets the value of the showFullId property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowFullId(Boolean value)
+ {
+ this.showFullId = value;
+ }
+
+ /**
+ * Gets the value of the rightAlignIds property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isRightAlignIds()
+ {
+ return rightAlignIds;
+ }
+
+ /**
+ * Sets the value of the rightAlignIds property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setRightAlignIds(Boolean value)
+ {
+ this.rightAlignIds = value;
+ }
- /**
- * Gets the value of the wrapAlignment property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isWrapAlignment() {
- return wrapAlignment;
- }
+ /**
+ * Gets the value of the showText property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowText()
+ {
+ return showText;
+ }
- /**
- * Sets the value of the wrapAlignment property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setWrapAlignment(Boolean value) {
- this.wrapAlignment = value;
- }
+ /**
+ * Sets the value of the showText property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowText(Boolean value)
+ {
+ this.showText = value;
+ }
- /**
- * Gets the value of the renderGaps property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isRenderGaps() {
- return renderGaps;
- }
+ /**
+ * Gets the value of the showColourText property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowColourText()
+ {
+ return showColourText;
+ }
- /**
- * Sets the value of the renderGaps property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setRenderGaps(Boolean value) {
- this.renderGaps = value;
- }
+ /**
+ * Sets the value of the showColourText property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowColourText(Boolean value)
+ {
+ this.showColourText = value;
+ }
- /**
- * Gets the value of the showSequenceFeatures property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowSequenceFeatures() {
- return showSequenceFeatures;
- }
+ /**
+ * Gets the value of the showUnconserved property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isShowUnconserved()
+ {
+ if (showUnconserved == null)
+ {
+ return false;
+ }
+ else
+ {
+ return showUnconserved;
+ }
+ }
- /**
- * Sets the value of the showSequenceFeatures property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowSequenceFeatures(Boolean value) {
- this.showSequenceFeatures = value;
- }
+ /**
+ * Sets the value of the showUnconserved property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowUnconserved(Boolean value)
+ {
+ this.showUnconserved = value;
+ }
- /**
- * Gets the value of the showNPfeatureTooltip property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowNPfeatureTooltip() {
- return showNPfeatureTooltip;
- }
+ /**
+ * Gets the value of the showBoxes property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowBoxes()
+ {
+ return showBoxes;
+ }
- /**
- * Sets the value of the showNPfeatureTooltip property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowNPfeatureTooltip(Boolean value) {
- this.showNPfeatureTooltip = value;
- }
+ /**
+ * Sets the value of the showBoxes property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowBoxes(Boolean value)
+ {
+ this.showBoxes = value;
+ }
- /**
- * Gets the value of the showDbRefTooltip property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowDbRefTooltip() {
- return showDbRefTooltip;
- }
+ /**
+ * Gets the value of the wrapAlignment property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isWrapAlignment()
+ {
+ return wrapAlignment;
+ }
- /**
- * Sets the value of the showDbRefTooltip property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowDbRefTooltip(Boolean value) {
- this.showDbRefTooltip = value;
- }
+ /**
+ * Sets the value of the wrapAlignment property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setWrapAlignment(Boolean value)
+ {
+ this.wrapAlignment = value;
+ }
- /**
- * Gets the value of the followHighlight property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isFollowHighlight() {
- if (followHighlight == null) {
- return true;
- } else {
- return followHighlight;
- }
- }
+ /**
+ * Gets the value of the renderGaps property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isRenderGaps()
+ {
+ return renderGaps;
+ }
- /**
- * Sets the value of the followHighlight property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setFollowHighlight(Boolean value) {
- this.followHighlight = value;
- }
+ /**
+ * Sets the value of the renderGaps property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setRenderGaps(Boolean value)
+ {
+ this.renderGaps = value;
+ }
- /**
- * Gets the value of the followSelection property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isFollowSelection() {
- if (followSelection == null) {
- return true;
- } else {
- return followSelection;
- }
- }
+ /**
+ * Gets the value of the showSequenceFeatures property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowSequenceFeatures()
+ {
+ return showSequenceFeatures;
+ }
- /**
- * Sets the value of the followSelection property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setFollowSelection(Boolean value) {
- this.followSelection = value;
- }
+ /**
+ * Sets the value of the showSequenceFeatures property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowSequenceFeatures(Boolean value)
+ {
+ this.showSequenceFeatures = value;
+ }
- /**
- * Gets the value of the showAnnotation property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowAnnotation() {
- return showAnnotation;
- }
+ /**
+ * Gets the value of the showNPfeatureTooltip property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowNPfeatureTooltip()
+ {
+ return showNPfeatureTooltip;
+ }
- /**
- * Sets the value of the showAnnotation property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowAnnotation(Boolean value) {
- this.showAnnotation = value;
- }
+ /**
+ * Sets the value of the showNPfeatureTooltip property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowNPfeatureTooltip(Boolean value)
+ {
+ this.showNPfeatureTooltip = value;
+ }
- /**
- * Gets the value of the centreColumnLabels property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isCentreColumnLabels() {
- if (centreColumnLabels == null) {
- return false;
- } else {
- return centreColumnLabels;
- }
- }
+ /**
+ * Gets the value of the showDbRefTooltip property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowDbRefTooltip()
+ {
+ return showDbRefTooltip;
+ }
- /**
- * Sets the value of the centreColumnLabels property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setCentreColumnLabels(Boolean value) {
- this.centreColumnLabels = value;
- }
+ /**
+ * Sets the value of the showDbRefTooltip property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowDbRefTooltip(Boolean value)
+ {
+ this.showDbRefTooltip = value;
+ }
- /**
- * Gets the value of the showGroupConservation property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isShowGroupConservation() {
- if (showGroupConservation == null) {
- return false;
- } else {
- return showGroupConservation;
- }
- }
+ /**
+ * Gets the value of the followHighlight property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isFollowHighlight()
+ {
+ if (followHighlight == null)
+ {
+ return true;
+ }
+ else
+ {
+ return followHighlight;
+ }
+ }
- /**
- * Sets the value of the showGroupConservation property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowGroupConservation(Boolean value) {
- this.showGroupConservation = value;
- }
+ /**
+ * Sets the value of the followHighlight property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setFollowHighlight(Boolean value)
+ {
+ this.followHighlight = value;
+ }
- /**
- * Gets the value of the showGroupConsensus property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isShowGroupConsensus() {
- if (showGroupConsensus == null) {
- return false;
- } else {
- return showGroupConsensus;
- }
- }
+ /**
+ * Gets the value of the followSelection property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isFollowSelection()
+ {
+ if (followSelection == null)
+ {
+ return true;
+ }
+ else
+ {
+ return followSelection;
+ }
+ }
- /**
- * Sets the value of the showGroupConsensus property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowGroupConsensus(Boolean value) {
- this.showGroupConsensus = value;
- }
+ /**
+ * Sets the value of the followSelection property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setFollowSelection(Boolean value)
+ {
+ this.followSelection = value;
+ }
- /**
- * Gets the value of the showConsensusHistogram property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isShowConsensusHistogram() {
- if (showConsensusHistogram == null) {
- return true;
- } else {
- return showConsensusHistogram;
- }
- }
+ /**
+ * Gets the value of the showAnnotation property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowAnnotation()
+ {
+ return showAnnotation;
+ }
- /**
- * Sets the value of the showConsensusHistogram property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowConsensusHistogram(Boolean value) {
- this.showConsensusHistogram = value;
- }
+ /**
+ * Sets the value of the showAnnotation property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowAnnotation(Boolean value)
+ {
+ this.showAnnotation = value;
+ }
- /**
- * Gets the value of the showSequenceLogo property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isShowSequenceLogo() {
- if (showSequenceLogo == null) {
- return false;
- } else {
- return showSequenceLogo;
- }
- }
+ /**
+ * Gets the value of the centreColumnLabels property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isCentreColumnLabels()
+ {
+ if (centreColumnLabels == null)
+ {
+ return false;
+ }
+ else
+ {
+ return centreColumnLabels;
+ }
+ }
+
+ /**
+ * Sets the value of the centreColumnLabels property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setCentreColumnLabels(Boolean value)
+ {
+ this.centreColumnLabels = value;
+ }
- /**
- * Sets the value of the showSequenceLogo property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowSequenceLogo(Boolean value) {
- this.showSequenceLogo = value;
- }
+ /**
+ * Gets the value of the showGroupConservation property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isShowGroupConservation()
+ {
+ if (showGroupConservation == null)
+ {
+ return false;
+ }
+ else
+ {
+ return showGroupConservation;
+ }
+ }
- /**
- * Gets the value of the normaliseSequenceLogo property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isNormaliseSequenceLogo() {
- if (normaliseSequenceLogo == null) {
- return false;
- } else {
- return normaliseSequenceLogo;
- }
- }
+ /**
+ * Sets the value of the showGroupConservation property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowGroupConservation(Boolean value)
+ {
+ this.showGroupConservation = value;
+ }
- /**
- * Sets the value of the normaliseSequenceLogo property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setNormaliseSequenceLogo(Boolean value) {
- this.normaliseSequenceLogo = value;
- }
+ /**
+ * Gets the value of the showGroupConsensus property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isShowGroupConsensus()
+ {
+ if (showGroupConsensus == null)
+ {
+ return false;
+ }
+ else
+ {
+ return showGroupConsensus;
+ }
+ }
- /**
- * Gets the value of the ignoreGapsinConsensus property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isIgnoreGapsinConsensus() {
- if (ignoreGapsinConsensus == null) {
- return true;
- } else {
- return ignoreGapsinConsensus;
- }
- }
+ /**
+ * Sets the value of the showGroupConsensus property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowGroupConsensus(Boolean value)
+ {
+ this.showGroupConsensus = value;
+ }
- /**
- * Sets the value of the ignoreGapsinConsensus property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setIgnoreGapsinConsensus(Boolean value) {
- this.ignoreGapsinConsensus = value;
- }
+ /**
+ * Gets the value of the showConsensusHistogram property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isShowConsensusHistogram()
+ {
+ if (showConsensusHistogram == null)
+ {
+ return true;
+ }
+ else
+ {
+ return showConsensusHistogram;
+ }
+ }
- /**
- * Gets the value of the startRes property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getStartRes() {
- return startRes;
- }
+ /**
+ * Sets the value of the showConsensusHistogram property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowConsensusHistogram(Boolean value)
+ {
+ this.showConsensusHistogram = value;
+ }
- /**
- * Sets the value of the startRes property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setStartRes(Integer value) {
- this.startRes = value;
- }
+ /**
+ * Gets the value of the showSequenceLogo property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isShowSequenceLogo()
+ {
+ if (showSequenceLogo == null)
+ {
+ return false;
+ }
+ else
+ {
+ return showSequenceLogo;
+ }
+ }
- /**
- * Gets the value of the startSeq property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getStartSeq() {
- return startSeq;
- }
+ /**
+ * Sets the value of the showSequenceLogo property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowSequenceLogo(Boolean value)
+ {
+ this.showSequenceLogo = value;
+ }
- /**
- * Sets the value of the startSeq property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setStartSeq(Integer value) {
- this.startSeq = value;
- }
+ /**
+ * Gets the value of the normaliseSequenceLogo property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isNormaliseSequenceLogo()
+ {
+ if (normaliseSequenceLogo == null)
+ {
+ return false;
+ }
+ else
+ {
+ return normaliseSequenceLogo;
+ }
+ }
- /**
- * Gets the value of the fontName property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getFontName() {
- return fontName;
- }
+ /**
+ * Sets the value of the normaliseSequenceLogo property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setNormaliseSequenceLogo(Boolean value)
+ {
+ this.normaliseSequenceLogo = value;
+ }
- /**
- * Sets the value of the fontName property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setFontName(String value) {
- this.fontName = value;
- }
+ /**
+ * Gets the value of the ignoreGapsinConsensus property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isIgnoreGapsinConsensus()
+ {
+ if (ignoreGapsinConsensus == null)
+ {
+ return true;
+ }
+ else
+ {
+ return ignoreGapsinConsensus;
+ }
+ }
- /**
- * Gets the value of the fontSize property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getFontSize() {
- return fontSize;
- }
+ /**
+ * Sets the value of the ignoreGapsinConsensus property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setIgnoreGapsinConsensus(Boolean value)
+ {
+ this.ignoreGapsinConsensus = value;
+ }
- /**
- * Sets the value of the fontSize property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setFontSize(Integer value) {
- this.fontSize = value;
- }
+ /**
+ * Gets the value of the startRes property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getStartRes()
+ {
+ return startRes;
+ }
- /**
- * Gets the value of the fontStyle property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getFontStyle() {
- return fontStyle;
- }
+ /**
+ * Sets the value of the startRes property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setStartRes(Integer value)
+ {
+ this.startRes = value;
+ }
- /**
- * Sets the value of the fontStyle property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setFontStyle(Integer value) {
- this.fontStyle = value;
- }
+ /**
+ * Gets the value of the startSeq property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getStartSeq()
+ {
+ return startSeq;
+ }
- /**
- * Gets the value of the scaleProteinAsCdna property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isScaleProteinAsCdna() {
- if (scaleProteinAsCdna == null) {
- return true;
- } else {
- return scaleProteinAsCdna;
- }
- }
+ /**
+ * Sets the value of the startSeq property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setStartSeq(Integer value)
+ {
+ this.startSeq = value;
+ }
- /**
- * Sets the value of the scaleProteinAsCdna property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setScaleProteinAsCdna(Boolean value) {
- this.scaleProteinAsCdna = value;
- }
+ /**
+ * Gets the value of the fontName property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getFontName()
+ {
+ return fontName;
+ }
- /**
- * Gets the value of the viewName property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getViewName() {
- return viewName;
- }
+ /**
+ * Sets the value of the fontName property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setFontName(String value)
+ {
+ this.fontName = value;
+ }
- /**
- * Sets the value of the viewName property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setViewName(String value) {
- this.viewName = value;
- }
+ /**
+ * Gets the value of the fontSize property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getFontSize()
+ {
+ return fontSize;
+ }
- /**
- * Gets the value of the sequenceSetId property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getSequenceSetId() {
- return sequenceSetId;
- }
+ /**
+ * Sets the value of the fontSize property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setFontSize(Integer value)
+ {
+ this.fontSize = value;
+ }
- /**
- * Sets the value of the sequenceSetId property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setSequenceSetId(String value) {
- this.sequenceSetId = value;
- }
+ /**
+ * Gets the value of the fontStyle property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getFontStyle()
+ {
+ return fontStyle;
+ }
- /**
- * Gets the value of the gatheredViews property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isGatheredViews() {
- return gatheredViews;
- }
+ /**
+ * Sets the value of the fontStyle property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setFontStyle(Integer value)
+ {
+ this.fontStyle = value;
+ }
- /**
- * Sets the value of the gatheredViews property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setGatheredViews(Boolean value) {
- this.gatheredViews = value;
- }
+ /**
+ * Gets the value of the scaleProteinAsCdna property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isScaleProteinAsCdna()
+ {
+ if (scaleProteinAsCdna == null)
+ {
+ return true;
+ }
+ else
+ {
+ return scaleProteinAsCdna;
+ }
+ }
- /**
- * Gets the value of the textCol1 property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getTextCol1() {
- return textCol1;
- }
+ /**
+ * Sets the value of the scaleProteinAsCdna property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setScaleProteinAsCdna(Boolean value)
+ {
+ this.scaleProteinAsCdna = value;
+ }
- /**
- * Sets the value of the textCol1 property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setTextCol1(Integer value) {
- this.textCol1 = value;
- }
+ /**
+ * Gets the value of the viewName property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getViewName()
+ {
+ return viewName;
+ }
+
+ /**
+ * Sets the value of the viewName property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setViewName(String value)
+ {
+ this.viewName = value;
+ }
- /**
- * Gets the value of the textCol2 property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getTextCol2() {
- return textCol2;
- }
+ /**
+ * Gets the value of the sequenceSetId property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getSequenceSetId()
+ {
+ return sequenceSetId;
+ }
- /**
- * Sets the value of the textCol2 property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setTextCol2(Integer value) {
- this.textCol2 = value;
- }
+ /**
+ * Sets the value of the sequenceSetId property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setSequenceSetId(String value)
+ {
+ this.sequenceSetId = value;
+ }
- /**
- * Gets the value of the textColThreshold property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getTextColThreshold() {
- return textColThreshold;
- }
+ /**
+ * Gets the value of the gatheredViews property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isGatheredViews()
+ {
+ return gatheredViews;
+ }
- /**
- * Sets the value of the textColThreshold property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setTextColThreshold(Integer value) {
- this.textColThreshold = value;
- }
+ /**
+ * Sets the value of the gatheredViews property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setGatheredViews(Boolean value)
+ {
+ this.gatheredViews = value;
+ }
- /**
- * Gets the value of the id property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getId() {
- return id;
- }
+ /**
+ * Gets the value of the textCol1 property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getTextCol1()
+ {
+ return textCol1;
+ }
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setId(String value) {
- this.id = value;
- }
+ /**
+ * Sets the value of the textCol1 property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setTextCol1(Integer value)
+ {
+ this.textCol1 = value;
+ }
- /**
- * Gets the value of the complementId property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getComplementId() {
- return complementId;
- }
+ /**
+ * Gets the value of the textCol2 property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getTextCol2()
+ {
+ return textCol2;
+ }
- /**
- * Sets the value of the complementId property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setComplementId(String value) {
- this.complementId = value;
- }
+ /**
+ * Sets the value of the textCol2 property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setTextCol2(Integer value)
+ {
+ this.textCol2 = value;
+ }
- /**
- * Gets the value of the width property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getWidth() {
- return width;
- }
+ /**
+ * Gets the value of the textColThreshold property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getTextColThreshold()
+ {
+ return textColThreshold;
+ }
- /**
- * Sets the value of the width property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setWidth(Integer value) {
- this.width = value;
- }
+ /**
+ * Sets the value of the textColThreshold property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setTextColThreshold(Integer value)
+ {
+ this.textColThreshold = value;
+ }
- /**
- * Gets the value of the height property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getHeight() {
- return height;
- }
+ /**
+ * Gets the value of the id property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getId()
+ {
+ return id;
+ }
- /**
- * Sets the value of the height property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setHeight(Integer value) {
- this.height = value;
- }
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setId(String value)
+ {
+ this.id = value;
+ }
- /**
- * Gets the value of the xpos property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getXpos() {
- return xpos;
- }
+ /**
+ * Gets the value of the complementId property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getComplementId()
+ {
+ return complementId;
+ }
- /**
- * Sets the value of the xpos property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setXpos(Integer value) {
- this.xpos = value;
- }
+ /**
+ * Sets the value of the complementId property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setComplementId(String value)
+ {
+ this.complementId = value;
+ }
- /**
- * Gets the value of the ypos property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getYpos() {
- return ypos;
- }
+ /**
+ * Gets the value of the width property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getWidth()
+ {
+ return width;
+ }
- /**
- * Sets the value of the ypos property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setYpos(Integer value) {
- this.ypos = value;
- }
+ /**
+ * Sets the value of the width property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setWidth(Integer value)
+ {
+ this.width = value;
+ }
+ /**
+ * Gets the value of the height property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getHeight()
+ {
+ return height;
+ }
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
- * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </extension>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class CalcIdParam
- extends WebServiceParameterSet
- {
+ /**
+ * Sets the value of the height property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setHeight(Integer value)
+ {
+ this.height = value;
+ }
- @XmlAttribute(name = "calcId", required = true)
- protected String calcId;
- @XmlAttribute(name = "needsUpdate")
- protected Boolean needsUpdate;
- @XmlAttribute(name = "autoUpdate", required = true)
- protected boolean autoUpdate;
-
- /**
- * Gets the value of the calcId property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getCalcId() {
- return calcId;
- }
-
- /**
- * Sets the value of the calcId property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setCalcId(String value) {
- this.calcId = value;
- }
-
- /**
- * Gets the value of the needsUpdate property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isNeedsUpdate() {
- if (needsUpdate == null) {
- return false;
- } else {
- return needsUpdate;
- }
- }
-
- /**
- * Sets the value of the needsUpdate property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setNeedsUpdate(Boolean value) {
- this.needsUpdate = value;
- }
-
- /**
- * Gets the value of the autoUpdate property.
- *
- */
- public boolean isAutoUpdate() {
- return autoUpdate;
- }
-
- /**
- * Sets the value of the autoUpdate property.
- *
- */
- public void setAutoUpdate(boolean value) {
- this.autoUpdate = value;
- }
+ /**
+ * Gets the value of the xpos property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getXpos()
+ {
+ return xpos;
+ }
- }
+ /**
+ * Sets the value of the xpos property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setXpos(Integer value)
+ {
+ this.xpos = value;
+ }
+ /**
+ * Gets the value of the ypos property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getYpos()
+ {
+ return ypos;
+ }
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class HiddenColumns {
-
- @XmlAttribute(name = "start")
- protected Integer start;
- @XmlAttribute(name = "end")
- protected Integer end;
-
- /**
- * Gets the value of the start property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getStart() {
- return start;
- }
-
- /**
- * Sets the value of the start property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setStart(Integer value) {
- this.start = value;
- }
-
- /**
- * Gets the value of the end property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getEnd() {
- return end;
- }
-
- /**
- * Sets the value of the end property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setEnd(Integer value) {
- this.end = value;
- }
+ /**
+ * Sets the value of the ypos property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setYpos(Integer value)
+ {
+ this.ypos = value;
+ }
+ /**
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
+ * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </extension>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class CalcIdParam extends WebServiceParameterSet
+ {
+
+ @XmlAttribute(name = "calcId", required = true)
+ protected String calcId;
+
+ @XmlAttribute(name = "needsUpdate")
+ protected Boolean needsUpdate;
+
+ @XmlAttribute(name = "autoUpdate", required = true)
+ protected boolean autoUpdate;
+
+ /**
+ * Gets the value of the calcId property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getCalcId()
+ {
+ return calcId;
+ }
+
+ /**
+ * Sets the value of the calcId property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setCalcId(String value)
+ {
+ this.calcId = value;
+ }
+
+ /**
+ * Gets the value of the needsUpdate property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isNeedsUpdate()
+ {
+ if (needsUpdate == null)
+ {
+ return false;
}
+ else
+ {
+ return needsUpdate;
+ }
+ }
+
+ /**
+ * Sets the value of the needsUpdate property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setNeedsUpdate(Boolean value)
+ {
+ this.needsUpdate = value;
+ }
+
+ /**
+ * Gets the value of the autoUpdate property.
+ *
+ */
+ public boolean isAutoUpdate()
+ {
+ return autoUpdate;
+ }
+
+ /**
+ * Sets the value of the autoUpdate property.
+ *
+ */
+ public void setAutoUpdate(boolean value)
+ {
+ this.autoUpdate = value;
+ }
+
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class HiddenColumns
+ {
+
+ @XmlAttribute(name = "start")
+ protected Integer start;
+
+ @XmlAttribute(name = "end")
+ protected Integer end;
+
+ /**
+ * Gets the value of the start property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getStart()
+ {
+ return start;
+ }
+
+ /**
+ * Sets the value of the start property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setStart(Integer value)
+ {
+ this.start = value;
+ }
+
+ /**
+ * Gets the value of the end property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getEnd()
+ {
+ return end;
+ }
+
+ /**
+ * Sets the value of the end property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setEnd(Integer value)
+ {
+ this.end = value;
+ }
}
+ }
+
}
// Generated on: 2021.08.30 at 11:05:22 AM BST
//
-
package jalview.xml.binding.jalview;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
-
/**
* <p>Java class for JalviewUserColours complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
*
- * <pre>
- * &lt;complexType name="JalviewUserColours"&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="Version" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
- * &lt;element name="colour" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="Name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="RGB" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="minRGB" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
- * &lt;attribute name="threshType" type="{www.jalview.org/colours}ThresholdType" /&gt;
- * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="filter" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet"/&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="featureType" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="schemeName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre> &lt;complexType name="JalviewUserColours"&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="Version"
+ * type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
+ * &lt;element name="colour" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="attributeName"
+ * type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2"
+ * minOccurs="0"/&gt; &lt;/sequence&gt; &lt;attribute
+ * name="Name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="RGB" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="minRGB" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="noValueColour"
+ * type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
+ * &lt;attribute name="threshType"
+ * type="{www.jalview.org/colours}ThresholdType" /&gt; &lt;attribute
+ * name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float"
+ * /&gt; &lt;attribute name="min"
+ * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute
+ * name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean"
+ * /&gt; &lt;attribute name="autoScale"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt; &lt;element
+ * name="filter" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="matcherSet"
+ * type="{www.jalview.org/colours}FeatureMatcherSet"/&gt;
+ * &lt;/sequence&gt; &lt;attribute name="featureType" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt;
+ * &lt;/sequence&gt; &lt;attribute name="schemeName"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "JalviewUserColours", namespace = "www.jalview.org/colours", propOrder = {
- "version",
- "colour",
- "filter"
-})
-public class JalviewUserColours {
-
- @XmlElement(name = "Version", namespace = "")
- protected String version;
- @XmlElement(namespace = "")
- protected List<JalviewUserColours.Colour> colour;
+@XmlType(
+ name = "JalviewUserColours",
+ namespace = "www.jalview.org/colours",
+ propOrder =
+ { "version", "colour", "filter" })
+public class JalviewUserColours
+{
+
+ @XmlElement(name = "Version", namespace = "")
+ protected String version;
+
+ @XmlElement(namespace = "")
+ protected List<JalviewUserColours.Colour> colour;
+
+ @XmlElement(namespace = "")
+ protected List<JalviewUserColours.Filter> filter;
+
+ @XmlAttribute(name = "schemeName")
+ protected String schemeName;
+
+ /**
+ * Gets the value of the version property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getVersion()
+ {
+ return version;
+ }
+
+ /**
+ * Sets the value of the version property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setVersion(String value)
+ {
+ this.version = value;
+ }
+
+ /**
+ * Gets the value of the colour property.
+ *
+ * <p> This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will be
+ * present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the colour property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getColour().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link JalviewUserColours.Colour }
+ *
+ *
+ */
+ public List<JalviewUserColours.Colour> getColour()
+ {
+ if (colour == null)
+ {
+ colour = new ArrayList<JalviewUserColours.Colour>();
+ }
+ return this.colour;
+ }
+
+ /**
+ * Gets the value of the filter property.
+ *
+ * <p> This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will be
+ * present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the filter property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getFilter().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link JalviewUserColours.Filter }
+ *
+ *
+ */
+ public List<JalviewUserColours.Filter> getFilter()
+ {
+ if (filter == null)
+ {
+ filter = new ArrayList<JalviewUserColours.Filter>();
+ }
+ return this.filter;
+ }
+
+ /**
+ * Gets the value of the schemeName property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getSchemeName()
+ {
+ return schemeName;
+ }
+
+ /**
+ * Sets the value of the schemeName property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setSchemeName(String value)
+ {
+ this.schemeName = value;
+ }
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
+ *
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="attributeName"
+ * type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2"
+ * minOccurs="0"/&gt; &lt;/sequence&gt; &lt;attribute
+ * name="Name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="RGB" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="minRGB" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="noValueColour"
+ * type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
+ * &lt;attribute name="threshType"
+ * type="{www.jalview.org/colours}ThresholdType" /&gt; &lt;attribute
+ * name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float"
+ * /&gt; &lt;attribute name="min"
+ * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute
+ * name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean"
+ * /&gt; &lt;attribute name="autoScale"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "attributeName" })
+ public static class Colour
+ {
+
@XmlElement(namespace = "")
- protected List<JalviewUserColours.Filter> filter;
- @XmlAttribute(name = "schemeName")
- protected String schemeName;
+ protected List<String> attributeName;
+
+ @XmlAttribute(name = "Name")
+ protected String name;
+
+ @XmlAttribute(name = "RGB", required = true)
+ protected String rgb;
+
+ @XmlAttribute(name = "minRGB")
+ protected String minRGB;
+
+ @XmlAttribute(name = "noValueColour")
+ protected NoValueColour noValueColour;
+
+ @XmlAttribute(name = "threshType")
+ protected ThresholdType threshType;
+
+ @XmlAttribute(name = "threshold")
+ protected Float threshold;
+
+ @XmlAttribute(name = "max")
+ protected Float max;
+
+ @XmlAttribute(name = "min")
+ protected Float min;
+
+ @XmlAttribute(name = "colourByLabel")
+ protected Boolean colourByLabel;
+
+ @XmlAttribute(name = "autoScale")
+ protected Boolean autoScale;
+
+ /**
+ * Gets the value of the attributeName property.
+ *
+ * <p> This accessor method returns a reference to the live list, not
+ * a snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the attributeName property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getAttributeName().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link String }
+ *
+ *
+ */
+ public List<String> getAttributeName()
+ {
+ if (attributeName == null)
+ {
+ attributeName = new ArrayList<String>();
+ }
+ return this.attributeName;
+ }
+
+ /**
+ * Gets the value of the name property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getName()
+ {
+ return name;
+ }
+
+ /**
+ * Sets the value of the name property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setName(String value)
+ {
+ this.name = value;
+ }
+
+ /**
+ * Gets the value of the rgb property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getRGB()
+ {
+ return rgb;
+ }
+
+ /**
+ * Sets the value of the rgb property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setRGB(String value)
+ {
+ this.rgb = value;
+ }
+
+ /**
+ * Gets the value of the minRGB property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getMinRGB()
+ {
+ return minRGB;
+ }
+
+ /**
+ * Sets the value of the minRGB property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setMinRGB(String value)
+ {
+ this.minRGB = value;
+ }
/**
- * Gets the value of the version property.
+ * Gets the value of the noValueColour property.
+ *
+ * @return possible object is {@link NoValueColour }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getVersion() {
- return version;
+ public NoValueColour getNoValueColour()
+ {
+ if (noValueColour == null)
+ {
+ return NoValueColour.MIN;
+ }
+ else
+ {
+ return noValueColour;
+ }
}
/**
- * Sets the value of the version property.
+ * Sets the value of the noValueColour property.
*
* @param value
- * allowed object is
- * {@link String }
- *
+ * allowed object is {@link NoValueColour }
+ *
*/
- public void setVersion(String value) {
- this.version = value;
+ public void setNoValueColour(NoValueColour value)
+ {
+ this.noValueColour = value;
}
/**
- * Gets the value of the colour property.
+ * Gets the value of the threshType property.
*
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the colour property.
+ * @return possible object is {@link ThresholdType }
*
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getColour().add(newItem);
- * </pre>
+ */
+ public ThresholdType getThreshType()
+ {
+ return threshType;
+ }
+
+ /**
+ * Sets the value of the threshType property.
*
+ * @param value
+ * allowed object is {@link ThresholdType }
*
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewUserColours.Colour }
+ */
+ public void setThreshType(ThresholdType value)
+ {
+ this.threshType = value;
+ }
+
+ /**
+ * Gets the value of the threshold property.
*
+ * @return possible object is {@link Float }
*
*/
- public List<JalviewUserColours.Colour> getColour() {
- if (colour == null) {
- colour = new ArrayList<JalviewUserColours.Colour>();
- }
- return this.colour;
+ public Float getThreshold()
+ {
+ return threshold;
}
/**
- * Gets the value of the filter property.
+ * Sets the value of the threshold property.
*
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the filter property.
+ * @param value
+ * allowed object is {@link Float }
*
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getFilter().add(newItem);
- * </pre>
+ */
+ public void setThreshold(Float value)
+ {
+ this.threshold = value;
+ }
+
+ /**
+ * Gets the value of the max property.
*
+ * @return possible object is {@link Float }
*
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewUserColours.Filter }
+ */
+ public Float getMax()
+ {
+ return max;
+ }
+
+ /**
+ * Sets the value of the max property.
*
+ * @param value
+ * allowed object is {@link Float }
*
*/
- public List<JalviewUserColours.Filter> getFilter() {
- if (filter == null) {
- filter = new ArrayList<JalviewUserColours.Filter>();
- }
- return this.filter;
+ public void setMax(Float value)
+ {
+ this.max = value;
}
/**
- * Gets the value of the schemeName property.
+ * Gets the value of the min property.
+ *
+ * @return possible object is {@link Float }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getSchemeName() {
- return schemeName;
+ public Float getMin()
+ {
+ return min;
}
/**
- * Sets the value of the schemeName property.
+ * Sets the value of the min property.
*
* @param value
- * allowed object is
- * {@link String }
- *
+ * allowed object is {@link Float }
+ *
+ */
+ public void setMin(Float value)
+ {
+ this.min = value;
+ }
+
+ /**
+ * Gets the value of the colourByLabel property.
+ *
+ * @return possible object is {@link Boolean }
+ *
*/
- public void setSchemeName(String value) {
- this.schemeName = value;
+ public Boolean isColourByLabel()
+ {
+ return colourByLabel;
}
+ /**
+ * Sets the value of the colourByLabel property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setColourByLabel(Boolean value)
+ {
+ this.colourByLabel = value;
+ }
/**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="Name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="RGB" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="minRGB" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
- * &lt;attribute name="threshType" type="{www.jalview.org/colours}ThresholdType" /&gt;
- * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * Gets the value of the autoScale property.
*
+ * @return possible object is {@link Boolean }
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "attributeName"
- })
- public static class Colour {
-
- @XmlElement(namespace = "")
- protected List<String> attributeName;
- @XmlAttribute(name = "Name")
- protected String name;
- @XmlAttribute(name = "RGB", required = true)
- protected String rgb;
- @XmlAttribute(name = "minRGB")
- protected String minRGB;
- @XmlAttribute(name = "noValueColour")
- protected NoValueColour noValueColour;
- @XmlAttribute(name = "threshType")
- protected ThresholdType threshType;
- @XmlAttribute(name = "threshold")
- protected Float threshold;
- @XmlAttribute(name = "max")
- protected Float max;
- @XmlAttribute(name = "min")
- protected Float min;
- @XmlAttribute(name = "colourByLabel")
- protected Boolean colourByLabel;
- @XmlAttribute(name = "autoScale")
- protected Boolean autoScale;
-
- /**
- * Gets the value of the attributeName property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the attributeName property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getAttributeName().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link String }
- *
- *
- */
- public List<String> getAttributeName() {
- if (attributeName == null) {
- attributeName = new ArrayList<String>();
- }
- return this.attributeName;
- }
-
- /**
- * Gets the value of the name property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getName() {
- return name;
- }
-
- /**
- * Sets the value of the name property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setName(String value) {
- this.name = value;
- }
-
- /**
- * Gets the value of the rgb property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getRGB() {
- return rgb;
- }
-
- /**
- * Sets the value of the rgb property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setRGB(String value) {
- this.rgb = value;
- }
-
- /**
- * Gets the value of the minRGB property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getMinRGB() {
- return minRGB;
- }
-
- /**
- * Sets the value of the minRGB property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setMinRGB(String value) {
- this.minRGB = value;
- }
-
- /**
- * Gets the value of the noValueColour property.
- *
- * @return
- * possible object is
- * {@link NoValueColour }
- *
- */
- public NoValueColour getNoValueColour() {
- if (noValueColour == null) {
- return NoValueColour.MIN;
- } else {
- return noValueColour;
- }
- }
-
- /**
- * Sets the value of the noValueColour property.
- *
- * @param value
- * allowed object is
- * {@link NoValueColour }
- *
- */
- public void setNoValueColour(NoValueColour value) {
- this.noValueColour = value;
- }
-
- /**
- * Gets the value of the threshType property.
- *
- * @return
- * possible object is
- * {@link ThresholdType }
- *
- */
- public ThresholdType getThreshType() {
- return threshType;
- }
-
- /**
- * Sets the value of the threshType property.
- *
- * @param value
- * allowed object is
- * {@link ThresholdType }
- *
- */
- public void setThreshType(ThresholdType value) {
- this.threshType = value;
- }
-
- /**
- * Gets the value of the threshold property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getThreshold() {
- return threshold;
- }
-
- /**
- * Sets the value of the threshold property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setThreshold(Float value) {
- this.threshold = value;
- }
-
- /**
- * Gets the value of the max property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getMax() {
- return max;
- }
-
- /**
- * Sets the value of the max property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setMax(Float value) {
- this.max = value;
- }
-
- /**
- * Gets the value of the min property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getMin() {
- return min;
- }
-
- /**
- * Sets the value of the min property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setMin(Float value) {
- this.min = value;
- }
-
- /**
- * Gets the value of the colourByLabel property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isColourByLabel() {
- return colourByLabel;
- }
-
- /**
- * Sets the value of the colourByLabel property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setColourByLabel(Boolean value) {
- this.colourByLabel = value;
- }
-
- /**
- * Gets the value of the autoScale property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isAutoScale() {
- return autoScale;
- }
-
- /**
- * Sets the value of the autoScale property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setAutoScale(Boolean value) {
- this.autoScale = value;
- }
+ public Boolean isAutoScale()
+ {
+ return autoScale;
+ }
+ /**
+ * Sets the value of the autoScale property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setAutoScale(Boolean value)
+ {
+ this.autoScale = value;
}
+ }
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
+ *
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="matcherSet"
+ * type="{www.jalview.org/colours}FeatureMatcherSet"/&gt;
+ * &lt;/sequence&gt; &lt;attribute name="featureType"
+ * use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "matcherSet" })
+ public static class Filter
+ {
+
+ @XmlElement(namespace = "", required = true)
+ protected FeatureMatcherSet matcherSet;
+
+ @XmlAttribute(name = "featureType", required = true)
+ protected String featureType;
/**
- * <p>Java class for anonymous complex type.
+ * Gets the value of the matcherSet property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * @return possible object is {@link FeatureMatcherSet }
*
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet"/&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="featureType" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ */
+ public FeatureMatcherSet getMatcherSet()
+ {
+ return matcherSet;
+ }
+
+ /**
+ * Sets the value of the matcherSet property.
*
+ * @param value
+ * allowed object is {@link FeatureMatcherSet }
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "matcherSet"
- })
- public static class Filter {
-
- @XmlElement(namespace = "", required = true)
- protected FeatureMatcherSet matcherSet;
- @XmlAttribute(name = "featureType", required = true)
- protected String featureType;
-
- /**
- * Gets the value of the matcherSet property.
- *
- * @return
- * possible object is
- * {@link FeatureMatcherSet }
- *
- */
- public FeatureMatcherSet getMatcherSet() {
- return matcherSet;
- }
-
- /**
- * Sets the value of the matcherSet property.
- *
- * @param value
- * allowed object is
- * {@link FeatureMatcherSet }
- *
- */
- public void setMatcherSet(FeatureMatcherSet value) {
- this.matcherSet = value;
- }
-
- /**
- * Gets the value of the featureType property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getFeatureType() {
- return featureType;
- }
-
- /**
- * Sets the value of the featureType property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setFeatureType(String value) {
- this.featureType = value;
- }
+ public void setMatcherSet(FeatureMatcherSet value)
+ {
+ this.matcherSet = value;
+ }
+ /**
+ * Gets the value of the featureType property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getFeatureType()
+ {
+ return featureType;
}
+ /**
+ * Sets the value of the featureType property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setFeatureType(String value)
+ {
+ this.featureType = value;
+ }
+
+ }
+
}
// Generated on: 2021.08.30 at 11:05:22 AM BST
//
-
package jalview.xml.binding.jalview;
import java.math.BigInteger;
import javax.xml.bind.annotation.XmlSeeAlso;
import javax.xml.bind.annotation.XmlType;
-
/**
*
- * This effectively represents a java.util.MapList object
- *
+ * This effectively represents a java.util.MapList object
+ *
*
* <p>Java class for mapListType complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
*
- * <pre>
- * &lt;complexType name="mapListType"&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="mapListFrom" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="mapListTo" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="mapFromUnit" use="required" type="{http://www.w3.org/2001/XMLSchema}positiveInteger" /&gt;
- * &lt;attribute name="mapToUnit" use="required" type="{http://www.w3.org/2001/XMLSchema}positiveInteger" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre> &lt;complexType name="mapListType"&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="mapListFrom"
+ * maxOccurs="unbounded" minOccurs="0"&gt; &lt;complexType&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
+ * name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
+ * /&gt; &lt;attribute name="end" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt; &lt;element
+ * name="mapListTo" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="start" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
+ * name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
+ * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt;
+ * &lt;/sequence&gt; &lt;attribute name="mapFromUnit" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}positiveInteger" /&gt;
+ * &lt;attribute name="mapToUnit" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}positiveInteger" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "mapListType", propOrder = {
- "mapListFrom",
- "mapListTo"
-})
-@XmlSeeAlso({
- Mapping.class
-})
-public class MapListType {
+@XmlType(name = "mapListType", propOrder = { "mapListFrom", "mapListTo" })
+@XmlSeeAlso({ Mapping.class })
+public class MapListType
+{
+
+ protected List<MapListType.MapListFrom> mapListFrom;
+
+ protected List<MapListType.MapListTo> mapListTo;
+
+ @XmlAttribute(name = "mapFromUnit", required = true)
+ @XmlSchemaType(name = "positiveInteger")
+ protected BigInteger mapFromUnit;
+
+ @XmlAttribute(name = "mapToUnit", required = true)
+ @XmlSchemaType(name = "positiveInteger")
+ protected BigInteger mapToUnit;
+
+ /**
+ * Gets the value of the mapListFrom property.
+ *
+ * <p> This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will be
+ * present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the mapListFrom property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getMapListFrom().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link MapListType.MapListFrom }
+ *
+ *
+ */
+ public List<MapListType.MapListFrom> getMapListFrom()
+ {
+ if (mapListFrom == null)
+ {
+ mapListFrom = new ArrayList<MapListType.MapListFrom>();
+ }
+ return this.mapListFrom;
+ }
+
+ /**
+ * Gets the value of the mapListTo property.
+ *
+ * <p> This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will be
+ * present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the mapListTo property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getMapListTo().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link MapListType.MapListTo }
+ *
+ *
+ */
+ public List<MapListType.MapListTo> getMapListTo()
+ {
+ if (mapListTo == null)
+ {
+ mapListTo = new ArrayList<MapListType.MapListTo>();
+ }
+ return this.mapListTo;
+ }
+
+ /**
+ * Gets the value of the mapFromUnit property.
+ *
+ * @return possible object is {@link BigInteger }
+ *
+ */
+ public BigInteger getMapFromUnit()
+ {
+ return mapFromUnit;
+ }
+
+ /**
+ * Sets the value of the mapFromUnit property.
+ *
+ * @param value
+ * allowed object is {@link BigInteger }
+ *
+ */
+ public void setMapFromUnit(BigInteger value)
+ {
+ this.mapFromUnit = value;
+ }
- protected List<MapListType.MapListFrom> mapListFrom;
- protected List<MapListType.MapListTo> mapListTo;
- @XmlAttribute(name = "mapFromUnit", required = true)
- @XmlSchemaType(name = "positiveInteger")
- protected BigInteger mapFromUnit;
- @XmlAttribute(name = "mapToUnit", required = true)
- @XmlSchemaType(name = "positiveInteger")
- protected BigInteger mapToUnit;
+ /**
+ * Gets the value of the mapToUnit property.
+ *
+ * @return possible object is {@link BigInteger }
+ *
+ */
+ public BigInteger getMapToUnit()
+ {
+ return mapToUnit;
+ }
+
+ /**
+ * Sets the value of the mapToUnit property.
+ *
+ * @param value
+ * allowed object is {@link BigInteger }
+ *
+ */
+ public void setMapToUnit(BigInteger value)
+ {
+ this.mapToUnit = value;
+ }
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
+ *
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
+ * name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
+ * /&gt; &lt;attribute name="end" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class MapListFrom
+ {
+
+ @XmlAttribute(name = "start", required = true)
+ protected int start;
+
+ @XmlAttribute(name = "end", required = true)
+ protected int end;
/**
- * Gets the value of the mapListFrom property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the mapListFrom property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getMapListFrom().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link MapListType.MapListFrom }
- *
+ * Gets the value of the start property.
*
*/
- public List<MapListType.MapListFrom> getMapListFrom() {
- if (mapListFrom == null) {
- mapListFrom = new ArrayList<MapListType.MapListFrom>();
- }
- return this.mapListFrom;
+ public int getStart()
+ {
+ return start;
}
/**
- * Gets the value of the mapListTo property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the mapListTo property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getMapListTo().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link MapListType.MapListTo }
- *
+ * Sets the value of the start property.
*
*/
- public List<MapListType.MapListTo> getMapListTo() {
- if (mapListTo == null) {
- mapListTo = new ArrayList<MapListType.MapListTo>();
- }
- return this.mapListTo;
+ public void setStart(int value)
+ {
+ this.start = value;
}
/**
- * Gets the value of the mapFromUnit property.
+ * Gets the value of the end property.
*
- * @return
- * possible object is
- * {@link BigInteger }
- *
*/
- public BigInteger getMapFromUnit() {
- return mapFromUnit;
+ public int getEnd()
+ {
+ return end;
}
/**
- * Sets the value of the mapFromUnit property.
+ * Sets the value of the end property.
*
- * @param value
- * allowed object is
- * {@link BigInteger }
- *
*/
- public void setMapFromUnit(BigInteger value) {
- this.mapFromUnit = value;
+ public void setEnd(int value)
+ {
+ this.end = value;
}
+ }
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
+ *
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
+ * name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
+ * /&gt; &lt;attribute name="end" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class MapListTo
+ {
+
+ @XmlAttribute(name = "start", required = true)
+ protected int start;
+
+ @XmlAttribute(name = "end", required = true)
+ protected int end;
+
/**
- * Gets the value of the mapToUnit property.
+ * Gets the value of the start property.
*
- * @return
- * possible object is
- * {@link BigInteger }
- *
*/
- public BigInteger getMapToUnit() {
- return mapToUnit;
+ public int getStart()
+ {
+ return start;
}
/**
- * Sets the value of the mapToUnit property.
+ * Sets the value of the start property.
*
- * @param value
- * allowed object is
- * {@link BigInteger }
- *
*/
- public void setMapToUnit(BigInteger value) {
- this.mapToUnit = value;
+ public void setStart(int value)
+ {
+ this.start = value;
}
-
/**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
- *
+ * Gets the value of the end property.
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class MapListFrom {
-
- @XmlAttribute(name = "start", required = true)
- protected int start;
- @XmlAttribute(name = "end", required = true)
- protected int end;
-
- /**
- * Gets the value of the start property.
- *
- */
- public int getStart() {
- return start;
- }
-
- /**
- * Sets the value of the start property.
- *
- */
- public void setStart(int value) {
- this.start = value;
- }
-
- /**
- * Gets the value of the end property.
- *
- */
- public int getEnd() {
- return end;
- }
-
- /**
- * Sets the value of the end property.
- *
- */
- public void setEnd(int value) {
- this.end = value;
- }
-
+ public int getEnd()
+ {
+ return end;
}
-
/**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
- *
+ * Sets the value of the end property.
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class MapListTo {
-
- @XmlAttribute(name = "start", required = true)
- protected int start;
- @XmlAttribute(name = "end", required = true)
- protected int end;
-
- /**
- * Gets the value of the start property.
- *
- */
- public int getStart() {
- return start;
- }
-
- /**
- * Sets the value of the start property.
- *
- */
- public void setStart(int value) {
- this.start = value;
- }
-
- /**
- * Gets the value of the end property.
- *
- */
- public int getEnd() {
- return end;
- }
-
- /**
- * Sets the value of the end property.
- *
- */
- public void setEnd(int value) {
- this.end = value;
- }
-
+ public void setEnd(int value)
+ {
+ this.end = value;
}
+ }
+
}
// Generated on: 2021.08.30 at 11:05:22 AM BST
//
-
package jalview.xml.binding.jalview;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlRootElement;
import javax.xml.bind.annotation.XmlType;
-
/**
*
- * Represent the jalview.datamodel.Mapping object - it also provides
- * a way of storing sequences that are mapped 'to' without adding them
- * to the sequence set (which will mean they are then added to the alignment too).
- *
+ * Represent the jalview.datamodel.Mapping object - it also provides a way of
+ * storing sequences that are mapped 'to' without adding them to the sequence
+ * set (which will mean they are then added to the alignment too).
+ *
*
* <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
*
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;extension base="{www.vamsas.ac.uk/jalview/version2}mapListType"&gt;
- * &lt;sequence&gt;
- * &lt;choice minOccurs="0"&gt;
- * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Sequence"/&gt;
- * &lt;element name="dseqFor"&gt;
- * &lt;simpleType&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt;
- * &lt;/restriction&gt;
- * &lt;/simpleType&gt;
- * &lt;/element&gt;
- * &lt;/choice&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="mappingType" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/extension&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;extension
+ * base="{www.vamsas.ac.uk/jalview/version2}mapListType"&gt;
+ * &lt;sequence&gt; &lt;choice minOccurs="0"&gt; &lt;element
+ * ref="{www.vamsas.ac.uk/jalview/version2}Sequence"/&gt; &lt;element
+ * name="dseqFor"&gt; &lt;simpleType&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}string"&gt;
+ * &lt;/restriction&gt; &lt;/simpleType&gt;
+ * &lt;/element&gt; &lt;/choice&gt; &lt;/sequence&gt;
+ * &lt;attribute name="mappingType"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/extension&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = {
- "sequence",
- "dseqFor"
-})
+@XmlType(name = "", propOrder = { "sequence", "dseqFor" })
@XmlRootElement(name = "Mapping")
-public class Mapping
- extends MapListType
+public class Mapping extends MapListType
{
- @XmlElement(name = "Sequence")
- protected Sequence sequence;
- protected String dseqFor;
- @XmlAttribute(name = "mappingType")
- protected String mappingType;
+ @XmlElement(name = "Sequence")
+ protected Sequence sequence;
+
+ protected String dseqFor;
+
+ @XmlAttribute(name = "mappingType")
+ protected String mappingType;
- /**
- * Gets the value of the sequence property.
- *
- * @return
- * possible object is
- * {@link Sequence }
- *
- */
- public Sequence getSequence() {
- return sequence;
- }
+ /**
+ * Gets the value of the sequence property.
+ *
+ * @return possible object is {@link Sequence }
+ *
+ */
+ public Sequence getSequence()
+ {
+ return sequence;
+ }
- /**
- * Sets the value of the sequence property.
- *
- * @param value
- * allowed object is
- * {@link Sequence }
- *
- */
- public void setSequence(Sequence value) {
- this.sequence = value;
- }
+ /**
+ * Sets the value of the sequence property.
+ *
+ * @param value
+ * allowed object is {@link Sequence }
+ *
+ */
+ public void setSequence(Sequence value)
+ {
+ this.sequence = value;
+ }
- /**
- * Gets the value of the dseqFor property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDseqFor() {
- return dseqFor;
- }
+ /**
+ * Gets the value of the dseqFor property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDseqFor()
+ {
+ return dseqFor;
+ }
- /**
- * Sets the value of the dseqFor property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDseqFor(String value) {
- this.dseqFor = value;
- }
+ /**
+ * Sets the value of the dseqFor property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setDseqFor(String value)
+ {
+ this.dseqFor = value;
+ }
- /**
- * Gets the value of the mappingType property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getMappingType() {
- return mappingType;
- }
+ /**
+ * Gets the value of the mappingType property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getMappingType()
+ {
+ return mappingType;
+ }
- /**
- * Sets the value of the mappingType property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setMappingType(String value) {
- this.mappingType = value;
- }
+ /**
+ * Sets the value of the mappingType property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setMappingType(String value)
+ {
+ this.mappingType = value;
+ }
}
// Generated on: 2021.08.30 at 11:05:22 AM BST
//
-
package jalview.xml.binding.jalview;
import javax.xml.bind.annotation.XmlEnum;
import javax.xml.bind.annotation.XmlEnumValue;
import javax.xml.bind.annotation.XmlType;
-
/**
* <p>Java class for NoValueColour.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
- * <pre>
- * &lt;simpleType name="NoValueColour"&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt;
- * &lt;enumeration value="None"/&gt;
- * &lt;enumeration value="Min"/&gt;
- * &lt;enumeration value="Max"/&gt;
- * &lt;/restriction&gt;
- * &lt;/simpleType&gt;
- * </pre>
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class. <pre> &lt;simpleType
+ * name="NoValueColour"&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}string"&gt; &lt;enumeration
+ * value="None"/&gt; &lt;enumeration value="Min"/&gt;
+ * &lt;enumeration value="Max"/&gt; &lt;/restriction&gt;
+ * &lt;/simpleType&gt; </pre>
*
*/
@XmlType(name = "NoValueColour", namespace = "www.jalview.org/colours")
@XmlEnum
-public enum NoValueColour {
-
- @XmlEnumValue("None")
- NONE("None"),
- @XmlEnumValue("Min")
- MIN("Min"),
- @XmlEnumValue("Max")
- MAX("Max");
- private final String value;
-
- NoValueColour(String v) {
- value = v;
- }
-
- public String value() {
- return value;
- }
-
- public static NoValueColour fromValue(String v) {
- for (NoValueColour c: NoValueColour.values()) {
- if (c.value.equals(v)) {
- return c;
- }
- }
- throw new IllegalArgumentException(v);
+public enum NoValueColour
+{
+
+ @XmlEnumValue("None")
+ NONE("None"), @XmlEnumValue("Min")
+ MIN("Min"), @XmlEnumValue("Max")
+ MAX("Max");
+
+ private final String value;
+
+ NoValueColour(String v)
+ {
+ value = v;
+ }
+
+ public String value()
+ {
+ return value;
+ }
+
+ public static NoValueColour fromValue(String v)
+ {
+ for (NoValueColour c : NoValueColour.values())
+ {
+ if (c.value.equals(v))
+ {
+ return c;
+ }
}
+ throw new IllegalArgumentException(v);
+ }
}
// Generated on: 2021.08.30 at 11:05:22 AM BST
//
-
package jalview.xml.binding.jalview;
import javax.xml.bind.JAXBElement;
import javax.xml.bind.annotation.XmlRegistry;
import javax.xml.namespace.QName;
-
/**
- * This object contains factory methods for each
- * Java content interface and Java element interface
- * generated in the jalview.xml.binding.jalview package.
- * <p>An ObjectFactory allows you to programatically
- * construct new instances of the Java representation
- * for XML content. The Java representation of XML
- * content can consist of schema derived interfaces
- * and classes representing the binding of schema
- * type definitions, element declarations and model
- * groups. Factory methods for each of these are
- * provided in this class.
+ * This object contains factory methods for each Java content interface and Java
+ * element interface generated in the jalview.xml.binding.jalview package.
+ * <p>An ObjectFactory allows you to programatically construct new
+ * instances of the Java representation for XML content. The Java representation
+ * of XML content can consist of schema derived interfaces and classes
+ * representing the binding of schema type definitions, element declarations and
+ * model groups. Factory methods for each of these are provided in this class.
*
*/
@XmlRegistry
-public class ObjectFactory {
-
- private final static QName _JalviewModel_QNAME = new QName("www.jalview.org", "JalviewModel");
- private final static QName _JalviewUserColours_QNAME = new QName("www.jalview.org/colours", "JalviewUserColours");
- private final static QName _WebServiceParameterSet_QNAME = new QName("www.jalview.org/xml/wsparamset", "WebServiceParameterSet");
-
- /**
- * Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: jalview.xml.binding.jalview
- *
- */
- public ObjectFactory() {
- }
-
- /**
- * Create an instance of {@link MapListType }
- *
- */
- public MapListType createMapListType() {
- return new MapListType();
- }
-
- /**
- * Create an instance of {@link Sequence }
- *
- */
- public Sequence createSequence() {
- return new Sequence();
- }
-
- /**
- * Create an instance of {@link AlcodonFrame }
- *
- */
- public AlcodonFrame createAlcodonFrame() {
- return new AlcodonFrame();
- }
-
- /**
- * Create an instance of {@link Annotation }
- *
- */
- public Annotation createAnnotation() {
- return new Annotation();
- }
-
- /**
- * Create an instance of {@link SequenceSet }
- *
- */
- public SequenceSet createSequenceSet() {
- return new SequenceSet();
- }
-
- /**
- * Create an instance of {@link FeatureMatcherSet }
- *
- */
- public FeatureMatcherSet createFeatureMatcherSet() {
- return new FeatureMatcherSet();
- }
-
- /**
- * Create an instance of {@link JalviewUserColours }
- *
- */
- public JalviewUserColours createJalviewUserColours() {
- return new JalviewUserColours();
- }
-
- /**
- * Create an instance of {@link Pdbentry }
- *
- */
- public Pdbentry createPdbentry() {
- return new Pdbentry();
- }
-
- /**
- * Create an instance of {@link Feature }
- *
- */
- public Feature createFeature() {
- return new Feature();
- }
-
- /**
- * Create an instance of {@link JalviewModel }
- *
- */
- public JalviewModel createJalviewModel() {
- return new JalviewModel();
- }
-
- /**
- * Create an instance of {@link JalviewModel.FeatureSettings }
- *
- */
- public JalviewModel.FeatureSettings createJalviewModelFeatureSettings() {
- return new JalviewModel.FeatureSettings();
- }
-
- /**
- * Create an instance of {@link JalviewModel.PcaViewer }
- *
- */
- public JalviewModel.PcaViewer createJalviewModelPcaViewer() {
- return new JalviewModel.PcaViewer();
- }
-
- /**
- * Create an instance of {@link JalviewModel.Viewport }
- *
- */
- public JalviewModel.Viewport createJalviewModelViewport() {
- return new JalviewModel.Viewport();
- }
-
- /**
- * Create an instance of {@link JalviewModel.JSeq }
- *
- */
- public JalviewModel.JSeq createJalviewModelJSeq() {
- return new JalviewModel.JSeq();
- }
-
- /**
- * Create an instance of {@link JalviewModel.JSeq.RnaViewer }
- *
- */
- public JalviewModel.JSeq.RnaViewer createJalviewModelJSeqRnaViewer() {
- return new JalviewModel.JSeq.RnaViewer();
- }
-
- /**
- * Create an instance of {@link JalviewModel.JSeq.Pdbids }
- *
- */
- public JalviewModel.JSeq.Pdbids createJalviewModelJSeqPdbids() {
- return new JalviewModel.JSeq.Pdbids();
- }
-
- /**
- * Create an instance of {@link AnnotationColourScheme }
- *
- */
- public AnnotationColourScheme createAnnotationColourScheme() {
- return new AnnotationColourScheme();
- }
-
- /**
- * Create an instance of {@link PcaDataType }
- *
- */
- public PcaDataType createPcaDataType() {
- return new PcaDataType();
- }
-
- /**
- * Create an instance of {@link DoubleVector }
- *
- */
- public DoubleVector createDoubleVector() {
- return new DoubleVector();
- }
-
- /**
- * Create an instance of {@link DoubleMatrix }
- *
- */
- public DoubleMatrix createDoubleMatrix() {
- return new DoubleMatrix();
- }
-
- /**
- * Create an instance of {@link Mapping }
- *
- */
- public Mapping createMapping() {
- return new Mapping();
- }
-
- /**
- * Create an instance of {@link MapListType.MapListFrom }
- *
- */
- public MapListType.MapListFrom createMapListTypeMapListFrom() {
- return new MapListType.MapListFrom();
- }
-
- /**
- * Create an instance of {@link MapListType.MapListTo }
- *
- */
- public MapListType.MapListTo createMapListTypeMapListTo() {
- return new MapListType.MapListTo();
- }
-
- /**
- * Create an instance of {@link SequenceType }
- *
- */
- public SequenceType createSequenceType() {
- return new SequenceType();
- }
-
- /**
- * Create an instance of {@link Sequence.DBRef }
- *
- */
- public Sequence.DBRef createSequenceDBRef() {
- return new Sequence.DBRef();
- }
-
- /**
- * Create an instance of {@link AlcodonFrame.Alcodon }
- *
- */
- public AlcodonFrame.Alcodon createAlcodonFrameAlcodon() {
- return new AlcodonFrame.Alcodon();
- }
-
- /**
- * Create an instance of {@link AlcodonFrame.AlcodMap }
- *
- */
- public AlcodonFrame.AlcodMap createAlcodonFrameAlcodMap() {
- return new AlcodonFrame.AlcodMap();
- }
-
- /**
- * Create an instance of {@link AnnotationElement }
- *
- */
- public AnnotationElement createAnnotationElement() {
- return new AnnotationElement();
- }
-
- /**
- * Create an instance of {@link Annotation.ThresholdLine }
- *
- */
- public Annotation.ThresholdLine createAnnotationThresholdLine() {
- return new Annotation.ThresholdLine();
- }
-
- /**
- * Create an instance of {@link Annotation.Property }
- *
- */
- public Annotation.Property createAnnotationProperty() {
- return new Annotation.Property();
- }
-
- /**
- * Create an instance of {@link SequenceSet.SequenceSetProperties }
- *
- */
- public SequenceSet.SequenceSetProperties createSequenceSetSequenceSetProperties() {
- return new SequenceSet.SequenceSetProperties();
- }
-
- /**
- * Create an instance of {@link VAMSAS }
- *
- */
- public VAMSAS createVAMSAS() {
- return new VAMSAS();
- }
-
- /**
- * Create an instance of {@link FeatureMatcher }
- *
- */
- public FeatureMatcher createFeatureMatcher() {
- return new FeatureMatcher();
- }
-
- /**
- * Create an instance of {@link WebServiceParameterSet }
- *
- */
- public WebServiceParameterSet createWebServiceParameterSet() {
- return new WebServiceParameterSet();
- }
-
- /**
- * Create an instance of {@link FeatureMatcherSet.CompoundMatcher }
- *
- */
- public FeatureMatcherSet.CompoundMatcher createFeatureMatcherSetCompoundMatcher() {
- return new FeatureMatcherSet.CompoundMatcher();
- }
-
- /**
- * Create an instance of {@link JalviewUserColours.Colour }
- *
- */
- public JalviewUserColours.Colour createJalviewUserColoursColour() {
- return new JalviewUserColours.Colour();
- }
-
- /**
- * Create an instance of {@link JalviewUserColours.Filter }
- *
- */
- public JalviewUserColours.Filter createJalviewUserColoursFilter() {
- return new JalviewUserColours.Filter();
- }
-
- /**
- * Create an instance of {@link Pdbentry.Property }
- *
- */
- public Pdbentry.Property createPdbentryProperty() {
- return new Pdbentry.Property();
- }
-
- /**
- * Create an instance of {@link Feature.OtherData }
- *
- */
- public Feature.OtherData createFeatureOtherData() {
- return new Feature.OtherData();
- }
-
- /**
- * Create an instance of {@link JalviewModel.JGroup }
- *
- */
- public JalviewModel.JGroup createJalviewModelJGroup() {
- return new JalviewModel.JGroup();
- }
-
- /**
- * Create an instance of {@link JalviewModel.UserColours }
- *
- */
- public JalviewModel.UserColours createJalviewModelUserColours() {
- return new JalviewModel.UserColours();
- }
-
- /**
- * Create an instance of {@link JalviewModel.Tree }
- *
- */
- public JalviewModel.Tree createJalviewModelTree() {
- return new JalviewModel.Tree();
- }
-
- /**
- * Create an instance of {@link JalviewModel.FeatureSettings.Setting }
- *
- */
- public JalviewModel.FeatureSettings.Setting createJalviewModelFeatureSettingsSetting() {
- return new JalviewModel.FeatureSettings.Setting();
- }
-
- /**
- * Create an instance of {@link JalviewModel.FeatureSettings.Group }
- *
- */
- public JalviewModel.FeatureSettings.Group createJalviewModelFeatureSettingsGroup() {
- return new JalviewModel.FeatureSettings.Group();
- }
-
- /**
- * Create an instance of {@link JalviewModel.PcaViewer.SequencePoint }
- *
- */
- public JalviewModel.PcaViewer.SequencePoint createJalviewModelPcaViewerSequencePoint() {
- return new JalviewModel.PcaViewer.SequencePoint();
- }
-
- /**
- * Create an instance of {@link JalviewModel.PcaViewer.Axis }
- *
- */
- public JalviewModel.PcaViewer.Axis createJalviewModelPcaViewerAxis() {
- return new JalviewModel.PcaViewer.Axis();
- }
-
- /**
- * Create an instance of {@link JalviewModel.PcaViewer.SeqPointMin }
- *
- */
- public JalviewModel.PcaViewer.SeqPointMin createJalviewModelPcaViewerSeqPointMin() {
- return new JalviewModel.PcaViewer.SeqPointMin();
- }
-
- /**
- * Create an instance of {@link JalviewModel.PcaViewer.SeqPointMax }
- *
- */
- public JalviewModel.PcaViewer.SeqPointMax createJalviewModelPcaViewerSeqPointMax() {
- return new JalviewModel.PcaViewer.SeqPointMax();
- }
-
- /**
- * Create an instance of {@link JalviewModel.Viewport.HiddenColumns }
- *
- */
- public JalviewModel.Viewport.HiddenColumns createJalviewModelViewportHiddenColumns() {
- return new JalviewModel.Viewport.HiddenColumns();
- }
-
- /**
- * Create an instance of {@link JalviewModel.Viewport.CalcIdParam }
- *
- */
- public JalviewModel.Viewport.CalcIdParam createJalviewModelViewportCalcIdParam() {
- return new JalviewModel.Viewport.CalcIdParam();
- }
-
- /**
- * Create an instance of {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
- *
- */
- public JalviewModel.JSeq.RnaViewer.SecondaryStructure createJalviewModelJSeqRnaViewerSecondaryStructure() {
- return new JalviewModel.JSeq.RnaViewer.SecondaryStructure();
- }
-
- /**
- * Create an instance of {@link JalviewModel.JSeq.Pdbids.StructureState }
- *
- */
- public JalviewModel.JSeq.Pdbids.StructureState createJalviewModelJSeqPdbidsStructureState() {
- return new JalviewModel.JSeq.Pdbids.StructureState();
- }
-
- /**
- * Create an instance of {@link JAXBElement }{@code <}{@link JalviewModel }{@code >}
- *
- * @param value
- * Java instance representing xml element's value.
- * @return
- * the new instance of {@link JAXBElement }{@code <}{@link JalviewModel }{@code >}
- */
- @XmlElementDecl(namespace = "www.jalview.org", name = "JalviewModel")
- public JAXBElement<JalviewModel> createJalviewModel(JalviewModel value) {
- return new JAXBElement<JalviewModel>(_JalviewModel_QNAME, JalviewModel.class, null, value);
- }
-
- /**
- * Create an instance of {@link JAXBElement }{@code <}{@link JalviewUserColours }{@code >}
- *
- * @param value
- * Java instance representing xml element's value.
- * @return
- * the new instance of {@link JAXBElement }{@code <}{@link JalviewUserColours }{@code >}
- */
- @XmlElementDecl(namespace = "www.jalview.org/colours", name = "JalviewUserColours")
- public JAXBElement<JalviewUserColours> createJalviewUserColours(JalviewUserColours value) {
- return new JAXBElement<JalviewUserColours>(_JalviewUserColours_QNAME, JalviewUserColours.class, null, value);
- }
-
- /**
- * Create an instance of {@link JAXBElement }{@code <}{@link WebServiceParameterSet }{@code >}
- *
- * @param value
- * Java instance representing xml element's value.
- * @return
- * the new instance of {@link JAXBElement }{@code <}{@link WebServiceParameterSet }{@code >}
- */
- @XmlElementDecl(namespace = "www.jalview.org/xml/wsparamset", name = "WebServiceParameterSet")
- public JAXBElement<WebServiceParameterSet> createWebServiceParameterSet(WebServiceParameterSet value) {
- return new JAXBElement<WebServiceParameterSet>(_WebServiceParameterSet_QNAME, WebServiceParameterSet.class, null, value);
- }
+public class ObjectFactory
+{
+
+ private final static QName _JalviewModel_QNAME = new QName(
+ "www.jalview.org", "JalviewModel");
+
+ private final static QName _JalviewUserColours_QNAME = new QName(
+ "www.jalview.org/colours", "JalviewUserColours");
+
+ private final static QName _WebServiceParameterSet_QNAME = new QName(
+ "www.jalview.org/xml/wsparamset", "WebServiceParameterSet");
+
+ /**
+ * Create a new ObjectFactory that can be used to create new instances of
+ * schema derived classes for package: jalview.xml.binding.jalview
+ *
+ */
+ public ObjectFactory()
+ {
+ }
+
+ /**
+ * Create an instance of {@link MapListType }
+ *
+ */
+ public MapListType createMapListType()
+ {
+ return new MapListType();
+ }
+
+ /**
+ * Create an instance of {@link Sequence }
+ *
+ */
+ public Sequence createSequence()
+ {
+ return new Sequence();
+ }
+
+ /**
+ * Create an instance of {@link AlcodonFrame }
+ *
+ */
+ public AlcodonFrame createAlcodonFrame()
+ {
+ return new AlcodonFrame();
+ }
+
+ /**
+ * Create an instance of {@link Annotation }
+ *
+ */
+ public Annotation createAnnotation()
+ {
+ return new Annotation();
+ }
+
+ /**
+ * Create an instance of {@link SequenceSet }
+ *
+ */
+ public SequenceSet createSequenceSet()
+ {
+ return new SequenceSet();
+ }
+
+ /**
+ * Create an instance of {@link FeatureMatcherSet }
+ *
+ */
+ public FeatureMatcherSet createFeatureMatcherSet()
+ {
+ return new FeatureMatcherSet();
+ }
+
+ /**
+ * Create an instance of {@link JalviewUserColours }
+ *
+ */
+ public JalviewUserColours createJalviewUserColours()
+ {
+ return new JalviewUserColours();
+ }
+
+ /**
+ * Create an instance of {@link Pdbentry }
+ *
+ */
+ public Pdbentry createPdbentry()
+ {
+ return new Pdbentry();
+ }
+
+ /**
+ * Create an instance of {@link Feature }
+ *
+ */
+ public Feature createFeature()
+ {
+ return new Feature();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel }
+ *
+ */
+ public JalviewModel createJalviewModel()
+ {
+ return new JalviewModel();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.FeatureSettings }
+ *
+ */
+ public JalviewModel.FeatureSettings createJalviewModelFeatureSettings()
+ {
+ return new JalviewModel.FeatureSettings();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.PcaViewer }
+ *
+ */
+ public JalviewModel.PcaViewer createJalviewModelPcaViewer()
+ {
+ return new JalviewModel.PcaViewer();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.Viewport }
+ *
+ */
+ public JalviewModel.Viewport createJalviewModelViewport()
+ {
+ return new JalviewModel.Viewport();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.JSeq }
+ *
+ */
+ public JalviewModel.JSeq createJalviewModelJSeq()
+ {
+ return new JalviewModel.JSeq();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.JSeq.RnaViewer }
+ *
+ */
+ public JalviewModel.JSeq.RnaViewer createJalviewModelJSeqRnaViewer()
+ {
+ return new JalviewModel.JSeq.RnaViewer();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.JSeq.Pdbids }
+ *
+ */
+ public JalviewModel.JSeq.Pdbids createJalviewModelJSeqPdbids()
+ {
+ return new JalviewModel.JSeq.Pdbids();
+ }
+
+ /**
+ * Create an instance of {@link AnnotationColourScheme }
+ *
+ */
+ public AnnotationColourScheme createAnnotationColourScheme()
+ {
+ return new AnnotationColourScheme();
+ }
+
+ /**
+ * Create an instance of {@link PcaDataType }
+ *
+ */
+ public PcaDataType createPcaDataType()
+ {
+ return new PcaDataType();
+ }
+
+ /**
+ * Create an instance of {@link DoubleVector }
+ *
+ */
+ public DoubleVector createDoubleVector()
+ {
+ return new DoubleVector();
+ }
+
+ /**
+ * Create an instance of {@link DoubleMatrix }
+ *
+ */
+ public DoubleMatrix createDoubleMatrix()
+ {
+ return new DoubleMatrix();
+ }
+
+ /**
+ * Create an instance of {@link Mapping }
+ *
+ */
+ public Mapping createMapping()
+ {
+ return new Mapping();
+ }
+
+ /**
+ * Create an instance of {@link MapListType.MapListFrom }
+ *
+ */
+ public MapListType.MapListFrom createMapListTypeMapListFrom()
+ {
+ return new MapListType.MapListFrom();
+ }
+
+ /**
+ * Create an instance of {@link MapListType.MapListTo }
+ *
+ */
+ public MapListType.MapListTo createMapListTypeMapListTo()
+ {
+ return new MapListType.MapListTo();
+ }
+
+ /**
+ * Create an instance of {@link SequenceType }
+ *
+ */
+ public SequenceType createSequenceType()
+ {
+ return new SequenceType();
+ }
+
+ /**
+ * Create an instance of {@link Sequence.DBRef }
+ *
+ */
+ public Sequence.DBRef createSequenceDBRef()
+ {
+ return new Sequence.DBRef();
+ }
+
+ /**
+ * Create an instance of {@link AlcodonFrame.Alcodon }
+ *
+ */
+ public AlcodonFrame.Alcodon createAlcodonFrameAlcodon()
+ {
+ return new AlcodonFrame.Alcodon();
+ }
+
+ /**
+ * Create an instance of {@link AlcodonFrame.AlcodMap }
+ *
+ */
+ public AlcodonFrame.AlcodMap createAlcodonFrameAlcodMap()
+ {
+ return new AlcodonFrame.AlcodMap();
+ }
+
+ /**
+ * Create an instance of {@link AnnotationElement }
+ *
+ */
+ public AnnotationElement createAnnotationElement()
+ {
+ return new AnnotationElement();
+ }
+
+ /**
+ * Create an instance of {@link Annotation.ThresholdLine }
+ *
+ */
+ public Annotation.ThresholdLine createAnnotationThresholdLine()
+ {
+ return new Annotation.ThresholdLine();
+ }
+
+ /**
+ * Create an instance of {@link Annotation.Property }
+ *
+ */
+ public Annotation.Property createAnnotationProperty()
+ {
+ return new Annotation.Property();
+ }
+
+ /**
+ * Create an instance of {@link SequenceSet.SequenceSetProperties }
+ *
+ */
+ public SequenceSet.SequenceSetProperties createSequenceSetSequenceSetProperties()
+ {
+ return new SequenceSet.SequenceSetProperties();
+ }
+
+ /**
+ * Create an instance of {@link VAMSAS }
+ *
+ */
+ public VAMSAS createVAMSAS()
+ {
+ return new VAMSAS();
+ }
+
+ /**
+ * Create an instance of {@link FeatureMatcher }
+ *
+ */
+ public FeatureMatcher createFeatureMatcher()
+ {
+ return new FeatureMatcher();
+ }
+
+ /**
+ * Create an instance of {@link WebServiceParameterSet }
+ *
+ */
+ public WebServiceParameterSet createWebServiceParameterSet()
+ {
+ return new WebServiceParameterSet();
+ }
+
+ /**
+ * Create an instance of {@link FeatureMatcherSet.CompoundMatcher }
+ *
+ */
+ public FeatureMatcherSet.CompoundMatcher createFeatureMatcherSetCompoundMatcher()
+ {
+ return new FeatureMatcherSet.CompoundMatcher();
+ }
+
+ /**
+ * Create an instance of {@link JalviewUserColours.Colour }
+ *
+ */
+ public JalviewUserColours.Colour createJalviewUserColoursColour()
+ {
+ return new JalviewUserColours.Colour();
+ }
+
+ /**
+ * Create an instance of {@link JalviewUserColours.Filter }
+ *
+ */
+ public JalviewUserColours.Filter createJalviewUserColoursFilter()
+ {
+ return new JalviewUserColours.Filter();
+ }
+
+ /**
+ * Create an instance of {@link Pdbentry.Property }
+ *
+ */
+ public Pdbentry.Property createPdbentryProperty()
+ {
+ return new Pdbentry.Property();
+ }
+
+ /**
+ * Create an instance of {@link Feature.OtherData }
+ *
+ */
+ public Feature.OtherData createFeatureOtherData()
+ {
+ return new Feature.OtherData();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.JGroup }
+ *
+ */
+ public JalviewModel.JGroup createJalviewModelJGroup()
+ {
+ return new JalviewModel.JGroup();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.UserColours }
+ *
+ */
+ public JalviewModel.UserColours createJalviewModelUserColours()
+ {
+ return new JalviewModel.UserColours();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.Tree }
+ *
+ */
+ public JalviewModel.Tree createJalviewModelTree()
+ {
+ return new JalviewModel.Tree();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.FeatureSettings.Setting }
+ *
+ */
+ public JalviewModel.FeatureSettings.Setting createJalviewModelFeatureSettingsSetting()
+ {
+ return new JalviewModel.FeatureSettings.Setting();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.FeatureSettings.Group }
+ *
+ */
+ public JalviewModel.FeatureSettings.Group createJalviewModelFeatureSettingsGroup()
+ {
+ return new JalviewModel.FeatureSettings.Group();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.PcaViewer.SequencePoint }
+ *
+ */
+ public JalviewModel.PcaViewer.SequencePoint createJalviewModelPcaViewerSequencePoint()
+ {
+ return new JalviewModel.PcaViewer.SequencePoint();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.PcaViewer.Axis }
+ *
+ */
+ public JalviewModel.PcaViewer.Axis createJalviewModelPcaViewerAxis()
+ {
+ return new JalviewModel.PcaViewer.Axis();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.PcaViewer.SeqPointMin }
+ *
+ */
+ public JalviewModel.PcaViewer.SeqPointMin createJalviewModelPcaViewerSeqPointMin()
+ {
+ return new JalviewModel.PcaViewer.SeqPointMin();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.PcaViewer.SeqPointMax }
+ *
+ */
+ public JalviewModel.PcaViewer.SeqPointMax createJalviewModelPcaViewerSeqPointMax()
+ {
+ return new JalviewModel.PcaViewer.SeqPointMax();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.Viewport.HiddenColumns }
+ *
+ */
+ public JalviewModel.Viewport.HiddenColumns createJalviewModelViewportHiddenColumns()
+ {
+ return new JalviewModel.Viewport.HiddenColumns();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.Viewport.CalcIdParam }
+ *
+ */
+ public JalviewModel.Viewport.CalcIdParam createJalviewModelViewportCalcIdParam()
+ {
+ return new JalviewModel.Viewport.CalcIdParam();
+ }
+
+ /**
+ * Create an instance of
+ * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
+ *
+ */
+ public JalviewModel.JSeq.RnaViewer.SecondaryStructure createJalviewModelJSeqRnaViewerSecondaryStructure()
+ {
+ return new JalviewModel.JSeq.RnaViewer.SecondaryStructure();
+ }
+
+ /**
+ * Create an instance of {@link JalviewModel.JSeq.Pdbids.StructureState }
+ *
+ */
+ public JalviewModel.JSeq.Pdbids.StructureState createJalviewModelJSeqPdbidsStructureState()
+ {
+ return new JalviewModel.JSeq.Pdbids.StructureState();
+ }
+
+ /**
+ * Create an instance of {@link JAXBElement }{@code <}{@link JalviewModel
+ * }{@code >}
+ *
+ * @param value
+ * Java instance representing xml element's value.
+ * @return the new instance of {@link JAXBElement
+ * }{@code <}{@link JalviewModel }{@code >}
+ */
+ @XmlElementDecl(namespace = "www.jalview.org", name = "JalviewModel")
+ public JAXBElement<JalviewModel> createJalviewModel(JalviewModel value)
+ {
+ return new JAXBElement<JalviewModel>(_JalviewModel_QNAME,
+ JalviewModel.class, null, value);
+ }
+
+ /**
+ * Create an instance of {@link JAXBElement
+ * }{@code <}{@link JalviewUserColours }{@code >}
+ *
+ * @param value
+ * Java instance representing xml element's value.
+ * @return the new instance of {@link JAXBElement
+ * }{@code <}{@link JalviewUserColours }{@code >}
+ */
+ @XmlElementDecl(
+ namespace = "www.jalview.org/colours",
+ name = "JalviewUserColours")
+ public JAXBElement<JalviewUserColours> createJalviewUserColours(
+ JalviewUserColours value)
+ {
+ return new JAXBElement<JalviewUserColours>(_JalviewUserColours_QNAME,
+ JalviewUserColours.class, null, value);
+ }
+
+ /**
+ * Create an instance of {@link JAXBElement
+ * }{@code <}{@link WebServiceParameterSet }{@code >}
+ *
+ * @param value
+ * Java instance representing xml element's value.
+ * @return the new instance of {@link JAXBElement
+ * }{@code <}{@link WebServiceParameterSet }{@code >}
+ */
+ @XmlElementDecl(
+ namespace = "www.jalview.org/xml/wsparamset",
+ name = "WebServiceParameterSet")
+ public JAXBElement<WebServiceParameterSet> createWebServiceParameterSet(
+ WebServiceParameterSet value)
+ {
+ return new JAXBElement<WebServiceParameterSet>(
+ _WebServiceParameterSet_QNAME, WebServiceParameterSet.class,
+ null, value);
+ }
}
// Generated on: 2021.08.30 at 11:05:22 AM BST
//
-
package jalview.xml.binding.jalview;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
-
/**
*
- * The results of a PCA calculation
- *
+ * The results of a PCA calculation
+ *
*
* <p>Java class for PcaDataType complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
*
- * <pre>
- * &lt;complexType name="PcaDataType"&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="pairwiseMatrix" type="{www.jalview.org}DoubleMatrix"/&gt;
- * &lt;element name="tridiagonalMatrix" type="{www.jalview.org}DoubleMatrix"/&gt;
- * &lt;element name="eigenMatrix" type="{www.jalview.org}DoubleMatrix"/&gt;
- * &lt;/sequence&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre> &lt;complexType name="PcaDataType"&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="pairwiseMatrix"
+ * type="{www.jalview.org}DoubleMatrix"/&gt; &lt;element
+ * name="tridiagonalMatrix" type="{www.jalview.org}DoubleMatrix"/&gt;
+ * &lt;element name="eigenMatrix"
+ * type="{www.jalview.org}DoubleMatrix"/&gt; &lt;/sequence&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "PcaDataType", namespace = "www.jalview.org", propOrder = {
- "pairwiseMatrix",
- "tridiagonalMatrix",
- "eigenMatrix"
-})
-public class PcaDataType {
+@XmlType(
+ name = "PcaDataType",
+ namespace = "www.jalview.org",
+ propOrder =
+ { "pairwiseMatrix", "tridiagonalMatrix", "eigenMatrix" })
+public class PcaDataType
+{
+
+ @XmlElement(required = true)
+ protected DoubleMatrix pairwiseMatrix;
+
+ @XmlElement(required = true)
+ protected DoubleMatrix tridiagonalMatrix;
- @XmlElement(required = true)
- protected DoubleMatrix pairwiseMatrix;
- @XmlElement(required = true)
- protected DoubleMatrix tridiagonalMatrix;
- @XmlElement(required = true)
- protected DoubleMatrix eigenMatrix;
+ @XmlElement(required = true)
+ protected DoubleMatrix eigenMatrix;
- /**
- * Gets the value of the pairwiseMatrix property.
- *
- * @return
- * possible object is
- * {@link DoubleMatrix }
- *
- */
- public DoubleMatrix getPairwiseMatrix() {
- return pairwiseMatrix;
- }
+ /**
+ * Gets the value of the pairwiseMatrix property.
+ *
+ * @return possible object is {@link DoubleMatrix }
+ *
+ */
+ public DoubleMatrix getPairwiseMatrix()
+ {
+ return pairwiseMatrix;
+ }
- /**
- * Sets the value of the pairwiseMatrix property.
- *
- * @param value
- * allowed object is
- * {@link DoubleMatrix }
- *
- */
- public void setPairwiseMatrix(DoubleMatrix value) {
- this.pairwiseMatrix = value;
- }
+ /**
+ * Sets the value of the pairwiseMatrix property.
+ *
+ * @param value
+ * allowed object is {@link DoubleMatrix }
+ *
+ */
+ public void setPairwiseMatrix(DoubleMatrix value)
+ {
+ this.pairwiseMatrix = value;
+ }
- /**
- * Gets the value of the tridiagonalMatrix property.
- *
- * @return
- * possible object is
- * {@link DoubleMatrix }
- *
- */
- public DoubleMatrix getTridiagonalMatrix() {
- return tridiagonalMatrix;
- }
+ /**
+ * Gets the value of the tridiagonalMatrix property.
+ *
+ * @return possible object is {@link DoubleMatrix }
+ *
+ */
+ public DoubleMatrix getTridiagonalMatrix()
+ {
+ return tridiagonalMatrix;
+ }
- /**
- * Sets the value of the tridiagonalMatrix property.
- *
- * @param value
- * allowed object is
- * {@link DoubleMatrix }
- *
- */
- public void setTridiagonalMatrix(DoubleMatrix value) {
- this.tridiagonalMatrix = value;
- }
+ /**
+ * Sets the value of the tridiagonalMatrix property.
+ *
+ * @param value
+ * allowed object is {@link DoubleMatrix }
+ *
+ */
+ public void setTridiagonalMatrix(DoubleMatrix value)
+ {
+ this.tridiagonalMatrix = value;
+ }
- /**
- * Gets the value of the eigenMatrix property.
- *
- * @return
- * possible object is
- * {@link DoubleMatrix }
- *
- */
- public DoubleMatrix getEigenMatrix() {
- return eigenMatrix;
- }
+ /**
+ * Gets the value of the eigenMatrix property.
+ *
+ * @return possible object is {@link DoubleMatrix }
+ *
+ */
+ public DoubleMatrix getEigenMatrix()
+ {
+ return eigenMatrix;
+ }
- /**
- * Sets the value of the eigenMatrix property.
- *
- * @param value
- * allowed object is
- * {@link DoubleMatrix }
- *
- */
- public void setEigenMatrix(DoubleMatrix value) {
- this.eigenMatrix = value;
- }
+ /**
+ * Sets the value of the eigenMatrix property.
+ *
+ * @param value
+ * allowed object is {@link DoubleMatrix }
+ *
+ */
+ public void setEigenMatrix(DoubleMatrix value)
+ {
+ this.eigenMatrix = value;
+ }
}
// Generated on: 2021.08.30 at 11:05:22 AM BST
//
-
package jalview.xml.binding.jalview;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlSeeAlso;
import javax.xml.bind.annotation.XmlType;
-
/**
* <p>Java class for pdbentry complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
*
- * <pre>
- * &lt;complexType name="pdbentry"&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;element name="property" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="file" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre> &lt;complexType name="pdbentry"&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;sequence
+ * maxOccurs="unbounded" minOccurs="0"&gt; &lt;element name="property"
+ * maxOccurs="unbounded" minOccurs="0"&gt; &lt;complexType&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
+ * name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
+ * /&gt; &lt;attribute name="value" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt;
+ * &lt;/sequence&gt; &lt;attribute name="id" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="file" type="{http://www.w3.org/2001/XMLSchema}string"
+ * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "pdbentry", namespace = "www.jalview.org", propOrder = {
- "property"
-})
-@XmlSeeAlso({
- jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids.class
-})
-public class Pdbentry {
-
- protected List<Pdbentry.Property> property;
- @XmlAttribute(name = "id", required = true)
- protected String id;
- @XmlAttribute(name = "type")
- protected String type;
- @XmlAttribute(name = "file")
- protected String file;
-
- /**
- * Gets the value of the property property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the property property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getProperty().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Pdbentry.Property }
- *
- *
- */
- public List<Pdbentry.Property> getProperty() {
- if (property == null) {
- property = new ArrayList<Pdbentry.Property>();
- }
- return this.property;
+@XmlType(
+ name = "pdbentry",
+ namespace = "www.jalview.org",
+ propOrder =
+ { "property" })
+@XmlSeeAlso({ jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids.class })
+public class Pdbentry
+{
+
+ protected List<Pdbentry.Property> property;
+
+ @XmlAttribute(name = "id", required = true)
+ protected String id;
+
+ @XmlAttribute(name = "type")
+ protected String type;
+
+ @XmlAttribute(name = "file")
+ protected String file;
+
+ /**
+ * Gets the value of the property property.
+ *
+ * <p> This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will be
+ * present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the property property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getProperty().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link Pdbentry.Property }
+ *
+ *
+ */
+ public List<Pdbentry.Property> getProperty()
+ {
+ if (property == null)
+ {
+ property = new ArrayList<Pdbentry.Property>();
}
+ return this.property;
+ }
+
+ /**
+ * Gets the value of the id property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getId()
+ {
+ return id;
+ }
+
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setId(String value)
+ {
+ this.id = value;
+ }
+
+ /**
+ * Gets the value of the type property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getType()
+ {
+ return type;
+ }
+
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setType(String value)
+ {
+ this.type = value;
+ }
+
+ /**
+ * Gets the value of the file property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getFile()
+ {
+ return file;
+ }
+
+ /**
+ * Sets the value of the file property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setFile(String value)
+ {
+ this.file = value;
+ }
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
+ *
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
+ * name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
+ * /&gt; &lt;attribute name="value" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Property
+ {
+
+ @XmlAttribute(name = "name", required = true)
+ protected String name;
+
+ @XmlAttribute(name = "value", required = true)
+ protected String value;
/**
- * Gets the value of the id property.
+ * Gets the value of the name property.
+ *
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getId() {
- return id;
+ public String getName()
+ {
+ return name;
}
/**
- * Sets the value of the id property.
+ * Sets the value of the name property.
*
* @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setId(String value) {
- this.id = value;
- }
-
- /**
- * Gets the value of the type property.
+ * allowed object is {@link String }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getType() {
- return type;
+ public void setName(String value)
+ {
+ this.name = value;
}
/**
- * Sets the value of the type property.
+ * Gets the value of the value property.
*
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setType(String value) {
- this.type = value;
- }
-
- /**
- * Gets the value of the file property.
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getFile() {
- return file;
+ public String getValue()
+ {
+ return value;
}
/**
- * Sets the value of the file property.
+ * Sets the value of the value property.
*
* @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setFile(String value) {
- this.file = value;
- }
-
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
- *
+ * allowed object is {@link String }
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class Property {
-
- @XmlAttribute(name = "name", required = true)
- protected String name;
- @XmlAttribute(name = "value", required = true)
- protected String value;
-
- /**
- * Gets the value of the name property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getName() {
- return name;
- }
-
- /**
- * Sets the value of the name property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setName(String value) {
- this.name = value;
- }
-
- /**
- * Gets the value of the value property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getValue() {
- return value;
- }
-
- /**
- * Sets the value of the value property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setValue(String value) {
- this.value = value;
- }
-
+ public void setValue(String value)
+ {
+ this.value = value;
}
+ }
+
}
// Generated on: 2021.08.30 at 11:05:22 AM BST
//
-
package jalview.xml.binding.jalview;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlRootElement;
import javax.xml.bind.annotation.XmlType;
-
/**
* <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
*
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;extension base="{www.vamsas.ac.uk/jalview/version2}SequenceType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="DBRef" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Mapping" minOccurs="0"/&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="source" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="version" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="accessionId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="locus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="canonical" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="dsseqid" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="biotype" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/extension&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;extension
+ * base="{www.vamsas.ac.uk/jalview/version2}SequenceType"&gt;
+ * &lt;sequence&gt; &lt;element name="DBRef" maxOccurs="unbounded"
+ * minOccurs="0"&gt; &lt;complexType&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element
+ * ref="{www.vamsas.ac.uk/jalview/version2}Mapping" minOccurs="0"/&gt;
+ * &lt;/sequence&gt; &lt;attribute name="source"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="version" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="accessionId"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="locus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false"
+ * /&gt; &lt;attribute name="canonical"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt;
+ * &lt;/sequence&gt; &lt;attribute name="dsseqid"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="biotype" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/extension&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = {
- "dbRef"
-})
+@XmlType(name = "", propOrder = { "dbRef" })
@XmlRootElement(name = "Sequence")
-public class Sequence
- extends SequenceType
+public class Sequence extends SequenceType
{
- @XmlElement(name = "DBRef")
- protected List<Sequence.DBRef> dbRef;
- @XmlAttribute(name = "dsseqid")
- protected String dsseqid;
- @XmlAttribute(name = "biotype")
- protected String biotype;
+ @XmlElement(name = "DBRef")
+ protected List<Sequence.DBRef> dbRef;
+
+ @XmlAttribute(name = "dsseqid")
+ protected String dsseqid;
+
+ @XmlAttribute(name = "biotype")
+ protected String biotype;
+
+ /**
+ * Gets the value of the dbRef property.
+ *
+ * <p> This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will be
+ * present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the dbRef property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getDBRef().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link Sequence.DBRef }
+ *
+ *
+ */
+ public List<Sequence.DBRef> getDBRef()
+ {
+ if (dbRef == null)
+ {
+ dbRef = new ArrayList<Sequence.DBRef>();
+ }
+ return this.dbRef;
+ }
+
+ /**
+ * Gets the value of the dsseqid property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDsseqid()
+ {
+ return dsseqid;
+ }
+
+ /**
+ * Sets the value of the dsseqid property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setDsseqid(String value)
+ {
+ this.dsseqid = value;
+ }
+
+ /**
+ * Gets the value of the biotype property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getBiotype()
+ {
+ return biotype;
+ }
+
+ /**
+ * Sets the value of the biotype property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setBiotype(String value)
+ {
+ this.biotype = value;
+ }
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
+ *
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element
+ * ref="{www.vamsas.ac.uk/jalview/version2}Mapping" minOccurs="0"/&gt;
+ * &lt;/sequence&gt; &lt;attribute name="source"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="version" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="accessionId"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="locus" type="{http://www.w3.org/2001/XMLSchema}boolean"
+ * default="false" /&gt; &lt;attribute name="canonical"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "mapping" })
+ public static class DBRef
+ {
+
+ @XmlElement(name = "Mapping")
+ protected Mapping mapping;
+
+ @XmlAttribute(name = "source")
+ protected String source;
+
+ @XmlAttribute(name = "version")
+ protected String version;
+
+ @XmlAttribute(name = "accessionId")
+ protected String accessionId;
+
+ @XmlAttribute(name = "locus")
+ protected Boolean locus;
+
+ @XmlAttribute(name = "canonical")
+ protected Boolean canonical;
/**
- * Gets the value of the dbRef property.
+ * Gets the value of the mapping property.
*
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the dbRef property.
+ * @return possible object is {@link Mapping }
*
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getDBRef().add(newItem);
- * </pre>
+ */
+ public Mapping getMapping()
+ {
+ return mapping;
+ }
+
+ /**
+ * Sets the value of the mapping property.
+ *
+ * @param value
+ * allowed object is {@link Mapping }
+ *
+ */
+ public void setMapping(Mapping value)
+ {
+ this.mapping = value;
+ }
+
+ /**
+ * Gets the value of the source property.
*
+ * @return possible object is {@link String }
*
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Sequence.DBRef }
+ */
+ public String getSource()
+ {
+ return source;
+ }
+
+ /**
+ * Sets the value of the source property.
*
+ * @param value
+ * allowed object is {@link String }
*
*/
- public List<Sequence.DBRef> getDBRef() {
- if (dbRef == null) {
- dbRef = new ArrayList<Sequence.DBRef>();
- }
- return this.dbRef;
+ public void setSource(String value)
+ {
+ this.source = value;
}
/**
- * Gets the value of the dsseqid property.
+ * Gets the value of the version property.
+ *
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getDsseqid() {
- return dsseqid;
+ public String getVersion()
+ {
+ return version;
}
/**
- * Sets the value of the dsseqid property.
+ * Sets the value of the version property.
*
* @param value
- * allowed object is
- * {@link String }
- *
+ * allowed object is {@link String }
+ *
*/
- public void setDsseqid(String value) {
- this.dsseqid = value;
+ public void setVersion(String value)
+ {
+ this.version = value;
}
/**
- * Gets the value of the biotype property.
+ * Gets the value of the accessionId property.
+ *
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getBiotype() {
- return biotype;
+ public String getAccessionId()
+ {
+ return accessionId;
}
/**
- * Sets the value of the biotype property.
+ * Sets the value of the accessionId property.
*
* @param value
- * allowed object is
- * {@link String }
- *
+ * allowed object is {@link String }
+ *
*/
- public void setBiotype(String value) {
- this.biotype = value;
+ public void setAccessionId(String value)
+ {
+ this.accessionId = value;
}
+ /**
+ * Gets the value of the locus property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isLocus()
+ {
+ if (locus == null)
+ {
+ return false;
+ }
+ else
+ {
+ return locus;
+ }
+ }
/**
- * <p>Java class for anonymous complex type.
+ * Sets the value of the locus property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * @param value
+ * allowed object is {@link Boolean }
*
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Mapping" minOccurs="0"/&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="source" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="version" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="accessionId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="locus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="canonical" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ */
+ public void setLocus(Boolean value)
+ {
+ this.locus = value;
+ }
+
+ /**
+ * Gets the value of the canonical property.
*
+ * @return possible object is {@link Boolean }
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "mapping"
- })
- public static class DBRef {
-
- @XmlElement(name = "Mapping")
- protected Mapping mapping;
- @XmlAttribute(name = "source")
- protected String source;
- @XmlAttribute(name = "version")
- protected String version;
- @XmlAttribute(name = "accessionId")
- protected String accessionId;
- @XmlAttribute(name = "locus")
- protected Boolean locus;
- @XmlAttribute(name = "canonical")
- protected Boolean canonical;
-
- /**
- * Gets the value of the mapping property.
- *
- * @return
- * possible object is
- * {@link Mapping }
- *
- */
- public Mapping getMapping() {
- return mapping;
- }
-
- /**
- * Sets the value of the mapping property.
- *
- * @param value
- * allowed object is
- * {@link Mapping }
- *
- */
- public void setMapping(Mapping value) {
- this.mapping = value;
- }
-
- /**
- * Gets the value of the source property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getSource() {
- return source;
- }
-
- /**
- * Sets the value of the source property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setSource(String value) {
- this.source = value;
- }
-
- /**
- * Gets the value of the version property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getVersion() {
- return version;
- }
-
- /**
- * Sets the value of the version property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setVersion(String value) {
- this.version = value;
- }
-
- /**
- * Gets the value of the accessionId property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getAccessionId() {
- return accessionId;
- }
-
- /**
- * Sets the value of the accessionId property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setAccessionId(String value) {
- this.accessionId = value;
- }
-
- /**
- * Gets the value of the locus property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isLocus() {
- if (locus == null) {
- return false;
- } else {
- return locus;
- }
- }
-
- /**
- * Sets the value of the locus property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setLocus(Boolean value) {
- this.locus = value;
- }
-
- /**
- * Gets the value of the canonical property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isCanonical() {
- if (canonical == null) {
- return false;
- } else {
- return canonical;
- }
- }
-
- /**
- * Sets the value of the canonical property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setCanonical(Boolean value) {
- this.canonical = value;
- }
+ public boolean isCanonical()
+ {
+ if (canonical == null)
+ {
+ return false;
+ }
+ else
+ {
+ return canonical;
+ }
+ }
+ /**
+ * Sets the value of the canonical property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setCanonical(Boolean value)
+ {
+ this.canonical = value;
}
+ }
+
}
// Generated on: 2021.08.30 at 11:05:22 AM BST
//
-
package jalview.xml.binding.jalview;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlRootElement;
import javax.xml.bind.annotation.XmlType;
-
/**
* <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
*
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Sequence" maxOccurs="unbounded" minOccurs="0"/&gt;
- * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Annotation" maxOccurs="unbounded" minOccurs="0"/&gt;
- * &lt;element name="sequenceSetProperties" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="key" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}AlcodonFrame" maxOccurs="unbounded" minOccurs="0"/&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="gapChar" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="datasetId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element
+ * ref="{www.vamsas.ac.uk/jalview/version2}Sequence" maxOccurs="unbounded"
+ * minOccurs="0"/&gt; &lt;element
+ * ref="{www.vamsas.ac.uk/jalview/version2}Annotation" maxOccurs="unbounded"
+ * minOccurs="0"/&gt; &lt;element name="sequenceSetProperties"
+ * maxOccurs="unbounded" minOccurs="0"&gt; &lt;complexType&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
+ * name="key" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="value"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; &lt;/element&gt; &lt;element
+ * ref="{www.vamsas.ac.uk/jalview/version2}AlcodonFrame" maxOccurs="unbounded"
+ * minOccurs="0"/&gt; &lt;/sequence&gt; &lt;attribute
+ * name="gapChar" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
+ * /&gt; &lt;attribute name="datasetId"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = {
- "sequence",
- "annotation",
- "sequenceSetProperties",
- "alcodonFrame"
-})
+@XmlType(
+ name = "",
+ propOrder =
+ { "sequence", "annotation", "sequenceSetProperties", "alcodonFrame" })
@XmlRootElement(name = "SequenceSet")
-public class SequenceSet {
+public class SequenceSet
+{
- @XmlElement(name = "Sequence")
- protected List<Sequence> sequence;
- @XmlElement(name = "Annotation")
- protected List<Annotation> annotation;
- protected List<SequenceSet.SequenceSetProperties> sequenceSetProperties;
- @XmlElement(name = "AlcodonFrame")
- protected List<AlcodonFrame> alcodonFrame;
- @XmlAttribute(name = "gapChar", required = true)
- protected String gapChar;
- @XmlAttribute(name = "datasetId")
- protected String datasetId;
+ @XmlElement(name = "Sequence")
+ protected List<Sequence> sequence;
- /**
- * Gets the value of the sequence property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the sequence property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getSequence().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Sequence }
- *
- *
- */
- public List<Sequence> getSequence() {
- if (sequence == null) {
- sequence = new ArrayList<Sequence>();
- }
- return this.sequence;
+ @XmlElement(name = "Annotation")
+ protected List<Annotation> annotation;
+
+ protected List<SequenceSet.SequenceSetProperties> sequenceSetProperties;
+
+ @XmlElement(name = "AlcodonFrame")
+ protected List<AlcodonFrame> alcodonFrame;
+
+ @XmlAttribute(name = "gapChar", required = true)
+ protected String gapChar;
+
+ @XmlAttribute(name = "datasetId")
+ protected String datasetId;
+
+ /**
+ * Gets the value of the sequence property.
+ *
+ * <p> This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will be
+ * present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the sequence property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getSequence().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link Sequence }
+ *
+ *
+ */
+ public List<Sequence> getSequence()
+ {
+ if (sequence == null)
+ {
+ sequence = new ArrayList<Sequence>();
}
+ return this.sequence;
+ }
- /**
- * Gets the value of the annotation property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the annotation property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getAnnotation().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Annotation }
- *
- *
- */
- public List<Annotation> getAnnotation() {
- if (annotation == null) {
- annotation = new ArrayList<Annotation>();
- }
- return this.annotation;
+ /**
+ * Gets the value of the annotation property.
+ *
+ * <p> This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will be
+ * present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the annotation property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getAnnotation().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link Annotation }
+ *
+ *
+ */
+ public List<Annotation> getAnnotation()
+ {
+ if (annotation == null)
+ {
+ annotation = new ArrayList<Annotation>();
}
+ return this.annotation;
+ }
- /**
- * Gets the value of the sequenceSetProperties property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the sequenceSetProperties property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getSequenceSetProperties().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link SequenceSet.SequenceSetProperties }
- *
- *
- */
- public List<SequenceSet.SequenceSetProperties> getSequenceSetProperties() {
- if (sequenceSetProperties == null) {
- sequenceSetProperties = new ArrayList<SequenceSet.SequenceSetProperties>();
- }
- return this.sequenceSetProperties;
+ /**
+ * Gets the value of the sequenceSetProperties property.
+ *
+ * <p> This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will be
+ * present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the sequenceSetProperties property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getSequenceSetProperties().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link SequenceSet.SequenceSetProperties }
+ *
+ *
+ */
+ public List<SequenceSet.SequenceSetProperties> getSequenceSetProperties()
+ {
+ if (sequenceSetProperties == null)
+ {
+ sequenceSetProperties = new ArrayList<SequenceSet.SequenceSetProperties>();
}
+ return this.sequenceSetProperties;
+ }
- /**
- * Gets the value of the alcodonFrame property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the alcodonFrame property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getAlcodonFrame().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link AlcodonFrame }
- *
- *
- */
- public List<AlcodonFrame> getAlcodonFrame() {
- if (alcodonFrame == null) {
- alcodonFrame = new ArrayList<AlcodonFrame>();
- }
- return this.alcodonFrame;
+ /**
+ * Gets the value of the alcodonFrame property.
+ *
+ * <p> This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will be
+ * present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the alcodonFrame property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getAlcodonFrame().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link AlcodonFrame }
+ *
+ *
+ */
+ public List<AlcodonFrame> getAlcodonFrame()
+ {
+ if (alcodonFrame == null)
+ {
+ alcodonFrame = new ArrayList<AlcodonFrame>();
}
+ return this.alcodonFrame;
+ }
+
+ /**
+ * Gets the value of the gapChar property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getGapChar()
+ {
+ return gapChar;
+ }
+
+ /**
+ * Sets the value of the gapChar property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setGapChar(String value)
+ {
+ this.gapChar = value;
+ }
+
+ /**
+ * Gets the value of the datasetId property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDatasetId()
+ {
+ return datasetId;
+ }
+
+ /**
+ * Sets the value of the datasetId property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setDatasetId(String value)
+ {
+ this.datasetId = value;
+ }
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
+ *
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt;
+ * &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
+ * name="key" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="value"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class SequenceSetProperties
+ {
+
+ @XmlAttribute(name = "key")
+ protected String key;
+
+ @XmlAttribute(name = "value")
+ protected String value;
/**
- * Gets the value of the gapChar property.
+ * Gets the value of the key property.
+ *
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getGapChar() {
- return gapChar;
+ public String getKey()
+ {
+ return key;
}
/**
- * Sets the value of the gapChar property.
+ * Sets the value of the key property.
*
* @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setGapChar(String value) {
- this.gapChar = value;
- }
-
- /**
- * Gets the value of the datasetId property.
+ * allowed object is {@link String }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getDatasetId() {
- return datasetId;
+ public void setKey(String value)
+ {
+ this.key = value;
}
/**
- * Sets the value of the datasetId property.
+ * Gets the value of the value property.
+ *
+ * @return possible object is {@link String }
*
- * @param value
- * allowed object is
- * {@link String }
- *
*/
- public void setDatasetId(String value) {
- this.datasetId = value;
+ public String getValue()
+ {
+ return value;
}
-
/**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="key" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * Sets the value of the value property.
*
+ * @param value
+ * allowed object is {@link String }
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class SequenceSetProperties {
-
- @XmlAttribute(name = "key")
- protected String key;
- @XmlAttribute(name = "value")
- protected String value;
-
- /**
- * Gets the value of the key property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getKey() {
- return key;
- }
-
- /**
- * Sets the value of the key property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setKey(String value) {
- this.key = value;
- }
-
- /**
- * Gets the value of the value property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getValue() {
- return value;
- }
-
- /**
- * Sets the value of the value property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setValue(String value) {
- this.value = value;
- }
-
+ public void setValue(String value)
+ {
+ this.value = value;
}
+ }
+
}
// Generated on: 2021.08.30 at 11:05:22 AM BST
//
-
package jalview.xml.binding.jalview;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlSeeAlso;
import javax.xml.bind.annotation.XmlType;
-
/**
* <p>Java class for SequenceType complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
*
- * <pre>
- * &lt;complexType name="SequenceType"&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="sequence" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
- * &lt;element name="name" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="description" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre> &lt;complexType name="SequenceType"&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="sequence"
+ * type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
+ * &lt;element name="name" type="{http://www.w3.org/2001/XMLSchema}string"
+ * minOccurs="0"/&gt; &lt;/sequence&gt; &lt;attribute name="id"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
+ * name="description" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "SequenceType", propOrder = {
- "sequence",
- "name"
-})
-@XmlSeeAlso({
- Sequence.class
-})
-public class SequenceType {
-
- protected String sequence;
- protected String name;
- @XmlAttribute(name = "id")
- protected String id;
- @XmlAttribute(name = "description")
- protected String description;
-
- /**
- * Gets the value of the sequence property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getSequence() {
- return sequence;
- }
-
- /**
- * Sets the value of the sequence property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setSequence(String value) {
- this.sequence = value;
- }
-
- /**
- * Gets the value of the name property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getName() {
- return name;
- }
-
- /**
- * Sets the value of the name property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setName(String value) {
- this.name = value;
- }
-
- /**
- * Gets the value of the id property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getId() {
- return id;
- }
-
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setId(String value) {
- this.id = value;
- }
-
- /**
- * Gets the value of the description property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDescription() {
- return description;
- }
-
- /**
- * Sets the value of the description property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDescription(String value) {
- this.description = value;
- }
+@XmlType(name = "SequenceType", propOrder = { "sequence", "name" })
+@XmlSeeAlso({ Sequence.class })
+public class SequenceType
+{
+
+ protected String sequence;
+
+ protected String name;
+
+ @XmlAttribute(name = "id")
+ protected String id;
+
+ @XmlAttribute(name = "description")
+ protected String description;
+
+ /**
+ * Gets the value of the sequence property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getSequence()
+ {
+ return sequence;
+ }
+
+ /**
+ * Sets the value of the sequence property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setSequence(String value)
+ {
+ this.sequence = value;
+ }
+
+ /**
+ * Gets the value of the name property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getName()
+ {
+ return name;
+ }
+
+ /**
+ * Sets the value of the name property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setName(String value)
+ {
+ this.name = value;
+ }
+
+ /**
+ * Gets the value of the id property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getId()
+ {
+ return id;
+ }
+
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setId(String value)
+ {
+ this.id = value;
+ }
+
+ /**
+ * Gets the value of the description property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDescription()
+ {
+ return description;
+ }
+
+ /**
+ * Sets the value of the description property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setDescription(String value)
+ {
+ this.description = value;
+ }
}
// Generated on: 2021.08.30 at 11:05:22 AM BST
//
-
package jalview.xml.binding.jalview;
import javax.xml.bind.annotation.XmlEnum;
import javax.xml.bind.annotation.XmlType;
-
/**
* <p>Java class for ThresholdType.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
- * <pre>
- * &lt;simpleType name="ThresholdType"&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt;
- * &lt;enumeration value="NONE"/&gt;
- * &lt;enumeration value="ABOVE"/&gt;
- * &lt;enumeration value="BELOW"/&gt;
- * &lt;/restriction&gt;
- * &lt;/simpleType&gt;
- * </pre>
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class. <pre> &lt;simpleType
+ * name="ThresholdType"&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}string"&gt; &lt;enumeration
+ * value="NONE"/&gt; &lt;enumeration value="ABOVE"/&gt;
+ * &lt;enumeration value="BELOW"/&gt; &lt;/restriction&gt;
+ * &lt;/simpleType&gt; </pre>
*
*/
@XmlType(name = "ThresholdType", namespace = "www.jalview.org/colours")
@XmlEnum
-public enum ThresholdType {
+public enum ThresholdType
+{
- NONE,
- ABOVE,
- BELOW;
+ NONE, ABOVE, BELOW;
- public String value() {
- return name();
- }
+ public String value()
+ {
+ return name();
+ }
- public static ThresholdType fromValue(String v) {
- return valueOf(v);
- }
+ public static ThresholdType fromValue(String v)
+ {
+ return valueOf(v);
+ }
}
// Generated on: 2021.08.30 at 11:05:22 AM BST
//
-
package jalview.xml.binding.jalview;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
-
/**
* <p>Java class for VAMSAS complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
*
- * <pre>
- * &lt;complexType name="VAMSAS"&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="Tree" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/&gt;
- * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}SequenceSet" maxOccurs="unbounded" minOccurs="0"/&gt;
- * &lt;/sequence&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre> &lt;complexType name="VAMSAS"&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="Tree"
+ * type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"
+ * minOccurs="0"/&gt; &lt;element
+ * ref="{www.vamsas.ac.uk/jalview/version2}SequenceSet" maxOccurs="unbounded"
+ * minOccurs="0"/&gt; &lt;/sequence&gt; &lt;/restriction&gt;
+ * &lt;/complexContent&gt; &lt;/complexType&gt; </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "VAMSAS", propOrder = {
- "tree",
- "sequenceSet"
-})
-public class VAMSAS {
+@XmlType(name = "VAMSAS", propOrder = { "tree", "sequenceSet" })
+public class VAMSAS
+{
+
+ @XmlElement(name = "Tree")
+ protected List<String> tree;
- @XmlElement(name = "Tree")
- protected List<String> tree;
- @XmlElement(name = "SequenceSet")
- protected List<SequenceSet> sequenceSet;
+ @XmlElement(name = "SequenceSet")
+ protected List<SequenceSet> sequenceSet;
- /**
- * Gets the value of the tree property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the tree property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getTree().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link String }
- *
- *
- */
- public List<String> getTree() {
- if (tree == null) {
- tree = new ArrayList<String>();
- }
- return this.tree;
+ /**
+ * Gets the value of the tree property.
+ *
+ * <p> This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will be
+ * present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the tree property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getTree().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link String }
+ *
+ *
+ */
+ public List<String> getTree()
+ {
+ if (tree == null)
+ {
+ tree = new ArrayList<String>();
}
+ return this.tree;
+ }
- /**
- * Gets the value of the sequenceSet property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the sequenceSet property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getSequenceSet().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link SequenceSet }
- *
- *
- */
- public List<SequenceSet> getSequenceSet() {
- if (sequenceSet == null) {
- sequenceSet = new ArrayList<SequenceSet>();
- }
- return this.sequenceSet;
+ /**
+ * Gets the value of the sequenceSet property.
+ *
+ * <p> This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will be
+ * present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the sequenceSet property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getSequenceSet().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link SequenceSet }
+ *
+ *
+ */
+ public List<SequenceSet> getSequenceSet()
+ {
+ if (sequenceSet == null)
+ {
+ sequenceSet = new ArrayList<SequenceSet>();
}
+ return this.sequenceSet;
+ }
}
// Generated on: 2021.08.30 at 11:05:22 AM BST
//
-
package jalview.xml.binding.jalview;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlSeeAlso;
import javax.xml.bind.annotation.XmlType;
-
/**
* <p>Java class for WebServiceParameterSet complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content
+ * contained within this class.
*
- * <pre>
- * &lt;complexType name="WebServiceParameterSet"&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="Version" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
- * &lt;element name="description" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
- * &lt;element name="serviceURL" type="{http://www.w3.org/2001/XMLSchema}anyURI" maxOccurs="unbounded"/&gt;
- * &lt;element name="parameters" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre> &lt;complexType name="WebServiceParameterSet"&gt;
+ * &lt;complexContent&gt; &lt;restriction
+ * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt; &lt;element name="Version"
+ * type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
+ * &lt;element name="description"
+ * type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
+ * &lt;element name="serviceURL"
+ * type="{http://www.w3.org/2001/XMLSchema}anyURI"
+ * maxOccurs="unbounded"/&gt; &lt;element name="parameters"
+ * type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
+ * &lt;/sequence&gt; &lt;attribute name="name" use="required"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt; &lt;/complexContent&gt;
+ * &lt;/complexType&gt; </pre>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "WebServiceParameterSet", namespace = "www.jalview.org/xml/wsparamset", propOrder = {
- "version",
- "description",
- "serviceURL",
- "parameters"
-})
+@XmlType(
+ name = "WebServiceParameterSet",
+ namespace = "www.jalview.org/xml/wsparamset",
+ propOrder =
+ { "version", "description", "serviceURL", "parameters" })
@XmlSeeAlso({
- jalview.xml.binding.jalview.JalviewModel.Viewport.CalcIdParam.class
-})
-public class WebServiceParameterSet {
-
- @XmlElement(name = "Version", namespace = "")
- protected String version;
- @XmlElement(namespace = "")
- protected String description;
- @XmlElement(namespace = "", required = true)
- @XmlSchemaType(name = "anyURI")
- protected List<String> serviceURL;
- @XmlElement(namespace = "", required = true)
- protected String parameters;
- @XmlAttribute(name = "name", required = true)
- protected String name;
-
- /**
- * Gets the value of the version property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getVersion() {
- return version;
- }
-
- /**
- * Sets the value of the version property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setVersion(String value) {
- this.version = value;
- }
-
- /**
- * Gets the value of the description property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDescription() {
- return description;
- }
-
- /**
- * Sets the value of the description property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDescription(String value) {
- this.description = value;
- }
-
- /**
- * Gets the value of the serviceURL property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the serviceURL property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getServiceURL().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link String }
- *
- *
- */
- public List<String> getServiceURL() {
- if (serviceURL == null) {
- serviceURL = new ArrayList<String>();
- }
- return this.serviceURL;
- }
-
- /**
- * Gets the value of the parameters property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getParameters() {
- return parameters;
- }
-
- /**
- * Sets the value of the parameters property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setParameters(String value) {
- this.parameters = value;
- }
-
- /**
- * Gets the value of the name property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getName() {
- return name;
- }
-
- /**
- * Sets the value of the name property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setName(String value) {
- this.name = value;
+ jalview.xml.binding.jalview.JalviewModel.Viewport.CalcIdParam.class })
+public class WebServiceParameterSet
+{
+
+ @XmlElement(name = "Version", namespace = "")
+ protected String version;
+
+ @XmlElement(namespace = "")
+ protected String description;
+
+ @XmlElement(namespace = "", required = true)
+ @XmlSchemaType(name = "anyURI")
+ protected List<String> serviceURL;
+
+ @XmlElement(namespace = "", required = true)
+ protected String parameters;
+
+ @XmlAttribute(name = "name", required = true)
+ protected String name;
+
+ /**
+ * Gets the value of the version property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getVersion()
+ {
+ return version;
+ }
+
+ /**
+ * Sets the value of the version property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setVersion(String value)
+ {
+ this.version = value;
+ }
+
+ /**
+ * Gets the value of the description property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDescription()
+ {
+ return description;
+ }
+
+ /**
+ * Sets the value of the description property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setDescription(String value)
+ {
+ this.description = value;
+ }
+
+ /**
+ * Gets the value of the serviceURL property.
+ *
+ * <p> This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will be
+ * present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the serviceURL property.
+ *
+ * <p> For example, to add a new item, do as follows: <pre>
+ * getServiceURL().add(newItem); </pre>
+ *
+ *
+ * <p> Objects of the following type(s) are allowed in the list
+ * {@link String }
+ *
+ *
+ */
+ public List<String> getServiceURL()
+ {
+ if (serviceURL == null)
+ {
+ serviceURL = new ArrayList<String>();
}
+ return this.serviceURL;
+ }
+
+ /**
+ * Gets the value of the parameters property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getParameters()
+ {
+ return parameters;
+ }
+
+ /**
+ * Sets the value of the parameters property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setParameters(String value)
+ {
+ this.parameters = value;
+ }
+
+ /**
+ * Gets the value of the name property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getName()
+ {
+ return name;
+ }
+
+ /**
+ * Sets the value of the name property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setName(String value)
+ {
+ this.name = value;
+ }
}
// Generated on: 2021.08.30 at 11:05:22 AM BST
//
-@javax.xml.bind.annotation.XmlSchema(namespace = "www.vamsas.ac.uk/jalview/version2", elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED)
+@javax.xml.bind.annotation.XmlSchema(
+ namespace = "www.vamsas.ac.uk/jalview/version2",
+ elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED)
package jalview.xml.binding.jalview;
// Generated on: 2015.10.09 at 03:18:33 PM BST
//
-
package jalview.xml.binding.sifts;
import java.math.BigInteger;
import javax.xml.bind.annotation.XmlType;
import javax.xml.bind.annotation.XmlValue;
-
/**
- * <p>Java class for anonymous complex type.
+ * <p>
+ * Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
*
* <pre>
* <complexType>
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = {
- "alignObject",
- "score",
- "block",
- "geo3D"
-})
+@XmlType(
+ name = "",
+ propOrder =
+ { "alignObject", "score", "block", "geo3D" })
@XmlRootElement(name = "alignment")
-public class Alignment {
-
- @XmlElement(required = true)
- protected List<Alignment.AlignObject> alignObject;
- protected List<Alignment.Score> score;
- @XmlElement(required = true)
- protected List<Alignment.Block> block;
- @XmlElement(name = "geo3d")
- protected List<Alignment.Geo3D> geo3D;
- @XmlAttribute(name = "alignType", required = true)
- protected String alignType;
+public class Alignment
+{
+
+ @XmlElement(required = true)
+ protected List<Alignment.AlignObject> alignObject;
+
+ protected List<Alignment.Score> score;
+
+ @XmlElement(required = true)
+ protected List<Alignment.Block> block;
+
+ @XmlElement(name = "geo3d")
+ protected List<Alignment.Geo3D> geo3D;
+
+ @XmlAttribute(name = "alignType", required = true)
+ protected String alignType;
+
+ /**
+ * Gets the value of the alignObject property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the alignObject property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getAlignObject().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Alignment.AlignObject }
+ *
+ *
+ */
+ public List<Alignment.AlignObject> getAlignObject()
+ {
+ if (alignObject == null)
+ {
+ alignObject = new ArrayList<Alignment.AlignObject>();
+ }
+ return this.alignObject;
+ }
+
+ /**
+ * Gets the value of the score property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the score property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getScore().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Alignment.Score }
+ *
+ *
+ */
+ public List<Alignment.Score> getScore()
+ {
+ if (score == null)
+ {
+ score = new ArrayList<Alignment.Score>();
+ }
+ return this.score;
+ }
+
+ /**
+ * Gets the value of the block property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the block property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getBlock().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Alignment.Block }
+ *
+ *
+ */
+ public List<Alignment.Block> getBlock()
+ {
+ if (block == null)
+ {
+ block = new ArrayList<Alignment.Block>();
+ }
+ return this.block;
+ }
+
+ /**
+ * Gets the value of the geo3D property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the geo3D property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getGeo3D().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Alignment.Geo3D }
+ *
+ *
+ */
+ public List<Alignment.Geo3D> getGeo3D()
+ {
+ if (geo3D == null)
+ {
+ geo3D = new ArrayList<Alignment.Geo3D>();
+ }
+ return this.geo3D;
+ }
+
+ /**
+ * Gets the value of the alignType property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getAlignType()
+ {
+ return alignType;
+ }
+
+ /**
+ * Sets the value of the alignType property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setAlignType(String value)
+ {
+ this.alignType = value;
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="alignObjectDetail" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}detail"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="sequence" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}region"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}dbRef"/>
+ * <attribute name="objectVersion" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="intObjectId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "alignObjectDetail", "sequence" })
+ public static class AlignObject
+ {
+
+ protected List<Alignment.AlignObject.AlignObjectDetail> alignObjectDetail;
+
+ protected Alignment.AlignObject.Sequence sequence;
+
+ @XmlAttribute(name = "objectVersion", required = true)
+ protected String objectVersion;
+
+ @XmlAttribute(name = "intObjectId", required = true)
+ protected String intObjectId;
+
+ @XmlAttribute(name = "type")
+ protected String type;
+
+ @XmlAttribute(name = "dbSource", required = true)
+ protected String dbSource;
+
+ @XmlAttribute(name = "dbCoordSys", required = true)
+ protected String dbCoordSys;
+
+ @XmlAttribute(name = "dbAccessionId", required = true)
+ protected String dbAccessionId;
+
+ @XmlAttribute(name = "dbEvidence")
+ protected String dbEvidence;
+
+ @XmlAttribute(name = "dbVersion")
+ protected String dbVersion;
/**
- * Gets the value of the alignObject property.
+ * Gets the value of the alignObjectDetail property.
*
* <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the alignObject property.
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the alignObjectDetail property.
*
* <p>
* For example, to add a new item, do as follows:
+ *
* <pre>
- * getAlignObject().add(newItem);
+ * getAlignObjectDetail().add(newItem);
* </pre>
*
*
* <p>
* Objects of the following type(s) are allowed in the list
- * {@link Alignment.AlignObject }
+ * {@link Alignment.AlignObject.AlignObjectDetail }
*
*
*/
- public List<Alignment.AlignObject> getAlignObject() {
- if (alignObject == null) {
- alignObject = new ArrayList<Alignment.AlignObject>();
- }
- return this.alignObject;
+ public List<Alignment.AlignObject.AlignObjectDetail> getAlignObjectDetail()
+ {
+ if (alignObjectDetail == null)
+ {
+ alignObjectDetail = new ArrayList<Alignment.AlignObject.AlignObjectDetail>();
+ }
+ return this.alignObjectDetail;
+ }
+
+ /**
+ * Gets the value of the sequence property.
+ *
+ * @return possible object is {@link Alignment.AlignObject.Sequence }
+ *
+ */
+ public Alignment.AlignObject.Sequence getSequence()
+ {
+ return sequence;
+ }
+
+ /**
+ * Sets the value of the sequence property.
+ *
+ * @param value
+ * allowed object is {@link Alignment.AlignObject.Sequence }
+ *
+ */
+ public void setSequence(Alignment.AlignObject.Sequence value)
+ {
+ this.sequence = value;
+ }
+
+ /**
+ * Gets the value of the objectVersion property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getObjectVersion()
+ {
+ return objectVersion;
+ }
+
+ /**
+ * Sets the value of the objectVersion property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setObjectVersion(String value)
+ {
+ this.objectVersion = value;
+ }
+
+ /**
+ * Gets the value of the intObjectId property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getIntObjectId()
+ {
+ return intObjectId;
}
/**
- * Gets the value of the score property.
+ * Sets the value of the intObjectId property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setIntObjectId(String value)
+ {
+ this.intObjectId = value;
+ }
+
+ /**
+ * Gets the value of the type property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getType()
+ {
+ return type;
+ }
+
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setType(String value)
+ {
+ this.type = value;
+ }
+
+ /**
+ * Gets the value of the dbSource property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDbSource()
+ {
+ return dbSource;
+ }
+
+ /**
+ * Sets the value of the dbSource property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setDbSource(String value)
+ {
+ this.dbSource = value;
+ }
+
+ /**
+ * Gets the value of the dbCoordSys property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDbCoordSys()
+ {
+ return dbCoordSys;
+ }
+
+ /**
+ * Sets the value of the dbCoordSys property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setDbCoordSys(String value)
+ {
+ this.dbCoordSys = value;
+ }
+
+ /**
+ * Gets the value of the dbAccessionId property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDbAccessionId()
+ {
+ return dbAccessionId;
+ }
+
+ /**
+ * Sets the value of the dbAccessionId property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setDbAccessionId(String value)
+ {
+ this.dbAccessionId = value;
+ }
+
+ /**
+ * Gets the value of the dbEvidence property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDbEvidence()
+ {
+ return dbEvidence;
+ }
+
+ /**
+ * Sets the value of the dbEvidence property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setDbEvidence(String value)
+ {
+ this.dbEvidence = value;
+ }
+
+ /**
+ * Gets the value of the dbVersion property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDbVersion()
+ {
+ return dbVersion;
+ }
+
+ /**
+ * Sets the value of the dbVersion property.
+ *
+ * @param value
+ * allowed object is {@link String }
*
+ */
+ public void setDbVersion(String value)
+ {
+ this.dbVersion = value;
+ }
+
+ /**
* <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the score property.
+ * Java class for anonymous complex type.
*
* <p>
- * For example, to add a new item, do as follows:
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
* <pre>
- * getScore().add(newItem);
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}detail"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
* </pre>
*
*
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "content" })
+ public static class AlignObjectDetail
+ {
+
+ @XmlValue
+ protected String content;
+
+ @XmlAttribute(name = "dbSource")
+ protected String dbSource;
+
+ @XmlAttribute(name = "property", required = true)
+ protected String property;
+
+ /**
+ * Gets the value of the content property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getContent()
+ {
+ return content;
+ }
+
+ /**
+ * Sets the value of the content property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setContent(String value)
+ {
+ this.content = value;
+ }
+
+ /**
+ * Gets the value of the dbSource property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDbSource()
+ {
+ return dbSource;
+ }
+
+ /**
+ * Sets the value of the dbSource property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setDbSource(String value)
+ {
+ this.dbSource = value;
+ }
+
+ /**
+ * Gets the value of the property property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getProperty()
+ {
+ return property;
+ }
+
+ /**
+ * Sets the value of the property property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setProperty(String value)
+ {
+ this.property = value;
+ }
+
+ }
+
+ /**
* <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Alignment.Score }
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}region"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
- public List<Alignment.Score> getScore() {
- if (score == null) {
- score = new ArrayList<Alignment.Score>();
- }
- return this.score;
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "content" })
+ public static class Sequence
+ {
+
+ @XmlValue
+ protected String content;
+
+ @XmlAttribute(name = "start")
+ protected String start;
+
+ @XmlAttribute(name = "end")
+ protected String end;
+
+ /**
+ * Gets the value of the content property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getContent()
+ {
+ return content;
+ }
+
+ /**
+ * Sets the value of the content property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setContent(String value)
+ {
+ this.content = value;
+ }
+
+ /**
+ * Gets the value of the start property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getStart()
+ {
+ return start;
+ }
+
+ /**
+ * Sets the value of the start property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setStart(String value)
+ {
+ this.start = value;
+ }
+
+ /**
+ * Gets the value of the end property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getEnd()
+ {
+ return end;
+ }
+
+ /**
+ * Sets the value of the end property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setEnd(String value)
+ {
+ this.end = value;
+ }
+
}
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="segment" maxOccurs="unbounded">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence minOccurs="0">
+ * <element name="cigar" type="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}cigarstring"/>
+ * </sequence>
+ * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}region"/>
+ * <attribute name="intObjectId" use="required" type="{http://www.w3.org/2001/XMLSchema}anySimpleType" />
+ * <attribute name="strand" type="{http://www.w3.org/2001/XMLSchema}anySimpleType" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attribute name="blockScore" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="blockOrder" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "segment" })
+ public static class Block
+ {
+
+ @XmlElement(required = true)
+ protected List<Alignment.Block.Segment> segment;
+
+ @XmlAttribute(name = "blockScore")
+ protected String blockScore;
+
+ @XmlAttribute(name = "blockOrder", required = true)
+ protected BigInteger blockOrder;
+
/**
- * Gets the value of the block property.
+ * Gets the value of the segment property.
*
* <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the block property.
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the segment property.
*
* <p>
* For example, to add a new item, do as follows:
+ *
* <pre>
- * getBlock().add(newItem);
+ * getSegment().add(newItem);
* </pre>
*
*
* <p>
* Objects of the following type(s) are allowed in the list
- * {@link Alignment.Block }
+ * {@link Alignment.Block.Segment }
*
*
*/
- public List<Alignment.Block> getBlock() {
- if (block == null) {
- block = new ArrayList<Alignment.Block>();
- }
- return this.block;
+ public List<Alignment.Block.Segment> getSegment()
+ {
+ if (segment == null)
+ {
+ segment = new ArrayList<Alignment.Block.Segment>();
+ }
+ return this.segment;
+ }
+
+ /**
+ * Gets the value of the blockScore property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getBlockScore()
+ {
+ return blockScore;
+ }
+
+ /**
+ * Sets the value of the blockScore property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setBlockScore(String value)
+ {
+ this.blockScore = value;
+ }
+
+ /**
+ * Gets the value of the blockOrder property.
+ *
+ * @return possible object is {@link BigInteger }
+ *
+ */
+ public BigInteger getBlockOrder()
+ {
+ return blockOrder;
+ }
+
+ /**
+ * Sets the value of the blockOrder property.
+ *
+ * @param value
+ * allowed object is {@link BigInteger }
+ *
+ */
+ public void setBlockOrder(BigInteger value)
+ {
+ this.blockOrder = value;
}
/**
- * Gets the value of the geo3D property.
+ * <p>
+ * Java class for anonymous complex type.
*
* <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the geo3D property.
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence minOccurs="0">
+ * <element name="cigar" type="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}cigarstring"/>
+ * </sequence>
+ * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}region"/>
+ * <attribute name="intObjectId" use="required" type="{http://www.w3.org/2001/XMLSchema}anySimpleType" />
+ * <attribute name="strand" type="{http://www.w3.org/2001/XMLSchema}anySimpleType" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "cigar" })
+ public static class Segment
+ {
+
+ protected String cigar;
+
+ @XmlAttribute(name = "intObjectId", required = true)
+ @XmlSchemaType(name = "anySimpleType")
+ protected String intObjectId;
+
+ @XmlAttribute(name = "strand")
+ @XmlSchemaType(name = "anySimpleType")
+ protected String strand;
+
+ @XmlAttribute(name = "start")
+ protected String start;
+
+ @XmlAttribute(name = "end")
+ protected String end;
+
+ /**
+ * Gets the value of the cigar property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getCigar()
+ {
+ return cigar;
+ }
+
+ /**
+ * Sets the value of the cigar property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setCigar(String value)
+ {
+ this.cigar = value;
+ }
+
+ /**
+ * Gets the value of the intObjectId property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getIntObjectId()
+ {
+ return intObjectId;
+ }
+
+ /**
+ * Sets the value of the intObjectId property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setIntObjectId(String value)
+ {
+ this.intObjectId = value;
+ }
+
+ /**
+ * Gets the value of the strand property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getStrand()
+ {
+ return strand;
+ }
+
+ /**
+ * Sets the value of the strand property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setStrand(String value)
+ {
+ this.strand = value;
+ }
+
+ /**
+ * Gets the value of the start property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getStart()
+ {
+ return start;
+ }
+
+ /**
+ * Sets the value of the start property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setStart(String value)
+ {
+ this.start = value;
+ }
+
+ /**
+ * Gets the value of the end property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getEnd()
+ {
+ return end;
+ }
+
+ /**
+ * Sets the value of the end property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setEnd(String value)
+ {
+ this.end = value;
+ }
+
+ }
+
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="vector">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="x" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="y" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="z" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="matrix" maxOccurs="unbounded">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="max11">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="coord" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="max12">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="coord" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="max13">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="coord" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="max21">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="coord" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="max22">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="coord" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="max23">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="coord" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="max31">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="coord" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="max32">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="coord" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="max33">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="coord" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attribute name="intObjectId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "vector", "matrix" })
+ public static class Geo3D
+ {
+
+ @XmlElement(required = true)
+ protected Alignment.Geo3D.Vector vector;
+
+ @XmlElement(required = true)
+ protected List<Alignment.Geo3D.Matrix> matrix;
+
+ @XmlAttribute(name = "intObjectId", required = true)
+ protected String intObjectId;
+
+ /**
+ * Gets the value of the vector property.
+ *
+ * @return possible object is {@link Alignment.Geo3D.Vector }
+ *
+ */
+ public Alignment.Geo3D.Vector getVector()
+ {
+ return vector;
+ }
+
+ /**
+ * Sets the value of the vector property.
+ *
+ * @param value
+ * allowed object is {@link Alignment.Geo3D.Vector }
+ *
+ */
+ public void setVector(Alignment.Geo3D.Vector value)
+ {
+ this.vector = value;
+ }
+
+ /**
+ * Gets the value of the matrix property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the matrix property.
*
* <p>
* For example, to add a new item, do as follows:
+ *
* <pre>
- * getGeo3D().add(newItem);
+ * getMatrix().add(newItem);
* </pre>
*
*
* <p>
* Objects of the following type(s) are allowed in the list
- * {@link Alignment.Geo3D }
+ * {@link Alignment.Geo3D.Matrix }
*
*
*/
- public List<Alignment.Geo3D> getGeo3D() {
- if (geo3D == null) {
- geo3D = new ArrayList<Alignment.Geo3D>();
- }
- return this.geo3D;
+ public List<Alignment.Geo3D.Matrix> getMatrix()
+ {
+ if (matrix == null)
+ {
+ matrix = new ArrayList<Alignment.Geo3D.Matrix>();
+ }
+ return this.matrix;
}
/**
- * Gets the value of the alignType property.
+ * Gets the value of the intObjectId property.
+ *
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getAlignType() {
- return alignType;
+ public String getIntObjectId()
+ {
+ return intObjectId;
}
/**
- * Sets the value of the alignType property.
+ * Sets the value of the intObjectId property.
*
* @param value
- * allowed object is
- * {@link String }
- *
+ * allowed object is {@link String }
+ *
*/
- public void setAlignType(String value) {
- this.alignType = value;
+ public void setIntObjectId(String value)
+ {
+ this.intObjectId = value;
}
-
/**
- * <p>Java class for anonymous complex type.
+ * <p>
+ * Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
*
* <pre>
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
* <sequence>
- * <element name="alignObjectDetail" maxOccurs="unbounded" minOccurs="0">
+ * <element name="max11">
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}detail"/>
+ * <attribute name="coord" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
* </restriction>
* </complexContent>
* </complexType>
* </element>
- * <element name="sequence" minOccurs="0">
+ * <element name="max12">
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}region"/>
+ * <attribute name="coord" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="max13">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="coord" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="max21">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="coord" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="max22">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="coord" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="max23">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="coord" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="max31">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="coord" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="max32">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="coord" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="max33">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="coord" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
* </restriction>
* </complexContent>
* </complexType>
* </element>
* </sequence>
- * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}dbRef"/>
- * <attribute name="objectVersion" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="intObjectId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
* </restriction>
* </complexContent>
* </complexType>
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "alignObjectDetail",
- "sequence"
- })
- public static class AlignObject {
-
- protected List<Alignment.AlignObject.AlignObjectDetail> alignObjectDetail;
- protected Alignment.AlignObject.Sequence sequence;
- @XmlAttribute(name = "objectVersion", required = true)
- protected String objectVersion;
- @XmlAttribute(name = "intObjectId", required = true)
- protected String intObjectId;
- @XmlAttribute(name = "type")
- protected String type;
- @XmlAttribute(name = "dbSource", required = true)
- protected String dbSource;
- @XmlAttribute(name = "dbCoordSys", required = true)
- protected String dbCoordSys;
- @XmlAttribute(name = "dbAccessionId", required = true)
- protected String dbAccessionId;
- @XmlAttribute(name = "dbEvidence")
- protected String dbEvidence;
- @XmlAttribute(name = "dbVersion")
- protected String dbVersion;
+ @XmlType(
+ name = "",
+ propOrder =
+ { "max11", "max12", "max13", "max21", "max22", "max23", "max31",
+ "max32", "max33" })
+ public static class Matrix
+ {
+
+ @XmlElement(required = true)
+ protected Alignment.Geo3D.Matrix.Max11 max11;
+
+ @XmlElement(required = true)
+ protected Alignment.Geo3D.Matrix.Max12 max12;
+
+ @XmlElement(required = true)
+ protected Alignment.Geo3D.Matrix.Max13 max13;
+
+ @XmlElement(required = true)
+ protected Alignment.Geo3D.Matrix.Max21 max21;
+
+ @XmlElement(required = true)
+ protected Alignment.Geo3D.Matrix.Max22 max22;
+
+ @XmlElement(required = true)
+ protected Alignment.Geo3D.Matrix.Max23 max23;
+
+ @XmlElement(required = true)
+ protected Alignment.Geo3D.Matrix.Max31 max31;
+
+ @XmlElement(required = true)
+ protected Alignment.Geo3D.Matrix.Max32 max32;
+
+ @XmlElement(required = true)
+ protected Alignment.Geo3D.Matrix.Max33 max33;
+
+ /**
+ * Gets the value of the max11 property.
+ *
+ * @return possible object is {@link Alignment.Geo3D.Matrix.Max11 }
+ *
+ */
+ public Alignment.Geo3D.Matrix.Max11 getMax11()
+ {
+ return max11;
+ }
+
+ /**
+ * Sets the value of the max11 property.
+ *
+ * @param value
+ * allowed object is {@link Alignment.Geo3D.Matrix.Max11 }
+ *
+ */
+ public void setMax11(Alignment.Geo3D.Matrix.Max11 value)
+ {
+ this.max11 = value;
+ }
+
+ /**
+ * Gets the value of the max12 property.
+ *
+ * @return possible object is {@link Alignment.Geo3D.Matrix.Max12 }
+ *
+ */
+ public Alignment.Geo3D.Matrix.Max12 getMax12()
+ {
+ return max12;
+ }
+
+ /**
+ * Sets the value of the max12 property.
+ *
+ * @param value
+ * allowed object is {@link Alignment.Geo3D.Matrix.Max12 }
+ *
+ */
+ public void setMax12(Alignment.Geo3D.Matrix.Max12 value)
+ {
+ this.max12 = value;
+ }
+
+ /**
+ * Gets the value of the max13 property.
+ *
+ * @return possible object is {@link Alignment.Geo3D.Matrix.Max13 }
+ *
+ */
+ public Alignment.Geo3D.Matrix.Max13 getMax13()
+ {
+ return max13;
+ }
+
+ /**
+ * Sets the value of the max13 property.
+ *
+ * @param value
+ * allowed object is {@link Alignment.Geo3D.Matrix.Max13 }
+ *
+ */
+ public void setMax13(Alignment.Geo3D.Matrix.Max13 value)
+ {
+ this.max13 = value;
+ }
+
+ /**
+ * Gets the value of the max21 property.
+ *
+ * @return possible object is {@link Alignment.Geo3D.Matrix.Max21 }
+ *
+ */
+ public Alignment.Geo3D.Matrix.Max21 getMax21()
+ {
+ return max21;
+ }
+
+ /**
+ * Sets the value of the max21 property.
+ *
+ * @param value
+ * allowed object is {@link Alignment.Geo3D.Matrix.Max21 }
+ *
+ */
+ public void setMax21(Alignment.Geo3D.Matrix.Max21 value)
+ {
+ this.max21 = value;
+ }
+
+ /**
+ * Gets the value of the max22 property.
+ *
+ * @return possible object is {@link Alignment.Geo3D.Matrix.Max22 }
+ *
+ */
+ public Alignment.Geo3D.Matrix.Max22 getMax22()
+ {
+ return max22;
+ }
+
+ /**
+ * Sets the value of the max22 property.
+ *
+ * @param value
+ * allowed object is {@link Alignment.Geo3D.Matrix.Max22 }
+ *
+ */
+ public void setMax22(Alignment.Geo3D.Matrix.Max22 value)
+ {
+ this.max22 = value;
+ }
+
+ /**
+ * Gets the value of the max23 property.
+ *
+ * @return possible object is {@link Alignment.Geo3D.Matrix.Max23 }
+ *
+ */
+ public Alignment.Geo3D.Matrix.Max23 getMax23()
+ {
+ return max23;
+ }
+
+ /**
+ * Sets the value of the max23 property.
+ *
+ * @param value
+ * allowed object is {@link Alignment.Geo3D.Matrix.Max23 }
+ *
+ */
+ public void setMax23(Alignment.Geo3D.Matrix.Max23 value)
+ {
+ this.max23 = value;
+ }
+
+ /**
+ * Gets the value of the max31 property.
+ *
+ * @return possible object is {@link Alignment.Geo3D.Matrix.Max31 }
+ *
+ */
+ public Alignment.Geo3D.Matrix.Max31 getMax31()
+ {
+ return max31;
+ }
+
+ /**
+ * Sets the value of the max31 property.
+ *
+ * @param value
+ * allowed object is {@link Alignment.Geo3D.Matrix.Max31 }
+ *
+ */
+ public void setMax31(Alignment.Geo3D.Matrix.Max31 value)
+ {
+ this.max31 = value;
+ }
+
+ /**
+ * Gets the value of the max32 property.
+ *
+ * @return possible object is {@link Alignment.Geo3D.Matrix.Max32 }
+ *
+ */
+ public Alignment.Geo3D.Matrix.Max32 getMax32()
+ {
+ return max32;
+ }
+
+ /**
+ * Sets the value of the max32 property.
+ *
+ * @param value
+ * allowed object is {@link Alignment.Geo3D.Matrix.Max32 }
+ *
+ */
+ public void setMax32(Alignment.Geo3D.Matrix.Max32 value)
+ {
+ this.max32 = value;
+ }
+
+ /**
+ * Gets the value of the max33 property.
+ *
+ * @return possible object is {@link Alignment.Geo3D.Matrix.Max33 }
+ *
+ */
+ public Alignment.Geo3D.Matrix.Max33 getMax33()
+ {
+ return max33;
+ }
+
+ /**
+ * Sets the value of the max33 property.
+ *
+ * @param value
+ * allowed object is {@link Alignment.Geo3D.Matrix.Max33 }
+ *
+ */
+ public void setMax33(Alignment.Geo3D.Matrix.Max33 value)
+ {
+ this.max33 = value;
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="coord" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Max11
+ {
+
+ @XmlAttribute(name = "coord", required = true)
+ protected float coord;
/**
- * Gets the value of the alignObjectDetail property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the alignObjectDetail property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getAlignObjectDetail().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Alignment.AlignObject.AlignObjectDetail }
- *
+ * Gets the value of the coord property.
*
*/
- public List<Alignment.AlignObject.AlignObjectDetail> getAlignObjectDetail() {
- if (alignObjectDetail == null) {
- alignObjectDetail = new ArrayList<Alignment.AlignObject.AlignObjectDetail>();
- }
- return this.alignObjectDetail;
+ public float getCoord()
+ {
+ return coord;
}
/**
- * Gets the value of the sequence property.
+ * Sets the value of the coord property.
*
- * @return
- * possible object is
- * {@link Alignment.AlignObject.Sequence }
- *
*/
- public Alignment.AlignObject.Sequence getSequence() {
- return sequence;
+ public void setCoord(float value)
+ {
+ this.coord = value;
}
- /**
- * Sets the value of the sequence property.
- *
- * @param value
- * allowed object is
- * {@link Alignment.AlignObject.Sequence }
- *
- */
- public void setSequence(Alignment.AlignObject.Sequence value) {
- this.sequence = value;
- }
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="coord" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Max12
+ {
+
+ @XmlAttribute(name = "coord", required = true)
+ protected float coord;
/**
- * Gets the value of the objectVersion property.
+ * Gets the value of the coord property.
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getObjectVersion() {
- return objectVersion;
+ public float getCoord()
+ {
+ return coord;
}
/**
- * Sets the value of the objectVersion property.
+ * Sets the value of the coord property.
*
- * @param value
- * allowed object is
- * {@link String }
- *
*/
- public void setObjectVersion(String value) {
- this.objectVersion = value;
+ public void setCoord(float value)
+ {
+ this.coord = value;
}
- /**
- * Gets the value of the intObjectId property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getIntObjectId() {
- return intObjectId;
- }
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="coord" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Max13
+ {
+
+ @XmlAttribute(name = "coord", required = true)
+ protected float coord;
/**
- * Sets the value of the intObjectId property.
+ * Gets the value of the coord property.
*
- * @param value
- * allowed object is
- * {@link String }
- *
*/
- public void setIntObjectId(String value) {
- this.intObjectId = value;
+ public float getCoord()
+ {
+ return coord;
}
/**
- * Gets the value of the type property.
+ * Sets the value of the coord property.
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getType() {
- return type;
+ public void setCoord(float value)
+ {
+ this.coord = value;
}
- /**
- * Sets the value of the type property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setType(String value) {
- this.type = value;
- }
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="coord" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Max21
+ {
+
+ @XmlAttribute(name = "coord", required = true)
+ protected float coord;
/**
- * Gets the value of the dbSource property.
+ * Gets the value of the coord property.
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getDbSource() {
- return dbSource;
+ public float getCoord()
+ {
+ return coord;
}
/**
- * Sets the value of the dbSource property.
+ * Sets the value of the coord property.
*
- * @param value
- * allowed object is
- * {@link String }
- *
*/
- public void setDbSource(String value) {
- this.dbSource = value;
+ public void setCoord(float value)
+ {
+ this.coord = value;
}
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="coord" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Max22
+ {
+
+ @XmlAttribute(name = "coord", required = true)
+ protected float coord;
+
/**
- * Gets the value of the dbCoordSys property.
+ * Gets the value of the coord property.
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getDbCoordSys() {
- return dbCoordSys;
+ public float getCoord()
+ {
+ return coord;
}
/**
- * Sets the value of the dbCoordSys property.
+ * Sets the value of the coord property.
*
- * @param value
- * allowed object is
- * {@link String }
- *
*/
- public void setDbCoordSys(String value) {
- this.dbCoordSys = value;
+ public void setCoord(float value)
+ {
+ this.coord = value;
}
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="coord" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Max23
+ {
+
+ @XmlAttribute(name = "coord", required = true)
+ protected float coord;
+
/**
- * Gets the value of the dbAccessionId property.
+ * Gets the value of the coord property.
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getDbAccessionId() {
- return dbAccessionId;
+ public float getCoord()
+ {
+ return coord;
}
/**
- * Sets the value of the dbAccessionId property.
+ * Sets the value of the coord property.
*
- * @param value
- * allowed object is
- * {@link String }
- *
*/
- public void setDbAccessionId(String value) {
- this.dbAccessionId = value;
+ public void setCoord(float value)
+ {
+ this.coord = value;
}
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="coord" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Max31
+ {
+
+ @XmlAttribute(name = "coord", required = true)
+ protected float coord;
+
/**
- * Gets the value of the dbEvidence property.
+ * Gets the value of the coord property.
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getDbEvidence() {
- return dbEvidence;
+ public float getCoord()
+ {
+ return coord;
}
/**
- * Sets the value of the dbEvidence property.
+ * Sets the value of the coord property.
*
- * @param value
- * allowed object is
- * {@link String }
- *
*/
- public void setDbEvidence(String value) {
- this.dbEvidence = value;
+ public void setCoord(float value)
+ {
+ this.coord = value;
}
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="coord" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Max32
+ {
+
+ @XmlAttribute(name = "coord", required = true)
+ protected float coord;
+
/**
- * Gets the value of the dbVersion property.
+ * Gets the value of the coord property.
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getDbVersion() {
- return dbVersion;
+ public float getCoord()
+ {
+ return coord;
}
/**
- * Sets the value of the dbVersion property.
+ * Sets the value of the coord property.
*
- * @param value
- * allowed object is
- * {@link String }
- *
*/
- public void setDbVersion(String value) {
- this.dbVersion = value;
+ public void setCoord(float value)
+ {
+ this.coord = value;
}
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="coord" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Max33
+ {
+
+ @XmlAttribute(name = "coord", required = true)
+ protected float coord;
/**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}detail"/>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
+ * Gets the value of the coord property.
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "content"
- })
- public static class AlignObjectDetail {
-
- @XmlValue
- protected String content;
- @XmlAttribute(name = "dbSource")
- protected String dbSource;
- @XmlAttribute(name = "property", required = true)
- protected String property;
-
- /**
- * Gets the value of the content property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getContent() {
- return content;
- }
-
- /**
- * Sets the value of the content property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setContent(String value) {
- this.content = value;
- }
-
- /**
- * Gets the value of the dbSource property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDbSource() {
- return dbSource;
- }
-
- /**
- * Sets the value of the dbSource property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDbSource(String value) {
- this.dbSource = value;
- }
-
- /**
- * Gets the value of the property property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getProperty() {
- return property;
- }
-
- /**
- * Sets the value of the property property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setProperty(String value) {
- this.property = value;
- }
-
+ public float getCoord()
+ {
+ return coord;
}
-
/**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}region"/>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
+ * Sets the value of the coord property.
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "content"
- })
- public static class Sequence {
-
- @XmlValue
- protected String content;
- @XmlAttribute(name = "start")
- protected String start;
- @XmlAttribute(name = "end")
- protected String end;
-
- /**
- * Gets the value of the content property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getContent() {
- return content;
- }
-
- /**
- * Sets the value of the content property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setContent(String value) {
- this.content = value;
- }
-
- /**
- * Gets the value of the start property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getStart() {
- return start;
- }
-
- /**
- * Sets the value of the start property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setStart(String value) {
- this.start = value;
- }
-
- /**
- * Gets the value of the end property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getEnd() {
- return end;
- }
-
- /**
- * Sets the value of the end property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setEnd(String value) {
- this.end = value;
- }
-
+ public void setCoord(float value)
+ {
+ this.coord = value;
}
- }
+ }
+ }
/**
- * <p>Java class for anonymous complex type.
+ * <p>
+ * Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
*
* <pre>
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="segment" maxOccurs="unbounded">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence minOccurs="0">
- * <element name="cigar" type="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}cigarstring"/>
- * </sequence>
- * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}region"/>
- * <attribute name="intObjectId" use="required" type="{http://www.w3.org/2001/XMLSchema}anySimpleType" />
- * <attribute name="strand" type="{http://www.w3.org/2001/XMLSchema}anySimpleType" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attribute name="blockScore" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="blockOrder" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ * <attribute name="x" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="y" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="z" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
* </restriction>
* </complexContent>
* </complexType>
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "segment"
- })
- public static class Block {
-
- @XmlElement(required = true)
- protected List<Alignment.Block.Segment> segment;
- @XmlAttribute(name = "blockScore")
- protected String blockScore;
- @XmlAttribute(name = "blockOrder", required = true)
- protected BigInteger blockOrder;
-
- /**
- * Gets the value of the segment property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the segment property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getSegment().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Alignment.Block.Segment }
- *
- *
- */
- public List<Alignment.Block.Segment> getSegment() {
- if (segment == null) {
- segment = new ArrayList<Alignment.Block.Segment>();
- }
- return this.segment;
- }
-
- /**
- * Gets the value of the blockScore property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getBlockScore() {
- return blockScore;
- }
-
- /**
- * Sets the value of the blockScore property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setBlockScore(String value) {
- this.blockScore = value;
- }
-
- /**
- * Gets the value of the blockOrder property.
- *
- * @return
- * possible object is
- * {@link BigInteger }
- *
- */
- public BigInteger getBlockOrder() {
- return blockOrder;
- }
-
- /**
- * Sets the value of the blockOrder property.
- *
- * @param value
- * allowed object is
- * {@link BigInteger }
- *
- */
- public void setBlockOrder(BigInteger value) {
- this.blockOrder = value;
- }
-
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence minOccurs="0">
- * <element name="cigar" type="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}cigarstring"/>
- * </sequence>
- * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}region"/>
- * <attribute name="intObjectId" use="required" type="{http://www.w3.org/2001/XMLSchema}anySimpleType" />
- * <attribute name="strand" type="{http://www.w3.org/2001/XMLSchema}anySimpleType" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "cigar"
- })
- public static class Segment {
-
- protected String cigar;
- @XmlAttribute(name = "intObjectId", required = true)
- @XmlSchemaType(name = "anySimpleType")
- protected String intObjectId;
- @XmlAttribute(name = "strand")
- @XmlSchemaType(name = "anySimpleType")
- protected String strand;
- @XmlAttribute(name = "start")
- protected String start;
- @XmlAttribute(name = "end")
- protected String end;
-
- /**
- * Gets the value of the cigar property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getCigar() {
- return cigar;
- }
-
- /**
- * Sets the value of the cigar property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setCigar(String value) {
- this.cigar = value;
- }
-
- /**
- * Gets the value of the intObjectId property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getIntObjectId() {
- return intObjectId;
- }
-
- /**
- * Sets the value of the intObjectId property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setIntObjectId(String value) {
- this.intObjectId = value;
- }
-
- /**
- * Gets the value of the strand property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getStrand() {
- return strand;
- }
-
- /**
- * Sets the value of the strand property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setStrand(String value) {
- this.strand = value;
- }
-
- /**
- * Gets the value of the start property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getStart() {
- return start;
- }
-
- /**
- * Sets the value of the start property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setStart(String value) {
- this.start = value;
- }
-
- /**
- * Gets the value of the end property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getEnd() {
- return end;
- }
-
- /**
- * Sets the value of the end property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setEnd(String value) {
- this.end = value;
- }
-
- }
+ @XmlType(name = "")
+ public static class Vector
+ {
+
+ @XmlAttribute(name = "x", required = true)
+ protected float x;
+
+ @XmlAttribute(name = "y", required = true)
+ protected float y;
+
+ @XmlAttribute(name = "z", required = true)
+ protected float z;
+
+ /**
+ * Gets the value of the x property.
+ *
+ */
+ public float getX()
+ {
+ return x;
+ }
+
+ /**
+ * Sets the value of the x property.
+ *
+ */
+ public void setX(float value)
+ {
+ this.x = value;
+ }
+
+ /**
+ * Gets the value of the y property.
+ *
+ */
+ public float getY()
+ {
+ return y;
+ }
+
+ /**
+ * Sets the value of the y property.
+ *
+ */
+ public void setY(float value)
+ {
+ this.y = value;
+ }
+
+ /**
+ * Gets the value of the z property.
+ *
+ */
+ public float getZ()
+ {
+ return z;
+ }
+
+ /**
+ * Sets the value of the z property.
+ *
+ */
+ public void setZ(float value)
+ {
+ this.z = value;
+ }
}
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="methodName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="scoreValue" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Score
+ {
+
+ @XmlAttribute(name = "methodName", required = true)
+ protected String methodName;
+
+ @XmlAttribute(name = "scoreValue", required = true)
+ protected String scoreValue;
/**
- * <p>Java class for anonymous complex type.
+ * Gets the value of the methodName property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * @return possible object is {@link String }
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="vector">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="x" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="y" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="z" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="matrix" maxOccurs="unbounded">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="max11">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="coord" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="max12">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="coord" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="max13">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="coord" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="max21">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="coord" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="max22">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="coord" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="max23">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="coord" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="max31">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="coord" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="max32">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="coord" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="max33">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="coord" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attribute name="intObjectId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ */
+ public String getMethodName()
+ {
+ return methodName;
+ }
+
+ /**
+ * Sets the value of the methodName property.
*
+ * @param value
+ * allowed object is {@link String }
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "vector",
- "matrix"
- })
- public static class Geo3D {
-
- @XmlElement(required = true)
- protected Alignment.Geo3D.Vector vector;
- @XmlElement(required = true)
- protected List<Alignment.Geo3D.Matrix> matrix;
- @XmlAttribute(name = "intObjectId", required = true)
- protected String intObjectId;
-
- /**
- * Gets the value of the vector property.
- *
- * @return
- * possible object is
- * {@link Alignment.Geo3D.Vector }
- *
- */
- public Alignment.Geo3D.Vector getVector() {
- return vector;
- }
-
- /**
- * Sets the value of the vector property.
- *
- * @param value
- * allowed object is
- * {@link Alignment.Geo3D.Vector }
- *
- */
- public void setVector(Alignment.Geo3D.Vector value) {
- this.vector = value;
- }
-
- /**
- * Gets the value of the matrix property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the matrix property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getMatrix().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Alignment.Geo3D.Matrix }
- *
- *
- */
- public List<Alignment.Geo3D.Matrix> getMatrix() {
- if (matrix == null) {
- matrix = new ArrayList<Alignment.Geo3D.Matrix>();
- }
- return this.matrix;
- }
-
- /**
- * Gets the value of the intObjectId property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getIntObjectId() {
- return intObjectId;
- }
-
- /**
- * Sets the value of the intObjectId property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setIntObjectId(String value) {
- this.intObjectId = value;
- }
-
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="max11">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="coord" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="max12">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="coord" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="max13">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="coord" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="max21">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="coord" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="max22">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="coord" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="max23">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="coord" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="max31">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="coord" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="max32">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="coord" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="max33">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="coord" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "max11",
- "max12",
- "max13",
- "max21",
- "max22",
- "max23",
- "max31",
- "max32",
- "max33"
- })
- public static class Matrix {
-
- @XmlElement(required = true)
- protected Alignment.Geo3D.Matrix.Max11 max11;
- @XmlElement(required = true)
- protected Alignment.Geo3D.Matrix.Max12 max12;
- @XmlElement(required = true)
- protected Alignment.Geo3D.Matrix.Max13 max13;
- @XmlElement(required = true)
- protected Alignment.Geo3D.Matrix.Max21 max21;
- @XmlElement(required = true)
- protected Alignment.Geo3D.Matrix.Max22 max22;
- @XmlElement(required = true)
- protected Alignment.Geo3D.Matrix.Max23 max23;
- @XmlElement(required = true)
- protected Alignment.Geo3D.Matrix.Max31 max31;
- @XmlElement(required = true)
- protected Alignment.Geo3D.Matrix.Max32 max32;
- @XmlElement(required = true)
- protected Alignment.Geo3D.Matrix.Max33 max33;
-
- /**
- * Gets the value of the max11 property.
- *
- * @return
- * possible object is
- * {@link Alignment.Geo3D.Matrix.Max11 }
- *
- */
- public Alignment.Geo3D.Matrix.Max11 getMax11() {
- return max11;
- }
-
- /**
- * Sets the value of the max11 property.
- *
- * @param value
- * allowed object is
- * {@link Alignment.Geo3D.Matrix.Max11 }
- *
- */
- public void setMax11(Alignment.Geo3D.Matrix.Max11 value) {
- this.max11 = value;
- }
-
- /**
- * Gets the value of the max12 property.
- *
- * @return
- * possible object is
- * {@link Alignment.Geo3D.Matrix.Max12 }
- *
- */
- public Alignment.Geo3D.Matrix.Max12 getMax12() {
- return max12;
- }
-
- /**
- * Sets the value of the max12 property.
- *
- * @param value
- * allowed object is
- * {@link Alignment.Geo3D.Matrix.Max12 }
- *
- */
- public void setMax12(Alignment.Geo3D.Matrix.Max12 value) {
- this.max12 = value;
- }
-
- /**
- * Gets the value of the max13 property.
- *
- * @return
- * possible object is
- * {@link Alignment.Geo3D.Matrix.Max13 }
- *
- */
- public Alignment.Geo3D.Matrix.Max13 getMax13() {
- return max13;
- }
-
- /**
- * Sets the value of the max13 property.
- *
- * @param value
- * allowed object is
- * {@link Alignment.Geo3D.Matrix.Max13 }
- *
- */
- public void setMax13(Alignment.Geo3D.Matrix.Max13 value) {
- this.max13 = value;
- }
-
- /**
- * Gets the value of the max21 property.
- *
- * @return
- * possible object is
- * {@link Alignment.Geo3D.Matrix.Max21 }
- *
- */
- public Alignment.Geo3D.Matrix.Max21 getMax21() {
- return max21;
- }
-
- /**
- * Sets the value of the max21 property.
- *
- * @param value
- * allowed object is
- * {@link Alignment.Geo3D.Matrix.Max21 }
- *
- */
- public void setMax21(Alignment.Geo3D.Matrix.Max21 value) {
- this.max21 = value;
- }
-
- /**
- * Gets the value of the max22 property.
- *
- * @return
- * possible object is
- * {@link Alignment.Geo3D.Matrix.Max22 }
- *
- */
- public Alignment.Geo3D.Matrix.Max22 getMax22() {
- return max22;
- }
-
- /**
- * Sets the value of the max22 property.
- *
- * @param value
- * allowed object is
- * {@link Alignment.Geo3D.Matrix.Max22 }
- *
- */
- public void setMax22(Alignment.Geo3D.Matrix.Max22 value) {
- this.max22 = value;
- }
-
- /**
- * Gets the value of the max23 property.
- *
- * @return
- * possible object is
- * {@link Alignment.Geo3D.Matrix.Max23 }
- *
- */
- public Alignment.Geo3D.Matrix.Max23 getMax23() {
- return max23;
- }
-
- /**
- * Sets the value of the max23 property.
- *
- * @param value
- * allowed object is
- * {@link Alignment.Geo3D.Matrix.Max23 }
- *
- */
- public void setMax23(Alignment.Geo3D.Matrix.Max23 value) {
- this.max23 = value;
- }
-
- /**
- * Gets the value of the max31 property.
- *
- * @return
- * possible object is
- * {@link Alignment.Geo3D.Matrix.Max31 }
- *
- */
- public Alignment.Geo3D.Matrix.Max31 getMax31() {
- return max31;
- }
-
- /**
- * Sets the value of the max31 property.
- *
- * @param value
- * allowed object is
- * {@link Alignment.Geo3D.Matrix.Max31 }
- *
- */
- public void setMax31(Alignment.Geo3D.Matrix.Max31 value) {
- this.max31 = value;
- }
-
- /**
- * Gets the value of the max32 property.
- *
- * @return
- * possible object is
- * {@link Alignment.Geo3D.Matrix.Max32 }
- *
- */
- public Alignment.Geo3D.Matrix.Max32 getMax32() {
- return max32;
- }
-
- /**
- * Sets the value of the max32 property.
- *
- * @param value
- * allowed object is
- * {@link Alignment.Geo3D.Matrix.Max32 }
- *
- */
- public void setMax32(Alignment.Geo3D.Matrix.Max32 value) {
- this.max32 = value;
- }
-
- /**
- * Gets the value of the max33 property.
- *
- * @return
- * possible object is
- * {@link Alignment.Geo3D.Matrix.Max33 }
- *
- */
- public Alignment.Geo3D.Matrix.Max33 getMax33() {
- return max33;
- }
-
- /**
- * Sets the value of the max33 property.
- *
- * @param value
- * allowed object is
- * {@link Alignment.Geo3D.Matrix.Max33 }
- *
- */
- public void setMax33(Alignment.Geo3D.Matrix.Max33 value) {
- this.max33 = value;
- }
-
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="coord" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class Max11 {
-
- @XmlAttribute(name = "coord", required = true)
- protected float coord;
-
- /**
- * Gets the value of the coord property.
- *
- */
- public float getCoord() {
- return coord;
- }
-
- /**
- * Sets the value of the coord property.
- *
- */
- public void setCoord(float value) {
- this.coord = value;
- }
-
- }
-
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="coord" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class Max12 {
-
- @XmlAttribute(name = "coord", required = true)
- protected float coord;
-
- /**
- * Gets the value of the coord property.
- *
- */
- public float getCoord() {
- return coord;
- }
-
- /**
- * Sets the value of the coord property.
- *
- */
- public void setCoord(float value) {
- this.coord = value;
- }
-
- }
-
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="coord" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class Max13 {
-
- @XmlAttribute(name = "coord", required = true)
- protected float coord;
-
- /**
- * Gets the value of the coord property.
- *
- */
- public float getCoord() {
- return coord;
- }
-
- /**
- * Sets the value of the coord property.
- *
- */
- public void setCoord(float value) {
- this.coord = value;
- }
-
- }
-
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="coord" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class Max21 {
-
- @XmlAttribute(name = "coord", required = true)
- protected float coord;
-
- /**
- * Gets the value of the coord property.
- *
- */
- public float getCoord() {
- return coord;
- }
-
- /**
- * Sets the value of the coord property.
- *
- */
- public void setCoord(float value) {
- this.coord = value;
- }
-
- }
-
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="coord" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class Max22 {
-
- @XmlAttribute(name = "coord", required = true)
- protected float coord;
-
- /**
- * Gets the value of the coord property.
- *
- */
- public float getCoord() {
- return coord;
- }
-
- /**
- * Sets the value of the coord property.
- *
- */
- public void setCoord(float value) {
- this.coord = value;
- }
-
- }
-
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="coord" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class Max23 {
-
- @XmlAttribute(name = "coord", required = true)
- protected float coord;
-
- /**
- * Gets the value of the coord property.
- *
- */
- public float getCoord() {
- return coord;
- }
-
- /**
- * Sets the value of the coord property.
- *
- */
- public void setCoord(float value) {
- this.coord = value;
- }
-
- }
-
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="coord" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class Max31 {
-
- @XmlAttribute(name = "coord", required = true)
- protected float coord;
-
- /**
- * Gets the value of the coord property.
- *
- */
- public float getCoord() {
- return coord;
- }
-
- /**
- * Sets the value of the coord property.
- *
- */
- public void setCoord(float value) {
- this.coord = value;
- }
-
- }
-
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="coord" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class Max32 {
-
- @XmlAttribute(name = "coord", required = true)
- protected float coord;
-
- /**
- * Gets the value of the coord property.
- *
- */
- public float getCoord() {
- return coord;
- }
-
- /**
- * Sets the value of the coord property.
- *
- */
- public void setCoord(float value) {
- this.coord = value;
- }
-
- }
-
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="coord" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class Max33 {
-
- @XmlAttribute(name = "coord", required = true)
- protected float coord;
-
- /**
- * Gets the value of the coord property.
- *
- */
- public float getCoord() {
- return coord;
- }
-
- /**
- * Sets the value of the coord property.
- *
- */
- public void setCoord(float value) {
- this.coord = value;
- }
-
- }
-
- }
-
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="x" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="y" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="z" use="required" type="{http://www.w3.org/2001/XMLSchema}float" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class Vector {
-
- @XmlAttribute(name = "x", required = true)
- protected float x;
- @XmlAttribute(name = "y", required = true)
- protected float y;
- @XmlAttribute(name = "z", required = true)
- protected float z;
-
- /**
- * Gets the value of the x property.
- *
- */
- public float getX() {
- return x;
- }
-
- /**
- * Sets the value of the x property.
- *
- */
- public void setX(float value) {
- this.x = value;
- }
-
- /**
- * Gets the value of the y property.
- *
- */
- public float getY() {
- return y;
- }
-
- /**
- * Sets the value of the y property.
- *
- */
- public void setY(float value) {
- this.y = value;
- }
-
- /**
- * Gets the value of the z property.
- *
- */
- public float getZ() {
- return z;
- }
-
- /**
- * Sets the value of the z property.
- *
- */
- public void setZ(float value) {
- this.z = value;
- }
-
- }
-
+ public void setMethodName(String value)
+ {
+ this.methodName = value;
}
-
/**
- * <p>Java class for anonymous complex type.
+ * Gets the value of the scoreValue property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * @return possible object is {@link String }
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="methodName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="scoreValue" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ */
+ public String getScoreValue()
+ {
+ return scoreValue;
+ }
+
+ /**
+ * Sets the value of the scoreValue property.
*
+ * @param value
+ * allowed object is {@link String }
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class Score {
-
- @XmlAttribute(name = "methodName", required = true)
- protected String methodName;
- @XmlAttribute(name = "scoreValue", required = true)
- protected String scoreValue;
-
- /**
- * Gets the value of the methodName property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getMethodName() {
- return methodName;
- }
-
- /**
- * Sets the value of the methodName property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setMethodName(String value) {
- this.methodName = value;
- }
-
- /**
- * Gets the value of the scoreValue property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getScoreValue() {
- return scoreValue;
- }
-
- /**
- * Sets the value of the scoreValue property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setScoreValue(String value) {
- this.scoreValue = value;
- }
-
+ public void setScoreValue(String value)
+ {
+ this.scoreValue = value;
}
+ }
+
}
// Generated on: 2015.10.09 at 03:18:33 PM BST
//
-
package jalview.xml.binding.sifts;
import javax.xml.bind.annotation.XmlEnum;
import javax.xml.bind.annotation.XmlEnumValue;
import javax.xml.bind.annotation.XmlType;
-
/**
- * <p>Java class for entityType.
+ * <p>
+ * Java class for entityType.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
* <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
+ * <p>
+ *
* <pre>
* <simpleType name="entityType">
* <restriction base="{http://www.w3.org/2001/XMLSchema}string">
* </pre>
*
*/
-@XmlType(name = "entityType", namespace = "http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd")
+@XmlType(
+ name = "entityType",
+ namespace = "http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd")
@XmlEnum
-public enum EntityType {
-
- @XmlEnumValue("protein")
- PROTEIN("protein"),
- RNA("RNA"),
- DNA("DNA"),
- @XmlEnumValue("domain")
- DOMAIN("domain");
- private final String value;
-
- EntityType(String v) {
- value = v;
- }
+public enum EntityType
+{
- public String value() {
- return value;
- }
+ @XmlEnumValue("protein")
+ PROTEIN("protein"), RNA("RNA"), DNA("DNA"), @XmlEnumValue("domain")
+ DOMAIN("domain");
+
+ private final String value;
+
+ EntityType(String v)
+ {
+ value = v;
+ }
+
+ public String value()
+ {
+ return value;
+ }
- public static EntityType fromValue(String v) {
- for (EntityType c: EntityType.values()) {
- if (c.value.equals(v)) {
- return c;
- }
- }
- throw new IllegalArgumentException(v);
+ public static EntityType fromValue(String v)
+ {
+ for (EntityType c : EntityType.values())
+ {
+ if (c.value.equals(v))
+ {
+ return c;
+ }
}
+ throw new IllegalArgumentException(v);
+ }
}
// Generated on: 2015.10.09 at 03:18:33 PM BST
//
-
package jalview.xml.binding.sifts;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlValue;
import javax.xml.datatype.XMLGregorianCalendar;
-
/**
- * <p>Java class for anonymous complex type.
+ * <p>
+ * Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
*
* <pre>
* <complexType>
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = {
- "listDB",
- "entryDetail",
- "entity",
- "alignment"
-})
+@XmlType(
+ name = "",
+ propOrder =
+ { "listDB", "entryDetail", "entity", "alignment" })
@XmlRootElement(name = "entry")
-public class Entry {
+public class Entry
+{
+
+ @XmlElement(required = true)
+ protected Entry.ListDB listDB;
+
+ protected List<Entry.EntryDetail> entryDetail;
+
+ @XmlElement(required = true)
+ protected List<Entry.Entity> entity;
+
+ protected List<Alignment> alignment;
+
+ @XmlAttribute(name = "date", required = true)
+ @XmlSchemaType(name = "date")
+ protected XMLGregorianCalendar date;
+
+ @XmlAttribute(name = "dbEntryVersion", required = true)
+ @XmlSchemaType(name = "date")
+ protected XMLGregorianCalendar dbEntryVersion;
+
+ @XmlAttribute(name = "dbSource", required = true)
+ protected String dbSource;
+
+ @XmlAttribute(name = "dbCoordSys", required = true)
+ protected String dbCoordSys;
+
+ @XmlAttribute(name = "dbAccessionId", required = true)
+ protected String dbAccessionId;
+
+ @XmlAttribute(name = "dbEvidence")
+ protected String dbEvidence;
+
+ @XmlAttribute(name = "dbVersion")
+ protected String dbVersion;
+
+ /**
+ * Gets the value of the listDB property.
+ *
+ * @return possible object is {@link Entry.ListDB }
+ *
+ */
+ public Entry.ListDB getListDB()
+ {
+ return listDB;
+ }
+
+ /**
+ * Sets the value of the listDB property.
+ *
+ * @param value
+ * allowed object is {@link Entry.ListDB }
+ *
+ */
+ public void setListDB(Entry.ListDB value)
+ {
+ this.listDB = value;
+ }
+
+ /**
+ * Gets the value of the entryDetail property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the entryDetail property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getEntryDetail().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Entry.EntryDetail }
+ *
+ *
+ */
+ public List<Entry.EntryDetail> getEntryDetail()
+ {
+ if (entryDetail == null)
+ {
+ entryDetail = new ArrayList<Entry.EntryDetail>();
+ }
+ return this.entryDetail;
+ }
+
+ /**
+ * Gets the value of the entity property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the entity property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getEntity().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Entry.Entity }
+ *
+ *
+ */
+ public List<Entry.Entity> getEntity()
+ {
+ if (entity == null)
+ {
+ entity = new ArrayList<Entry.Entity>();
+ }
+ return this.entity;
+ }
+
+ /**
+ * Gets the value of the alignment property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the alignment property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getAlignment().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link Alignment }
+ *
+ *
+ */
+ public List<Alignment> getAlignment()
+ {
+ if (alignment == null)
+ {
+ alignment = new ArrayList<Alignment>();
+ }
+ return this.alignment;
+ }
+
+ /**
+ * Gets the value of the date property.
+ *
+ * @return possible object is {@link XMLGregorianCalendar }
+ *
+ */
+ public XMLGregorianCalendar getDate()
+ {
+ return date;
+ }
+
+ /**
+ * Sets the value of the date property.
+ *
+ * @param value
+ * allowed object is {@link XMLGregorianCalendar }
+ *
+ */
+ public void setDate(XMLGregorianCalendar value)
+ {
+ this.date = value;
+ }
+
+ /**
+ * Gets the value of the dbEntryVersion property.
+ *
+ * @return possible object is {@link XMLGregorianCalendar }
+ *
+ */
+ public XMLGregorianCalendar getDbEntryVersion()
+ {
+ return dbEntryVersion;
+ }
+
+ /**
+ * Sets the value of the dbEntryVersion property.
+ *
+ * @param value
+ * allowed object is {@link XMLGregorianCalendar }
+ *
+ */
+ public void setDbEntryVersion(XMLGregorianCalendar value)
+ {
+ this.dbEntryVersion = value;
+ }
+
+ /**
+ * Gets the value of the dbSource property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDbSource()
+ {
+ return dbSource;
+ }
+
+ /**
+ * Sets the value of the dbSource property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setDbSource(String value)
+ {
+ this.dbSource = value;
+ }
+
+ /**
+ * Gets the value of the dbCoordSys property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDbCoordSys()
+ {
+ return dbCoordSys;
+ }
+
+ /**
+ * Sets the value of the dbCoordSys property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setDbCoordSys(String value)
+ {
+ this.dbCoordSys = value;
+ }
+
+ /**
+ * Gets the value of the dbAccessionId property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDbAccessionId()
+ {
+ return dbAccessionId;
+ }
+
+ /**
+ * Sets the value of the dbAccessionId property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setDbAccessionId(String value)
+ {
+ this.dbAccessionId = value;
+ }
+
+ /**
+ * Gets the value of the dbEvidence property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDbEvidence()
+ {
+ return dbEvidence;
+ }
+
+ /**
+ * Sets the value of the dbEvidence property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setDbEvidence(String value)
+ {
+ this.dbEvidence = value;
+ }
+
+ /**
+ * Gets the value of the dbVersion property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDbVersion()
+ {
+ return dbVersion;
+ }
+
+ /**
+ * Sets the value of the dbVersion property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setDbVersion(String value)
+ {
+ this.dbVersion = value;
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="entityDetail" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}detail"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="segment" maxOccurs="unbounded">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="listResidue" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="residue" maxOccurs="unbounded">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="crossRefDb" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}dbRef"/>
+ * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}resRef"/>
+ * <attribute name="dbChainId" type="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}chainId" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="residueDetail" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}detail"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}resRef"/>
+ * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}listdbRef"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="listMapRegion" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="mapRegion" maxOccurs="unbounded">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="db">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="dbDetail" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}detail"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}dbRef"/>
+ * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}region"/>
+ * <attribute name="dbChainId" type="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}dbChainId" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}region"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="segmentDetail" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}detail"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}region"/>
+ * <attribute name="segId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attribute name="type" use="required" type="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}entityType" />
+ * <attribute name="entityId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "entityDetail", "segment" })
+ public static class Entity
+ {
+
+ protected List<Entry.Entity.EntityDetail> entityDetail;
@XmlElement(required = true)
- protected Entry.ListDB listDB;
- protected List<Entry.EntryDetail> entryDetail;
- @XmlElement(required = true)
- protected List<Entry.Entity> entity;
- protected List<Alignment> alignment;
- @XmlAttribute(name = "date", required = true)
- @XmlSchemaType(name = "date")
- protected XMLGregorianCalendar date;
- @XmlAttribute(name = "dbEntryVersion", required = true)
- @XmlSchemaType(name = "date")
- protected XMLGregorianCalendar dbEntryVersion;
- @XmlAttribute(name = "dbSource", required = true)
- protected String dbSource;
- @XmlAttribute(name = "dbCoordSys", required = true)
- protected String dbCoordSys;
- @XmlAttribute(name = "dbAccessionId", required = true)
- protected String dbAccessionId;
- @XmlAttribute(name = "dbEvidence")
- protected String dbEvidence;
- @XmlAttribute(name = "dbVersion")
- protected String dbVersion;
+ protected List<Entry.Entity.Segment> segment;
- /**
- * Gets the value of the listDB property.
- *
- * @return
- * possible object is
- * {@link Entry.ListDB }
- *
- */
- public Entry.ListDB getListDB() {
- return listDB;
- }
+ @XmlAttribute(name = "type", required = true)
+ protected EntityType type;
- /**
- * Sets the value of the listDB property.
- *
- * @param value
- * allowed object is
- * {@link Entry.ListDB }
- *
- */
- public void setListDB(Entry.ListDB value) {
- this.listDB = value;
- }
+ @XmlAttribute(name = "entityId", required = true)
+ protected String entityId;
/**
- * Gets the value of the entryDetail property.
+ * Gets the value of the entityDetail property.
*
* <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the entryDetail property.
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the entityDetail property.
*
* <p>
* For example, to add a new item, do as follows:
- * <pre>
- * getEntryDetail().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Entry.EntryDetail }
- *
- *
- */
- public List<Entry.EntryDetail> getEntryDetail() {
- if (entryDetail == null) {
- entryDetail = new ArrayList<Entry.EntryDetail>();
- }
- return this.entryDetail;
- }
-
- /**
- * Gets the value of the entity property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the entity property.
*
- * <p>
- * For example, to add a new item, do as follows:
* <pre>
- * getEntity().add(newItem);
+ * getEntityDetail().add(newItem);
* </pre>
*
*
* <p>
* Objects of the following type(s) are allowed in the list
- * {@link Entry.Entity }
+ * {@link Entry.Entity.EntityDetail }
*
*
*/
- public List<Entry.Entity> getEntity() {
- if (entity == null) {
- entity = new ArrayList<Entry.Entity>();
- }
- return this.entity;
+ public List<Entry.Entity.EntityDetail> getEntityDetail()
+ {
+ if (entityDetail == null)
+ {
+ entityDetail = new ArrayList<Entry.Entity.EntityDetail>();
+ }
+ return this.entityDetail;
}
/**
- * Gets the value of the alignment property.
+ * Gets the value of the segment property.
*
* <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the alignment property.
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the segment property.
*
* <p>
* For example, to add a new item, do as follows:
+ *
* <pre>
- * getAlignment().add(newItem);
+ * getSegment().add(newItem);
* </pre>
*
*
* <p>
* Objects of the following type(s) are allowed in the list
- * {@link Alignment }
- *
+ * {@link Entry.Entity.Segment }
*
- */
- public List<Alignment> getAlignment() {
- if (alignment == null) {
- alignment = new ArrayList<Alignment>();
- }
- return this.alignment;
- }
-
- /**
- * Gets the value of the date property.
*
- * @return
- * possible object is
- * {@link XMLGregorianCalendar }
- *
*/
- public XMLGregorianCalendar getDate() {
- return date;
+ public List<Entry.Entity.Segment> getSegment()
+ {
+ if (segment == null)
+ {
+ segment = new ArrayList<Entry.Entity.Segment>();
+ }
+ return this.segment;
}
/**
- * Sets the value of the date property.
+ * Gets the value of the type property.
*
- * @param value
- * allowed object is
- * {@link XMLGregorianCalendar }
- *
- */
- public void setDate(XMLGregorianCalendar value) {
- this.date = value;
- }
-
- /**
- * Gets the value of the dbEntryVersion property.
+ * @return possible object is {@link EntityType }
*
- * @return
- * possible object is
- * {@link XMLGregorianCalendar }
- *
*/
- public XMLGregorianCalendar getDbEntryVersion() {
- return dbEntryVersion;
+ public EntityType getType()
+ {
+ return type;
}
/**
- * Sets the value of the dbEntryVersion property.
+ * Sets the value of the type property.
*
* @param value
- * allowed object is
- * {@link XMLGregorianCalendar }
- *
- */
- public void setDbEntryVersion(XMLGregorianCalendar value) {
- this.dbEntryVersion = value;
- }
-
- /**
- * Gets the value of the dbSource property.
+ * allowed object is {@link EntityType }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getDbSource() {
- return dbSource;
+ public void setType(EntityType value)
+ {
+ this.type = value;
}
/**
- * Sets the value of the dbSource property.
+ * Gets the value of the entityId property.
*
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDbSource(String value) {
- this.dbSource = value;
- }
-
- /**
- * Gets the value of the dbCoordSys property.
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getDbCoordSys() {
- return dbCoordSys;
+ public String getEntityId()
+ {
+ return entityId;
}
/**
- * Sets the value of the dbCoordSys property.
+ * Sets the value of the entityId property.
*
* @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDbCoordSys(String value) {
- this.dbCoordSys = value;
- }
-
- /**
- * Gets the value of the dbAccessionId property.
+ * allowed object is {@link String }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getDbAccessionId() {
- return dbAccessionId;
+ public void setEntityId(String value)
+ {
+ this.entityId = value;
}
/**
- * Sets the value of the dbAccessionId property.
+ * <p>
+ * Java class for anonymous complex type.
*
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDbAccessionId(String value) {
- this.dbAccessionId = value;
- }
-
- /**
- * Gets the value of the dbEvidence property.
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
*
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDbEvidence() {
- return dbEvidence;
- }
-
- /**
- * Sets the value of the dbEvidence property.
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}detail"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDbEvidence(String value) {
- this.dbEvidence = value;
- }
-
- /**
- * Gets the value of the dbVersion property.
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getDbVersion() {
- return dbVersion;
- }
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "content" })
+ public static class EntityDetail
+ {
+
+ @XmlValue
+ protected String content;
+
+ @XmlAttribute(name = "dbSource")
+ protected String dbSource;
+
+ @XmlAttribute(name = "property", required = true)
+ protected String property;
+
+ /**
+ * Gets the value of the content property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getContent()
+ {
+ return content;
+ }
+
+ /**
+ * Sets the value of the content property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setContent(String value)
+ {
+ this.content = value;
+ }
+
+ /**
+ * Gets the value of the dbSource property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDbSource()
+ {
+ return dbSource;
+ }
+
+ /**
+ * Sets the value of the dbSource property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setDbSource(String value)
+ {
+ this.dbSource = value;
+ }
+
+ /**
+ * Gets the value of the property property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getProperty()
+ {
+ return property;
+ }
+
+ /**
+ * Sets the value of the property property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setProperty(String value)
+ {
+ this.property = value;
+ }
- /**
- * Sets the value of the dbVersion property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDbVersion(String value) {
- this.dbVersion = value;
}
-
/**
- * <p>Java class for anonymous complex type.
+ * <p>
+ * Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
*
* <pre>
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
* <sequence>
- * <element name="entityDetail" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}detail"/>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="segment" maxOccurs="unbounded">
+ * <element name="listResidue" minOccurs="0">
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
* <sequence>
- * <element name="listResidue" minOccurs="0">
+ * <element name="residue" maxOccurs="unbounded">
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
* <sequence>
- * <element name="residue" maxOccurs="unbounded">
+ * <element name="crossRefDb" maxOccurs="unbounded" minOccurs="0">
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="crossRefDb" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}dbRef"/>
- * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}resRef"/>
- * <attribute name="dbChainId" type="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}chainId" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="residueDetail" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}detail"/>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
+ * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}dbRef"/>
* <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}resRef"/>
- * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}listdbRef"/>
+ * <attribute name="dbChainId" type="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}chainId" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="residueDetail" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}detail"/>
* </restriction>
* </complexContent>
* </complexType>
* </element>
* </sequence>
+ * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}resRef"/>
+ * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}listdbRef"/>
* </restriction>
* </complexContent>
* </complexType>
* </element>
- * <element name="listMapRegion" minOccurs="0">
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="listMapRegion" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="mapRegion" maxOccurs="unbounded">
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
* <sequence>
- * <element name="mapRegion" maxOccurs="unbounded">
+ * <element name="db">
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
* <sequence>
- * <element name="db">
+ * <element name="dbDetail" maxOccurs="unbounded" minOccurs="0">
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="dbDetail" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}detail"/>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}dbRef"/>
- * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}region"/>
- * <attribute name="dbChainId" type="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}dbChainId" />
+ * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}detail"/>
* </restriction>
* </complexContent>
* </complexType>
* </element>
* </sequence>
+ * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}dbRef"/>
* <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}region"/>
+ * <attribute name="dbChainId" type="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}dbChainId" />
* </restriction>
* </complexContent>
* </complexType>
* </element>
* </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="segmentDetail" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}detail"/>
+ * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}region"/>
* </restriction>
* </complexContent>
* </complexType>
* </element>
* </sequence>
- * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}region"/>
- * <attribute name="segId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="segmentDetail" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}detail"/>
* </restriction>
* </complexContent>
* </complexType>
* </element>
* </sequence>
- * <attribute name="type" use="required" type="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}entityType" />
- * <attribute name="entityId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}region"/>
+ * <attribute name="segId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
* </restriction>
* </complexContent>
* </complexType>
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "entityDetail",
- "segment"
- })
- public static class Entity {
+ @XmlType(
+ name = "",
+ propOrder =
+ { "listResidue", "listMapRegion", "segmentDetail" })
+ public static class Segment
+ {
+
+ protected Entry.Entity.Segment.ListResidue listResidue;
+
+ protected Entry.Entity.Segment.ListMapRegion listMapRegion;
+
+ protected List<Entry.Entity.Segment.SegmentDetail> segmentDetail;
+
+ @XmlAttribute(name = "segId", required = true)
+ protected String segId;
+
+ @XmlAttribute(name = "start")
+ protected String start;
+
+ @XmlAttribute(name = "end")
+ protected String end;
+
+ /**
+ * Gets the value of the listResidue property.
+ *
+ * @return possible object is {@link Entry.Entity.Segment.ListResidue }
+ *
+ */
+ public Entry.Entity.Segment.ListResidue getListResidue()
+ {
+ return listResidue;
+ }
+
+ /**
+ * Sets the value of the listResidue property.
+ *
+ * @param value
+ * allowed object is {@link Entry.Entity.Segment.ListResidue }
+ *
+ */
+ public void setListResidue(Entry.Entity.Segment.ListResidue value)
+ {
+ this.listResidue = value;
+ }
+
+ /**
+ * Gets the value of the listMapRegion property.
+ *
+ * @return possible object is {@link Entry.Entity.Segment.ListMapRegion }
+ *
+ */
+ public Entry.Entity.Segment.ListMapRegion getListMapRegion()
+ {
+ return listMapRegion;
+ }
+
+ /**
+ * Sets the value of the listMapRegion property.
+ *
+ * @param value
+ * allowed object is {@link Entry.Entity.Segment.ListMapRegion }
+ *
+ */
+ public void setListMapRegion(Entry.Entity.Segment.ListMapRegion value)
+ {
+ this.listMapRegion = value;
+ }
+
+ /**
+ * Gets the value of the segmentDetail property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the segmentDetail property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getSegmentDetail().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Entry.Entity.Segment.SegmentDetail }
+ *
+ *
+ */
+ public List<Entry.Entity.Segment.SegmentDetail> getSegmentDetail()
+ {
+ if (segmentDetail == null)
+ {
+ segmentDetail = new ArrayList<Entry.Entity.Segment.SegmentDetail>();
+ }
+ return this.segmentDetail;
+ }
+
+ /**
+ * Gets the value of the segId property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getSegId()
+ {
+ return segId;
+ }
+
+ /**
+ * Sets the value of the segId property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setSegId(String value)
+ {
+ this.segId = value;
+ }
+
+ /**
+ * Gets the value of the start property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getStart()
+ {
+ return start;
+ }
+
+ /**
+ * Sets the value of the start property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setStart(String value)
+ {
+ this.start = value;
+ }
+
+ /**
+ * Gets the value of the end property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getEnd()
+ {
+ return end;
+ }
+
+ /**
+ * Sets the value of the end property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setEnd(String value)
+ {
+ this.end = value;
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="mapRegion" maxOccurs="unbounded">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="db">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="dbDetail" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}detail"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}dbRef"/>
+ * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}region"/>
+ * <attribute name="dbChainId" type="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}dbChainId" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}region"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "mapRegion" })
+ public static class ListMapRegion
+ {
- protected List<Entry.Entity.EntityDetail> entityDetail;
@XmlElement(required = true)
- protected List<Entry.Entity.Segment> segment;
- @XmlAttribute(name = "type", required = true)
- protected EntityType type;
- @XmlAttribute(name = "entityId", required = true)
- protected String entityId;
+ protected List<Entry.Entity.Segment.ListMapRegion.MapRegion> mapRegion;
/**
- * Gets the value of the entityDetail property.
+ * Gets the value of the mapRegion property.
*
* <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the entityDetail property.
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list
+ * will be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the mapRegion property.
*
* <p>
* For example, to add a new item, do as follows:
+ *
* <pre>
- * getEntityDetail().add(newItem);
+ * getMapRegion().add(newItem);
* </pre>
*
*
* <p>
* Objects of the following type(s) are allowed in the list
- * {@link Entry.Entity.EntityDetail }
+ * {@link Entry.Entity.Segment.ListMapRegion.MapRegion }
*
*
*/
- public List<Entry.Entity.EntityDetail> getEntityDetail() {
- if (entityDetail == null) {
- entityDetail = new ArrayList<Entry.Entity.EntityDetail>();
- }
- return this.entityDetail;
+ public List<Entry.Entity.Segment.ListMapRegion.MapRegion> getMapRegion()
+ {
+ if (mapRegion == null)
+ {
+ mapRegion = new ArrayList<Entry.Entity.Segment.ListMapRegion.MapRegion>();
+ }
+ return this.mapRegion;
}
/**
- * Gets the value of the segment property.
- *
* <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the segment property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getSegment().add(newItem);
- * </pre>
- *
+ * Java class for anonymous complex type.
*
* <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Entry.Entity.Segment }
- *
- *
- */
- public List<Entry.Entity.Segment> getSegment() {
- if (segment == null) {
- segment = new ArrayList<Entry.Entity.Segment>();
- }
- return this.segment;
- }
-
- /**
- * Gets the value of the type property.
- *
- * @return
- * possible object is
- * {@link EntityType }
- *
- */
- public EntityType getType() {
- return type;
- }
-
- /**
- * Sets the value of the type property.
- *
- * @param value
- * allowed object is
- * {@link EntityType }
- *
- */
- public void setType(EntityType value) {
- this.type = value;
- }
-
- /**
- * Gets the value of the entityId property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getEntityId() {
- return entityId;
- }
-
- /**
- * Sets the value of the entityId property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setEntityId(String value) {
- this.entityId = value;
- }
-
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * The following schema fragment specifies the expected content
+ * contained within this class.
*
* <pre>
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}detail"/>
+ * <sequence>
+ * <element name="db">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="dbDetail" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}detail"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}dbRef"/>
+ * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}region"/>
+ * <attribute name="dbChainId" type="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}dbChainId" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}region"/>
* </restriction>
* </complexContent>
* </complexType>
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "content"
- })
- public static class EntityDetail {
+ @XmlType(name = "", propOrder = { "db" })
+ public static class MapRegion
+ {
+
+ @XmlElement(required = true)
+ protected Entry.Entity.Segment.ListMapRegion.MapRegion.Db db;
+
+ @XmlAttribute(name = "start")
+ protected String start;
+
+ @XmlAttribute(name = "end")
+ protected String end;
+
+ /**
+ * Gets the value of the db property.
+ *
+ * @return possible object is
+ * {@link Entry.Entity.Segment.ListMapRegion.MapRegion.Db }
+ *
+ */
+ public Entry.Entity.Segment.ListMapRegion.MapRegion.Db getDb()
+ {
+ return db;
+ }
+
+ /**
+ * Sets the value of the db property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Entry.Entity.Segment.ListMapRegion.MapRegion.Db }
+ *
+ */
+ public void setDb(
+ Entry.Entity.Segment.ListMapRegion.MapRegion.Db value)
+ {
+ this.db = value;
+ }
+
+ /**
+ * Gets the value of the start property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getStart()
+ {
+ return start;
+ }
+
+ /**
+ * Sets the value of the start property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setStart(String value)
+ {
+ this.start = value;
+ }
+
+ /**
+ * Gets the value of the end property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getEnd()
+ {
+ return end;
+ }
+
+ /**
+ * Sets the value of the end property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setEnd(String value)
+ {
+ this.end = value;
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content
+ * contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="dbDetail" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}detail"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}dbRef"/>
+ * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}region"/>
+ * <attribute name="dbChainId" type="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}dbChainId" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "dbDetail" })
+ public static class Db
+ {
+
+ protected List<Entry.Entity.Segment.ListMapRegion.MapRegion.Db.DbDetail> dbDetail;
+
+ @XmlAttribute(name = "dbChainId")
+ protected String dbChainId;
- @XmlValue
- protected String content;
- @XmlAttribute(name = "dbSource")
+ @XmlAttribute(name = "dbSource", required = true)
protected String dbSource;
- @XmlAttribute(name = "property", required = true)
- protected String property;
+
+ @XmlAttribute(name = "dbCoordSys", required = true)
+ protected String dbCoordSys;
+
+ @XmlAttribute(name = "dbAccessionId", required = true)
+ protected String dbAccessionId;
+
+ @XmlAttribute(name = "dbEvidence")
+ protected String dbEvidence;
+
+ @XmlAttribute(name = "dbVersion")
+ protected String dbVersion;
+
+ @XmlAttribute(name = "start")
+ protected String start;
+
+ @XmlAttribute(name = "end")
+ protected String end;
/**
- * Gets the value of the content property.
+ * Gets the value of the dbDetail property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned
+ * list will be present inside the JAXB object. This is why there is
+ * not a <CODE>set</CODE> method for the dbDetail property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getDbDetail().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Entry.Entity.Segment.ListMapRegion.MapRegion.Db.DbDetail }
+ *
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getContent() {
- return content;
+ public List<Entry.Entity.Segment.ListMapRegion.MapRegion.Db.DbDetail> getDbDetail()
+ {
+ if (dbDetail == null)
+ {
+ dbDetail = new ArrayList<Entry.Entity.Segment.ListMapRegion.MapRegion.Db.DbDetail>();
+ }
+ return this.dbDetail;
}
/**
- * Sets the value of the content property.
+ * Gets the value of the dbChainId property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDbChainId()
+ {
+ return dbChainId;
+ }
+
+ /**
+ * Sets the value of the dbChainId property.
*
* @param value
- * allowed object is
- * {@link String }
- *
+ * allowed object is {@link String }
+ *
*/
- public void setContent(String value) {
- this.content = value;
+ public void setDbChainId(String value)
+ {
+ this.dbChainId = value;
}
/**
* Gets the value of the dbSource property.
*
- * @return
- * possible object is
- * {@link String }
- *
+ * @return possible object is {@link String }
+ *
*/
- public String getDbSource() {
- return dbSource;
+ public String getDbSource()
+ {
+ return dbSource;
}
/**
* Sets the value of the dbSource property.
*
* @param value
- * allowed object is
- * {@link String }
- *
+ * allowed object is {@link String }
+ *
*/
- public void setDbSource(String value) {
- this.dbSource = value;
+ public void setDbSource(String value)
+ {
+ this.dbSource = value;
}
/**
- * Gets the value of the property property.
+ * Gets the value of the dbCoordSys property.
+ *
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getProperty() {
- return property;
+ public String getDbCoordSys()
+ {
+ return dbCoordSys;
}
/**
- * Sets the value of the property property.
+ * Sets the value of the dbCoordSys property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setDbCoordSys(String value)
+ {
+ this.dbCoordSys = value;
+ }
+
+ /**
+ * Gets the value of the dbAccessionId property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDbAccessionId()
+ {
+ return dbAccessionId;
+ }
+
+ /**
+ * Sets the value of the dbAccessionId property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setDbAccessionId(String value)
+ {
+ this.dbAccessionId = value;
+ }
+
+ /**
+ * Gets the value of the dbEvidence property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDbEvidence()
+ {
+ return dbEvidence;
+ }
+
+ /**
+ * Sets the value of the dbEvidence property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setDbEvidence(String value)
+ {
+ this.dbEvidence = value;
+ }
+
+ /**
+ * Gets the value of the dbVersion property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDbVersion()
+ {
+ return dbVersion;
+ }
+
+ /**
+ * Sets the value of the dbVersion property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setDbVersion(String value)
+ {
+ this.dbVersion = value;
+ }
+
+ /**
+ * Gets the value of the start property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getStart()
+ {
+ return start;
+ }
+
+ /**
+ * Sets the value of the start property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setStart(String value)
+ {
+ this.start = value;
+ }
+
+ /**
+ * Gets the value of the end property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getEnd()
+ {
+ return end;
+ }
+
+ /**
+ * Sets the value of the end property.
*
* @param value
- * allowed object is
- * {@link String }
- *
+ * allowed object is {@link String }
+ *
*/
- public void setProperty(String value) {
+ public void setEnd(String value)
+ {
+ this.end = value;
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content
+ * contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}detail"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "content" })
+ public static class DbDetail
+ {
+
+ @XmlValue
+ protected String content;
+
+ @XmlAttribute(name = "dbSource")
+ protected String dbSource;
+
+ @XmlAttribute(name = "property", required = true)
+ protected String property;
+
+ /**
+ * Gets the value of the content property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getContent()
+ {
+ return content;
+ }
+
+ /**
+ * Sets the value of the content property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setContent(String value)
+ {
+ this.content = value;
+ }
+
+ /**
+ * Gets the value of the dbSource property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDbSource()
+ {
+ return dbSource;
+ }
+
+ /**
+ * Sets the value of the dbSource property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setDbSource(String value)
+ {
+ this.dbSource = value;
+ }
+
+ /**
+ * Gets the value of the property property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getProperty()
+ {
+ return property;
+ }
+
+ /**
+ * Sets the value of the property property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setProperty(String value)
+ {
this.property = value;
+ }
+
}
+ }
+
}
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="residue" maxOccurs="unbounded">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="crossRefDb" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}dbRef"/>
+ * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}resRef"/>
+ * <attribute name="dbChainId" type="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}chainId" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="residueDetail" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}detail"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}resRef"/>
+ * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}listdbRef"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "residue" })
+ public static class ListResidue
+ {
+
+ @XmlElement(required = true)
+ protected List<Entry.Entity.Segment.ListResidue.Residue> residue;
+
+ /**
+ * Gets the value of the residue property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list
+ * will be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the residue property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getResidue().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Entry.Entity.Segment.ListResidue.Residue }
+ *
+ *
+ */
+ public List<Entry.Entity.Segment.ListResidue.Residue> getResidue()
+ {
+ if (residue == null)
+ {
+ residue = new ArrayList<Entry.Entity.Segment.ListResidue.Residue>();
+ }
+ return this.residue;
+ }
/**
- * <p>Java class for anonymous complex type.
+ * <p>
+ * Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content
+ * contained within this class.
*
* <pre>
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
* <sequence>
- * <element name="listResidue" minOccurs="0">
+ * <element name="crossRefDb" maxOccurs="unbounded" minOccurs="0">
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="residue" maxOccurs="unbounded">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="crossRefDb" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}dbRef"/>
- * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}resRef"/>
- * <attribute name="dbChainId" type="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}chainId" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="residueDetail" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}detail"/>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}resRef"/>
- * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}listdbRef"/>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
+ * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}dbRef"/>
+ * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}resRef"/>
+ * <attribute name="dbChainId" type="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}chainId" />
* </restriction>
* </complexContent>
* </complexType>
* </element>
- * <element name="listMapRegion" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="mapRegion" maxOccurs="unbounded">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="db">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="dbDetail" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}detail"/>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}dbRef"/>
- * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}region"/>
- * <attribute name="dbChainId" type="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}dbChainId" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}region"/>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="segmentDetail" maxOccurs="unbounded" minOccurs="0">
+ * <element name="residueDetail" maxOccurs="unbounded" minOccurs="0">
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
* </complexType>
* </element>
* </sequence>
- * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}region"/>
- * <attribute name="segId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}resRef"/>
+ * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}listdbRef"/>
* </restriction>
* </complexContent>
* </complexType>
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "listResidue",
- "listMapRegion",
- "segmentDetail"
- })
- public static class Segment {
-
- protected Entry.Entity.Segment.ListResidue listResidue;
- protected Entry.Entity.Segment.ListMapRegion listMapRegion;
- protected List<Entry.Entity.Segment.SegmentDetail> segmentDetail;
- @XmlAttribute(name = "segId", required = true)
- protected String segId;
- @XmlAttribute(name = "start")
- protected String start;
- @XmlAttribute(name = "end")
- protected String end;
+ @XmlType(name = "", propOrder = { "crossRefDb", "residueDetail" })
+ public static class Residue
+ {
+
+ protected List<Entry.Entity.Segment.ListResidue.Residue.CrossRefDb> crossRefDb;
+
+ protected List<Entry.Entity.Segment.ListResidue.Residue.ResidueDetail> residueDetail;
+
+ @XmlAttribute(name = "dbResNum", required = true)
+ protected String dbResNum;
+
+ @XmlAttribute(name = "dbResName", required = true)
+ protected String dbResName;
+
+ @XmlAttribute(name = "dbVersion")
+ protected String dbVersion;
+
+ @XmlAttribute(name = "dbSource", required = true)
+ protected String dbSource;
+
+ @XmlAttribute(name = "dbCoordSys", required = true)
+ protected String dbCoordSys;
+
+ /**
+ * Gets the value of the crossRefDb property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list
+ * will be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the crossRefDb property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getCrossRefDb().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Entry.Entity.Segment.ListResidue.Residue.CrossRefDb }
+ *
+ *
+ */
+ public List<Entry.Entity.Segment.ListResidue.Residue.CrossRefDb> getCrossRefDb()
+ {
+ if (crossRefDb == null)
+ {
+ crossRefDb = new ArrayList<Entry.Entity.Segment.ListResidue.Residue.CrossRefDb>();
+ }
+ return this.crossRefDb;
+ }
+
+ /**
+ * Gets the value of the residueDetail property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list
+ * will be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the residueDetail property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getResidueDetail().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Entry.Entity.Segment.ListResidue.Residue.ResidueDetail }
+ *
+ *
+ */
+ public List<Entry.Entity.Segment.ListResidue.Residue.ResidueDetail> getResidueDetail()
+ {
+ if (residueDetail == null)
+ {
+ residueDetail = new ArrayList<Entry.Entity.Segment.ListResidue.Residue.ResidueDetail>();
+ }
+ return this.residueDetail;
+ }
+
+ /**
+ * Gets the value of the dbResNum property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDbResNum()
+ {
+ return dbResNum;
+ }
+
+ /**
+ * Sets the value of the dbResNum property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setDbResNum(String value)
+ {
+ this.dbResNum = value;
+ }
+
+ /**
+ * Gets the value of the dbResName property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDbResName()
+ {
+ return dbResName;
+ }
+
+ /**
+ * Sets the value of the dbResName property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setDbResName(String value)
+ {
+ this.dbResName = value;
+ }
+
+ /**
+ * Gets the value of the dbVersion property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDbVersion()
+ {
+ return dbVersion;
+ }
+
+ /**
+ * Sets the value of the dbVersion property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setDbVersion(String value)
+ {
+ this.dbVersion = value;
+ }
+
+ /**
+ * Gets the value of the dbSource property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDbSource()
+ {
+ return dbSource;
+ }
+
+ /**
+ * Sets the value of the dbSource property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setDbSource(String value)
+ {
+ this.dbSource = value;
+ }
+
+ /**
+ * Gets the value of the dbCoordSys property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDbCoordSys()
+ {
+ return dbCoordSys;
+ }
+
+ /**
+ * Sets the value of the dbCoordSys property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setDbCoordSys(String value)
+ {
+ this.dbCoordSys = value;
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content
+ * contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}dbRef"/>
+ * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}resRef"/>
+ * <attribute name="dbChainId" type="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}chainId" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class CrossRefDb
+ {
+
+ @XmlAttribute(name = "dbChainId")
+ protected String dbChainId;
+
+ @XmlAttribute(name = "dbSource", required = true)
+ protected String dbSource;
+
+ @XmlAttribute(name = "dbCoordSys", required = true)
+ protected String dbCoordSys;
+
+ @XmlAttribute(name = "dbAccessionId", required = true)
+ protected String dbAccessionId;
+
+ @XmlAttribute(name = "dbEvidence")
+ protected String dbEvidence;
+
+ @XmlAttribute(name = "dbVersion")
+ protected String dbVersion;
+
+ @XmlAttribute(name = "dbResNum", required = true)
+ protected String dbResNum;
+
+ @XmlAttribute(name = "dbResName", required = true)
+ protected String dbResName;
/**
- * Gets the value of the listResidue property.
+ * Gets the value of the dbChainId property.
+ *
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link Entry.Entity.Segment.ListResidue }
- *
*/
- public Entry.Entity.Segment.ListResidue getListResidue() {
- return listResidue;
+ public String getDbChainId()
+ {
+ return dbChainId;
}
/**
- * Sets the value of the listResidue property.
+ * Sets the value of the dbChainId property.
*
* @param value
- * allowed object is
- * {@link Entry.Entity.Segment.ListResidue }
- *
+ * allowed object is {@link String }
+ *
*/
- public void setListResidue(Entry.Entity.Segment.ListResidue value) {
- this.listResidue = value;
+ public void setDbChainId(String value)
+ {
+ this.dbChainId = value;
}
/**
- * Gets the value of the listMapRegion property.
+ * Gets the value of the dbSource property.
+ *
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link Entry.Entity.Segment.ListMapRegion }
- *
*/
- public Entry.Entity.Segment.ListMapRegion getListMapRegion() {
- return listMapRegion;
+ public String getDbSource()
+ {
+ return dbSource;
}
/**
- * Sets the value of the listMapRegion property.
+ * Sets the value of the dbSource property.
*
* @param value
- * allowed object is
- * {@link Entry.Entity.Segment.ListMapRegion }
- *
+ * allowed object is {@link String }
+ *
*/
- public void setListMapRegion(Entry.Entity.Segment.ListMapRegion value) {
- this.listMapRegion = value;
+ public void setDbSource(String value)
+ {
+ this.dbSource = value;
}
/**
- * Gets the value of the segmentDetail property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the segmentDetail property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getSegmentDetail().add(newItem);
- * </pre>
+ * Gets the value of the dbCoordSys property.
*
+ * @return possible object is {@link String }
*
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Entry.Entity.Segment.SegmentDetail }
+ */
+ public String getDbCoordSys()
+ {
+ return dbCoordSys;
+ }
+
+ /**
+ * Sets the value of the dbCoordSys property.
*
+ * @param value
+ * allowed object is {@link String }
*
*/
- public List<Entry.Entity.Segment.SegmentDetail> getSegmentDetail() {
- if (segmentDetail == null) {
- segmentDetail = new ArrayList<Entry.Entity.Segment.SegmentDetail>();
- }
- return this.segmentDetail;
+ public void setDbCoordSys(String value)
+ {
+ this.dbCoordSys = value;
}
/**
- * Gets the value of the segId property.
+ * Gets the value of the dbAccessionId property.
+ *
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getSegId() {
- return segId;
+ public String getDbAccessionId()
+ {
+ return dbAccessionId;
}
/**
- * Sets the value of the segId property.
+ * Sets the value of the dbAccessionId property.
*
* @param value
- * allowed object is
- * {@link String }
- *
+ * allowed object is {@link String }
+ *
*/
- public void setSegId(String value) {
- this.segId = value;
+ public void setDbAccessionId(String value)
+ {
+ this.dbAccessionId = value;
}
/**
- * Gets the value of the start property.
+ * Gets the value of the dbEvidence property.
+ *
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getStart() {
- return start;
+ public String getDbEvidence()
+ {
+ return dbEvidence;
}
/**
- * Sets the value of the start property.
+ * Sets the value of the dbEvidence property.
*
* @param value
- * allowed object is
- * {@link String }
- *
+ * allowed object is {@link String }
+ *
*/
- public void setStart(String value) {
- this.start = value;
+ public void setDbEvidence(String value)
+ {
+ this.dbEvidence = value;
}
/**
- * Gets the value of the end property.
+ * Gets the value of the dbVersion property.
+ *
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getEnd() {
- return end;
+ public String getDbVersion()
+ {
+ return dbVersion;
}
/**
- * Sets the value of the end property.
+ * Sets the value of the dbVersion property.
*
* @param value
- * allowed object is
- * {@link String }
- *
+ * allowed object is {@link String }
+ *
*/
- public void setEnd(String value) {
- this.end = value;
+ public void setDbVersion(String value)
+ {
+ this.dbVersion = value;
}
+ /**
+ * Gets the value of the dbResNum property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDbResNum()
+ {
+ return dbResNum;
+ }
/**
- * <p>Java class for anonymous complex type.
+ * Sets the value of the dbResNum property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * @param value
+ * allowed object is {@link String }
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="mapRegion" maxOccurs="unbounded">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="db">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="dbDetail" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}detail"/>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}dbRef"/>
- * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}region"/>
- * <attribute name="dbChainId" type="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}dbChainId" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}region"/>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ */
+ public void setDbResNum(String value)
+ {
+ this.dbResNum = value;
+ }
+
+ /**
+ * Gets the value of the dbResName property.
*
+ * @return possible object is {@link String }
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "mapRegion"
- })
- public static class ListMapRegion {
-
- @XmlElement(required = true)
- protected List<Entry.Entity.Segment.ListMapRegion.MapRegion> mapRegion;
-
- /**
- * Gets the value of the mapRegion property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the mapRegion property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getMapRegion().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Entry.Entity.Segment.ListMapRegion.MapRegion }
- *
- *
- */
- public List<Entry.Entity.Segment.ListMapRegion.MapRegion> getMapRegion() {
- if (mapRegion == null) {
- mapRegion = new ArrayList<Entry.Entity.Segment.ListMapRegion.MapRegion>();
- }
- return this.mapRegion;
- }
-
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="db">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="dbDetail" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}detail"/>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}dbRef"/>
- * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}region"/>
- * <attribute name="dbChainId" type="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}dbChainId" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}region"/>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "db"
- })
- public static class MapRegion {
-
- @XmlElement(required = true)
- protected Entry.Entity.Segment.ListMapRegion.MapRegion.Db db;
- @XmlAttribute(name = "start")
- protected String start;
- @XmlAttribute(name = "end")
- protected String end;
-
- /**
- * Gets the value of the db property.
- *
- * @return
- * possible object is
- * {@link Entry.Entity.Segment.ListMapRegion.MapRegion.Db }
- *
- */
- public Entry.Entity.Segment.ListMapRegion.MapRegion.Db getDb() {
- return db;
- }
-
- /**
- * Sets the value of the db property.
- *
- * @param value
- * allowed object is
- * {@link Entry.Entity.Segment.ListMapRegion.MapRegion.Db }
- *
- */
- public void setDb(Entry.Entity.Segment.ListMapRegion.MapRegion.Db value) {
- this.db = value;
- }
-
- /**
- * Gets the value of the start property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getStart() {
- return start;
- }
-
- /**
- * Sets the value of the start property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setStart(String value) {
- this.start = value;
- }
-
- /**
- * Gets the value of the end property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getEnd() {
- return end;
- }
-
- /**
- * Sets the value of the end property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setEnd(String value) {
- this.end = value;
- }
-
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="dbDetail" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}detail"/>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}dbRef"/>
- * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}region"/>
- * <attribute name="dbChainId" type="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}dbChainId" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "dbDetail"
- })
- public static class Db {
-
- protected List<Entry.Entity.Segment.ListMapRegion.MapRegion.Db.DbDetail> dbDetail;
- @XmlAttribute(name = "dbChainId")
- protected String dbChainId;
- @XmlAttribute(name = "dbSource", required = true)
- protected String dbSource;
- @XmlAttribute(name = "dbCoordSys", required = true)
- protected String dbCoordSys;
- @XmlAttribute(name = "dbAccessionId", required = true)
- protected String dbAccessionId;
- @XmlAttribute(name = "dbEvidence")
- protected String dbEvidence;
- @XmlAttribute(name = "dbVersion")
- protected String dbVersion;
- @XmlAttribute(name = "start")
- protected String start;
- @XmlAttribute(name = "end")
- protected String end;
-
- /**
- * Gets the value of the dbDetail property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the dbDetail property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getDbDetail().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Entry.Entity.Segment.ListMapRegion.MapRegion.Db.DbDetail }
- *
- *
- */
- public List<Entry.Entity.Segment.ListMapRegion.MapRegion.Db.DbDetail> getDbDetail() {
- if (dbDetail == null) {
- dbDetail = new ArrayList<Entry.Entity.Segment.ListMapRegion.MapRegion.Db.DbDetail>();
- }
- return this.dbDetail;
- }
-
- /**
- * Gets the value of the dbChainId property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDbChainId() {
- return dbChainId;
- }
-
- /**
- * Sets the value of the dbChainId property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDbChainId(String value) {
- this.dbChainId = value;
- }
-
- /**
- * Gets the value of the dbSource property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDbSource() {
- return dbSource;
- }
-
- /**
- * Sets the value of the dbSource property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDbSource(String value) {
- this.dbSource = value;
- }
-
- /**
- * Gets the value of the dbCoordSys property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDbCoordSys() {
- return dbCoordSys;
- }
-
- /**
- * Sets the value of the dbCoordSys property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDbCoordSys(String value) {
- this.dbCoordSys = value;
- }
-
- /**
- * Gets the value of the dbAccessionId property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDbAccessionId() {
- return dbAccessionId;
- }
-
- /**
- * Sets the value of the dbAccessionId property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDbAccessionId(String value) {
- this.dbAccessionId = value;
- }
-
- /**
- * Gets the value of the dbEvidence property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDbEvidence() {
- return dbEvidence;
- }
-
- /**
- * Sets the value of the dbEvidence property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDbEvidence(String value) {
- this.dbEvidence = value;
- }
-
- /**
- * Gets the value of the dbVersion property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDbVersion() {
- return dbVersion;
- }
-
- /**
- * Sets the value of the dbVersion property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDbVersion(String value) {
- this.dbVersion = value;
- }
-
- /**
- * Gets the value of the start property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getStart() {
- return start;
- }
-
- /**
- * Sets the value of the start property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setStart(String value) {
- this.start = value;
- }
-
- /**
- * Gets the value of the end property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getEnd() {
- return end;
- }
-
- /**
- * Sets the value of the end property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setEnd(String value) {
- this.end = value;
- }
-
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}detail"/>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "content"
- })
- public static class DbDetail {
-
- @XmlValue
- protected String content;
- @XmlAttribute(name = "dbSource")
- protected String dbSource;
- @XmlAttribute(name = "property", required = true)
- protected String property;
-
- /**
- * Gets the value of the content property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getContent() {
- return content;
- }
-
- /**
- * Sets the value of the content property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setContent(String value) {
- this.content = value;
- }
-
- /**
- * Gets the value of the dbSource property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDbSource() {
- return dbSource;
- }
-
- /**
- * Sets the value of the dbSource property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDbSource(String value) {
- this.dbSource = value;
- }
-
- /**
- * Gets the value of the property property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getProperty() {
- return property;
- }
-
- /**
- * Sets the value of the property property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setProperty(String value) {
- this.property = value;
- }
-
- }
-
- }
-
- }
+ public String getDbResName()
+ {
+ return dbResName;
+ }
+ /**
+ * Sets the value of the dbResName property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setDbResName(String value)
+ {
+ this.dbResName = value;
}
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content
+ * contained within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}detail"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "content" })
+ public static class ResidueDetail
+ {
+
+ @XmlValue
+ protected String content;
+
+ @XmlAttribute(name = "dbSource")
+ protected String dbSource;
+
+ @XmlAttribute(name = "property", required = true)
+ protected String property;
/**
- * <p>Java class for anonymous complex type.
+ * Gets the value of the content property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * @return possible object is {@link String }
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="residue" maxOccurs="unbounded">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="crossRefDb" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}dbRef"/>
- * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}resRef"/>
- * <attribute name="dbChainId" type="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}chainId" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="residueDetail" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}detail"/>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}resRef"/>
- * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}listdbRef"/>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ */
+ public String getContent()
+ {
+ return content;
+ }
+
+ /**
+ * Sets the value of the content property.
*
+ * @param value
+ * allowed object is {@link String }
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "residue"
- })
- public static class ListResidue {
-
- @XmlElement(required = true)
- protected List<Entry.Entity.Segment.ListResidue.Residue> residue;
-
- /**
- * Gets the value of the residue property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the residue property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getResidue().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Entry.Entity.Segment.ListResidue.Residue }
- *
- *
- */
- public List<Entry.Entity.Segment.ListResidue.Residue> getResidue() {
- if (residue == null) {
- residue = new ArrayList<Entry.Entity.Segment.ListResidue.Residue>();
- }
- return this.residue;
- }
-
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="crossRefDb" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}dbRef"/>
- * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}resRef"/>
- * <attribute name="dbChainId" type="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}chainId" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * <element name="residueDetail" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}detail"/>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}resRef"/>
- * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}listdbRef"/>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "crossRefDb",
- "residueDetail"
- })
- public static class Residue {
-
- protected List<Entry.Entity.Segment.ListResidue.Residue.CrossRefDb> crossRefDb;
- protected List<Entry.Entity.Segment.ListResidue.Residue.ResidueDetail> residueDetail;
- @XmlAttribute(name = "dbResNum", required = true)
- protected String dbResNum;
- @XmlAttribute(name = "dbResName", required = true)
- protected String dbResName;
- @XmlAttribute(name = "dbVersion")
- protected String dbVersion;
- @XmlAttribute(name = "dbSource", required = true)
- protected String dbSource;
- @XmlAttribute(name = "dbCoordSys", required = true)
- protected String dbCoordSys;
-
- /**
- * Gets the value of the crossRefDb property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the crossRefDb property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getCrossRefDb().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Entry.Entity.Segment.ListResidue.Residue.CrossRefDb }
- *
- *
- */
- public List<Entry.Entity.Segment.ListResidue.Residue.CrossRefDb> getCrossRefDb() {
- if (crossRefDb == null) {
- crossRefDb = new ArrayList<Entry.Entity.Segment.ListResidue.Residue.CrossRefDb>();
- }
- return this.crossRefDb;
- }
-
- /**
- * Gets the value of the residueDetail property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the residueDetail property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getResidueDetail().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Entry.Entity.Segment.ListResidue.Residue.ResidueDetail }
- *
- *
- */
- public List<Entry.Entity.Segment.ListResidue.Residue.ResidueDetail> getResidueDetail() {
- if (residueDetail == null) {
- residueDetail = new ArrayList<Entry.Entity.Segment.ListResidue.Residue.ResidueDetail>();
- }
- return this.residueDetail;
- }
-
- /**
- * Gets the value of the dbResNum property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDbResNum() {
- return dbResNum;
- }
-
- /**
- * Sets the value of the dbResNum property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDbResNum(String value) {
- this.dbResNum = value;
- }
-
- /**
- * Gets the value of the dbResName property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDbResName() {
- return dbResName;
- }
-
- /**
- * Sets the value of the dbResName property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDbResName(String value) {
- this.dbResName = value;
- }
-
- /**
- * Gets the value of the dbVersion property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDbVersion() {
- return dbVersion;
- }
-
- /**
- * Sets the value of the dbVersion property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDbVersion(String value) {
- this.dbVersion = value;
- }
-
- /**
- * Gets the value of the dbSource property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDbSource() {
- return dbSource;
- }
-
- /**
- * Sets the value of the dbSource property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDbSource(String value) {
- this.dbSource = value;
- }
-
- /**
- * Gets the value of the dbCoordSys property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDbCoordSys() {
- return dbCoordSys;
- }
-
- /**
- * Sets the value of the dbCoordSys property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDbCoordSys(String value) {
- this.dbCoordSys = value;
- }
-
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}dbRef"/>
- * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}resRef"/>
- * <attribute name="dbChainId" type="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}chainId" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class CrossRefDb {
-
- @XmlAttribute(name = "dbChainId")
- protected String dbChainId;
- @XmlAttribute(name = "dbSource", required = true)
- protected String dbSource;
- @XmlAttribute(name = "dbCoordSys", required = true)
- protected String dbCoordSys;
- @XmlAttribute(name = "dbAccessionId", required = true)
- protected String dbAccessionId;
- @XmlAttribute(name = "dbEvidence")
- protected String dbEvidence;
- @XmlAttribute(name = "dbVersion")
- protected String dbVersion;
- @XmlAttribute(name = "dbResNum", required = true)
- protected String dbResNum;
- @XmlAttribute(name = "dbResName", required = true)
- protected String dbResName;
-
- /**
- * Gets the value of the dbChainId property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDbChainId() {
- return dbChainId;
- }
-
- /**
- * Sets the value of the dbChainId property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDbChainId(String value) {
- this.dbChainId = value;
- }
-
- /**
- * Gets the value of the dbSource property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDbSource() {
- return dbSource;
- }
-
- /**
- * Sets the value of the dbSource property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDbSource(String value) {
- this.dbSource = value;
- }
-
- /**
- * Gets the value of the dbCoordSys property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDbCoordSys() {
- return dbCoordSys;
- }
-
- /**
- * Sets the value of the dbCoordSys property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDbCoordSys(String value) {
- this.dbCoordSys = value;
- }
-
- /**
- * Gets the value of the dbAccessionId property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDbAccessionId() {
- return dbAccessionId;
- }
-
- /**
- * Sets the value of the dbAccessionId property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDbAccessionId(String value) {
- this.dbAccessionId = value;
- }
-
- /**
- * Gets the value of the dbEvidence property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDbEvidence() {
- return dbEvidence;
- }
-
- /**
- * Sets the value of the dbEvidence property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDbEvidence(String value) {
- this.dbEvidence = value;
- }
-
- /**
- * Gets the value of the dbVersion property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDbVersion() {
- return dbVersion;
- }
-
- /**
- * Sets the value of the dbVersion property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDbVersion(String value) {
- this.dbVersion = value;
- }
-
- /**
- * Gets the value of the dbResNum property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDbResNum() {
- return dbResNum;
- }
-
- /**
- * Sets the value of the dbResNum property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDbResNum(String value) {
- this.dbResNum = value;
- }
-
- /**
- * Gets the value of the dbResName property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDbResName() {
- return dbResName;
- }
-
- /**
- * Sets the value of the dbResName property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDbResName(String value) {
- this.dbResName = value;
- }
-
- }
-
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}detail"/>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "content"
- })
- public static class ResidueDetail {
-
- @XmlValue
- protected String content;
- @XmlAttribute(name = "dbSource")
- protected String dbSource;
- @XmlAttribute(name = "property", required = true)
- protected String property;
-
- /**
- * Gets the value of the content property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getContent() {
- return content;
- }
-
- /**
- * Sets the value of the content property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setContent(String value) {
- this.content = value;
- }
-
- /**
- * Gets the value of the dbSource property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDbSource() {
- return dbSource;
- }
-
- /**
- * Sets the value of the dbSource property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDbSource(String value) {
- this.dbSource = value;
- }
-
- /**
- * Gets the value of the property property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getProperty() {
- return property;
- }
-
- /**
- * Sets the value of the property property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setProperty(String value) {
- this.property = value;
- }
-
- }
-
- }
-
+ public void setContent(String value)
+ {
+ this.content = value;
}
-
/**
- * <p>Java class for anonymous complex type.
+ * Gets the value of the dbSource property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * @return possible object is {@link String }
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}detail"/>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ */
+ public String getDbSource()
+ {
+ return dbSource;
+ }
+
+ /**
+ * Sets the value of the dbSource property.
*
+ * @param value
+ * allowed object is {@link String }
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "content"
- })
- public static class SegmentDetail {
-
- @XmlValue
- protected String content;
- @XmlAttribute(name = "dbSource")
- protected String dbSource;
- @XmlAttribute(name = "property", required = true)
- protected String property;
-
- /**
- * Gets the value of the content property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getContent() {
- return content;
- }
-
- /**
- * Sets the value of the content property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setContent(String value) {
- this.content = value;
- }
-
- /**
- * Gets the value of the dbSource property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDbSource() {
- return dbSource;
- }
-
- /**
- * Sets the value of the dbSource property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDbSource(String value) {
- this.dbSource = value;
- }
-
- /**
- * Gets the value of the property property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getProperty() {
- return property;
- }
-
- /**
- * Sets the value of the property property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setProperty(String value) {
- this.property = value;
- }
+ public void setDbSource(String value)
+ {
+ this.dbSource = value;
+ }
+ /**
+ * Gets the value of the property property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getProperty()
+ {
+ return property;
}
- }
+ /**
+ * Sets the value of the property property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setProperty(String value)
+ {
+ this.property = value;
+ }
- }
+ }
+ }
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}detail"/>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "content"
- })
- public static class EntryDetail {
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}detail"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "content" })
+ public static class SegmentDetail
+ {
@XmlValue
protected String content;
+
@XmlAttribute(name = "dbSource")
protected String dbSource;
+
@XmlAttribute(name = "property", required = true)
protected String property;
/**
* Gets the value of the content property.
*
- * @return
- * possible object is
- * {@link String }
- *
+ * @return possible object is {@link String }
+ *
*/
- public String getContent() {
- return content;
+ public String getContent()
+ {
+ return content;
}
/**
* Sets the value of the content property.
*
* @param value
- * allowed object is
- * {@link String }
- *
+ * allowed object is {@link String }
+ *
*/
- public void setContent(String value) {
- this.content = value;
+ public void setContent(String value)
+ {
+ this.content = value;
}
/**
* Gets the value of the dbSource property.
*
- * @return
- * possible object is
- * {@link String }
- *
+ * @return possible object is {@link String }
+ *
*/
- public String getDbSource() {
- return dbSource;
+ public String getDbSource()
+ {
+ return dbSource;
}
/**
* Sets the value of the dbSource property.
*
* @param value
- * allowed object is
- * {@link String }
- *
+ * allowed object is {@link String }
+ *
*/
- public void setDbSource(String value) {
- this.dbSource = value;
+ public void setDbSource(String value)
+ {
+ this.dbSource = value;
}
/**
* Gets the value of the property property.
*
- * @return
- * possible object is
- * {@link String }
- *
+ * @return possible object is {@link String }
+ *
*/
- public String getProperty() {
- return property;
+ public String getProperty()
+ {
+ return property;
}
/**
* Sets the value of the property property.
*
* @param value
- * allowed object is
- * {@link String }
- *
+ * allowed object is {@link String }
+ *
*/
- public void setProperty(String value) {
- this.property = value;
+ public void setProperty(String value)
+ {
+ this.property = value;
}
+ }
+
}
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}detail"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "content" })
+ public static class EntryDetail
+ {
+
+ @XmlValue
+ protected String content;
+
+ @XmlAttribute(name = "dbSource")
+ protected String dbSource;
+
+ @XmlAttribute(name = "property", required = true)
+ protected String property;
+
+ /**
+ * Gets the value of the content property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getContent()
+ {
+ return content;
+ }
/**
- * <p>Java class for anonymous complex type.
+ * Sets the value of the content property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setContent(String value)
+ {
+ this.content = value;
+ }
+
+ /**
+ * Gets the value of the dbSource property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDbSource()
+ {
+ return dbSource;
+ }
+
+ /**
+ * Sets the value of the dbSource property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setDbSource(String value)
+ {
+ this.dbSource = value;
+ }
+
+ /**
+ * Gets the value of the property property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getProperty()
+ {
+ return property;
+ }
+
+ /**
+ * Sets the value of the property property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setProperty(String value)
+ {
+ this.property = value;
+ }
+
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence maxOccurs="unbounded">
+ * <element name="db">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}listdbRef"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "db" })
+ public static class ListDB
+ {
+
+ @XmlElement(required = true)
+ protected List<Entry.ListDB.Db> db;
+
+ /**
+ * Gets the value of the db property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the db property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getDb().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link Entry.ListDB.Db }
+ *
+ *
+ */
+ public List<Entry.ListDB.Db> getDb()
+ {
+ if (db == null)
+ {
+ db = new ArrayList<Entry.ListDB.Db>();
+ }
+ return this.db;
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
*
* <pre>
* <complexType>
* <complexContent>
* <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence maxOccurs="unbounded">
- * <element name="db">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}listdbRef"/>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
+ * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}listdbRef"/>
* </restriction>
* </complexContent>
* </complexType>
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "db"
- })
- public static class ListDB {
-
- @XmlElement(required = true)
- protected List<Entry.ListDB.Db> db;
-
- /**
- * Gets the value of the db property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the db property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getDb().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Entry.ListDB.Db }
- *
- *
- */
- public List<Entry.ListDB.Db> getDb() {
- if (db == null) {
- db = new ArrayList<Entry.ListDB.Db>();
- }
- return this.db;
- }
-
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{http://www.ebi.ac.uk/pdbe/docs/sifts/dataTypes.xsd}listdbRef"/>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class Db {
-
- @XmlAttribute(name = "dbVersion")
- protected String dbVersion;
- @XmlAttribute(name = "dbSource", required = true)
- protected String dbSource;
- @XmlAttribute(name = "dbCoordSys", required = true)
- protected String dbCoordSys;
-
- /**
- * Gets the value of the dbVersion property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDbVersion() {
- return dbVersion;
- }
-
- /**
- * Sets the value of the dbVersion property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDbVersion(String value) {
- this.dbVersion = value;
- }
-
- /**
- * Gets the value of the dbSource property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDbSource() {
- return dbSource;
- }
-
- /**
- * Sets the value of the dbSource property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDbSource(String value) {
- this.dbSource = value;
- }
-
- /**
- * Gets the value of the dbCoordSys property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDbCoordSys() {
- return dbCoordSys;
- }
-
- /**
- * Sets the value of the dbCoordSys property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDbCoordSys(String value) {
- this.dbCoordSys = value;
- }
-
- }
+ @XmlType(name = "")
+ public static class Db
+ {
+
+ @XmlAttribute(name = "dbVersion")
+ protected String dbVersion;
+
+ @XmlAttribute(name = "dbSource", required = true)
+ protected String dbSource;
+
+ @XmlAttribute(name = "dbCoordSys", required = true)
+ protected String dbCoordSys;
+
+ /**
+ * Gets the value of the dbVersion property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDbVersion()
+ {
+ return dbVersion;
+ }
+
+ /**
+ * Sets the value of the dbVersion property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setDbVersion(String value)
+ {
+ this.dbVersion = value;
+ }
+
+ /**
+ * Gets the value of the dbSource property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDbSource()
+ {
+ return dbSource;
+ }
+
+ /**
+ * Sets the value of the dbSource property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setDbSource(String value)
+ {
+ this.dbSource = value;
+ }
+
+ /**
+ * Gets the value of the dbCoordSys property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDbCoordSys()
+ {
+ return dbCoordSys;
+ }
+
+ /**
+ * Sets the value of the dbCoordSys property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setDbCoordSys(String value)
+ {
+ this.dbCoordSys = value;
+ }
}
+ }
+
}
// Generated on: 2015.10.09 at 03:18:33 PM BST
//
-
package jalview.xml.binding.sifts;
import javax.xml.bind.annotation.XmlRegistry;
-
/**
- * This object contains factory methods for each
- * Java content interface and Java element interface
- * generated in the jalview.xml.binding.sifts package.
- * <p>An ObjectFactory allows you to programatically
- * construct new instances of the Java representation
- * for XML content. The Java representation of XML
- * content can consist of schema derived interfaces
- * and classes representing the binding of schema
- * type definitions, element declarations and model
- * groups. Factory methods for each of these are
- * provided in this class.
+ * This object contains factory methods for each Java content interface and Java
+ * element interface generated in the jalview.xml.binding.sifts package.
+ * <p>
+ * An ObjectFactory allows you to programatically construct new instances of the
+ * Java representation for XML content. The Java representation of XML content
+ * can consist of schema derived interfaces and classes representing the binding
+ * of schema type definitions, element declarations and model groups. Factory
+ * methods for each of these are provided in this class.
*
*/
@XmlRegistry
-public class ObjectFactory {
-
-
- /**
- * Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: jalview.xml.binding.sifts
- *
- */
- public ObjectFactory() {
- }
-
- /**
- * Create an instance of {@link Entry }
- *
- */
- public Entry createEntry() {
- return new Entry();
- }
-
- /**
- * Create an instance of {@link Alignment }
- *
- */
- public Alignment createAlignment() {
- return new Alignment();
- }
-
- /**
- * Create an instance of {@link Alignment.Geo3D }
- *
- */
- public Alignment.Geo3D createAlignmentGeo3D() {
- return new Alignment.Geo3D();
- }
-
- /**
- * Create an instance of {@link Alignment.Geo3D.Matrix }
- *
- */
- public Alignment.Geo3D.Matrix createAlignmentGeo3DMatrix() {
- return new Alignment.Geo3D.Matrix();
- }
-
- /**
- * Create an instance of {@link Alignment.Block }
- *
- */
- public Alignment.Block createAlignmentBlock() {
- return new Alignment.Block();
- }
-
- /**
- * Create an instance of {@link Alignment.AlignObject }
- *
- */
- public Alignment.AlignObject createAlignmentAlignObject() {
- return new Alignment.AlignObject();
- }
-
- /**
- * Create an instance of {@link Entry.Entity }
- *
- */
- public Entry.Entity createEntryEntity() {
- return new Entry.Entity();
- }
-
- /**
- * Create an instance of {@link Entry.Entity.Segment }
- *
- */
- public Entry.Entity.Segment createEntryEntitySegment() {
- return new Entry.Entity.Segment();
- }
-
- /**
- * Create an instance of {@link Entry.Entity.Segment.ListMapRegion }
- *
- */
- public Entry.Entity.Segment.ListMapRegion createEntryEntitySegmentListMapRegion() {
- return new Entry.Entity.Segment.ListMapRegion();
- }
-
- /**
- * Create an instance of {@link Entry.Entity.Segment.ListMapRegion.MapRegion }
- *
- */
- public Entry.Entity.Segment.ListMapRegion.MapRegion createEntryEntitySegmentListMapRegionMapRegion() {
- return new Entry.Entity.Segment.ListMapRegion.MapRegion();
- }
-
- /**
- * Create an instance of {@link Entry.Entity.Segment.ListMapRegion.MapRegion.Db }
- *
- */
- public Entry.Entity.Segment.ListMapRegion.MapRegion.Db createEntryEntitySegmentListMapRegionMapRegionDb() {
- return new Entry.Entity.Segment.ListMapRegion.MapRegion.Db();
- }
-
- /**
- * Create an instance of {@link Entry.Entity.Segment.ListResidue }
- *
- */
- public Entry.Entity.Segment.ListResidue createEntryEntitySegmentListResidue() {
- return new Entry.Entity.Segment.ListResidue();
- }
-
- /**
- * Create an instance of {@link Entry.Entity.Segment.ListResidue.Residue }
- *
- */
- public Entry.Entity.Segment.ListResidue.Residue createEntryEntitySegmentListResidueResidue() {
- return new Entry.Entity.Segment.ListResidue.Residue();
- }
-
- /**
- * Create an instance of {@link Entry.ListDB }
- *
- */
- public Entry.ListDB createEntryListDB() {
- return new Entry.ListDB();
- }
-
- /**
- * Create an instance of {@link Entry.EntryDetail }
- *
- */
- public Entry.EntryDetail createEntryEntryDetail() {
- return new Entry.EntryDetail();
- }
-
- /**
- * Create an instance of {@link Alignment.Score }
- *
- */
- public Alignment.Score createAlignmentScore() {
- return new Alignment.Score();
- }
-
- /**
- * Create an instance of {@link Alignment.Geo3D.Vector }
- *
- */
- public Alignment.Geo3D.Vector createAlignmentGeo3DVector() {
- return new Alignment.Geo3D.Vector();
- }
-
- /**
- * Create an instance of {@link Alignment.Geo3D.Matrix.Max11 }
- *
- */
- public Alignment.Geo3D.Matrix.Max11 createAlignmentGeo3DMatrixMax11() {
- return new Alignment.Geo3D.Matrix.Max11();
- }
-
- /**
- * Create an instance of {@link Alignment.Geo3D.Matrix.Max12 }
- *
- */
- public Alignment.Geo3D.Matrix.Max12 createAlignmentGeo3DMatrixMax12() {
- return new Alignment.Geo3D.Matrix.Max12();
- }
-
- /**
- * Create an instance of {@link Alignment.Geo3D.Matrix.Max13 }
- *
- */
- public Alignment.Geo3D.Matrix.Max13 createAlignmentGeo3DMatrixMax13() {
- return new Alignment.Geo3D.Matrix.Max13();
- }
-
- /**
- * Create an instance of {@link Alignment.Geo3D.Matrix.Max21 }
- *
- */
- public Alignment.Geo3D.Matrix.Max21 createAlignmentGeo3DMatrixMax21() {
- return new Alignment.Geo3D.Matrix.Max21();
- }
-
- /**
- * Create an instance of {@link Alignment.Geo3D.Matrix.Max22 }
- *
- */
- public Alignment.Geo3D.Matrix.Max22 createAlignmentGeo3DMatrixMax22() {
- return new Alignment.Geo3D.Matrix.Max22();
- }
-
- /**
- * Create an instance of {@link Alignment.Geo3D.Matrix.Max23 }
- *
- */
- public Alignment.Geo3D.Matrix.Max23 createAlignmentGeo3DMatrixMax23() {
- return new Alignment.Geo3D.Matrix.Max23();
- }
-
- /**
- * Create an instance of {@link Alignment.Geo3D.Matrix.Max31 }
- *
- */
- public Alignment.Geo3D.Matrix.Max31 createAlignmentGeo3DMatrixMax31() {
- return new Alignment.Geo3D.Matrix.Max31();
- }
-
- /**
- * Create an instance of {@link Alignment.Geo3D.Matrix.Max32 }
- *
- */
- public Alignment.Geo3D.Matrix.Max32 createAlignmentGeo3DMatrixMax32() {
- return new Alignment.Geo3D.Matrix.Max32();
- }
-
- /**
- * Create an instance of {@link Alignment.Geo3D.Matrix.Max33 }
- *
- */
- public Alignment.Geo3D.Matrix.Max33 createAlignmentGeo3DMatrixMax33() {
- return new Alignment.Geo3D.Matrix.Max33();
- }
-
- /**
- * Create an instance of {@link Alignment.Block.Segment }
- *
- */
- public Alignment.Block.Segment createAlignmentBlockSegment() {
- return new Alignment.Block.Segment();
- }
-
- /**
- * Create an instance of {@link Alignment.AlignObject.AlignObjectDetail }
- *
- */
- public Alignment.AlignObject.AlignObjectDetail createAlignmentAlignObjectAlignObjectDetail() {
- return new Alignment.AlignObject.AlignObjectDetail();
- }
-
- /**
- * Create an instance of {@link Alignment.AlignObject.Sequence }
- *
- */
- public Alignment.AlignObject.Sequence createAlignmentAlignObjectSequence() {
- return new Alignment.AlignObject.Sequence();
- }
-
- /**
- * Create an instance of {@link Entry.Entity.EntityDetail }
- *
- */
- public Entry.Entity.EntityDetail createEntryEntityEntityDetail() {
- return new Entry.Entity.EntityDetail();
- }
-
- /**
- * Create an instance of {@link Entry.Entity.Segment.SegmentDetail }
- *
- */
- public Entry.Entity.Segment.SegmentDetail createEntryEntitySegmentSegmentDetail() {
- return new Entry.Entity.Segment.SegmentDetail();
- }
-
- /**
- * Create an instance of {@link Entry.Entity.Segment.ListMapRegion.MapRegion.Db.DbDetail }
- *
- */
- public Entry.Entity.Segment.ListMapRegion.MapRegion.Db.DbDetail createEntryEntitySegmentListMapRegionMapRegionDbDbDetail() {
- return new Entry.Entity.Segment.ListMapRegion.MapRegion.Db.DbDetail();
- }
-
- /**
- * Create an instance of {@link Entry.Entity.Segment.ListResidue.Residue.CrossRefDb }
- *
- */
- public Entry.Entity.Segment.ListResidue.Residue.CrossRefDb createEntryEntitySegmentListResidueResidueCrossRefDb() {
- return new Entry.Entity.Segment.ListResidue.Residue.CrossRefDb();
- }
-
- /**
- * Create an instance of {@link Entry.Entity.Segment.ListResidue.Residue.ResidueDetail }
- *
- */
- public Entry.Entity.Segment.ListResidue.Residue.ResidueDetail createEntryEntitySegmentListResidueResidueResidueDetail() {
- return new Entry.Entity.Segment.ListResidue.Residue.ResidueDetail();
- }
-
- /**
- * Create an instance of {@link Entry.ListDB.Db }
- *
- */
- public Entry.ListDB.Db createEntryListDBDb() {
- return new Entry.ListDB.Db();
- }
+public class ObjectFactory
+{
+
+ /**
+ * Create a new ObjectFactory that can be used to create new instances of
+ * schema derived classes for package: jalview.xml.binding.sifts
+ *
+ */
+ public ObjectFactory()
+ {
+ }
+
+ /**
+ * Create an instance of {@link Entry }
+ *
+ */
+ public Entry createEntry()
+ {
+ return new Entry();
+ }
+
+ /**
+ * Create an instance of {@link Alignment }
+ *
+ */
+ public Alignment createAlignment()
+ {
+ return new Alignment();
+ }
+
+ /**
+ * Create an instance of {@link Alignment.Geo3D }
+ *
+ */
+ public Alignment.Geo3D createAlignmentGeo3D()
+ {
+ return new Alignment.Geo3D();
+ }
+
+ /**
+ * Create an instance of {@link Alignment.Geo3D.Matrix }
+ *
+ */
+ public Alignment.Geo3D.Matrix createAlignmentGeo3DMatrix()
+ {
+ return new Alignment.Geo3D.Matrix();
+ }
+
+ /**
+ * Create an instance of {@link Alignment.Block }
+ *
+ */
+ public Alignment.Block createAlignmentBlock()
+ {
+ return new Alignment.Block();
+ }
+
+ /**
+ * Create an instance of {@link Alignment.AlignObject }
+ *
+ */
+ public Alignment.AlignObject createAlignmentAlignObject()
+ {
+ return new Alignment.AlignObject();
+ }
+
+ /**
+ * Create an instance of {@link Entry.Entity }
+ *
+ */
+ public Entry.Entity createEntryEntity()
+ {
+ return new Entry.Entity();
+ }
+
+ /**
+ * Create an instance of {@link Entry.Entity.Segment }
+ *
+ */
+ public Entry.Entity.Segment createEntryEntitySegment()
+ {
+ return new Entry.Entity.Segment();
+ }
+
+ /**
+ * Create an instance of {@link Entry.Entity.Segment.ListMapRegion }
+ *
+ */
+ public Entry.Entity.Segment.ListMapRegion createEntryEntitySegmentListMapRegion()
+ {
+ return new Entry.Entity.Segment.ListMapRegion();
+ }
+
+ /**
+ * Create an instance of {@link Entry.Entity.Segment.ListMapRegion.MapRegion }
+ *
+ */
+ public Entry.Entity.Segment.ListMapRegion.MapRegion createEntryEntitySegmentListMapRegionMapRegion()
+ {
+ return new Entry.Entity.Segment.ListMapRegion.MapRegion();
+ }
+
+ /**
+ * Create an instance of
+ * {@link Entry.Entity.Segment.ListMapRegion.MapRegion.Db }
+ *
+ */
+ public Entry.Entity.Segment.ListMapRegion.MapRegion.Db createEntryEntitySegmentListMapRegionMapRegionDb()
+ {
+ return new Entry.Entity.Segment.ListMapRegion.MapRegion.Db();
+ }
+
+ /**
+ * Create an instance of {@link Entry.Entity.Segment.ListResidue }
+ *
+ */
+ public Entry.Entity.Segment.ListResidue createEntryEntitySegmentListResidue()
+ {
+ return new Entry.Entity.Segment.ListResidue();
+ }
+
+ /**
+ * Create an instance of {@link Entry.Entity.Segment.ListResidue.Residue }
+ *
+ */
+ public Entry.Entity.Segment.ListResidue.Residue createEntryEntitySegmentListResidueResidue()
+ {
+ return new Entry.Entity.Segment.ListResidue.Residue();
+ }
+
+ /**
+ * Create an instance of {@link Entry.ListDB }
+ *
+ */
+ public Entry.ListDB createEntryListDB()
+ {
+ return new Entry.ListDB();
+ }
+
+ /**
+ * Create an instance of {@link Entry.EntryDetail }
+ *
+ */
+ public Entry.EntryDetail createEntryEntryDetail()
+ {
+ return new Entry.EntryDetail();
+ }
+
+ /**
+ * Create an instance of {@link Alignment.Score }
+ *
+ */
+ public Alignment.Score createAlignmentScore()
+ {
+ return new Alignment.Score();
+ }
+
+ /**
+ * Create an instance of {@link Alignment.Geo3D.Vector }
+ *
+ */
+ public Alignment.Geo3D.Vector createAlignmentGeo3DVector()
+ {
+ return new Alignment.Geo3D.Vector();
+ }
+
+ /**
+ * Create an instance of {@link Alignment.Geo3D.Matrix.Max11 }
+ *
+ */
+ public Alignment.Geo3D.Matrix.Max11 createAlignmentGeo3DMatrixMax11()
+ {
+ return new Alignment.Geo3D.Matrix.Max11();
+ }
+
+ /**
+ * Create an instance of {@link Alignment.Geo3D.Matrix.Max12 }
+ *
+ */
+ public Alignment.Geo3D.Matrix.Max12 createAlignmentGeo3DMatrixMax12()
+ {
+ return new Alignment.Geo3D.Matrix.Max12();
+ }
+
+ /**
+ * Create an instance of {@link Alignment.Geo3D.Matrix.Max13 }
+ *
+ */
+ public Alignment.Geo3D.Matrix.Max13 createAlignmentGeo3DMatrixMax13()
+ {
+ return new Alignment.Geo3D.Matrix.Max13();
+ }
+
+ /**
+ * Create an instance of {@link Alignment.Geo3D.Matrix.Max21 }
+ *
+ */
+ public Alignment.Geo3D.Matrix.Max21 createAlignmentGeo3DMatrixMax21()
+ {
+ return new Alignment.Geo3D.Matrix.Max21();
+ }
+
+ /**
+ * Create an instance of {@link Alignment.Geo3D.Matrix.Max22 }
+ *
+ */
+ public Alignment.Geo3D.Matrix.Max22 createAlignmentGeo3DMatrixMax22()
+ {
+ return new Alignment.Geo3D.Matrix.Max22();
+ }
+
+ /**
+ * Create an instance of {@link Alignment.Geo3D.Matrix.Max23 }
+ *
+ */
+ public Alignment.Geo3D.Matrix.Max23 createAlignmentGeo3DMatrixMax23()
+ {
+ return new Alignment.Geo3D.Matrix.Max23();
+ }
+
+ /**
+ * Create an instance of {@link Alignment.Geo3D.Matrix.Max31 }
+ *
+ */
+ public Alignment.Geo3D.Matrix.Max31 createAlignmentGeo3DMatrixMax31()
+ {
+ return new Alignment.Geo3D.Matrix.Max31();
+ }
+
+ /**
+ * Create an instance of {@link Alignment.Geo3D.Matrix.Max32 }
+ *
+ */
+ public Alignment.Geo3D.Matrix.Max32 createAlignmentGeo3DMatrixMax32()
+ {
+ return new Alignment.Geo3D.Matrix.Max32();
+ }
+
+ /**
+ * Create an instance of {@link Alignment.Geo3D.Matrix.Max33 }
+ *
+ */
+ public Alignment.Geo3D.Matrix.Max33 createAlignmentGeo3DMatrixMax33()
+ {
+ return new Alignment.Geo3D.Matrix.Max33();
+ }
+
+ /**
+ * Create an instance of {@link Alignment.Block.Segment }
+ *
+ */
+ public Alignment.Block.Segment createAlignmentBlockSegment()
+ {
+ return new Alignment.Block.Segment();
+ }
+
+ /**
+ * Create an instance of {@link Alignment.AlignObject.AlignObjectDetail }
+ *
+ */
+ public Alignment.AlignObject.AlignObjectDetail createAlignmentAlignObjectAlignObjectDetail()
+ {
+ return new Alignment.AlignObject.AlignObjectDetail();
+ }
+
+ /**
+ * Create an instance of {@link Alignment.AlignObject.Sequence }
+ *
+ */
+ public Alignment.AlignObject.Sequence createAlignmentAlignObjectSequence()
+ {
+ return new Alignment.AlignObject.Sequence();
+ }
+
+ /**
+ * Create an instance of {@link Entry.Entity.EntityDetail }
+ *
+ */
+ public Entry.Entity.EntityDetail createEntryEntityEntityDetail()
+ {
+ return new Entry.Entity.EntityDetail();
+ }
+
+ /**
+ * Create an instance of {@link Entry.Entity.Segment.SegmentDetail }
+ *
+ */
+ public Entry.Entity.Segment.SegmentDetail createEntryEntitySegmentSegmentDetail()
+ {
+ return new Entry.Entity.Segment.SegmentDetail();
+ }
+
+ /**
+ * Create an instance of
+ * {@link Entry.Entity.Segment.ListMapRegion.MapRegion.Db.DbDetail }
+ *
+ */
+ public Entry.Entity.Segment.ListMapRegion.MapRegion.Db.DbDetail createEntryEntitySegmentListMapRegionMapRegionDbDbDetail()
+ {
+ return new Entry.Entity.Segment.ListMapRegion.MapRegion.Db.DbDetail();
+ }
+
+ /**
+ * Create an instance of
+ * {@link Entry.Entity.Segment.ListResidue.Residue.CrossRefDb }
+ *
+ */
+ public Entry.Entity.Segment.ListResidue.Residue.CrossRefDb createEntryEntitySegmentListResidueResidueCrossRefDb()
+ {
+ return new Entry.Entity.Segment.ListResidue.Residue.CrossRefDb();
+ }
+
+ /**
+ * Create an instance of
+ * {@link Entry.Entity.Segment.ListResidue.Residue.ResidueDetail }
+ *
+ */
+ public Entry.Entity.Segment.ListResidue.Residue.ResidueDetail createEntryEntitySegmentListResidueResidueResidueDetail()
+ {
+ return new Entry.Entity.Segment.ListResidue.Residue.ResidueDetail();
+ }
+
+ /**
+ * Create an instance of {@link Entry.ListDB.Db }
+ *
+ */
+ public Entry.ListDB.Db createEntryListDBDb()
+ {
+ return new Entry.ListDB.Db();
+ }
}
// Generated on: 2015.10.09 at 03:18:33 PM BST
//
-@javax.xml.bind.annotation.XmlSchema(namespace = "http://www.ebi.ac.uk/pdbe/docs/sifts/eFamily.xsd", elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED)
+@javax.xml.bind.annotation.XmlSchema(
+ namespace = "http://www.ebi.ac.uk/pdbe/docs/sifts/eFamily.xsd",
+ elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED)
package jalview.xml.binding.sifts;
// Generated on: 2019.04.05 at 08:01:44 AM BST
//
-
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlType;
-
/**
- * Describes different types of citations.
- * Equivalent to the flat file RX-, RG-, RA-, RT- and RL-lines.
+ * Describes different types of citations. Equivalent to the flat file RX-, RG-,
+ * RA-, RT- and RL-lines.
*
- * <p>Java class for citationType complex type.
+ * <p>
+ * Java class for citationType complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
*
* <pre>
* <complexType name="citationType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "citationType", propOrder = {
- "title",
- "editorList",
- "authorList",
- "locator",
- "dbReference"
-})
-public class CitationType {
-
- protected String title;
- protected NameListType editorList;
- protected NameListType authorList;
- protected String locator;
- protected List<DbReferenceType> dbReference;
- @XmlAttribute(name = "type", required = true)
- protected String type;
- @XmlAttribute(name = "date")
- protected String date;
- @XmlAttribute(name = "name")
- protected String name;
- @XmlAttribute(name = "volume")
- protected String volume;
- @XmlAttribute(name = "first")
- protected String first;
- @XmlAttribute(name = "last")
- protected String last;
- @XmlAttribute(name = "publisher")
- protected String publisher;
- @XmlAttribute(name = "city")
- protected String city;
- @XmlAttribute(name = "db")
- protected String db;
- @XmlAttribute(name = "number")
- protected String number;
- @XmlAttribute(name = "institute")
- protected String institute;
- @XmlAttribute(name = "country")
- protected String country;
-
- /**
- * Gets the value of the title property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getTitle() {
- return title;
- }
-
- /**
- * Sets the value of the title property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setTitle(String value) {
- this.title = value;
- }
-
- /**
- * Gets the value of the editorList property.
- *
- * @return
- * possible object is
- * {@link NameListType }
- *
- */
- public NameListType getEditorList() {
- return editorList;
- }
-
- /**
- * Sets the value of the editorList property.
- *
- * @param value
- * allowed object is
- * {@link NameListType }
- *
- */
- public void setEditorList(NameListType value) {
- this.editorList = value;
- }
-
- /**
- * Gets the value of the authorList property.
- *
- * @return
- * possible object is
- * {@link NameListType }
- *
- */
- public NameListType getAuthorList() {
- return authorList;
- }
-
- /**
- * Sets the value of the authorList property.
- *
- * @param value
- * allowed object is
- * {@link NameListType }
- *
- */
- public void setAuthorList(NameListType value) {
- this.authorList = value;
- }
-
- /**
- * Gets the value of the locator property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getLocator() {
- return locator;
- }
-
- /**
- * Sets the value of the locator property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setLocator(String value) {
- this.locator = value;
- }
-
- /**
- * Gets the value of the dbReference property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the dbReference property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getDbReference().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link DbReferenceType }
- *
- *
- */
- public List<DbReferenceType> getDbReference() {
- if (dbReference == null) {
- dbReference = new ArrayList<DbReferenceType>();
- }
- return this.dbReference;
- }
-
- /**
- * Gets the value of the type property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getType() {
- return type;
- }
-
- /**
- * Sets the value of the type property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setType(String value) {
- this.type = value;
- }
-
- /**
- * Gets the value of the date property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDate() {
- return date;
- }
-
- /**
- * Sets the value of the date property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDate(String value) {
- this.date = value;
- }
-
- /**
- * Gets the value of the name property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getName() {
- return name;
- }
-
- /**
- * Sets the value of the name property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setName(String value) {
- this.name = value;
- }
-
- /**
- * Gets the value of the volume property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getVolume() {
- return volume;
- }
-
- /**
- * Sets the value of the volume property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setVolume(String value) {
- this.volume = value;
- }
-
- /**
- * Gets the value of the first property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getFirst() {
- return first;
- }
-
- /**
- * Sets the value of the first property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setFirst(String value) {
- this.first = value;
- }
-
- /**
- * Gets the value of the last property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getLast() {
- return last;
- }
-
- /**
- * Sets the value of the last property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setLast(String value) {
- this.last = value;
- }
-
- /**
- * Gets the value of the publisher property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getPublisher() {
- return publisher;
- }
-
- /**
- * Sets the value of the publisher property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setPublisher(String value) {
- this.publisher = value;
- }
-
- /**
- * Gets the value of the city property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getCity() {
- return city;
- }
-
- /**
- * Sets the value of the city property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setCity(String value) {
- this.city = value;
- }
-
- /**
- * Gets the value of the db property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDb() {
- return db;
- }
-
- /**
- * Sets the value of the db property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDb(String value) {
- this.db = value;
- }
-
- /**
- * Gets the value of the number property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getNumber() {
- return number;
- }
-
- /**
- * Sets the value of the number property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setNumber(String value) {
- this.number = value;
- }
-
- /**
- * Gets the value of the institute property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getInstitute() {
- return institute;
- }
-
- /**
- * Sets the value of the institute property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setInstitute(String value) {
- this.institute = value;
- }
-
- /**
- * Gets the value of the country property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getCountry() {
- return country;
- }
-
- /**
- * Sets the value of the country property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setCountry(String value) {
- this.country = value;
- }
+@XmlType(
+ name = "citationType",
+ propOrder =
+ { "title", "editorList", "authorList", "locator", "dbReference" })
+public class CitationType
+{
+
+ protected String title;
+
+ protected NameListType editorList;
+
+ protected NameListType authorList;
+
+ protected String locator;
+
+ protected List<DbReferenceType> dbReference;
+
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
+
+ @XmlAttribute(name = "date")
+ protected String date;
+
+ @XmlAttribute(name = "name")
+ protected String name;
+
+ @XmlAttribute(name = "volume")
+ protected String volume;
+
+ @XmlAttribute(name = "first")
+ protected String first;
+
+ @XmlAttribute(name = "last")
+ protected String last;
+
+ @XmlAttribute(name = "publisher")
+ protected String publisher;
+
+ @XmlAttribute(name = "city")
+ protected String city;
+
+ @XmlAttribute(name = "db")
+ protected String db;
+
+ @XmlAttribute(name = "number")
+ protected String number;
+
+ @XmlAttribute(name = "institute")
+ protected String institute;
+
+ @XmlAttribute(name = "country")
+ protected String country;
+
+ /**
+ * Gets the value of the title property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getTitle()
+ {
+ return title;
+ }
+
+ /**
+ * Sets the value of the title property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setTitle(String value)
+ {
+ this.title = value;
+ }
+
+ /**
+ * Gets the value of the editorList property.
+ *
+ * @return possible object is {@link NameListType }
+ *
+ */
+ public NameListType getEditorList()
+ {
+ return editorList;
+ }
+
+ /**
+ * Sets the value of the editorList property.
+ *
+ * @param value
+ * allowed object is {@link NameListType }
+ *
+ */
+ public void setEditorList(NameListType value)
+ {
+ this.editorList = value;
+ }
+
+ /**
+ * Gets the value of the authorList property.
+ *
+ * @return possible object is {@link NameListType }
+ *
+ */
+ public NameListType getAuthorList()
+ {
+ return authorList;
+ }
+
+ /**
+ * Sets the value of the authorList property.
+ *
+ * @param value
+ * allowed object is {@link NameListType }
+ *
+ */
+ public void setAuthorList(NameListType value)
+ {
+ this.authorList = value;
+ }
+
+ /**
+ * Gets the value of the locator property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getLocator()
+ {
+ return locator;
+ }
+
+ /**
+ * Sets the value of the locator property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setLocator(String value)
+ {
+ this.locator = value;
+ }
+
+ /**
+ * Gets the value of the dbReference property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the dbReference property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getDbReference().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link DbReferenceType }
+ *
+ *
+ */
+ public List<DbReferenceType> getDbReference()
+ {
+ if (dbReference == null)
+ {
+ dbReference = new ArrayList<DbReferenceType>();
+ }
+ return this.dbReference;
+ }
+
+ /**
+ * Gets the value of the type property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getType()
+ {
+ return type;
+ }
+
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setType(String value)
+ {
+ this.type = value;
+ }
+
+ /**
+ * Gets the value of the date property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDate()
+ {
+ return date;
+ }
+
+ /**
+ * Sets the value of the date property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setDate(String value)
+ {
+ this.date = value;
+ }
+
+ /**
+ * Gets the value of the name property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getName()
+ {
+ return name;
+ }
+
+ /**
+ * Sets the value of the name property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setName(String value)
+ {
+ this.name = value;
+ }
+
+ /**
+ * Gets the value of the volume property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getVolume()
+ {
+ return volume;
+ }
+
+ /**
+ * Sets the value of the volume property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setVolume(String value)
+ {
+ this.volume = value;
+ }
+
+ /**
+ * Gets the value of the first property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getFirst()
+ {
+ return first;
+ }
+
+ /**
+ * Sets the value of the first property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setFirst(String value)
+ {
+ this.first = value;
+ }
+
+ /**
+ * Gets the value of the last property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getLast()
+ {
+ return last;
+ }
+
+ /**
+ * Sets the value of the last property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setLast(String value)
+ {
+ this.last = value;
+ }
+
+ /**
+ * Gets the value of the publisher property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getPublisher()
+ {
+ return publisher;
+ }
+
+ /**
+ * Sets the value of the publisher property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setPublisher(String value)
+ {
+ this.publisher = value;
+ }
+
+ /**
+ * Gets the value of the city property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getCity()
+ {
+ return city;
+ }
+
+ /**
+ * Sets the value of the city property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setCity(String value)
+ {
+ this.city = value;
+ }
+
+ /**
+ * Gets the value of the db property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDb()
+ {
+ return db;
+ }
+
+ /**
+ * Sets the value of the db property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setDb(String value)
+ {
+ this.db = value;
+ }
+
+ /**
+ * Gets the value of the number property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getNumber()
+ {
+ return number;
+ }
+
+ /**
+ * Sets the value of the number property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setNumber(String value)
+ {
+ this.number = value;
+ }
+
+ /**
+ * Gets the value of the institute property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getInstitute()
+ {
+ return institute;
+ }
+
+ /**
+ * Sets the value of the institute property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setInstitute(String value)
+ {
+ this.institute = value;
+ }
+
+ /**
+ * Gets the value of the country property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getCountry()
+ {
+ return country;
+ }
+
+ /**
+ * Sets the value of the country property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setCountry(String value)
+ {
+ this.country = value;
+ }
}
// Generated on: 2019.04.05 at 08:01:44 AM BST
//
-
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
-
/**
* Describes a cofactor.
*
- * <p>Java class for cofactorType complex type.
+ * <p>
+ * Java class for cofactorType complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
*
* <pre>
* <complexType name="cofactorType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "cofactorType", propOrder = {
- "name",
- "dbReference"
-})
-public class CofactorType {
+@XmlType(name = "cofactorType", propOrder = { "name", "dbReference" })
+public class CofactorType
+{
- @XmlElement(required = true)
- protected String name;
- @XmlElement(required = true)
- protected DbReferenceType dbReference;
- @XmlAttribute(name = "evidence")
- protected List<Integer> evidence;
+ @XmlElement(required = true)
+ protected String name;
- /**
- * Gets the value of the name property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getName() {
- return name;
- }
+ @XmlElement(required = true)
+ protected DbReferenceType dbReference;
- /**
- * Sets the value of the name property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setName(String value) {
- this.name = value;
- }
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
- /**
- * Gets the value of the dbReference property.
- *
- * @return
- * possible object is
- * {@link DbReferenceType }
- *
- */
- public DbReferenceType getDbReference() {
- return dbReference;
- }
+ /**
+ * Gets the value of the name property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getName()
+ {
+ return name;
+ }
- /**
- * Sets the value of the dbReference property.
- *
- * @param value
- * allowed object is
- * {@link DbReferenceType }
- *
- */
- public void setDbReference(DbReferenceType value) {
- this.dbReference = value;
- }
+ /**
+ * Sets the value of the name property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setName(String value)
+ {
+ this.name = value;
+ }
+
+ /**
+ * Gets the value of the dbReference property.
+ *
+ * @return possible object is {@link DbReferenceType }
+ *
+ */
+ public DbReferenceType getDbReference()
+ {
+ return dbReference;
+ }
+
+ /**
+ * Sets the value of the dbReference property.
+ *
+ * @param value
+ * allowed object is {@link DbReferenceType }
+ *
+ */
+ public void setDbReference(DbReferenceType value)
+ {
+ this.dbReference = value;
+ }
- /**
- * Gets the value of the evidence property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the evidence property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getEvidence().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Integer }
- *
- *
- */
- public List<Integer> getEvidence() {
- if (evidence == null) {
- evidence = new ArrayList<Integer>();
- }
- return this.evidence;
+ /**
+ * Gets the value of the evidence property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getEvidence()
+ {
+ if (evidence == null)
+ {
+ evidence = new ArrayList<Integer>();
}
+ return this.evidence;
+ }
}
// Generated on: 2019.04.05 at 08:01:44 AM BST
//
-
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlSchemaType;
import javax.xml.bind.annotation.XmlType;
-
/**
- * Describes different types of general annotations.
- * Equivalent to the flat file CC-line.
+ * Describes different types of general annotations. Equivalent to the flat file
+ * CC-line.
*
- * <p>Java class for commentType complex type.
+ * <p>
+ * Java class for commentType complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
*
* <pre>
* <complexType name="commentType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "commentType", propOrder = {
- "molecule",
- "absorption",
- "kinetics",
- "phDependence",
- "redoxPotential",
- "temperatureDependence",
- "reaction",
- "physiologicalReaction",
- "cofactor",
- "subcellularLocation",
- "conflict",
- "link",
- "event",
- "isoform",
- "interactant",
- "organismsDiffer",
- "experiments",
- "disease",
- "location",
- "text"
-})
-public class CommentType {
-
- protected MoleculeType molecule;
- protected CommentType.Absorption absorption;
- protected CommentType.Kinetics kinetics;
- protected CommentType.PhDependence phDependence;
- protected CommentType.RedoxPotential redoxPotential;
- protected CommentType.TemperatureDependence temperatureDependence;
- protected ReactionType reaction;
- protected List<PhysiologicalReactionType> physiologicalReaction;
- protected List<CofactorType> cofactor;
- protected List<SubcellularLocationType> subcellularLocation;
- protected CommentType.Conflict conflict;
- protected List<CommentType.Link> link;
- protected List<EventType> event;
- protected List<IsoformType> isoform;
- protected List<InteractantType> interactant;
- @XmlElement(defaultValue = "false")
- protected Boolean organismsDiffer;
- protected Integer experiments;
- protected CommentType.Disease disease;
- protected List<LocationType> location;
- protected List<EvidencedStringType> text;
- @XmlAttribute(name = "type", required = true)
- protected String type;
- @XmlAttribute(name = "locationType")
- protected String locationType;
- @XmlAttribute(name = "name")
- protected String name;
- @XmlAttribute(name = "mass")
- protected Float mass;
- @XmlAttribute(name = "error")
- protected String error;
- @XmlAttribute(name = "method")
- protected String method;
- @XmlAttribute(name = "evidence")
- protected List<Integer> evidence;
+@XmlType(
+ name = "commentType",
+ propOrder =
+ { "molecule", "absorption", "kinetics", "phDependence", "redoxPotential",
+ "temperatureDependence", "reaction", "physiologicalReaction",
+ "cofactor", "subcellularLocation", "conflict", "link", "event",
+ "isoform", "interactant", "organismsDiffer", "experiments", "disease",
+ "location", "text" })
+public class CommentType
+{
- /**
- * Gets the value of the molecule property.
- *
- * @return
- * possible object is
- * {@link MoleculeType }
- *
- */
- public MoleculeType getMolecule() {
- return molecule;
- }
+ protected MoleculeType molecule;
- /**
- * Sets the value of the molecule property.
- *
- * @param value
- * allowed object is
- * {@link MoleculeType }
- *
- */
- public void setMolecule(MoleculeType value) {
- this.molecule = value;
- }
+ protected CommentType.Absorption absorption;
- /**
- * Gets the value of the absorption property.
- *
- * @return
- * possible object is
- * {@link CommentType.Absorption }
- *
- */
- public CommentType.Absorption getAbsorption() {
- return absorption;
- }
+ protected CommentType.Kinetics kinetics;
- /**
- * Sets the value of the absorption property.
- *
- * @param value
- * allowed object is
- * {@link CommentType.Absorption }
- *
- */
- public void setAbsorption(CommentType.Absorption value) {
- this.absorption = value;
- }
+ protected CommentType.PhDependence phDependence;
- /**
- * Gets the value of the kinetics property.
- *
- * @return
- * possible object is
- * {@link CommentType.Kinetics }
- *
- */
- public CommentType.Kinetics getKinetics() {
- return kinetics;
- }
+ protected CommentType.RedoxPotential redoxPotential;
- /**
- * Sets the value of the kinetics property.
- *
- * @param value
- * allowed object is
- * {@link CommentType.Kinetics }
- *
- */
- public void setKinetics(CommentType.Kinetics value) {
- this.kinetics = value;
- }
+ protected CommentType.TemperatureDependence temperatureDependence;
- /**
- * Gets the value of the phDependence property.
- *
- * @return
- * possible object is
- * {@link CommentType.PhDependence }
- *
- */
- public CommentType.PhDependence getPhDependence() {
- return phDependence;
- }
+ protected ReactionType reaction;
- /**
- * Sets the value of the phDependence property.
- *
- * @param value
- * allowed object is
- * {@link CommentType.PhDependence }
- *
- */
- public void setPhDependence(CommentType.PhDependence value) {
- this.phDependence = value;
- }
+ protected List<PhysiologicalReactionType> physiologicalReaction;
- /**
- * Gets the value of the redoxPotential property.
- *
- * @return
- * possible object is
- * {@link CommentType.RedoxPotential }
- *
- */
- public CommentType.RedoxPotential getRedoxPotential() {
- return redoxPotential;
- }
+ protected List<CofactorType> cofactor;
- /**
- * Sets the value of the redoxPotential property.
- *
- * @param value
- * allowed object is
- * {@link CommentType.RedoxPotential }
- *
- */
- public void setRedoxPotential(CommentType.RedoxPotential value) {
- this.redoxPotential = value;
- }
+ protected List<SubcellularLocationType> subcellularLocation;
- /**
- * Gets the value of the temperatureDependence property.
- *
- * @return
- * possible object is
- * {@link CommentType.TemperatureDependence }
- *
- */
- public CommentType.TemperatureDependence getTemperatureDependence() {
- return temperatureDependence;
- }
+ protected CommentType.Conflict conflict;
- /**
- * Sets the value of the temperatureDependence property.
- *
- * @param value
- * allowed object is
- * {@link CommentType.TemperatureDependence }
- *
- */
- public void setTemperatureDependence(CommentType.TemperatureDependence value) {
- this.temperatureDependence = value;
+ protected List<CommentType.Link> link;
+
+ protected List<EventType> event;
+
+ protected List<IsoformType> isoform;
+
+ protected List<InteractantType> interactant;
+
+ @XmlElement(defaultValue = "false")
+ protected Boolean organismsDiffer;
+
+ protected Integer experiments;
+
+ protected CommentType.Disease disease;
+
+ protected List<LocationType> location;
+
+ protected List<EvidencedStringType> text;
+
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
+
+ @XmlAttribute(name = "locationType")
+ protected String locationType;
+
+ @XmlAttribute(name = "name")
+ protected String name;
+
+ @XmlAttribute(name = "mass")
+ protected Float mass;
+
+ @XmlAttribute(name = "error")
+ protected String error;
+
+ @XmlAttribute(name = "method")
+ protected String method;
+
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
+
+ /**
+ * Gets the value of the molecule property.
+ *
+ * @return possible object is {@link MoleculeType }
+ *
+ */
+ public MoleculeType getMolecule()
+ {
+ return molecule;
+ }
+
+ /**
+ * Sets the value of the molecule property.
+ *
+ * @param value
+ * allowed object is {@link MoleculeType }
+ *
+ */
+ public void setMolecule(MoleculeType value)
+ {
+ this.molecule = value;
+ }
+
+ /**
+ * Gets the value of the absorption property.
+ *
+ * @return possible object is {@link CommentType.Absorption }
+ *
+ */
+ public CommentType.Absorption getAbsorption()
+ {
+ return absorption;
+ }
+
+ /**
+ * Sets the value of the absorption property.
+ *
+ * @param value
+ * allowed object is {@link CommentType.Absorption }
+ *
+ */
+ public void setAbsorption(CommentType.Absorption value)
+ {
+ this.absorption = value;
+ }
+
+ /**
+ * Gets the value of the kinetics property.
+ *
+ * @return possible object is {@link CommentType.Kinetics }
+ *
+ */
+ public CommentType.Kinetics getKinetics()
+ {
+ return kinetics;
+ }
+
+ /**
+ * Sets the value of the kinetics property.
+ *
+ * @param value
+ * allowed object is {@link CommentType.Kinetics }
+ *
+ */
+ public void setKinetics(CommentType.Kinetics value)
+ {
+ this.kinetics = value;
+ }
+
+ /**
+ * Gets the value of the phDependence property.
+ *
+ * @return possible object is {@link CommentType.PhDependence }
+ *
+ */
+ public CommentType.PhDependence getPhDependence()
+ {
+ return phDependence;
+ }
+
+ /**
+ * Sets the value of the phDependence property.
+ *
+ * @param value
+ * allowed object is {@link CommentType.PhDependence }
+ *
+ */
+ public void setPhDependence(CommentType.PhDependence value)
+ {
+ this.phDependence = value;
+ }
+
+ /**
+ * Gets the value of the redoxPotential property.
+ *
+ * @return possible object is {@link CommentType.RedoxPotential }
+ *
+ */
+ public CommentType.RedoxPotential getRedoxPotential()
+ {
+ return redoxPotential;
+ }
+
+ /**
+ * Sets the value of the redoxPotential property.
+ *
+ * @param value
+ * allowed object is {@link CommentType.RedoxPotential }
+ *
+ */
+ public void setRedoxPotential(CommentType.RedoxPotential value)
+ {
+ this.redoxPotential = value;
+ }
+
+ /**
+ * Gets the value of the temperatureDependence property.
+ *
+ * @return possible object is {@link CommentType.TemperatureDependence }
+ *
+ */
+ public CommentType.TemperatureDependence getTemperatureDependence()
+ {
+ return temperatureDependence;
+ }
+
+ /**
+ * Sets the value of the temperatureDependence property.
+ *
+ * @param value
+ * allowed object is {@link CommentType.TemperatureDependence }
+ *
+ */
+ public void setTemperatureDependence(
+ CommentType.TemperatureDependence value)
+ {
+ this.temperatureDependence = value;
+ }
+
+ /**
+ * Gets the value of the reaction property.
+ *
+ * @return possible object is {@link ReactionType }
+ *
+ */
+ public ReactionType getReaction()
+ {
+ return reaction;
+ }
+
+ /**
+ * Sets the value of the reaction property.
+ *
+ * @param value
+ * allowed object is {@link ReactionType }
+ *
+ */
+ public void setReaction(ReactionType value)
+ {
+ this.reaction = value;
+ }
+
+ /**
+ * Gets the value of the physiologicalReaction property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the physiologicalReaction property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getPhysiologicalReaction().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link PhysiologicalReactionType }
+ *
+ *
+ */
+ public List<PhysiologicalReactionType> getPhysiologicalReaction()
+ {
+ if (physiologicalReaction == null)
+ {
+ physiologicalReaction = new ArrayList<PhysiologicalReactionType>();
+ }
+ return this.physiologicalReaction;
+ }
+
+ /**
+ * Gets the value of the cofactor property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the cofactor property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getCofactor().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link CofactorType }
+ *
+ *
+ */
+ public List<CofactorType> getCofactor()
+ {
+ if (cofactor == null)
+ {
+ cofactor = new ArrayList<CofactorType>();
+ }
+ return this.cofactor;
+ }
+
+ /**
+ * Gets the value of the subcellularLocation property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the subcellularLocation property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getSubcellularLocation().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link SubcellularLocationType }
+ *
+ *
+ */
+ public List<SubcellularLocationType> getSubcellularLocation()
+ {
+ if (subcellularLocation == null)
+ {
+ subcellularLocation = new ArrayList<SubcellularLocationType>();
+ }
+ return this.subcellularLocation;
+ }
+
+ /**
+ * Gets the value of the conflict property.
+ *
+ * @return possible object is {@link CommentType.Conflict }
+ *
+ */
+ public CommentType.Conflict getConflict()
+ {
+ return conflict;
+ }
+
+ /**
+ * Sets the value of the conflict property.
+ *
+ * @param value
+ * allowed object is {@link CommentType.Conflict }
+ *
+ */
+ public void setConflict(CommentType.Conflict value)
+ {
+ this.conflict = value;
+ }
+
+ /**
+ * Gets the value of the link property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the link property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getLink().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link CommentType.Link }
+ *
+ *
+ */
+ public List<CommentType.Link> getLink()
+ {
+ if (link == null)
+ {
+ link = new ArrayList<CommentType.Link>();
}
+ return this.link;
+ }
+
+ /**
+ * Gets the value of the event property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the event property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getEvent().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link EventType }
+ *
+ *
+ */
+ public List<EventType> getEvent()
+ {
+ if (event == null)
+ {
+ event = new ArrayList<EventType>();
+ }
+ return this.event;
+ }
+
+ /**
+ * Gets the value of the isoform property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the isoform property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getIsoform().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link IsoformType
+ * }
+ *
+ *
+ */
+ public List<IsoformType> getIsoform()
+ {
+ if (isoform == null)
+ {
+ isoform = new ArrayList<IsoformType>();
+ }
+ return this.isoform;
+ }
+
+ /**
+ * Gets the value of the interactant property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the interactant property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getInteractant().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link InteractantType }
+ *
+ *
+ */
+ public List<InteractantType> getInteractant()
+ {
+ if (interactant == null)
+ {
+ interactant = new ArrayList<InteractantType>();
+ }
+ return this.interactant;
+ }
+
+ /**
+ * Gets the value of the organismsDiffer property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isOrganismsDiffer()
+ {
+ return organismsDiffer;
+ }
+
+ /**
+ * Sets the value of the organismsDiffer property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setOrganismsDiffer(Boolean value)
+ {
+ this.organismsDiffer = value;
+ }
+
+ /**
+ * Gets the value of the experiments property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getExperiments()
+ {
+ return experiments;
+ }
+
+ /**
+ * Sets the value of the experiments property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setExperiments(Integer value)
+ {
+ this.experiments = value;
+ }
+
+ /**
+ * Gets the value of the disease property.
+ *
+ * @return possible object is {@link CommentType.Disease }
+ *
+ */
+ public CommentType.Disease getDisease()
+ {
+ return disease;
+ }
+
+ /**
+ * Sets the value of the disease property.
+ *
+ * @param value
+ * allowed object is {@link CommentType.Disease }
+ *
+ */
+ public void setDisease(CommentType.Disease value)
+ {
+ this.disease = value;
+ }
+
+ /**
+ * Gets the value of the location property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the location property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getLocation().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link LocationType }
+ *
+ *
+ */
+ public List<LocationType> getLocation()
+ {
+ if (location == null)
+ {
+ location = new ArrayList<LocationType>();
+ }
+ return this.location;
+ }
+
+ /**
+ * Gets the value of the text property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the text property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getText().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getText()
+ {
+ if (text == null)
+ {
+ text = new ArrayList<EvidencedStringType>();
+ }
+ return this.text;
+ }
+
+ /**
+ * Gets the value of the type property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getType()
+ {
+ return type;
+ }
+
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setType(String value)
+ {
+ this.type = value;
+ }
+
+ /**
+ * Gets the value of the locationType property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getLocationType()
+ {
+ return locationType;
+ }
+
+ /**
+ * Sets the value of the locationType property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setLocationType(String value)
+ {
+ this.locationType = value;
+ }
+
+ /**
+ * Gets the value of the name property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getName()
+ {
+ return name;
+ }
+
+ /**
+ * Sets the value of the name property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setName(String value)
+ {
+ this.name = value;
+ }
+
+ /**
+ * Gets the value of the mass property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getMass()
+ {
+ return mass;
+ }
+
+ /**
+ * Sets the value of the mass property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setMass(Float value)
+ {
+ this.mass = value;
+ }
+
+ /**
+ * Gets the value of the error property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getError()
+ {
+ return error;
+ }
+
+ /**
+ * Sets the value of the error property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setError(String value)
+ {
+ this.error = value;
+ }
+
+ /**
+ * Gets the value of the method property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getMethod()
+ {
+ return method;
+ }
+
+ /**
+ * Sets the value of the method property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setMethod(String value)
+ {
+ this.method = value;
+ }
+
+ /**
+ * Gets the value of the evidence property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getEvidence()
+ {
+ if (evidence == null)
+ {
+ evidence = new ArrayList<Integer>();
+ }
+ return this.evidence;
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="max" type="{http://uniprot.org/uniprot}evidencedStringType" minOccurs="0"/>
+ * <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "max", "text" })
+ public static class Absorption
+ {
+
+ protected EvidencedStringType max;
+
+ protected List<EvidencedStringType> text;
/**
- * Gets the value of the reaction property.
+ * Gets the value of the max property.
+ *
+ * @return possible object is {@link EvidencedStringType }
*
- * @return
- * possible object is
- * {@link ReactionType }
- *
*/
- public ReactionType getReaction() {
- return reaction;
+ public EvidencedStringType getMax()
+ {
+ return max;
}
/**
- * Sets the value of the reaction property.
+ * Sets the value of the max property.
*
* @param value
- * allowed object is
- * {@link ReactionType }
- *
+ * allowed object is {@link EvidencedStringType }
+ *
*/
- public void setReaction(ReactionType value) {
- this.reaction = value;
+ public void setMax(EvidencedStringType value)
+ {
+ this.max = value;
}
/**
- * Gets the value of the physiologicalReaction property.
+ * Gets the value of the text property.
*
* <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the physiologicalReaction property.
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the text property.
*
* <p>
* For example, to add a new item, do as follows:
+ *
* <pre>
- * getPhysiologicalReaction().add(newItem);
+ * getText().add(newItem);
* </pre>
*
*
* <p>
* Objects of the following type(s) are allowed in the list
- * {@link PhysiologicalReactionType }
+ * {@link EvidencedStringType }
*
*
*/
- public List<PhysiologicalReactionType> getPhysiologicalReaction() {
- if (physiologicalReaction == null) {
- physiologicalReaction = new ArrayList<PhysiologicalReactionType>();
- }
- return this.physiologicalReaction;
+ public List<EvidencedStringType> getText()
+ {
+ if (text == null)
+ {
+ text = new ArrayList<EvidencedStringType>();
+ }
+ return this.text;
}
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="sequence" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="resource" use="required">
+ * <simpleType>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ * <enumeration value="EMBL-CDS"/>
+ * <enumeration value="EMBL"/>
+ * </restriction>
+ * </simpleType>
+ * </attribute>
+ * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="version" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attribute name="type" use="required">
+ * <simpleType>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ * <enumeration value="frameshift"/>
+ * <enumeration value="erroneous initiation"/>
+ * <enumeration value="erroneous termination"/>
+ * <enumeration value="erroneous gene model prediction"/>
+ * <enumeration value="erroneous translation"/>
+ * <enumeration value="miscellaneous discrepancy"/>
+ * </restriction>
+ * </simpleType>
+ * </attribute>
+ * <attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "sequence" })
+ public static class Conflict
+ {
+
+ protected CommentType.Conflict.Sequence sequence;
+
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
+
+ @XmlAttribute(name = "ref")
+ protected String ref;
+
/**
- * Gets the value of the cofactor property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the cofactor property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getCofactor().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link CofactorType }
+ * Gets the value of the sequence property.
*
+ * @return possible object is {@link CommentType.Conflict.Sequence }
*
*/
- public List<CofactorType> getCofactor() {
- if (cofactor == null) {
- cofactor = new ArrayList<CofactorType>();
- }
- return this.cofactor;
+ public CommentType.Conflict.Sequence getSequence()
+ {
+ return sequence;
}
/**
- * Gets the value of the subcellularLocation property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the subcellularLocation property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getSubcellularLocation().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link SubcellularLocationType }
+ * Sets the value of the sequence property.
*
+ * @param value
+ * allowed object is {@link CommentType.Conflict.Sequence }
*
*/
- public List<SubcellularLocationType> getSubcellularLocation() {
- if (subcellularLocation == null) {
- subcellularLocation = new ArrayList<SubcellularLocationType>();
- }
- return this.subcellularLocation;
+ public void setSequence(CommentType.Conflict.Sequence value)
+ {
+ this.sequence = value;
}
/**
- * Gets the value of the conflict property.
+ * Gets the value of the type property.
*
- * @return
- * possible object is
- * {@link CommentType.Conflict }
- *
- */
- public CommentType.Conflict getConflict() {
- return conflict;
- }
-
- /**
- * Sets the value of the conflict property.
+ * @return possible object is {@link String }
*
- * @param value
- * allowed object is
- * {@link CommentType.Conflict }
- *
*/
- public void setConflict(CommentType.Conflict value) {
- this.conflict = value;
+ public String getType()
+ {
+ return type;
}
/**
- * Gets the value of the link property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the link property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getLink().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link CommentType.Link }
+ * Sets the value of the type property.
*
+ * @param value
+ * allowed object is {@link String }
*
*/
- public List<CommentType.Link> getLink() {
- if (link == null) {
- link = new ArrayList<CommentType.Link>();
- }
- return this.link;
+ public void setType(String value)
+ {
+ this.type = value;
}
/**
- * Gets the value of the event property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the event property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getEvent().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EventType }
+ * Gets the value of the ref property.
*
+ * @return possible object is {@link String }
*
*/
- public List<EventType> getEvent() {
- if (event == null) {
- event = new ArrayList<EventType>();
- }
- return this.event;
+ public String getRef()
+ {
+ return ref;
}
/**
- * Gets the value of the isoform property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the isoform property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getIsoform().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link IsoformType }
+ * Sets the value of the ref property.
*
+ * @param value
+ * allowed object is {@link String }
*
*/
- public List<IsoformType> getIsoform() {
- if (isoform == null) {
- isoform = new ArrayList<IsoformType>();
- }
- return this.isoform;
+ public void setRef(String value)
+ {
+ this.ref = value;
}
/**
- * Gets the value of the interactant property.
- *
* <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the interactant property.
+ * Java class for anonymous complex type.
*
* <p>
- * For example, to add a new item, do as follows:
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
* <pre>
- * getInteractant().add(newItem);
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="resource" use="required">
+ * <simpleType>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ * <enumeration value="EMBL-CDS"/>
+ * <enumeration value="EMBL"/>
+ * </restriction>
+ * </simpleType>
+ * </attribute>
+ * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="version" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
* </pre>
*
*
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link InteractantType }
- *
- *
*/
- public List<InteractantType> getInteractant() {
- if (interactant == null) {
- interactant = new ArrayList<InteractantType>();
- }
- return this.interactant;
- }
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Sequence
+ {
+
+ @XmlAttribute(name = "resource", required = true)
+ protected String resource;
+
+ @XmlAttribute(name = "id", required = true)
+ protected String id;
+
+ @XmlAttribute(name = "version")
+ protected Integer version;
+
+ /**
+ * Gets the value of the resource property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getResource()
+ {
+ return resource;
+ }
+
+ /**
+ * Sets the value of the resource property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setResource(String value)
+ {
+ this.resource = value;
+ }
+
+ /**
+ * Gets the value of the id property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getId()
+ {
+ return id;
+ }
+
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setId(String value)
+ {
+ this.id = value;
+ }
+
+ /**
+ * Gets the value of the version property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getVersion()
+ {
+ return version;
+ }
+
+ /**
+ * Sets the value of the version property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setVersion(Integer value)
+ {
+ this.version = value;
+ }
- /**
- * Gets the value of the organismsDiffer property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isOrganismsDiffer() {
- return organismsDiffer;
}
- /**
- * Sets the value of the organismsDiffer property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setOrganismsDiffer(Boolean value) {
- this.organismsDiffer = value;
- }
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="name" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * <element name="acronym" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * <element name="description" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * <element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType"/>
+ * </sequence>
+ * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(
+ name = "",
+ propOrder =
+ { "name", "acronym", "description", "dbReference" })
+ public static class Disease
+ {
+
+ @XmlElement(required = true)
+ protected String name;
- /**
- * Gets the value of the experiments property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getExperiments() {
- return experiments;
- }
+ @XmlElement(required = true)
+ protected String acronym;
- /**
- * Sets the value of the experiments property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setExperiments(Integer value) {
- this.experiments = value;
- }
+ @XmlElement(required = true)
+ protected String description;
- /**
- * Gets the value of the disease property.
- *
- * @return
- * possible object is
- * {@link CommentType.Disease }
- *
- */
- public CommentType.Disease getDisease() {
- return disease;
- }
+ @XmlElement(required = true)
+ protected DbReferenceType dbReference;
- /**
- * Sets the value of the disease property.
- *
- * @param value
- * allowed object is
- * {@link CommentType.Disease }
- *
- */
- public void setDisease(CommentType.Disease value) {
- this.disease = value;
- }
+ @XmlAttribute(name = "id", required = true)
+ protected String id;
/**
- * Gets the value of the location property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the location property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getLocation().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link LocationType }
+ * Gets the value of the name property.
*
+ * @return possible object is {@link String }
*
*/
- public List<LocationType> getLocation() {
- if (location == null) {
- location = new ArrayList<LocationType>();
- }
- return this.location;
+ public String getName()
+ {
+ return name;
}
/**
- * Gets the value of the text property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the text property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getText().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
+ * Sets the value of the name property.
*
+ * @param value
+ * allowed object is {@link String }
*
*/
- public List<EvidencedStringType> getText() {
- if (text == null) {
- text = new ArrayList<EvidencedStringType>();
- }
- return this.text;
+ public void setName(String value)
+ {
+ this.name = value;
}
/**
- * Gets the value of the type property.
+ * Gets the value of the acronym property.
+ *
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getType() {
- return type;
+ public String getAcronym()
+ {
+ return acronym;
}
/**
- * Sets the value of the type property.
+ * Sets the value of the acronym property.
*
* @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setType(String value) {
- this.type = value;
- }
-
- /**
- * Gets the value of the locationType property.
+ * allowed object is {@link String }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getLocationType() {
- return locationType;
+ public void setAcronym(String value)
+ {
+ this.acronym = value;
}
/**
- * Sets the value of the locationType property.
+ * Gets the value of the description property.
*
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setLocationType(String value) {
- this.locationType = value;
- }
-
- /**
- * Gets the value of the name property.
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getName() {
- return name;
+ public String getDescription()
+ {
+ return description;
}
/**
- * Sets the value of the name property.
+ * Sets the value of the description property.
*
* @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setName(String value) {
- this.name = value;
- }
-
- /**
- * Gets the value of the mass property.
+ * allowed object is {@link String }
*
- * @return
- * possible object is
- * {@link Float }
- *
*/
- public Float getMass() {
- return mass;
+ public void setDescription(String value)
+ {
+ this.description = value;
}
/**
- * Sets the value of the mass property.
+ * Gets the value of the dbReference property.
*
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setMass(Float value) {
- this.mass = value;
- }
-
- /**
- * Gets the value of the error property.
+ * @return possible object is {@link DbReferenceType }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getError() {
- return error;
+ public DbReferenceType getDbReference()
+ {
+ return dbReference;
}
/**
- * Sets the value of the error property.
+ * Sets the value of the dbReference property.
*
* @param value
- * allowed object is
- * {@link String }
- *
+ * allowed object is {@link DbReferenceType }
+ *
*/
- public void setError(String value) {
- this.error = value;
+ public void setDbReference(DbReferenceType value)
+ {
+ this.dbReference = value;
}
/**
- * Gets the value of the method property.
+ * Gets the value of the id property.
+ *
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getMethod() {
- return method;
+ public String getId()
+ {
+ return id;
}
/**
- * Sets the value of the method property.
+ * Sets the value of the id property.
*
* @param value
- * allowed object is
- * {@link String }
- *
+ * allowed object is {@link String }
+ *
*/
- public void setMethod(String value) {
- this.method = value;
+ public void setId(String value)
+ {
+ this.id = value;
}
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="KM" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="Vmax" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "km", "vmax", "text" })
+ public static class Kinetics
+ {
+
+ @XmlElement(name = "KM")
+ protected List<EvidencedStringType> km;
+
+ @XmlElement(name = "Vmax")
+ protected List<EvidencedStringType> vmax;
+
+ protected List<EvidencedStringType> text;
+
/**
- * Gets the value of the evidence property.
+ * Gets the value of the km property.
*
* <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the evidence property.
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the km property.
*
* <p>
* For example, to add a new item, do as follows:
+ *
* <pre>
- * getEvidence().add(newItem);
+ * getKM().add(newItem);
* </pre>
*
*
* <p>
* Objects of the following type(s) are allowed in the list
- * {@link Integer }
+ * {@link EvidencedStringType }
*
*
*/
- public List<Integer> getEvidence() {
- if (evidence == null) {
- evidence = new ArrayList<Integer>();
- }
- return this.evidence;
+ public List<EvidencedStringType> getKM()
+ {
+ if (km == null)
+ {
+ km = new ArrayList<EvidencedStringType>();
+ }
+ return this.km;
}
-
/**
- * <p>Java class for anonymous complex type.
+ * Gets the value of the vmax property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the vmax property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
*
* <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="max" type="{http://uniprot.org/uniprot}evidencedStringType" minOccurs="0"/>
- * <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
+ * getVmax().add(newItem);
* </pre>
*
*
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "max",
- "text"
- })
- public static class Absorption {
-
- protected EvidencedStringType max;
- protected List<EvidencedStringType> text;
-
- /**
- * Gets the value of the max property.
- *
- * @return
- * possible object is
- * {@link EvidencedStringType }
- *
- */
- public EvidencedStringType getMax() {
- return max;
- }
-
- /**
- * Sets the value of the max property.
- *
- * @param value
- * allowed object is
- * {@link EvidencedStringType }
- *
- */
- public void setMax(EvidencedStringType value) {
- this.max = value;
- }
-
- /**
- * Gets the value of the text property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the text property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getText().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
- *
- *
- */
- public List<EvidencedStringType> getText() {
- if (text == null) {
- text = new ArrayList<EvidencedStringType>();
- }
- return this.text;
- }
-
- }
-
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="sequence" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="resource" use="required">
- * <simpleType>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
- * <enumeration value="EMBL-CDS"/>
- * <enumeration value="EMBL"/>
- * </restriction>
- * </simpleType>
- * </attribute>
- * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="version" type="{http://www.w3.org/2001/XMLSchema}int" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attribute name="type" use="required">
- * <simpleType>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
- * <enumeration value="frameshift"/>
- * <enumeration value="erroneous initiation"/>
- * <enumeration value="erroneous termination"/>
- * <enumeration value="erroneous gene model prediction"/>
- * <enumeration value="erroneous translation"/>
- * <enumeration value="miscellaneous discrepancy"/>
- * </restriction>
- * </simpleType>
- * </attribute>
- * <attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
*
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "sequence"
- })
- public static class Conflict {
-
- protected CommentType.Conflict.Sequence sequence;
- @XmlAttribute(name = "type", required = true)
- protected String type;
- @XmlAttribute(name = "ref")
- protected String ref;
-
- /**
- * Gets the value of the sequence property.
- *
- * @return
- * possible object is
- * {@link CommentType.Conflict.Sequence }
- *
- */
- public CommentType.Conflict.Sequence getSequence() {
- return sequence;
- }
-
- /**
- * Sets the value of the sequence property.
- *
- * @param value
- * allowed object is
- * {@link CommentType.Conflict.Sequence }
- *
- */
- public void setSequence(CommentType.Conflict.Sequence value) {
- this.sequence = value;
- }
-
- /**
- * Gets the value of the type property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getType() {
- return type;
- }
-
- /**
- * Sets the value of the type property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setType(String value) {
- this.type = value;
- }
-
- /**
- * Gets the value of the ref property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getRef() {
- return ref;
- }
-
- /**
- * Sets the value of the ref property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setRef(String value) {
- this.ref = value;
- }
-
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="resource" use="required">
- * <simpleType>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
- * <enumeration value="EMBL-CDS"/>
- * <enumeration value="EMBL"/>
- * </restriction>
- * </simpleType>
- * </attribute>
- * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="version" type="{http://www.w3.org/2001/XMLSchema}int" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class Sequence {
-
- @XmlAttribute(name = "resource", required = true)
- protected String resource;
- @XmlAttribute(name = "id", required = true)
- protected String id;
- @XmlAttribute(name = "version")
- protected Integer version;
-
- /**
- * Gets the value of the resource property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getResource() {
- return resource;
- }
-
- /**
- * Sets the value of the resource property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setResource(String value) {
- this.resource = value;
- }
-
- /**
- * Gets the value of the id property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getId() {
- return id;
- }
-
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setId(String value) {
- this.id = value;
- }
-
- /**
- * Gets the value of the version property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getVersion() {
- return version;
- }
-
- /**
- * Sets the value of the version property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setVersion(Integer value) {
- this.version = value;
- }
-
- }
-
+ public List<EvidencedStringType> getVmax()
+ {
+ if (vmax == null)
+ {
+ vmax = new ArrayList<EvidencedStringType>();
+ }
+ return this.vmax;
}
-
/**
- * <p>Java class for anonymous complex type.
+ * Gets the value of the text property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the text property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * For example, to add a new item, do as follows:
*
* <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="name" type="{http://www.w3.org/2001/XMLSchema}string"/>
- * <element name="acronym" type="{http://www.w3.org/2001/XMLSchema}string"/>
- * <element name="description" type="{http://www.w3.org/2001/XMLSchema}string"/>
- * <element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType"/>
- * </sequence>
- * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
+ * getText().add(newItem);
* </pre>
*
*
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "name",
- "acronym",
- "description",
- "dbReference"
- })
- public static class Disease {
-
- @XmlElement(required = true)
- protected String name;
- @XmlElement(required = true)
- protected String acronym;
- @XmlElement(required = true)
- protected String description;
- @XmlElement(required = true)
- protected DbReferenceType dbReference;
- @XmlAttribute(name = "id", required = true)
- protected String id;
-
- /**
- * Gets the value of the name property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getName() {
- return name;
- }
-
- /**
- * Sets the value of the name property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setName(String value) {
- this.name = value;
- }
-
- /**
- * Gets the value of the acronym property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getAcronym() {
- return acronym;
- }
-
- /**
- * Sets the value of the acronym property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setAcronym(String value) {
- this.acronym = value;
- }
-
- /**
- * Gets the value of the description property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDescription() {
- return description;
- }
-
- /**
- * Sets the value of the description property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDescription(String value) {
- this.description = value;
- }
-
- /**
- * Gets the value of the dbReference property.
- *
- * @return
- * possible object is
- * {@link DbReferenceType }
- *
- */
- public DbReferenceType getDbReference() {
- return dbReference;
- }
-
- /**
- * Sets the value of the dbReference property.
- *
- * @param value
- * allowed object is
- * {@link DbReferenceType }
- *
- */
- public void setDbReference(DbReferenceType value) {
- this.dbReference = value;
- }
-
- /**
- * Gets the value of the id property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getId() {
- return id;
- }
-
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setId(String value) {
- this.id = value;
- }
-
+ public List<EvidencedStringType> getText()
+ {
+ if (text == null)
+ {
+ text = new ArrayList<EvidencedStringType>();
+ }
+ return this.text;
}
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="uri" use="required" type="{http://www.w3.org/2001/XMLSchema}anyURI" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Link
+ {
+
+ @XmlAttribute(name = "uri", required = true)
+ @XmlSchemaType(name = "anyURI")
+ protected String uri;
/**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="KM" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
- * <element name="Vmax" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
- * <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * Gets the value of the uri property.
*
+ * @return possible object is {@link String }
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "km",
- "vmax",
- "text"
- })
- public static class Kinetics {
-
- @XmlElement(name = "KM")
- protected List<EvidencedStringType> km;
- @XmlElement(name = "Vmax")
- protected List<EvidencedStringType> vmax;
- protected List<EvidencedStringType> text;
-
- /**
- * Gets the value of the km property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the km property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getKM().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
- *
- *
- */
- public List<EvidencedStringType> getKM() {
- if (km == null) {
- km = new ArrayList<EvidencedStringType>();
- }
- return this.km;
- }
-
- /**
- * Gets the value of the vmax property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the vmax property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getVmax().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
- *
- *
- */
- public List<EvidencedStringType> getVmax() {
- if (vmax == null) {
- vmax = new ArrayList<EvidencedStringType>();
- }
- return this.vmax;
- }
-
- /**
- * Gets the value of the text property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the text property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getText().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
- *
- *
- */
- public List<EvidencedStringType> getText() {
- if (text == null) {
- text = new ArrayList<EvidencedStringType>();
- }
- return this.text;
- }
-
+ public String getUri()
+ {
+ return uri;
}
-
/**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="uri" use="required" type="{http://www.w3.org/2001/XMLSchema}anyURI" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * Sets the value of the uri property.
*
+ * @param value
+ * allowed object is {@link String }
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class Link {
-
- @XmlAttribute(name = "uri", required = true)
- @XmlSchemaType(name = "anyURI")
- protected String uri;
-
- /**
- * Gets the value of the uri property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getUri() {
- return uri;
- }
-
- /**
- * Sets the value of the uri property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setUri(String value) {
- this.uri = value;
- }
-
+ public void setUri(String value)
+ {
+ this.uri = value;
}
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "text" })
+ public static class PhDependence
+ {
+
+ @XmlElement(required = true)
+ protected List<EvidencedStringType> text;
/**
- * <p>Java class for anonymous complex type.
+ * Gets the value of the text property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the text property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * For example, to add a new item, do as follows:
*
* <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
+ * getText().add(newItem);
* </pre>
*
*
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "text"
- })
- public static class PhDependence {
-
- @XmlElement(required = true)
- protected List<EvidencedStringType> text;
-
- /**
- * Gets the value of the text property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the text property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getText().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
- *
- *
- */
- public List<EvidencedStringType> getText() {
- if (text == null) {
- text = new ArrayList<EvidencedStringType>();
- }
- return this.text;
- }
-
+ public List<EvidencedStringType> getText()
+ {
+ if (text == null)
+ {
+ text = new ArrayList<EvidencedStringType>();
+ }
+ return this.text;
}
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "text" })
+ public static class RedoxPotential
+ {
+
+ @XmlElement(required = true)
+ protected List<EvidencedStringType> text;
/**
- * <p>Java class for anonymous complex type.
+ * Gets the value of the text property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the text property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
*
* <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
+ * getText().add(newItem);
* </pre>
*
*
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "text"
- })
- public static class RedoxPotential {
-
- @XmlElement(required = true)
- protected List<EvidencedStringType> text;
-
- /**
- * Gets the value of the text property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the text property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getText().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
- *
- *
- */
- public List<EvidencedStringType> getText() {
- if (text == null) {
- text = new ArrayList<EvidencedStringType>();
- }
- return this.text;
- }
-
+ public List<EvidencedStringType> getText()
+ {
+ if (text == null)
+ {
+ text = new ArrayList<EvidencedStringType>();
+ }
+ return this.text;
}
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "text" })
+ public static class TemperatureDependence
+ {
+
+ @XmlElement(required = true)
+ protected List<EvidencedStringType> text;
/**
- * <p>Java class for anonymous complex type.
+ * Gets the value of the text property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the text property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
*
* <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
+ * getText().add(newItem);
* </pre>
*
*
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "text"
- })
- public static class TemperatureDependence {
-
- @XmlElement(required = true)
- protected List<EvidencedStringType> text;
-
- /**
- * Gets the value of the text property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the text property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getText().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
- *
- *
- */
- public List<EvidencedStringType> getText() {
- if (text == null) {
- text = new ArrayList<EvidencedStringType>();
- }
- return this.text;
- }
-
+ public List<EvidencedStringType> getText()
+ {
+ if (text == null)
+ {
+ text = new ArrayList<EvidencedStringType>();
+ }
+ return this.text;
}
+ }
+
}
// Generated on: 2019.04.05 at 08:01:44 AM BST
//
-
package jalview.xml.binding.uniprot;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlType;
-
/**
- * Describes the authors of a citation when these are represented by a consortium.
- * Equivalent to the flat file RG-line.
+ * Describes the authors of a citation when these are represented by a
+ * consortium. Equivalent to the flat file RG-line.
*
- * <p>Java class for consortiumType complex type.
+ * <p>
+ * Java class for consortiumType complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
*
* <pre>
* <complexType name="consortiumType">
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "consortiumType")
-public class ConsortiumType {
+public class ConsortiumType
+{
- @XmlAttribute(name = "name", required = true)
- protected String name;
+ @XmlAttribute(name = "name", required = true)
+ protected String name;
- /**
- * Gets the value of the name property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getName() {
- return name;
- }
+ /**
+ * Gets the value of the name property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getName()
+ {
+ return name;
+ }
- /**
- * Sets the value of the name property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setName(String value) {
- this.name = value;
- }
+ /**
+ * Sets the value of the name property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setName(String value)
+ {
+ this.name = value;
+ }
}
// Generated on: 2019.04.05 at 08:01:44 AM BST
//
-
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlType;
-
/**
- * Describes a database cross-reference.
- * Equivalent to the flat file DR-line.
- *
+ * Describes a database cross-reference. Equivalent to the flat file DR-line.
*
- * <p>Java class for dbReferenceType complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * Java class for dbReferenceType complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
*
* <pre>
* <complexType name="dbReferenceType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "dbReferenceType", propOrder = {
- "molecule",
- "property"
-})
-public class DbReferenceType {
-
- protected MoleculeType molecule;
- protected List<PropertyType> property;
- @XmlAttribute(name = "type", required = true)
- protected String type;
- @XmlAttribute(name = "id", required = true)
- protected String id;
- @XmlAttribute(name = "evidence")
- protected List<Integer> evidence;
-
- /**
- * Gets the value of the molecule property.
- *
- * @return
- * possible object is
- * {@link MoleculeType }
- *
- */
- public MoleculeType getMolecule() {
- return molecule;
- }
+@XmlType(name = "dbReferenceType", propOrder = { "molecule", "property" })
+public class DbReferenceType
+{
- /**
- * Sets the value of the molecule property.
- *
- * @param value
- * allowed object is
- * {@link MoleculeType }
- *
- */
- public void setMolecule(MoleculeType value) {
- this.molecule = value;
- }
+ protected MoleculeType molecule;
- /**
- * Gets the value of the property property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the property property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getProperty().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link PropertyType }
- *
- *
- */
- public List<PropertyType> getProperty() {
- if (property == null) {
- property = new ArrayList<PropertyType>();
- }
- return this.property;
- }
+ protected List<PropertyType> property;
- /**
- * Gets the value of the type property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getType() {
- return type;
- }
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
- /**
- * Sets the value of the type property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setType(String value) {
- this.type = value;
- }
+ @XmlAttribute(name = "id", required = true)
+ protected String id;
- /**
- * Gets the value of the id property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getId() {
- return id;
- }
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
+
+ /**
+ * Gets the value of the molecule property.
+ *
+ * @return possible object is {@link MoleculeType }
+ *
+ */
+ public MoleculeType getMolecule()
+ {
+ return molecule;
+ }
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setId(String value) {
- this.id = value;
+ /**
+ * Sets the value of the molecule property.
+ *
+ * @param value
+ * allowed object is {@link MoleculeType }
+ *
+ */
+ public void setMolecule(MoleculeType value)
+ {
+ this.molecule = value;
+ }
+
+ /**
+ * Gets the value of the property property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the property property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getProperty().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link PropertyType }
+ *
+ *
+ */
+ public List<PropertyType> getProperty()
+ {
+ if (property == null)
+ {
+ property = new ArrayList<PropertyType>();
}
+ return this.property;
+ }
+
+ /**
+ * Gets the value of the type property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getType()
+ {
+ return type;
+ }
+
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setType(String value)
+ {
+ this.type = value;
+ }
+
+ /**
+ * Gets the value of the id property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getId()
+ {
+ return id;
+ }
+
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setId(String value)
+ {
+ this.id = value;
+ }
- /**
- * Gets the value of the evidence property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the evidence property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getEvidence().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Integer }
- *
- *
- */
- public List<Integer> getEvidence() {
- if (evidence == null) {
- evidence = new ArrayList<Integer>();
- }
- return this.evidence;
+ /**
+ * Gets the value of the evidence property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getEvidence()
+ {
+ if (evidence == null)
+ {
+ evidence = new ArrayList<Integer>();
}
+ return this.evidence;
+ }
}
// Generated on: 2019.04.05 at 08:01:44 AM BST
//
-
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlType;
import javax.xml.datatype.XMLGregorianCalendar;
-
/**
- * <p>Java class for anonymous complex type.
+ * <p>
+ * Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
*
* <pre>
* <complexType>
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = {
- "accession",
- "name",
- "protein",
- "gene",
- "organism",
- "organismHost",
- "geneLocation",
- "reference",
- "comment",
- "dbReference",
- "proteinExistence",
- "keyword",
- "feature",
- "evidence",
- "sequence"
-})
+@XmlType(
+ name = "",
+ propOrder =
+ { "accession", "name", "protein", "gene", "organism", "organismHost",
+ "geneLocation", "reference", "comment", "dbReference",
+ "proteinExistence", "keyword", "feature", "evidence", "sequence" })
@XmlRootElement(name = "entry")
-public class Entry {
-
- @XmlElement(required = true)
- protected List<String> accession;
- @XmlElement(required = true)
- protected List<String> name;
- @XmlElement(required = true)
- protected ProteinType protein;
- protected List<GeneType> gene;
- @XmlElement(required = true)
- protected OrganismType organism;
- protected List<OrganismType> organismHost;
- protected List<GeneLocationType> geneLocation;
- @XmlElement(required = true)
- protected List<ReferenceType> reference;
- @XmlElement(nillable = true)
- protected List<CommentType> comment;
- protected List<DbReferenceType> dbReference;
- @XmlElement(required = true)
- protected ProteinExistenceType proteinExistence;
- protected List<KeywordType> keyword;
- protected List<FeatureType> feature;
- protected List<EvidenceType> evidence;
- @XmlElement(required = true)
- protected SequenceType sequence;
- @XmlAttribute(name = "dataset", required = true)
- protected String dataset;
- @XmlAttribute(name = "created", required = true)
- @XmlSchemaType(name = "date")
- protected XMLGregorianCalendar created;
- @XmlAttribute(name = "modified", required = true)
- @XmlSchemaType(name = "date")
- protected XMLGregorianCalendar modified;
- @XmlAttribute(name = "version", required = true)
- protected int version;
-
- /**
- * Gets the value of the accession property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the accession property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getAccession().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link String }
- *
- *
- */
- public List<String> getAccession() {
- if (accession == null) {
- accession = new ArrayList<String>();
- }
- return this.accession;
- }
+public class Entry
+{
- /**
- * Gets the value of the name property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the name property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getName().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link String }
- *
- *
- */
- public List<String> getName() {
- if (name == null) {
- name = new ArrayList<String>();
- }
- return this.name;
- }
+ @XmlElement(required = true)
+ protected List<String> accession;
- /**
- * Gets the value of the protein property.
- *
- * @return
- * possible object is
- * {@link ProteinType }
- *
- */
- public ProteinType getProtein() {
- return protein;
- }
+ @XmlElement(required = true)
+ protected List<String> name;
- /**
- * Sets the value of the protein property.
- *
- * @param value
- * allowed object is
- * {@link ProteinType }
- *
- */
- public void setProtein(ProteinType value) {
- this.protein = value;
- }
+ @XmlElement(required = true)
+ protected ProteinType protein;
- /**
- * Gets the value of the gene property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the gene property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getGene().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link GeneType }
- *
- *
- */
- public List<GeneType> getGene() {
- if (gene == null) {
- gene = new ArrayList<GeneType>();
- }
- return this.gene;
- }
+ protected List<GeneType> gene;
- /**
- * Gets the value of the organism property.
- *
- * @return
- * possible object is
- * {@link OrganismType }
- *
- */
- public OrganismType getOrganism() {
- return organism;
- }
+ @XmlElement(required = true)
+ protected OrganismType organism;
- /**
- * Sets the value of the organism property.
- *
- * @param value
- * allowed object is
- * {@link OrganismType }
- *
- */
- public void setOrganism(OrganismType value) {
- this.organism = value;
- }
+ protected List<OrganismType> organismHost;
- /**
- * Gets the value of the organismHost property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the organismHost property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getOrganismHost().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link OrganismType }
- *
- *
- */
- public List<OrganismType> getOrganismHost() {
- if (organismHost == null) {
- organismHost = new ArrayList<OrganismType>();
- }
- return this.organismHost;
- }
+ protected List<GeneLocationType> geneLocation;
- /**
- * Gets the value of the geneLocation property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the geneLocation property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getGeneLocation().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link GeneLocationType }
- *
- *
- */
- public List<GeneLocationType> getGeneLocation() {
- if (geneLocation == null) {
- geneLocation = new ArrayList<GeneLocationType>();
- }
- return this.geneLocation;
- }
+ @XmlElement(required = true)
+ protected List<ReferenceType> reference;
- /**
- * Gets the value of the reference property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the reference property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getReference().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link ReferenceType }
- *
- *
- */
- public List<ReferenceType> getReference() {
- if (reference == null) {
- reference = new ArrayList<ReferenceType>();
- }
- return this.reference;
- }
+ @XmlElement(nillable = true)
+ protected List<CommentType> comment;
- /**
- * Gets the value of the comment property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the comment property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getComment().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link CommentType }
- *
- *
- */
- public List<CommentType> getComment() {
- if (comment == null) {
- comment = new ArrayList<CommentType>();
- }
- return this.comment;
- }
+ protected List<DbReferenceType> dbReference;
- /**
- * Gets the value of the dbReference property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the dbReference property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getDbReference().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link DbReferenceType }
- *
- *
- */
- public List<DbReferenceType> getDbReference() {
- if (dbReference == null) {
- dbReference = new ArrayList<DbReferenceType>();
- }
- return this.dbReference;
- }
+ @XmlElement(required = true)
+ protected ProteinExistenceType proteinExistence;
- /**
- * Gets the value of the proteinExistence property.
- *
- * @return
- * possible object is
- * {@link ProteinExistenceType }
- *
- */
- public ProteinExistenceType getProteinExistence() {
- return proteinExistence;
- }
+ protected List<KeywordType> keyword;
- /**
- * Sets the value of the proteinExistence property.
- *
- * @param value
- * allowed object is
- * {@link ProteinExistenceType }
- *
- */
- public void setProteinExistence(ProteinExistenceType value) {
- this.proteinExistence = value;
- }
+ protected List<FeatureType> feature;
- /**
- * Gets the value of the keyword property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the keyword property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getKeyword().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link KeywordType }
- *
- *
- */
- public List<KeywordType> getKeyword() {
- if (keyword == null) {
- keyword = new ArrayList<KeywordType>();
- }
- return this.keyword;
- }
+ protected List<EvidenceType> evidence;
- /**
- * Gets the value of the feature property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the feature property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getFeature().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link FeatureType }
- *
- *
- */
- public List<FeatureType> getFeature() {
- if (feature == null) {
- feature = new ArrayList<FeatureType>();
- }
- return this.feature;
- }
+ @XmlElement(required = true)
+ protected SequenceType sequence;
- /**
- * Gets the value of the evidence property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the evidence property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getEvidence().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidenceType }
- *
- *
- */
- public List<EvidenceType> getEvidence() {
- if (evidence == null) {
- evidence = new ArrayList<EvidenceType>();
- }
- return this.evidence;
- }
+ @XmlAttribute(name = "dataset", required = true)
+ protected String dataset;
- /**
- * Gets the value of the sequence property.
- *
- * @return
- * possible object is
- * {@link SequenceType }
- *
- */
- public SequenceType getSequence() {
- return sequence;
- }
+ @XmlAttribute(name = "created", required = true)
+ @XmlSchemaType(name = "date")
+ protected XMLGregorianCalendar created;
- /**
- * Sets the value of the sequence property.
- *
- * @param value
- * allowed object is
- * {@link SequenceType }
- *
- */
- public void setSequence(SequenceType value) {
- this.sequence = value;
- }
+ @XmlAttribute(name = "modified", required = true)
+ @XmlSchemaType(name = "date")
+ protected XMLGregorianCalendar modified;
- /**
- * Gets the value of the dataset property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDataset() {
- return dataset;
- }
+ @XmlAttribute(name = "version", required = true)
+ protected int version;
- /**
- * Sets the value of the dataset property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDataset(String value) {
- this.dataset = value;
+ /**
+ * Gets the value of the accession property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the accession property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getAccession().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link String }
+ *
+ *
+ */
+ public List<String> getAccession()
+ {
+ if (accession == null)
+ {
+ accession = new ArrayList<String>();
}
-
- /**
- * Gets the value of the created property.
- *
- * @return
- * possible object is
- * {@link XMLGregorianCalendar }
- *
- */
- public XMLGregorianCalendar getCreated() {
- return created;
+ return this.accession;
+ }
+
+ /**
+ * Gets the value of the name property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the name property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link String }
+ *
+ *
+ */
+ public List<String> getName()
+ {
+ if (name == null)
+ {
+ name = new ArrayList<String>();
}
-
- /**
- * Sets the value of the created property.
- *
- * @param value
- * allowed object is
- * {@link XMLGregorianCalendar }
- *
- */
- public void setCreated(XMLGregorianCalendar value) {
- this.created = value;
+ return this.name;
+ }
+
+ /**
+ * Gets the value of the protein property.
+ *
+ * @return possible object is {@link ProteinType }
+ *
+ */
+ public ProteinType getProtein()
+ {
+ return protein;
+ }
+
+ /**
+ * Sets the value of the protein property.
+ *
+ * @param value
+ * allowed object is {@link ProteinType }
+ *
+ */
+ public void setProtein(ProteinType value)
+ {
+ this.protein = value;
+ }
+
+ /**
+ * Gets the value of the gene property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the gene property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getGene().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link GeneType }
+ *
+ *
+ */
+ public List<GeneType> getGene()
+ {
+ if (gene == null)
+ {
+ gene = new ArrayList<GeneType>();
}
-
- /**
- * Gets the value of the modified property.
- *
- * @return
- * possible object is
- * {@link XMLGregorianCalendar }
- *
- */
- public XMLGregorianCalendar getModified() {
- return modified;
+ return this.gene;
+ }
+
+ /**
+ * Gets the value of the organism property.
+ *
+ * @return possible object is {@link OrganismType }
+ *
+ */
+ public OrganismType getOrganism()
+ {
+ return organism;
+ }
+
+ /**
+ * Sets the value of the organism property.
+ *
+ * @param value
+ * allowed object is {@link OrganismType }
+ *
+ */
+ public void setOrganism(OrganismType value)
+ {
+ this.organism = value;
+ }
+
+ /**
+ * Gets the value of the organismHost property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the organismHost property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getOrganismHost().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link OrganismType }
+ *
+ *
+ */
+ public List<OrganismType> getOrganismHost()
+ {
+ if (organismHost == null)
+ {
+ organismHost = new ArrayList<OrganismType>();
}
-
- /**
- * Sets the value of the modified property.
- *
- * @param value
- * allowed object is
- * {@link XMLGregorianCalendar }
- *
- */
- public void setModified(XMLGregorianCalendar value) {
- this.modified = value;
+ return this.organismHost;
+ }
+
+ /**
+ * Gets the value of the geneLocation property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the geneLocation property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getGeneLocation().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link GeneLocationType }
+ *
+ *
+ */
+ public List<GeneLocationType> getGeneLocation()
+ {
+ if (geneLocation == null)
+ {
+ geneLocation = new ArrayList<GeneLocationType>();
}
-
- /**
- * Gets the value of the version property.
- *
- */
- public int getVersion() {
- return version;
+ return this.geneLocation;
+ }
+
+ /**
+ * Gets the value of the reference property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the reference property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getReference().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link ReferenceType }
+ *
+ *
+ */
+ public List<ReferenceType> getReference()
+ {
+ if (reference == null)
+ {
+ reference = new ArrayList<ReferenceType>();
}
-
- /**
- * Sets the value of the version property.
- *
- */
- public void setVersion(int value) {
- this.version = value;
+ return this.reference;
+ }
+
+ /**
+ * Gets the value of the comment property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the comment property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getComment().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link CommentType
+ * }
+ *
+ *
+ */
+ public List<CommentType> getComment()
+ {
+ if (comment == null)
+ {
+ comment = new ArrayList<CommentType>();
+ }
+ return this.comment;
+ }
+
+ /**
+ * Gets the value of the dbReference property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the dbReference property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getDbReference().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link DbReferenceType }
+ *
+ *
+ */
+ public List<DbReferenceType> getDbReference()
+ {
+ if (dbReference == null)
+ {
+ dbReference = new ArrayList<DbReferenceType>();
+ }
+ return this.dbReference;
+ }
+
+ /**
+ * Gets the value of the proteinExistence property.
+ *
+ * @return possible object is {@link ProteinExistenceType }
+ *
+ */
+ public ProteinExistenceType getProteinExistence()
+ {
+ return proteinExistence;
+ }
+
+ /**
+ * Sets the value of the proteinExistence property.
+ *
+ * @param value
+ * allowed object is {@link ProteinExistenceType }
+ *
+ */
+ public void setProteinExistence(ProteinExistenceType value)
+ {
+ this.proteinExistence = value;
+ }
+
+ /**
+ * Gets the value of the keyword property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the keyword property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getKeyword().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link KeywordType
+ * }
+ *
+ *
+ */
+ public List<KeywordType> getKeyword()
+ {
+ if (keyword == null)
+ {
+ keyword = new ArrayList<KeywordType>();
+ }
+ return this.keyword;
+ }
+
+ /**
+ * Gets the value of the feature property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the feature property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getFeature().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link FeatureType
+ * }
+ *
+ *
+ */
+ public List<FeatureType> getFeature()
+ {
+ if (feature == null)
+ {
+ feature = new ArrayList<FeatureType>();
+ }
+ return this.feature;
+ }
+
+ /**
+ * Gets the value of the evidence property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidenceType }
+ *
+ *
+ */
+ public List<EvidenceType> getEvidence()
+ {
+ if (evidence == null)
+ {
+ evidence = new ArrayList<EvidenceType>();
}
+ return this.evidence;
+ }
+
+ /**
+ * Gets the value of the sequence property.
+ *
+ * @return possible object is {@link SequenceType }
+ *
+ */
+ public SequenceType getSequence()
+ {
+ return sequence;
+ }
+
+ /**
+ * Sets the value of the sequence property.
+ *
+ * @param value
+ * allowed object is {@link SequenceType }
+ *
+ */
+ public void setSequence(SequenceType value)
+ {
+ this.sequence = value;
+ }
+
+ /**
+ * Gets the value of the dataset property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDataset()
+ {
+ return dataset;
+ }
+
+ /**
+ * Sets the value of the dataset property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setDataset(String value)
+ {
+ this.dataset = value;
+ }
+
+ /**
+ * Gets the value of the created property.
+ *
+ * @return possible object is {@link XMLGregorianCalendar }
+ *
+ */
+ public XMLGregorianCalendar getCreated()
+ {
+ return created;
+ }
+
+ /**
+ * Sets the value of the created property.
+ *
+ * @param value
+ * allowed object is {@link XMLGregorianCalendar }
+ *
+ */
+ public void setCreated(XMLGregorianCalendar value)
+ {
+ this.created = value;
+ }
+
+ /**
+ * Gets the value of the modified property.
+ *
+ * @return possible object is {@link XMLGregorianCalendar }
+ *
+ */
+ public XMLGregorianCalendar getModified()
+ {
+ return modified;
+ }
+
+ /**
+ * Sets the value of the modified property.
+ *
+ * @param value
+ * allowed object is {@link XMLGregorianCalendar }
+ *
+ */
+ public void setModified(XMLGregorianCalendar value)
+ {
+ this.modified = value;
+ }
+
+ /**
+ * Gets the value of the version property.
+ *
+ */
+ public int getVersion()
+ {
+ return version;
+ }
+
+ /**
+ * Sets the value of the version property.
+ *
+ */
+ public void setVersion(int value)
+ {
+ this.version = value;
+ }
}
// Generated on: 2019.04.05 at 08:01:44 AM BST
//
-
package jalview.xml.binding.uniprot;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlType;
-
/**
* Describes the type of events that cause alternative products.
*
- * <p>Java class for eventType complex type.
+ * <p>
+ * Java class for eventType complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
*
* <pre>
* <complexType name="eventType">
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "eventType")
-public class EventType {
+public class EventType
+{
- @XmlAttribute(name = "type", required = true)
- protected String type;
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
- /**
- * Gets the value of the type property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getType() {
- return type;
- }
+ /**
+ * Gets the value of the type property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getType()
+ {
+ return type;
+ }
- /**
- * Sets the value of the type property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setType(String value) {
- this.type = value;
- }
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setType(String value)
+ {
+ this.type = value;
+ }
}
// Generated on: 2019.04.05 at 08:01:44 AM BST
//
-
package jalview.xml.binding.uniprot;
import java.math.BigInteger;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlType;
-
/**
- * Describes the evidence for an annotation.
- * No flat file equivalent.
+ * Describes the evidence for an annotation. No flat file equivalent.
*
- * <p>Java class for evidenceType complex type.
+ * <p>
+ * Java class for evidenceType complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
*
* <pre>
* <complexType name="evidenceType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "evidenceType", propOrder = {
- "source",
- "importedFrom"
-})
-public class EvidenceType {
-
- protected SourceType source;
- protected ImportedFromType importedFrom;
- @XmlAttribute(name = "type", required = true)
- protected String type;
- @XmlAttribute(name = "key", required = true)
- protected BigInteger key;
-
- /**
- * Gets the value of the source property.
- *
- * @return
- * possible object is
- * {@link SourceType }
- *
- */
- public SourceType getSource() {
- return source;
- }
-
- /**
- * Sets the value of the source property.
- *
- * @param value
- * allowed object is
- * {@link SourceType }
- *
- */
- public void setSource(SourceType value) {
- this.source = value;
- }
-
- /**
- * Gets the value of the importedFrom property.
- *
- * @return
- * possible object is
- * {@link ImportedFromType }
- *
- */
- public ImportedFromType getImportedFrom() {
- return importedFrom;
- }
-
- /**
- * Sets the value of the importedFrom property.
- *
- * @param value
- * allowed object is
- * {@link ImportedFromType }
- *
- */
- public void setImportedFrom(ImportedFromType value) {
- this.importedFrom = value;
- }
-
- /**
- * Gets the value of the type property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getType() {
- return type;
- }
-
- /**
- * Sets the value of the type property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setType(String value) {
- this.type = value;
- }
-
- /**
- * Gets the value of the key property.
- *
- * @return
- * possible object is
- * {@link BigInteger }
- *
- */
- public BigInteger getKey() {
- return key;
- }
-
- /**
- * Sets the value of the key property.
- *
- * @param value
- * allowed object is
- * {@link BigInteger }
- *
- */
- public void setKey(BigInteger value) {
- this.key = value;
- }
+@XmlType(name = "evidenceType", propOrder = { "source", "importedFrom" })
+public class EvidenceType
+{
+
+ protected SourceType source;
+
+ protected ImportedFromType importedFrom;
+
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
+
+ @XmlAttribute(name = "key", required = true)
+ protected BigInteger key;
+
+ /**
+ * Gets the value of the source property.
+ *
+ * @return possible object is {@link SourceType }
+ *
+ */
+ public SourceType getSource()
+ {
+ return source;
+ }
+
+ /**
+ * Sets the value of the source property.
+ *
+ * @param value
+ * allowed object is {@link SourceType }
+ *
+ */
+ public void setSource(SourceType value)
+ {
+ this.source = value;
+ }
+
+ /**
+ * Gets the value of the importedFrom property.
+ *
+ * @return possible object is {@link ImportedFromType }
+ *
+ */
+ public ImportedFromType getImportedFrom()
+ {
+ return importedFrom;
+ }
+
+ /**
+ * Sets the value of the importedFrom property.
+ *
+ * @param value
+ * allowed object is {@link ImportedFromType }
+ *
+ */
+ public void setImportedFrom(ImportedFromType value)
+ {
+ this.importedFrom = value;
+ }
+
+ /**
+ * Gets the value of the type property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getType()
+ {
+ return type;
+ }
+
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setType(String value)
+ {
+ this.type = value;
+ }
+
+ /**
+ * Gets the value of the key property.
+ *
+ * @return possible object is {@link BigInteger }
+ *
+ */
+ public BigInteger getKey()
+ {
+ return key;
+ }
+
+ /**
+ * Sets the value of the key property.
+ *
+ * @param value
+ * allowed object is {@link BigInteger }
+ *
+ */
+ public void setKey(BigInteger value)
+ {
+ this.key = value;
+ }
}
// Generated on: 2019.04.05 at 08:01:44 AM BST
//
-
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlType;
import javax.xml.bind.annotation.XmlValue;
-
/**
- * <p>Java class for evidencedStringType complex type.
+ * <p>
+ * Java class for evidencedStringType complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
*
* <pre>
* <complexType name="evidencedStringType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "evidencedStringType", propOrder = {
- "value"
-})
-public class EvidencedStringType {
+@XmlType(name = "evidencedStringType", propOrder = { "value" })
+public class EvidencedStringType
+{
- @XmlValue
- protected String value;
- @XmlAttribute(name = "evidence")
- protected List<Integer> evidence;
- @XmlAttribute(name = "status")
- protected String status;
+ @XmlValue
+ protected String value;
- /**
- * Gets the value of the value property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getValue() {
- return value;
- }
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
- /**
- * Sets the value of the value property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setValue(String value) {
- this.value = value;
- }
+ @XmlAttribute(name = "status")
+ protected String status;
- /**
- * Gets the value of the evidence property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the evidence property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getEvidence().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Integer }
- *
- *
- */
- public List<Integer> getEvidence() {
- if (evidence == null) {
- evidence = new ArrayList<Integer>();
- }
- return this.evidence;
- }
+ /**
+ * Gets the value of the value property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getValue()
+ {
+ return value;
+ }
- /**
- * Gets the value of the status property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getStatus() {
- return status;
- }
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setValue(String value)
+ {
+ this.value = value;
+ }
- /**
- * Sets the value of the status property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setStatus(String value) {
- this.status = value;
+ /**
+ * Gets the value of the evidence property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getEvidence()
+ {
+ if (evidence == null)
+ {
+ evidence = new ArrayList<Integer>();
}
+ return this.evidence;
+ }
+
+ /**
+ * Gets the value of the status property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getStatus()
+ {
+ return status;
+ }
+
+ /**
+ * Sets the value of the status property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setStatus(String value)
+ {
+ this.status = value;
+ }
}
// Generated on: 2019.04.05 at 08:01:44 AM BST
//
-
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
-
/**
- * Describes different types of sequence annotations.
- * Equivalent to the flat file FT-line.
+ * Describes different types of sequence annotations. Equivalent to the flat
+ * file FT-line.
*
- * <p>Java class for featureType complex type.
+ * <p>
+ * Java class for featureType complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
*
* <pre>
* <complexType name="featureType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "featureType", propOrder = {
- "original",
- "variation",
- "location"
-})
-public class FeatureType {
+@XmlType(
+ name = "featureType",
+ propOrder =
+ { "original", "variation", "location" })
+public class FeatureType
+{
- protected String original;
- protected List<String> variation;
- @XmlElement(required = true)
- protected LocationType location;
- @XmlAttribute(name = "type", required = true)
- protected String type;
- @XmlAttribute(name = "status")
- protected String status;
- @XmlAttribute(name = "id")
- protected String id;
- @XmlAttribute(name = "description")
- protected String description;
- @XmlAttribute(name = "evidence")
- protected List<Integer> evidence;
- @XmlAttribute(name = "ref")
- protected String ref;
+ protected String original;
- /**
- * Gets the value of the original property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getOriginal() {
- return original;
- }
+ protected List<String> variation;
- /**
- * Sets the value of the original property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setOriginal(String value) {
- this.original = value;
- }
+ @XmlElement(required = true)
+ protected LocationType location;
- /**
- * Gets the value of the variation property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the variation property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getVariation().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link String }
- *
- *
- */
- public List<String> getVariation() {
- if (variation == null) {
- variation = new ArrayList<String>();
- }
- return this.variation;
- }
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
- /**
- * Gets the value of the location property.
- *
- * @return
- * possible object is
- * {@link LocationType }
- *
- */
- public LocationType getLocation() {
- return location;
- }
+ @XmlAttribute(name = "status")
+ protected String status;
- /**
- * Sets the value of the location property.
- *
- * @param value
- * allowed object is
- * {@link LocationType }
- *
- */
- public void setLocation(LocationType value) {
- this.location = value;
- }
+ @XmlAttribute(name = "id")
+ protected String id;
- /**
- * Gets the value of the type property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getType() {
- return type;
- }
+ @XmlAttribute(name = "description")
+ protected String description;
- /**
- * Sets the value of the type property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setType(String value) {
- this.type = value;
- }
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
- /**
- * Gets the value of the status property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getStatus() {
- return status;
- }
+ @XmlAttribute(name = "ref")
+ protected String ref;
- /**
- * Sets the value of the status property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setStatus(String value) {
- this.status = value;
- }
+ /**
+ * Gets the value of the original property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getOriginal()
+ {
+ return original;
+ }
- /**
- * Gets the value of the id property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getId() {
- return id;
- }
+ /**
+ * Sets the value of the original property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setOriginal(String value)
+ {
+ this.original = value;
+ }
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setId(String value) {
- this.id = value;
+ /**
+ * Gets the value of the variation property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the variation property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getVariation().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link String }
+ *
+ *
+ */
+ public List<String> getVariation()
+ {
+ if (variation == null)
+ {
+ variation = new ArrayList<String>();
}
+ return this.variation;
+ }
- /**
- * Gets the value of the description property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDescription() {
- return description;
- }
+ /**
+ * Gets the value of the location property.
+ *
+ * @return possible object is {@link LocationType }
+ *
+ */
+ public LocationType getLocation()
+ {
+ return location;
+ }
- /**
- * Sets the value of the description property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDescription(String value) {
- this.description = value;
- }
+ /**
+ * Sets the value of the location property.
+ *
+ * @param value
+ * allowed object is {@link LocationType }
+ *
+ */
+ public void setLocation(LocationType value)
+ {
+ this.location = value;
+ }
- /**
- * Gets the value of the evidence property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the evidence property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getEvidence().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Integer }
- *
- *
- */
- public List<Integer> getEvidence() {
- if (evidence == null) {
- evidence = new ArrayList<Integer>();
- }
- return this.evidence;
- }
+ /**
+ * Gets the value of the type property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getType()
+ {
+ return type;
+ }
- /**
- * Gets the value of the ref property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getRef() {
- return ref;
- }
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setType(String value)
+ {
+ this.type = value;
+ }
+
+ /**
+ * Gets the value of the status property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getStatus()
+ {
+ return status;
+ }
+
+ /**
+ * Sets the value of the status property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setStatus(String value)
+ {
+ this.status = value;
+ }
- /**
- * Sets the value of the ref property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setRef(String value) {
- this.ref = value;
+ /**
+ * Gets the value of the id property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getId()
+ {
+ return id;
+ }
+
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setId(String value)
+ {
+ this.id = value;
+ }
+
+ /**
+ * Gets the value of the description property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDescription()
+ {
+ return description;
+ }
+
+ /**
+ * Sets the value of the description property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setDescription(String value)
+ {
+ this.description = value;
+ }
+
+ /**
+ * Gets the value of the evidence property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getEvidence()
+ {
+ if (evidence == null)
+ {
+ evidence = new ArrayList<Integer>();
}
+ return this.evidence;
+ }
+
+ /**
+ * Gets the value of the ref property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getRef()
+ {
+ return ref;
+ }
+
+ /**
+ * Sets the value of the ref property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setRef(String value)
+ {
+ this.ref = value;
+ }
}
// Generated on: 2019.04.05 at 08:01:44 AM BST
//
-
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlType;
-
/**
- * Describes non-nuclear gene locations (organelles and plasmids).
- * Equivalent to the flat file OG-line.
+ * Describes non-nuclear gene locations (organelles and plasmids). Equivalent to
+ * the flat file OG-line.
*
- * <p>Java class for geneLocationType complex type.
+ * <p>
+ * Java class for geneLocationType complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
*
* <pre>
* <complexType name="geneLocationType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "geneLocationType", propOrder = {
- "name"
-})
-public class GeneLocationType {
+@XmlType(name = "geneLocationType", propOrder = { "name" })
+public class GeneLocationType
+{
- protected List<StatusType> name;
- @XmlAttribute(name = "type", required = true)
- protected String type;
- @XmlAttribute(name = "evidence")
- protected List<Integer> evidence;
+ protected List<StatusType> name;
- /**
- * Gets the value of the name property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the name property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getName().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link StatusType }
- *
- *
- */
- public List<StatusType> getName() {
- if (name == null) {
- name = new ArrayList<StatusType>();
- }
- return this.name;
- }
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
- /**
- * Gets the value of the type property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getType() {
- return type;
- }
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
- /**
- * Sets the value of the type property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setType(String value) {
- this.type = value;
+ /**
+ * Gets the value of the name property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the name property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link StatusType
+ * }
+ *
+ *
+ */
+ public List<StatusType> getName()
+ {
+ if (name == null)
+ {
+ name = new ArrayList<StatusType>();
}
+ return this.name;
+ }
+
+ /**
+ * Gets the value of the type property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getType()
+ {
+ return type;
+ }
+
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setType(String value)
+ {
+ this.type = value;
+ }
- /**
- * Gets the value of the evidence property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the evidence property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getEvidence().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Integer }
- *
- *
- */
- public List<Integer> getEvidence() {
- if (evidence == null) {
- evidence = new ArrayList<Integer>();
- }
- return this.evidence;
+ /**
+ * Gets the value of the evidence property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getEvidence()
+ {
+ if (evidence == null)
+ {
+ evidence = new ArrayList<Integer>();
}
+ return this.evidence;
+ }
}
// Generated on: 2019.04.05 at 08:01:44 AM BST
//
-
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlType;
import javax.xml.bind.annotation.XmlValue;
-
/**
- * Describes different types of gene designations.
- * Equivalent to the flat file GN-line.
+ * Describes different types of gene designations. Equivalent to the flat file
+ * GN-line.
*
- * <p>Java class for geneNameType complex type.
+ * <p>
+ * Java class for geneNameType complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
*
* <pre>
* <complexType name="geneNameType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "geneNameType", propOrder = {
- "value"
-})
-public class GeneNameType {
+@XmlType(name = "geneNameType", propOrder = { "value" })
+public class GeneNameType
+{
- @XmlValue
- protected String value;
- @XmlAttribute(name = "evidence")
- protected List<Integer> evidence;
- @XmlAttribute(name = "type", required = true)
- protected String type;
+ @XmlValue
+ protected String value;
- /**
- * Gets the value of the value property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getValue() {
- return value;
- }
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
- /**
- * Sets the value of the value property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setValue(String value) {
- this.value = value;
- }
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
- /**
- * Gets the value of the evidence property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the evidence property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getEvidence().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Integer }
- *
- *
- */
- public List<Integer> getEvidence() {
- if (evidence == null) {
- evidence = new ArrayList<Integer>();
- }
- return this.evidence;
- }
+ /**
+ * Gets the value of the value property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getValue()
+ {
+ return value;
+ }
- /**
- * Gets the value of the type property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getType() {
- return type;
- }
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setValue(String value)
+ {
+ this.value = value;
+ }
- /**
- * Sets the value of the type property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setType(String value) {
- this.type = value;
+ /**
+ * Gets the value of the evidence property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getEvidence()
+ {
+ if (evidence == null)
+ {
+ evidence = new ArrayList<Integer>();
}
+ return this.evidence;
+ }
+
+ /**
+ * Gets the value of the type property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getType()
+ {
+ return type;
+ }
+
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setType(String value)
+ {
+ this.type = value;
+ }
}
// Generated on: 2019.04.05 at 08:01:44 AM BST
//
-
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
-
/**
- * Describes a gene.
- * Equivalent to the flat file GN-line.
+ * Describes a gene. Equivalent to the flat file GN-line.
*
- * <p>Java class for geneType complex type.
+ * <p>
+ * Java class for geneType complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
*
* <pre>
* <complexType name="geneType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "geneType", propOrder = {
- "name"
-})
-public class GeneType {
+@XmlType(name = "geneType", propOrder = { "name" })
+public class GeneType
+{
- @XmlElement(required = true)
- protected List<GeneNameType> name;
+ @XmlElement(required = true)
+ protected List<GeneNameType> name;
- /**
- * Gets the value of the name property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the name property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getName().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link GeneNameType }
- *
- *
- */
- public List<GeneNameType> getName() {
- if (name == null) {
- name = new ArrayList<GeneNameType>();
- }
- return this.name;
+ /**
+ * Gets the value of the name property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the name property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link GeneNameType }
+ *
+ *
+ */
+ public List<GeneNameType> getName()
+ {
+ if (name == null)
+ {
+ name = new ArrayList<GeneNameType>();
}
+ return this.name;
+ }
}
// Generated on: 2019.04.05 at 08:01:44 AM BST
//
-
package jalview.xml.binding.uniprot;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
-
/**
- * Describes the source of the evidence, when it is not assigned by UniProt, but imported from an external database.
+ * Describes the source of the evidence, when it is not assigned by UniProt, but
+ * imported from an external database.
*
- * <p>Java class for importedFromType complex type.
+ * <p>
+ * Java class for importedFromType complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
*
* <pre>
* <complexType name="importedFromType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "importedFromType", propOrder = {
- "dbReference"
-})
-public class ImportedFromType {
+@XmlType(name = "importedFromType", propOrder = { "dbReference" })
+public class ImportedFromType
+{
- @XmlElement(required = true)
- protected DbReferenceType dbReference;
+ @XmlElement(required = true)
+ protected DbReferenceType dbReference;
- /**
- * Gets the value of the dbReference property.
- *
- * @return
- * possible object is
- * {@link DbReferenceType }
- *
- */
- public DbReferenceType getDbReference() {
- return dbReference;
- }
+ /**
+ * Gets the value of the dbReference property.
+ *
+ * @return possible object is {@link DbReferenceType }
+ *
+ */
+ public DbReferenceType getDbReference()
+ {
+ return dbReference;
+ }
- /**
- * Sets the value of the dbReference property.
- *
- * @param value
- * allowed object is
- * {@link DbReferenceType }
- *
- */
- public void setDbReference(DbReferenceType value) {
- this.dbReference = value;
- }
+ /**
+ * Sets the value of the dbReference property.
+ *
+ * @param value
+ * allowed object is {@link DbReferenceType }
+ *
+ */
+ public void setDbReference(DbReferenceType value)
+ {
+ this.dbReference = value;
+ }
}
// Generated on: 2019.04.05 at 08:01:44 AM BST
//
-
package jalview.xml.binding.uniprot;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlType;
-
/**
- * <p>Java class for interactantType complex type.
+ * <p>
+ * Java class for interactantType complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
*
* <pre>
* <complexType name="interactantType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "interactantType", propOrder = {
- "id",
- "label"
-})
-public class InteractantType {
+@XmlType(name = "interactantType", propOrder = { "id", "label" })
+public class InteractantType
+{
+
+ protected String id;
+
+ protected String label;
- protected String id;
- protected String label;
- @XmlAttribute(name = "intactId", required = true)
- protected String intactId;
+ @XmlAttribute(name = "intactId", required = true)
+ protected String intactId;
- /**
- * Gets the value of the id property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getId() {
- return id;
- }
+ /**
+ * Gets the value of the id property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getId()
+ {
+ return id;
+ }
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setId(String value) {
- this.id = value;
- }
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setId(String value)
+ {
+ this.id = value;
+ }
- /**
- * Gets the value of the label property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getLabel() {
- return label;
- }
+ /**
+ * Gets the value of the label property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getLabel()
+ {
+ return label;
+ }
- /**
- * Sets the value of the label property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setLabel(String value) {
- this.label = value;
- }
+ /**
+ * Sets the value of the label property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setLabel(String value)
+ {
+ this.label = value;
+ }
- /**
- * Gets the value of the intactId property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getIntactId() {
- return intactId;
- }
+ /**
+ * Gets the value of the intactId property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getIntactId()
+ {
+ return intactId;
+ }
- /**
- * Sets the value of the intactId property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setIntactId(String value) {
- this.intactId = value;
- }
+ /**
+ * Sets the value of the intactId property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setIntactId(String value)
+ {
+ this.intactId = value;
+ }
}
// Generated on: 2019.04.05 at 08:01:44 AM BST
//
-
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlType;
import javax.xml.bind.annotation.XmlValue;
-
/**
* Describes isoforms in 'alternative products' annotations.
*
- * <p>Java class for isoformType complex type.
+ * <p>
+ * Java class for isoformType complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
*
* <pre>
* <complexType name="isoformType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "isoformType", propOrder = {
- "id",
- "name",
- "sequence",
- "text"
-})
-public class IsoformType {
+@XmlType(
+ name = "isoformType",
+ propOrder =
+ { "id", "name", "sequence", "text" })
+public class IsoformType
+{
- @XmlElement(required = true)
- protected List<String> id;
- @XmlElement(required = true)
- protected List<IsoformType.Name> name;
- @XmlElement(required = true)
- protected IsoformType.Sequence sequence;
- protected List<EvidencedStringType> text;
+ @XmlElement(required = true)
+ protected List<String> id;
- /**
- * Gets the value of the id property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the id property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getId().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link String }
- *
- *
- */
- public List<String> getId() {
- if (id == null) {
- id = new ArrayList<String>();
- }
- return this.id;
+ @XmlElement(required = true)
+ protected List<IsoformType.Name> name;
+
+ @XmlElement(required = true)
+ protected IsoformType.Sequence sequence;
+
+ protected List<EvidencedStringType> text;
+
+ /**
+ * Gets the value of the id property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the id property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getId().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link String }
+ *
+ *
+ */
+ public List<String> getId()
+ {
+ if (id == null)
+ {
+ id = new ArrayList<String>();
}
+ return this.id;
+ }
- /**
- * Gets the value of the name property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the name property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getName().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link IsoformType.Name }
- *
- *
- */
- public List<IsoformType.Name> getName() {
- if (name == null) {
- name = new ArrayList<IsoformType.Name>();
- }
- return this.name;
+ /**
+ * Gets the value of the name property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the name property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link IsoformType.Name }
+ *
+ *
+ */
+ public List<IsoformType.Name> getName()
+ {
+ if (name == null)
+ {
+ name = new ArrayList<IsoformType.Name>();
+ }
+ return this.name;
+ }
+
+ /**
+ * Gets the value of the sequence property.
+ *
+ * @return possible object is {@link IsoformType.Sequence }
+ *
+ */
+ public IsoformType.Sequence getSequence()
+ {
+ return sequence;
+ }
+
+ /**
+ * Sets the value of the sequence property.
+ *
+ * @param value
+ * allowed object is {@link IsoformType.Sequence }
+ *
+ */
+ public void setSequence(IsoformType.Sequence value)
+ {
+ this.sequence = value;
+ }
+
+ /**
+ * Gets the value of the text property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the text property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getText().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getText()
+ {
+ if (text == null)
+ {
+ text = new ArrayList<EvidencedStringType>();
}
+ return this.text;
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <simpleContent>
+ * <extension base="<http://www.w3.org/2001/XMLSchema>string">
+ * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+ * </extension>
+ * </simpleContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "value" })
+ public static class Name
+ {
+
+ @XmlValue
+ protected String value;
+
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
/**
- * Gets the value of the sequence property.
+ * Gets the value of the value property.
+ *
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link IsoformType.Sequence }
- *
*/
- public IsoformType.Sequence getSequence() {
- return sequence;
+ public String getValue()
+ {
+ return value;
}
/**
- * Sets the value of the sequence property.
+ * Sets the value of the value property.
*
* @param value
- * allowed object is
- * {@link IsoformType.Sequence }
- *
+ * allowed object is {@link String }
+ *
*/
- public void setSequence(IsoformType.Sequence value) {
- this.sequence = value;
+ public void setValue(String value)
+ {
+ this.value = value;
}
/**
- * Gets the value of the text property.
+ * Gets the value of the evidence property.
*
* <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the text property.
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the evidence property.
*
* <p>
* For example, to add a new item, do as follows:
+ *
* <pre>
- * getText().add(newItem);
+ * getEvidence().add(newItem);
* </pre>
*
*
* <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
+ * Objects of the following type(s) are allowed in the list {@link Integer }
*
*
*/
- public List<EvidencedStringType> getText() {
- if (text == null) {
- text = new ArrayList<EvidencedStringType>();
- }
- return this.text;
+ public List<Integer> getEvidence()
+ {
+ if (evidence == null)
+ {
+ evidence = new ArrayList<Integer>();
+ }
+ return this.evidence;
}
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="type" use="required">
+ * <simpleType>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ * <enumeration value="not described"/>
+ * <enumeration value="described"/>
+ * <enumeration value="displayed"/>
+ * <enumeration value="external"/>
+ * </restriction>
+ * </simpleType>
+ * </attribute>
+ * <attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Sequence
+ {
+
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
+
+ @XmlAttribute(name = "ref")
+ protected String ref;
/**
- * <p>Java class for anonymous complex type.
+ * Gets the value of the type property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * @return possible object is {@link String }
*
- * <pre>
- * <complexType>
- * <simpleContent>
- * <extension base="<http://www.w3.org/2001/XMLSchema>string">
- * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
- * </extension>
- * </simpleContent>
- * </complexType>
- * </pre>
+ */
+ public String getType()
+ {
+ return type;
+ }
+
+ /**
+ * Sets the value of the type property.
*
+ * @param value
+ * allowed object is {@link String }
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "value"
- })
- public static class Name {
-
- @XmlValue
- protected String value;
- @XmlAttribute(name = "evidence")
- protected List<Integer> evidence;
-
- /**
- * Gets the value of the value property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getValue() {
- return value;
- }
-
- /**
- * Sets the value of the value property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setValue(String value) {
- this.value = value;
- }
-
- /**
- * Gets the value of the evidence property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the evidence property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getEvidence().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Integer }
- *
- *
- */
- public List<Integer> getEvidence() {
- if (evidence == null) {
- evidence = new ArrayList<Integer>();
- }
- return this.evidence;
- }
-
+ public void setType(String value)
+ {
+ this.type = value;
}
-
/**
- * <p>Java class for anonymous complex type.
+ * Gets the value of the ref property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * @return possible object is {@link String }
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="type" use="required">
- * <simpleType>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
- * <enumeration value="not described"/>
- * <enumeration value="described"/>
- * <enumeration value="displayed"/>
- * <enumeration value="external"/>
- * </restriction>
- * </simpleType>
- * </attribute>
- * <attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ */
+ public String getRef()
+ {
+ return ref;
+ }
+
+ /**
+ * Sets the value of the ref property.
*
+ * @param value
+ * allowed object is {@link String }
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class Sequence {
-
- @XmlAttribute(name = "type", required = true)
- protected String type;
- @XmlAttribute(name = "ref")
- protected String ref;
-
- /**
- * Gets the value of the type property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getType() {
- return type;
- }
-
- /**
- * Sets the value of the type property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setType(String value) {
- this.type = value;
- }
-
- /**
- * Gets the value of the ref property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getRef() {
- return ref;
- }
-
- /**
- * Sets the value of the ref property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setRef(String value) {
- this.ref = value;
- }
-
+ public void setRef(String value)
+ {
+ this.ref = value;
}
+ }
+
}
// Generated on: 2019.04.05 at 08:01:44 AM BST
//
-
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlType;
import javax.xml.bind.annotation.XmlValue;
-
/**
- * <p>Java class for keywordType complex type.
+ * <p>
+ * Java class for keywordType complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
*
* <pre>
* <complexType name="keywordType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "keywordType", propOrder = {
- "value"
-})
-public class KeywordType {
+@XmlType(name = "keywordType", propOrder = { "value" })
+public class KeywordType
+{
- @XmlValue
- protected String value;
- @XmlAttribute(name = "evidence")
- protected List<Integer> evidence;
- @XmlAttribute(name = "id", required = true)
- protected String id;
+ @XmlValue
+ protected String value;
- /**
- * Gets the value of the value property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getValue() {
- return value;
- }
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
- /**
- * Sets the value of the value property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setValue(String value) {
- this.value = value;
- }
+ @XmlAttribute(name = "id", required = true)
+ protected String id;
- /**
- * Gets the value of the evidence property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the evidence property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getEvidence().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Integer }
- *
- *
- */
- public List<Integer> getEvidence() {
- if (evidence == null) {
- evidence = new ArrayList<Integer>();
- }
- return this.evidence;
- }
+ /**
+ * Gets the value of the value property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getValue()
+ {
+ return value;
+ }
- /**
- * Gets the value of the id property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getId() {
- return id;
- }
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setValue(String value)
+ {
+ this.value = value;
+ }
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setId(String value) {
- this.id = value;
+ /**
+ * Gets the value of the evidence property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getEvidence()
+ {
+ if (evidence == null)
+ {
+ evidence = new ArrayList<Integer>();
}
+ return this.evidence;
+ }
+
+ /**
+ * Gets the value of the id property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getId()
+ {
+ return id;
+ }
+
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setId(String value)
+ {
+ this.id = value;
+ }
}
// Generated on: 2019.04.05 at 08:01:44 AM BST
//
-
package jalview.xml.binding.uniprot;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlType;
-
/**
- * Describes a sequence location as either a range with a begin and end or as a position. The 'sequence' attribute is only used when the location is not on the canonical sequence displayed in the current entry.
+ * Describes a sequence location as either a range with a begin and end or as a
+ * position. The 'sequence' attribute is only used when the location is not on
+ * the canonical sequence displayed in the current entry.
*
- * <p>Java class for locationType complex type.
+ * <p>
+ * Java class for locationType complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
*
* <pre>
* <complexType name="locationType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "locationType", propOrder = {
- "begin",
- "end",
- "position"
-})
-public class LocationType {
-
- protected PositionType begin;
- protected PositionType end;
- protected PositionType position;
- @XmlAttribute(name = "sequence")
- protected String sequence;
-
- /**
- * Gets the value of the begin property.
- *
- * @return
- * possible object is
- * {@link PositionType }
- *
- */
- public PositionType getBegin() {
- return begin;
- }
-
- /**
- * Sets the value of the begin property.
- *
- * @param value
- * allowed object is
- * {@link PositionType }
- *
- */
- public void setBegin(PositionType value) {
- this.begin = value;
- }
-
- /**
- * Gets the value of the end property.
- *
- * @return
- * possible object is
- * {@link PositionType }
- *
- */
- public PositionType getEnd() {
- return end;
- }
-
- /**
- * Sets the value of the end property.
- *
- * @param value
- * allowed object is
- * {@link PositionType }
- *
- */
- public void setEnd(PositionType value) {
- this.end = value;
- }
-
- /**
- * Gets the value of the position property.
- *
- * @return
- * possible object is
- * {@link PositionType }
- *
- */
- public PositionType getPosition() {
- return position;
- }
-
- /**
- * Sets the value of the position property.
- *
- * @param value
- * allowed object is
- * {@link PositionType }
- *
- */
- public void setPosition(PositionType value) {
- this.position = value;
- }
-
- /**
- * Gets the value of the sequence property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getSequence() {
- return sequence;
- }
-
- /**
- * Sets the value of the sequence property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setSequence(String value) {
- this.sequence = value;
- }
+@XmlType(name = "locationType", propOrder = { "begin", "end", "position" })
+public class LocationType
+{
+
+ protected PositionType begin;
+
+ protected PositionType end;
+
+ protected PositionType position;
+
+ @XmlAttribute(name = "sequence")
+ protected String sequence;
+
+ /**
+ * Gets the value of the begin property.
+ *
+ * @return possible object is {@link PositionType }
+ *
+ */
+ public PositionType getBegin()
+ {
+ return begin;
+ }
+
+ /**
+ * Sets the value of the begin property.
+ *
+ * @param value
+ * allowed object is {@link PositionType }
+ *
+ */
+ public void setBegin(PositionType value)
+ {
+ this.begin = value;
+ }
+
+ /**
+ * Gets the value of the end property.
+ *
+ * @return possible object is {@link PositionType }
+ *
+ */
+ public PositionType getEnd()
+ {
+ return end;
+ }
+
+ /**
+ * Sets the value of the end property.
+ *
+ * @param value
+ * allowed object is {@link PositionType }
+ *
+ */
+ public void setEnd(PositionType value)
+ {
+ this.end = value;
+ }
+
+ /**
+ * Gets the value of the position property.
+ *
+ * @return possible object is {@link PositionType }
+ *
+ */
+ public PositionType getPosition()
+ {
+ return position;
+ }
+
+ /**
+ * Sets the value of the position property.
+ *
+ * @param value
+ * allowed object is {@link PositionType }
+ *
+ */
+ public void setPosition(PositionType value)
+ {
+ this.position = value;
+ }
+
+ /**
+ * Gets the value of the sequence property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getSequence()
+ {
+ return sequence;
+ }
+
+ /**
+ * Sets the value of the sequence property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setSequence(String value)
+ {
+ this.sequence = value;
+ }
}
// Generated on: 2019.04.05 at 08:01:44 AM BST
//
-
package jalview.xml.binding.uniprot;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlType;
import javax.xml.bind.annotation.XmlValue;
-
/**
* Describes a molecule by name or unique identifier.
*
- * <p>Java class for moleculeType complex type.
+ * <p>
+ * Java class for moleculeType complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
*
* <pre>
* <complexType name="moleculeType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "moleculeType", propOrder = {
- "value"
-})
-public class MoleculeType {
+@XmlType(name = "moleculeType", propOrder = { "value" })
+public class MoleculeType
+{
+
+ @XmlValue
+ protected String value;
- @XmlValue
- protected String value;
- @XmlAttribute(name = "id")
- protected String id;
+ @XmlAttribute(name = "id")
+ protected String id;
- /**
- * Gets the value of the value property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getValue() {
- return value;
- }
+ /**
+ * Gets the value of the value property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getValue()
+ {
+ return value;
+ }
- /**
- * Sets the value of the value property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setValue(String value) {
- this.value = value;
- }
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setValue(String value)
+ {
+ this.value = value;
+ }
- /**
- * Gets the value of the id property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getId() {
- return id;
- }
+ /**
+ * Gets the value of the id property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getId()
+ {
+ return id;
+ }
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setId(String value) {
- this.id = value;
- }
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setId(String value)
+ {
+ this.id = value;
+ }
}
// Generated on: 2019.04.05 at 08:01:44 AM BST
//
-
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlElements;
import javax.xml.bind.annotation.XmlType;
-
/**
- * <p>Java class for nameListType complex type.
+ * <p>
+ * Java class for nameListType complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
*
* <pre>
* <complexType name="nameListType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "nameListType", propOrder = {
- "consortiumOrPerson"
-})
-public class NameListType {
+@XmlType(name = "nameListType", propOrder = { "consortiumOrPerson" })
+public class NameListType
+{
- @XmlElements({
- @XmlElement(name = "consortium", type = ConsortiumType.class),
- @XmlElement(name = "person", type = PersonType.class)
- })
- protected List<Object> consortiumOrPerson;
+ @XmlElements({
+ @XmlElement(name = "consortium", type = ConsortiumType.class),
+ @XmlElement(name = "person", type = PersonType.class) })
+ protected List<Object> consortiumOrPerson;
- /**
- * Gets the value of the consortiumOrPerson property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the consortiumOrPerson property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getConsortiumOrPerson().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link ConsortiumType }
- * {@link PersonType }
- *
- *
- */
- public List<Object> getConsortiumOrPerson() {
- if (consortiumOrPerson == null) {
- consortiumOrPerson = new ArrayList<Object>();
- }
- return this.consortiumOrPerson;
+ /**
+ * Gets the value of the consortiumOrPerson property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the consortiumOrPerson property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getConsortiumOrPerson().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link ConsortiumType } {@link PersonType }
+ *
+ *
+ */
+ public List<Object> getConsortiumOrPerson()
+ {
+ if (consortiumOrPerson == null)
+ {
+ consortiumOrPerson = new ArrayList<Object>();
}
+ return this.consortiumOrPerson;
+ }
}
// Generated on: 2019.04.05 at 08:01:44 AM BST
//
-
package jalview.xml.binding.uniprot;
import javax.xml.bind.JAXBElement;
import javax.xml.bind.annotation.XmlRegistry;
import javax.xml.namespace.QName;
-
/**
- * This object contains factory methods for each
- * Java content interface and Java element interface
- * generated in the jalview.xml.binding.uniprot package.
- * <p>An ObjectFactory allows you to programatically
- * construct new instances of the Java representation
- * for XML content. The Java representation of XML
- * content can consist of schema derived interfaces
- * and classes representing the binding of schema
- * type definitions, element declarations and model
- * groups. Factory methods for each of these are
- * provided in this class.
+ * This object contains factory methods for each Java content interface and Java
+ * element interface generated in the jalview.xml.binding.uniprot package.
+ * <p>
+ * An ObjectFactory allows you to programatically construct new instances of the
+ * Java representation for XML content. The Java representation of XML content
+ * can consist of schema derived interfaces and classes representing the binding
+ * of schema type definitions, element declarations and model groups. Factory
+ * methods for each of these are provided in this class.
*
*/
@XmlRegistry
-public class ObjectFactory {
-
- private final static QName _Copyright_QNAME = new QName("http://uniprot.org/uniprot", "copyright");
-
- /**
- * Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: jalview.xml.binding.uniprot
- *
- */
- public ObjectFactory() {
- }
-
- /**
- * Create an instance of {@link SourceDataType }
- *
- */
- public SourceDataType createSourceDataType() {
- return new SourceDataType();
- }
-
- /**
- * Create an instance of {@link IsoformType }
- *
- */
- public IsoformType createIsoformType() {
- return new IsoformType();
- }
-
- /**
- * Create an instance of {@link CommentType }
- *
- */
- public CommentType createCommentType() {
- return new CommentType();
- }
-
- /**
- * Create an instance of {@link CommentType.Conflict }
- *
- */
- public CommentType.Conflict createCommentTypeConflict() {
- return new CommentType.Conflict();
- }
-
- /**
- * Create an instance of {@link OrganismType }
- *
- */
- public OrganismType createOrganismType() {
- return new OrganismType();
- }
-
- /**
- * Create an instance of {@link ProteinType }
- *
- */
- public ProteinType createProteinType() {
- return new ProteinType();
- }
-
- /**
- * Create an instance of {@link Entry }
- *
- */
- public Entry createEntry() {
- return new Entry();
- }
-
- /**
- * Create an instance of {@link GeneType }
- *
- */
- public GeneType createGeneType() {
- return new GeneType();
- }
-
- /**
- * Create an instance of {@link GeneLocationType }
- *
- */
- public GeneLocationType createGeneLocationType() {
- return new GeneLocationType();
- }
-
- /**
- * Create an instance of {@link ReferenceType }
- *
- */
- public ReferenceType createReferenceType() {
- return new ReferenceType();
- }
-
- /**
- * Create an instance of {@link DbReferenceType }
- *
- */
- public DbReferenceType createDbReferenceType() {
- return new DbReferenceType();
- }
-
- /**
- * Create an instance of {@link ProteinExistenceType }
- *
- */
- public ProteinExistenceType createProteinExistenceType() {
- return new ProteinExistenceType();
- }
-
- /**
- * Create an instance of {@link KeywordType }
- *
- */
- public KeywordType createKeywordType() {
- return new KeywordType();
- }
-
- /**
- * Create an instance of {@link FeatureType }
- *
- */
- public FeatureType createFeatureType() {
- return new FeatureType();
- }
-
- /**
- * Create an instance of {@link EvidenceType }
- *
- */
- public EvidenceType createEvidenceType() {
- return new EvidenceType();
- }
-
- /**
- * Create an instance of {@link SequenceType }
- *
- */
- public SequenceType createSequenceType() {
- return new SequenceType();
- }
-
- /**
- * Create an instance of {@link Uniprot }
- *
- */
- public Uniprot createUniprot() {
- return new Uniprot();
- }
-
- /**
- * Create an instance of {@link StatusType }
- *
- */
- public StatusType createStatusType() {
- return new StatusType();
- }
-
- /**
- * Create an instance of {@link PositionType }
- *
- */
- public PositionType createPositionType() {
- return new PositionType();
- }
-
- /**
- * Create an instance of {@link ConsortiumType }
- *
- */
- public ConsortiumType createConsortiumType() {
- return new ConsortiumType();
- }
-
- /**
- * Create an instance of {@link GeneNameType }
- *
- */
- public GeneNameType createGeneNameType() {
- return new GeneNameType();
- }
-
- /**
- * Create an instance of {@link LocationType }
- *
- */
- public LocationType createLocationType() {
- return new LocationType();
- }
-
- /**
- * Create an instance of {@link CitationType }
- *
- */
- public CitationType createCitationType() {
- return new CitationType();
- }
-
- /**
- * Create an instance of {@link PropertyType }
- *
- */
- public PropertyType createPropertyType() {
- return new PropertyType();
- }
-
- /**
- * Create an instance of {@link PhysiologicalReactionType }
- *
- */
- public PhysiologicalReactionType createPhysiologicalReactionType() {
- return new PhysiologicalReactionType();
- }
-
- /**
- * Create an instance of {@link CofactorType }
- *
- */
- public CofactorType createCofactorType() {
- return new CofactorType();
- }
-
- /**
- * Create an instance of {@link EvidencedStringType }
- *
- */
- public EvidencedStringType createEvidencedStringType() {
- return new EvidencedStringType();
- }
-
- /**
- * Create an instance of {@link PersonType }
- *
- */
- public PersonType createPersonType() {
- return new PersonType();
- }
-
- /**
- * Create an instance of {@link ImportedFromType }
- *
- */
- public ImportedFromType createImportedFromType() {
- return new ImportedFromType();
- }
-
- /**
- * Create an instance of {@link EventType }
- *
- */
- public EventType createEventType() {
- return new EventType();
- }
-
- /**
- * Create an instance of {@link InteractantType }
- *
- */
- public InteractantType createInteractantType() {
- return new InteractantType();
- }
-
- /**
- * Create an instance of {@link NameListType }
- *
- */
- public NameListType createNameListType() {
- return new NameListType();
- }
-
- /**
- * Create an instance of {@link ReactionType }
- *
- */
- public ReactionType createReactionType() {
- return new ReactionType();
- }
-
- /**
- * Create an instance of {@link SourceType }
- *
- */
- public SourceType createSourceType() {
- return new SourceType();
- }
-
- /**
- * Create an instance of {@link MoleculeType }
- *
- */
- public MoleculeType createMoleculeType() {
- return new MoleculeType();
- }
-
- /**
- * Create an instance of {@link OrganismNameType }
- *
- */
- public OrganismNameType createOrganismNameType() {
- return new OrganismNameType();
- }
-
- /**
- * Create an instance of {@link SubcellularLocationType }
- *
- */
- public SubcellularLocationType createSubcellularLocationType() {
- return new SubcellularLocationType();
- }
-
- /**
- * Create an instance of {@link SourceDataType.Strain }
- *
- */
- public SourceDataType.Strain createSourceDataTypeStrain() {
- return new SourceDataType.Strain();
- }
-
- /**
- * Create an instance of {@link SourceDataType.Plasmid }
- *
- */
- public SourceDataType.Plasmid createSourceDataTypePlasmid() {
- return new SourceDataType.Plasmid();
- }
-
- /**
- * Create an instance of {@link SourceDataType.Transposon }
- *
- */
- public SourceDataType.Transposon createSourceDataTypeTransposon() {
- return new SourceDataType.Transposon();
- }
-
- /**
- * Create an instance of {@link SourceDataType.Tissue }
- *
- */
- public SourceDataType.Tissue createSourceDataTypeTissue() {
- return new SourceDataType.Tissue();
- }
-
- /**
- * Create an instance of {@link IsoformType.Name }
- *
- */
- public IsoformType.Name createIsoformTypeName() {
- return new IsoformType.Name();
- }
-
- /**
- * Create an instance of {@link IsoformType.Sequence }
- *
- */
- public IsoformType.Sequence createIsoformTypeSequence() {
- return new IsoformType.Sequence();
- }
-
- /**
- * Create an instance of {@link CommentType.Absorption }
- *
- */
- public CommentType.Absorption createCommentTypeAbsorption() {
- return new CommentType.Absorption();
- }
-
- /**
- * Create an instance of {@link CommentType.Kinetics }
- *
- */
- public CommentType.Kinetics createCommentTypeKinetics() {
- return new CommentType.Kinetics();
- }
-
- /**
- * Create an instance of {@link CommentType.PhDependence }
- *
- */
- public CommentType.PhDependence createCommentTypePhDependence() {
- return new CommentType.PhDependence();
- }
-
- /**
- * Create an instance of {@link CommentType.RedoxPotential }
- *
- */
- public CommentType.RedoxPotential createCommentTypeRedoxPotential() {
- return new CommentType.RedoxPotential();
- }
-
- /**
- * Create an instance of {@link CommentType.TemperatureDependence }
- *
- */
- public CommentType.TemperatureDependence createCommentTypeTemperatureDependence() {
- return new CommentType.TemperatureDependence();
- }
-
- /**
- * Create an instance of {@link CommentType.Link }
- *
- */
- public CommentType.Link createCommentTypeLink() {
- return new CommentType.Link();
- }
-
- /**
- * Create an instance of {@link CommentType.Disease }
- *
- */
- public CommentType.Disease createCommentTypeDisease() {
- return new CommentType.Disease();
- }
-
- /**
- * Create an instance of {@link CommentType.Conflict.Sequence }
- *
- */
- public CommentType.Conflict.Sequence createCommentTypeConflictSequence() {
- return new CommentType.Conflict.Sequence();
- }
-
- /**
- * Create an instance of {@link OrganismType.Lineage }
- *
- */
- public OrganismType.Lineage createOrganismTypeLineage() {
- return new OrganismType.Lineage();
- }
-
- /**
- * Create an instance of {@link ProteinType.RecommendedName }
- *
- */
- public ProteinType.RecommendedName createProteinTypeRecommendedName() {
- return new ProteinType.RecommendedName();
- }
-
- /**
- * Create an instance of {@link ProteinType.AlternativeName }
- *
- */
- public ProteinType.AlternativeName createProteinTypeAlternativeName() {
- return new ProteinType.AlternativeName();
- }
-
- /**
- * Create an instance of {@link ProteinType.SubmittedName }
- *
- */
- public ProteinType.SubmittedName createProteinTypeSubmittedName() {
- return new ProteinType.SubmittedName();
- }
-
- /**
- * Create an instance of {@link ProteinType.Domain }
- *
- */
- public ProteinType.Domain createProteinTypeDomain() {
- return new ProteinType.Domain();
- }
-
- /**
- * Create an instance of {@link ProteinType.Component }
- *
- */
- public ProteinType.Component createProteinTypeComponent() {
- return new ProteinType.Component();
- }
-
- /**
- * Create an instance of {@link JAXBElement }{@code <}{@link String }{@code >}}
- *
- */
- @XmlElementDecl(namespace = "http://uniprot.org/uniprot", name = "copyright")
- public JAXBElement<String> createCopyright(String value) {
- return new JAXBElement<String>(_Copyright_QNAME, String.class, null, value);
- }
+public class ObjectFactory
+{
+
+ private final static QName _Copyright_QNAME = new QName(
+ "http://uniprot.org/uniprot", "copyright");
+
+ /**
+ * Create a new ObjectFactory that can be used to create new instances of
+ * schema derived classes for package: jalview.xml.binding.uniprot
+ *
+ */
+ public ObjectFactory()
+ {
+ }
+
+ /**
+ * Create an instance of {@link SourceDataType }
+ *
+ */
+ public SourceDataType createSourceDataType()
+ {
+ return new SourceDataType();
+ }
+
+ /**
+ * Create an instance of {@link IsoformType }
+ *
+ */
+ public IsoformType createIsoformType()
+ {
+ return new IsoformType();
+ }
+
+ /**
+ * Create an instance of {@link CommentType }
+ *
+ */
+ public CommentType createCommentType()
+ {
+ return new CommentType();
+ }
+
+ /**
+ * Create an instance of {@link CommentType.Conflict }
+ *
+ */
+ public CommentType.Conflict createCommentTypeConflict()
+ {
+ return new CommentType.Conflict();
+ }
+
+ /**
+ * Create an instance of {@link OrganismType }
+ *
+ */
+ public OrganismType createOrganismType()
+ {
+ return new OrganismType();
+ }
+
+ /**
+ * Create an instance of {@link ProteinType }
+ *
+ */
+ public ProteinType createProteinType()
+ {
+ return new ProteinType();
+ }
+
+ /**
+ * Create an instance of {@link Entry }
+ *
+ */
+ public Entry createEntry()
+ {
+ return new Entry();
+ }
+
+ /**
+ * Create an instance of {@link GeneType }
+ *
+ */
+ public GeneType createGeneType()
+ {
+ return new GeneType();
+ }
+
+ /**
+ * Create an instance of {@link GeneLocationType }
+ *
+ */
+ public GeneLocationType createGeneLocationType()
+ {
+ return new GeneLocationType();
+ }
+
+ /**
+ * Create an instance of {@link ReferenceType }
+ *
+ */
+ public ReferenceType createReferenceType()
+ {
+ return new ReferenceType();
+ }
+
+ /**
+ * Create an instance of {@link DbReferenceType }
+ *
+ */
+ public DbReferenceType createDbReferenceType()
+ {
+ return new DbReferenceType();
+ }
+
+ /**
+ * Create an instance of {@link ProteinExistenceType }
+ *
+ */
+ public ProteinExistenceType createProteinExistenceType()
+ {
+ return new ProteinExistenceType();
+ }
+
+ /**
+ * Create an instance of {@link KeywordType }
+ *
+ */
+ public KeywordType createKeywordType()
+ {
+ return new KeywordType();
+ }
+
+ /**
+ * Create an instance of {@link FeatureType }
+ *
+ */
+ public FeatureType createFeatureType()
+ {
+ return new FeatureType();
+ }
+
+ /**
+ * Create an instance of {@link EvidenceType }
+ *
+ */
+ public EvidenceType createEvidenceType()
+ {
+ return new EvidenceType();
+ }
+
+ /**
+ * Create an instance of {@link SequenceType }
+ *
+ */
+ public SequenceType createSequenceType()
+ {
+ return new SequenceType();
+ }
+
+ /**
+ * Create an instance of {@link Uniprot }
+ *
+ */
+ public Uniprot createUniprot()
+ {
+ return new Uniprot();
+ }
+
+ /**
+ * Create an instance of {@link StatusType }
+ *
+ */
+ public StatusType createStatusType()
+ {
+ return new StatusType();
+ }
+
+ /**
+ * Create an instance of {@link PositionType }
+ *
+ */
+ public PositionType createPositionType()
+ {
+ return new PositionType();
+ }
+
+ /**
+ * Create an instance of {@link ConsortiumType }
+ *
+ */
+ public ConsortiumType createConsortiumType()
+ {
+ return new ConsortiumType();
+ }
+
+ /**
+ * Create an instance of {@link GeneNameType }
+ *
+ */
+ public GeneNameType createGeneNameType()
+ {
+ return new GeneNameType();
+ }
+
+ /**
+ * Create an instance of {@link LocationType }
+ *
+ */
+ public LocationType createLocationType()
+ {
+ return new LocationType();
+ }
+
+ /**
+ * Create an instance of {@link CitationType }
+ *
+ */
+ public CitationType createCitationType()
+ {
+ return new CitationType();
+ }
+
+ /**
+ * Create an instance of {@link PropertyType }
+ *
+ */
+ public PropertyType createPropertyType()
+ {
+ return new PropertyType();
+ }
+
+ /**
+ * Create an instance of {@link PhysiologicalReactionType }
+ *
+ */
+ public PhysiologicalReactionType createPhysiologicalReactionType()
+ {
+ return new PhysiologicalReactionType();
+ }
+
+ /**
+ * Create an instance of {@link CofactorType }
+ *
+ */
+ public CofactorType createCofactorType()
+ {
+ return new CofactorType();
+ }
+
+ /**
+ * Create an instance of {@link EvidencedStringType }
+ *
+ */
+ public EvidencedStringType createEvidencedStringType()
+ {
+ return new EvidencedStringType();
+ }
+
+ /**
+ * Create an instance of {@link PersonType }
+ *
+ */
+ public PersonType createPersonType()
+ {
+ return new PersonType();
+ }
+
+ /**
+ * Create an instance of {@link ImportedFromType }
+ *
+ */
+ public ImportedFromType createImportedFromType()
+ {
+ return new ImportedFromType();
+ }
+
+ /**
+ * Create an instance of {@link EventType }
+ *
+ */
+ public EventType createEventType()
+ {
+ return new EventType();
+ }
+
+ /**
+ * Create an instance of {@link InteractantType }
+ *
+ */
+ public InteractantType createInteractantType()
+ {
+ return new InteractantType();
+ }
+
+ /**
+ * Create an instance of {@link NameListType }
+ *
+ */
+ public NameListType createNameListType()
+ {
+ return new NameListType();
+ }
+
+ /**
+ * Create an instance of {@link ReactionType }
+ *
+ */
+ public ReactionType createReactionType()
+ {
+ return new ReactionType();
+ }
+
+ /**
+ * Create an instance of {@link SourceType }
+ *
+ */
+ public SourceType createSourceType()
+ {
+ return new SourceType();
+ }
+
+ /**
+ * Create an instance of {@link MoleculeType }
+ *
+ */
+ public MoleculeType createMoleculeType()
+ {
+ return new MoleculeType();
+ }
+
+ /**
+ * Create an instance of {@link OrganismNameType }
+ *
+ */
+ public OrganismNameType createOrganismNameType()
+ {
+ return new OrganismNameType();
+ }
+
+ /**
+ * Create an instance of {@link SubcellularLocationType }
+ *
+ */
+ public SubcellularLocationType createSubcellularLocationType()
+ {
+ return new SubcellularLocationType();
+ }
+
+ /**
+ * Create an instance of {@link SourceDataType.Strain }
+ *
+ */
+ public SourceDataType.Strain createSourceDataTypeStrain()
+ {
+ return new SourceDataType.Strain();
+ }
+
+ /**
+ * Create an instance of {@link SourceDataType.Plasmid }
+ *
+ */
+ public SourceDataType.Plasmid createSourceDataTypePlasmid()
+ {
+ return new SourceDataType.Plasmid();
+ }
+
+ /**
+ * Create an instance of {@link SourceDataType.Transposon }
+ *
+ */
+ public SourceDataType.Transposon createSourceDataTypeTransposon()
+ {
+ return new SourceDataType.Transposon();
+ }
+
+ /**
+ * Create an instance of {@link SourceDataType.Tissue }
+ *
+ */
+ public SourceDataType.Tissue createSourceDataTypeTissue()
+ {
+ return new SourceDataType.Tissue();
+ }
+
+ /**
+ * Create an instance of {@link IsoformType.Name }
+ *
+ */
+ public IsoformType.Name createIsoformTypeName()
+ {
+ return new IsoformType.Name();
+ }
+
+ /**
+ * Create an instance of {@link IsoformType.Sequence }
+ *
+ */
+ public IsoformType.Sequence createIsoformTypeSequence()
+ {
+ return new IsoformType.Sequence();
+ }
+
+ /**
+ * Create an instance of {@link CommentType.Absorption }
+ *
+ */
+ public CommentType.Absorption createCommentTypeAbsorption()
+ {
+ return new CommentType.Absorption();
+ }
+
+ /**
+ * Create an instance of {@link CommentType.Kinetics }
+ *
+ */
+ public CommentType.Kinetics createCommentTypeKinetics()
+ {
+ return new CommentType.Kinetics();
+ }
+
+ /**
+ * Create an instance of {@link CommentType.PhDependence }
+ *
+ */
+ public CommentType.PhDependence createCommentTypePhDependence()
+ {
+ return new CommentType.PhDependence();
+ }
+
+ /**
+ * Create an instance of {@link CommentType.RedoxPotential }
+ *
+ */
+ public CommentType.RedoxPotential createCommentTypeRedoxPotential()
+ {
+ return new CommentType.RedoxPotential();
+ }
+
+ /**
+ * Create an instance of {@link CommentType.TemperatureDependence }
+ *
+ */
+ public CommentType.TemperatureDependence createCommentTypeTemperatureDependence()
+ {
+ return new CommentType.TemperatureDependence();
+ }
+
+ /**
+ * Create an instance of {@link CommentType.Link }
+ *
+ */
+ public CommentType.Link createCommentTypeLink()
+ {
+ return new CommentType.Link();
+ }
+
+ /**
+ * Create an instance of {@link CommentType.Disease }
+ *
+ */
+ public CommentType.Disease createCommentTypeDisease()
+ {
+ return new CommentType.Disease();
+ }
+
+ /**
+ * Create an instance of {@link CommentType.Conflict.Sequence }
+ *
+ */
+ public CommentType.Conflict.Sequence createCommentTypeConflictSequence()
+ {
+ return new CommentType.Conflict.Sequence();
+ }
+
+ /**
+ * Create an instance of {@link OrganismType.Lineage }
+ *
+ */
+ public OrganismType.Lineage createOrganismTypeLineage()
+ {
+ return new OrganismType.Lineage();
+ }
+
+ /**
+ * Create an instance of {@link ProteinType.RecommendedName }
+ *
+ */
+ public ProteinType.RecommendedName createProteinTypeRecommendedName()
+ {
+ return new ProteinType.RecommendedName();
+ }
+
+ /**
+ * Create an instance of {@link ProteinType.AlternativeName }
+ *
+ */
+ public ProteinType.AlternativeName createProteinTypeAlternativeName()
+ {
+ return new ProteinType.AlternativeName();
+ }
+
+ /**
+ * Create an instance of {@link ProteinType.SubmittedName }
+ *
+ */
+ public ProteinType.SubmittedName createProteinTypeSubmittedName()
+ {
+ return new ProteinType.SubmittedName();
+ }
+
+ /**
+ * Create an instance of {@link ProteinType.Domain }
+ *
+ */
+ public ProteinType.Domain createProteinTypeDomain()
+ {
+ return new ProteinType.Domain();
+ }
+
+ /**
+ * Create an instance of {@link ProteinType.Component }
+ *
+ */
+ public ProteinType.Component createProteinTypeComponent()
+ {
+ return new ProteinType.Component();
+ }
+
+ /**
+ * Create an instance of {@link JAXBElement }{@code <}{@link String
+ * }{@code >}}
+ *
+ */
+ @XmlElementDecl(
+ namespace = "http://uniprot.org/uniprot",
+ name = "copyright")
+ public JAXBElement<String> createCopyright(String value)
+ {
+ return new JAXBElement<String>(_Copyright_QNAME, String.class, null,
+ value);
+ }
}
// Generated on: 2019.04.05 at 08:01:44 AM BST
//
-
package jalview.xml.binding.uniprot;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlType;
import javax.xml.bind.annotation.XmlValue;
-
/**
* Describes different types of source organism names.
*
- * <p>Java class for organismNameType complex type.
+ * <p>
+ * Java class for organismNameType complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
*
* <pre>
* <complexType name="organismNameType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "organismNameType", propOrder = {
- "value"
-})
-public class OrganismNameType {
+@XmlType(name = "organismNameType", propOrder = { "value" })
+public class OrganismNameType
+{
+
+ @XmlValue
+ protected String value;
- @XmlValue
- protected String value;
- @XmlAttribute(name = "type", required = true)
- protected String type;
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
- /**
- * Gets the value of the value property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getValue() {
- return value;
- }
+ /**
+ * Gets the value of the value property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getValue()
+ {
+ return value;
+ }
- /**
- * Sets the value of the value property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setValue(String value) {
- this.value = value;
- }
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setValue(String value)
+ {
+ this.value = value;
+ }
- /**
- * Gets the value of the type property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getType() {
- return type;
- }
+ /**
+ * Gets the value of the type property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getType()
+ {
+ return type;
+ }
- /**
- * Sets the value of the type property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setType(String value) {
- this.type = value;
- }
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setType(String value)
+ {
+ this.type = value;
+ }
}
// Generated on: 2019.04.05 at 08:01:44 AM BST
//
-
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
-
/**
* Describes the source organism.
*
- * <p>Java class for organismType complex type.
+ * <p>
+ * Java class for organismType complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
*
* <pre>
* <complexType name="organismType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "organismType", propOrder = {
- "name",
- "dbReference",
- "lineage"
-})
-public class OrganismType {
-
- @XmlElement(required = true)
- protected List<OrganismNameType> name;
- @XmlElement(required = true)
- protected List<DbReferenceType> dbReference;
- protected OrganismType.Lineage lineage;
- @XmlAttribute(name = "evidence")
- protected List<Integer> evidence;
-
- /**
- * Gets the value of the name property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the name property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getName().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link OrganismNameType }
- *
- *
- */
- public List<OrganismNameType> getName() {
- if (name == null) {
- name = new ArrayList<OrganismNameType>();
- }
- return this.name;
+@XmlType(
+ name = "organismType",
+ propOrder =
+ { "name", "dbReference", "lineage" })
+public class OrganismType
+{
+
+ @XmlElement(required = true)
+ protected List<OrganismNameType> name;
+
+ @XmlElement(required = true)
+ protected List<DbReferenceType> dbReference;
+
+ protected OrganismType.Lineage lineage;
+
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
+
+ /**
+ * Gets the value of the name property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the name property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link OrganismNameType }
+ *
+ *
+ */
+ public List<OrganismNameType> getName()
+ {
+ if (name == null)
+ {
+ name = new ArrayList<OrganismNameType>();
}
-
- /**
- * Gets the value of the dbReference property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the dbReference property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getDbReference().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link DbReferenceType }
- *
- *
- */
- public List<DbReferenceType> getDbReference() {
- if (dbReference == null) {
- dbReference = new ArrayList<DbReferenceType>();
- }
- return this.dbReference;
+ return this.name;
+ }
+
+ /**
+ * Gets the value of the dbReference property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the dbReference property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getDbReference().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link DbReferenceType }
+ *
+ *
+ */
+ public List<DbReferenceType> getDbReference()
+ {
+ if (dbReference == null)
+ {
+ dbReference = new ArrayList<DbReferenceType>();
}
-
- /**
- * Gets the value of the lineage property.
- *
- * @return
- * possible object is
- * {@link OrganismType.Lineage }
- *
- */
- public OrganismType.Lineage getLineage() {
- return lineage;
+ return this.dbReference;
+ }
+
+ /**
+ * Gets the value of the lineage property.
+ *
+ * @return possible object is {@link OrganismType.Lineage }
+ *
+ */
+ public OrganismType.Lineage getLineage()
+ {
+ return lineage;
+ }
+
+ /**
+ * Sets the value of the lineage property.
+ *
+ * @param value
+ * allowed object is {@link OrganismType.Lineage }
+ *
+ */
+ public void setLineage(OrganismType.Lineage value)
+ {
+ this.lineage = value;
+ }
+
+ /**
+ * Gets the value of the evidence property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getEvidence()
+ {
+ if (evidence == null)
+ {
+ evidence = new ArrayList<Integer>();
}
+ return this.evidence;
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="taxon" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "taxon" })
+ public static class Lineage
+ {
- /**
- * Sets the value of the lineage property.
- *
- * @param value
- * allowed object is
- * {@link OrganismType.Lineage }
- *
- */
- public void setLineage(OrganismType.Lineage value) {
- this.lineage = value;
- }
+ @XmlElement(required = true)
+ protected List<String> taxon;
/**
- * Gets the value of the evidence property.
+ * Gets the value of the taxon property.
*
* <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the evidence property.
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the taxon property.
*
* <p>
* For example, to add a new item, do as follows:
+ *
* <pre>
- * getEvidence().add(newItem);
+ * getTaxon().add(newItem);
* </pre>
*
*
* <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Integer }
+ * Objects of the following type(s) are allowed in the list {@link String }
*
*
*/
- public List<Integer> getEvidence() {
- if (evidence == null) {
- evidence = new ArrayList<Integer>();
- }
- return this.evidence;
+ public List<String> getTaxon()
+ {
+ if (taxon == null)
+ {
+ taxon = new ArrayList<String>();
+ }
+ return this.taxon;
}
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="taxon" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "taxon"
- })
- public static class Lineage {
-
- @XmlElement(required = true)
- protected List<String> taxon;
-
- /**
- * Gets the value of the taxon property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the taxon property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getTaxon().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link String }
- *
- *
- */
- public List<String> getTaxon() {
- if (taxon == null) {
- taxon = new ArrayList<String>();
- }
- return this.taxon;
- }
-
- }
+ }
}
// Generated on: 2019.04.05 at 08:01:44 AM BST
//
-
package jalview.xml.binding.uniprot;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlType;
-
/**
- * <p>Java class for personType complex type.
+ * <p>
+ * Java class for personType complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
*
* <pre>
* <complexType name="personType">
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "personType")
-public class PersonType {
+public class PersonType
+{
- @XmlAttribute(name = "name", required = true)
- protected String name;
+ @XmlAttribute(name = "name", required = true)
+ protected String name;
- /**
- * Gets the value of the name property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getName() {
- return name;
- }
+ /**
+ * Gets the value of the name property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getName()
+ {
+ return name;
+ }
- /**
- * Sets the value of the name property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setName(String value) {
- this.name = value;
- }
+ /**
+ * Sets the value of the name property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setName(String value)
+ {
+ this.name = value;
+ }
}
// Generated on: 2019.04.05 at 08:01:44 AM BST
//
-
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
-
/**
* Describes a physiological reaction.
*
- * <p>Java class for physiologicalReactionType complex type.
+ * <p>
+ * Java class for physiologicalReactionType complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
*
* <pre>
* <complexType name="physiologicalReactionType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "physiologicalReactionType", propOrder = {
- "dbReference"
-})
-public class PhysiologicalReactionType {
+@XmlType(name = "physiologicalReactionType", propOrder = { "dbReference" })
+public class PhysiologicalReactionType
+{
- @XmlElement(required = true)
- protected DbReferenceType dbReference;
- @XmlAttribute(name = "direction", required = true)
- protected String direction;
- @XmlAttribute(name = "evidence")
- protected List<Integer> evidence;
+ @XmlElement(required = true)
+ protected DbReferenceType dbReference;
- /**
- * Gets the value of the dbReference property.
- *
- * @return
- * possible object is
- * {@link DbReferenceType }
- *
- */
- public DbReferenceType getDbReference() {
- return dbReference;
- }
+ @XmlAttribute(name = "direction", required = true)
+ protected String direction;
- /**
- * Sets the value of the dbReference property.
- *
- * @param value
- * allowed object is
- * {@link DbReferenceType }
- *
- */
- public void setDbReference(DbReferenceType value) {
- this.dbReference = value;
- }
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
- /**
- * Gets the value of the direction property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getDirection() {
- return direction;
- }
+ /**
+ * Gets the value of the dbReference property.
+ *
+ * @return possible object is {@link DbReferenceType }
+ *
+ */
+ public DbReferenceType getDbReference()
+ {
+ return dbReference;
+ }
- /**
- * Sets the value of the direction property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setDirection(String value) {
- this.direction = value;
- }
+ /**
+ * Sets the value of the dbReference property.
+ *
+ * @param value
+ * allowed object is {@link DbReferenceType }
+ *
+ */
+ public void setDbReference(DbReferenceType value)
+ {
+ this.dbReference = value;
+ }
+
+ /**
+ * Gets the value of the direction property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getDirection()
+ {
+ return direction;
+ }
+
+ /**
+ * Sets the value of the direction property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setDirection(String value)
+ {
+ this.direction = value;
+ }
- /**
- * Gets the value of the evidence property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the evidence property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getEvidence().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Integer }
- *
- *
- */
- public List<Integer> getEvidence() {
- if (evidence == null) {
- evidence = new ArrayList<Integer>();
- }
- return this.evidence;
+ /**
+ * Gets the value of the evidence property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getEvidence()
+ {
+ if (evidence == null)
+ {
+ evidence = new ArrayList<Integer>();
}
+ return this.evidence;
+ }
}
// Generated on: 2019.04.05 at 08:01:44 AM BST
//
-
package jalview.xml.binding.uniprot;
import java.math.BigInteger;
import javax.xml.bind.annotation.XmlSchemaType;
import javax.xml.bind.annotation.XmlType;
-
/**
- * <p>Java class for positionType complex type.
+ * <p>
+ * Java class for positionType complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
*
* <pre>
* <complexType name="positionType">
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "positionType")
-public class PositionType {
+public class PositionType
+{
- @XmlAttribute(name = "position")
- @XmlSchemaType(name = "unsignedLong")
- protected BigInteger position;
- @XmlAttribute(name = "status")
- protected String status;
- @XmlAttribute(name = "evidence")
- protected List<Integer> evidence;
+ @XmlAttribute(name = "position")
+ @XmlSchemaType(name = "unsignedLong")
+ protected BigInteger position;
- /**
- * Gets the value of the position property.
- *
- * @return
- * possible object is
- * {@link BigInteger }
- *
- */
- public BigInteger getPosition() {
- return position;
- }
+ @XmlAttribute(name = "status")
+ protected String status;
- /**
- * Sets the value of the position property.
- *
- * @param value
- * allowed object is
- * {@link BigInteger }
- *
- */
- public void setPosition(BigInteger value) {
- this.position = value;
- }
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
- /**
- * Gets the value of the status property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getStatus() {
- if (status == null) {
- return "certain";
- } else {
- return status;
- }
- }
+ /**
+ * Gets the value of the position property.
+ *
+ * @return possible object is {@link BigInteger }
+ *
+ */
+ public BigInteger getPosition()
+ {
+ return position;
+ }
+
+ /**
+ * Sets the value of the position property.
+ *
+ * @param value
+ * allowed object is {@link BigInteger }
+ *
+ */
+ public void setPosition(BigInteger value)
+ {
+ this.position = value;
+ }
- /**
- * Sets the value of the status property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setStatus(String value) {
- this.status = value;
+ /**
+ * Gets the value of the status property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getStatus()
+ {
+ if (status == null)
+ {
+ return "certain";
}
+ else
+ {
+ return status;
+ }
+ }
+
+ /**
+ * Sets the value of the status property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setStatus(String value)
+ {
+ this.status = value;
+ }
- /**
- * Gets the value of the evidence property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the evidence property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getEvidence().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Integer }
- *
- *
- */
- public List<Integer> getEvidence() {
- if (evidence == null) {
- evidence = new ArrayList<Integer>();
- }
- return this.evidence;
+ /**
+ * Gets the value of the evidence property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getEvidence()
+ {
+ if (evidence == null)
+ {
+ evidence = new ArrayList<Integer>();
}
+ return this.evidence;
+ }
}
// Generated on: 2019.04.05 at 08:01:44 AM BST
//
-
package jalview.xml.binding.uniprot;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlType;
-
/**
- * <p>Java class for propertyType complex type.
+ * <p>
+ * Java class for propertyType complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
*
* <pre>
* <complexType name="propertyType">
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "propertyType")
-public class PropertyType {
+public class PropertyType
+{
+
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
- @XmlAttribute(name = "type", required = true)
- protected String type;
- @XmlAttribute(name = "value", required = true)
- protected String value;
+ @XmlAttribute(name = "value", required = true)
+ protected String value;
- /**
- * Gets the value of the type property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getType() {
- return type;
- }
+ /**
+ * Gets the value of the type property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getType()
+ {
+ return type;
+ }
- /**
- * Sets the value of the type property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setType(String value) {
- this.type = value;
- }
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setType(String value)
+ {
+ this.type = value;
+ }
- /**
- * Gets the value of the value property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getValue() {
- return value;
- }
+ /**
+ * Gets the value of the value property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getValue()
+ {
+ return value;
+ }
- /**
- * Sets the value of the value property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setValue(String value) {
- this.value = value;
- }
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setValue(String value)
+ {
+ this.value = value;
+ }
}
// Generated on: 2019.04.05 at 08:01:44 AM BST
//
-
package jalview.xml.binding.uniprot;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlType;
-
/**
- * Describes the evidence for the protein's existence.
- * Equivalent to the flat file PE-line.
+ * Describes the evidence for the protein's existence. Equivalent to the flat
+ * file PE-line.
*
- * <p>Java class for proteinExistenceType complex type.
+ * <p>
+ * Java class for proteinExistenceType complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
*
* <pre>
* <complexType name="proteinExistenceType">
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "proteinExistenceType")
-public class ProteinExistenceType {
+public class ProteinExistenceType
+{
- @XmlAttribute(name = "type", required = true)
- protected String type;
+ @XmlAttribute(name = "type", required = true)
+ protected String type;
- /**
- * Gets the value of the type property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getType() {
- return type;
- }
+ /**
+ * Gets the value of the type property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getType()
+ {
+ return type;
+ }
- /**
- * Sets the value of the type property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setType(String value) {
- this.type = value;
- }
+ /**
+ * Sets the value of the type property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setType(String value)
+ {
+ this.type = value;
+ }
}
// Generated on: 2019.04.05 at 08:01:44 AM BST
//
-
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
-
/**
- * Describes the names for the protein and parts thereof.
- * Equivalent to the flat file DE-line.
+ * Describes the names for the protein and parts thereof. Equivalent to the flat
+ * file DE-line.
*
- * <p>Java class for proteinType complex type.
+ * <p>
+ * Java class for proteinType complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
*
* <pre>
* <complexType name="proteinType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "proteinType", propOrder = {
- "recommendedName",
- "alternativeName",
- "submittedName",
- "allergenName",
- "biotechName",
- "cdAntigenName",
- "innName",
- "domain",
- "component"
-})
-public class ProteinType {
+@XmlType(
+ name = "proteinType",
+ propOrder =
+ { "recommendedName", "alternativeName", "submittedName", "allergenName",
+ "biotechName", "cdAntigenName", "innName", "domain", "component" })
+public class ProteinType
+{
+
+ protected ProteinType.RecommendedName recommendedName;
+
+ protected List<ProteinType.AlternativeName> alternativeName;
+
+ protected List<ProteinType.SubmittedName> submittedName;
+
+ protected EvidencedStringType allergenName;
+
+ protected EvidencedStringType biotechName;
+
+ protected List<EvidencedStringType> cdAntigenName;
+
+ protected List<EvidencedStringType> innName;
+
+ protected List<ProteinType.Domain> domain;
+
+ protected List<ProteinType.Component> component;
+
+ /**
+ * Gets the value of the recommendedName property.
+ *
+ * @return possible object is {@link ProteinType.RecommendedName }
+ *
+ */
+ public ProteinType.RecommendedName getRecommendedName()
+ {
+ return recommendedName;
+ }
+
+ /**
+ * Sets the value of the recommendedName property.
+ *
+ * @param value
+ * allowed object is {@link ProteinType.RecommendedName }
+ *
+ */
+ public void setRecommendedName(ProteinType.RecommendedName value)
+ {
+ this.recommendedName = value;
+ }
+
+ /**
+ * Gets the value of the alternativeName property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the alternativeName property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getAlternativeName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link ProteinType.AlternativeName }
+ *
+ *
+ */
+ public List<ProteinType.AlternativeName> getAlternativeName()
+ {
+ if (alternativeName == null)
+ {
+ alternativeName = new ArrayList<ProteinType.AlternativeName>();
+ }
+ return this.alternativeName;
+ }
+
+ /**
+ * Gets the value of the submittedName property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the submittedName property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getSubmittedName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link ProteinType.SubmittedName }
+ *
+ *
+ */
+ public List<ProteinType.SubmittedName> getSubmittedName()
+ {
+ if (submittedName == null)
+ {
+ submittedName = new ArrayList<ProteinType.SubmittedName>();
+ }
+ return this.submittedName;
+ }
+
+ /**
+ * Gets the value of the allergenName property.
+ *
+ * @return possible object is {@link EvidencedStringType }
+ *
+ */
+ public EvidencedStringType getAllergenName()
+ {
+ return allergenName;
+ }
+
+ /**
+ * Sets the value of the allergenName property.
+ *
+ * @param value
+ * allowed object is {@link EvidencedStringType }
+ *
+ */
+ public void setAllergenName(EvidencedStringType value)
+ {
+ this.allergenName = value;
+ }
+
+ /**
+ * Gets the value of the biotechName property.
+ *
+ * @return possible object is {@link EvidencedStringType }
+ *
+ */
+ public EvidencedStringType getBiotechName()
+ {
+ return biotechName;
+ }
+
+ /**
+ * Sets the value of the biotechName property.
+ *
+ * @param value
+ * allowed object is {@link EvidencedStringType }
+ *
+ */
+ public void setBiotechName(EvidencedStringType value)
+ {
+ this.biotechName = value;
+ }
+
+ /**
+ * Gets the value of the cdAntigenName property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the cdAntigenName property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getCdAntigenName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getCdAntigenName()
+ {
+ if (cdAntigenName == null)
+ {
+ cdAntigenName = new ArrayList<EvidencedStringType>();
+ }
+ return this.cdAntigenName;
+ }
+
+ /**
+ * Gets the value of the innName property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the innName property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getInnName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getInnName()
+ {
+ if (innName == null)
+ {
+ innName = new ArrayList<EvidencedStringType>();
+ }
+ return this.innName;
+ }
+
+ /**
+ * Gets the value of the domain property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the domain property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getDomain().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link ProteinType.Domain }
+ *
+ *
+ */
+ public List<ProteinType.Domain> getDomain()
+ {
+ if (domain == null)
+ {
+ domain = new ArrayList<ProteinType.Domain>();
+ }
+ return this.domain;
+ }
+
+ /**
+ * Gets the value of the component property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the component property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getComponent().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link ProteinType.Component }
+ *
+ *
+ */
+ public List<ProteinType.Component> getComponent()
+ {
+ if (component == null)
+ {
+ component = new ArrayList<ProteinType.Component>();
+ }
+ return this.component;
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="fullName" type="{http://uniprot.org/uniprot}evidencedStringType" minOccurs="0"/>
+ * <element name="shortName" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="ecNumber" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "fullName", "shortName", "ecNumber" })
+ public static class AlternativeName
+ {
+
+ protected EvidencedStringType fullName;
+
+ protected List<EvidencedStringType> shortName;
+
+ protected List<EvidencedStringType> ecNumber;
+
+ /**
+ * Gets the value of the fullName property.
+ *
+ * @return possible object is {@link EvidencedStringType }
+ *
+ */
+ public EvidencedStringType getFullName()
+ {
+ return fullName;
+ }
+
+ /**
+ * Sets the value of the fullName property.
+ *
+ * @param value
+ * allowed object is {@link EvidencedStringType }
+ *
+ */
+ public void setFullName(EvidencedStringType value)
+ {
+ this.fullName = value;
+ }
+
+ /**
+ * Gets the value of the shortName property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the shortName property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getShortName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getShortName()
+ {
+ if (shortName == null)
+ {
+ shortName = new ArrayList<EvidencedStringType>();
+ }
+ return this.shortName;
+ }
+
+ /**
+ * Gets the value of the ecNumber property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the ecNumber property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getEcNumber().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getEcNumber()
+ {
+ if (ecNumber == null)
+ {
+ ecNumber = new ArrayList<EvidencedStringType>();
+ }
+ return this.ecNumber;
+ }
+
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <group ref="{http://uniprot.org/uniprot}proteinNameGroup"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(
+ name = "",
+ propOrder =
+ { "recommendedName", "alternativeName", "submittedName", "allergenName",
+ "biotechName", "cdAntigenName", "innName" })
+ public static class Component
+ {
protected ProteinType.RecommendedName recommendedName;
+
protected List<ProteinType.AlternativeName> alternativeName;
+
protected List<ProteinType.SubmittedName> submittedName;
+
protected EvidencedStringType allergenName;
+
protected EvidencedStringType biotechName;
+
protected List<EvidencedStringType> cdAntigenName;
+
protected List<EvidencedStringType> innName;
- protected List<ProteinType.Domain> domain;
- protected List<ProteinType.Component> component;
/**
* Gets the value of the recommendedName property.
*
- * @return
- * possible object is
- * {@link ProteinType.RecommendedName }
- *
+ * @return possible object is {@link ProteinType.RecommendedName }
+ *
*/
- public ProteinType.RecommendedName getRecommendedName() {
- return recommendedName;
+ public ProteinType.RecommendedName getRecommendedName()
+ {
+ return recommendedName;
}
/**
* Sets the value of the recommendedName property.
*
* @param value
- * allowed object is
- * {@link ProteinType.RecommendedName }
- *
+ * allowed object is {@link ProteinType.RecommendedName }
+ *
*/
- public void setRecommendedName(ProteinType.RecommendedName value) {
- this.recommendedName = value;
+ public void setRecommendedName(ProteinType.RecommendedName value)
+ {
+ this.recommendedName = value;
}
/**
* Gets the value of the alternativeName property.
*
* <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the alternativeName property.
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the alternativeName property.
*
* <p>
* For example, to add a new item, do as follows:
+ *
* <pre>
- * getAlternativeName().add(newItem);
+ * getAlternativeName().add(newItem);
* </pre>
*
*
*
*
*/
- public List<ProteinType.AlternativeName> getAlternativeName() {
- if (alternativeName == null) {
- alternativeName = new ArrayList<ProteinType.AlternativeName>();
- }
- return this.alternativeName;
+ public List<ProteinType.AlternativeName> getAlternativeName()
+ {
+ if (alternativeName == null)
+ {
+ alternativeName = new ArrayList<ProteinType.AlternativeName>();
+ }
+ return this.alternativeName;
}
/**
* Gets the value of the submittedName property.
*
* <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the submittedName property.
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the submittedName property.
*
* <p>
* For example, to add a new item, do as follows:
+ *
* <pre>
- * getSubmittedName().add(newItem);
+ * getSubmittedName().add(newItem);
* </pre>
*
*
*
*
*/
- public List<ProteinType.SubmittedName> getSubmittedName() {
- if (submittedName == null) {
- submittedName = new ArrayList<ProteinType.SubmittedName>();
- }
- return this.submittedName;
+ public List<ProteinType.SubmittedName> getSubmittedName()
+ {
+ if (submittedName == null)
+ {
+ submittedName = new ArrayList<ProteinType.SubmittedName>();
+ }
+ return this.submittedName;
}
/**
* Gets the value of the allergenName property.
*
- * @return
- * possible object is
- * {@link EvidencedStringType }
- *
+ * @return possible object is {@link EvidencedStringType }
+ *
*/
- public EvidencedStringType getAllergenName() {
- return allergenName;
+ public EvidencedStringType getAllergenName()
+ {
+ return allergenName;
}
/**
* Sets the value of the allergenName property.
*
* @param value
- * allowed object is
- * {@link EvidencedStringType }
- *
+ * allowed object is {@link EvidencedStringType }
+ *
*/
- public void setAllergenName(EvidencedStringType value) {
- this.allergenName = value;
+ public void setAllergenName(EvidencedStringType value)
+ {
+ this.allergenName = value;
}
/**
* Gets the value of the biotechName property.
*
- * @return
- * possible object is
- * {@link EvidencedStringType }
- *
+ * @return possible object is {@link EvidencedStringType }
+ *
*/
- public EvidencedStringType getBiotechName() {
- return biotechName;
+ public EvidencedStringType getBiotechName()
+ {
+ return biotechName;
}
/**
* Sets the value of the biotechName property.
*
* @param value
- * allowed object is
- * {@link EvidencedStringType }
- *
+ * allowed object is {@link EvidencedStringType }
+ *
*/
- public void setBiotechName(EvidencedStringType value) {
- this.biotechName = value;
+ public void setBiotechName(EvidencedStringType value)
+ {
+ this.biotechName = value;
}
/**
* Gets the value of the cdAntigenName property.
*
* <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the cdAntigenName property.
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the cdAntigenName property.
*
* <p>
* For example, to add a new item, do as follows:
+ *
* <pre>
- * getCdAntigenName().add(newItem);
+ * getCdAntigenName().add(newItem);
* </pre>
*
*
*
*
*/
- public List<EvidencedStringType> getCdAntigenName() {
- if (cdAntigenName == null) {
- cdAntigenName = new ArrayList<EvidencedStringType>();
- }
- return this.cdAntigenName;
+ public List<EvidencedStringType> getCdAntigenName()
+ {
+ if (cdAntigenName == null)
+ {
+ cdAntigenName = new ArrayList<EvidencedStringType>();
+ }
+ return this.cdAntigenName;
}
/**
* Gets the value of the innName property.
*
* <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the innName property.
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the innName property.
*
* <p>
* For example, to add a new item, do as follows:
+ *
* <pre>
- * getInnName().add(newItem);
+ * getInnName().add(newItem);
* </pre>
*
*
*
*
*/
- public List<EvidencedStringType> getInnName() {
- if (innName == null) {
- innName = new ArrayList<EvidencedStringType>();
- }
- return this.innName;
+ public List<EvidencedStringType> getInnName()
+ {
+ if (innName == null)
+ {
+ innName = new ArrayList<EvidencedStringType>();
+ }
+ return this.innName;
+ }
+
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <group ref="{http://uniprot.org/uniprot}proteinNameGroup"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(
+ name = "",
+ propOrder =
+ { "recommendedName", "alternativeName", "submittedName", "allergenName",
+ "biotechName", "cdAntigenName", "innName" })
+ public static class Domain
+ {
+
+ protected ProteinType.RecommendedName recommendedName;
+
+ protected List<ProteinType.AlternativeName> alternativeName;
+
+ protected List<ProteinType.SubmittedName> submittedName;
+
+ protected EvidencedStringType allergenName;
+
+ protected EvidencedStringType biotechName;
+
+ protected List<EvidencedStringType> cdAntigenName;
+
+ protected List<EvidencedStringType> innName;
+
+ /**
+ * Gets the value of the recommendedName property.
+ *
+ * @return possible object is {@link ProteinType.RecommendedName }
+ *
+ */
+ public ProteinType.RecommendedName getRecommendedName()
+ {
+ return recommendedName;
}
/**
- * Gets the value of the domain property.
+ * Sets the value of the recommendedName property.
+ *
+ * @param value
+ * allowed object is {@link ProteinType.RecommendedName }
+ *
+ */
+ public void setRecommendedName(ProteinType.RecommendedName value)
+ {
+ this.recommendedName = value;
+ }
+
+ /**
+ * Gets the value of the alternativeName property.
*
* <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the domain property.
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the alternativeName property.
*
* <p>
* For example, to add a new item, do as follows:
+ *
* <pre>
- * getDomain().add(newItem);
+ * getAlternativeName().add(newItem);
* </pre>
*
*
* <p>
* Objects of the following type(s) are allowed in the list
- * {@link ProteinType.Domain }
+ * {@link ProteinType.AlternativeName }
*
*
*/
- public List<ProteinType.Domain> getDomain() {
- if (domain == null) {
- domain = new ArrayList<ProteinType.Domain>();
- }
- return this.domain;
+ public List<ProteinType.AlternativeName> getAlternativeName()
+ {
+ if (alternativeName == null)
+ {
+ alternativeName = new ArrayList<ProteinType.AlternativeName>();
+ }
+ return this.alternativeName;
}
/**
- * Gets the value of the component property.
+ * Gets the value of the submittedName property.
*
* <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the component property.
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the submittedName property.
*
* <p>
* For example, to add a new item, do as follows:
+ *
* <pre>
- * getComponent().add(newItem);
+ * getSubmittedName().add(newItem);
* </pre>
*
*
* <p>
* Objects of the following type(s) are allowed in the list
- * {@link ProteinType.Component }
+ * {@link ProteinType.SubmittedName }
*
*
*/
- public List<ProteinType.Component> getComponent() {
- if (component == null) {
- component = new ArrayList<ProteinType.Component>();
- }
- return this.component;
+ public List<ProteinType.SubmittedName> getSubmittedName()
+ {
+ if (submittedName == null)
+ {
+ submittedName = new ArrayList<ProteinType.SubmittedName>();
+ }
+ return this.submittedName;
}
+ /**
+ * Gets the value of the allergenName property.
+ *
+ * @return possible object is {@link EvidencedStringType }
+ *
+ */
+ public EvidencedStringType getAllergenName()
+ {
+ return allergenName;
+ }
/**
- * <p>Java class for anonymous complex type.
+ * Sets the value of the allergenName property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * @param value
+ * allowed object is {@link EvidencedStringType }
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="fullName" type="{http://uniprot.org/uniprot}evidencedStringType" minOccurs="0"/>
- * <element name="shortName" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
- * <element name="ecNumber" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ */
+ public void setAllergenName(EvidencedStringType value)
+ {
+ this.allergenName = value;
+ }
+
+ /**
+ * Gets the value of the biotechName property.
*
+ * @return possible object is {@link EvidencedStringType }
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "fullName",
- "shortName",
- "ecNumber"
- })
- public static class AlternativeName {
-
- protected EvidencedStringType fullName;
- protected List<EvidencedStringType> shortName;
- protected List<EvidencedStringType> ecNumber;
-
- /**
- * Gets the value of the fullName property.
- *
- * @return
- * possible object is
- * {@link EvidencedStringType }
- *
- */
- public EvidencedStringType getFullName() {
- return fullName;
- }
-
- /**
- * Sets the value of the fullName property.
- *
- * @param value
- * allowed object is
- * {@link EvidencedStringType }
- *
- */
- public void setFullName(EvidencedStringType value) {
- this.fullName = value;
- }
-
- /**
- * Gets the value of the shortName property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the shortName property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getShortName().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
- *
- *
- */
- public List<EvidencedStringType> getShortName() {
- if (shortName == null) {
- shortName = new ArrayList<EvidencedStringType>();
- }
- return this.shortName;
- }
-
- /**
- * Gets the value of the ecNumber property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the ecNumber property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getEcNumber().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
- *
- *
- */
- public List<EvidencedStringType> getEcNumber() {
- if (ecNumber == null) {
- ecNumber = new ArrayList<EvidencedStringType>();
- }
- return this.ecNumber;
- }
+ public EvidencedStringType getBiotechName()
+ {
+ return biotechName;
+ }
+ /**
+ * Sets the value of the biotechName property.
+ *
+ * @param value
+ * allowed object is {@link EvidencedStringType }
+ *
+ */
+ public void setBiotechName(EvidencedStringType value)
+ {
+ this.biotechName = value;
}
+ /**
+ * Gets the value of the cdAntigenName property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the cdAntigenName property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getCdAntigenName().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getCdAntigenName()
+ {
+ if (cdAntigenName == null)
+ {
+ cdAntigenName = new ArrayList<EvidencedStringType>();
+ }
+ return this.cdAntigenName;
+ }
/**
- * <p>Java class for anonymous complex type.
+ * Gets the value of the innName property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the innName property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
*
* <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <group ref="{http://uniprot.org/uniprot}proteinNameGroup"/>
- * </restriction>
- * </complexContent>
- * </complexType>
+ * getInnName().add(newItem);
* </pre>
*
*
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "recommendedName",
- "alternativeName",
- "submittedName",
- "allergenName",
- "biotechName",
- "cdAntigenName",
- "innName"
- })
- public static class Component {
-
- protected ProteinType.RecommendedName recommendedName;
- protected List<ProteinType.AlternativeName> alternativeName;
- protected List<ProteinType.SubmittedName> submittedName;
- protected EvidencedStringType allergenName;
- protected EvidencedStringType biotechName;
- protected List<EvidencedStringType> cdAntigenName;
- protected List<EvidencedStringType> innName;
-
- /**
- * Gets the value of the recommendedName property.
- *
- * @return
- * possible object is
- * {@link ProteinType.RecommendedName }
- *
- */
- public ProteinType.RecommendedName getRecommendedName() {
- return recommendedName;
- }
-
- /**
- * Sets the value of the recommendedName property.
- *
- * @param value
- * allowed object is
- * {@link ProteinType.RecommendedName }
- *
- */
- public void setRecommendedName(ProteinType.RecommendedName value) {
- this.recommendedName = value;
- }
-
- /**
- * Gets the value of the alternativeName property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the alternativeName property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getAlternativeName().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link ProteinType.AlternativeName }
- *
- *
- */
- public List<ProteinType.AlternativeName> getAlternativeName() {
- if (alternativeName == null) {
- alternativeName = new ArrayList<ProteinType.AlternativeName>();
- }
- return this.alternativeName;
- }
-
- /**
- * Gets the value of the submittedName property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the submittedName property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getSubmittedName().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link ProteinType.SubmittedName }
- *
- *
- */
- public List<ProteinType.SubmittedName> getSubmittedName() {
- if (submittedName == null) {
- submittedName = new ArrayList<ProteinType.SubmittedName>();
- }
- return this.submittedName;
- }
-
- /**
- * Gets the value of the allergenName property.
- *
- * @return
- * possible object is
- * {@link EvidencedStringType }
- *
- */
- public EvidencedStringType getAllergenName() {
- return allergenName;
- }
-
- /**
- * Sets the value of the allergenName property.
- *
- * @param value
- * allowed object is
- * {@link EvidencedStringType }
- *
- */
- public void setAllergenName(EvidencedStringType value) {
- this.allergenName = value;
- }
-
- /**
- * Gets the value of the biotechName property.
- *
- * @return
- * possible object is
- * {@link EvidencedStringType }
- *
- */
- public EvidencedStringType getBiotechName() {
- return biotechName;
- }
-
- /**
- * Sets the value of the biotechName property.
- *
- * @param value
- * allowed object is
- * {@link EvidencedStringType }
- *
- */
- public void setBiotechName(EvidencedStringType value) {
- this.biotechName = value;
- }
-
- /**
- * Gets the value of the cdAntigenName property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the cdAntigenName property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getCdAntigenName().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
- *
- *
- */
- public List<EvidencedStringType> getCdAntigenName() {
- if (cdAntigenName == null) {
- cdAntigenName = new ArrayList<EvidencedStringType>();
- }
- return this.cdAntigenName;
- }
-
- /**
- * Gets the value of the innName property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the innName property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getInnName().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
- *
- *
- */
- public List<EvidencedStringType> getInnName() {
- if (innName == null) {
- innName = new ArrayList<EvidencedStringType>();
- }
- return this.innName;
- }
+ public List<EvidencedStringType> getInnName()
+ {
+ if (innName == null)
+ {
+ innName = new ArrayList<EvidencedStringType>();
+ }
+ return this.innName;
+ }
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="fullName" type="{http://uniprot.org/uniprot}evidencedStringType"/>
+ * <element name="shortName" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="ecNumber" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "fullName", "shortName", "ecNumber" })
+ public static class RecommendedName
+ {
+
+ @XmlElement(required = true)
+ protected EvidencedStringType fullName;
+
+ protected List<EvidencedStringType> shortName;
+
+ protected List<EvidencedStringType> ecNumber;
+
+ /**
+ * Gets the value of the fullName property.
+ *
+ * @return possible object is {@link EvidencedStringType }
+ *
+ */
+ public EvidencedStringType getFullName()
+ {
+ return fullName;
}
+ /**
+ * Sets the value of the fullName property.
+ *
+ * @param value
+ * allowed object is {@link EvidencedStringType }
+ *
+ */
+ public void setFullName(EvidencedStringType value)
+ {
+ this.fullName = value;
+ }
/**
- * <p>Java class for anonymous complex type.
+ * Gets the value of the shortName property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the shortName property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
*
* <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <group ref="{http://uniprot.org/uniprot}proteinNameGroup"/>
- * </restriction>
- * </complexContent>
- * </complexType>
+ * getShortName().add(newItem);
* </pre>
*
*
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "recommendedName",
- "alternativeName",
- "submittedName",
- "allergenName",
- "biotechName",
- "cdAntigenName",
- "innName"
- })
- public static class Domain {
-
- protected ProteinType.RecommendedName recommendedName;
- protected List<ProteinType.AlternativeName> alternativeName;
- protected List<ProteinType.SubmittedName> submittedName;
- protected EvidencedStringType allergenName;
- protected EvidencedStringType biotechName;
- protected List<EvidencedStringType> cdAntigenName;
- protected List<EvidencedStringType> innName;
-
- /**
- * Gets the value of the recommendedName property.
- *
- * @return
- * possible object is
- * {@link ProteinType.RecommendedName }
- *
- */
- public ProteinType.RecommendedName getRecommendedName() {
- return recommendedName;
- }
-
- /**
- * Sets the value of the recommendedName property.
- *
- * @param value
- * allowed object is
- * {@link ProteinType.RecommendedName }
- *
- */
- public void setRecommendedName(ProteinType.RecommendedName value) {
- this.recommendedName = value;
- }
-
- /**
- * Gets the value of the alternativeName property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the alternativeName property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getAlternativeName().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link ProteinType.AlternativeName }
- *
- *
- */
- public List<ProteinType.AlternativeName> getAlternativeName() {
- if (alternativeName == null) {
- alternativeName = new ArrayList<ProteinType.AlternativeName>();
- }
- return this.alternativeName;
- }
-
- /**
- * Gets the value of the submittedName property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the submittedName property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getSubmittedName().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link ProteinType.SubmittedName }
- *
- *
- */
- public List<ProteinType.SubmittedName> getSubmittedName() {
- if (submittedName == null) {
- submittedName = new ArrayList<ProteinType.SubmittedName>();
- }
- return this.submittedName;
- }
-
- /**
- * Gets the value of the allergenName property.
- *
- * @return
- * possible object is
- * {@link EvidencedStringType }
- *
- */
- public EvidencedStringType getAllergenName() {
- return allergenName;
- }
-
- /**
- * Sets the value of the allergenName property.
- *
- * @param value
- * allowed object is
- * {@link EvidencedStringType }
- *
- */
- public void setAllergenName(EvidencedStringType value) {
- this.allergenName = value;
- }
-
- /**
- * Gets the value of the biotechName property.
- *
- * @return
- * possible object is
- * {@link EvidencedStringType }
- *
- */
- public EvidencedStringType getBiotechName() {
- return biotechName;
- }
-
- /**
- * Sets the value of the biotechName property.
- *
- * @param value
- * allowed object is
- * {@link EvidencedStringType }
- *
- */
- public void setBiotechName(EvidencedStringType value) {
- this.biotechName = value;
- }
-
- /**
- * Gets the value of the cdAntigenName property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the cdAntigenName property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getCdAntigenName().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
- *
- *
- */
- public List<EvidencedStringType> getCdAntigenName() {
- if (cdAntigenName == null) {
- cdAntigenName = new ArrayList<EvidencedStringType>();
- }
- return this.cdAntigenName;
- }
-
- /**
- * Gets the value of the innName property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the innName property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getInnName().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
- *
- *
- */
- public List<EvidencedStringType> getInnName() {
- if (innName == null) {
- innName = new ArrayList<EvidencedStringType>();
- }
- return this.innName;
- }
-
+ public List<EvidencedStringType> getShortName()
+ {
+ if (shortName == null)
+ {
+ shortName = new ArrayList<EvidencedStringType>();
+ }
+ return this.shortName;
}
-
/**
- * <p>Java class for anonymous complex type.
+ * Gets the value of the ecNumber property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the ecNumber property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * For example, to add a new item, do as follows:
*
* <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="fullName" type="{http://uniprot.org/uniprot}evidencedStringType"/>
- * <element name="shortName" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
- * <element name="ecNumber" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
+ * getEcNumber().add(newItem);
* </pre>
*
*
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "fullName",
- "shortName",
- "ecNumber"
- })
- public static class RecommendedName {
-
- @XmlElement(required = true)
- protected EvidencedStringType fullName;
- protected List<EvidencedStringType> shortName;
- protected List<EvidencedStringType> ecNumber;
-
- /**
- * Gets the value of the fullName property.
- *
- * @return
- * possible object is
- * {@link EvidencedStringType }
- *
- */
- public EvidencedStringType getFullName() {
- return fullName;
- }
-
- /**
- * Sets the value of the fullName property.
- *
- * @param value
- * allowed object is
- * {@link EvidencedStringType }
- *
- */
- public void setFullName(EvidencedStringType value) {
- this.fullName = value;
- }
-
- /**
- * Gets the value of the shortName property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the shortName property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getShortName().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
- *
- *
- */
- public List<EvidencedStringType> getShortName() {
- if (shortName == null) {
- shortName = new ArrayList<EvidencedStringType>();
- }
- return this.shortName;
- }
-
- /**
- * Gets the value of the ecNumber property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the ecNumber property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getEcNumber().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
- *
- *
- */
- public List<EvidencedStringType> getEcNumber() {
- if (ecNumber == null) {
- ecNumber = new ArrayList<EvidencedStringType>();
- }
- return this.ecNumber;
- }
+ public List<EvidencedStringType> getEcNumber()
+ {
+ if (ecNumber == null)
+ {
+ ecNumber = new ArrayList<EvidencedStringType>();
+ }
+ return this.ecNumber;
+ }
+
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="fullName" type="{http://uniprot.org/uniprot}evidencedStringType"/>
+ * <element name="ecNumber" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "fullName", "ecNumber" })
+ public static class SubmittedName
+ {
+
+ @XmlElement(required = true)
+ protected EvidencedStringType fullName;
+
+ protected List<EvidencedStringType> ecNumber;
+ /**
+ * Gets the value of the fullName property.
+ *
+ * @return possible object is {@link EvidencedStringType }
+ *
+ */
+ public EvidencedStringType getFullName()
+ {
+ return fullName;
}
+ /**
+ * Sets the value of the fullName property.
+ *
+ * @param value
+ * allowed object is {@link EvidencedStringType }
+ *
+ */
+ public void setFullName(EvidencedStringType value)
+ {
+ this.fullName = value;
+ }
/**
- * <p>Java class for anonymous complex type.
+ * Gets the value of the ecNumber property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the ecNumber property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
*
* <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="fullName" type="{http://uniprot.org/uniprot}evidencedStringType"/>
- * <element name="ecNumber" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
+ * getEcNumber().add(newItem);
* </pre>
*
*
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "fullName",
- "ecNumber"
- })
- public static class SubmittedName {
-
- @XmlElement(required = true)
- protected EvidencedStringType fullName;
- protected List<EvidencedStringType> ecNumber;
-
- /**
- * Gets the value of the fullName property.
- *
- * @return
- * possible object is
- * {@link EvidencedStringType }
- *
- */
- public EvidencedStringType getFullName() {
- return fullName;
- }
-
- /**
- * Sets the value of the fullName property.
- *
- * @param value
- * allowed object is
- * {@link EvidencedStringType }
- *
- */
- public void setFullName(EvidencedStringType value) {
- this.fullName = value;
- }
-
- /**
- * Gets the value of the ecNumber property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the ecNumber property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getEcNumber().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
- *
- *
- */
- public List<EvidencedStringType> getEcNumber() {
- if (ecNumber == null) {
- ecNumber = new ArrayList<EvidencedStringType>();
- }
- return this.ecNumber;
- }
-
+ public List<EvidencedStringType> getEcNumber()
+ {
+ if (ecNumber == null)
+ {
+ ecNumber = new ArrayList<EvidencedStringType>();
+ }
+ return this.ecNumber;
}
+ }
+
}
// Generated on: 2019.04.05 at 08:01:44 AM BST
//
-
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
-
/**
* Describes a chemical reaction.
*
- * <p>Java class for reactionType complex type.
+ * <p>
+ * Java class for reactionType complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
*
* <pre>
* <complexType name="reactionType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "reactionType", propOrder = {
- "text",
- "dbReference"
-})
-public class ReactionType {
+@XmlType(name = "reactionType", propOrder = { "text", "dbReference" })
+public class ReactionType
+{
- @XmlElement(required = true)
- protected String text;
- @XmlElement(required = true)
- protected List<DbReferenceType> dbReference;
- @XmlAttribute(name = "evidence")
- protected List<Integer> evidence;
+ @XmlElement(required = true)
+ protected String text;
- /**
- * Gets the value of the text property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getText() {
- return text;
- }
+ @XmlElement(required = true)
+ protected List<DbReferenceType> dbReference;
- /**
- * Sets the value of the text property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setText(String value) {
- this.text = value;
- }
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
+
+ /**
+ * Gets the value of the text property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getText()
+ {
+ return text;
+ }
+
+ /**
+ * Sets the value of the text property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setText(String value)
+ {
+ this.text = value;
+ }
- /**
- * Gets the value of the dbReference property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the dbReference property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getDbReference().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link DbReferenceType }
- *
- *
- */
- public List<DbReferenceType> getDbReference() {
- if (dbReference == null) {
- dbReference = new ArrayList<DbReferenceType>();
- }
- return this.dbReference;
+ /**
+ * Gets the value of the dbReference property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the dbReference property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getDbReference().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link DbReferenceType }
+ *
+ *
+ */
+ public List<DbReferenceType> getDbReference()
+ {
+ if (dbReference == null)
+ {
+ dbReference = new ArrayList<DbReferenceType>();
}
+ return this.dbReference;
+ }
- /**
- * Gets the value of the evidence property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the evidence property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getEvidence().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Integer }
- *
- *
- */
- public List<Integer> getEvidence() {
- if (evidence == null) {
- evidence = new ArrayList<Integer>();
- }
- return this.evidence;
+ /**
+ * Gets the value of the evidence property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getEvidence()
+ {
+ if (evidence == null)
+ {
+ evidence = new ArrayList<Integer>();
}
+ return this.evidence;
+ }
}
// Generated on: 2019.04.05 at 08:01:44 AM BST
//
-
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
-
/**
- * Describes a citation and a summary of its content.
- * Equivalent to the flat file RN-, RP-, RC-, RX-, RG-, RA-, RT- and RL-lines.
+ * Describes a citation and a summary of its content. Equivalent to the flat
+ * file RN-, RP-, RC-, RX-, RG-, RA-, RT- and RL-lines.
*
- * <p>Java class for referenceType complex type.
+ * <p>
+ * Java class for referenceType complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
*
* <pre>
* <complexType name="referenceType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "referenceType", propOrder = {
- "citation",
- "scope",
- "source"
-})
-public class ReferenceType {
-
- @XmlElement(required = true)
- protected CitationType citation;
- @XmlElement(required = true)
- protected List<String> scope;
- protected SourceDataType source;
- @XmlAttribute(name = "evidence")
- protected List<Integer> evidence;
- @XmlAttribute(name = "key", required = true)
- protected String key;
-
- /**
- * Gets the value of the citation property.
- *
- * @return
- * possible object is
- * {@link CitationType }
- *
- */
- public CitationType getCitation() {
- return citation;
- }
+@XmlType(
+ name = "referenceType",
+ propOrder =
+ { "citation", "scope", "source" })
+public class ReferenceType
+{
- /**
- * Sets the value of the citation property.
- *
- * @param value
- * allowed object is
- * {@link CitationType }
- *
- */
- public void setCitation(CitationType value) {
- this.citation = value;
- }
+ @XmlElement(required = true)
+ protected CitationType citation;
- /**
- * Gets the value of the scope property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the scope property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getScope().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link String }
- *
- *
- */
- public List<String> getScope() {
- if (scope == null) {
- scope = new ArrayList<String>();
- }
- return this.scope;
- }
+ @XmlElement(required = true)
+ protected List<String> scope;
- /**
- * Gets the value of the source property.
- *
- * @return
- * possible object is
- * {@link SourceDataType }
- *
- */
- public SourceDataType getSource() {
- return source;
- }
+ protected SourceDataType source;
- /**
- * Sets the value of the source property.
- *
- * @param value
- * allowed object is
- * {@link SourceDataType }
- *
- */
- public void setSource(SourceDataType value) {
- this.source = value;
- }
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
- /**
- * Gets the value of the evidence property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the evidence property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getEvidence().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Integer }
- *
- *
- */
- public List<Integer> getEvidence() {
- if (evidence == null) {
- evidence = new ArrayList<Integer>();
- }
- return this.evidence;
- }
+ @XmlAttribute(name = "key", required = true)
+ protected String key;
+
+ /**
+ * Gets the value of the citation property.
+ *
+ * @return possible object is {@link CitationType }
+ *
+ */
+ public CitationType getCitation()
+ {
+ return citation;
+ }
- /**
- * Gets the value of the key property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getKey() {
- return key;
+ /**
+ * Sets the value of the citation property.
+ *
+ * @param value
+ * allowed object is {@link CitationType }
+ *
+ */
+ public void setCitation(CitationType value)
+ {
+ this.citation = value;
+ }
+
+ /**
+ * Gets the value of the scope property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the scope property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getScope().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link String }
+ *
+ *
+ */
+ public List<String> getScope()
+ {
+ if (scope == null)
+ {
+ scope = new ArrayList<String>();
}
+ return this.scope;
+ }
+
+ /**
+ * Gets the value of the source property.
+ *
+ * @return possible object is {@link SourceDataType }
+ *
+ */
+ public SourceDataType getSource()
+ {
+ return source;
+ }
- /**
- * Sets the value of the key property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setKey(String value) {
- this.key = value;
+ /**
+ * Sets the value of the source property.
+ *
+ * @param value
+ * allowed object is {@link SourceDataType }
+ *
+ */
+ public void setSource(SourceDataType value)
+ {
+ this.source = value;
+ }
+
+ /**
+ * Gets the value of the evidence property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getEvidence().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link Integer }
+ *
+ *
+ */
+ public List<Integer> getEvidence()
+ {
+ if (evidence == null)
+ {
+ evidence = new ArrayList<Integer>();
}
+ return this.evidence;
+ }
+
+ /**
+ * Gets the value of the key property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getKey()
+ {
+ return key;
+ }
+
+ /**
+ * Sets the value of the key property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setKey(String value)
+ {
+ this.key = value;
+ }
}
// Generated on: 2019.04.05 at 08:01:44 AM BST
//
-
package jalview.xml.binding.uniprot;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlValue;
import javax.xml.datatype.XMLGregorianCalendar;
-
/**
- * <p>Java class for sequenceType complex type.
+ * <p>
+ * Java class for sequenceType complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
*
* <pre>
* <complexType name="sequenceType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "sequenceType", propOrder = {
- "value"
-})
-public class SequenceType {
-
- @XmlValue
- protected String value;
- @XmlAttribute(name = "length", required = true)
- protected int length;
- @XmlAttribute(name = "mass", required = true)
- protected int mass;
- @XmlAttribute(name = "checksum", required = true)
- protected String checksum;
- @XmlAttribute(name = "modified", required = true)
- @XmlSchemaType(name = "date")
- protected XMLGregorianCalendar modified;
- @XmlAttribute(name = "version", required = true)
- protected int version;
- @XmlAttribute(name = "precursor")
- protected Boolean precursor;
- @XmlAttribute(name = "fragment")
- protected String fragment;
-
- /**
- * Gets the value of the value property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getValue() {
- return value;
- }
-
- /**
- * Sets the value of the value property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setValue(String value) {
- this.value = value;
- }
-
- /**
- * Gets the value of the length property.
- *
- */
- public int getLength() {
- return length;
- }
-
- /**
- * Sets the value of the length property.
- *
- */
- public void setLength(int value) {
- this.length = value;
- }
-
- /**
- * Gets the value of the mass property.
- *
- */
- public int getMass() {
- return mass;
- }
-
- /**
- * Sets the value of the mass property.
- *
- */
- public void setMass(int value) {
- this.mass = value;
- }
-
- /**
- * Gets the value of the checksum property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getChecksum() {
- return checksum;
- }
-
- /**
- * Sets the value of the checksum property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setChecksum(String value) {
- this.checksum = value;
- }
-
- /**
- * Gets the value of the modified property.
- *
- * @return
- * possible object is
- * {@link XMLGregorianCalendar }
- *
- */
- public XMLGregorianCalendar getModified() {
- return modified;
- }
-
- /**
- * Sets the value of the modified property.
- *
- * @param value
- * allowed object is
- * {@link XMLGregorianCalendar }
- *
- */
- public void setModified(XMLGregorianCalendar value) {
- this.modified = value;
- }
-
- /**
- * Gets the value of the version property.
- *
- */
- public int getVersion() {
- return version;
- }
-
- /**
- * Sets the value of the version property.
- *
- */
- public void setVersion(int value) {
- this.version = value;
- }
-
- /**
- * Gets the value of the precursor property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isPrecursor() {
- return precursor;
- }
-
- /**
- * Sets the value of the precursor property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setPrecursor(Boolean value) {
- this.precursor = value;
- }
-
- /**
- * Gets the value of the fragment property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getFragment() {
- return fragment;
- }
-
- /**
- * Sets the value of the fragment property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setFragment(String value) {
- this.fragment = value;
- }
+@XmlType(name = "sequenceType", propOrder = { "value" })
+public class SequenceType
+{
+
+ @XmlValue
+ protected String value;
+
+ @XmlAttribute(name = "length", required = true)
+ protected int length;
+
+ @XmlAttribute(name = "mass", required = true)
+ protected int mass;
+
+ @XmlAttribute(name = "checksum", required = true)
+ protected String checksum;
+
+ @XmlAttribute(name = "modified", required = true)
+ @XmlSchemaType(name = "date")
+ protected XMLGregorianCalendar modified;
+
+ @XmlAttribute(name = "version", required = true)
+ protected int version;
+
+ @XmlAttribute(name = "precursor")
+ protected Boolean precursor;
+
+ @XmlAttribute(name = "fragment")
+ protected String fragment;
+
+ /**
+ * Gets the value of the value property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getValue()
+ {
+ return value;
+ }
+
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setValue(String value)
+ {
+ this.value = value;
+ }
+
+ /**
+ * Gets the value of the length property.
+ *
+ */
+ public int getLength()
+ {
+ return length;
+ }
+
+ /**
+ * Sets the value of the length property.
+ *
+ */
+ public void setLength(int value)
+ {
+ this.length = value;
+ }
+
+ /**
+ * Gets the value of the mass property.
+ *
+ */
+ public int getMass()
+ {
+ return mass;
+ }
+
+ /**
+ * Sets the value of the mass property.
+ *
+ */
+ public void setMass(int value)
+ {
+ this.mass = value;
+ }
+
+ /**
+ * Gets the value of the checksum property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getChecksum()
+ {
+ return checksum;
+ }
+
+ /**
+ * Sets the value of the checksum property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setChecksum(String value)
+ {
+ this.checksum = value;
+ }
+
+ /**
+ * Gets the value of the modified property.
+ *
+ * @return possible object is {@link XMLGregorianCalendar }
+ *
+ */
+ public XMLGregorianCalendar getModified()
+ {
+ return modified;
+ }
+
+ /**
+ * Sets the value of the modified property.
+ *
+ * @param value
+ * allowed object is {@link XMLGregorianCalendar }
+ *
+ */
+ public void setModified(XMLGregorianCalendar value)
+ {
+ this.modified = value;
+ }
+
+ /**
+ * Gets the value of the version property.
+ *
+ */
+ public int getVersion()
+ {
+ return version;
+ }
+
+ /**
+ * Sets the value of the version property.
+ *
+ */
+ public void setVersion(int value)
+ {
+ this.version = value;
+ }
+
+ /**
+ * Gets the value of the precursor property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isPrecursor()
+ {
+ return precursor;
+ }
+
+ /**
+ * Sets the value of the precursor property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setPrecursor(Boolean value)
+ {
+ this.precursor = value;
+ }
+
+ /**
+ * Gets the value of the fragment property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getFragment()
+ {
+ return fragment;
+ }
+
+ /**
+ * Sets the value of the fragment property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setFragment(String value)
+ {
+ this.fragment = value;
+ }
}
// Generated on: 2019.04.05 at 08:01:44 AM BST
//
-
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlType;
import javax.xml.bind.annotation.XmlValue;
-
/**
- * Describes the source of the sequence according to the citation.
- * Equivalent to the flat file RC-line.
+ * Describes the source of the sequence according to the citation. Equivalent to
+ * the flat file RC-line.
*
- * <p>Java class for sourceDataType complex type.
+ * <p>
+ * Java class for sourceDataType complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
*
* <pre>
* <complexType name="sourceDataType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "sourceDataType", propOrder = {
- "strainOrPlasmidOrTransposon"
-})
-public class SourceDataType {
-
- @XmlElements({
- @XmlElement(name = "strain", type = SourceDataType.Strain.class),
- @XmlElement(name = "plasmid", type = SourceDataType.Plasmid.class),
- @XmlElement(name = "transposon", type = SourceDataType.Transposon.class),
- @XmlElement(name = "tissue", type = SourceDataType.Tissue.class)
- })
- protected List<Object> strainOrPlasmidOrTransposon;
+@XmlType(
+ name = "sourceDataType",
+ propOrder =
+ { "strainOrPlasmidOrTransposon" })
+public class SourceDataType
+{
+
+ @XmlElements({
+ @XmlElement(name = "strain", type = SourceDataType.Strain.class),
+ @XmlElement(name = "plasmid", type = SourceDataType.Plasmid.class),
+ @XmlElement(
+ name = "transposon",
+ type = SourceDataType.Transposon.class),
+ @XmlElement(name = "tissue", type = SourceDataType.Tissue.class) })
+ protected List<Object> strainOrPlasmidOrTransposon;
+
+ /**
+ * Gets the value of the strainOrPlasmidOrTransposon property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the strainOrPlasmidOrTransposon property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getStrainOrPlasmidOrTransposon().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link SourceDataType.Strain } {@link SourceDataType.Plasmid }
+ * {@link SourceDataType.Transposon } {@link SourceDataType.Tissue }
+ *
+ *
+ */
+ public List<Object> getStrainOrPlasmidOrTransposon()
+ {
+ if (strainOrPlasmidOrTransposon == null)
+ {
+ strainOrPlasmidOrTransposon = new ArrayList<Object>();
+ }
+ return this.strainOrPlasmidOrTransposon;
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <simpleContent>
+ * <extension base="<http://www.w3.org/2001/XMLSchema>string">
+ * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+ * </extension>
+ * </simpleContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "value" })
+ public static class Plasmid
+ {
+
+ @XmlValue
+ protected String value;
+
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
+
+ /**
+ * Gets the value of the value property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getValue()
+ {
+ return value;
+ }
/**
- * Gets the value of the strainOrPlasmidOrTransposon property.
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setValue(String value)
+ {
+ this.value = value;
+ }
+
+ /**
+ * Gets the value of the evidence property.
*
* <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the strainOrPlasmidOrTransposon property.
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the evidence property.
*
* <p>
* For example, to add a new item, do as follows:
+ *
* <pre>
- * getStrainOrPlasmidOrTransposon().add(newItem);
+ * getEvidence().add(newItem);
* </pre>
*
*
* <p>
- * Objects of the following type(s) are allowed in the list
- * {@link SourceDataType.Strain }
- * {@link SourceDataType.Plasmid }
- * {@link SourceDataType.Transposon }
- * {@link SourceDataType.Tissue }
+ * Objects of the following type(s) are allowed in the list {@link Integer }
*
*
*/
- public List<Object> getStrainOrPlasmidOrTransposon() {
- if (strainOrPlasmidOrTransposon == null) {
- strainOrPlasmidOrTransposon = new ArrayList<Object>();
- }
- return this.strainOrPlasmidOrTransposon;
+ public List<Integer> getEvidence()
+ {
+ if (evidence == null)
+ {
+ evidence = new ArrayList<Integer>();
+ }
+ return this.evidence;
}
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <simpleContent>
+ * <extension base="<http://www.w3.org/2001/XMLSchema>string">
+ * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+ * </extension>
+ * </simpleContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "value" })
+ public static class Strain
+ {
+
+ @XmlValue
+ protected String value;
+
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
/**
- * <p>Java class for anonymous complex type.
+ * Gets the value of the value property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * @return possible object is {@link String }
*
- * <pre>
- * <complexType>
- * <simpleContent>
- * <extension base="<http://www.w3.org/2001/XMLSchema>string">
- * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
- * </extension>
- * </simpleContent>
- * </complexType>
- * </pre>
+ */
+ public String getValue()
+ {
+ return value;
+ }
+
+ /**
+ * Sets the value of the value property.
*
+ * @param value
+ * allowed object is {@link String }
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "value"
- })
- public static class Plasmid {
-
- @XmlValue
- protected String value;
- @XmlAttribute(name = "evidence")
- protected List<Integer> evidence;
-
- /**
- * Gets the value of the value property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getValue() {
- return value;
- }
-
- /**
- * Sets the value of the value property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setValue(String value) {
- this.value = value;
- }
-
- /**
- * Gets the value of the evidence property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the evidence property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getEvidence().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Integer }
- *
- *
- */
- public List<Integer> getEvidence() {
- if (evidence == null) {
- evidence = new ArrayList<Integer>();
- }
- return this.evidence;
- }
-
+ public void setValue(String value)
+ {
+ this.value = value;
}
-
/**
- * <p>Java class for anonymous complex type.
+ * Gets the value of the evidence property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
*
* <pre>
- * <complexType>
- * <simpleContent>
- * <extension base="<http://www.w3.org/2001/XMLSchema>string">
- * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
- * </extension>
- * </simpleContent>
- * </complexType>
+ * getEvidence().add(newItem);
* </pre>
*
*
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link Integer }
+ *
+ *
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "value"
- })
- public static class Strain {
-
- @XmlValue
- protected String value;
- @XmlAttribute(name = "evidence")
- protected List<Integer> evidence;
-
- /**
- * Gets the value of the value property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getValue() {
- return value;
- }
-
- /**
- * Sets the value of the value property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setValue(String value) {
- this.value = value;
- }
-
- /**
- * Gets the value of the evidence property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the evidence property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getEvidence().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Integer }
- *
- *
- */
- public List<Integer> getEvidence() {
- if (evidence == null) {
- evidence = new ArrayList<Integer>();
- }
- return this.evidence;
- }
+ public List<Integer> getEvidence()
+ {
+ if (evidence == null)
+ {
+ evidence = new ArrayList<Integer>();
+ }
+ return this.evidence;
+ }
+
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <simpleContent>
+ * <extension base="<http://www.w3.org/2001/XMLSchema>string">
+ * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+ * </extension>
+ * </simpleContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "value" })
+ public static class Tissue
+ {
+
+ @XmlValue
+ protected String value;
+
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
+ /**
+ * Gets the value of the value property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getValue()
+ {
+ return value;
}
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setValue(String value)
+ {
+ this.value = value;
+ }
/**
- * <p>Java class for anonymous complex type.
+ * Gets the value of the evidence property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
*
* <pre>
- * <complexType>
- * <simpleContent>
- * <extension base="<http://www.w3.org/2001/XMLSchema>string">
- * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
- * </extension>
- * </simpleContent>
- * </complexType>
+ * getEvidence().add(newItem);
* </pre>
*
*
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link Integer }
+ *
+ *
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "value"
- })
- public static class Tissue {
-
- @XmlValue
- protected String value;
- @XmlAttribute(name = "evidence")
- protected List<Integer> evidence;
-
- /**
- * Gets the value of the value property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getValue() {
- return value;
- }
-
- /**
- * Sets the value of the value property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setValue(String value) {
- this.value = value;
- }
-
- /**
- * Gets the value of the evidence property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the evidence property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getEvidence().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Integer }
- *
- *
- */
- public List<Integer> getEvidence() {
- if (evidence == null) {
- evidence = new ArrayList<Integer>();
- }
- return this.evidence;
- }
+ public List<Integer> getEvidence()
+ {
+ if (evidence == null)
+ {
+ evidence = new ArrayList<Integer>();
+ }
+ return this.evidence;
+ }
+ }
+
+ /**
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <simpleContent>
+ * <extension base="<http://www.w3.org/2001/XMLSchema>string">
+ * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+ * </extension>
+ * </simpleContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "value" })
+ public static class Transposon
+ {
+
+ @XmlValue
+ protected String value;
+
+ @XmlAttribute(name = "evidence")
+ protected List<Integer> evidence;
+
+ /**
+ * Gets the value of the value property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getValue()
+ {
+ return value;
}
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setValue(String value)
+ {
+ this.value = value;
+ }
/**
- * <p>Java class for anonymous complex type.
+ * Gets the value of the evidence property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the evidence property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
*
* <pre>
- * <complexType>
- * <simpleContent>
- * <extension base="<http://www.w3.org/2001/XMLSchema>string">
- * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
- * </extension>
- * </simpleContent>
- * </complexType>
+ * getEvidence().add(newItem);
* </pre>
*
*
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link Integer }
+ *
+ *
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "value"
- })
- public static class Transposon {
-
- @XmlValue
- protected String value;
- @XmlAttribute(name = "evidence")
- protected List<Integer> evidence;
-
- /**
- * Gets the value of the value property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getValue() {
- return value;
- }
-
- /**
- * Sets the value of the value property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setValue(String value) {
- this.value = value;
- }
-
- /**
- * Gets the value of the evidence property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the evidence property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getEvidence().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Integer }
- *
- *
- */
- public List<Integer> getEvidence() {
- if (evidence == null) {
- evidence = new ArrayList<Integer>();
- }
- return this.evidence;
- }
-
+ public List<Integer> getEvidence()
+ {
+ if (evidence == null)
+ {
+ evidence = new ArrayList<Integer>();
+ }
+ return this.evidence;
}
+ }
+
}
// Generated on: 2019.04.05 at 08:01:44 AM BST
//
-
package jalview.xml.binding.uniprot;
import java.math.BigInteger;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlType;
-
/**
- * Describes the source of the data using a database cross-reference (or a 'ref' attribute when the source cannot be found in a public data source, such as PubMed, and is cited only within the UniProtKB entry).
+ * Describes the source of the data using a database cross-reference (or a 'ref'
+ * attribute when the source cannot be found in a public data source, such as
+ * PubMed, and is cited only within the UniProtKB entry).
*
- * <p>Java class for sourceType complex type.
+ * <p>
+ * Java class for sourceType complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
*
* <pre>
* <complexType name="sourceType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "sourceType", propOrder = {
- "dbReference"
-})
-public class SourceType {
+@XmlType(name = "sourceType", propOrder = { "dbReference" })
+public class SourceType
+{
+
+ protected DbReferenceType dbReference;
- protected DbReferenceType dbReference;
- @XmlAttribute(name = "ref")
- protected BigInteger ref;
+ @XmlAttribute(name = "ref")
+ protected BigInteger ref;
- /**
- * Gets the value of the dbReference property.
- *
- * @return
- * possible object is
- * {@link DbReferenceType }
- *
- */
- public DbReferenceType getDbReference() {
- return dbReference;
- }
+ /**
+ * Gets the value of the dbReference property.
+ *
+ * @return possible object is {@link DbReferenceType }
+ *
+ */
+ public DbReferenceType getDbReference()
+ {
+ return dbReference;
+ }
- /**
- * Sets the value of the dbReference property.
- *
- * @param value
- * allowed object is
- * {@link DbReferenceType }
- *
- */
- public void setDbReference(DbReferenceType value) {
- this.dbReference = value;
- }
+ /**
+ * Sets the value of the dbReference property.
+ *
+ * @param value
+ * allowed object is {@link DbReferenceType }
+ *
+ */
+ public void setDbReference(DbReferenceType value)
+ {
+ this.dbReference = value;
+ }
- /**
- * Gets the value of the ref property.
- *
- * @return
- * possible object is
- * {@link BigInteger }
- *
- */
- public BigInteger getRef() {
- return ref;
- }
+ /**
+ * Gets the value of the ref property.
+ *
+ * @return possible object is {@link BigInteger }
+ *
+ */
+ public BigInteger getRef()
+ {
+ return ref;
+ }
- /**
- * Sets the value of the ref property.
- *
- * @param value
- * allowed object is
- * {@link BigInteger }
- *
- */
- public void setRef(BigInteger value) {
- this.ref = value;
- }
+ /**
+ * Sets the value of the ref property.
+ *
+ * @param value
+ * allowed object is {@link BigInteger }
+ *
+ */
+ public void setRef(BigInteger value)
+ {
+ this.ref = value;
+ }
}
// Generated on: 2019.04.05 at 08:01:44 AM BST
//
-
package jalview.xml.binding.uniprot;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlType;
import javax.xml.bind.annotation.XmlValue;
-
/**
* Indicates whether the name of a plasmid is known or unknown.
*
- * <p>Java class for statusType complex type.
+ * <p>
+ * Java class for statusType complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
*
* <pre>
* <complexType name="statusType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "statusType", propOrder = {
- "value"
-})
-public class StatusType {
+@XmlType(name = "statusType", propOrder = { "value" })
+public class StatusType
+{
- @XmlValue
- protected String value;
- @XmlAttribute(name = "status")
- protected String status;
+ @XmlValue
+ protected String value;
- /**
- * Gets the value of the value property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getValue() {
- return value;
- }
+ @XmlAttribute(name = "status")
+ protected String status;
- /**
- * Sets the value of the value property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setValue(String value) {
- this.value = value;
- }
+ /**
+ * Gets the value of the value property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getValue()
+ {
+ return value;
+ }
- /**
- * Gets the value of the status property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getStatus() {
- if (status == null) {
- return "known";
- } else {
- return status;
- }
- }
+ /**
+ * Sets the value of the value property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setValue(String value)
+ {
+ this.value = value;
+ }
- /**
- * Sets the value of the status property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setStatus(String value) {
- this.status = value;
+ /**
+ * Gets the value of the status property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getStatus()
+ {
+ if (status == null)
+ {
+ return "known";
+ }
+ else
+ {
+ return status;
}
+ }
+
+ /**
+ * Sets the value of the status property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setStatus(String value)
+ {
+ this.status = value;
+ }
}
// Generated on: 2019.04.05 at 08:01:44 AM BST
//
-
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlType;
-
/**
- * Describes the subcellular location and optionally the topology and orientation of a molecule.
+ * Describes the subcellular location and optionally the topology and
+ * orientation of a molecule.
*
- * <p>Java class for subcellularLocationType complex type.
+ * <p>
+ * Java class for subcellularLocationType complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
*
* <pre>
* <complexType name="subcellularLocationType">
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "subcellularLocationType", propOrder = {
- "location",
- "topology",
- "orientation"
-})
-public class SubcellularLocationType {
+@XmlType(
+ name = "subcellularLocationType",
+ propOrder =
+ { "location", "topology", "orientation" })
+public class SubcellularLocationType
+{
+
+ @XmlElement(required = true)
+ protected List<EvidencedStringType> location;
+
+ protected List<EvidencedStringType> topology;
- @XmlElement(required = true)
- protected List<EvidencedStringType> location;
- protected List<EvidencedStringType> topology;
- protected List<EvidencedStringType> orientation;
+ protected List<EvidencedStringType> orientation;
- /**
- * Gets the value of the location property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the location property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getLocation().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
- *
- *
- */
- public List<EvidencedStringType> getLocation() {
- if (location == null) {
- location = new ArrayList<EvidencedStringType>();
- }
- return this.location;
+ /**
+ * Gets the value of the location property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the location property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getLocation().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getLocation()
+ {
+ if (location == null)
+ {
+ location = new ArrayList<EvidencedStringType>();
}
+ return this.location;
+ }
- /**
- * Gets the value of the topology property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the topology property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getTopology().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
- *
- *
- */
- public List<EvidencedStringType> getTopology() {
- if (topology == null) {
- topology = new ArrayList<EvidencedStringType>();
- }
- return this.topology;
+ /**
+ * Gets the value of the topology property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the topology property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getTopology().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getTopology()
+ {
+ if (topology == null)
+ {
+ topology = new ArrayList<EvidencedStringType>();
}
+ return this.topology;
+ }
- /**
- * Gets the value of the orientation property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the orientation property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getOrientation().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link EvidencedStringType }
- *
- *
- */
- public List<EvidencedStringType> getOrientation() {
- if (orientation == null) {
- orientation = new ArrayList<EvidencedStringType>();
- }
- return this.orientation;
+ /**
+ * Gets the value of the orientation property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the orientation property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getOrientation().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link EvidencedStringType }
+ *
+ *
+ */
+ public List<EvidencedStringType> getOrientation()
+ {
+ if (orientation == null)
+ {
+ orientation = new ArrayList<EvidencedStringType>();
}
+ return this.orientation;
+ }
}
// Generated on: 2019.04.05 at 08:01:44 AM BST
//
-
package jalview.xml.binding.uniprot;
import java.util.ArrayList;
import javax.xml.bind.annotation.XmlRootElement;
import javax.xml.bind.annotation.XmlType;
-
/**
- * <p>Java class for anonymous complex type.
+ * <p>
+ * Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
*
* <pre>
* <complexType>
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = {
- "entry",
- "copyright"
-})
+@XmlType(name = "", propOrder = { "entry", "copyright" })
@XmlRootElement(name = "uniprot")
-public class Uniprot {
+public class Uniprot
+{
- @XmlElement(required = true)
- protected List<Entry> entry;
- protected String copyright;
+ @XmlElement(required = true)
+ protected List<Entry> entry;
- /**
- * Gets the value of the entry property.
- *
- * <p>
- * This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the
- * returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the entry property.
- *
- * <p>
- * For example, to add a new item, do as follows:
- * <pre>
- * getEntry().add(newItem);
- * </pre>
- *
- *
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link Entry }
- *
- *
- */
- public List<Entry> getEntry() {
- if (entry == null) {
- entry = new ArrayList<Entry>();
- }
- return this.entry;
- }
+ protected String copyright;
- /**
- * Gets the value of the copyright property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getCopyright() {
- return copyright;
+ /**
+ * Gets the value of the entry property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the entry property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ *
+ * <pre>
+ * getEntry().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link Entry }
+ *
+ *
+ */
+ public List<Entry> getEntry()
+ {
+ if (entry == null)
+ {
+ entry = new ArrayList<Entry>();
}
+ return this.entry;
+ }
- /**
- * Sets the value of the copyright property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setCopyright(String value) {
- this.copyright = value;
- }
+ /**
+ * Gets the value of the copyright property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getCopyright()
+ {
+ return copyright;
+ }
+
+ /**
+ * Sets the value of the copyright property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setCopyright(String value)
+ {
+ this.copyright = value;
+ }
}
// Generated on: 2019.04.05 at 08:01:44 AM BST
//
-@javax.xml.bind.annotation.XmlSchema(namespace = "http://uniprot.org/uniprot", elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED)
+@javax.xml.bind.annotation.XmlSchema(
+ namespace = "http://uniprot.org/uniprot",
+ elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED)
package jalview.xml.binding.uniprot;
zappo.addActionListener(this);
taylor.setLabel(MessageManager.getString("label.colourScheme_taylor"));
taylor.addActionListener(this);
- helix.setLabel(MessageManager
- .getString("label.colourScheme_helixpropensity"));
+ helix.setLabel(
+ MessageManager.getString("label.colourScheme_helixpropensity"));
helix.addActionListener(this);
strand.setLabel(MessageManager
.getString("label.colourScheme_strandpropensity"));
String tfacName = "Temperature Factor";
-
- public PDBChain(String thePdbid, String theId, String tempFactorColumnName)
+ public PDBChain(String thePdbid, String theId,
+ String tempFactorColumnName)
{
- this.pdbid = thePdbid == null ? thePdbid : thePdbid.toLowerCase(Locale.ROOT);
+ this.pdbid = thePdbid == null ? thePdbid
+ : thePdbid.toLowerCase(Locale.ROOT);
this.id = theId;
- if (tempFactorColumnName!=null && tempFactorColumnName.length()>0)
+ if (tempFactorColumnName != null && tempFactorColumnName.length() > 0)
{
tfacName = tempFactorColumnName;
}
}
/**
- * import chain data assuming Temperature Factor is in the Temperature Factor column
+ * import chain data assuming Temperature Factor is in the Temperature Factor
+ * column
+ *
* @param thePdbid
* @param theId
*/
public PDBChain(String thePdbid, String theId)
{
- this(thePdbid,theId, null);
+ this(thePdbid, theId, null);
}
/**
}
char seqchar = ds.getCharAt(seqpos - ds.getStart());
- boolean sameResidue = Comparison.isSameResidue(
- seqchar, strchar, false);
+ boolean sameResidue = Comparison.isSameResidue(seqchar, strchar,
+ false);
if (sameResidue)
{
for (Atom atom : res.atoms)
* @param status
* The Status of the transferred annotation
*
- * @param altPDBID the group id for the features on the destination sequence (e.g. the official accession ID)
+ * @param altPDBID
+ * the group id for the features on the destination sequence (e.g.
+ * the official accession ID)
*/
- public void transferRESNUMFeatures(SequenceI seq,
- String status, String altPDBID)
+ public void transferRESNUMFeatures(SequenceI seq, String status,
+ String altPDBID)
{
- if (altPDBID==null)
+ if (altPDBID == null)
{
altPDBID = pdbid;
}
if (feature.getFeatureGroup() != null
&& feature.getFeatureGroup().equals(pdbid))
{
- int newBegin = 1 + residues.elementAt(feature.getBegin() - offset).atoms
- .elementAt(0).alignmentMapping;
+ int newBegin = 1
+ + residues.elementAt(feature.getBegin() - offset).atoms
+ .elementAt(0).alignmentMapping;
int newEnd = 1 + residues.elementAt(feature.getEnd() - offset).atoms
.elementAt(0).alignmentMapping;
SequenceFeature tx = new SequenceFeature(feature, newBegin, newEnd,
{
String desc = currAtom.resName + ":" + currAtom.resNumIns + " "
+ pdbid + id;
- SequenceFeature sf = new SequenceFeature("INSERTION", desc, offset
- + count - 1, offset + count - 1, "PDB_INS");
+ SequenceFeature sf = new SequenceFeature("INSERTION", desc,
+ offset + count - 1, offset + count - 1, "PDB_INS");
resFeatures.addElement(sf);
residues.lastElement().atoms.addAll(resAtoms);
}
Residue tmpres = residues.lastElement();
Atom tmpat = tmpres.atoms.get(0);
// Make A new SequenceFeature for the current residue numbering
- String desc = tmpat.resName
- + ":" + tmpat.resNumIns + " " + pdbid + id;
+ String desc = tmpat.resName + ":" + tmpat.resNumIns + " " + pdbid
+ + id;
SequenceFeature sf = new SequenceFeature(RESNUM_FEATURE, desc,
offset + count, offset + count, pdbid);
resFeatures.addElement(sf);
min = Math.min(min, annots[i].value);
resAnnotation.setElementAt(null, i);
}
- AlignmentAnnotation tfactorann = new AlignmentAnnotation(
- tfacName, tfacName + " for " + pdbid + id,
- annots, min, max, AlignmentAnnotation.LINE_GRAPH);
-
+ AlignmentAnnotation tfactorann = new AlignmentAnnotation(tfacName,
+ tfacName + " for " + pdbid + id, annots, min, max,
+ AlignmentAnnotation.LINE_GRAPH);
+
tfactorann.setCalcId(getClass().getName());
tfactorann.setSequenceRef(sequence);
}
}
-
/**
* Colour start/end of bonds by charge
* <ul>
if (tmpchain != null)
{
tmpchain.atoms.addElement(tmpatom);
- } else
+ }
+ else
{
// PDBfile never handles alphafold models
tmpchain = new PDBChain(getId(), tmpatom.chain);
* This represents an EPS document. Several EpsGraphics2D objects may point to
* the same EpsDocument.
* <p>
- * Copyright Paul Mutton, <a
- * href="http://www.jibble.org/">http://www.jibble.org/</a>
+ * Copyright Paul Mutton,
+ * <a href="http://www.jibble.org/">http://www.jibble.org/</a>
*
*/
public class EpsDocument
this.minY = minY;
this.maxX = maxX;
this.maxY = maxY;
- _bufferedWriter = new BufferedWriter(new OutputStreamWriter(
- outputStream));
+ _bufferedWriter = new BufferedWriter(
+ new OutputStreamWriter(outputStream));
write(_bufferedWriter);
}
}
else
{
- writer.write(offsetX + " " + ((maxY - minY) - offsetY)
- + " translate\n");
+ writer.write(
+ offsetX + " " + ((maxY - minY) - offsetY) + " translate\n");
}
writer.flush();
* <p>
* Not all methods are implemented yet. Those that are not are clearly labelled.
* <p>
- * Copyright Paul Mutton, <a
- * href="http://www.jibble.org/">http://www.jibble.org/</a>
+ * Copyright Paul Mutton,
+ * <a href="http://www.jibble.org/">http://www.jibble.org/</a>
*
*/
public class EpsGraphics2D extends java.awt.Graphics2D
int minY, int maxX, int maxY) throws IOException
{
this(title);
- _document = new EpsDocument(title, outputStream, minX, minY, maxX, maxY);
+ _document = new EpsDocument(title, outputStream, minX, minY, maxX,
+ maxY);
}
/**
private void methodNotSupported()
{
EpsException e = new EpsException(MessageManager.formatMessage(
- "exception.eps_method_not_supported", new String[] { VERSION }));
+ "exception.eps_method_not_supported", new String[]
+ { VERSION }));
e.printStackTrace(System.err);
}
* the top left.
*/
@Override
- public void draw3DRect(int x, int y, int width, int height, boolean raised)
+ public void draw3DRect(int x, int y, int width, int height,
+ boolean raised)
{
Color originalColor = getColor();
Stroke originalStroke = getStroke();
* come from the top left.
*/
@Override
- public void fill3DRect(int x, int y, int width, int height, boolean raised)
+ public void fill3DRect(int x, int y, int width, int height,
+ boolean raised)
{
Color originalColor = getColor();
WritableRaster wr = img.copyData(null);
BufferedImage img1 = new BufferedImage(cm, wr,
cm.isAlphaPremultiplied(), properties);
- AffineTransform at = AffineTransform.getTranslateInstance(
- img.getMinX(), img.getMinY());
+ AffineTransform at = AffineTransform.getTranslateInstance(img.getMinX(),
+ img.getMinY());
at.preConcatenate(xform);
drawImage(img1, at, null);
}
* Draws a RenderableImage by invoking its createDefaultRendering method.
*/
@Override
- public void drawRenderableImage(RenderableImage img, AffineTransform xform)
+ public void drawRenderableImage(RenderableImage img,
+ AffineTransform xform)
{
drawRenderedImage(img.createDefaultRendering(), xform);
}
if (getAccurateTextMode())
{
TextLayout layout = new TextLayout(iterator, getFontRenderContext());
- Shape shape = layout.getOutline(AffineTransform.getTranslateInstance(
- x, y));
+ Shape shape = layout
+ .getOutline(AffineTransform.getTranslateInstance(x, y));
draw(shape, "fill");
}
else
Point2D location = transform(x, y);
append(location.getX() + " " + location.getY() + " moveto");
StringBuffer buffer = new StringBuffer();
- for (char ch = iterator.first(); ch != CharacterIterator.DONE; ch = iterator
- .next())
+ for (char ch = iterator
+ .first(); ch != CharacterIterator.DONE; ch = iterator.next())
{
if (ch == '(' || ch == ')')
{
} catch (Exception e)
{
throw new EpsException(MessageManager.formatMessage(
- "exception.eps_unable_to_get_inverse_matrix",
- new String[] { _transform.toString() }));
+ "exception.eps_unable_to_get_inverse_matrix", new String[]
+ { _transform.toString() }));
}
}
}
public void drawArc(int x, int y, int width, int height, int startAngle,
int arcAngle)
{
- Shape shape = new Arc2D.Float(x, y, width, height, startAngle,
- arcAngle, Arc2D.OPEN);
+ Shape shape = new Arc2D.Float(x, y, width, height, startAngle, arcAngle,
+ Arc2D.OPEN);
draw(shape);
}
public void fillArc(int x, int y, int width, int height, int startAngle,
int arcAngle)
{
- Shape shape = new Arc2D.Float(x, y, width, height, startAngle,
- arcAngle, Arc2D.PIE);
+ Shape shape = new Arc2D.Float(x, y, width, height, startAngle, arcAngle,
+ Arc2D.PIE);
draw(shape, "fill");
}
} catch (Exception e)
{
throw new EpsException(MessageManager.formatMessage(
- "exception.eps_unable_to_get_inverse_matrix",
- new String[] { matrix.toString() }));
+ "exception.eps_unable_to_get_inverse_matrix", new String[]
+ { matrix.toString() }));
}
matrix.scale(1, -1);
matrix.getMatrix(m);
for (int x = 0; x < width; x++)
{
Color color = new Color(pixels[x + width * y]);
- line.append(toHexString(color.getRed())
- + toHexString(color.getGreen())
- + toHexString(color.getBlue()));
+ line.append(
+ toHexString(color.getRed()) + toHexString(color.getGreen())
+ + toHexString(color.getBlue()));
if (line.length() > 64)
{
append(line.toString());
* delimited text is a very popular format for data interchange. It is
* understood by most database, spreadsheet, and organizer programs.
* <p>
- * Each row of text represents a row in a table or a data record. Each row
- * ends with a NEWLINE character. Each row contains one or more values.
- * Values are separated by commas. A value can contain any character except
- * for comma, unless is is wrapped in single quotes or double quotes.
+ * Each row of text represents a row in a table or a data record. Each row ends
+ * with a NEWLINE character. Each row contains one or more values. Values are
+ * separated by commas. A value can contain any character except for comma,
+ * unless is is wrapped in single quotes or double quotes.
* <p>
* The first row usually contains the names of the columns.
* <p>
- * A comma delimited list can be converted into a JSONArray of JSONObjects.
- * The names for the elements in the JSONObjects can be taken from the names
- * in the first row.
+ * A comma delimited list can be converted into a JSONArray of JSONObjects. The
+ * names for the elements in the JSONObjects can be taken from the names in the
+ * first row.
+ *
* @author JSON.org
* @version 2016-05-01
*/
-public class CDL {
+public class CDL
+{
- /**
- * Get the next value. The value can be wrapped in quotes. The value can
- * be empty.
- * @param x A JSONTokener of the source text.
- * @return The value string, or null if empty.
- * @throws JSONException if the quoted string is badly formed.
- */
- private static String getValue(JSONTokener x) throws JSONException {
- char c;
- char q;
- StringBuffer sb;
- do {
- c = x.next();
- } while (c == ' ' || c == '\t');
- switch (c) {
- case 0:
- return null;
- case '"':
- case '\'':
- q = c;
- sb = new StringBuffer();
- for (;;) {
- c = x.next();
- if (c == q) {
- //Handle escaped double-quote
- char nextC = x.next();
- if(nextC != '\"') {
- // if our quote was the end of the file, don't step
- if(nextC > 0) {
- x.back();
- }
- break;
- }
- }
- if (c == 0 || c == '\n' || c == '\r') {
- throw x.syntaxError("Missing close quote '" + q + "'.");
- }
- sb.append(c);
+ /**
+ * Get the next value. The value can be wrapped in quotes. The value can be
+ * empty.
+ *
+ * @param x
+ * A JSONTokener of the source text.
+ * @return The value string, or null if empty.
+ * @throws JSONException
+ * if the quoted string is badly formed.
+ */
+ private static String getValue(JSONTokener x) throws JSONException
+ {
+ char c;
+ char q;
+ StringBuffer sb;
+ do
+ {
+ c = x.next();
+ } while (c == ' ' || c == '\t');
+ switch (c)
+ {
+ case 0:
+ return null;
+ case '"':
+ case '\'':
+ q = c;
+ sb = new StringBuffer();
+ for (;;)
+ {
+ c = x.next();
+ if (c == q)
+ {
+ // Handle escaped double-quote
+ char nextC = x.next();
+ if (nextC != '\"')
+ {
+ // if our quote was the end of the file, don't step
+ if (nextC > 0)
+ {
+ x.back();
}
- return sb.toString();
- case ',':
- x.back();
- return "";
- default:
- x.back();
- return x.nextTo(',');
+ break;
+ }
}
+ if (c == 0 || c == '\n' || c == '\r')
+ {
+ throw x.syntaxError("Missing close quote '" + q + "'.");
+ }
+ sb.append(c);
+ }
+ return sb.toString();
+ case ',':
+ x.back();
+ return "";
+ default:
+ x.back();
+ return x.nextTo(',');
}
+ }
- /**
- * Produce a JSONArray of strings from a row of comma delimited values.
- * @param x A JSONTokener of the source text.
- * @return A JSONArray of strings.
- * @throws JSONException
- */
- public static JSONArray rowToJSONArray(JSONTokener x) throws JSONException {
- JSONArray ja = new JSONArray();
- for (;;) {
- String value = getValue(x);
- char c = x.next();
- if (value == null ||
- (ja.length() == 0 && value.length() == 0 && c != ',')) {
- return null;
- }
- ja.put(value);
- for (;;) {
- if (c == ',') {
- break;
- }
- if (c != ' ') {
- if (c == '\n' || c == '\r' || c == 0) {
- return ja;
- }
- throw x.syntaxError("Bad character '" + c + "' (" +
- (int)c + ").");
- }
- c = x.next();
- }
+ /**
+ * Produce a JSONArray of strings from a row of comma delimited values.
+ *
+ * @param x
+ * A JSONTokener of the source text.
+ * @return A JSONArray of strings.
+ * @throws JSONException
+ */
+ public static JSONArray rowToJSONArray(JSONTokener x) throws JSONException
+ {
+ JSONArray ja = new JSONArray();
+ for (;;)
+ {
+ String value = getValue(x);
+ char c = x.next();
+ if (value == null
+ || (ja.length() == 0 && value.length() == 0 && c != ','))
+ {
+ return null;
+ }
+ ja.put(value);
+ for (;;)
+ {
+ if (c == ',')
+ {
+ break;
}
+ if (c != ' ')
+ {
+ if (c == '\n' || c == '\r' || c == 0)
+ {
+ return ja;
+ }
+ throw x.syntaxError(
+ "Bad character '" + c + "' (" + (int) c + ").");
+ }
+ c = x.next();
+ }
}
+ }
- /**
- * Produce a JSONObject from a row of comma delimited text, using a
- * parallel JSONArray of strings to provides the names of the elements.
- * @param names A JSONArray of names. This is commonly obtained from the
- * first row of a comma delimited text file using the rowToJSONArray
- * method.
- * @param x A JSONTokener of the source text.
- * @return A JSONObject combining the names and values.
- * @throws JSONException
- */
- public static JSONObject rowToJSONObject(JSONArray names, JSONTokener x)
- throws JSONException {
- JSONArray ja = rowToJSONArray(x);
- return ja != null ? ja.toJSONObject(names) : null;
- }
+ /**
+ * Produce a JSONObject from a row of comma delimited text, using a parallel
+ * JSONArray of strings to provides the names of the elements.
+ *
+ * @param names
+ * A JSONArray of names. This is commonly obtained from the first row
+ * of a comma delimited text file using the rowToJSONArray method.
+ * @param x
+ * A JSONTokener of the source text.
+ * @return A JSONObject combining the names and values.
+ * @throws JSONException
+ */
+ public static JSONObject rowToJSONObject(JSONArray names, JSONTokener x)
+ throws JSONException
+ {
+ JSONArray ja = rowToJSONArray(x);
+ return ja != null ? ja.toJSONObject(names) : null;
+ }
- /**
- * Produce a comma delimited text row from a JSONArray. Values containing
- * the comma character will be quoted. Troublesome characters may be
- * removed.
- * @param ja A JSONArray of strings.
- * @return A string ending in NEWLINE.
- */
- public static String rowToString(JSONArray ja) {
- StringBuilder sb = new StringBuilder();
- for (int i = 0; i < ja.length(); i += 1) {
- if (i > 0) {
- sb.append(',');
- }
- Object object = ja.opt(i);
- if (object != null) {
- String string = object.toString();
- if (string.length() > 0 && (string.indexOf(',') >= 0 ||
- string.indexOf('\n') >= 0 || string.indexOf('\r') >= 0 ||
- string.indexOf(0) >= 0 || string.charAt(0) == '"')) {
- sb.append('"');
- int length = string.length();
- for (int j = 0; j < length; j += 1) {
- char c = string.charAt(j);
- if (c >= ' ' && c != '"') {
- sb.append(c);
- }
- }
- sb.append('"');
- } else {
- sb.append(string);
- }
+ /**
+ * Produce a comma delimited text row from a JSONArray. Values containing the
+ * comma character will be quoted. Troublesome characters may be removed.
+ *
+ * @param ja
+ * A JSONArray of strings.
+ * @return A string ending in NEWLINE.
+ */
+ public static String rowToString(JSONArray ja)
+ {
+ StringBuilder sb = new StringBuilder();
+ for (int i = 0; i < ja.length(); i += 1)
+ {
+ if (i > 0)
+ {
+ sb.append(',');
+ }
+ Object object = ja.opt(i);
+ if (object != null)
+ {
+ String string = object.toString();
+ if (string.length() > 0 && (string.indexOf(',') >= 0
+ || string.indexOf('\n') >= 0 || string.indexOf('\r') >= 0
+ || string.indexOf(0) >= 0 || string.charAt(0) == '"'))
+ {
+ sb.append('"');
+ int length = string.length();
+ for (int j = 0; j < length; j += 1)
+ {
+ char c = string.charAt(j);
+ if (c >= ' ' && c != '"')
+ {
+ sb.append(c);
}
+ }
+ sb.append('"');
}
- sb.append('\n');
- return sb.toString();
+ else
+ {
+ sb.append(string);
+ }
+ }
}
+ sb.append('\n');
+ return sb.toString();
+ }
- /**
- * Produce a JSONArray of JSONObjects from a comma delimited text string,
- * using the first row as a source of names.
- * @param string The comma delimited text.
- * @return A JSONArray of JSONObjects.
- * @throws JSONException
- */
- public static JSONArray toJSONArray(String string) throws JSONException {
- return toJSONArray(new JSONTokener(string));
- }
+ /**
+ * Produce a JSONArray of JSONObjects from a comma delimited text string,
+ * using the first row as a source of names.
+ *
+ * @param string
+ * The comma delimited text.
+ * @return A JSONArray of JSONObjects.
+ * @throws JSONException
+ */
+ public static JSONArray toJSONArray(String string) throws JSONException
+ {
+ return toJSONArray(new JSONTokener(string));
+ }
- /**
- * Produce a JSONArray of JSONObjects from a comma delimited text string,
- * using the first row as a source of names.
- * @param x The JSONTokener containing the comma delimited text.
- * @return A JSONArray of JSONObjects.
- * @throws JSONException
- */
- public static JSONArray toJSONArray(JSONTokener x) throws JSONException {
- return toJSONArray(rowToJSONArray(x), x);
- }
+ /**
+ * Produce a JSONArray of JSONObjects from a comma delimited text string,
+ * using the first row as a source of names.
+ *
+ * @param x
+ * The JSONTokener containing the comma delimited text.
+ * @return A JSONArray of JSONObjects.
+ * @throws JSONException
+ */
+ public static JSONArray toJSONArray(JSONTokener x) throws JSONException
+ {
+ return toJSONArray(rowToJSONArray(x), x);
+ }
- /**
- * Produce a JSONArray of JSONObjects from a comma delimited text string
- * using a supplied JSONArray as the source of element names.
- * @param names A JSONArray of strings.
- * @param string The comma delimited text.
- * @return A JSONArray of JSONObjects.
- * @throws JSONException
- */
- public static JSONArray toJSONArray(JSONArray names, String string)
- throws JSONException {
- return toJSONArray(names, new JSONTokener(string));
- }
+ /**
+ * Produce a JSONArray of JSONObjects from a comma delimited text string using
+ * a supplied JSONArray as the source of element names.
+ *
+ * @param names
+ * A JSONArray of strings.
+ * @param string
+ * The comma delimited text.
+ * @return A JSONArray of JSONObjects.
+ * @throws JSONException
+ */
+ public static JSONArray toJSONArray(JSONArray names, String string)
+ throws JSONException
+ {
+ return toJSONArray(names, new JSONTokener(string));
+ }
- /**
- * Produce a JSONArray of JSONObjects from a comma delimited text string
- * using a supplied JSONArray as the source of element names.
- * @param names A JSONArray of strings.
- * @param x A JSONTokener of the source text.
- * @return A JSONArray of JSONObjects.
- * @throws JSONException
- */
- public static JSONArray toJSONArray(JSONArray names, JSONTokener x)
- throws JSONException {
- if (names == null || names.length() == 0) {
- return null;
- }
- JSONArray ja = new JSONArray();
- for (;;) {
- JSONObject jo = rowToJSONObject(names, x);
- if (jo == null) {
- break;
- }
- ja.put(jo);
- }
- if (ja.length() == 0) {
- return null;
- }
- return ja;
+ /**
+ * Produce a JSONArray of JSONObjects from a comma delimited text string using
+ * a supplied JSONArray as the source of element names.
+ *
+ * @param names
+ * A JSONArray of strings.
+ * @param x
+ * A JSONTokener of the source text.
+ * @return A JSONArray of JSONObjects.
+ * @throws JSONException
+ */
+ public static JSONArray toJSONArray(JSONArray names, JSONTokener x)
+ throws JSONException
+ {
+ if (names == null || names.length() == 0)
+ {
+ return null;
}
+ JSONArray ja = new JSONArray();
+ for (;;)
+ {
+ JSONObject jo = rowToJSONObject(names, x);
+ if (jo == null)
+ {
+ break;
+ }
+ ja.put(jo);
+ }
+ if (ja.length() == 0)
+ {
+ return null;
+ }
+ return ja;
+ }
-
- /**
- * Produce a comma delimited text from a JSONArray of JSONObjects. The
- * first row will be a list of names obtained by inspecting the first
- * JSONObject.
- * @param ja A JSONArray of JSONObjects.
- * @return A comma delimited text.
- * @throws JSONException
- */
- public static String toString(JSONArray ja) throws JSONException {
- JSONObject jo = ja.optJSONObject(0);
- if (jo != null) {
- JSONArray names = jo.names();
- if (names != null) {
- return rowToString(names) + toString(names, ja);
- }
- }
- return null;
+ /**
+ * Produce a comma delimited text from a JSONArray of JSONObjects. The first
+ * row will be a list of names obtained by inspecting the first JSONObject.
+ *
+ * @param ja
+ * A JSONArray of JSONObjects.
+ * @return A comma delimited text.
+ * @throws JSONException
+ */
+ public static String toString(JSONArray ja) throws JSONException
+ {
+ JSONObject jo = ja.optJSONObject(0);
+ if (jo != null)
+ {
+ JSONArray names = jo.names();
+ if (names != null)
+ {
+ return rowToString(names) + toString(names, ja);
+ }
}
+ return null;
+ }
- /**
- * Produce a comma delimited text from a JSONArray of JSONObjects using
- * a provided list of names. The list of names is not included in the
- * output.
- * @param names A JSONArray of strings.
- * @param ja A JSONArray of JSONObjects.
- * @return A comma delimited text.
- * @throws JSONException
- */
- public static String toString(JSONArray names, JSONArray ja)
- throws JSONException {
- if (names == null || names.length() == 0) {
- return null;
- }
- StringBuffer sb = new StringBuffer();
- for (int i = 0; i < ja.length(); i += 1) {
- JSONObject jo = ja.optJSONObject(i);
- if (jo != null) {
- sb.append(rowToString(jo.toJSONArray(names)));
- }
- }
- return sb.toString();
+ /**
+ * Produce a comma delimited text from a JSONArray of JSONObjects using a
+ * provided list of names. The list of names is not included in the output.
+ *
+ * @param names
+ * A JSONArray of strings.
+ * @param ja
+ * A JSONArray of JSONObjects.
+ * @return A comma delimited text.
+ * @throws JSONException
+ */
+ public static String toString(JSONArray names, JSONArray ja)
+ throws JSONException
+ {
+ if (names == null || names.length() == 0)
+ {
+ return null;
+ }
+ StringBuffer sb = new StringBuffer();
+ for (int i = 0; i < ja.length(); i += 1)
+ {
+ JSONObject jo = ja.optJSONObject(i);
+ if (jo != null)
+ {
+ sb.append(rowToString(jo.toJSONArray(names)));
+ }
}
+ return sb.toString();
+ }
}
*/
/**
- * Convert a web browser cookie specification to a JSONObject and back.
- * JSON and Cookies are both notations for name/value pairs.
+ * Convert a web browser cookie specification to a JSONObject and back. JSON and
+ * Cookies are both notations for name/value pairs.
+ *
* @author JSON.org
* @version 2015-12-09
*/
-public class Cookie {
+public class Cookie
+{
- /**
- * Produce a copy of a string in which the characters '+', '%', '=', ';'
- * and control characters are replaced with "%hh". This is a gentle form
- * of URL encoding, attempting to cause as little distortion to the
- * string as possible. The characters '=' and ';' are meta characters in
- * cookies. By convention, they are escaped using the URL-encoding. This is
- * only a convention, not a standard. Often, cookies are expected to have
- * encoded values. We encode '=' and ';' because we must. We encode '%' and
- * '+' because they are meta characters in URL encoding.
- * @param string The source string.
- * @return The escaped result.
- */
- public static String escape(String string) {
- char c;
- String s = string.trim();
- int length = s.length();
- StringBuilder sb = new StringBuilder(length);
- for (int i = 0; i < length; i += 1) {
- c = s.charAt(i);
- if (c < ' ' || c == '+' || c == '%' || c == '=' || c == ';') {
- sb.append('%');
- sb.append(Character.forDigit((char)((c >>> 4) & 0x0f), 16));
- sb.append(Character.forDigit((char)(c & 0x0f), 16));
- } else {
- sb.append(c);
- }
- }
- return sb.toString();
+ /**
+ * Produce a copy of a string in which the characters '+', '%', '=', ';' and
+ * control characters are replaced with "%hh". This is a gentle form of URL
+ * encoding, attempting to cause as little distortion to the string as
+ * possible. The characters '=' and ';' are meta characters in cookies. By
+ * convention, they are escaped using the URL-encoding. This is only a
+ * convention, not a standard. Often, cookies are expected to have encoded
+ * values. We encode '=' and ';' because we must. We encode '%' and '+'
+ * because they are meta characters in URL encoding.
+ *
+ * @param string
+ * The source string.
+ * @return The escaped result.
+ */
+ public static String escape(String string)
+ {
+ char c;
+ String s = string.trim();
+ int length = s.length();
+ StringBuilder sb = new StringBuilder(length);
+ for (int i = 0; i < length; i += 1)
+ {
+ c = s.charAt(i);
+ if (c < ' ' || c == '+' || c == '%' || c == '=' || c == ';')
+ {
+ sb.append('%');
+ sb.append(Character.forDigit((char) ((c >>> 4) & 0x0f), 16));
+ sb.append(Character.forDigit((char) (c & 0x0f), 16));
+ }
+ else
+ {
+ sb.append(c);
+ }
}
+ return sb.toString();
+ }
-
- /**
- * Convert a cookie specification string into a JSONObject. The string
- * will contain a name value pair separated by '='. The name and the value
- * will be unescaped, possibly converting '+' and '%' sequences. The
- * cookie properties may follow, separated by ';', also represented as
- * name=value (except the secure property, which does not have a value).
- * The name will be stored under the key "name", and the value will be
- * stored under the key "value". This method does not do checking or
- * validation of the parameters. It only converts the cookie string into
- * a JSONObject.
- * @param string The cookie specification string.
- * @return A JSONObject containing "name", "value", and possibly other
- * members.
- * @throws JSONException
- */
- public static JSONObject toJSONObject(String string) throws JSONException {
- String name;
- JSONObject jo = new JSONObject();
- Object value;
- JSONTokener x = new JSONTokener(string);
- jo.put("name", x.nextTo('='));
- x.next('=');
- jo.put("value", x.nextTo(';'));
- x.next();
- while (x.more()) {
- name = unescape(x.nextTo("=;"));
- if (x.next() != '=') {
- if (name.equals("secure")) {
- value = Boolean.TRUE;
- } else {
- throw x.syntaxError("Missing '=' in cookie parameter.");
- }
- } else {
- value = unescape(x.nextTo(';'));
- x.next();
- }
- jo.put(name, value);
+ /**
+ * Convert a cookie specification string into a JSONObject. The string will
+ * contain a name value pair separated by '='. The name and the value will be
+ * unescaped, possibly converting '+' and '%' sequences. The cookie properties
+ * may follow, separated by ';', also represented as name=value (except the
+ * secure property, which does not have a value). The name will be stored
+ * under the key "name", and the value will be stored under the key "value".
+ * This method does not do checking or validation of the parameters. It only
+ * converts the cookie string into a JSONObject.
+ *
+ * @param string
+ * The cookie specification string.
+ * @return A JSONObject containing "name", "value", and possibly other
+ * members.
+ * @throws JSONException
+ */
+ public static JSONObject toJSONObject(String string) throws JSONException
+ {
+ String name;
+ JSONObject jo = new JSONObject();
+ Object value;
+ JSONTokener x = new JSONTokener(string);
+ jo.put("name", x.nextTo('='));
+ x.next('=');
+ jo.put("value", x.nextTo(';'));
+ x.next();
+ while (x.more())
+ {
+ name = unescape(x.nextTo("=;"));
+ if (x.next() != '=')
+ {
+ if (name.equals("secure"))
+ {
+ value = Boolean.TRUE;
+ }
+ else
+ {
+ throw x.syntaxError("Missing '=' in cookie parameter.");
}
- return jo;
+ }
+ else
+ {
+ value = unescape(x.nextTo(';'));
+ x.next();
+ }
+ jo.put(name, value);
}
+ return jo;
+ }
+ /**
+ * Convert a JSONObject into a cookie specification string. The JSONObject
+ * must contain "name" and "value" members. If the JSONObject contains
+ * "expires", "domain", "path", or "secure" members, they will be appended to
+ * the cookie specification string. All other members are ignored.
+ *
+ * @param jo
+ * A JSONObject
+ * @return A cookie specification string
+ * @throws JSONException
+ */
+ public static String toString(JSONObject jo) throws JSONException
+ {
+ StringBuilder sb = new StringBuilder();
- /**
- * Convert a JSONObject into a cookie specification string. The JSONObject
- * must contain "name" and "value" members.
- * If the JSONObject contains "expires", "domain", "path", or "secure"
- * members, they will be appended to the cookie specification string.
- * All other members are ignored.
- * @param jo A JSONObject
- * @return A cookie specification string
- * @throws JSONException
- */
- public static String toString(JSONObject jo) throws JSONException {
- StringBuilder sb = new StringBuilder();
-
- sb.append(escape(jo.getString("name")));
- sb.append("=");
- sb.append(escape(jo.getString("value")));
- if (jo.has("expires")) {
- sb.append(";expires=");
- sb.append(jo.getString("expires"));
- }
- if (jo.has("domain")) {
- sb.append(";domain=");
- sb.append(escape(jo.getString("domain")));
- }
- if (jo.has("path")) {
- sb.append(";path=");
- sb.append(escape(jo.getString("path")));
- }
- if (jo.optBoolean("secure")) {
- sb.append(";secure");
- }
- return sb.toString();
+ sb.append(escape(jo.getString("name")));
+ sb.append("=");
+ sb.append(escape(jo.getString("value")));
+ if (jo.has("expires"))
+ {
+ sb.append(";expires=");
+ sb.append(jo.getString("expires"));
+ }
+ if (jo.has("domain"))
+ {
+ sb.append(";domain=");
+ sb.append(escape(jo.getString("domain")));
+ }
+ if (jo.has("path"))
+ {
+ sb.append(";path=");
+ sb.append(escape(jo.getString("path")));
+ }
+ if (jo.optBoolean("secure"))
+ {
+ sb.append(";secure");
}
+ return sb.toString();
+ }
- /**
- * Convert <code>%</code><i>hh</i> sequences to single characters, and
- * convert plus to space.
- * @param string A string that may contain
- * <code>+</code> <small>(plus)</small> and
- * <code>%</code><i>hh</i> sequences.
- * @return The unescaped string.
- */
- public static String unescape(String string) {
- int length = string.length();
- StringBuilder sb = new StringBuilder(length);
- for (int i = 0; i < length; ++i) {
- char c = string.charAt(i);
- if (c == '+') {
- c = ' ';
- } else if (c == '%' && i + 2 < length) {
- int d = JSONTokener.dehexchar(string.charAt(i + 1));
- int e = JSONTokener.dehexchar(string.charAt(i + 2));
- if (d >= 0 && e >= 0) {
- c = (char)(d * 16 + e);
- i += 2;
- }
- }
- sb.append(c);
+ /**
+ * Convert <code>%</code><i>hh</i> sequences to single characters, and convert
+ * plus to space.
+ *
+ * @param string
+ * A string that may contain
+ * <code>+</code> <small>(plus)</small> and
+ * <code>%</code><i>hh</i> sequences.
+ * @return The unescaped string.
+ */
+ public static String unescape(String string)
+ {
+ int length = string.length();
+ StringBuilder sb = new StringBuilder(length);
+ for (int i = 0; i < length; ++i)
+ {
+ char c = string.charAt(i);
+ if (c == '+')
+ {
+ c = ' ';
+ }
+ else if (c == '%' && i + 2 < length)
+ {
+ int d = JSONTokener.dehexchar(string.charAt(i + 1));
+ int e = JSONTokener.dehexchar(string.charAt(i + 2));
+ if (d >= 0 && e >= 0)
+ {
+ c = (char) (d * 16 + e);
+ i += 2;
}
- return sb.toString();
+ }
+ sb.append(c);
}
+ return sb.toString();
+ }
}
/**
* Convert a web browser cookie list string to a JSONObject and back.
+ *
* @author JSON.org
* @version 2015-12-09
*/
-public class CookieList {
+public class CookieList
+{
- /**
- * Convert a cookie list into a JSONObject. A cookie list is a sequence
- * of name/value pairs. The names are separated from the values by '='.
- * The pairs are separated by ';'. The names and the values
- * will be unescaped, possibly converting '+' and '%' sequences.
- *
- * To add a cookie to a cookie list,
- * cookielistJSONObject.put(cookieJSONObject.getString("name"),
- * cookieJSONObject.getString("value"));
- * @param string A cookie list string
- * @return A JSONObject
- * @throws JSONException
- */
- public static JSONObject toJSONObject(String string) throws JSONException {
- JSONObject jo = new JSONObject();
- JSONTokener x = new JSONTokener(string);
- while (x.more()) {
- String name = Cookie.unescape(x.nextTo('='));
- x.next('=');
- jo.put(name, Cookie.unescape(x.nextTo(';')));
- x.next();
- }
- return jo;
+ /**
+ * Convert a cookie list into a JSONObject. A cookie list is a sequence of
+ * name/value pairs. The names are separated from the values by '='. The pairs
+ * are separated by ';'. The names and the values will be unescaped, possibly
+ * converting '+' and '%' sequences.
+ *
+ * To add a cookie to a cookie list,
+ * cookielistJSONObject.put(cookieJSONObject.getString("name"),
+ * cookieJSONObject.getString("value"));
+ *
+ * @param string
+ * A cookie list string
+ * @return A JSONObject
+ * @throws JSONException
+ */
+ public static JSONObject toJSONObject(String string) throws JSONException
+ {
+ JSONObject jo = new JSONObject();
+ JSONTokener x = new JSONTokener(string);
+ while (x.more())
+ {
+ String name = Cookie.unescape(x.nextTo('='));
+ x.next('=');
+ jo.put(name, Cookie.unescape(x.nextTo(';')));
+ x.next();
}
+ return jo;
+ }
- /**
- * Convert a JSONObject into a cookie list. A cookie list is a sequence
- * of name/value pairs. The names are separated from the values by '='.
- * The pairs are separated by ';'. The characters '%', '+', '=', and ';'
- * in the names and values are replaced by "%hh".
- * @param jo A JSONObject
- * @return A cookie list string
- * @throws JSONException
- */
- public static String toString(JSONObject jo) throws JSONException {
- boolean b = false;
- final StringBuilder sb = new StringBuilder();
- // Don't use the new entrySet API to maintain Android support
- for (final String key : jo.keySet()) {
- final Object value = jo.opt(key);
- if (!JSONObject.NULL.equals(value)) {
- if (b) {
- sb.append(';');
- }
- sb.append(Cookie.escape(key));
- sb.append("=");
- sb.append(Cookie.escape(value.toString()));
- b = true;
- }
+ /**
+ * Convert a JSONObject into a cookie list. A cookie list is a sequence of
+ * name/value pairs. The names are separated from the values by '='. The pairs
+ * are separated by ';'. The characters '%', '+', '=', and ';' in the names
+ * and values are replaced by "%hh".
+ *
+ * @param jo
+ * A JSONObject
+ * @return A cookie list string
+ * @throws JSONException
+ */
+ public static String toString(JSONObject jo) throws JSONException
+ {
+ boolean b = false;
+ final StringBuilder sb = new StringBuilder();
+ // Don't use the new entrySet API to maintain Android support
+ for (final String key : jo.keySet())
+ {
+ final Object value = jo.opt(key);
+ if (!JSONObject.NULL.equals(value))
+ {
+ if (b)
+ {
+ sb.append(';');
}
- return sb.toString();
+ sb.append(Cookie.escape(key));
+ sb.append("=");
+ sb.append(Cookie.escape(value.toString()));
+ b = true;
+ }
}
+ return sb.toString();
+ }
}
/**
* Convert an HTTP header to a JSONObject and back.
+ *
* @author JSON.org
* @version 2015-12-09
*/
-public class HTTP {
-
- /** Carriage return/line feed. */
- public static final String CRLF = "\r\n";
-
- /**
- * Convert an HTTP header string into a JSONObject. It can be a request
- * header or a response header. A request header will contain
- * <pre>{
- * Method: "POST" (for example),
- * "Request-URI": "/" (for example),
- * "HTTP-Version": "HTTP/1.1" (for example)
- * }</pre>
- * A response header will contain
- * <pre>{
- * "HTTP-Version": "HTTP/1.1" (for example),
- * "Status-Code": "200" (for example),
- * "Reason-Phrase": "OK" (for example)
- * }</pre>
- * In addition, the other parameters in the header will be captured, using
- * the HTTP field names as JSON names, so that <pre>
- * Date: Sun, 26 May 2002 18:06:04 GMT
- * Cookie: Q=q2=PPEAsg--; B=677gi6ouf29bn&b=2&f=s
- * Cache-Control: no-cache</pre>
- * become
- * <pre>{...
- * Date: "Sun, 26 May 2002 18:06:04 GMT",
- * Cookie: "Q=q2=PPEAsg--; B=677gi6ouf29bn&b=2&f=s",
- * "Cache-Control": "no-cache",
- * ...}</pre>
- * It does no further checking or conversion. It does not parse dates.
- * It does not do '%' transforms on URLs.
- * @param string An HTTP header string.
- * @return A JSONObject containing the elements and attributes
- * of the XML string.
- * @throws JSONException
- */
- public static JSONObject toJSONObject(String string) throws JSONException {
- JSONObject jo = new JSONObject();
- HTTPTokener x = new HTTPTokener(string);
- String token;
-
- token = x.nextToken();
- if (token.toUpperCase(Locale.ROOT).startsWith("HTTP")) {
-
-// Response
-
- jo.put("HTTP-Version", token);
- jo.put("Status-Code", x.nextToken());
- jo.put("Reason-Phrase", x.nextTo('\0'));
- x.next();
-
- } else {
-
-// Request
-
- jo.put("Method", token);
- jo.put("Request-URI", x.nextToken());
- jo.put("HTTP-Version", x.nextToken());
- }
-
-// Fields
-
- while (x.more()) {
- String name = x.nextTo(':');
- x.next(':');
- jo.put(name, x.nextTo('\0'));
- x.next();
- }
- return jo;
+public class HTTP
+{
+
+ /** Carriage return/line feed. */
+ public static final String CRLF = "\r\n";
+
+ /**
+ * Convert an HTTP header string into a JSONObject. It can be a request header
+ * or a response header. A request header will contain
+ *
+ * <pre>
+ * {
+ * Method: "POST" (for example),
+ * "Request-URI": "/" (for example),
+ * "HTTP-Version": "HTTP/1.1" (for example)
+ * }
+ * </pre>
+ *
+ * A response header will contain
+ *
+ * <pre>
+ * {
+ * "HTTP-Version": "HTTP/1.1" (for example),
+ * "Status-Code": "200" (for example),
+ * "Reason-Phrase": "OK" (for example)
+ * }
+ * </pre>
+ *
+ * In addition, the other parameters in the header will be captured, using the
+ * HTTP field names as JSON names, so that
+ *
+ * <pre>
+ * Date: Sun, 26 May 2002 18:06:04 GMT
+ * Cookie: Q=q2=PPEAsg--; B=677gi6ouf29bn&b=2&f=s
+ * Cache-Control: no-cache
+ * </pre>
+ *
+ * become
+ *
+ * <pre>
+ * {...
+ * Date: "Sun, 26 May 2002 18:06:04 GMT",
+ * Cookie: "Q=q2=PPEAsg--; B=677gi6ouf29bn&b=2&f=s",
+ * "Cache-Control": "no-cache",
+ * ...}
+ * </pre>
+ *
+ * It does no further checking or conversion. It does not parse dates. It does
+ * not do '%' transforms on URLs.
+ *
+ * @param string
+ * An HTTP header string.
+ * @return A JSONObject containing the elements and attributes of the XML
+ * string.
+ * @throws JSONException
+ */
+ public static JSONObject toJSONObject(String string) throws JSONException
+ {
+ JSONObject jo = new JSONObject();
+ HTTPTokener x = new HTTPTokener(string);
+ String token;
+
+ token = x.nextToken();
+ if (token.toUpperCase(Locale.ROOT).startsWith("HTTP"))
+ {
+
+ // Response
+
+ jo.put("HTTP-Version", token);
+ jo.put("Status-Code", x.nextToken());
+ jo.put("Reason-Phrase", x.nextTo('\0'));
+ x.next();
+
}
+ else
+ {
+ // Request
- /**
- * Convert a JSONObject into an HTTP header. A request header must contain
- * <pre>{
- * Method: "POST" (for example),
- * "Request-URI": "/" (for example),
- * "HTTP-Version": "HTTP/1.1" (for example)
- * }</pre>
- * A response header must contain
- * <pre>{
- * "HTTP-Version": "HTTP/1.1" (for example),
- * "Status-Code": "200" (for example),
- * "Reason-Phrase": "OK" (for example)
- * }</pre>
- * Any other members of the JSONObject will be output as HTTP fields.
- * The result will end with two CRLF pairs.
- * @param jo A JSONObject
- * @return An HTTP header string.
- * @throws JSONException if the object does not contain enough
- * information.
- */
- public static String toString(JSONObject jo) throws JSONException {
- StringBuilder sb = new StringBuilder();
- if (jo.has("Status-Code") && jo.has("Reason-Phrase")) {
- sb.append(jo.getString("HTTP-Version"));
- sb.append(' ');
- sb.append(jo.getString("Status-Code"));
- sb.append(' ');
- sb.append(jo.getString("Reason-Phrase"));
- } else if (jo.has("Method") && jo.has("Request-URI")) {
- sb.append(jo.getString("Method"));
- sb.append(' ');
- sb.append('"');
- sb.append(jo.getString("Request-URI"));
- sb.append('"');
- sb.append(' ');
- sb.append(jo.getString("HTTP-Version"));
- } else {
- throw new JSONException("Not enough material for an HTTP header.");
- }
- sb.append(CRLF);
- // Don't use the new entrySet API to maintain Android support
- for (final String key : jo.keySet()) {
- String value = jo.optString(key);
- if (!"HTTP-Version".equals(key) && !"Status-Code".equals(key) &&
- !"Reason-Phrase".equals(key) && !"Method".equals(key) &&
- !"Request-URI".equals(key) && !JSONObject.NULL.equals(value)) {
- sb.append(key);
- sb.append(": ");
- sb.append(jo.optString(key));
- sb.append(CRLF);
- }
- }
+ jo.put("Method", token);
+ jo.put("Request-URI", x.nextToken());
+ jo.put("HTTP-Version", x.nextToken());
+ }
+
+ // Fields
+
+ while (x.more())
+ {
+ String name = x.nextTo(':');
+ x.next(':');
+ jo.put(name, x.nextTo('\0'));
+ x.next();
+ }
+ return jo;
+ }
+
+ /**
+ * Convert a JSONObject into an HTTP header. A request header must contain
+ *
+ * <pre>
+ * {
+ * Method: "POST" (for example),
+ * "Request-URI": "/" (for example),
+ * "HTTP-Version": "HTTP/1.1" (for example)
+ * }
+ * </pre>
+ *
+ * A response header must contain
+ *
+ * <pre>
+ * {
+ * "HTTP-Version": "HTTP/1.1" (for example),
+ * "Status-Code": "200" (for example),
+ * "Reason-Phrase": "OK" (for example)
+ * }
+ * </pre>
+ *
+ * Any other members of the JSONObject will be output as HTTP fields. The
+ * result will end with two CRLF pairs.
+ *
+ * @param jo
+ * A JSONObject
+ * @return An HTTP header string.
+ * @throws JSONException
+ * if the object does not contain enough information.
+ */
+ public static String toString(JSONObject jo) throws JSONException
+ {
+ StringBuilder sb = new StringBuilder();
+ if (jo.has("Status-Code") && jo.has("Reason-Phrase"))
+ {
+ sb.append(jo.getString("HTTP-Version"));
+ sb.append(' ');
+ sb.append(jo.getString("Status-Code"));
+ sb.append(' ');
+ sb.append(jo.getString("Reason-Phrase"));
+ }
+ else if (jo.has("Method") && jo.has("Request-URI"))
+ {
+ sb.append(jo.getString("Method"));
+ sb.append(' ');
+ sb.append('"');
+ sb.append(jo.getString("Request-URI"));
+ sb.append('"');
+ sb.append(' ');
+ sb.append(jo.getString("HTTP-Version"));
+ }
+ else
+ {
+ throw new JSONException("Not enough material for an HTTP header.");
+ }
+ sb.append(CRLF);
+ // Don't use the new entrySet API to maintain Android support
+ for (final String key : jo.keySet())
+ {
+ String value = jo.optString(key);
+ if (!"HTTP-Version".equals(key) && !"Status-Code".equals(key)
+ && !"Reason-Phrase".equals(key) && !"Method".equals(key)
+ && !"Request-URI".equals(key)
+ && !JSONObject.NULL.equals(value))
+ {
+ sb.append(key);
+ sb.append(": ");
+ sb.append(jo.optString(key));
sb.append(CRLF);
- return sb.toString();
+ }
}
+ sb.append(CRLF);
+ return sb.toString();
+ }
}
*/
/**
- * The HTTPTokener extends the JSONTokener to provide additional methods
- * for the parsing of HTTP headers.
+ * The HTTPTokener extends the JSONTokener to provide additional methods for the
+ * parsing of HTTP headers.
+ *
* @author JSON.org
* @version 2015-12-09
*/
-public class HTTPTokener extends JSONTokener {
-
- /**
- * Construct an HTTPTokener from a string.
- * @param string A source string.
- */
- public HTTPTokener(String string) {
- super(string);
- }
+public class HTTPTokener extends JSONTokener
+{
+ /**
+ * Construct an HTTPTokener from a string.
+ *
+ * @param string
+ * A source string.
+ */
+ public HTTPTokener(String string)
+ {
+ super(string);
+ }
- /**
- * Get the next token or string. This is used in parsing HTTP headers.
- * @throws JSONException
- * @return A String.
- */
- public String nextToken() throws JSONException {
- char c;
- char q;
- StringBuilder sb = new StringBuilder();
- do {
- c = next();
- } while (Character.isWhitespace(c));
- if (c == '"' || c == '\'') {
- q = c;
- for (;;) {
- c = next();
- if (c < ' ') {
- throw syntaxError("Unterminated string.");
- }
- if (c == q) {
- return sb.toString();
- }
- sb.append(c);
- }
+ /**
+ * Get the next token or string. This is used in parsing HTTP headers.
+ *
+ * @throws JSONException
+ * @return A String.
+ */
+ public String nextToken() throws JSONException
+ {
+ char c;
+ char q;
+ StringBuilder sb = new StringBuilder();
+ do
+ {
+ c = next();
+ } while (Character.isWhitespace(c));
+ if (c == '"' || c == '\'')
+ {
+ q = c;
+ for (;;)
+ {
+ c = next();
+ if (c < ' ')
+ {
+ throw syntaxError("Unterminated string.");
}
- for (;;) {
- if (c == 0 || Character.isWhitespace(c)) {
- return sb.toString();
- }
- sb.append(c);
- c = next();
+ if (c == q)
+ {
+ return sb.toString();
}
+ sb.append(c);
+ }
+ }
+ for (;;)
+ {
+ if (c == 0 || Character.isWhitespace(c))
+ {
+ return sb.toString();
+ }
+ sb.append(c);
+ c = next();
}
+ }
}
import java.util.List;
import java.util.Map;
-
/**
* A JSONArray is an ordered sequence of values. Its external text form is a
* string wrapped in square brackets with commas separating the values. The
* <li>Strings do not need to be quoted at all if they do not begin with a quote
* or single quote, and if they do not contain leading or trailing spaces, and
* if they do not contain any of these characters:
- * <code>{ } [ ] / \ : , #</code> and if they do not look like numbers and
- * if they are not the reserved words <code>true</code>, <code>false</code>, or
+ * <code>{ } [ ] / \ : , #</code> and if they do not look like numbers and if
+ * they are not the reserved words <code>true</code>, <code>false</code>, or
* <code>null</code>.</li>
* </ul>
*
* @author JSON.org
* @version 2016-08/15
*/
-public class JSONArray implements Iterable<Object> {
-
- /**
- * The arrayList where the JSONArray's properties are kept.
- */
- private final ArrayList<Object> myArrayList;
-
- /**
- * Construct an empty JSONArray.
- */
- public JSONArray() {
- this.myArrayList = new ArrayList<Object>();
- }
-
- /**
- * Construct a JSONArray from a JSONTokener.
- *
- * @param x
- * A JSONTokener
- * @throws JSONException
- * If there is a syntax error.
- */
- public JSONArray(JSONTokener x) throws JSONException {
- this();
- if (x.nextClean() != '[') {
- throw x.syntaxError("A JSONArray text must start with '['");
+public class JSONArray implements Iterable<Object>
+{
+
+ /**
+ * The arrayList where the JSONArray's properties are kept.
+ */
+ private final ArrayList<Object> myArrayList;
+
+ /**
+ * Construct an empty JSONArray.
+ */
+ public JSONArray()
+ {
+ this.myArrayList = new ArrayList<Object>();
+ }
+
+ /**
+ * Construct a JSONArray from a JSONTokener.
+ *
+ * @param x
+ * A JSONTokener
+ * @throws JSONException
+ * If there is a syntax error.
+ */
+ public JSONArray(JSONTokener x) throws JSONException
+ {
+ this();
+ if (x.nextClean() != '[')
+ {
+ throw x.syntaxError("A JSONArray text must start with '['");
+ }
+
+ char nextChar = x.nextClean();
+ if (nextChar == 0)
+ {
+ // array is unclosed. No ']' found, instead EOF
+ throw x.syntaxError("Expected a ',' or ']'");
+ }
+ if (nextChar != ']')
+ {
+ x.back();
+ for (;;)
+ {
+ if (x.nextClean() == ',')
+ {
+ x.back();
+ this.myArrayList.add(JSONObject.NULL);
+ }
+ else
+ {
+ x.back();
+ this.myArrayList.add(x.nextValue());
}
-
- char nextChar = x.nextClean();
- if (nextChar == 0) {
+ switch (x.nextClean())
+ {
+ case 0:
+ // array is unclosed. No ']' found, instead EOF
+ throw x.syntaxError("Expected a ',' or ']'");
+ case ',':
+ nextChar = x.nextClean();
+ if (nextChar == 0)
+ {
// array is unclosed. No ']' found, instead EOF
throw x.syntaxError("Expected a ',' or ']'");
+ }
+ if (nextChar == ']')
+ {
+ return;
+ }
+ x.back();
+ break;
+ case ']':
+ return;
+ default:
+ throw x.syntaxError("Expected a ',' or ']'");
}
- if (nextChar != ']') {
- x.back();
- for (;;) {
- if (x.nextClean() == ',') {
- x.back();
- this.myArrayList.add(JSONObject.NULL);
- } else {
- x.back();
- this.myArrayList.add(x.nextValue());
- }
- switch (x.nextClean()) {
- case 0:
- // array is unclosed. No ']' found, instead EOF
- throw x.syntaxError("Expected a ',' or ']'");
- case ',':
- nextChar = x.nextClean();
- if (nextChar == 0) {
- // array is unclosed. No ']' found, instead EOF
- throw x.syntaxError("Expected a ',' or ']'");
- }
- if (nextChar == ']') {
- return;
- }
- x.back();
- break;
- case ']':
- return;
- default:
- throw x.syntaxError("Expected a ',' or ']'");
- }
- }
- }
- }
-
- /**
- * Construct a JSONArray from a source JSON text.
- *
- * @param source
- * A string that begins with <code>[</code> <small>(left
- * bracket)</small> and ends with <code>]</code>
- * <small>(right bracket)</small>.
- * @throws JSONException
- * If there is a syntax error.
- */
- public JSONArray(String source) throws JSONException {
- this(new JSONTokener(source));
- }
-
- /**
- * Construct a JSONArray from a Collection.
- *
- * @param collection
- * A Collection.
- */
- public JSONArray(Collection<?> collection) {
- if (collection == null) {
- this.myArrayList = new ArrayList<Object>();
- } else {
- this.myArrayList = new ArrayList<Object>(collection.size());
- for (Object o: collection){
- this.myArrayList.add(JSONObject.wrap(o));
- }
- }
- }
-
- /**
- * Construct a JSONArray from an array
- *
- * @throws JSONException
- * If not an array or if an array value is non-finite number.
- */
- public JSONArray(Object array) throws JSONException {
- this();
- if (array.getClass().isArray()) {
- int length = Array.getLength(array);
- this.myArrayList.ensureCapacity(length);
- for (int i = 0; i < length; i += 1) {
- this.put(JSONObject.wrap(Array.get(array, i)));
- }
- } else {
- throw new JSONException(
- "JSONArray initial value should be a string or collection or array.");
- }
- }
-
- @Override
- public Iterator<Object> iterator() {
- return this.myArrayList.iterator();
- }
-
- /**
- * Get the object value associated with an index.
- *
- * @param index
- * The index must be between 0 and length() - 1.
- * @return An object value.
- * @throws JSONException
- * If there is no value for the index.
- */
- public Object get(int index) throws JSONException {
- Object object = this.opt(index);
- if (object == null) {
- throw new JSONException("JSONArray[" + index + "] not found.");
- }
- return object;
- }
-
- /**
- * Get the boolean value associated with an index. The string values "true"
- * and "false" are converted to boolean.
- *
- * @param index
- * The index must be between 0 and length() - 1.
- * @return The truth.
- * @throws JSONException
- * If there is no value for the index or if the value is not
- * convertible to boolean.
- */
- public boolean getBoolean(int index) throws JSONException {
- Object object = this.get(index);
- if (object.equals(Boolean.FALSE)
- || (object instanceof String && ((String) object)
- .equalsIgnoreCase("false"))) {
- return false;
- } else if (object.equals(Boolean.TRUE)
- || (object instanceof String && ((String) object)
- .equalsIgnoreCase("true"))) {
- return true;
- }
- throw new JSONException("JSONArray[" + index + "] is not a boolean.");
- }
-
- /**
- * Get the double value associated with an index.
- *
- * @param index
- * The index must be between 0 and length() - 1.
- * @return The value.
- * @throws JSONException
- * If the key is not found or if the value cannot be converted
- * to a number.
- */
- public double getDouble(int index) throws JSONException {
- Object object = this.get(index);
- try {
- return object instanceof Number ? ((Number) object).doubleValue()
- : Double.parseDouble((String) object);
- } catch (Exception e) {
- throw new JSONException("JSONArray[" + index + "] is not a number.", e);
- }
- }
-
- /**
- * Get the float value associated with a key.
- *
- * @param index
- * The index must be between 0 and length() - 1.
- * @return The numeric value.
- * @throws JSONException
- * if the key is not found or if the value is not a Number
- * object and cannot be converted to a number.
- */
- public float getFloat(int index) throws JSONException {
- Object object = this.get(index);
- try {
- return object instanceof Number ? ((Number) object).floatValue()
- : Float.parseFloat(object.toString());
- } catch (Exception e) {
- throw new JSONException("JSONArray[" + index
- + "] is not a number.", e);
- }
- }
-
- /**
- * Get the Number value associated with a key.
- *
- * @param index
- * The index must be between 0 and length() - 1.
- * @return The numeric value.
- * @throws JSONException
- * if the key is not found or if the value is not a Number
- * object and cannot be converted to a number.
- */
- public Number getNumber(int index) throws JSONException {
- Object object = this.get(index);
- try {
- if (object instanceof Number) {
- return (Number)object;
- }
- return JSONObject.stringToNumber(object.toString());
- } catch (Exception e) {
- throw new JSONException("JSONArray[" + index + "] is not a number.", e);
- }
- }
-
- /**
- * Get the enum value associated with an index.
- *
- * @param clazz
- * The type of enum to retrieve.
- * @param index
- * The index must be between 0 and length() - 1.
- * @return The enum value at the index location
- * @throws JSONException
- * if the key is not found or if the value cannot be converted
- * to an enum.
- */
- public <E extends Enum<E>> E getEnum(Class<E> clazz, int index) throws JSONException {
- E val = optEnum(clazz, index);
- if(val==null) {
- // JSONException should really take a throwable argument.
- // If it did, I would re-implement this with the Enum.valueOf
- // method and place any thrown exception in the JSONException
- throw new JSONException("JSONArray[" + index + "] is not an enum of type "
- + JSONObject.quote(clazz.getSimpleName()) + ".");
- }
- return val;
- }
-
- /**
- * Get the BigDecimal value associated with an index.
- *
- * @param index
- * The index must be between 0 and length() - 1.
- * @return The value.
- * @throws JSONException
- * If the key is not found or if the value cannot be converted
- * to a BigDecimal.
- */
- public BigDecimal getBigDecimal (int index) throws JSONException {
- Object object = this.get(index);
- try {
- return new BigDecimal(object.toString());
- } catch (Exception e) {
- throw new JSONException("JSONArray[" + index +
- "] could not convert to BigDecimal.", e);
- }
- }
-
- /**
- * Get the BigInteger value associated with an index.
- *
- * @param index
- * The index must be between 0 and length() - 1.
- * @return The value.
- * @throws JSONException
- * If the key is not found or if the value cannot be converted
- * to a BigInteger.
- */
- public BigInteger getBigInteger (int index) throws JSONException {
- Object object = this.get(index);
- try {
- return new BigInteger(object.toString());
- } catch (Exception e) {
- throw new JSONException("JSONArray[" + index +
- "] could not convert to BigInteger.", e);
- }
- }
-
- /**
- * Get the int value associated with an index.
- *
- * @param index
- * The index must be between 0 and length() - 1.
- * @return The value.
- * @throws JSONException
- * If the key is not found or if the value is not a number.
- */
- public int getInt(int index) throws JSONException {
- Object object = this.get(index);
- try {
- return object instanceof Number ? ((Number) object).intValue()
- : Integer.parseInt((String) object);
- } catch (Exception e) {
- throw new JSONException("JSONArray[" + index + "] is not a number.", e);
- }
- }
-
- /**
- * Get the JSONArray associated with an index.
- *
- * @param index
- * The index must be between 0 and length() - 1.
- * @return A JSONArray value.
- * @throws JSONException
- * If there is no value for the index. or if the value is not a
- * JSONArray
- */
- public JSONArray getJSONArray(int index) throws JSONException {
- Object object = this.get(index);
- if (object instanceof JSONArray) {
- return (JSONArray) object;
- }
- throw new JSONException("JSONArray[" + index + "] is not a JSONArray.");
- }
-
- /**
- * Get the JSONObject associated with an index.
- *
- * @param index
- * subscript
- * @return A JSONObject value.
- * @throws JSONException
- * If there is no value for the index or if the value is not a
- * JSONObject
- */
- public JSONObject getJSONObject(int index) throws JSONException {
- Object object = this.get(index);
- if (object instanceof JSONObject) {
- return (JSONObject) object;
- }
- throw new JSONException("JSONArray[" + index + "] is not a JSONObject.");
- }
-
- /**
- * Get the long value associated with an index.
- *
- * @param index
- * The index must be between 0 and length() - 1.
- * @return The value.
- * @throws JSONException
- * If the key is not found or if the value cannot be converted
- * to a number.
- */
- public long getLong(int index) throws JSONException {
- Object object = this.get(index);
- try {
- return object instanceof Number ? ((Number) object).longValue()
- : Long.parseLong((String) object);
- } catch (Exception e) {
- throw new JSONException("JSONArray[" + index + "] is not a number.", e);
- }
- }
-
- /**
- * Get the string associated with an index.
- *
- * @param index
- * The index must be between 0 and length() - 1.
- * @return A string value.
- * @throws JSONException
- * If there is no string value for the index.
- */
- public String getString(int index) throws JSONException {
- Object object = this.get(index);
- if (object instanceof String) {
- return (String) object;
- }
- throw new JSONException("JSONArray[" + index + "] not a string.");
- }
-
- /**
- * Determine if the value is <code>null</code>.
- *
- * @param index
- * The index must be between 0 and length() - 1.
- * @return true if the value at the index is <code>null</code>, or if there is no value.
- */
- public boolean isNull(int index) {
- return JSONObject.NULL.equals(this.opt(index));
- }
-
- /**
- * Make a string from the contents of this JSONArray. The
- * <code>separator</code> string is inserted between each element. Warning:
- * This method assumes that the data structure is acyclical.
- *
- * @param separator
- * A string that will be inserted between the elements.
- * @return a string.
- * @throws JSONException
- * If the array contains an invalid number.
- */
- public String join(String separator) throws JSONException {
- int len = this.length();
- StringBuilder sb = new StringBuilder();
-
- for (int i = 0; i < len; i += 1) {
- if (i > 0) {
- sb.append(separator);
- }
- sb.append(JSONObject.valueToString(this.myArrayList.get(i)));
- }
- return sb.toString();
- }
-
- /**
- * Get the number of elements in the JSONArray, included nulls.
- *
- * @return The length (or size).
- */
- public int length() {
- return this.myArrayList.size();
- }
-
- /**
- * Get the optional object value associated with an index.
- *
- * @param index
- * The index must be between 0 and length() - 1. If not, null is returned.
- * @return An object value, or null if there is no object at that index.
- */
- public Object opt(int index) {
- return (index < 0 || index >= this.length()) ? null : this.myArrayList
- .get(index);
- }
-
- /**
- * Get the optional boolean value associated with an index. It returns false
- * if there is no value at that index, or if the value is not Boolean.TRUE
- * or the String "true".
- *
- * @param index
- * The index must be between 0 and length() - 1.
- * @return The truth.
- */
- public boolean optBoolean(int index) {
- return this.optBoolean(index, false);
- }
-
- /**
- * Get the optional boolean value associated with an index. It returns the
- * defaultValue if there is no value at that index or if it is not a Boolean
- * or the String "true" or "false" (case insensitive).
- *
- * @param index
- * The index must be between 0 and length() - 1.
- * @param defaultValue
- * A boolean default.
- * @return The truth.
- */
- public boolean optBoolean(int index, boolean defaultValue) {
- try {
- return this.getBoolean(index);
- } catch (Exception e) {
- return defaultValue;
- }
- }
-
- /**
- * Get the optional double value associated with an index. NaN is returned
- * if there is no value for the index, or if the value is not a number and
- * cannot be converted to a number.
- *
- * @param index
- * The index must be between 0 and length() - 1.
- * @return The value.
- */
- public double optDouble(int index) {
- return this.optDouble(index, Double.NaN);
- }
-
- /**
- * Get the optional double value associated with an index. The defaultValue
- * is returned if there is no value for the index, or if the value is not a
- * number and cannot be converted to a number.
- *
- * @param index
- * subscript
- * @param defaultValue
- * The default value.
- * @return The value.
- */
- public double optDouble(int index, double defaultValue) {
- Object val = this.opt(index);
- if (JSONObject.NULL.equals(val)) {
- return defaultValue;
- }
- if (val instanceof Number){
- return ((Number) val).doubleValue();
- }
- if (val instanceof String) {
- try {
- return Double.parseDouble((String) val);
- } catch (Exception e) {
- return defaultValue;
- }
- }
+ }
+ }
+ }
+
+ /**
+ * Construct a JSONArray from a source JSON text.
+ *
+ * @param source
+ * A string that begins with <code>[</code> <small>(left
+ * bracket)</small> and ends with <code>]</code> <small>(right
+ * bracket)</small>.
+ * @throws JSONException
+ * If there is a syntax error.
+ */
+ public JSONArray(String source) throws JSONException
+ {
+ this(new JSONTokener(source));
+ }
+
+ /**
+ * Construct a JSONArray from a Collection.
+ *
+ * @param collection
+ * A Collection.
+ */
+ public JSONArray(Collection<?> collection)
+ {
+ if (collection == null)
+ {
+ this.myArrayList = new ArrayList<Object>();
+ }
+ else
+ {
+ this.myArrayList = new ArrayList<Object>(collection.size());
+ for (Object o : collection)
+ {
+ this.myArrayList.add(JSONObject.wrap(o));
+ }
+ }
+ }
+
+ /**
+ * Construct a JSONArray from an array
+ *
+ * @throws JSONException
+ * If not an array or if an array value is non-finite number.
+ */
+ public JSONArray(Object array) throws JSONException
+ {
+ this();
+ if (array.getClass().isArray())
+ {
+ int length = Array.getLength(array);
+ this.myArrayList.ensureCapacity(length);
+ for (int i = 0; i < length; i += 1)
+ {
+ this.put(JSONObject.wrap(Array.get(array, i)));
+ }
+ }
+ else
+ {
+ throw new JSONException(
+ "JSONArray initial value should be a string or collection or array.");
+ }
+ }
+
+ @Override
+ public Iterator<Object> iterator()
+ {
+ return this.myArrayList.iterator();
+ }
+
+ /**
+ * Get the object value associated with an index.
+ *
+ * @param index
+ * The index must be between 0 and length() - 1.
+ * @return An object value.
+ * @throws JSONException
+ * If there is no value for the index.
+ */
+ public Object get(int index) throws JSONException
+ {
+ Object object = this.opt(index);
+ if (object == null)
+ {
+ throw new JSONException("JSONArray[" + index + "] not found.");
+ }
+ return object;
+ }
+
+ /**
+ * Get the boolean value associated with an index. The string values "true"
+ * and "false" are converted to boolean.
+ *
+ * @param index
+ * The index must be between 0 and length() - 1.
+ * @return The truth.
+ * @throws JSONException
+ * If there is no value for the index or if the value is not
+ * convertible to boolean.
+ */
+ public boolean getBoolean(int index) throws JSONException
+ {
+ Object object = this.get(index);
+ if (object.equals(Boolean.FALSE) || (object instanceof String
+ && ((String) object).equalsIgnoreCase("false")))
+ {
+ return false;
+ }
+ else if (object.equals(Boolean.TRUE) || (object instanceof String
+ && ((String) object).equalsIgnoreCase("true")))
+ {
+ return true;
+ }
+ throw new JSONException("JSONArray[" + index + "] is not a boolean.");
+ }
+
+ /**
+ * Get the double value associated with an index.
+ *
+ * @param index
+ * The index must be between 0 and length() - 1.
+ * @return The value.
+ * @throws JSONException
+ * If the key is not found or if the value cannot be converted to a
+ * number.
+ */
+ public double getDouble(int index) throws JSONException
+ {
+ Object object = this.get(index);
+ try
+ {
+ return object instanceof Number ? ((Number) object).doubleValue()
+ : Double.parseDouble((String) object);
+ } catch (Exception e)
+ {
+ throw new JSONException("JSONArray[" + index + "] is not a number.",
+ e);
+ }
+ }
+
+ /**
+ * Get the float value associated with a key.
+ *
+ * @param index
+ * The index must be between 0 and length() - 1.
+ * @return The numeric value.
+ * @throws JSONException
+ * if the key is not found or if the value is not a Number object
+ * and cannot be converted to a number.
+ */
+ public float getFloat(int index) throws JSONException
+ {
+ Object object = this.get(index);
+ try
+ {
+ return object instanceof Number ? ((Number) object).floatValue()
+ : Float.parseFloat(object.toString());
+ } catch (Exception e)
+ {
+ throw new JSONException("JSONArray[" + index + "] is not a number.",
+ e);
+ }
+ }
+
+ /**
+ * Get the Number value associated with a key.
+ *
+ * @param index
+ * The index must be between 0 and length() - 1.
+ * @return The numeric value.
+ * @throws JSONException
+ * if the key is not found or if the value is not a Number object
+ * and cannot be converted to a number.
+ */
+ public Number getNumber(int index) throws JSONException
+ {
+ Object object = this.get(index);
+ try
+ {
+ if (object instanceof Number)
+ {
+ return (Number) object;
+ }
+ return JSONObject.stringToNumber(object.toString());
+ } catch (Exception e)
+ {
+ throw new JSONException("JSONArray[" + index + "] is not a number.",
+ e);
+ }
+ }
+
+ /**
+ * Get the enum value associated with an index.
+ *
+ * @param clazz
+ * The type of enum to retrieve.
+ * @param index
+ * The index must be between 0 and length() - 1.
+ * @return The enum value at the index location
+ * @throws JSONException
+ * if the key is not found or if the value cannot be converted to an
+ * enum.
+ */
+ public <E extends Enum<E>> E getEnum(Class<E> clazz, int index)
+ throws JSONException
+ {
+ E val = optEnum(clazz, index);
+ if (val == null)
+ {
+ // JSONException should really take a throwable argument.
+ // If it did, I would re-implement this with the Enum.valueOf
+ // method and place any thrown exception in the JSONException
+ throw new JSONException(
+ "JSONArray[" + index + "] is not an enum of type "
+ + JSONObject.quote(clazz.getSimpleName()) + ".");
+ }
+ return val;
+ }
+
+ /**
+ * Get the BigDecimal value associated with an index.
+ *
+ * @param index
+ * The index must be between 0 and length() - 1.
+ * @return The value.
+ * @throws JSONException
+ * If the key is not found or if the value cannot be converted to a
+ * BigDecimal.
+ */
+ public BigDecimal getBigDecimal(int index) throws JSONException
+ {
+ Object object = this.get(index);
+ try
+ {
+ return new BigDecimal(object.toString());
+ } catch (Exception e)
+ {
+ throw new JSONException(
+ "JSONArray[" + index + "] could not convert to BigDecimal.",
+ e);
+ }
+ }
+
+ /**
+ * Get the BigInteger value associated with an index.
+ *
+ * @param index
+ * The index must be between 0 and length() - 1.
+ * @return The value.
+ * @throws JSONException
+ * If the key is not found or if the value cannot be converted to a
+ * BigInteger.
+ */
+ public BigInteger getBigInteger(int index) throws JSONException
+ {
+ Object object = this.get(index);
+ try
+ {
+ return new BigInteger(object.toString());
+ } catch (Exception e)
+ {
+ throw new JSONException(
+ "JSONArray[" + index + "] could not convert to BigInteger.",
+ e);
+ }
+ }
+
+ /**
+ * Get the int value associated with an index.
+ *
+ * @param index
+ * The index must be between 0 and length() - 1.
+ * @return The value.
+ * @throws JSONException
+ * If the key is not found or if the value is not a number.
+ */
+ public int getInt(int index) throws JSONException
+ {
+ Object object = this.get(index);
+ try
+ {
+ return object instanceof Number ? ((Number) object).intValue()
+ : Integer.parseInt((String) object);
+ } catch (Exception e)
+ {
+ throw new JSONException("JSONArray[" + index + "] is not a number.",
+ e);
+ }
+ }
+
+ /**
+ * Get the JSONArray associated with an index.
+ *
+ * @param index
+ * The index must be between 0 and length() - 1.
+ * @return A JSONArray value.
+ * @throws JSONException
+ * If there is no value for the index. or if the value is not a
+ * JSONArray
+ */
+ public JSONArray getJSONArray(int index) throws JSONException
+ {
+ Object object = this.get(index);
+ if (object instanceof JSONArray)
+ {
+ return (JSONArray) object;
+ }
+ throw new JSONException("JSONArray[" + index + "] is not a JSONArray.");
+ }
+
+ /**
+ * Get the JSONObject associated with an index.
+ *
+ * @param index
+ * subscript
+ * @return A JSONObject value.
+ * @throws JSONException
+ * If there is no value for the index or if the value is not a
+ * JSONObject
+ */
+ public JSONObject getJSONObject(int index) throws JSONException
+ {
+ Object object = this.get(index);
+ if (object instanceof JSONObject)
+ {
+ return (JSONObject) object;
+ }
+ throw new JSONException(
+ "JSONArray[" + index + "] is not a JSONObject.");
+ }
+
+ /**
+ * Get the long value associated with an index.
+ *
+ * @param index
+ * The index must be between 0 and length() - 1.
+ * @return The value.
+ * @throws JSONException
+ * If the key is not found or if the value cannot be converted to a
+ * number.
+ */
+ public long getLong(int index) throws JSONException
+ {
+ Object object = this.get(index);
+ try
+ {
+ return object instanceof Number ? ((Number) object).longValue()
+ : Long.parseLong((String) object);
+ } catch (Exception e)
+ {
+ throw new JSONException("JSONArray[" + index + "] is not a number.",
+ e);
+ }
+ }
+
+ /**
+ * Get the string associated with an index.
+ *
+ * @param index
+ * The index must be between 0 and length() - 1.
+ * @return A string value.
+ * @throws JSONException
+ * If there is no string value for the index.
+ */
+ public String getString(int index) throws JSONException
+ {
+ Object object = this.get(index);
+ if (object instanceof String)
+ {
+ return (String) object;
+ }
+ throw new JSONException("JSONArray[" + index + "] not a string.");
+ }
+
+ /**
+ * Determine if the value is <code>null</code>.
+ *
+ * @param index
+ * The index must be between 0 and length() - 1.
+ * @return true if the value at the index is <code>null</code>, or if there is
+ * no value.
+ */
+ public boolean isNull(int index)
+ {
+ return JSONObject.NULL.equals(this.opt(index));
+ }
+
+ /**
+ * Make a string from the contents of this JSONArray. The
+ * <code>separator</code> string is inserted between each element. Warning:
+ * This method assumes that the data structure is acyclical.
+ *
+ * @param separator
+ * A string that will be inserted between the elements.
+ * @return a string.
+ * @throws JSONException
+ * If the array contains an invalid number.
+ */
+ public String join(String separator) throws JSONException
+ {
+ int len = this.length();
+ StringBuilder sb = new StringBuilder();
+
+ for (int i = 0; i < len; i += 1)
+ {
+ if (i > 0)
+ {
+ sb.append(separator);
+ }
+ sb.append(JSONObject.valueToString(this.myArrayList.get(i)));
+ }
+ return sb.toString();
+ }
+
+ /**
+ * Get the number of elements in the JSONArray, included nulls.
+ *
+ * @return The length (or size).
+ */
+ public int length()
+ {
+ return this.myArrayList.size();
+ }
+
+ /**
+ * Get the optional object value associated with an index.
+ *
+ * @param index
+ * The index must be between 0 and length() - 1. If not, null is
+ * returned.
+ * @return An object value, or null if there is no object at that index.
+ */
+ public Object opt(int index)
+ {
+ return (index < 0 || index >= this.length()) ? null
+ : this.myArrayList.get(index);
+ }
+
+ /**
+ * Get the optional boolean value associated with an index. It returns false
+ * if there is no value at that index, or if the value is not Boolean.TRUE or
+ * the String "true".
+ *
+ * @param index
+ * The index must be between 0 and length() - 1.
+ * @return The truth.
+ */
+ public boolean optBoolean(int index)
+ {
+ return this.optBoolean(index, false);
+ }
+
+ /**
+ * Get the optional boolean value associated with an index. It returns the
+ * defaultValue if there is no value at that index or if it is not a Boolean
+ * or the String "true" or "false" (case insensitive).
+ *
+ * @param index
+ * The index must be between 0 and length() - 1.
+ * @param defaultValue
+ * A boolean default.
+ * @return The truth.
+ */
+ public boolean optBoolean(int index, boolean defaultValue)
+ {
+ try
+ {
+ return this.getBoolean(index);
+ } catch (Exception e)
+ {
+ return defaultValue;
+ }
+ }
+
+ /**
+ * Get the optional double value associated with an index. NaN is returned if
+ * there is no value for the index, or if the value is not a number and cannot
+ * be converted to a number.
+ *
+ * @param index
+ * The index must be between 0 and length() - 1.
+ * @return The value.
+ */
+ public double optDouble(int index)
+ {
+ return this.optDouble(index, Double.NaN);
+ }
+
+ /**
+ * Get the optional double value associated with an index. The defaultValue is
+ * returned if there is no value for the index, or if the value is not a
+ * number and cannot be converted to a number.
+ *
+ * @param index
+ * subscript
+ * @param defaultValue
+ * The default value.
+ * @return The value.
+ */
+ public double optDouble(int index, double defaultValue)
+ {
+ Object val = this.opt(index);
+ if (JSONObject.NULL.equals(val))
+ {
+ return defaultValue;
+ }
+ if (val instanceof Number)
+ {
+ return ((Number) val).doubleValue();
+ }
+ if (val instanceof String)
+ {
+ try
+ {
+ return Double.parseDouble((String) val);
+ } catch (Exception e)
+ {
return defaultValue;
- }
-
- /**
- * Get the optional float value associated with an index. NaN is returned
- * if there is no value for the index, or if the value is not a number and
- * cannot be converted to a number.
- *
- * @param index
- * The index must be between 0 and length() - 1.
- * @return The value.
- */
- public float optFloat(int index) {
- return this.optFloat(index, Float.NaN);
- }
-
- /**
- * Get the optional float value associated with an index. The defaultValue
- * is returned if there is no value for the index, or if the value is not a
- * number and cannot be converted to a number.
- *
- * @param index
- * subscript
- * @param defaultValue
- * The default value.
- * @return The value.
- */
- public float optFloat(int index, float defaultValue) {
- Object val = this.opt(index);
- if (JSONObject.NULL.equals(val)) {
- return defaultValue;
- }
- if (val instanceof Number){
- return ((Number) val).floatValue();
- }
- if (val instanceof String) {
- try {
- return Float.parseFloat((String) val);
- } catch (Exception e) {
- return defaultValue;
- }
- }
+ }
+ }
+ return defaultValue;
+ }
+
+ /**
+ * Get the optional float value associated with an index. NaN is returned if
+ * there is no value for the index, or if the value is not a number and cannot
+ * be converted to a number.
+ *
+ * @param index
+ * The index must be between 0 and length() - 1.
+ * @return The value.
+ */
+ public float optFloat(int index)
+ {
+ return this.optFloat(index, Float.NaN);
+ }
+
+ /**
+ * Get the optional float value associated with an index. The defaultValue is
+ * returned if there is no value for the index, or if the value is not a
+ * number and cannot be converted to a number.
+ *
+ * @param index
+ * subscript
+ * @param defaultValue
+ * The default value.
+ * @return The value.
+ */
+ public float optFloat(int index, float defaultValue)
+ {
+ Object val = this.opt(index);
+ if (JSONObject.NULL.equals(val))
+ {
+ return defaultValue;
+ }
+ if (val instanceof Number)
+ {
+ return ((Number) val).floatValue();
+ }
+ if (val instanceof String)
+ {
+ try
+ {
+ return Float.parseFloat((String) val);
+ } catch (Exception e)
+ {
return defaultValue;
- }
-
- /**
- * Get the optional int value associated with an index. Zero is returned if
- * there is no value for the index, or if the value is not a number and
- * cannot be converted to a number.
- *
- * @param index
- * The index must be between 0 and length() - 1.
- * @return The value.
- */
- public int optInt(int index) {
- return this.optInt(index, 0);
- }
-
- /**
- * Get the optional int value associated with an index. The defaultValue is
- * returned if there is no value for the index, or if the value is not a
- * number and cannot be converted to a number.
- *
- * @param index
- * The index must be between 0 and length() - 1.
- * @param defaultValue
- * The default value.
- * @return The value.
- */
- public int optInt(int index, int defaultValue) {
- Object val = this.opt(index);
- if (JSONObject.NULL.equals(val)) {
- return defaultValue;
- }
- if (val instanceof Number){
- return ((Number) val).intValue();
- }
-
- if (val instanceof String) {
- try {
- return new BigDecimal(val.toString()).intValue();
- } catch (Exception e) {
- return defaultValue;
- }
- }
+ }
+ }
+ return defaultValue;
+ }
+
+ /**
+ * Get the optional int value associated with an index. Zero is returned if
+ * there is no value for the index, or if the value is not a number and cannot
+ * be converted to a number.
+ *
+ * @param index
+ * The index must be between 0 and length() - 1.
+ * @return The value.
+ */
+ public int optInt(int index)
+ {
+ return this.optInt(index, 0);
+ }
+
+ /**
+ * Get the optional int value associated with an index. The defaultValue is
+ * returned if there is no value for the index, or if the value is not a
+ * number and cannot be converted to a number.
+ *
+ * @param index
+ * The index must be between 0 and length() - 1.
+ * @param defaultValue
+ * The default value.
+ * @return The value.
+ */
+ public int optInt(int index, int defaultValue)
+ {
+ Object val = this.opt(index);
+ if (JSONObject.NULL.equals(val))
+ {
+ return defaultValue;
+ }
+ if (val instanceof Number)
+ {
+ return ((Number) val).intValue();
+ }
+
+ if (val instanceof String)
+ {
+ try
+ {
+ return new BigDecimal(val.toString()).intValue();
+ } catch (Exception e)
+ {
return defaultValue;
- }
-
- /**
- * Get the enum value associated with a key.
- *
- * @param clazz
- * The type of enum to retrieve.
- * @param index
- * The index must be between 0 and length() - 1.
- * @return The enum value at the index location or null if not found
- */
- public <E extends Enum<E>> E optEnum(Class<E> clazz, int index) {
- return this.optEnum(clazz, index, null);
- }
-
- /**
- * Get the enum value associated with a key.
- *
- * @param clazz
- * The type of enum to retrieve.
- * @param index
- * The index must be between 0 and length() - 1.
- * @param defaultValue
- * The default in case the value is not found
- * @return The enum value at the index location or defaultValue if
- * the value is not found or cannot be assigned to clazz
- */
- public <E extends Enum<E>> E optEnum(Class<E> clazz, int index, E defaultValue) {
- try {
- Object val = this.opt(index);
- if (JSONObject.NULL.equals(val)) {
- return defaultValue;
- }
- if (clazz.isAssignableFrom(val.getClass())) {
- // we just checked it!
- @SuppressWarnings("unchecked")
- E myE = (E) val;
- return myE;
- }
- return Enum.valueOf(clazz, val.toString());
- } catch (IllegalArgumentException e) {
- return defaultValue;
- } catch (NullPointerException e) {
- return defaultValue;
- }
- }
-
-
- /**
- * Get the optional BigInteger value associated with an index. The
- * defaultValue is returned if there is no value for the index, or if the
- * value is not a number and cannot be converted to a number.
- *
- * @param index
- * The index must be between 0 and length() - 1.
- * @param defaultValue
- * The default value.
- * @return The value.
- */
- public BigInteger optBigInteger(int index, BigInteger defaultValue) {
- Object val = this.opt(index);
- if (JSONObject.NULL.equals(val)) {
- return defaultValue;
- }
- if (val instanceof BigInteger){
- return (BigInteger) val;
- }
- if (val instanceof BigDecimal){
- return ((BigDecimal) val).toBigInteger();
- }
- if (val instanceof Double || val instanceof Float){
- return new BigDecimal(((Number) val).doubleValue()).toBigInteger();
- }
- if (val instanceof Long || val instanceof Integer
- || val instanceof Short || val instanceof Byte){
- return BigInteger.valueOf(((Number) val).longValue());
- }
- try {
- final String valStr = val.toString();
- if(JSONObject.isDecimalNotation(valStr)) {
- return new BigDecimal(valStr).toBigInteger();
- }
- return new BigInteger(valStr);
- } catch (Exception e) {
- return defaultValue;
- }
- }
-
- /**
- * Get the optional BigDecimal value associated with an index. The
- * defaultValue is returned if there is no value for the index, or if the
- * value is not a number and cannot be converted to a number.
- *
- * @param index
- * The index must be between 0 and length() - 1.
- * @param defaultValue
- * The default value.
- * @return The value.
- */
- public BigDecimal optBigDecimal(int index, BigDecimal defaultValue) {
- Object val = this.opt(index);
- if (JSONObject.NULL.equals(val)) {
- return defaultValue;
- }
- if (val instanceof BigDecimal){
- return (BigDecimal) val;
- }
- if (val instanceof BigInteger){
- return new BigDecimal((BigInteger) val);
- }
- if (val instanceof Double || val instanceof Float){
- return new BigDecimal(((Number) val).doubleValue());
- }
- if (val instanceof Long || val instanceof Integer
- || val instanceof Short || val instanceof Byte){
- return new BigDecimal(((Number) val).longValue());
- }
- try {
- return new BigDecimal(val.toString());
- } catch (Exception e) {
- return defaultValue;
- }
- }
-
- /**
- * Get the optional JSONArray associated with an index.
- *
- * @param index
- * subscript
- * @return A JSONArray value, or null if the index has no value, or if the
- * value is not a JSONArray.
- */
- public JSONArray optJSONArray(int index) {
- Object o = this.opt(index);
- return o instanceof JSONArray ? (JSONArray) o : null;
- }
-
- /**
- * Get the optional JSONObject associated with an index. Null is returned if
- * the key is not found, or null if the index has no value, or if the value
- * is not a JSONObject.
- *
- * @param index
- * The index must be between 0 and length() - 1.
- * @return A JSONObject value.
- */
- public JSONObject optJSONObject(int index) {
- Object o = this.opt(index);
- return o instanceof JSONObject ? (JSONObject) o : null;
- }
-
- /**
- * Get the optional long value associated with an index. Zero is returned if
- * there is no value for the index, or if the value is not a number and
- * cannot be converted to a number.
- *
- * @param index
- * The index must be between 0 and length() - 1.
- * @return The value.
- */
- public long optLong(int index) {
- return this.optLong(index, 0);
- }
-
- /**
- * Get the optional long value associated with an index. The defaultValue is
- * returned if there is no value for the index, or if the value is not a
- * number and cannot be converted to a number.
- *
- * @param index
- * The index must be between 0 and length() - 1.
- * @param defaultValue
- * The default value.
- * @return The value.
- */
- public long optLong(int index, long defaultValue) {
- Object val = this.opt(index);
- if (JSONObject.NULL.equals(val)) {
- return defaultValue;
- }
- if (val instanceof Number){
- return ((Number) val).longValue();
- }
-
- if (val instanceof String) {
- try {
- return new BigDecimal(val.toString()).longValue();
- } catch (Exception e) {
- return defaultValue;
- }
- }
+ }
+ }
+ return defaultValue;
+ }
+
+ /**
+ * Get the enum value associated with a key.
+ *
+ * @param clazz
+ * The type of enum to retrieve.
+ * @param index
+ * The index must be between 0 and length() - 1.
+ * @return The enum value at the index location or null if not found
+ */
+ public <E extends Enum<E>> E optEnum(Class<E> clazz, int index)
+ {
+ return this.optEnum(clazz, index, null);
+ }
+
+ /**
+ * Get the enum value associated with a key.
+ *
+ * @param clazz
+ * The type of enum to retrieve.
+ * @param index
+ * The index must be between 0 and length() - 1.
+ * @param defaultValue
+ * The default in case the value is not found
+ * @return The enum value at the index location or defaultValue if the value
+ * is not found or cannot be assigned to clazz
+ */
+ public <E extends Enum<E>> E optEnum(Class<E> clazz, int index,
+ E defaultValue)
+ {
+ try
+ {
+ Object val = this.opt(index);
+ if (JSONObject.NULL.equals(val))
+ {
return defaultValue;
- }
-
- /**
- * Get an optional {@link Number} value associated with a key, or <code>null</code>
- * if there is no such key or if the value is not a number. If the value is a string,
- * an attempt will be made to evaluate it as a number ({@link BigDecimal}). This method
- * would be used in cases where type coercion of the number value is unwanted.
- *
- * @param index
- * The index must be between 0 and length() - 1.
- * @return An object which is the value.
- */
- public Number optNumber(int index) {
- return this.optNumber(index, null);
- }
-
- /**
- * Get an optional {@link Number} value associated with a key, or the default if there
- * is no such key or if the value is not a number. If the value is a string,
- * an attempt will be made to evaluate it as a number ({@link BigDecimal}). This method
- * would be used in cases where type coercion of the number value is unwanted.
- *
- * @param index
- * The index must be between 0 and length() - 1.
- * @param defaultValue
- * The default.
- * @return An object which is the value.
- */
- public Number optNumber(int index, Number defaultValue) {
- Object val = this.opt(index);
- if (JSONObject.NULL.equals(val)) {
- return defaultValue;
- }
- if (val instanceof Number){
- return (Number) val;
- }
-
- if (val instanceof String) {
- try {
- return JSONObject.stringToNumber((String) val);
- } catch (Exception e) {
- return defaultValue;
- }
- }
+ }
+ if (clazz.isAssignableFrom(val.getClass()))
+ {
+ // we just checked it!
+ @SuppressWarnings("unchecked")
+ E myE = (E) val;
+ return myE;
+ }
+ return Enum.valueOf(clazz, val.toString());
+ } catch (IllegalArgumentException e)
+ {
+ return defaultValue;
+ } catch (NullPointerException e)
+ {
+ return defaultValue;
+ }
+ }
+
+ /**
+ * Get the optional BigInteger value associated with an index. The
+ * defaultValue is returned if there is no value for the index, or if the
+ * value is not a number and cannot be converted to a number.
+ *
+ * @param index
+ * The index must be between 0 and length() - 1.
+ * @param defaultValue
+ * The default value.
+ * @return The value.
+ */
+ public BigInteger optBigInteger(int index, BigInteger defaultValue)
+ {
+ Object val = this.opt(index);
+ if (JSONObject.NULL.equals(val))
+ {
+ return defaultValue;
+ }
+ if (val instanceof BigInteger)
+ {
+ return (BigInteger) val;
+ }
+ if (val instanceof BigDecimal)
+ {
+ return ((BigDecimal) val).toBigInteger();
+ }
+ if (val instanceof Double || val instanceof Float)
+ {
+ return new BigDecimal(((Number) val).doubleValue()).toBigInteger();
+ }
+ if (val instanceof Long || val instanceof Integer
+ || val instanceof Short || val instanceof Byte)
+ {
+ return BigInteger.valueOf(((Number) val).longValue());
+ }
+ try
+ {
+ final String valStr = val.toString();
+ if (JSONObject.isDecimalNotation(valStr))
+ {
+ return new BigDecimal(valStr).toBigInteger();
+ }
+ return new BigInteger(valStr);
+ } catch (Exception e)
+ {
+ return defaultValue;
+ }
+ }
+
+ /**
+ * Get the optional BigDecimal value associated with an index. The
+ * defaultValue is returned if there is no value for the index, or if the
+ * value is not a number and cannot be converted to a number.
+ *
+ * @param index
+ * The index must be between 0 and length() - 1.
+ * @param defaultValue
+ * The default value.
+ * @return The value.
+ */
+ public BigDecimal optBigDecimal(int index, BigDecimal defaultValue)
+ {
+ Object val = this.opt(index);
+ if (JSONObject.NULL.equals(val))
+ {
+ return defaultValue;
+ }
+ if (val instanceof BigDecimal)
+ {
+ return (BigDecimal) val;
+ }
+ if (val instanceof BigInteger)
+ {
+ return new BigDecimal((BigInteger) val);
+ }
+ if (val instanceof Double || val instanceof Float)
+ {
+ return new BigDecimal(((Number) val).doubleValue());
+ }
+ if (val instanceof Long || val instanceof Integer
+ || val instanceof Short || val instanceof Byte)
+ {
+ return new BigDecimal(((Number) val).longValue());
+ }
+ try
+ {
+ return new BigDecimal(val.toString());
+ } catch (Exception e)
+ {
+ return defaultValue;
+ }
+ }
+
+ /**
+ * Get the optional JSONArray associated with an index.
+ *
+ * @param index
+ * subscript
+ * @return A JSONArray value, or null if the index has no value, or if the
+ * value is not a JSONArray.
+ */
+ public JSONArray optJSONArray(int index)
+ {
+ Object o = this.opt(index);
+ return o instanceof JSONArray ? (JSONArray) o : null;
+ }
+
+ /**
+ * Get the optional JSONObject associated with an index. Null is returned if
+ * the key is not found, or null if the index has no value, or if the value is
+ * not a JSONObject.
+ *
+ * @param index
+ * The index must be between 0 and length() - 1.
+ * @return A JSONObject value.
+ */
+ public JSONObject optJSONObject(int index)
+ {
+ Object o = this.opt(index);
+ return o instanceof JSONObject ? (JSONObject) o : null;
+ }
+
+ /**
+ * Get the optional long value associated with an index. Zero is returned if
+ * there is no value for the index, or if the value is not a number and cannot
+ * be converted to a number.
+ *
+ * @param index
+ * The index must be between 0 and length() - 1.
+ * @return The value.
+ */
+ public long optLong(int index)
+ {
+ return this.optLong(index, 0);
+ }
+
+ /**
+ * Get the optional long value associated with an index. The defaultValue is
+ * returned if there is no value for the index, or if the value is not a
+ * number and cannot be converted to a number.
+ *
+ * @param index
+ * The index must be between 0 and length() - 1.
+ * @param defaultValue
+ * The default value.
+ * @return The value.
+ */
+ public long optLong(int index, long defaultValue)
+ {
+ Object val = this.opt(index);
+ if (JSONObject.NULL.equals(val))
+ {
+ return defaultValue;
+ }
+ if (val instanceof Number)
+ {
+ return ((Number) val).longValue();
+ }
+
+ if (val instanceof String)
+ {
+ try
+ {
+ return new BigDecimal(val.toString()).longValue();
+ } catch (Exception e)
+ {
return defaultValue;
- }
-
- /**
- * Get the optional string value associated with an index. It returns an
- * empty string if there is no value at that index. If the value is not a
- * string and is not null, then it is converted to a string.
- *
- * @param index
- * The index must be between 0 and length() - 1.
- * @return A String value.
- */
- public String optString(int index) {
- return this.optString(index, "");
- }
-
- /**
- * Get the optional string associated with an index. The defaultValue is
- * returned if the key is not found.
- *
- * @param index
- * The index must be between 0 and length() - 1.
- * @param defaultValue
- * The default value.
- * @return A String value.
- */
- public String optString(int index, String defaultValue) {
- Object object = this.opt(index);
- return JSONObject.NULL.equals(object) ? defaultValue : object
- .toString();
- }
-
- /**
- * Append a boolean value. This increases the array's length by one.
- *
- * @param value
- * A boolean value.
- * @return this.
- */
- public JSONArray put(boolean value) {
- return this.put(value ? Boolean.TRUE : Boolean.FALSE);
- }
-
- /**
- * Put a value in the JSONArray, where the value will be a JSONArray which
- * is produced from a Collection.
- *
- * @param value
- * A Collection value.
- * @return this.
- * @throws JSONException
- * If the value is non-finite number.
- */
- public JSONArray put(Collection<?> value) {
- return this.put(new JSONArray(value));
- }
-
- /**
- * Append a double value. This increases the array's length by one.
- *
- * @param value
- * A double value.
- * @return this.
- * @throws JSONException
- * if the value is not finite.
- */
- public JSONArray put(double value) throws JSONException {
- return this.put(Double.valueOf(value));
- }
-
- /**
- * Append a float value. This increases the array's length by one.
- *
- * @param value
- * A float value.
- * @return this.
- * @throws JSONException
- * if the value is not finite.
- */
- public JSONArray put(float value) throws JSONException {
- return this.put(Float.valueOf(value));
- }
-
- /**
- * Append an int value. This increases the array's length by one.
- *
- * @param value
- * An int value.
- * @return this.
- */
- public JSONArray put(int value) {
- return this.put(Integer.valueOf(value));
- }
-
- /**
- * Append an long value. This increases the array's length by one.
- *
- * @param value
- * A long value.
- * @return this.
- */
- public JSONArray put(long value) {
- return this.put(Long.valueOf(value));
- }
-
- /**
- * Put a value in the JSONArray, where the value will be a JSONObject which
- * is produced from a Map.
- *
- * @param value
- * A Map value.
- * @return this.
- * @throws JSONException
- * If a value in the map is non-finite number.
- * @throws NullPointerException
- * If a key in the map is <code>null</code>
- */
- public JSONArray put(Map<?, ?> value) {
- return this.put(new JSONObject(value));
- }
-
- /**
- * Append an object value. This increases the array's length by one.
- *
- * @param value
- * An object value. The value should be a Boolean, Double,
- * Integer, JSONArray, JSONObject, Long, or String, or the
- * JSONObject.NULL object.
- * @return this.
- * @throws JSONException
- * If the value is non-finite number.
- */
- public JSONArray put(Object value) {
- JSONObject.testValidity(value);
- this.myArrayList.add(value);
- return this;
- }
-
- /**
- * Put or replace a boolean value in the JSONArray. If the index is greater
- * than the length of the JSONArray, then null elements will be added as
- * necessary to pad it out.
- *
- * @param index
- * The subscript.
- * @param value
- * A boolean value.
- * @return this.
- * @throws JSONException
- * If the index is negative.
- */
- public JSONArray put(int index, boolean value) throws JSONException {
- return this.put(index, value ? Boolean.TRUE : Boolean.FALSE);
- }
-
- /**
- * Put a value in the JSONArray, where the value will be a JSONArray which
- * is produced from a Collection.
- *
- * @param index
- * The subscript.
- * @param value
- * A Collection value.
- * @return this.
- * @throws JSONException
- * If the index is negative or if the value is non-finite.
- */
- public JSONArray put(int index, Collection<?> value) throws JSONException {
- return this.put(index, new JSONArray(value));
- }
-
- /**
- * Put or replace a double value. If the index is greater than the length of
- * the JSONArray, then null elements will be added as necessary to pad it
- * out.
- *
- * @param index
- * The subscript.
- * @param value
- * A double value.
- * @return this.
- * @throws JSONException
- * If the index is negative or if the value is non-finite.
- */
- public JSONArray put(int index, double value) throws JSONException {
- return this.put(index, Double.valueOf(value));
- }
-
- /**
- * Put or replace a float value. If the index is greater than the length of
- * the JSONArray, then null elements will be added as necessary to pad it
- * out.
- *
- * @param index
- * The subscript.
- * @param value
- * A float value.
- * @return this.
- * @throws JSONException
- * If the index is negative or if the value is non-finite.
- */
- public JSONArray put(int index, float value) throws JSONException {
- return this.put(index, Float.valueOf(value));
- }
-
- /**
- * Put or replace an int value. If the index is greater than the length of
- * the JSONArray, then null elements will be added as necessary to pad it
- * out.
- *
- * @param index
- * The subscript.
- * @param value
- * An int value.
- * @return this.
- * @throws JSONException
- * If the index is negative.
- */
- public JSONArray put(int index, int value) throws JSONException {
- return this.put(index, Integer.valueOf(value));
- }
-
- /**
- * Put or replace a long value. If the index is greater than the length of
- * the JSONArray, then null elements will be added as necessary to pad it
- * out.
- *
- * @param index
- * The subscript.
- * @param value
- * A long value.
- * @return this.
- * @throws JSONException
- * If the index is negative.
- */
- public JSONArray put(int index, long value) throws JSONException {
- return this.put(index, Long.valueOf(value));
- }
-
- /**
- * Put a value in the JSONArray, where the value will be a JSONObject that
- * is produced from a Map.
- *
- * @param index
- * The subscript.
- * @param value
- * The Map value.
- * @return this.
- * @throws JSONException
- * If the index is negative or if the the value is an invalid
- * number.
- * @throws NullPointerException
- * If a key in the map is <code>null</code>
- */
- public JSONArray put(int index, Map<?, ?> value) throws JSONException {
- this.put(index, new JSONObject(value));
- return this;
- }
-
- /**
- * Put or replace an object value in the JSONArray. If the index is greater
- * than the length of the JSONArray, then null elements will be added as
- * necessary to pad it out.
- *
- * @param index
- * The subscript.
- * @param value
- * The value to put into the array. The value should be a
- * Boolean, Double, Integer, JSONArray, JSONObject, Long, or
- * String, or the JSONObject.NULL object.
- * @return this.
- * @throws JSONException
- * If the index is negative or if the the value is an invalid
- * number.
- */
- public JSONArray put(int index, Object value) throws JSONException {
- if (index < 0) {
- throw new JSONException("JSONArray[" + index + "] not found.");
- }
- if (index < this.length()) {
- JSONObject.testValidity(value);
- this.myArrayList.set(index, value);
- return this;
- }
- if(index == this.length()){
- // simple append
- return this.put(value);
- }
- // if we are inserting past the length, we want to grow the array all at once
- // instead of incrementally.
- this.myArrayList.ensureCapacity(index + 1);
- while (index != this.length()) {
- // we don't need to test validity of NULL objects
- this.myArrayList.add(JSONObject.NULL);
- }
- return this.put(value);
- }
-
- /**
- * Creates a JSONPointer using an initialization string and tries to
- * match it to an item within this JSONArray. For example, given a
- * JSONArray initialized with this document:
- * <pre>
- * [
- * {"b":"c"}
- * ]
- * </pre>
- * and this JSONPointer string:
- * <pre>
- * "/0/b"
- * </pre>
- * Then this method will return the String "c"
- * A JSONPointerException may be thrown from code called by this method.
- *
- * @param jsonPointer string that can be used to create a JSONPointer
- * @return the item matched by the JSONPointer, otherwise null
- */
- public Object query(String jsonPointer) {
- return query(new JSONPointer(jsonPointer));
- }
-
- /**
- * Uses a uaer initialized JSONPointer and tries to
- * match it to an item whithin this JSONArray. For example, given a
- * JSONArray initialized with this document:
- * <pre>
- * [
- * {"b":"c"}
- * ]
- * </pre>
- * and this JSONPointer:
- * <pre>
- * "/0/b"
- * </pre>
- * Then this method will return the String "c"
- * A JSONPointerException may be thrown from code called by this method.
- *
- * @param jsonPointer string that can be used to create a JSONPointer
- * @return the item matched by the JSONPointer, otherwise null
- */
- public Object query(JSONPointer jsonPointer) {
- return jsonPointer.queryFrom(this);
- }
-
- /**
- * Queries and returns a value from this object using {@code jsonPointer}, or
- * returns null if the query fails due to a missing key.
- *
- * @param jsonPointer the string representation of the JSON pointer
- * @return the queried value or {@code null}
- * @throws IllegalArgumentException if {@code jsonPointer} has invalid syntax
- */
- public Object optQuery(String jsonPointer) {
- return optQuery(new JSONPointer(jsonPointer));
- }
-
- /**
- * Queries and returns a value from this object using {@code jsonPointer}, or
- * returns null if the query fails due to a missing key.
- *
- * @param jsonPointer The JSON pointer
- * @return the queried value or {@code null}
- * @throws IllegalArgumentException if {@code jsonPointer} has invalid syntax
- */
- public Object optQuery(JSONPointer jsonPointer) {
- try {
- return jsonPointer.queryFrom(this);
- } catch (JSONPointerException e) {
- return null;
- }
- }
-
- /**
- * Remove an index and close the hole.
- *
- * @param index
- * The index of the element to be removed.
- * @return The value that was associated with the index, or null if there
- * was no value.
- */
- public Object remove(int index) {
- return index >= 0 && index < this.length()
+ }
+ }
+ return defaultValue;
+ }
+
+ /**
+ * Get an optional {@link Number} value associated with a key, or
+ * <code>null</code> if there is no such key or if the value is not a number.
+ * If the value is a string, an attempt will be made to evaluate it as a
+ * number ({@link BigDecimal}). This method would be used in cases where type
+ * coercion of the number value is unwanted.
+ *
+ * @param index
+ * The index must be between 0 and length() - 1.
+ * @return An object which is the value.
+ */
+ public Number optNumber(int index)
+ {
+ return this.optNumber(index, null);
+ }
+
+ /**
+ * Get an optional {@link Number} value associated with a key, or the default
+ * if there is no such key or if the value is not a number. If the value is a
+ * string, an attempt will be made to evaluate it as a number
+ * ({@link BigDecimal}). This method would be used in cases where type
+ * coercion of the number value is unwanted.
+ *
+ * @param index
+ * The index must be between 0 and length() - 1.
+ * @param defaultValue
+ * The default.
+ * @return An object which is the value.
+ */
+ public Number optNumber(int index, Number defaultValue)
+ {
+ Object val = this.opt(index);
+ if (JSONObject.NULL.equals(val))
+ {
+ return defaultValue;
+ }
+ if (val instanceof Number)
+ {
+ return (Number) val;
+ }
+
+ if (val instanceof String)
+ {
+ try
+ {
+ return JSONObject.stringToNumber((String) val);
+ } catch (Exception e)
+ {
+ return defaultValue;
+ }
+ }
+ return defaultValue;
+ }
+
+ /**
+ * Get the optional string value associated with an index. It returns an empty
+ * string if there is no value at that index. If the value is not a string and
+ * is not null, then it is converted to a string.
+ *
+ * @param index
+ * The index must be between 0 and length() - 1.
+ * @return A String value.
+ */
+ public String optString(int index)
+ {
+ return this.optString(index, "");
+ }
+
+ /**
+ * Get the optional string associated with an index. The defaultValue is
+ * returned if the key is not found.
+ *
+ * @param index
+ * The index must be between 0 and length() - 1.
+ * @param defaultValue
+ * The default value.
+ * @return A String value.
+ */
+ public String optString(int index, String defaultValue)
+ {
+ Object object = this.opt(index);
+ return JSONObject.NULL.equals(object) ? defaultValue
+ : object.toString();
+ }
+
+ /**
+ * Append a boolean value. This increases the array's length by one.
+ *
+ * @param value
+ * A boolean value.
+ * @return this.
+ */
+ public JSONArray put(boolean value)
+ {
+ return this.put(value ? Boolean.TRUE : Boolean.FALSE);
+ }
+
+ /**
+ * Put a value in the JSONArray, where the value will be a JSONArray which is
+ * produced from a Collection.
+ *
+ * @param value
+ * A Collection value.
+ * @return this.
+ * @throws JSONException
+ * If the value is non-finite number.
+ */
+ public JSONArray put(Collection<?> value)
+ {
+ return this.put(new JSONArray(value));
+ }
+
+ /**
+ * Append a double value. This increases the array's length by one.
+ *
+ * @param value
+ * A double value.
+ * @return this.
+ * @throws JSONException
+ * if the value is not finite.
+ */
+ public JSONArray put(double value) throws JSONException
+ {
+ return this.put(Double.valueOf(value));
+ }
+
+ /**
+ * Append a float value. This increases the array's length by one.
+ *
+ * @param value
+ * A float value.
+ * @return this.
+ * @throws JSONException
+ * if the value is not finite.
+ */
+ public JSONArray put(float value) throws JSONException
+ {
+ return this.put(Float.valueOf(value));
+ }
+
+ /**
+ * Append an int value. This increases the array's length by one.
+ *
+ * @param value
+ * An int value.
+ * @return this.
+ */
+ public JSONArray put(int value)
+ {
+ return this.put(Integer.valueOf(value));
+ }
+
+ /**
+ * Append an long value. This increases the array's length by one.
+ *
+ * @param value
+ * A long value.
+ * @return this.
+ */
+ public JSONArray put(long value)
+ {
+ return this.put(Long.valueOf(value));
+ }
+
+ /**
+ * Put a value in the JSONArray, where the value will be a JSONObject which is
+ * produced from a Map.
+ *
+ * @param value
+ * A Map value.
+ * @return this.
+ * @throws JSONException
+ * If a value in the map is non-finite number.
+ * @throws NullPointerException
+ * If a key in the map is <code>null</code>
+ */
+ public JSONArray put(Map<?, ?> value)
+ {
+ return this.put(new JSONObject(value));
+ }
+
+ /**
+ * Append an object value. This increases the array's length by one.
+ *
+ * @param value
+ * An object value. The value should be a Boolean, Double, Integer,
+ * JSONArray, JSONObject, Long, or String, or the JSONObject.NULL
+ * object.
+ * @return this.
+ * @throws JSONException
+ * If the value is non-finite number.
+ */
+ public JSONArray put(Object value)
+ {
+ JSONObject.testValidity(value);
+ this.myArrayList.add(value);
+ return this;
+ }
+
+ /**
+ * Put or replace a boolean value in the JSONArray. If the index is greater
+ * than the length of the JSONArray, then null elements will be added as
+ * necessary to pad it out.
+ *
+ * @param index
+ * The subscript.
+ * @param value
+ * A boolean value.
+ * @return this.
+ * @throws JSONException
+ * If the index is negative.
+ */
+ public JSONArray put(int index, boolean value) throws JSONException
+ {
+ return this.put(index, value ? Boolean.TRUE : Boolean.FALSE);
+ }
+
+ /**
+ * Put a value in the JSONArray, where the value will be a JSONArray which is
+ * produced from a Collection.
+ *
+ * @param index
+ * The subscript.
+ * @param value
+ * A Collection value.
+ * @return this.
+ * @throws JSONException
+ * If the index is negative or if the value is non-finite.
+ */
+ public JSONArray put(int index, Collection<?> value) throws JSONException
+ {
+ return this.put(index, new JSONArray(value));
+ }
+
+ /**
+ * Put or replace a double value. If the index is greater than the length of
+ * the JSONArray, then null elements will be added as necessary to pad it out.
+ *
+ * @param index
+ * The subscript.
+ * @param value
+ * A double value.
+ * @return this.
+ * @throws JSONException
+ * If the index is negative or if the value is non-finite.
+ */
+ public JSONArray put(int index, double value) throws JSONException
+ {
+ return this.put(index, Double.valueOf(value));
+ }
+
+ /**
+ * Put or replace a float value. If the index is greater than the length of
+ * the JSONArray, then null elements will be added as necessary to pad it out.
+ *
+ * @param index
+ * The subscript.
+ * @param value
+ * A float value.
+ * @return this.
+ * @throws JSONException
+ * If the index is negative or if the value is non-finite.
+ */
+ public JSONArray put(int index, float value) throws JSONException
+ {
+ return this.put(index, Float.valueOf(value));
+ }
+
+ /**
+ * Put or replace an int value. If the index is greater than the length of the
+ * JSONArray, then null elements will be added as necessary to pad it out.
+ *
+ * @param index
+ * The subscript.
+ * @param value
+ * An int value.
+ * @return this.
+ * @throws JSONException
+ * If the index is negative.
+ */
+ public JSONArray put(int index, int value) throws JSONException
+ {
+ return this.put(index, Integer.valueOf(value));
+ }
+
+ /**
+ * Put or replace a long value. If the index is greater than the length of the
+ * JSONArray, then null elements will be added as necessary to pad it out.
+ *
+ * @param index
+ * The subscript.
+ * @param value
+ * A long value.
+ * @return this.
+ * @throws JSONException
+ * If the index is negative.
+ */
+ public JSONArray put(int index, long value) throws JSONException
+ {
+ return this.put(index, Long.valueOf(value));
+ }
+
+ /**
+ * Put a value in the JSONArray, where the value will be a JSONObject that is
+ * produced from a Map.
+ *
+ * @param index
+ * The subscript.
+ * @param value
+ * The Map value.
+ * @return this.
+ * @throws JSONException
+ * If the index is negative or if the the value is an invalid
+ * number.
+ * @throws NullPointerException
+ * If a key in the map is <code>null</code>
+ */
+ public JSONArray put(int index, Map<?, ?> value) throws JSONException
+ {
+ this.put(index, new JSONObject(value));
+ return this;
+ }
+
+ /**
+ * Put or replace an object value in the JSONArray. If the index is greater
+ * than the length of the JSONArray, then null elements will be added as
+ * necessary to pad it out.
+ *
+ * @param index
+ * The subscript.
+ * @param value
+ * The value to put into the array. The value should be a Boolean,
+ * Double, Integer, JSONArray, JSONObject, Long, or String, or the
+ * JSONObject.NULL object.
+ * @return this.
+ * @throws JSONException
+ * If the index is negative or if the the value is an invalid
+ * number.
+ */
+ public JSONArray put(int index, Object value) throws JSONException
+ {
+ if (index < 0)
+ {
+ throw new JSONException("JSONArray[" + index + "] not found.");
+ }
+ if (index < this.length())
+ {
+ JSONObject.testValidity(value);
+ this.myArrayList.set(index, value);
+ return this;
+ }
+ if (index == this.length())
+ {
+ // simple append
+ return this.put(value);
+ }
+ // if we are inserting past the length, we want to grow the array all at
+ // once
+ // instead of incrementally.
+ this.myArrayList.ensureCapacity(index + 1);
+ while (index != this.length())
+ {
+ // we don't need to test validity of NULL objects
+ this.myArrayList.add(JSONObject.NULL);
+ }
+ return this.put(value);
+ }
+
+ /**
+ * Creates a JSONPointer using an initialization string and tries to match it
+ * to an item within this JSONArray. For example, given a JSONArray
+ * initialized with this document:
+ *
+ * <pre>
+ * [
+ * {"b":"c"}
+ * ]
+ * </pre>
+ *
+ * and this JSONPointer string:
+ *
+ * <pre>
+ * "/0/b"
+ * </pre>
+ *
+ * Then this method will return the String "c" A JSONPointerException may be
+ * thrown from code called by this method.
+ *
+ * @param jsonPointer
+ * string that can be used to create a JSONPointer
+ * @return the item matched by the JSONPointer, otherwise null
+ */
+ public Object query(String jsonPointer)
+ {
+ return query(new JSONPointer(jsonPointer));
+ }
+
+ /**
+ * Uses a uaer initialized JSONPointer and tries to match it to an item
+ * whithin this JSONArray. For example, given a JSONArray initialized with
+ * this document:
+ *
+ * <pre>
+ * [
+ * {"b":"c"}
+ * ]
+ * </pre>
+ *
+ * and this JSONPointer:
+ *
+ * <pre>
+ * "/0/b"
+ * </pre>
+ *
+ * Then this method will return the String "c" A JSONPointerException may be
+ * thrown from code called by this method.
+ *
+ * @param jsonPointer
+ * string that can be used to create a JSONPointer
+ * @return the item matched by the JSONPointer, otherwise null
+ */
+ public Object query(JSONPointer jsonPointer)
+ {
+ return jsonPointer.queryFrom(this);
+ }
+
+ /**
+ * Queries and returns a value from this object using {@code jsonPointer}, or
+ * returns null if the query fails due to a missing key.
+ *
+ * @param jsonPointer
+ * the string representation of the JSON pointer
+ * @return the queried value or {@code null}
+ * @throws IllegalArgumentException
+ * if {@code jsonPointer} has invalid syntax
+ */
+ public Object optQuery(String jsonPointer)
+ {
+ return optQuery(new JSONPointer(jsonPointer));
+ }
+
+ /**
+ * Queries and returns a value from this object using {@code jsonPointer}, or
+ * returns null if the query fails due to a missing key.
+ *
+ * @param jsonPointer
+ * The JSON pointer
+ * @return the queried value or {@code null}
+ * @throws IllegalArgumentException
+ * if {@code jsonPointer} has invalid syntax
+ */
+ public Object optQuery(JSONPointer jsonPointer)
+ {
+ try
+ {
+ return jsonPointer.queryFrom(this);
+ } catch (JSONPointerException e)
+ {
+ return null;
+ }
+ }
+
+ /**
+ * Remove an index and close the hole.
+ *
+ * @param index
+ * The index of the element to be removed.
+ * @return The value that was associated with the index, or null if there was
+ * no value.
+ */
+ public Object remove(int index)
+ {
+ return index >= 0 && index < this.length()
? this.myArrayList.remove(index)
: null;
- }
-
- /**
- * Determine if two JSONArrays are similar.
- * They must contain similar sequences.
- *
- * @param other The other JSONArray
- * @return true if they are equal
- */
- public boolean similar(Object other) {
- if (!(other instanceof JSONArray)) {
- return false;
+ }
+
+ /**
+ * Determine if two JSONArrays are similar. They must contain similar
+ * sequences.
+ *
+ * @param other
+ * The other JSONArray
+ * @return true if they are equal
+ */
+ public boolean similar(Object other)
+ {
+ if (!(other instanceof JSONArray))
+ {
+ return false;
+ }
+ int len = this.length();
+ if (len != ((JSONArray) other).length())
+ {
+ return false;
+ }
+ for (int i = 0; i < len; i += 1)
+ {
+ Object valueThis = this.myArrayList.get(i);
+ Object valueOther = ((JSONArray) other).myArrayList.get(i);
+ if (valueThis == valueOther)
+ {
+ continue;
+ }
+ if (valueThis == null)
+ {
+ return false;
+ }
+ if (valueThis instanceof JSONObject)
+ {
+ if (!((JSONObject) valueThis).similar(valueOther))
+ {
+ return false;
}
- int len = this.length();
- if (len != ((JSONArray)other).length()) {
- return false;
+ }
+ else if (valueThis instanceof JSONArray)
+ {
+ if (!((JSONArray) valueThis).similar(valueOther))
+ {
+ return false;
}
- for (int i = 0; i < len; i += 1) {
- Object valueThis = this.myArrayList.get(i);
- Object valueOther = ((JSONArray)other).myArrayList.get(i);
- if(valueThis == valueOther) {
- continue;
- }
- if(valueThis == null) {
- return false;
- }
- if (valueThis instanceof JSONObject) {
- if (!((JSONObject)valueThis).similar(valueOther)) {
- return false;
- }
- } else if (valueThis instanceof JSONArray) {
- if (!((JSONArray)valueThis).similar(valueOther)) {
- return false;
- }
- } else if (!valueThis.equals(valueOther)) {
- return false;
- }
+ }
+ else if (!valueThis.equals(valueOther))
+ {
+ return false;
+ }
+ }
+ return true;
+ }
+
+ /**
+ * Produce a JSONObject by combining a JSONArray of names with the values of
+ * this JSONArray.
+ *
+ * @param names
+ * A JSONArray containing a list of key strings. These will be paired
+ * with the values.
+ * @return A JSONObject, or null if there are no names or if this JSONArray
+ * has no values.
+ * @throws JSONException
+ * If any of the names are null.
+ */
+ public JSONObject toJSONObject(JSONArray names) throws JSONException
+ {
+ if (names == null || names.isEmpty() || this.isEmpty())
+ {
+ return null;
+ }
+ JSONObject jo = new JSONObject(names.length());
+ for (int i = 0; i < names.length(); i += 1)
+ {
+ jo.put(names.getString(i), this.opt(i));
+ }
+ return jo;
+ }
+
+ /**
+ * Make a JSON text of this JSONArray. For compactness, no unnecessary
+ * whitespace is added. If it is not possible to produce a syntactically
+ * correct JSON text then null will be returned instead. This could occur if
+ * the array contains an invalid number.
+ * <p>
+ * <b> Warning: This method assumes that the data structure is acyclical. </b>
+ *
+ * @return a printable, displayable, transmittable representation of the
+ * array.
+ */
+ @Override
+ public String toString()
+ {
+ try
+ {
+ return this.toString(0);
+ } catch (Exception e)
+ {
+ return null;
+ }
+ }
+
+ /**
+ * Make a pretty-printed JSON text of this JSONArray.
+ *
+ * <p>
+ * If <code>indentFactor > 0</code> and the {@link JSONArray} has only one
+ * element, then the array will be output on a single line:
+ *
+ * <pre>
+ * {@code [1]}
+ * </pre>
+ *
+ * <p>
+ * If an array has 2 or more elements, then it will be output across multiple
+ * lines:
+ *
+ * <pre>
+ * {@code
+ * [
+ * 1,
+ * "value 2",
+ * 3
+ * ]
+ * }
+ * </pre>
+ * <p>
+ * <b> Warning: This method assumes that the data structure is acyclical. </b>
+ *
+ * @param indentFactor
+ * The number of spaces to add to each level of indentation.
+ * @return a printable, displayable, transmittable representation of the
+ * object, beginning with <code>[</code> <small>(left
+ * bracket)</small> and ending with <code>]</code> <small>(right
+ * bracket)</small>.
+ * @throws JSONException
+ */
+ public String toString(int indentFactor) throws JSONException
+ {
+ StringWriter sw = new StringWriter();
+ synchronized (sw.getBuffer())
+ {
+ return this.write(sw, indentFactor, 0).toString();
+ }
+ }
+
+ /**
+ * Write the contents of the JSONArray as JSON text to a writer. For
+ * compactness, no whitespace is added.
+ * <p>
+ * <b> Warning: This method assumes that the data structure is acyclical. </b>
+ *
+ * @return The writer.
+ * @throws JSONException
+ */
+ public Writer write(Writer writer) throws JSONException
+ {
+ return this.write(writer, 0, 0);
+ }
+
+ /**
+ * Write the contents of the JSONArray as JSON text to a writer.
+ *
+ * <p>
+ * If <code>indentFactor > 0</code> and the {@link JSONArray} has only one
+ * element, then the array will be output on a single line:
+ *
+ * <pre>
+ * {@code [1]}
+ * </pre>
+ *
+ * <p>
+ * If an array has 2 or more elements, then it will be output across multiple
+ * lines:
+ *
+ * <pre>
+ * {@code
+ * [
+ * 1,
+ * "value 2",
+ * 3
+ * ]
+ * }
+ * </pre>
+ * <p>
+ * <b> Warning: This method assumes that the data structure is acyclical. </b>
+ *
+ * @param writer
+ * Writes the serialized JSON
+ * @param indentFactor
+ * The number of spaces to add to each level of indentation.
+ * @param indent
+ * The indentation of the top level.
+ * @return The writer.
+ * @throws JSONException
+ */
+ public Writer write(Writer writer, int indentFactor, int indent)
+ throws JSONException
+ {
+ try
+ {
+ boolean commanate = false;
+ int length = this.length();
+ writer.write('[');
+
+ if (length == 1)
+ {
+ try
+ {
+ JSONObject.writeValue(writer, this.myArrayList.get(0),
+ indentFactor, indent);
+ } catch (Exception e)
+ {
+ throw new JSONException(
+ "Unable to write JSONArray value at index: 0", e);
}
- return true;
- }
-
- /**
- * Produce a JSONObject by combining a JSONArray of names with the values of
- * this JSONArray.
- *
- * @param names
- * A JSONArray containing a list of key strings. These will be
- * paired with the values.
- * @return A JSONObject, or null if there are no names or if this JSONArray
- * has no values.
- * @throws JSONException
- * If any of the names are null.
- */
- public JSONObject toJSONObject(JSONArray names) throws JSONException {
- if (names == null || names.isEmpty() || this.isEmpty()) {
- return null;
- }
- JSONObject jo = new JSONObject(names.length());
- for (int i = 0; i < names.length(); i += 1) {
- jo.put(names.getString(i), this.opt(i));
- }
- return jo;
- }
-
- /**
- * Make a JSON text of this JSONArray. For compactness, no unnecessary
- * whitespace is added. If it is not possible to produce a syntactically
- * correct JSON text then null will be returned instead. This could occur if
- * the array contains an invalid number.
- * <p><b>
- * Warning: This method assumes that the data structure is acyclical.
- * </b>
- *
- * @return a printable, displayable, transmittable representation of the
- * array.
- */
- @Override
- public String toString() {
- try {
- return this.toString(0);
- } catch (Exception e) {
- return null;
- }
- }
-
- /**
- * Make a pretty-printed JSON text of this JSONArray.
- *
- * <p>If <code>indentFactor > 0</code> and the {@link JSONArray} has only
- * one element, then the array will be output on a single line:
- * <pre>{@code [1]}</pre>
- *
- * <p>If an array has 2 or more elements, then it will be output across
- * multiple lines: <pre>{@code
- * [
- * 1,
- * "value 2",
- * 3
- * ]
- * }</pre>
- * <p><b>
- * Warning: This method assumes that the data structure is acyclical.
- * </b>
- *
- * @param indentFactor
- * The number of spaces to add to each level of indentation.
- * @return a printable, displayable, transmittable representation of the
- * object, beginning with <code>[</code> <small>(left
- * bracket)</small> and ending with <code>]</code>
- * <small>(right bracket)</small>.
- * @throws JSONException
- */
- public String toString(int indentFactor) throws JSONException {
- StringWriter sw = new StringWriter();
- synchronized (sw.getBuffer()) {
- return this.write(sw, indentFactor, 0).toString();
- }
- }
-
- /**
- * Write the contents of the JSONArray as JSON text to a writer. For
- * compactness, no whitespace is added.
- * <p><b>
- * Warning: This method assumes that the data structure is acyclical.
- *</b>
- *
- * @return The writer.
- * @throws JSONException
- */
- public Writer write(Writer writer) throws JSONException {
- return this.write(writer, 0, 0);
- }
-
- /**
- * Write the contents of the JSONArray as JSON text to a writer.
- *
- * <p>If <code>indentFactor > 0</code> and the {@link JSONArray} has only
- * one element, then the array will be output on a single line:
- * <pre>{@code [1]}</pre>
- *
- * <p>If an array has 2 or more elements, then it will be output across
- * multiple lines: <pre>{@code
- * [
- * 1,
- * "value 2",
- * 3
- * ]
- * }</pre>
- * <p><b>
- * Warning: This method assumes that the data structure is acyclical.
- * </b>
- *
- * @param writer
- * Writes the serialized JSON
- * @param indentFactor
- * The number of spaces to add to each level of indentation.
- * @param indent
- * The indentation of the top level.
- * @return The writer.
- * @throws JSONException
- */
- public Writer write(Writer writer, int indentFactor, int indent)
- throws JSONException {
- try {
- boolean commanate = false;
- int length = this.length();
- writer.write('[');
-
- if (length == 1) {
- try {
- JSONObject.writeValue(writer, this.myArrayList.get(0),
- indentFactor, indent);
- } catch (Exception e) {
- throw new JSONException("Unable to write JSONArray value at index: 0", e);
- }
- } else if (length != 0) {
- final int newindent = indent + indentFactor;
-
- for (int i = 0; i < length; i += 1) {
- if (commanate) {
- writer.write(',');
- }
- if (indentFactor > 0) {
- writer.write('\n');
- }
- JSONObject.indent(writer, newindent);
- try {
- JSONObject.writeValue(writer, this.myArrayList.get(i),
- indentFactor, newindent);
- } catch (Exception e) {
- throw new JSONException("Unable to write JSONArray value at index: " + i, e);
- }
- commanate = true;
- }
- if (indentFactor > 0) {
- writer.write('\n');
- }
- JSONObject.indent(writer, indent);
- }
- writer.write(']');
- return writer;
- } catch (IOException e) {
- throw new JSONException(e);
+ }
+ else if (length != 0)
+ {
+ final int newindent = indent + indentFactor;
+
+ for (int i = 0; i < length; i += 1)
+ {
+ if (commanate)
+ {
+ writer.write(',');
+ }
+ if (indentFactor > 0)
+ {
+ writer.write('\n');
+ }
+ JSONObject.indent(writer, newindent);
+ try
+ {
+ JSONObject.writeValue(writer, this.myArrayList.get(i),
+ indentFactor, newindent);
+ } catch (Exception e)
+ {
+ throw new JSONException(
+ "Unable to write JSONArray value at index: " + i, e);
+ }
+ commanate = true;
}
- }
-
- /**
- * Returns a java.util.List containing all of the elements in this array.
- * If an element in the array is a JSONArray or JSONObject it will also
- * be converted.
- * <p>
- * Warning: This method assumes that the data structure is acyclical.
- *
- * @return a java.util.List containing the elements of this array
- */
- public List<Object> toList() {
- List<Object> results = new ArrayList<Object>(this.myArrayList.size());
- for (Object element : this.myArrayList) {
- if (element == null || JSONObject.NULL.equals(element)) {
- results.add(null);
- } else if (element instanceof JSONArray) {
- results.add(((JSONArray) element).toList());
- } else if (element instanceof JSONObject) {
- results.add(((JSONObject) element).toMap());
- } else {
- results.add(element);
- }
+ if (indentFactor > 0)
+ {
+ writer.write('\n');
}
- return results;
- }
-
- /**
- * Check if JSONArray is empty.
- *
- * @return true if JSONArray is empty, otherwise false.
- */
- public boolean isEmpty() {
- return myArrayList.isEmpty();
- }
+ JSONObject.indent(writer, indent);
+ }
+ writer.write(']');
+ return writer;
+ } catch (IOException e)
+ {
+ throw new JSONException(e);
+ }
+ }
+
+ /**
+ * Returns a java.util.List containing all of the elements in this array. If
+ * an element in the array is a JSONArray or JSONObject it will also be
+ * converted.
+ * <p>
+ * Warning: This method assumes that the data structure is acyclical.
+ *
+ * @return a java.util.List containing the elements of this array
+ */
+ public List<Object> toList()
+ {
+ List<Object> results = new ArrayList<Object>(this.myArrayList.size());
+ for (Object element : this.myArrayList)
+ {
+ if (element == null || JSONObject.NULL.equals(element))
+ {
+ results.add(null);
+ }
+ else if (element instanceof JSONArray)
+ {
+ results.add(((JSONArray) element).toList());
+ }
+ else if (element instanceof JSONObject)
+ {
+ results.add(((JSONObject) element).toMap());
+ }
+ else
+ {
+ results.add(element);
+ }
+ }
+ return results;
+ }
+
+ /**
+ * Check if JSONArray is empty.
+ *
+ * @return true if JSONArray is empty, otherwise false.
+ */
+ public boolean isEmpty()
+ {
+ return myArrayList.isEmpty();
+ }
}
* @author JSON.org
* @version 2015-12-09
*/
-public class JSONException extends RuntimeException {
- /** Serialization ID */
- private static final long serialVersionUID = 0;
+public class JSONException extends RuntimeException
+{
+ /** Serialization ID */
+ private static final long serialVersionUID = 0;
- /**
- * Constructs a JSONException with an explanatory message.
- *
- * @param message
- * Detail about the reason for the exception.
- */
- public JSONException(final String message) {
- super(message);
- }
+ /**
+ * Constructs a JSONException with an explanatory message.
+ *
+ * @param message
+ * Detail about the reason for the exception.
+ */
+ public JSONException(final String message)
+ {
+ super(message);
+ }
- /**
- * Constructs a JSONException with an explanatory message and cause.
- *
- * @param message
- * Detail about the reason for the exception.
- * @param cause
- * The cause.
- */
- public JSONException(final String message, final Throwable cause) {
- super(message, cause);
- }
+ /**
+ * Constructs a JSONException with an explanatory message and cause.
+ *
+ * @param message
+ * Detail about the reason for the exception.
+ * @param cause
+ * The cause.
+ */
+ public JSONException(final String message, final Throwable cause)
+ {
+ super(message, cause);
+ }
- /**
- * Constructs a new JSONException with the specified cause.
- *
- * @param cause
- * The cause.
- */
- public JSONException(final Throwable cause) {
- super(cause.getMessage(), cause);
- }
+ /**
+ * Constructs a new JSONException with the specified cause.
+ *
+ * @param cause
+ * The cause.
+ */
+ public JSONException(final Throwable cause)
+ {
+ super(cause.getMessage(), cause);
+ }
}
* @author JSON.org
* @version 2016-01-30
*/
-public class JSONML {
- /**
- * Parse XML values and store them in a JSONArray.
- * @param x The XMLTokener containing the source string.
- * @param arrayForm true if array form, false if object form.
- * @param ja The JSONArray that is containing the current tag or null
- * if we are at the outermost level.
- * @param keepStrings Don't type-convert text nodes and attribute values
- * @return A JSONArray if the value is the outermost tag, otherwise null.
- * @throws JSONException
- */
- private static Object parse(
- XMLTokener x,
- boolean arrayForm,
- JSONArray ja,
- boolean keepStrings
- ) throws JSONException {
- String attribute;
- char c;
- String closeTag = null;
- int i;
- JSONArray newja = null;
- JSONObject newjo = null;
- Object token;
- String tagName = null;
-
-// Test for and skip past these forms:
-// <!-- ... -->
-// <![ ... ]]>
-// <! ... >
-// <? ... ?>
-
- while (true) {
- if (!x.more()) {
- throw x.syntaxError("Bad XML");
+public class JSONML
+{
+ /**
+ * Parse XML values and store them in a JSONArray.
+ *
+ * @param x
+ * The XMLTokener containing the source string.
+ * @param arrayForm
+ * true if array form, false if object form.
+ * @param ja
+ * The JSONArray that is containing the current tag or null if we are
+ * at the outermost level.
+ * @param keepStrings
+ * Don't type-convert text nodes and attribute values
+ * @return A JSONArray if the value is the outermost tag, otherwise null.
+ * @throws JSONException
+ */
+ private static Object parse(XMLTokener x, boolean arrayForm, JSONArray ja,
+ boolean keepStrings) throws JSONException
+ {
+ String attribute;
+ char c;
+ String closeTag = null;
+ int i;
+ JSONArray newja = null;
+ JSONObject newjo = null;
+ Object token;
+ String tagName = null;
+
+ // Test for and skip past these forms:
+ // <!-- ... -->
+ // <![ ... ]]>
+ // <! ... >
+ // <? ... ?>
+
+ while (true)
+ {
+ if (!x.more())
+ {
+ throw x.syntaxError("Bad XML");
+ }
+ token = x.nextContent();
+ if (token == XML.LT)
+ {
+ token = x.nextToken();
+ if (token instanceof Character)
+ {
+ if (token == XML.SLASH)
+ {
+
+ // Close tag </
+
+ token = x.nextToken();
+ if (!(token instanceof String))
+ {
+ throw new JSONException("Expected a closing name instead of '"
+ + token + "'.");
}
- token = x.nextContent();
- if (token == XML.LT) {
- token = x.nextToken();
- if (token instanceof Character) {
- if (token == XML.SLASH) {
-
-// Close tag </
-
- token = x.nextToken();
- if (!(token instanceof String)) {
- throw new JSONException(
- "Expected a closing name instead of '" +
- token + "'.");
- }
- if (x.nextToken() != XML.GT) {
- throw x.syntaxError("Misshaped close tag");
- }
- return token;
- } else if (token == XML.BANG) {
-
-// <!
-
- c = x.next();
- if (c == '-') {
- if (x.next() == '-') {
- x.skipPast("-->");
- } else {
- x.back();
- }
- } else if (c == '[') {
- token = x.nextToken();
- if (token.equals("CDATA") && x.next() == '[') {
- if (ja != null) {
- ja.put(x.nextCDATA());
- }
- } else {
- throw x.syntaxError("Expected 'CDATA['");
- }
- } else {
- i = 1;
- do {
- token = x.nextMeta();
- if (token == null) {
- throw x.syntaxError("Missing '>' after '<!'.");
- } else if (token == XML.LT) {
- i += 1;
- } else if (token == XML.GT) {
- i -= 1;
- }
- } while (i > 0);
- }
- } else if (token == XML.QUEST) {
-
-// <?
-
- x.skipPast("?>");
- } else {
- throw x.syntaxError("Misshaped tag");
- }
-
-// Open tag <
-
- } else {
- if (!(token instanceof String)) {
- throw x.syntaxError("Bad tagName '" + token + "'.");
- }
- tagName = (String)token;
- newja = new JSONArray();
- newjo = new JSONObject();
- if (arrayForm) {
- newja.put(tagName);
- if (ja != null) {
- ja.put(newja);
- }
- } else {
- newjo.put("tagName", tagName);
- if (ja != null) {
- ja.put(newjo);
- }
- }
- token = null;
- for (;;) {
- if (token == null) {
- token = x.nextToken();
- }
- if (token == null) {
- throw x.syntaxError("Misshaped tag");
- }
- if (!(token instanceof String)) {
- break;
- }
-
-// attribute = value
-
- attribute = (String)token;
- if (!arrayForm && ("tagName".equals(attribute) || "childNode".equals(attribute))) {
- throw x.syntaxError("Reserved attribute.");
- }
- token = x.nextToken();
- if (token == XML.EQ) {
- token = x.nextToken();
- if (!(token instanceof String)) {
- throw x.syntaxError("Missing value");
- }
- newjo.accumulate(attribute, keepStrings ? ((String)token) :XML.stringToValue((String)token));
- token = null;
- } else {
- newjo.accumulate(attribute, "");
- }
- }
- if (arrayForm && newjo.length() > 0) {
- newja.put(newjo);
- }
-
-// Empty tag <.../>
-
- if (token == XML.SLASH) {
- if (x.nextToken() != XML.GT) {
- throw x.syntaxError("Misshaped tag");
- }
- if (ja == null) {
- if (arrayForm) {
- return newja;
- }
- return newjo;
- }
-
-// Content, between <...> and </...>
-
- } else {
- if (token != XML.GT) {
- throw x.syntaxError("Misshaped tag");
- }
- closeTag = (String)parse(x, arrayForm, newja, keepStrings);
- if (closeTag != null) {
- if (!closeTag.equals(tagName)) {
- throw x.syntaxError("Mismatched '" + tagName +
- "' and '" + closeTag + "'");
- }
- tagName = null;
- if (!arrayForm && newja.length() > 0) {
- newjo.put("childNodes", newja);
- }
- if (ja == null) {
- if (arrayForm) {
- return newja;
- }
- return newjo;
- }
- }
- }
+ if (x.nextToken() != XML.GT)
+ {
+ throw x.syntaxError("Misshaped close tag");
+ }
+ return token;
+ }
+ else if (token == XML.BANG)
+ {
+
+ // <!
+
+ c = x.next();
+ if (c == '-')
+ {
+ if (x.next() == '-')
+ {
+ x.skipPast("-->");
+ }
+ else
+ {
+ x.back();
+ }
+ }
+ else if (c == '[')
+ {
+ token = x.nextToken();
+ if (token.equals("CDATA") && x.next() == '[')
+ {
+ if (ja != null)
+ {
+ ja.put(x.nextCDATA());
+ }
+ }
+ else
+ {
+ throw x.syntaxError("Expected 'CDATA['");
+ }
+ }
+ else
+ {
+ i = 1;
+ do
+ {
+ token = x.nextMeta();
+ if (token == null)
+ {
+ throw x.syntaxError("Missing '>' after '<!'.");
+ }
+ else if (token == XML.LT)
+ {
+ i += 1;
}
- } else {
- if (ja != null) {
- ja.put(token instanceof String
- ? keepStrings ? XML.unescape((String)token) :XML.stringToValue((String)token)
- : token);
+ else if (token == XML.GT)
+ {
+ i -= 1;
}
+ } while (i > 0);
}
- }
- }
-
-
- /**
- * Convert a well-formed (but not necessarily valid) XML string into a
- * JSONArray using the JsonML transform. Each XML tag is represented as
- * a JSONArray in which the first element is the tag name. If the tag has
- * attributes, then the second element will be JSONObject containing the
- * name/value pairs. If the tag contains children, then strings and
- * JSONArrays will represent the child tags.
- * Comments, prologs, DTDs, and <code><[ [ ]]></code> are ignored.
- * @param string The source string.
- * @return A JSONArray containing the structured data from the XML string.
- * @throws JSONException Thrown on error converting to a JSONArray
- */
- public static JSONArray toJSONArray(String string) throws JSONException {
- return (JSONArray)parse(new XMLTokener(string), true, null, false);
- }
+ }
+ else if (token == XML.QUEST)
+ {
+ // <?
- /**
- * Convert a well-formed (but not necessarily valid) XML string into a
- * JSONArray using the JsonML transform. Each XML tag is represented as
- * a JSONArray in which the first element is the tag name. If the tag has
- * attributes, then the second element will be JSONObject containing the
- * name/value pairs. If the tag contains children, then strings and
- * JSONArrays will represent the child tags.
- * As opposed to toJSONArray this method does not attempt to convert
- * any text node or attribute value to any type
- * but just leaves it as a string.
- * Comments, prologs, DTDs, and <code><[ [ ]]></code> are ignored.
- * @param string The source string.
- * @param keepStrings If true, then values will not be coerced into boolean
- * or numeric values and will instead be left as strings
- * @return A JSONArray containing the structured data from the XML string.
- * @throws JSONException Thrown on error converting to a JSONArray
- */
- public static JSONArray toJSONArray(String string, boolean keepStrings) throws JSONException {
- return (JSONArray)parse(new XMLTokener(string), true, null, keepStrings);
- }
+ x.skipPast("?>");
+ }
+ else
+ {
+ throw x.syntaxError("Misshaped tag");
+ }
+ // Open tag <
- /**
- * Convert a well-formed (but not necessarily valid) XML string into a
- * JSONArray using the JsonML transform. Each XML tag is represented as
- * a JSONArray in which the first element is the tag name. If the tag has
- * attributes, then the second element will be JSONObject containing the
- * name/value pairs. If the tag contains children, then strings and
- * JSONArrays will represent the child content and tags.
- * As opposed to toJSONArray this method does not attempt to convert
- * any text node or attribute value to any type
- * but just leaves it as a string.
- * Comments, prologs, DTDs, and <code><[ [ ]]></code> are ignored.
- * @param x An XMLTokener.
- * @param keepStrings If true, then values will not be coerced into boolean
- * or numeric values and will instead be left as strings
- * @return A JSONArray containing the structured data from the XML string.
- * @throws JSONException Thrown on error converting to a JSONArray
- */
- public static JSONArray toJSONArray(XMLTokener x, boolean keepStrings) throws JSONException {
- return (JSONArray)parse(x, true, null, keepStrings);
- }
+ }
+ else
+ {
+ if (!(token instanceof String))
+ {
+ throw x.syntaxError("Bad tagName '" + token + "'.");
+ }
+ tagName = (String) token;
+ newja = new JSONArray();
+ newjo = new JSONObject();
+ if (arrayForm)
+ {
+ newja.put(tagName);
+ if (ja != null)
+ {
+ ja.put(newja);
+ }
+ }
+ else
+ {
+ newjo.put("tagName", tagName);
+ if (ja != null)
+ {
+ ja.put(newjo);
+ }
+ }
+ token = null;
+ for (;;)
+ {
+ if (token == null)
+ {
+ token = x.nextToken();
+ }
+ if (token == null)
+ {
+ throw x.syntaxError("Misshaped tag");
+ }
+ if (!(token instanceof String))
+ {
+ break;
+ }
+ // attribute = value
- /**
- * Convert a well-formed (but not necessarily valid) XML string into a
- * JSONArray using the JsonML transform. Each XML tag is represented as
- * a JSONArray in which the first element is the tag name. If the tag has
- * attributes, then the second element will be JSONObject containing the
- * name/value pairs. If the tag contains children, then strings and
- * JSONArrays will represent the child content and tags.
- * Comments, prologs, DTDs, and <code><[ [ ]]></code> are ignored.
- * @param x An XMLTokener.
- * @return A JSONArray containing the structured data from the XML string.
- * @throws JSONException Thrown on error converting to a JSONArray
- */
- public static JSONArray toJSONArray(XMLTokener x) throws JSONException {
- return (JSONArray)parse(x, true, null, false);
- }
+ attribute = (String) token;
+ if (!arrayForm && ("tagName".equals(attribute)
+ || "childNode".equals(attribute)))
+ {
+ throw x.syntaxError("Reserved attribute.");
+ }
+ token = x.nextToken();
+ if (token == XML.EQ)
+ {
+ token = x.nextToken();
+ if (!(token instanceof String))
+ {
+ throw x.syntaxError("Missing value");
+ }
+ newjo.accumulate(attribute, keepStrings ? ((String) token)
+ : XML.stringToValue((String) token));
+ token = null;
+ }
+ else
+ {
+ newjo.accumulate(attribute, "");
+ }
+ }
+ if (arrayForm && newjo.length() > 0)
+ {
+ newja.put(newjo);
+ }
+
+ // Empty tag <.../>
+
+ if (token == XML.SLASH)
+ {
+ if (x.nextToken() != XML.GT)
+ {
+ throw x.syntaxError("Misshaped tag");
+ }
+ if (ja == null)
+ {
+ if (arrayForm)
+ {
+ return newja;
+ }
+ return newjo;
+ }
+ // Content, between <...> and </...>
- /**
- * Convert a well-formed (but not necessarily valid) XML string into a
- * JSONObject using the JsonML transform. Each XML tag is represented as
- * a JSONObject with a "tagName" property. If the tag has attributes, then
- * the attributes will be in the JSONObject as properties. If the tag
- * contains children, the object will have a "childNodes" property which
- * will be an array of strings and JsonML JSONObjects.
-
- * Comments, prologs, DTDs, and <code><[ [ ]]></code> are ignored.
- * @param string The XML source text.
- * @return A JSONObject containing the structured data from the XML string.
- * @throws JSONException Thrown on error converting to a JSONObject
- */
- public static JSONObject toJSONObject(String string) throws JSONException {
- return (JSONObject)parse(new XMLTokener(string), false, null, false);
+ }
+ else
+ {
+ if (token != XML.GT)
+ {
+ throw x.syntaxError("Misshaped tag");
+ }
+ closeTag = (String) parse(x, arrayForm, newja, keepStrings);
+ if (closeTag != null)
+ {
+ if (!closeTag.equals(tagName))
+ {
+ throw x.syntaxError("Mismatched '" + tagName + "' and '"
+ + closeTag + "'");
+ }
+ tagName = null;
+ if (!arrayForm && newja.length() > 0)
+ {
+ newjo.put("childNodes", newja);
+ }
+ if (ja == null)
+ {
+ if (arrayForm)
+ {
+ return newja;
+ }
+ return newjo;
+ }
+ }
+ }
+ }
+ }
+ else
+ {
+ if (ja != null)
+ {
+ ja.put(token instanceof String
+ ? keepStrings ? XML.unescape((String) token)
+ : XML.stringToValue((String) token)
+ : token);
+ }
+ }
}
-
-
- /**
- * Convert a well-formed (but not necessarily valid) XML string into a
- * JSONObject using the JsonML transform. Each XML tag is represented as
- * a JSONObject with a "tagName" property. If the tag has attributes, then
- * the attributes will be in the JSONObject as properties. If the tag
- * contains children, the object will have a "childNodes" property which
- * will be an array of strings and JsonML JSONObjects.
-
- * Comments, prologs, DTDs, and <code><[ [ ]]></code> are ignored.
- * @param string The XML source text.
- * @param keepStrings If true, then values will not be coerced into boolean
- * or numeric values and will instead be left as strings
- * @return A JSONObject containing the structured data from the XML string.
- * @throws JSONException Thrown on error converting to a JSONObject
- */
- public static JSONObject toJSONObject(String string, boolean keepStrings) throws JSONException {
- return (JSONObject)parse(new XMLTokener(string), false, null, keepStrings);
+ }
+
+ /**
+ * Convert a well-formed (but not necessarily valid) XML string into a
+ * JSONArray using the JsonML transform. Each XML tag is represented as a
+ * JSONArray in which the first element is the tag name. If the tag has
+ * attributes, then the second element will be JSONObject containing the
+ * name/value pairs. If the tag contains children, then strings and JSONArrays
+ * will represent the child tags. Comments, prologs, DTDs, and
+ * <code><[ [ ]]></code> are ignored.
+ *
+ * @param string
+ * The source string.
+ * @return A JSONArray containing the structured data from the XML string.
+ * @throws JSONException
+ * Thrown on error converting to a JSONArray
+ */
+ public static JSONArray toJSONArray(String string) throws JSONException
+ {
+ return (JSONArray) parse(new XMLTokener(string), true, null, false);
+ }
+
+ /**
+ * Convert a well-formed (but not necessarily valid) XML string into a
+ * JSONArray using the JsonML transform. Each XML tag is represented as a
+ * JSONArray in which the first element is the tag name. If the tag has
+ * attributes, then the second element will be JSONObject containing the
+ * name/value pairs. If the tag contains children, then strings and JSONArrays
+ * will represent the child tags. As opposed to toJSONArray this method does
+ * not attempt to convert any text node or attribute value to any type but
+ * just leaves it as a string. Comments, prologs, DTDs, and
+ * <code><[ [ ]]></code> are ignored.
+ *
+ * @param string
+ * The source string.
+ * @param keepStrings
+ * If true, then values will not be coerced into boolean or numeric
+ * values and will instead be left as strings
+ * @return A JSONArray containing the structured data from the XML string.
+ * @throws JSONException
+ * Thrown on error converting to a JSONArray
+ */
+ public static JSONArray toJSONArray(String string, boolean keepStrings)
+ throws JSONException
+ {
+ return (JSONArray) parse(new XMLTokener(string), true, null,
+ keepStrings);
+ }
+
+ /**
+ * Convert a well-formed (but not necessarily valid) XML string into a
+ * JSONArray using the JsonML transform. Each XML tag is represented as a
+ * JSONArray in which the first element is the tag name. If the tag has
+ * attributes, then the second element will be JSONObject containing the
+ * name/value pairs. If the tag contains children, then strings and JSONArrays
+ * will represent the child content and tags. As opposed to toJSONArray this
+ * method does not attempt to convert any text node or attribute value to any
+ * type but just leaves it as a string. Comments, prologs, DTDs, and
+ * <code><[ [ ]]></code> are ignored.
+ *
+ * @param x
+ * An XMLTokener.
+ * @param keepStrings
+ * If true, then values will not be coerced into boolean or numeric
+ * values and will instead be left as strings
+ * @return A JSONArray containing the structured data from the XML string.
+ * @throws JSONException
+ * Thrown on error converting to a JSONArray
+ */
+ public static JSONArray toJSONArray(XMLTokener x, boolean keepStrings)
+ throws JSONException
+ {
+ return (JSONArray) parse(x, true, null, keepStrings);
+ }
+
+ /**
+ * Convert a well-formed (but not necessarily valid) XML string into a
+ * JSONArray using the JsonML transform. Each XML tag is represented as a
+ * JSONArray in which the first element is the tag name. If the tag has
+ * attributes, then the second element will be JSONObject containing the
+ * name/value pairs. If the tag contains children, then strings and JSONArrays
+ * will represent the child content and tags. Comments, prologs, DTDs, and
+ * <code><[ [ ]]></code> are ignored.
+ *
+ * @param x
+ * An XMLTokener.
+ * @return A JSONArray containing the structured data from the XML string.
+ * @throws JSONException
+ * Thrown on error converting to a JSONArray
+ */
+ public static JSONArray toJSONArray(XMLTokener x) throws JSONException
+ {
+ return (JSONArray) parse(x, true, null, false);
+ }
+
+ /**
+ * Convert a well-formed (but not necessarily valid) XML string into a
+ * JSONObject using the JsonML transform. Each XML tag is represented as a
+ * JSONObject with a "tagName" property. If the tag has attributes, then the
+ * attributes will be in the JSONObject as properties. If the tag contains
+ * children, the object will have a "childNodes" property which will be an
+ * array of strings and JsonML JSONObjects.
+ *
+ * Comments, prologs, DTDs, and <code><[ [ ]]></code> are ignored.
+ *
+ * @param string
+ * The XML source text.
+ * @return A JSONObject containing the structured data from the XML string.
+ * @throws JSONException
+ * Thrown on error converting to a JSONObject
+ */
+ public static JSONObject toJSONObject(String string) throws JSONException
+ {
+ return (JSONObject) parse(new XMLTokener(string), false, null, false);
+ }
+
+ /**
+ * Convert a well-formed (but not necessarily valid) XML string into a
+ * JSONObject using the JsonML transform. Each XML tag is represented as a
+ * JSONObject with a "tagName" property. If the tag has attributes, then the
+ * attributes will be in the JSONObject as properties. If the tag contains
+ * children, the object will have a "childNodes" property which will be an
+ * array of strings and JsonML JSONObjects.
+ *
+ * Comments, prologs, DTDs, and <code><[ [ ]]></code> are ignored.
+ *
+ * @param string
+ * The XML source text.
+ * @param keepStrings
+ * If true, then values will not be coerced into boolean or numeric
+ * values and will instead be left as strings
+ * @return A JSONObject containing the structured data from the XML string.
+ * @throws JSONException
+ * Thrown on error converting to a JSONObject
+ */
+ public static JSONObject toJSONObject(String string, boolean keepStrings)
+ throws JSONException
+ {
+ return (JSONObject) parse(new XMLTokener(string), false, null,
+ keepStrings);
+ }
+
+ /**
+ * Convert a well-formed (but not necessarily valid) XML string into a
+ * JSONObject using the JsonML transform. Each XML tag is represented as a
+ * JSONObject with a "tagName" property. If the tag has attributes, then the
+ * attributes will be in the JSONObject as properties. If the tag contains
+ * children, the object will have a "childNodes" property which will be an
+ * array of strings and JsonML JSONObjects.
+ *
+ * Comments, prologs, DTDs, and <code><[ [ ]]></code> are ignored.
+ *
+ * @param x
+ * An XMLTokener of the XML source text.
+ * @return A JSONObject containing the structured data from the XML string.
+ * @throws JSONException
+ * Thrown on error converting to a JSONObject
+ */
+ public static JSONObject toJSONObject(XMLTokener x) throws JSONException
+ {
+ return (JSONObject) parse(x, false, null, false);
+ }
+
+ /**
+ * Convert a well-formed (but not necessarily valid) XML string into a
+ * JSONObject using the JsonML transform. Each XML tag is represented as a
+ * JSONObject with a "tagName" property. If the tag has attributes, then the
+ * attributes will be in the JSONObject as properties. If the tag contains
+ * children, the object will have a "childNodes" property which will be an
+ * array of strings and JsonML JSONObjects.
+ *
+ * Comments, prologs, DTDs, and <code><[ [ ]]></code> are ignored.
+ *
+ * @param x
+ * An XMLTokener of the XML source text.
+ * @param keepStrings
+ * If true, then values will not be coerced into boolean or numeric
+ * values and will instead be left as strings
+ * @return A JSONObject containing the structured data from the XML string.
+ * @throws JSONException
+ * Thrown on error converting to a JSONObject
+ */
+ public static JSONObject toJSONObject(XMLTokener x, boolean keepStrings)
+ throws JSONException
+ {
+ return (JSONObject) parse(x, false, null, keepStrings);
+ }
+
+ /**
+ * Reverse the JSONML transformation, making an XML text from a JSONArray.
+ *
+ * @param ja
+ * A JSONArray.
+ * @return An XML string.
+ * @throws JSONException
+ * Thrown on error converting to a string
+ */
+ public static String toString(JSONArray ja) throws JSONException
+ {
+ int i;
+ JSONObject jo;
+ int length;
+ Object object;
+ StringBuilder sb = new StringBuilder();
+ String tagName;
+
+ // Emit <tagName
+
+ tagName = ja.getString(0);
+ XML.noSpace(tagName);
+ tagName = XML.escape(tagName);
+ sb.append('<');
+ sb.append(tagName);
+
+ object = ja.opt(1);
+ if (object instanceof JSONObject)
+ {
+ i = 2;
+ jo = (JSONObject) object;
+
+ // Emit the attributes
+
+ // Don't use the new entrySet API to maintain Android support
+ for (final String key : jo.keySet())
+ {
+ final Object value = jo.opt(key);
+ XML.noSpace(key);
+ if (value != null)
+ {
+ sb.append(' ');
+ sb.append(XML.escape(key));
+ sb.append('=');
+ sb.append('"');
+ sb.append(XML.escape(value.toString()));
+ sb.append('"');
+ }
+ }
}
-
-
- /**
- * Convert a well-formed (but not necessarily valid) XML string into a
- * JSONObject using the JsonML transform. Each XML tag is represented as
- * a JSONObject with a "tagName" property. If the tag has attributes, then
- * the attributes will be in the JSONObject as properties. If the tag
- * contains children, the object will have a "childNodes" property which
- * will be an array of strings and JsonML JSONObjects.
-
- * Comments, prologs, DTDs, and <code><[ [ ]]></code> are ignored.
- * @param x An XMLTokener of the XML source text.
- * @return A JSONObject containing the structured data from the XML string.
- * @throws JSONException Thrown on error converting to a JSONObject
- */
- public static JSONObject toJSONObject(XMLTokener x) throws JSONException {
- return (JSONObject)parse(x, false, null, false);
+ else
+ {
+ i = 1;
}
+ // Emit content in body
- /**
- * Convert a well-formed (but not necessarily valid) XML string into a
- * JSONObject using the JsonML transform. Each XML tag is represented as
- * a JSONObject with a "tagName" property. If the tag has attributes, then
- * the attributes will be in the JSONObject as properties. If the tag
- * contains children, the object will have a "childNodes" property which
- * will be an array of strings and JsonML JSONObjects.
-
- * Comments, prologs, DTDs, and <code><[ [ ]]></code> are ignored.
- * @param x An XMLTokener of the XML source text.
- * @param keepStrings If true, then values will not be coerced into boolean
- * or numeric values and will instead be left as strings
- * @return A JSONObject containing the structured data from the XML string.
- * @throws JSONException Thrown on error converting to a JSONObject
- */
- public static JSONObject toJSONObject(XMLTokener x, boolean keepStrings) throws JSONException {
- return (JSONObject)parse(x, false, null, keepStrings);
+ length = ja.length();
+ if (i >= length)
+ {
+ sb.append('/');
+ sb.append('>');
}
-
-
- /**
- * Reverse the JSONML transformation, making an XML text from a JSONArray.
- * @param ja A JSONArray.
- * @return An XML string.
- * @throws JSONException Thrown on error converting to a string
- */
- public static String toString(JSONArray ja) throws JSONException {
- int i;
- JSONObject jo;
- int length;
- Object object;
- StringBuilder sb = new StringBuilder();
- String tagName;
-
-// Emit <tagName
-
- tagName = ja.getString(0);
- XML.noSpace(tagName);
- tagName = XML.escape(tagName);
- sb.append('<');
- sb.append(tagName);
-
- object = ja.opt(1);
- if (object instanceof JSONObject) {
- i = 2;
- jo = (JSONObject)object;
-
-// Emit the attributes
-
- // Don't use the new entrySet API to maintain Android support
- for (final String key : jo.keySet()) {
- final Object value = jo.opt(key);
- XML.noSpace(key);
- if (value != null) {
- sb.append(' ');
- sb.append(XML.escape(key));
- sb.append('=');
- sb.append('"');
- sb.append(XML.escape(value.toString()));
- sb.append('"');
- }
- }
- } else {
- i = 1;
+ else
+ {
+ sb.append('>');
+ do
+ {
+ object = ja.get(i);
+ i += 1;
+ if (object != null)
+ {
+ if (object instanceof String)
+ {
+ sb.append(XML.escape(object.toString()));
+ }
+ else if (object instanceof JSONObject)
+ {
+ sb.append(toString((JSONObject) object));
+ }
+ else if (object instanceof JSONArray)
+ {
+ sb.append(toString((JSONArray) object));
+ }
+ else
+ {
+ sb.append(object.toString());
+ }
}
-
-// Emit content in body
-
- length = ja.length();
- if (i >= length) {
- sb.append('/');
- sb.append('>');
- } else {
- sb.append('>');
- do {
- object = ja.get(i);
- i += 1;
- if (object != null) {
- if (object instanceof String) {
- sb.append(XML.escape(object.toString()));
- } else if (object instanceof JSONObject) {
- sb.append(toString((JSONObject)object));
- } else if (object instanceof JSONArray) {
- sb.append(toString((JSONArray)object));
- } else {
- sb.append(object.toString());
- }
- }
- } while (i < length);
- sb.append('<');
- sb.append('/');
- sb.append(tagName);
- sb.append('>');
+ } while (i < length);
+ sb.append('<');
+ sb.append('/');
+ sb.append(tagName);
+ sb.append('>');
+ }
+ return sb.toString();
+ }
+
+ /**
+ * Reverse the JSONML transformation, making an XML text from a JSONObject.
+ * The JSONObject must contain a "tagName" property. If it has children, then
+ * it must have a "childNodes" property containing an array of objects. The
+ * other properties are attributes with string values.
+ *
+ * @param jo
+ * A JSONObject.
+ * @return An XML string.
+ * @throws JSONException
+ * Thrown on error converting to a string
+ */
+ public static String toString(JSONObject jo) throws JSONException
+ {
+ StringBuilder sb = new StringBuilder();
+ int i;
+ JSONArray ja;
+ int length;
+ Object object;
+ String tagName;
+ Object value;
+
+ // Emit <tagName
+
+ tagName = jo.optString("tagName");
+ if (tagName == null)
+ {
+ return XML.escape(jo.toString());
+ }
+ XML.noSpace(tagName);
+ tagName = XML.escape(tagName);
+ sb.append('<');
+ sb.append(tagName);
+
+ // Emit the attributes
+
+ // Don't use the new entrySet API to maintain Android support
+ for (final String key : jo.keySet())
+ {
+ if (!"tagName".equals(key) && !"childNodes".equals(key))
+ {
+ XML.noSpace(key);
+ value = jo.opt(key);
+ if (value != null)
+ {
+ sb.append(' ');
+ sb.append(XML.escape(key));
+ sb.append('=');
+ sb.append('"');
+ sb.append(XML.escape(value.toString()));
+ sb.append('"');
}
- return sb.toString();
+ }
}
- /**
- * Reverse the JSONML transformation, making an XML text from a JSONObject.
- * The JSONObject must contain a "tagName" property. If it has children,
- * then it must have a "childNodes" property containing an array of objects.
- * The other properties are attributes with string values.
- * @param jo A JSONObject.
- * @return An XML string.
- * @throws JSONException Thrown on error converting to a string
- */
- public static String toString(JSONObject jo) throws JSONException {
- StringBuilder sb = new StringBuilder();
- int i;
- JSONArray ja;
- int length;
- Object object;
- String tagName;
- Object value;
-
-//Emit <tagName
-
- tagName = jo.optString("tagName");
- if (tagName == null) {
- return XML.escape(jo.toString());
- }
- XML.noSpace(tagName);
- tagName = XML.escape(tagName);
- sb.append('<');
- sb.append(tagName);
-
-//Emit the attributes
-
- // Don't use the new entrySet API to maintain Android support
- for (final String key : jo.keySet()) {
- if (!"tagName".equals(key) && !"childNodes".equals(key)) {
- XML.noSpace(key);
- value = jo.opt(key);
- if (value != null) {
- sb.append(' ');
- sb.append(XML.escape(key));
- sb.append('=');
- sb.append('"');
- sb.append(XML.escape(value.toString()));
- sb.append('"');
- }
- }
- }
+ // Emit content in body
-//Emit content in body
-
- ja = jo.optJSONArray("childNodes");
- if (ja == null) {
- sb.append('/');
- sb.append('>');
- } else {
- sb.append('>');
- length = ja.length();
- for (i = 0; i < length; i += 1) {
- object = ja.get(i);
- if (object != null) {
- if (object instanceof String) {
- sb.append(XML.escape(object.toString()));
- } else if (object instanceof JSONObject) {
- sb.append(toString((JSONObject)object));
- } else if (object instanceof JSONArray) {
- sb.append(toString((JSONArray)object));
- } else {
- sb.append(object.toString());
- }
- }
- }
- sb.append('<');
- sb.append('/');
- sb.append(tagName);
- sb.append('>');
+ ja = jo.optJSONArray("childNodes");
+ if (ja == null)
+ {
+ sb.append('/');
+ sb.append('>');
+ }
+ else
+ {
+ sb.append('>');
+ length = ja.length();
+ for (i = 0; i < length; i += 1)
+ {
+ object = ja.get(i);
+ if (object != null)
+ {
+ if (object instanceof String)
+ {
+ sb.append(XML.escape(object.toString()));
+ }
+ else if (object instanceof JSONObject)
+ {
+ sb.append(toString((JSONObject) object));
+ }
+ else if (object instanceof JSONArray)
+ {
+ sb.append(toString((JSONArray) object));
+ }
+ else
+ {
+ sb.append(object.toString());
+ }
}
- return sb.toString();
+ }
+ sb.append('<');
+ sb.append('/');
+ sb.append(tagName);
+ sb.append('>');
}
+ return sb.toString();
+ }
}
* @author JSON.org
* @version 2016-08-15
*/
-public class JSONObject {
- /**
- * JSONObject.NULL is equivalent to the value that JavaScript calls null, whilst
- * Java's null is equivalent to the value that JavaScript calls undefined.
- */
- private static final class Null {
-
- /**
- * There is only intended to be a single instance of the NULL object, so the
- * clone method returns itself.
- *
- * @return NULL.
- */
- @Override
- protected final Object clone() {
- return this;
- }
-
- /**
- * A Null object is equal to the null value and to itself.
- *
- * @param object An object to test for nullness.
- * @return true if the object parameter is the JSONObject.NULL object or null.
- */
- @Override
- public boolean equals(Object object) {
- return object == null || object == this;
- }
-
- /**
- * A Null object is equal to the null value and to itself.
- *
- * @return always returns 0.
- */
- @Override
- public int hashCode() {
- return 0;
- }
-
- /**
- * Get the "null" string value.
- *
- * @return The string "null".
- */
- @Override
- public String toString() {
- return "null";
- }
- }
-
- /**
- * The map where the JSONObject's properties are kept.
- */
- private final Map<String, Object> map;
-
- /**
- * It is sometimes more convenient and less ambiguous to have a
- * <code>NULL</code> object than to use Java's <code>null</code> value.
- * <code>JSONObject.NULL.equals(null)</code> returns <code>true</code>.
- * <code>JSONObject.NULL.toString()</code> returns <code>"null"</code>.
- */
- public static final Object NULL = new Null();
-
- /**
- * Construct an empty JSONObject.
- */
- public JSONObject() {
- // HashMap is used on purpose to ensure that elements are unordered by
- // the specification.
- // JSON tends to be a portable transfer format to allows the container
- // implementations to rearrange their items for a faster element
- // retrieval based on associative access.
- // Therefore, an implementation mustn't rely on the order of the item.
- this.map = new HashMap<String, Object>();
- }
-
- /**
- * Construct a JSONObject from a subset of another JSONObject. An array of
- * strings is used to identify the keys that should be copied. Missing keys are
- * ignored.
- *
- * @param jo A JSONObject.
- * @param names An array of strings.
- */
- public JSONObject(JSONObject jo, String[] names) {
- this(names.length);
- for (int i = 0; i < names.length; i += 1) {
- try {
- this.putOnce(names[i], jo.opt(names[i]));
- } catch (Exception ignore) {
- }
- }
- }
-
- /**
- * Construct a JSONObject from a JSONTokener.
- *
- * @param x A JSONTokener object containing the source string.
- * @throws JSONException If there is a syntax error in the source string or a
- * duplicated key.
- */
- public JSONObject(JSONTokener x) throws JSONException {
- this();
- char c;
- String key;
-
- if (x.nextClean() != '{') {
- throw x.syntaxError("A JSONObject text must begin with '{'");
- }
- for (;;) {
- c = x.nextClean();
- switch (c) {
- case 0:
- throw x.syntaxError("A JSONObject text must end with '}'");
- case '}':
- return;
- default:
- x.back();
- key = x.nextValue().toString();
- }
-
- // The key is followed by ':'.
-
- c = x.nextClean();
- if (c != ':') {
- throw x.syntaxError("Expected a ':' after a key");
- }
-
- // Use syntaxError(..) to include error location
-
- if (key != null) {
- // Check if key exists
- if (this.opt(key) != null) {
- // key already exists
- throw x.syntaxError("Duplicate key \"" + key + "\"");
- }
- // Only add value if non-null
- Object value = x.nextValue();
- if (value != null) {
- this.put(key, value);
- }
- }
-
- // Pairs are separated by ','.
-
- switch (x.nextClean()) {
- case ';':
- case ',':
- if (x.nextClean() == '}') {
- return;
- }
- x.back();
- break;
- case '}':
- return;
- default:
- throw x.syntaxError("Expected a ',' or '}'");
- }
- }
- }
-
- /**
- * Construct a JSONObject from a Map.
- *
- * @param m A map object that can be used to initialize the contents of the
- * JSONObject.
- * @throws JSONException If a value in the map is non-finite number.
- * @throws NullPointerException If a key in the map is <code>null</code>
- */
- public JSONObject(Map<?, ?> m) {
- if (m == null) {
- this.map = new HashMap<String, Object>();
- } else {
- this.map = new HashMap<String, Object>(m.size());
- for (final Entry<?, ?> e : m.entrySet()) {
- if (e.getKey() == null) {
- throw new NullPointerException("Null key.");
- }
- final Object value = e.getValue();
- if (value != null) {
- this.map.put(String.valueOf(e.getKey()), wrap(value));
- }
- }
- }
- }
-
- /**
- * Construct a JSONObject from an Object using bean getters. It reflects on all
- * of the public methods of the object. For each of the methods with no
- * parameters and a name starting with <code>"get"</code> or <code>"is"</code>
- * followed by an uppercase letter, the method is invoked, and a key and the
- * value returned from the getter method are put into the new JSONObject.
- * <p>
- * The key is formed by removing the <code>"get"</code> or <code>"is"</code>
- * prefix. If the second remaining character is not upper case, then the first
- * character is converted to lower case.
- * <p>
- * Methods that are <code>static</code>, return <code>void</code>, have
- * parameters, or are "bridge" methods, are ignored.
- * <p>
- * For example, if an object has a method named <code>"getName"</code>, and if
- * the result of calling <code>object.getName()</code> is
- * <code>"Larry Fine"</code>, then the JSONObject will contain
- * <code>"name": "Larry Fine"</code>.
- * <p>
- * The {@link JSONPropertyName} annotation can be used on a bean getter to
- * override key name used in the JSONObject. For example, using the object above
- * with the <code>getName</code> method, if we annotated it with:
- *
- * <pre>
- * @JSONPropertyName("FullName")
- * public String getName() {
- * return this.name;
- * }
- * </pre>
- *
- * The resulting JSON object would contain <code>"FullName": "Larry Fine"</code>
- * <p>
- * Similarly, the {@link JSONPropertyName} annotation can be used on non-
- * <code>get</code> and <code>is</code> methods. We can also override key name
- * used in the JSONObject as seen below even though the field would normally be
- * ignored:
- *
- * <pre>
- * @JSONPropertyName("FullName")
- * public String fullName() {
- * return this.name;
- * }
- * </pre>
- *
- * The resulting JSON object would contain <code>"FullName": "Larry Fine"</code>
- * <p>
- * The {@link JSONPropertyIgnore} annotation can be used to force the bean
- * property to not be serialized into JSON. If both {@link JSONPropertyIgnore}
- * and {@link JSONPropertyName} are defined on the same method, a depth
- * comparison is performed and the one closest to the concrete class being
- * serialized is used. If both annotations are at the same level, then the
- * {@link JSONPropertyIgnore} annotation takes precedent and the field is not
- * serialized. For example, the following declaration would prevent the
- * <code>getName</code> method from being serialized:
- *
- * <pre>
- * @JSONPropertyName("FullName")
- * @JSONPropertyIgnore
- * public String getName() {
- * return this.name;
- * }
- * </pre>
- * <p>
- *
- * @param bean An object that has getter methods that should be used to make a
- * JSONObject.
- */
- public JSONObject(Object bean) {
- this();
- this.populateMap(bean);
- }
-
- /**
- * Construct a JSONObject from an Object, using reflection to find the public
- * members. The resulting JSONObject's keys will be the strings from the names
- * array, and the values will be the field values associated with those keys in
- * the object. If a key is not found or not visible, then it will not be copied
- * into the new JSONObject.
- *
- * @param object An object that has fields that should be used to make a
- * JSONObject.
- * @param names An array of strings, the names of the fields to be obtained
- * from the object.
- */
- public JSONObject(Object object, String names[]) {
- this(names.length);
- Class<?> c = object.getClass();
- for (int i = 0; i < names.length; i += 1) {
- String name = names[i];
- try {
- this.putOpt(name, c.getField(name).get(object));
- } catch (Exception ignore) {
- }
- }
- }
-
- /**
- * Construct a JSONObject from a source JSON text string. This is the most
- * commonly used JSONObject constructor.
- *
- * @param source A string beginning with <code>{</code> <small>(left
- * brace)</small> and ending with <code>}</code>
- * <small>(right brace)</small>.
- * @exception JSONException If there is a syntax error in the source string or a
- * duplicated key.
- */
- public JSONObject(String source) throws JSONException {
- this(new JSONTokener(source));
- }
-
- /**
- * Construct a JSONObject from a ResourceBundle.
- *
- * @param baseName The ResourceBundle base name.
- * @param locale The Locale to load the ResourceBundle for.
- * @throws JSONException If any JSONExceptions are detected.
- */
- public JSONObject(String baseName, Locale locale) throws JSONException {
- this();
- ResourceBundle bundle = ResourceBundle.getBundle(baseName, locale,
- Thread.currentThread().getContextClassLoader());
-
-// Iterate through the keys in the bundle.
-
- Enumeration<String> keys = bundle.getKeys();
- while (keys.hasMoreElements()) {
- Object key = keys.nextElement();
- if (key != null) {
-
-// Go through the path, ensuring that there is a nested JSONObject for each
-// segment except the last. Add the value using the last segment's name into
-// the deepest nested JSONObject.
-
- String[] path = ((String) key).split("\\.");
- int last = path.length - 1;
- JSONObject target = this;
- for (int i = 0; i < last; i += 1) {
- String segment = path[i];
- JSONObject nextTarget = target.optJSONObject(segment);
- if (nextTarget == null) {
- nextTarget = new JSONObject();
- target.put(segment, nextTarget);
- }
- target = nextTarget;
- }
- target.put(path[last], bundle.getString((String) key));
- }
- }
- }
-
- /**
- * Constructor to specify an initial capacity of the internal map. Useful for
- * library internal calls where we know, or at least can best guess, how big
- * this JSONObject will be.
- *
- * @param initialCapacity initial capacity of the internal map.
- */
- protected JSONObject(int initialCapacity) {
- this.map = new HashMap<String, Object>(initialCapacity);
- }
-
- /**
- * Accumulate values under a key. It is similar to the put method except that if
- * there is already an object stored under the key then a JSONArray is stored
- * under the key to hold all of the accumulated values. If there is already a
- * JSONArray, then the new value is appended to it. In contrast, the put method
- * replaces the previous value.
- *
- * If only one value is accumulated that is not a JSONArray, then the result
- * will be the same as using put. But if multiple values are accumulated, then
- * the result will be like append.
- *
- * @param key A key string.
- * @param value An object to be accumulated under the key.
- * @return this.
- * @throws JSONException If the value is non-finite number.
- * @throws NullPointerException If the key is <code>null</code>.
- */
- public JSONObject accumulate(String key, Object value) throws JSONException {
- testValidity(value);
- Object object = this.opt(key);
- if (object == null) {
- this.put(key, value instanceof JSONArray ? new JSONArray().put(value) : value);
- } else if (object instanceof JSONArray) {
- ((JSONArray) object).put(value);
- } else {
- this.put(key, new JSONArray().put(object).put(value));
- }
- return this;
- }
-
- /**
- * Append values to the array under a key. If the key does not exist in the
- * JSONObject, then the key is put in the JSONObject with its value being a
- * JSONArray containing the value parameter. If the key was already associated
- * with a JSONArray, then the value parameter is appended to it.
- *
- * @param key A key string.
- * @param value An object to be accumulated under the key.
- * @return this.
- * @throws JSONException If the value is non-finite number or if the
- * current value associated with the key is not a
- * JSONArray.
- * @throws NullPointerException If the key is <code>null</code>.
- */
- public JSONObject append(String key, Object value) throws JSONException {
- testValidity(value);
- Object object = this.opt(key);
- if (object == null) {
- this.put(key, new JSONArray().put(value));
- } else if (object instanceof JSONArray) {
- this.put(key, ((JSONArray) object).put(value));
- } else {
- throw new JSONException("JSONObject[" + key + "] is not a JSONArray.");
- }
- return this;
- }
-
- /**
- * Produce a string from a double. The string "null" will be returned if the
- * number is not finite.
- *
- * @param d A double.
- * @return A String.
- */
- public static String doubleToString(double d) {
- if (Double.isInfinite(d) || Double.isNaN(d)) {
- return "null";
- }
-
-// Shave off trailing zeros and decimal point, if possible.
-
- String string = Double.toString(d);
- if (string.indexOf('.') > 0 && string.indexOf('e') < 0 && string.indexOf('E') < 0) {
- while (string.endsWith("0")) {
- string = string.substring(0, string.length() - 1);
- }
- if (string.endsWith(".")) {
- string = string.substring(0, string.length() - 1);
- }
- }
- return string;
- }
-
- /**
- * Get the value object associated with a key.
- *
- * @param key A key string.
- * @return The object associated with the key.
- * @throws JSONException if the key is not found.
- */
- public Object get(String key) throws JSONException {
- if (key == null) {
- throw new JSONException("Null key.");
- }
- Object object = this.opt(key);
- if (object == null) {
- throw new JSONException("JSONObject[" + quote(key) + "] not found.");
- }
- return object;
- }
-
- /**
- * Get the enum value associated with a key.
- *
- * @param clazz The type of enum to retrieve.
- * @param key A key string.
- * @return The enum value associated with the key
- * @throws JSONException if the key is not found or if the value cannot be
- * converted to an enum.
- */
- public <E extends Enum<E>> E getEnum(Class<E> clazz, String key) throws JSONException {
- E val = optEnum(clazz, key);
- if (val == null) {
- // JSONException should really take a throwable argument.
- // If it did, I would re-implement this with the Enum.valueOf
- // method and place any thrown exception in the JSONException
- throw new JSONException(
- "JSONObject[" + quote(key) + "] is not an enum of type " + quote(clazz.getSimpleName()) + ".");
- }
- return val;
- }
-
- /**
- * Get the boolean value associated with a key.
- *
- * @param key A key string.
- * @return The truth.
- * @throws JSONException if the value is not a Boolean or the String "true" or
- * "false".
- */
- public boolean getBoolean(String key) throws JSONException {
- Object object = this.get(key);
- if (object.equals(Boolean.FALSE) || (object instanceof String && ((String) object).equalsIgnoreCase("false"))) {
- return false;
- } else if (object.equals(Boolean.TRUE)
- || (object instanceof String && ((String) object).equalsIgnoreCase("true"))) {
- return true;
- }
- throw new JSONException("JSONObject[" + quote(key) + "] is not a Boolean.");
- }
-
- /**
- * Get the BigInteger value associated with a key.
- *
- * @param key A key string.
- * @return The numeric value.
- * @throws JSONException if the key is not found or if the value cannot be
- * converted to BigInteger.
- */
- public BigInteger getBigInteger(String key) throws JSONException {
- Object object = this.get(key);
- try {
- return new BigInteger(object.toString());
- } catch (Exception e) {
- throw new JSONException("JSONObject[" + quote(key) + "] could not be converted to BigInteger.", e);
- }
- }
-
- /**
- * Get the BigDecimal value associated with a key.
- *
- * @param key A key string.
- * @return The numeric value.
- * @throws JSONException if the key is not found or if the value cannot be
- * converted to BigDecimal.
- */
- public BigDecimal getBigDecimal(String key) throws JSONException {
- Object object = this.get(key);
- if (object instanceof BigDecimal) {
- return (BigDecimal) object;
- }
- try {
- return new BigDecimal(object.toString());
- } catch (Exception e) {
- throw new JSONException("JSONObject[" + quote(key) + "] could not be converted to BigDecimal.", e);
- }
- }
-
- /**
- * Get the double value associated with a key.
- *
- * @param key A key string.
- * @return The numeric value.
- * @throws JSONException if the key is not found or if the value is not a Number
- * object and cannot be converted to a number.
- */
- public double getDouble(String key) throws JSONException {
- Object object = this.get(key);
- try {
- return object instanceof Number ? ((Number) object).doubleValue() : Double.parseDouble(object.toString());
- } catch (Exception e) {
- throw new JSONException("JSONObject[" + quote(key) + "] is not a number.", e);
- }
- }
-
- /**
- * Get the float value associated with a key.
- *
- * @param key A key string.
- * @return The numeric value.
- * @throws JSONException if the key is not found or if the value is not a Number
- * object and cannot be converted to a number.
- */
- public float getFloat(String key) throws JSONException {
- Object object = this.get(key);
- try {
- return object instanceof Number ? ((Number) object).floatValue() : Float.parseFloat(object.toString());
- } catch (Exception e) {
- throw new JSONException("JSONObject[" + quote(key) + "] is not a number.", e);
- }
- }
-
- /**
- * Get the Number value associated with a key.
- *
- * @param key A key string.
- * @return The numeric value.
- * @throws JSONException if the key is not found or if the value is not a Number
- * object and cannot be converted to a number.
- */
- public Number getNumber(String key) throws JSONException {
- Object object = this.get(key);
- try {
- if (object instanceof Number) {
- return (Number) object;
- }
- return stringToNumber(object.toString());
- } catch (Exception e) {
- throw new JSONException("JSONObject[" + quote(key) + "] is not a number.", e);
- }
- }
-
- /**
- * Get the int value associated with a key.
- *
- * @param key A key string.
- * @return The integer value.
- * @throws JSONException if the key is not found or if the value cannot be
- * converted to an integer.
- */
- public int getInt(String key) throws JSONException {
- Object object = this.get(key);
- try {
- return object instanceof Number ? ((Number) object).intValue() : Integer.parseInt((String) object);
- } catch (Exception e) {
- throw new JSONException("JSONObject[" + quote(key) + "] is not an int.", e);
- }
- }
-
- /**
- * Get the JSONArray value associated with a key.
- *
- * @param key A key string.
- * @return A JSONArray which is the value.
- * @throws JSONException if the key is not found or if the value is not a
- * JSONArray.
- */
- public JSONArray getJSONArray(String key) throws JSONException {
- Object object = this.get(key);
- if (object instanceof JSONArray) {
- return (JSONArray) object;
- }
- throw new JSONException("JSONObject[" + quote(key) + "] is not a JSONArray.");
- }
-
- /**
- * Get the JSONObject value associated with a key.
- *
- * @param key A key string.
- * @return A JSONObject which is the value.
- * @throws JSONException if the key is not found or if the value is not a
- * JSONObject.
- */
- public JSONObject getJSONObject(String key) throws JSONException {
- Object object = this.get(key);
- if (object instanceof JSONObject) {
- return (JSONObject) object;
- }
- throw new JSONException("JSONObject[" + quote(key) + "] is not a JSONObject.");
- }
-
- /**
- * Get the long value associated with a key.
- *
- * @param key A key string.
- * @return The long value.
- * @throws JSONException if the key is not found or if the value cannot be
- * converted to a long.
- */
- public long getLong(String key) throws JSONException {
- Object object = this.get(key);
- try {
- return object instanceof Number ? ((Number) object).longValue() : Long.parseLong((String) object);
- } catch (Exception e) {
- throw new JSONException("JSONObject[" + quote(key) + "] is not a long.", e);
- }
- }
-
- /**
- * Get an array of field names from a JSONObject.
- *
- * @return An array of field names, or null if there are no names.
- */
- public static String[] getNames(JSONObject jo) {
- if (jo.isEmpty()) {
- return null;
- }
- return jo.keySet().toArray(new String[jo.length()]);
- }
-
- /**
- * Get an array of field names from an Object.
- *
- * @return An array of field names, or null if there are no names.
- */
- public static String[] getNames(Object object) {
- if (object == null) {
- return null;
- }
- Class<?> klass = object.getClass();
- Field[] fields = klass.getFields();
- int length = fields.length;
- if (length == 0) {
- return null;
- }
- String[] names = new String[length];
- for (int i = 0; i < length; i += 1) {
- names[i] = fields[i].getName();
- }
- return names;
- }
-
- /**
- * Get the string associated with a key.
- *
- * @param key A key string.
- * @return A string which is the value.
- * @throws JSONException if there is no string value for the key.
- */
- public String getString(String key) throws JSONException {
- Object object = this.get(key);
- if (object instanceof String) {
- return (String) object;
- }
- throw new JSONException("JSONObject[" + quote(key) + "] not a string.");
- }
-
- /**
- * Determine if the JSONObject contains a specific key.
- *
- * @param key A key string.
- * @return true if the key exists in the JSONObject.
- */
- public boolean has(String key) {
- return this.map.containsKey(key);
- }
-
- /**
- * Increment a property of a JSONObject. If there is no such property, create
- * one with a value of 1. If there is such a property, and if it is an Integer,
- * Long, Double, or Float, then add one to it.
- *
- * @param key A key string.
- * @return this.
- * @throws JSONException If there is already a property with this name that is
- * not an Integer, Long, Double, or Float.
- */
- public JSONObject increment(String key) throws JSONException {
- Object value = this.opt(key);
- if (value == null) {
- this.put(key, 1);
- } else if (value instanceof BigInteger) {
- this.put(key, ((BigInteger) value).add(BigInteger.ONE));
- } else if (value instanceof BigDecimal) {
- this.put(key, ((BigDecimal) value).add(BigDecimal.ONE));
- } else if (value instanceof Integer) {
- this.put(key, ((Integer) value).intValue() + 1);
- } else if (value instanceof Long) {
- this.put(key, ((Long) value).longValue() + 1L);
- } else if (value instanceof Double) {
- this.put(key, ((Double) value).doubleValue() + 1.0d);
- } else if (value instanceof Float) {
- this.put(key, ((Float) value).floatValue() + 1.0f);
- } else {
- throw new JSONException("Unable to increment [" + quote(key) + "].");
- }
- return this;
- }
-
- /**
- * Determine if the value associated with the key is <code>null</code> or if
- * there is no value.
- *
- * @param key A key string.
- * @return true if there is no value associated with the key or if the value is
- * the JSONObject.NULL object.
- */
- public boolean isNull(String key) {
- return JSONObject.NULL.equals(this.opt(key));
- }
-
- /**
- * Get an enumeration of the keys of the JSONObject. Modifying this key Set will
- * also modify the JSONObject. Use with caution.
- *
- * @see Set#iterator()
- *
- * @return An iterator of the keys.
- */
- public Iterator<String> keys() {
- return this.keySet().iterator();
- }
-
- /**
- * Get a set of keys of the JSONObject. Modifying this key Set will also modify
- * the JSONObject. Use with caution.
- *
- * @see Map#keySet()
- *
- * @return A keySet.
- */
- public Set<String> keySet() {
- return this.map.keySet();
- }
-
- /**
- * Get a set of entries of the JSONObject. These are raw values and may not
- * match what is returned by the JSONObject get* and opt* functions. Modifying
- * the returned EntrySet or the Entry objects contained therein will modify the
- * backing JSONObject. This does not return a clone or a read-only view.
- *
- * Use with caution.
- *
- * @see Map#entrySet()
- *
- * @return An Entry Set
- */
- protected Set<Entry<String, Object>> entrySet() {
- return this.map.entrySet();
- }
-
- /**
- * Get the number of keys stored in the JSONObject.
- *
- * @return The number of keys in the JSONObject.
- */
- public int length() {
- return this.map.size();
- }
-
- /**
- * Check if JSONObject is empty.
- *
- * @return true if JSONObject is empty, otherwise false.
- */
- public boolean isEmpty() {
- return map.isEmpty();
- }
-
- /**
- * Produce a JSONArray containing the names of the elements of this JSONObject.
- *
- * @return A JSONArray containing the key strings, or null if the JSONObject is
- * empty.
- */
- public JSONArray names() {
- if (this.map.isEmpty()) {
- return null;
- }
- return new JSONArray(this.map.keySet());
- }
-
- /**
- * Produce a string from a Number.
- *
- * @param number A Number
- * @return A String.
- * @throws JSONException If n is a non-finite number.
- */
- public static String numberToString(Number number) throws JSONException {
- if (number == null) {
- throw new JSONException("Null pointer");
- }
- testValidity(number);
-
- // Shave off trailing zeros and decimal point, if possible.
-
- String string = number.toString();
- if (string.indexOf('.') > 0 && string.indexOf('e') < 0 && string.indexOf('E') < 0) {
- while (string.endsWith("0")) {
- string = string.substring(0, string.length() - 1);
- }
- if (string.endsWith(".")) {
- string = string.substring(0, string.length() - 1);
- }
- }
- return string;
- }
-
- /**
- * Get an optional value associated with a key.
- *
- * @param key A key string.
- * @return An object which is the value, or null if there is no value.
- */
- public Object opt(String key) {
- return key == null ? null : this.map.get(key);
- }
-
- /**
- * Get the enum value associated with a key.
- *
- * @param clazz The type of enum to retrieve.
- * @param key A key string.
- * @return The enum value associated with the key or null if not found
- */
- public <E extends Enum<E>> E optEnum(Class<E> clazz, String key) {
- return this.optEnum(clazz, key, null);
- }
-
- /**
- * Get the enum value associated with a key.
- *
- * @param clazz The type of enum to retrieve.
- * @param key A key string.
- * @param defaultValue The default in case the value is not found
- * @return The enum value associated with the key or defaultValue if the value
- * is not found or cannot be assigned to <code>clazz</code>
- */
- public <E extends Enum<E>> E optEnum(Class<E> clazz, String key, E defaultValue) {
- try {
- Object val = this.opt(key);
- if (NULL.equals(val)) {
- return defaultValue;
- }
- if (clazz.isAssignableFrom(val.getClass())) {
- // we just checked it!
- @SuppressWarnings("unchecked")
- E myE = (E) val;
- return myE;
- }
- return Enum.valueOf(clazz, val.toString());
- } catch (IllegalArgumentException e) {
- return defaultValue;
- } catch (NullPointerException e) {
- return defaultValue;
- }
- }
-
- /**
- * Get an optional boolean associated with a key. It returns false if there is
- * no such key, or if the value is not Boolean.TRUE or the String "true".
- *
- * @param key A key string.
- * @return The truth.
- */
- public boolean optBoolean(String key) {
- return this.optBoolean(key, false);
- }
-
- /**
- * Get an optional boolean associated with a key. It returns the defaultValue if
- * there is no such key, or if it is not a Boolean or the String "true" or
- * "false" (case insensitive).
- *
- * @param key A key string.
- * @param defaultValue The default.
- * @return The truth.
- */
- public boolean optBoolean(String key, boolean defaultValue) {
- Object val = this.opt(key);
- if (NULL.equals(val)) {
- return defaultValue;
- }
- if (val instanceof Boolean) {
- return ((Boolean) val).booleanValue();
- }
- try {
- // we'll use the get anyway because it does string conversion.
- return this.getBoolean(key);
- } catch (Exception e) {
- return defaultValue;
- }
- }
-
- /**
- * Get an optional BigDecimal associated with a key, or the defaultValue if
- * there is no such key or if its value is not a number. If the value is a
- * string, an attempt will be made to evaluate it as a number.
- *
- * @param key A key string.
- * @param defaultValue The default.
- * @return An object which is the value.
- */
- public BigDecimal optBigDecimal(String key, BigDecimal defaultValue) {
- Object val = this.opt(key);
- if (NULL.equals(val)) {
- return defaultValue;
- }
- if (val instanceof BigDecimal) {
- return (BigDecimal) val;
- }
- if (val instanceof BigInteger) {
- return new BigDecimal((BigInteger) val);
- }
- if (val instanceof Double || val instanceof Float) {
- return new BigDecimal(((Number) val).doubleValue());
- }
- if (val instanceof Long || val instanceof Integer || val instanceof Short || val instanceof Byte) {
- return new BigDecimal(((Number) val).longValue());
- }
- // don't check if it's a string in case of unchecked Number subclasses
- try {
- return new BigDecimal(val.toString());
- } catch (Exception e) {
- return defaultValue;
- }
- }
-
- /**
- * Get an optional BigInteger associated with a key, or the defaultValue if
- * there is no such key or if its value is not a number. If the value is a
- * string, an attempt will be made to evaluate it as a number.
- *
- * @param key A key string.
- * @param defaultValue The default.
- * @return An object which is the value.
- */
- public BigInteger optBigInteger(String key, BigInteger defaultValue) {
- Object val = this.opt(key);
- if (NULL.equals(val)) {
- return defaultValue;
- }
- if (val instanceof BigInteger) {
- return (BigInteger) val;
- }
- if (val instanceof BigDecimal) {
- return ((BigDecimal) val).toBigInteger();
- }
- if (val instanceof Double || val instanceof Float) {
- return new BigDecimal(((Number) val).doubleValue()).toBigInteger();
- }
- if (val instanceof Long || val instanceof Integer || val instanceof Short || val instanceof Byte) {
- return BigInteger.valueOf(((Number) val).longValue());
- }
- // don't check if it's a string in case of unchecked Number subclasses
- try {
- // the other opt functions handle implicit conversions, i.e.
- // jo.put("double",1.1d);
- // jo.optInt("double"); -- will return 1, not an error
- // this conversion to BigDecimal then to BigInteger is to maintain
- // that type cast support that may truncate the decimal.
- final String valStr = val.toString();
- if (isDecimalNotation(valStr)) {
- return new BigDecimal(valStr).toBigInteger();
- }
- return new BigInteger(valStr);
- } catch (Exception e) {
- return defaultValue;
- }
- }
-
- /**
- * Get an optional double associated with a key, or NaN if there is no such key
- * or if its value is not a number. If the value is a string, an attempt will be
- * made to evaluate it as a number.
- *
- * @param key A string which is the key.
- * @return An object which is the value.
- */
- public double optDouble(String key) {
- return this.optDouble(key, Double.NaN);
- }
-
- /**
- * Get an optional double associated with a key, or the defaultValue if there is
- * no such key or if its value is not a number. If the value is a string, an
- * attempt will be made to evaluate it as a number.
- *
- * @param key A key string.
- * @param defaultValue The default.
- * @return An object which is the value.
- */
- public double optDouble(String key, double defaultValue) {
- Object val = this.opt(key);
- if (NULL.equals(val)) {
- return defaultValue;
- }
- if (val instanceof Number) {
- return ((Number) val).doubleValue();
- }
- if (val instanceof String) {
- try {
- return Double.parseDouble((String) val);
- } catch (Exception e) {
- return defaultValue;
- }
- }
- return defaultValue;
- }
-
- /**
- * Get the optional double value associated with an index. NaN is returned if
- * there is no value for the index, or if the value is not a number and cannot
- * be converted to a number.
- *
- * @param key A key string.
- * @return The value.
- */
- public float optFloat(String key) {
- return this.optFloat(key, Float.NaN);
- }
-
- /**
- * Get the optional double value associated with an index. The defaultValue is
- * returned if there is no value for the index, or if the value is not a number
- * and cannot be converted to a number.
- *
- * @param key A key string.
- * @param defaultValue The default value.
- * @return The value.
- */
- public float optFloat(String key, float defaultValue) {
- Object val = this.opt(key);
- if (JSONObject.NULL.equals(val)) {
- return defaultValue;
- }
- if (val instanceof Number) {
- return ((Number) val).floatValue();
- }
- if (val instanceof String) {
- try {
- return Float.parseFloat((String) val);
- } catch (Exception e) {
- return defaultValue;
- }
- }
- return defaultValue;
- }
-
- /**
- * Get an optional int value associated with a key, or zero if there is no such
- * key or if the value is not a number. If the value is a string, an attempt
- * will be made to evaluate it as a number.
- *
- * @param key A key string.
- * @return An object which is the value.
- */
- public int optInt(String key) {
- return this.optInt(key, 0);
- }
-
- /**
- * Get an optional int value associated with a key, or the default if there is
- * no such key or if the value is not a number. If the value is a string, an
- * attempt will be made to evaluate it as a number.
- *
- * @param key A key string.
- * @param defaultValue The default.
- * @return An object which is the value.
- */
- public int optInt(String key, int defaultValue) {
- Object val = this.opt(key);
- if (NULL.equals(val)) {
- return defaultValue;
- }
- if (val instanceof Number) {
- return ((Number) val).intValue();
- }
-
- if (val instanceof String) {
- try {
- return new BigDecimal((String) val).intValue();
- } catch (Exception e) {
- return defaultValue;
- }
- }
- return defaultValue;
- }
-
- /**
- * Get an optional JSONArray associated with a key. It returns null if there is
- * no such key, or if its value is not a JSONArray.
- *
- * @param key A key string.
- * @return A JSONArray which is the value.
- */
- public JSONArray optJSONArray(String key) {
- Object o = this.opt(key);
- return o instanceof JSONArray ? (JSONArray) o : null;
- }
-
- /**
- * Get an optional JSONObject associated with a key. It returns null if there is
- * no such key, or if its value is not a JSONObject.
- *
- * @param key A key string.
- * @return A JSONObject which is the value.
- */
- public JSONObject optJSONObject(String key) {
- Object object = this.opt(key);
- return object instanceof JSONObject ? (JSONObject) object : null;
- }
-
- /**
- * Get an optional long value associated with a key, or zero if there is no such
- * key or if the value is not a number. If the value is a string, an attempt
- * will be made to evaluate it as a number.
- *
- * @param key A key string.
- * @return An object which is the value.
- */
- public long optLong(String key) {
- return this.optLong(key, 0);
- }
-
- /**
- * Get an optional long value associated with a key, or the default if there is
- * no such key or if the value is not a number. If the value is a string, an
- * attempt will be made to evaluate it as a number.
- *
- * @param key A key string.
- * @param defaultValue The default.
- * @return An object which is the value.
- */
- public long optLong(String key, long defaultValue) {
- Object val = this.opt(key);
- if (NULL.equals(val)) {
- return defaultValue;
- }
- if (val instanceof Number) {
- return ((Number) val).longValue();
- }
-
- if (val instanceof String) {
- try {
- return new BigDecimal((String) val).longValue();
- } catch (Exception e) {
- return defaultValue;
- }
- }
- return defaultValue;
- }
-
- /**
- * Get an optional {@link Number} value associated with a key, or
- * <code>null</code> if there is no such key or if the value is not a number. If
- * the value is a string, an attempt will be made to evaluate it as a number
- * ({@link BigDecimal}). This method would be used in cases where type coercion
- * of the number value is unwanted.
- *
- * @param key A key string.
- * @return An object which is the value.
- */
- public Number optNumber(String key) {
- return this.optNumber(key, null);
- }
-
- /**
- * Get an optional {@link Number} value associated with a key, or the default if
- * there is no such key or if the value is not a number. If the value is a
- * string, an attempt will be made to evaluate it as a number. This method would
- * be used in cases where type coercion of the number value is unwanted.
- *
- * @param key A key string.
- * @param defaultValue The default.
- * @return An object which is the value.
- */
- public Number optNumber(String key, Number defaultValue) {
- Object val = this.opt(key);
- if (NULL.equals(val)) {
- return defaultValue;
- }
- if (val instanceof Number) {
- return (Number) val;
- }
-
- if (val instanceof String) {
- try {
- return stringToNumber((String) val);
- } catch (Exception e) {
- return defaultValue;
- }
- }
- return defaultValue;
- }
-
- /**
- * Get an optional string associated with a key. It returns an empty string if
- * there is no such key. If the value is not a string and is not null, then it
- * is converted to a string.
- *
- * @param key A key string.
- * @return A string which is the value.
- */
- public String optString(String key) {
- return this.optString(key, "");
- }
-
- /**
- * Get an optional string associated with a key. It returns the defaultValue if
- * there is no such key.
- *
- * @param key A key string.
- * @param defaultValue The default.
- * @return A string which is the value.
- */
- public String optString(String key, String defaultValue) {
- Object object = this.opt(key);
- return NULL.equals(object) ? defaultValue : object.toString();
- }
-
- /**
- * Populates the internal map of the JSONObject with the bean properties. The
- * bean can not be recursive.
- *
- * @see JSONObject#JSONObject(Object)
- *
- * @param bean the bean
- */
- private void populateMap(Object bean) {
- Class<?> klass = bean.getClass();
-
- // If klass is a System class then set includeSuperClass to false.
-
- boolean includeSuperClass = klass.getClassLoader() != null;
-
- Method[] methods = includeSuperClass ? klass.getMethods() : klass.getDeclaredMethods();
- for (final Method method : methods) {
- final int modifiers = method.getModifiers();
- if (Modifier.isPublic(modifiers) && !Modifier.isStatic(modifiers) && method.getParameterTypes().length == 0
- && !method.isBridge() && method.getReturnType() != Void.TYPE
- && isValidMethodName(method.getName())) {
- final String key = getKeyNameFromMethod(method);
- if (key != null && !key.isEmpty()) {
- try {
- final Object result = method.invoke(bean);
- if (result != null) {
- this.map.put(key, wrap(result));
- // we don't use the result anywhere outside of wrap
- // if it's a resource we should be sure to close it
- // after calling toString
- if (result instanceof Closeable) {
- try {
- ((Closeable) result).close();
- } catch (IOException ignore) {
- }
- }
- }
- } catch (IllegalAccessException ignore) {
- } catch (IllegalArgumentException ignore) {
- } catch (InvocationTargetException ignore) {
- }
- }
- }
- }
- }
-
- private boolean isValidMethodName(String name) {
- return !"getClass".equals(name) && !"getDeclaringClass".equals(name);
- }
-
- private String getKeyNameFromMethod(Method method) {
- final int ignoreDepth = -1;// getAnnotationDepth(method, JSONPropertyIgnore.class);
-// if (ignoreDepth > 0) {
-// final int forcedNameDepth = getAnnotationDepth(method, JSONPropertyName.class);
-// if (forcedNameDepth < 0 || ignoreDepth <= forcedNameDepth) {
-// // the hierarchy asked to ignore, and the nearest name override
-// // was higher or non-existent
-// return null;
-// }
-// }
-// JSONPropertyName annotation = getAnnotation(method, JSONPropertyName.class);
-// if (annotation != null && annotation.value() != null && !annotation.value().isEmpty()) {
-// return annotation.value();
-// }
- String key;
- final String name = method.getName();
- if (name.startsWith("get") && name.length() > 3) {
- key = name.substring(3);
- } else if (name.startsWith("is") && name.length() > 2) {
- key = name.substring(2);
- } else {
- return null;
- }
- // if the first letter in the key is not uppercase, then skip.
- // This is to maintain backwards compatibility before PR406
- // (https://github.com/stleary/JSON-java/pull/406/)
- if (Character.isLowerCase(key.charAt(0))) {
- return null;
- }
- if (key.length() == 1) {
- key = key.toLowerCase(Locale.ROOT);
- } else if (!Character.isUpperCase(key.charAt(1))) {
- key = key.substring(0, 1).toLowerCase(Locale.ROOT) + key.substring(1);
- }
- return (/** @j2sNative 1 ? key.split("$")[0] : */
- key);
- }
-
-// /**
-// * Searches the class hierarchy to see if the method or it's super
-// * implementations and interfaces has the annotation.
-// *
-// * @param <A>
-// * type of the annotation
-// *
-// * @param m
-// * method to check
-// * @param annotationClass
-// * annotation to look for
-// * @return the {@link Annotation} if the annotation exists on the current method
-// * or one of it's super class definitions
-// */
-// private static <A extends Annotation> A getAnnotation(final Method m, final Class<A> annotationClass) {
-// return null;
-// // if we have invalid data the result is null
-// if (true || m == null || annotationClass == null) {
-// return null;
-// }
-//
-// if (m.isAnnotationPresent(annotationClass)) {
-// return m.getAnnotation(annotationClass);
-// }
-//
-// // if we've already reached the Object class, return null;
-// Class<?> c = m.getDeclaringClass();
-// if (c.getSuperclass() == null) {
-// return null;
-// }
-//
-// // check directly implemented interfaces for the method being checked
-// for (Class<?> i : c.getInterfaces()) {
-// try {
-// Method im = i.getMethod(m.getName(), m.getParameterTypes());
-// return getAnnotation(im, annotationClass);
-// } catch (final SecurityException ex) {
-// continue;
-// } catch (final NoSuchMethodException ex) {
-// continue;
-// }
-// }
-//
-// try {
-// return getAnnotation(
-// c.getSuperclass().getMethod(m.getName(), m.getParameterTypes()),
-// annotationClass);
-// } catch (final SecurityException ex) {
-// return null;
-// } catch (final NoSuchMethodException ex) {
-// return null;
-// }
-// }
-//
-// /**
-// * Searches the class hierarchy to see if the method or it's super
-// * implementations and interfaces has the annotation. Returns the depth of the
-// * annotation in the hierarchy.
-// *
-// * @param <A>
-// * type of the annotation
-// *
-// * @param m
-// * method to check
-// * @param annotationClass
-// * annotation to look for
-// * @return Depth of the annotation or -1 if the annotation is not on the method.
-// */
-// private static int getAnnotationDepth(final Method m, final Class<? extends Annotation> annotationClass) {
-// // if we have invalid data the result is -1
-// if (m == null || annotationClass == null) {
-// return -1;
-// }
-// if (m.isAnnotationPresent(annotationClass)) {
-// return 1;
-// }
-//
-// // if we've already reached the Object class, return -1;
-// Class<?> c = m.getDeclaringClass();
-// if (c.getSuperclass() == null) {
-// return -1;
-// }
-//
-// // check directly implemented interfaces for the method being checked
-// for (Class<?> i : c.getInterfaces()) {
-// try {
-// Method im = i.getMethod(m.getName(), m.getParameterTypes());
-// int d = getAnnotationDepth(im, annotationClass);
-// if (d > 0) {
-// // since the annotation was on the interface, add 1
-// return d + 1;
-// }
-// } catch (final SecurityException ex) {
-// continue;
-// } catch (final NoSuchMethodException ex) {
-// continue;
-// }
-// }
-//
-// try {
-// int d = getAnnotationDepth(
-// c.getSuperclass().getMethod(m.getName(), m.getParameterTypes()),
-// annotationClass);
-// if (d > 0) {
-// // since the annotation was on the superclass, add 1
-// return d + 1;
-// }
-// return -1;
-// } catch (final SecurityException ex) {
-// return -1;
-// } catch (final NoSuchMethodException ex) {
-// return -1;
-// }
-// }
-
- /**
- * Put a key/boolean pair in the JSONObject.
- *
- * @param key A key string.
- * @param value A boolean which is the value.
- * @return this.
- * @throws JSONException If the value is non-finite number.
- * @throws NullPointerException If the key is <code>null</code>.
- */
- public JSONObject put(String key, boolean value) throws JSONException {
- return this.put(key, value ? Boolean.TRUE : Boolean.FALSE);
- }
-
- /**
- * Put a key/value pair in the JSONObject, where the value will be a JSONArray
- * which is produced from a Collection.
- *
- * @param key A key string.
- * @param value A Collection value.
- * @return this.
- * @throws JSONException If the value is non-finite number.
- * @throws NullPointerException If the key is <code>null</code>.
- */
- public JSONObject put(String key, Collection<?> value) throws JSONException {
- return this.put(key, new JSONArray(value));
- }
-
- /**
- * Put a key/double pair in the JSONObject.
- *
- * @param key A key string.
- * @param value A double which is the value.
- * @return this.
- * @throws JSONException If the value is non-finite number.
- * @throws NullPointerException If the key is <code>null</code>.
- */
- public JSONObject put(String key, double value) throws JSONException {
- return this.put(key, Double.valueOf(value));
- }
-
- /**
- * Put a key/float pair in the JSONObject.
- *
- * @param key A key string.
- * @param value A float which is the value.
- * @return this.
- * @throws JSONException If the value is non-finite number.
- * @throws NullPointerException If the key is <code>null</code>.
- */
- public JSONObject put(String key, float value) throws JSONException {
- return this.put(key, Float.valueOf(value));
- }
-
- /**
- * Put a key/int pair in the JSONObject.
- *
- * @param key A key string.
- * @param value An int which is the value.
- * @return this.
- * @throws JSONException If the value is non-finite number.
- * @throws NullPointerException If the key is <code>null</code>.
- */
- public JSONObject put(String key, int value) throws JSONException {
- return this.put(key, Integer.valueOf(value));
- }
-
- /**
- * Put a key/long pair in the JSONObject.
- *
- * @param key A key string.
- * @param value A long which is the value.
- * @return this.
- * @throws JSONException If the value is non-finite number.
- * @throws NullPointerException If the key is <code>null</code>.
- */
- public JSONObject put(String key, long value) throws JSONException {
- return this.put(key, Long.valueOf(value));
- }
-
- /**
- * Put a key/value pair in the JSONObject, where the value will be a JSONObject
- * which is produced from a Map.
- *
- * @param key A key string.
- * @param value A Map value.
- * @return this.
- * @throws JSONException If the value is non-finite number.
- * @throws NullPointerException If the key is <code>null</code>.
- */
- public JSONObject put(String key, Map<?, ?> value) throws JSONException {
- return this.put(key, new JSONObject(value));
- }
-
- /**
- * Put a key/value pair in the JSONObject. If the value is <code>null</code>,
- * then the key will be removed from the JSONObject if it is present.
- *
- * @param key A key string.
- * @param value An object which is the value. It should be of one of these
- * types: Boolean, Double, Integer, JSONArray, JSONObject, Long,
- * String, or the JSONObject.NULL object.
- * @return this.
- * @throws JSONException If the value is non-finite number.
- * @throws NullPointerException If the key is <code>null</code>.
- */
- public JSONObject put(String key, Object value) throws JSONException {
- if (key == null) {
- throw new NullPointerException("Null key.");
- }
- if (value != null) {
- testValidity(value);
- this.map.put(key, value);
- } else {
- this.remove(key);
- }
- return this;
- }
-
- /**
- * Put a key/value pair in the JSONObject, but only if the key and the value are
- * both non-null, and only if there is not already a member with that name.
- *
- * @param key string
- * @param value object
- * @return this.
- * @throws JSONException if the key is a duplicate
- */
- public JSONObject putOnce(String key, Object value) throws JSONException {
- if (key != null && value != null) {
- if (this.opt(key) != null) {
- throw new JSONException("Duplicate key \"" + key + "\"");
- }
- return this.put(key, value);
- }
- return this;
- }
-
- /**
- * Put a key/value pair in the JSONObject, but only if the key and the value are
- * both non-null.
- *
- * @param key A key string.
- * @param value An object which is the value. It should be of one of these
- * types: Boolean, Double, Integer, JSONArray, JSONObject, Long,
- * String, or the JSONObject.NULL object.
- * @return this.
- * @throws JSONException If the value is a non-finite number.
- */
- public JSONObject putOpt(String key, Object value) throws JSONException {
- if (key != null && value != null) {
- return this.put(key, value);
- }
- return this;
- }
-
- /**
- * Creates a JSONPointer using an initialization string and tries to match it to
- * an item within this JSONObject. For example, given a JSONObject initialized
- * with this document:
- *
- * <pre>
- * {
- * "a":{"b":"c"}
- * }
- * </pre>
- *
- * and this JSONPointer string:
- *
- * <pre>
- * "/a/b"
- * </pre>
- *
- * Then this method will return the String "c". A JSONPointerException may be
- * thrown from code called by this method.
- *
- * @param jsonPointer string that can be used to create a JSONPointer
- * @return the item matched by the JSONPointer, otherwise null
- */
- public Object query(String jsonPointer) {
- return query(new JSONPointer(jsonPointer));
- }
-
- /**
- * Uses a user initialized JSONPointer and tries to match it to an item within
- * this JSONObject. For example, given a JSONObject initialized with this
- * document:
- *
- * <pre>
- * {
- * "a":{"b":"c"}
- * }
- * </pre>
- *
- * and this JSONPointer:
- *
- * <pre>
- * "/a/b"
- * </pre>
- *
- * Then this method will return the String "c". A JSONPointerException may be
- * thrown from code called by this method.
- *
- * @param jsonPointer string that can be used to create a JSONPointer
- * @return the item matched by the JSONPointer, otherwise null
- */
- public Object query(JSONPointer jsonPointer) {
- return jsonPointer.queryFrom(this);
- }
-
- /**
- * Queries and returns a value from this object using {@code jsonPointer}, or
- * returns null if the query fails due to a missing key.
- *
- * @param jsonPointer the string representation of the JSON pointer
- * @return the queried value or {@code null}
- * @throws IllegalArgumentException if {@code jsonPointer} has invalid syntax
- */
- public Object optQuery(String jsonPointer) {
- return optQuery(new JSONPointer(jsonPointer));
- }
-
- /**
- * Queries and returns a value from this object using {@code jsonPointer}, or
- * returns null if the query fails due to a missing key.
- *
- * @param jsonPointer The JSON pointer
- * @return the queried value or {@code null}
- * @throws IllegalArgumentException if {@code jsonPointer} has invalid syntax
- */
- public Object optQuery(JSONPointer jsonPointer) {
- try {
- return jsonPointer.queryFrom(this);
- } catch (JSONPointerException e) {
- return null;
- }
- }
-
- /**
- * Produce a string in double quotes with backslash sequences in all the right
- * places. A backslash will be inserted within </, producing <\/, allowing JSON
- * text to be delivered in HTML. In JSON text, a string cannot contain a control
- * character or an unescaped quote or backslash.
- *
- * @param string A String
- * @return A String correctly formatted for insertion in a JSON text.
- */
- public static String quote(String string) {
- StringWriter sw = new StringWriter();
- synchronized (sw.getBuffer()) {
- try {
- return quote(string, sw).toString();
- } catch (IOException ignored) {
- // will never happen - we are writing to a string writer
- return "";
- }
- }
- }
-
- public static Writer quote(String string, Writer w) throws IOException {
- if (string == null || string.isEmpty()) {
- w.write("\"\"");
- return w;
- }
-
- char b;
- char c = 0;
- String hhhh;
- int i;
- int len = string.length();
-
- w.write('"');
- for (i = 0; i < len; i += 1) {
- b = c;
- c = string.charAt(i);
- switch (c) {
- case '\\':
- case '"':
- w.write('\\');
- w.write(c);
- break;
- case '/':
- if (b == '<') {
- w.write('\\');
- }
- w.write(c);
- break;
- case '\b':
- w.write("\\b");
- break;
- case '\t':
- w.write("\\t");
- break;
- case '\n':
- w.write("\\n");
- break;
- case '\f':
- w.write("\\f");
- break;
- case '\r':
- w.write("\\r");
- break;
- default:
- if (c < ' ' || (c >= '\u0080' && c < '\u00a0') || (c >= '\u2000' && c < '\u2100')) {
- w.write("\\u");
- hhhh = Integer.toHexString(c);
- w.write("0000", 0, 4 - hhhh.length());
- w.write(hhhh);
- } else {
- w.write(c);
- }
- }
- }
- w.write('"');
- return w;
- }
-
- /**
- * Remove a name and its value, if present.
- *
- * @param key The name to be removed.
- * @return The value that was associated with the name, or null if there was no
- * value.
- */
- public Object remove(String key) {
- return this.map.remove(key);
- }
-
- /**
- * Determine if two JSONObjects are similar. They must contain the same set of
- * names which must be associated with similar values.
- *
- * @param other The other JSONObject
- * @return true if they are equal
- */
- public boolean similar(Object other) {
- try {
- if (!(other instanceof JSONObject)) {
- return false;
- }
- if (!this.keySet().equals(((JSONObject) other).keySet())) {
- return false;
- }
- for (final Entry<String, ?> entry : this.entrySet()) {
- String name = entry.getKey();
- Object valueThis = entry.getValue();
- Object valueOther = ((JSONObject) other).get(name);
- if (valueThis == valueOther) {
- continue;
- }
- if (valueThis == null) {
- return false;
- }
- if (valueThis instanceof JSONObject) {
- if (!((JSONObject) valueThis).similar(valueOther)) {
- return false;
- }
- } else if (valueThis instanceof JSONArray) {
- if (!((JSONArray) valueThis).similar(valueOther)) {
- return false;
- }
- } else if (!valueThis.equals(valueOther)) {
- return false;
- }
- }
- return true;
- } catch (Throwable exception) {
- return false;
- }
- }
-
- /**
- * Tests if the value should be tried as a decimal. It makes no test if there
- * are actual digits.
- *
- * @param val value to test
- * @return true if the string is "-0" or if it contains '.', 'e', or 'E', false
- * otherwise.
- */
- protected static boolean isDecimalNotation(final String val) {
- return val.indexOf('.') > -1 || val.indexOf('e') > -1 || val.indexOf('E') > -1 || "-0".equals(val);
- }
-
- /**
- * Converts a string to a number using the narrowest possible type. Possible
- * returns for this function are BigDecimal, Double, BigInteger, Long, and
- * Integer. When a Double is returned, it should always be a valid Double and
- * not NaN or +-infinity.
- *
- * @param val value to convert
- * @return Number representation of the value.
- * @throws NumberFormatException thrown if the value is not a valid number. A
- * public caller should catch this and wrap it in
- * a {@link JSONException} if applicable.
- */
- protected static Number stringToNumber(final String val) throws NumberFormatException {
- char initial = val.charAt(0);
- if ((initial >= '0' && initial <= '9') || initial == '-') {
- // decimal representation
- if (isDecimalNotation(val)) {
- // quick dirty way to see if we need a BigDecimal instead of a Double
- // this only handles some cases of overflow or underflow
- if (val.length() > 14) {
- return new BigDecimal(val);
- }
- final Double d = Double.valueOf(val);
- if (d.isInfinite() || d.isNaN()) {
- // if we can't parse it as a double, go up to BigDecimal
- // this is probably due to underflow like 4.32e-678
- // or overflow like 4.65e5324. The size of the string is small
- // but can't be held in a Double.
- return new BigDecimal(val);
- }
- return d;
- }
- // integer representation.
- // This will narrow any values to the smallest reasonable Object representation
- // (Integer, Long, or BigInteger)
-
- // string version
- // The compare string length method reduces GC,
- // but leads to smaller integers being placed in larger wrappers even though not
- // needed. i.e. 1,000,000,000 -> Long even though it's an Integer
- // 1,000,000,000,000,000,000 -> BigInteger even though it's a Long
- // if(val.length()<=9){
- // return Integer.valueOf(val);
- // }
- // if(val.length()<=18){
- // return Long.valueOf(val);
- // }
- // return new BigInteger(val);
-
- // BigInteger version: We use a similar bitLenth compare as
- // BigInteger#intValueExact uses. Increases GC, but objects hold
- // only what they need. i.e. Less runtime overhead if the value is
- // long lived. Which is the better tradeoff? This is closer to what's
- // in stringToValue.
- BigInteger bi = new BigInteger(val);
- if (bi.bitLength() <= 31) {
- return Integer.valueOf(bi.intValue());
- }
- if (bi.bitLength() <= 63) {
- return Long.valueOf(bi.longValue());
- }
- return bi;
- }
- throw new NumberFormatException("val [" + val + "] is not a valid number.");
- }
-
- /**
- * Try to convert a string into a number, boolean, or null. If the string can't
- * be converted, return the string.
- *
- * @param string A String.
- * @return A simple JSON value.
- */
- // Changes to this method must be copied to the corresponding method in
- // the XML class to keep full support for Android
- public static Object stringToValue(String string) {
- if (string.equals("")) {
- return string;
- }
- if (string.equalsIgnoreCase("true")) {
- return Boolean.TRUE;
- }
- if (string.equalsIgnoreCase("false")) {
- return Boolean.FALSE;
- }
- if (string.equalsIgnoreCase("null")) {
- return JSONObject.NULL;
- }
-
- /*
- * If it might be a number, try converting it. If a number cannot be produced,
- * then the value will just be a string.
- */
-
- char initial = string.charAt(0);
- if ((initial >= '0' && initial <= '9') || initial == '-') {
- try {
- // if we want full Big Number support this block can be replaced with:
- // return stringToNumber(string);
- if (isDecimalNotation(string)) {
- Double d = Double.valueOf(string);
- if (!d.isInfinite() && !d.isNaN()) {
- return d;
- }
- } else {
- Long myLong = Long.valueOf(string);
- if (string.equals(myLong.toString())) {
- if (myLong.longValue() == myLong.intValue()) {
- return Integer.valueOf(myLong.intValue());
- }
- return myLong;
- }
- }
- } catch (Exception ignore) {
- }
- }
- return string;
- }
-
- /**
- * Throw an exception if the object is a NaN or infinite number.
- *
- * @param o The object to test.
- * @throws JSONException If o is a non-finite number.
- */
- public static void testValidity(Object o) throws JSONException {
- if (o != null) {
- if (o instanceof Double) {
- if (((Double) o).isInfinite() || ((Double) o).isNaN()) {
- throw new JSONException("JSON does not allow non-finite numbers.");
- }
- } else if (o instanceof Float) {
- if (((Float) o).isInfinite() || ((Float) o).isNaN()) {
- throw new JSONException("JSON does not allow non-finite numbers.");
- }
- }
- }
- }
-
- /**
- * Produce a JSONArray containing the values of the members of this JSONObject.
- *
- * @param names A JSONArray containing a list of key strings. This determines
- * the sequence of the values in the result.
- * @return A JSONArray of values.
- * @throws JSONException If any of the values are non-finite numbers.
- */
- public JSONArray toJSONArray(JSONArray names) throws JSONException {
- if (names == null || names.isEmpty()) {
- return null;
- }
- JSONArray ja = new JSONArray();
- for (int i = 0; i < names.length(); i += 1) {
- ja.put(this.opt(names.getString(i)));
- }
- return ja;
- }
-
- /**
- * Make a JSON text of this JSONObject. For compactness, no whitespace is added.
- * If this would not result in a syntactically correct JSON text, then null will
- * be returned instead.
- * <p>
- * <b> Warning: This method assumes that the data structure is acyclical. </b>
- *
- * @return a printable, displayable, portable, transmittable representation of
- * the object, beginning with <code>{</code> <small>(left
- * brace)</small> and ending with <code>}</code> <small>(right
- * brace)</small>.
- */
- @Override
- public String toString() {
- try {
- return this.toString(0);
- } catch (Exception e) {
- return null;
- }
- }
-
- /**
- * Make a pretty-printed JSON text of this JSONObject.
- *
- * <p>
- * If <code>indentFactor > 0</code> and the {@link JSONObject} has only one key,
- * then the object will be output on a single line:
- *
- * <pre>
- * {@code {"key": 1}}
- * </pre>
- *
- * <p>
- * If an object has 2 or more keys, then it will be output across multiple
- * lines: <code><pre>{
- * "key1": 1,
- * "key2": "value 2",
- * "key3": 3
- * }</pre></code>
- * <p>
- * <b> Warning: This method assumes that the data structure is acyclical. </b>
- *
- * @param indentFactor The number of spaces to add to each level of indentation.
- * @return a printable, displayable, portable, transmittable representation of
- * the object, beginning with <code>{</code> <small>(left
- * brace)</small> and ending with <code>}</code> <small>(right
- * brace)</small>.
- * @throws JSONException If the object contains an invalid number.
- */
- public String toString(int indentFactor) throws JSONException {
- StringWriter w = new StringWriter();
- synchronized (w.getBuffer()) {
- return this.write(w, indentFactor, 0).toString();
- }
- }
-
- /**
- * Make a JSON text of an Object value. If the object has an
- * value.toJSONString() method, then that method will be used to produce the
- * JSON text. The method is required to produce a strictly conforming text. If
- * the object does not contain a toJSONString method (which is the most common
- * case), then a text will be produced by other means. If the value is an array
- * or Collection, then a JSONArray will be made from it and its toJSONString
- * method will be called. If the value is a MAP, then a JSONObject will be made
- * from it and its toJSONString method will be called. Otherwise, the value's
- * toString method will be called, and the result will be quoted.
- *
- * <p>
- * Warning: This method assumes that the data structure is acyclical.
- *
- * @param value The value to be serialized.
- * @return a printable, displayable, transmittable representation of the object,
- * beginning with <code>{</code> <small>(left brace)</small> and
- * ending with <code>}</code> <small>(right brace)</small>.
- * @throws JSONException If the value is or contains an invalid number.
- */
- public static String valueToString(Object value) throws JSONException {
- // moves the implementation to JSONWriter as:
- // 1. It makes more sense to be part of the writer class
- // 2. For Android support this method is not available. By implementing it in
- // the Writer
- // Android users can use the writer with the built in Android JSONObject
- // implementation.
- return JSONWriter.valueToString(value);
- }
-
- /**
- * Wrap an object, if necessary. If the object is <code>null</code>, return the
- * NULL object. If it is an array or collection, wrap it in a JSONArray. If it
- * is a map, wrap it in a JSONObject. If it is a standard property (Double,
- * String, et al) then it is already wrapped. Otherwise, if it comes from one of
- * the java packages, turn it into a string. And if it doesn't, try to wrap it
- * in a JSONObject. If the wrapping fails, then null is returned.
- *
- * @param object The object to wrap
- * @return The wrapped value
- */
- public static Object wrap(Object object) {
- try {
- if (object == null) {
- return NULL;
- }
- if (object instanceof JSONObject || object instanceof JSONArray || NULL.equals(object)
- || object instanceof JSONString || object instanceof Byte || object instanceof Character
- || object instanceof Short || object instanceof Integer || object instanceof Long
- || object instanceof Boolean || object instanceof Float || object instanceof Double
- || object instanceof String || object instanceof BigInteger || object instanceof BigDecimal
- || object instanceof Enum) {
- return object;
- }
-
- if (object instanceof Collection) {
- Collection<?> coll = (Collection<?>) object;
- return new JSONArray(coll);
- }
- if (object.getClass().isArray()) {
- return new JSONArray(object);
- }
- if (object instanceof Map) {
- Map<?, ?> map = (Map<?, ?>) object;
- return new JSONObject(map);
- }
- Package objectPackage = object.getClass().getPackage();
- String objectPackageName = objectPackage != null ? objectPackage.getName() : "";
- if (objectPackageName.startsWith("java.") || objectPackageName.startsWith("javax.")
- || object.getClass().getClassLoader() == null) {
- return object.toString();
- }
- return new JSONObject(object);
- } catch (Exception exception) {
- return null;
- }
- }
-
- /**
- * Write the contents of the JSONObject as JSON text to a writer. For
- * compactness, no whitespace is added.
- * <p>
- * <b> Warning: This method assumes that the data structure is acyclical. </b>
- *
- * @return The writer.
- * @throws JSONException
- */
- public Writer write(Writer writer) throws JSONException {
- return this.write(writer, 0, 0);
- }
-
- static final Writer writeValue(Writer writer, Object value, int indentFactor, int indent)
- throws JSONException, IOException {
- if (value == null || value.equals(null)) {
- writer.write("null");
- } else if (value instanceof JSONString) {
- Object o;
- try {
- o = ((JSONString) value).toJSONString();
- } catch (Exception e) {
- throw new JSONException(e);
- }
- writer.write(o != null ? o.toString() : quote(value.toString()));
- } else if (value instanceof Number) {
- // not all Numbers may match actual JSON Numbers. i.e. fractions or Imaginary
- final String numberAsString = numberToString((Number) value);
- try {
- // Use the BigDecimal constructor for its parser to validate the format.
- @SuppressWarnings("unused")
- BigDecimal testNum = new BigDecimal(numberAsString);
- // Close enough to a JSON number that we will use it unquoted
- writer.write(numberAsString);
- } catch (NumberFormatException ex) {
- // The Number value is not a valid JSON number.
- // Instead we will quote it as a string
- quote(numberAsString, writer);
- }
- } else if (value instanceof Boolean) {
- writer.write(value.toString());
- } else if (value instanceof Enum<?>) {
- writer.write(quote(((Enum<?>) value).name()));
- } else if (value instanceof JSONObject) {
- ((JSONObject) value).write(writer, indentFactor, indent);
- } else if (value instanceof JSONArray) {
- ((JSONArray) value).write(writer, indentFactor, indent);
- } else if (value instanceof Map) {
- Map<?, ?> map = (Map<?, ?>) value;
- new JSONObject(map).write(writer, indentFactor, indent);
- } else if (value instanceof Collection) {
- Collection<?> coll = (Collection<?>) value;
- new JSONArray(coll).write(writer, indentFactor, indent);
- } else if (value.getClass().isArray()) {
- new JSONArray(value).write(writer, indentFactor, indent);
- } else {
- quote(value.toString(), writer);
- }
- return writer;
- }
-
- static final void indent(Writer writer, int indent) throws IOException {
- for (int i = 0; i < indent; i += 1) {
- writer.write(' ');
- }
- }
-
- /**
- * Write the contents of the JSONObject as JSON text to a writer.
- *
- * <p>
- * If <code>indentFactor > 0</code> and the {@link JSONObject} has only one key,
- * then the object will be output on a single line:
- *
- * <pre>
- * {@code {"key": 1}}
- * </pre>
- *
- * <p>
- * If an object has 2 or more keys, then it will be output across multiple
- * lines: <code><pre>{
- * "key1": 1,
- * "key2": "value 2",
- * "key3": 3
- * }</pre></code>
- * <p>
- * <b> Warning: This method assumes that the data structure is acyclical. </b>
- *
- * @param writer Writes the serialized JSON
- * @param indentFactor The number of spaces to add to each level of indentation.
- * @param indent The indentation of the top level.
- * @return The writer.
- * @throws JSONException
- */
- public Writer write(Writer writer, int indentFactor, int indent) throws JSONException {
- try {
- boolean commanate = false;
- final int length = this.length();
- writer.write('{');
-
- if (length == 1) {
- final Entry<String, ?> entry = this.entrySet().iterator().next();
- final String key = entry.getKey();
- writer.write(quote(key));
- writer.write(':');
- if (indentFactor > 0) {
- writer.write(' ');
- }
- try {
- writeValue(writer, entry.getValue(), indentFactor, indent);
- } catch (Exception e) {
- throw new JSONException("Unable to write JSONObject value for key: " + key, e);
- }
- } else if (length != 0) {
- final int newindent = indent + indentFactor;
- for (final Entry<String, ?> entry : this.entrySet()) {
- if (commanate) {
- writer.write(',');
- }
- if (indentFactor > 0) {
- writer.write('\n');
- }
- indent(writer, newindent);
- final String key = entry.getKey();
- writer.write(quote(key));
- writer.write(':');
- if (indentFactor > 0) {
- writer.write(' ');
- }
- try {
- writeValue(writer, entry.getValue(), indentFactor, newindent);
- } catch (Exception e) {
- throw new JSONException("Unable to write JSONObject value for key: " + key, e);
- }
- commanate = true;
- }
- if (indentFactor > 0) {
- writer.write('\n');
- }
- indent(writer, indent);
- }
- writer.write('}');
- return writer;
- } catch (IOException exception) {
- throw new JSONException(exception);
- }
- }
-
- /**
- * Returns a java.util.Map containing all of the entries in this object. If an
- * entry in the object is a JSONArray or JSONObject it will also be converted.
- * <p>
- * Warning: This method assumes that the data structure is acyclical.
- *
- * @return a java.util.Map containing the entries of this object
- */
- public Map<String, Object> toMap() {
- Map<String, Object> results = new HashMap<String, Object>();
- for (Entry<String, Object> entry : this.entrySet()) {
- Object value;
- if (entry.getValue() == null || NULL.equals(entry.getValue())) {
- value = null;
- } else if (entry.getValue() instanceof JSONObject) {
- value = ((JSONObject) entry.getValue()).toMap();
- } else if (entry.getValue() instanceof JSONArray) {
- value = ((JSONArray) entry.getValue()).toList();
- } else {
- value = entry.getValue();
- }
- results.put(entry.getKey(), value);
- }
- return results;
- }
+public class JSONObject
+{
+ /**
+ * JSONObject.NULL is equivalent to the value that JavaScript calls null,
+ * whilst Java's null is equivalent to the value that JavaScript calls
+ * undefined.
+ */
+ private static final class Null
+ {
+
+ /**
+ * There is only intended to be a single instance of the NULL object, so the
+ * clone method returns itself.
+ *
+ * @return NULL.
+ */
+ @Override
+ protected final Object clone()
+ {
+ return this;
+ }
+
+ /**
+ * A Null object is equal to the null value and to itself.
+ *
+ * @param object
+ * An object to test for nullness.
+ * @return true if the object parameter is the JSONObject.NULL object or
+ * null.
+ */
+ @Override
+ public boolean equals(Object object)
+ {
+ return object == null || object == this;
+ }
+
+ /**
+ * A Null object is equal to the null value and to itself.
+ *
+ * @return always returns 0.
+ */
+ @Override
+ public int hashCode()
+ {
+ return 0;
+ }
+
+ /**
+ * Get the "null" string value.
+ *
+ * @return The string "null".
+ */
+ @Override
+ public String toString()
+ {
+ return "null";
+ }
+ }
+
+ /**
+ * The map where the JSONObject's properties are kept.
+ */
+ private final Map<String, Object> map;
+
+ /**
+ * It is sometimes more convenient and less ambiguous to have a
+ * <code>NULL</code> object than to use Java's <code>null</code> value.
+ * <code>JSONObject.NULL.equals(null)</code> returns <code>true</code>.
+ * <code>JSONObject.NULL.toString()</code> returns <code>"null"</code>.
+ */
+ public static final Object NULL = new Null();
+
+ /**
+ * Construct an empty JSONObject.
+ */
+ public JSONObject()
+ {
+ // HashMap is used on purpose to ensure that elements are unordered by
+ // the specification.
+ // JSON tends to be a portable transfer format to allows the container
+ // implementations to rearrange their items for a faster element
+ // retrieval based on associative access.
+ // Therefore, an implementation mustn't rely on the order of the item.
+ this.map = new HashMap<String, Object>();
+ }
+
+ /**
+ * Construct a JSONObject from a subset of another JSONObject. An array of
+ * strings is used to identify the keys that should be copied. Missing keys
+ * are ignored.
+ *
+ * @param jo
+ * A JSONObject.
+ * @param names
+ * An array of strings.
+ */
+ public JSONObject(JSONObject jo, String[] names)
+ {
+ this(names.length);
+ for (int i = 0; i < names.length; i += 1)
+ {
+ try
+ {
+ this.putOnce(names[i], jo.opt(names[i]));
+ } catch (Exception ignore)
+ {
+ }
+ }
+ }
+
+ /**
+ * Construct a JSONObject from a JSONTokener.
+ *
+ * @param x
+ * A JSONTokener object containing the source string.
+ * @throws JSONException
+ * If there is a syntax error in the source string or a duplicated
+ * key.
+ */
+ public JSONObject(JSONTokener x) throws JSONException
+ {
+ this();
+ char c;
+ String key;
+
+ if (x.nextClean() != '{')
+ {
+ throw x.syntaxError("A JSONObject text must begin with '{'");
+ }
+ for (;;)
+ {
+ c = x.nextClean();
+ switch (c)
+ {
+ case 0:
+ throw x.syntaxError("A JSONObject text must end with '}'");
+ case '}':
+ return;
+ default:
+ x.back();
+ key = x.nextValue().toString();
+ }
+
+ // The key is followed by ':'.
+
+ c = x.nextClean();
+ if (c != ':')
+ {
+ throw x.syntaxError("Expected a ':' after a key");
+ }
+
+ // Use syntaxError(..) to include error location
+
+ if (key != null)
+ {
+ // Check if key exists
+ if (this.opt(key) != null)
+ {
+ // key already exists
+ throw x.syntaxError("Duplicate key \"" + key + "\"");
+ }
+ // Only add value if non-null
+ Object value = x.nextValue();
+ if (value != null)
+ {
+ this.put(key, value);
+ }
+ }
+
+ // Pairs are separated by ','.
+
+ switch (x.nextClean())
+ {
+ case ';':
+ case ',':
+ if (x.nextClean() == '}')
+ {
+ return;
+ }
+ x.back();
+ break;
+ case '}':
+ return;
+ default:
+ throw x.syntaxError("Expected a ',' or '}'");
+ }
+ }
+ }
+
+ /**
+ * Construct a JSONObject from a Map.
+ *
+ * @param m
+ * A map object that can be used to initialize the contents of the
+ * JSONObject.
+ * @throws JSONException
+ * If a value in the map is non-finite number.
+ * @throws NullPointerException
+ * If a key in the map is <code>null</code>
+ */
+ public JSONObject(Map<?, ?> m)
+ {
+ if (m == null)
+ {
+ this.map = new HashMap<String, Object>();
+ }
+ else
+ {
+ this.map = new HashMap<String, Object>(m.size());
+ for (final Entry<?, ?> e : m.entrySet())
+ {
+ if (e.getKey() == null)
+ {
+ throw new NullPointerException("Null key.");
+ }
+ final Object value = e.getValue();
+ if (value != null)
+ {
+ this.map.put(String.valueOf(e.getKey()), wrap(value));
+ }
+ }
+ }
+ }
+
+ /**
+ * Construct a JSONObject from an Object using bean getters. It reflects on
+ * all of the public methods of the object. For each of the methods with no
+ * parameters and a name starting with <code>"get"</code> or <code>"is"</code>
+ * followed by an uppercase letter, the method is invoked, and a key and the
+ * value returned from the getter method are put into the new JSONObject.
+ * <p>
+ * The key is formed by removing the <code>"get"</code> or <code>"is"</code>
+ * prefix. If the second remaining character is not upper case, then the first
+ * character is converted to lower case.
+ * <p>
+ * Methods that are <code>static</code>, return <code>void</code>, have
+ * parameters, or are "bridge" methods, are ignored.
+ * <p>
+ * For example, if an object has a method named <code>"getName"</code>, and if
+ * the result of calling <code>object.getName()</code> is
+ * <code>"Larry Fine"</code>, then the JSONObject will contain
+ * <code>"name": "Larry Fine"</code>.
+ * <p>
+ * The {@link JSONPropertyName} annotation can be used on a bean getter to
+ * override key name used in the JSONObject. For example, using the object
+ * above with the <code>getName</code> method, if we annotated it with:
+ *
+ * <pre>
+ * @JSONPropertyName("FullName")
+ * public String getName()
+ * {
+ * return this.name;
+ * }
+ * </pre>
+ *
+ * The resulting JSON object would contain
+ * <code>"FullName": "Larry Fine"</code>
+ * <p>
+ * Similarly, the {@link JSONPropertyName} annotation can be used on non-
+ * <code>get</code> and <code>is</code> methods. We can also override key name
+ * used in the JSONObject as seen below even though the field would normally
+ * be ignored:
+ *
+ * <pre>
+ * @JSONPropertyName("FullName")
+ * public String fullName()
+ * {
+ * return this.name;
+ * }
+ * </pre>
+ *
+ * The resulting JSON object would contain
+ * <code>"FullName": "Larry Fine"</code>
+ * <p>
+ * The {@link JSONPropertyIgnore} annotation can be used to force the bean
+ * property to not be serialized into JSON. If both {@link JSONPropertyIgnore}
+ * and {@link JSONPropertyName} are defined on the same method, a depth
+ * comparison is performed and the one closest to the concrete class being
+ * serialized is used. If both annotations are at the same level, then the
+ * {@link JSONPropertyIgnore} annotation takes precedent and the field is not
+ * serialized. For example, the following declaration would prevent the
+ * <code>getName</code> method from being serialized:
+ *
+ * <pre>
+ * @JSONPropertyName("FullName")
+ * @JSONPropertyIgnore
+ * public String getName()
+ * {
+ * return this.name;
+ * }
+ * </pre>
+ * <p>
+ *
+ * @param bean
+ * An object that has getter methods that should be used to make a
+ * JSONObject.
+ */
+ public JSONObject(Object bean)
+ {
+ this();
+ this.populateMap(bean);
+ }
+
+ /**
+ * Construct a JSONObject from an Object, using reflection to find the public
+ * members. The resulting JSONObject's keys will be the strings from the names
+ * array, and the values will be the field values associated with those keys
+ * in the object. If a key is not found or not visible, then it will not be
+ * copied into the new JSONObject.
+ *
+ * @param object
+ * An object that has fields that should be used to make a
+ * JSONObject.
+ * @param names
+ * An array of strings, the names of the fields to be obtained from
+ * the object.
+ */
+ public JSONObject(Object object, String names[])
+ {
+ this(names.length);
+ Class<?> c = object.getClass();
+ for (int i = 0; i < names.length; i += 1)
+ {
+ String name = names[i];
+ try
+ {
+ this.putOpt(name, c.getField(name).get(object));
+ } catch (Exception ignore)
+ {
+ }
+ }
+ }
+
+ /**
+ * Construct a JSONObject from a source JSON text string. This is the most
+ * commonly used JSONObject constructor.
+ *
+ * @param source
+ * A string beginning with <code>{</code> <small>(left
+ * brace)</small> and ending with <code>}</code> <small>(right
+ * brace)</small>.
+ * @exception JSONException
+ * If there is a syntax error in the source string or a
+ * duplicated key.
+ */
+ public JSONObject(String source) throws JSONException
+ {
+ this(new JSONTokener(source));
+ }
+
+ /**
+ * Construct a JSONObject from a ResourceBundle.
+ *
+ * @param baseName
+ * The ResourceBundle base name.
+ * @param locale
+ * The Locale to load the ResourceBundle for.
+ * @throws JSONException
+ * If any JSONExceptions are detected.
+ */
+ public JSONObject(String baseName, Locale locale) throws JSONException
+ {
+ this();
+ ResourceBundle bundle = ResourceBundle.getBundle(baseName, locale,
+ Thread.currentThread().getContextClassLoader());
+
+ // Iterate through the keys in the bundle.
+
+ Enumeration<String> keys = bundle.getKeys();
+ while (keys.hasMoreElements())
+ {
+ Object key = keys.nextElement();
+ if (key != null)
+ {
+
+ // Go through the path, ensuring that there is a nested JSONObject for
+ // each
+ // segment except the last. Add the value using the last segment's name
+ // into
+ // the deepest nested JSONObject.
+
+ String[] path = ((String) key).split("\\.");
+ int last = path.length - 1;
+ JSONObject target = this;
+ for (int i = 0; i < last; i += 1)
+ {
+ String segment = path[i];
+ JSONObject nextTarget = target.optJSONObject(segment);
+ if (nextTarget == null)
+ {
+ nextTarget = new JSONObject();
+ target.put(segment, nextTarget);
+ }
+ target = nextTarget;
+ }
+ target.put(path[last], bundle.getString((String) key));
+ }
+ }
+ }
+
+ /**
+ * Constructor to specify an initial capacity of the internal map. Useful for
+ * library internal calls where we know, or at least can best guess, how big
+ * this JSONObject will be.
+ *
+ * @param initialCapacity
+ * initial capacity of the internal map.
+ */
+ protected JSONObject(int initialCapacity)
+ {
+ this.map = new HashMap<String, Object>(initialCapacity);
+ }
+
+ /**
+ * Accumulate values under a key. It is similar to the put method except that
+ * if there is already an object stored under the key then a JSONArray is
+ * stored under the key to hold all of the accumulated values. If there is
+ * already a JSONArray, then the new value is appended to it. In contrast, the
+ * put method replaces the previous value.
+ *
+ * If only one value is accumulated that is not a JSONArray, then the result
+ * will be the same as using put. But if multiple values are accumulated, then
+ * the result will be like append.
+ *
+ * @param key
+ * A key string.
+ * @param value
+ * An object to be accumulated under the key.
+ * @return this.
+ * @throws JSONException
+ * If the value is non-finite number.
+ * @throws NullPointerException
+ * If the key is <code>null</code>.
+ */
+ public JSONObject accumulate(String key, Object value)
+ throws JSONException
+ {
+ testValidity(value);
+ Object object = this.opt(key);
+ if (object == null)
+ {
+ this.put(key, value instanceof JSONArray ? new JSONArray().put(value)
+ : value);
+ }
+ else if (object instanceof JSONArray)
+ {
+ ((JSONArray) object).put(value);
+ }
+ else
+ {
+ this.put(key, new JSONArray().put(object).put(value));
+ }
+ return this;
+ }
+
+ /**
+ * Append values to the array under a key. If the key does not exist in the
+ * JSONObject, then the key is put in the JSONObject with its value being a
+ * JSONArray containing the value parameter. If the key was already associated
+ * with a JSONArray, then the value parameter is appended to it.
+ *
+ * @param key
+ * A key string.
+ * @param value
+ * An object to be accumulated under the key.
+ * @return this.
+ * @throws JSONException
+ * If the value is non-finite number or if the current value
+ * associated with the key is not a JSONArray.
+ * @throws NullPointerException
+ * If the key is <code>null</code>.
+ */
+ public JSONObject append(String key, Object value) throws JSONException
+ {
+ testValidity(value);
+ Object object = this.opt(key);
+ if (object == null)
+ {
+ this.put(key, new JSONArray().put(value));
+ }
+ else if (object instanceof JSONArray)
+ {
+ this.put(key, ((JSONArray) object).put(value));
+ }
+ else
+ {
+ throw new JSONException(
+ "JSONObject[" + key + "] is not a JSONArray.");
+ }
+ return this;
+ }
+
+ /**
+ * Produce a string from a double. The string "null" will be returned if the
+ * number is not finite.
+ *
+ * @param d
+ * A double.
+ * @return A String.
+ */
+ public static String doubleToString(double d)
+ {
+ if (Double.isInfinite(d) || Double.isNaN(d))
+ {
+ return "null";
+ }
+
+ // Shave off trailing zeros and decimal point, if possible.
+
+ String string = Double.toString(d);
+ if (string.indexOf('.') > 0 && string.indexOf('e') < 0
+ && string.indexOf('E') < 0)
+ {
+ while (string.endsWith("0"))
+ {
+ string = string.substring(0, string.length() - 1);
+ }
+ if (string.endsWith("."))
+ {
+ string = string.substring(0, string.length() - 1);
+ }
+ }
+ return string;
+ }
+
+ /**
+ * Get the value object associated with a key.
+ *
+ * @param key
+ * A key string.
+ * @return The object associated with the key.
+ * @throws JSONException
+ * if the key is not found.
+ */
+ public Object get(String key) throws JSONException
+ {
+ if (key == null)
+ {
+ throw new JSONException("Null key.");
+ }
+ Object object = this.opt(key);
+ if (object == null)
+ {
+ throw new JSONException("JSONObject[" + quote(key) + "] not found.");
+ }
+ return object;
+ }
+
+ /**
+ * Get the enum value associated with a key.
+ *
+ * @param clazz
+ * The type of enum to retrieve.
+ * @param key
+ * A key string.
+ * @return The enum value associated with the key
+ * @throws JSONException
+ * if the key is not found or if the value cannot be converted to an
+ * enum.
+ */
+ public <E extends Enum<E>> E getEnum(Class<E> clazz, String key)
+ throws JSONException
+ {
+ E val = optEnum(clazz, key);
+ if (val == null)
+ {
+ // JSONException should really take a throwable argument.
+ // If it did, I would re-implement this with the Enum.valueOf
+ // method and place any thrown exception in the JSONException
+ throw new JSONException(
+ "JSONObject[" + quote(key) + "] is not an enum of type "
+ + quote(clazz.getSimpleName()) + ".");
+ }
+ return val;
+ }
+
+ /**
+ * Get the boolean value associated with a key.
+ *
+ * @param key
+ * A key string.
+ * @return The truth.
+ * @throws JSONException
+ * if the value is not a Boolean or the String "true" or "false".
+ */
+ public boolean getBoolean(String key) throws JSONException
+ {
+ Object object = this.get(key);
+ if (object.equals(Boolean.FALSE) || (object instanceof String
+ && ((String) object).equalsIgnoreCase("false")))
+ {
+ return false;
+ }
+ else if (object.equals(Boolean.TRUE) || (object instanceof String
+ && ((String) object).equalsIgnoreCase("true")))
+ {
+ return true;
+ }
+ throw new JSONException(
+ "JSONObject[" + quote(key) + "] is not a Boolean.");
+ }
+
+ /**
+ * Get the BigInteger value associated with a key.
+ *
+ * @param key
+ * A key string.
+ * @return The numeric value.
+ * @throws JSONException
+ * if the key is not found or if the value cannot be converted to
+ * BigInteger.
+ */
+ public BigInteger getBigInteger(String key) throws JSONException
+ {
+ Object object = this.get(key);
+ try
+ {
+ return new BigInteger(object.toString());
+ } catch (Exception e)
+ {
+ throw new JSONException("JSONObject[" + quote(key)
+ + "] could not be converted to BigInteger.", e);
+ }
+ }
+
+ /**
+ * Get the BigDecimal value associated with a key.
+ *
+ * @param key
+ * A key string.
+ * @return The numeric value.
+ * @throws JSONException
+ * if the key is not found or if the value cannot be converted to
+ * BigDecimal.
+ */
+ public BigDecimal getBigDecimal(String key) throws JSONException
+ {
+ Object object = this.get(key);
+ if (object instanceof BigDecimal)
+ {
+ return (BigDecimal) object;
+ }
+ try
+ {
+ return new BigDecimal(object.toString());
+ } catch (Exception e)
+ {
+ throw new JSONException("JSONObject[" + quote(key)
+ + "] could not be converted to BigDecimal.", e);
+ }
+ }
+
+ /**
+ * Get the double value associated with a key.
+ *
+ * @param key
+ * A key string.
+ * @return The numeric value.
+ * @throws JSONException
+ * if the key is not found or if the value is not a Number object
+ * and cannot be converted to a number.
+ */
+ public double getDouble(String key) throws JSONException
+ {
+ Object object = this.get(key);
+ try
+ {
+ return object instanceof Number ? ((Number) object).doubleValue()
+ : Double.parseDouble(object.toString());
+ } catch (Exception e)
+ {
+ throw new JSONException(
+ "JSONObject[" + quote(key) + "] is not a number.", e);
+ }
+ }
+
+ /**
+ * Get the float value associated with a key.
+ *
+ * @param key
+ * A key string.
+ * @return The numeric value.
+ * @throws JSONException
+ * if the key is not found or if the value is not a Number object
+ * and cannot be converted to a number.
+ */
+ public float getFloat(String key) throws JSONException
+ {
+ Object object = this.get(key);
+ try
+ {
+ return object instanceof Number ? ((Number) object).floatValue()
+ : Float.parseFloat(object.toString());
+ } catch (Exception e)
+ {
+ throw new JSONException(
+ "JSONObject[" + quote(key) + "] is not a number.", e);
+ }
+ }
+
+ /**
+ * Get the Number value associated with a key.
+ *
+ * @param key
+ * A key string.
+ * @return The numeric value.
+ * @throws JSONException
+ * if the key is not found or if the value is not a Number object
+ * and cannot be converted to a number.
+ */
+ public Number getNumber(String key) throws JSONException
+ {
+ Object object = this.get(key);
+ try
+ {
+ if (object instanceof Number)
+ {
+ return (Number) object;
+ }
+ return stringToNumber(object.toString());
+ } catch (Exception e)
+ {
+ throw new JSONException(
+ "JSONObject[" + quote(key) + "] is not a number.", e);
+ }
+ }
+
+ /**
+ * Get the int value associated with a key.
+ *
+ * @param key
+ * A key string.
+ * @return The integer value.
+ * @throws JSONException
+ * if the key is not found or if the value cannot be converted to an
+ * integer.
+ */
+ public int getInt(String key) throws JSONException
+ {
+ Object object = this.get(key);
+ try
+ {
+ return object instanceof Number ? ((Number) object).intValue()
+ : Integer.parseInt((String) object);
+ } catch (Exception e)
+ {
+ throw new JSONException(
+ "JSONObject[" + quote(key) + "] is not an int.", e);
+ }
+ }
+
+ /**
+ * Get the JSONArray value associated with a key.
+ *
+ * @param key
+ * A key string.
+ * @return A JSONArray which is the value.
+ * @throws JSONException
+ * if the key is not found or if the value is not a JSONArray.
+ */
+ public JSONArray getJSONArray(String key) throws JSONException
+ {
+ Object object = this.get(key);
+ if (object instanceof JSONArray)
+ {
+ return (JSONArray) object;
+ }
+ throw new JSONException(
+ "JSONObject[" + quote(key) + "] is not a JSONArray.");
+ }
+
+ /**
+ * Get the JSONObject value associated with a key.
+ *
+ * @param key
+ * A key string.
+ * @return A JSONObject which is the value.
+ * @throws JSONException
+ * if the key is not found or if the value is not a JSONObject.
+ */
+ public JSONObject getJSONObject(String key) throws JSONException
+ {
+ Object object = this.get(key);
+ if (object instanceof JSONObject)
+ {
+ return (JSONObject) object;
+ }
+ throw new JSONException(
+ "JSONObject[" + quote(key) + "] is not a JSONObject.");
+ }
+
+ /**
+ * Get the long value associated with a key.
+ *
+ * @param key
+ * A key string.
+ * @return The long value.
+ * @throws JSONException
+ * if the key is not found or if the value cannot be converted to a
+ * long.
+ */
+ public long getLong(String key) throws JSONException
+ {
+ Object object = this.get(key);
+ try
+ {
+ return object instanceof Number ? ((Number) object).longValue()
+ : Long.parseLong((String) object);
+ } catch (Exception e)
+ {
+ throw new JSONException(
+ "JSONObject[" + quote(key) + "] is not a long.", e);
+ }
+ }
+
+ /**
+ * Get an array of field names from a JSONObject.
+ *
+ * @return An array of field names, or null if there are no names.
+ */
+ public static String[] getNames(JSONObject jo)
+ {
+ if (jo.isEmpty())
+ {
+ return null;
+ }
+ return jo.keySet().toArray(new String[jo.length()]);
+ }
+
+ /**
+ * Get an array of field names from an Object.
+ *
+ * @return An array of field names, or null if there are no names.
+ */
+ public static String[] getNames(Object object)
+ {
+ if (object == null)
+ {
+ return null;
+ }
+ Class<?> klass = object.getClass();
+ Field[] fields = klass.getFields();
+ int length = fields.length;
+ if (length == 0)
+ {
+ return null;
+ }
+ String[] names = new String[length];
+ for (int i = 0; i < length; i += 1)
+ {
+ names[i] = fields[i].getName();
+ }
+ return names;
+ }
+
+ /**
+ * Get the string associated with a key.
+ *
+ * @param key
+ * A key string.
+ * @return A string which is the value.
+ * @throws JSONException
+ * if there is no string value for the key.
+ */
+ public String getString(String key) throws JSONException
+ {
+ Object object = this.get(key);
+ if (object instanceof String)
+ {
+ return (String) object;
+ }
+ throw new JSONException("JSONObject[" + quote(key) + "] not a string.");
+ }
+
+ /**
+ * Determine if the JSONObject contains a specific key.
+ *
+ * @param key
+ * A key string.
+ * @return true if the key exists in the JSONObject.
+ */
+ public boolean has(String key)
+ {
+ return this.map.containsKey(key);
+ }
+
+ /**
+ * Increment a property of a JSONObject. If there is no such property, create
+ * one with a value of 1. If there is such a property, and if it is an
+ * Integer, Long, Double, or Float, then add one to it.
+ *
+ * @param key
+ * A key string.
+ * @return this.
+ * @throws JSONException
+ * If there is already a property with this name that is not an
+ * Integer, Long, Double, or Float.
+ */
+ public JSONObject increment(String key) throws JSONException
+ {
+ Object value = this.opt(key);
+ if (value == null)
+ {
+ this.put(key, 1);
+ }
+ else if (value instanceof BigInteger)
+ {
+ this.put(key, ((BigInteger) value).add(BigInteger.ONE));
+ }
+ else if (value instanceof BigDecimal)
+ {
+ this.put(key, ((BigDecimal) value).add(BigDecimal.ONE));
+ }
+ else if (value instanceof Integer)
+ {
+ this.put(key, ((Integer) value).intValue() + 1);
+ }
+ else if (value instanceof Long)
+ {
+ this.put(key, ((Long) value).longValue() + 1L);
+ }
+ else if (value instanceof Double)
+ {
+ this.put(key, ((Double) value).doubleValue() + 1.0d);
+ }
+ else if (value instanceof Float)
+ {
+ this.put(key, ((Float) value).floatValue() + 1.0f);
+ }
+ else
+ {
+ throw new JSONException("Unable to increment [" + quote(key) + "].");
+ }
+ return this;
+ }
+
+ /**
+ * Determine if the value associated with the key is <code>null</code> or if
+ * there is no value.
+ *
+ * @param key
+ * A key string.
+ * @return true if there is no value associated with the key or if the value
+ * is the JSONObject.NULL object.
+ */
+ public boolean isNull(String key)
+ {
+ return JSONObject.NULL.equals(this.opt(key));
+ }
+
+ /**
+ * Get an enumeration of the keys of the JSONObject. Modifying this key Set
+ * will also modify the JSONObject. Use with caution.
+ *
+ * @see Set#iterator()
+ *
+ * @return An iterator of the keys.
+ */
+ public Iterator<String> keys()
+ {
+ return this.keySet().iterator();
+ }
+
+ /**
+ * Get a set of keys of the JSONObject. Modifying this key Set will also
+ * modify the JSONObject. Use with caution.
+ *
+ * @see Map#keySet()
+ *
+ * @return A keySet.
+ */
+ public Set<String> keySet()
+ {
+ return this.map.keySet();
+ }
+
+ /**
+ * Get a set of entries of the JSONObject. These are raw values and may not
+ * match what is returned by the JSONObject get* and opt* functions. Modifying
+ * the returned EntrySet or the Entry objects contained therein will modify
+ * the backing JSONObject. This does not return a clone or a read-only view.
+ *
+ * Use with caution.
+ *
+ * @see Map#entrySet()
+ *
+ * @return An Entry Set
+ */
+ protected Set<Entry<String, Object>> entrySet()
+ {
+ return this.map.entrySet();
+ }
+
+ /**
+ * Get the number of keys stored in the JSONObject.
+ *
+ * @return The number of keys in the JSONObject.
+ */
+ public int length()
+ {
+ return this.map.size();
+ }
+
+ /**
+ * Check if JSONObject is empty.
+ *
+ * @return true if JSONObject is empty, otherwise false.
+ */
+ public boolean isEmpty()
+ {
+ return map.isEmpty();
+ }
+
+ /**
+ * Produce a JSONArray containing the names of the elements of this
+ * JSONObject.
+ *
+ * @return A JSONArray containing the key strings, or null if the JSONObject
+ * is empty.
+ */
+ public JSONArray names()
+ {
+ if (this.map.isEmpty())
+ {
+ return null;
+ }
+ return new JSONArray(this.map.keySet());
+ }
+
+ /**
+ * Produce a string from a Number.
+ *
+ * @param number
+ * A Number
+ * @return A String.
+ * @throws JSONException
+ * If n is a non-finite number.
+ */
+ public static String numberToString(Number number) throws JSONException
+ {
+ if (number == null)
+ {
+ throw new JSONException("Null pointer");
+ }
+ testValidity(number);
+
+ // Shave off trailing zeros and decimal point, if possible.
+
+ String string = number.toString();
+ if (string.indexOf('.') > 0 && string.indexOf('e') < 0
+ && string.indexOf('E') < 0)
+ {
+ while (string.endsWith("0"))
+ {
+ string = string.substring(0, string.length() - 1);
+ }
+ if (string.endsWith("."))
+ {
+ string = string.substring(0, string.length() - 1);
+ }
+ }
+ return string;
+ }
+
+ /**
+ * Get an optional value associated with a key.
+ *
+ * @param key
+ * A key string.
+ * @return An object which is the value, or null if there is no value.
+ */
+ public Object opt(String key)
+ {
+ return key == null ? null : this.map.get(key);
+ }
+
+ /**
+ * Get the enum value associated with a key.
+ *
+ * @param clazz
+ * The type of enum to retrieve.
+ * @param key
+ * A key string.
+ * @return The enum value associated with the key or null if not found
+ */
+ public <E extends Enum<E>> E optEnum(Class<E> clazz, String key)
+ {
+ return this.optEnum(clazz, key, null);
+ }
+
+ /**
+ * Get the enum value associated with a key.
+ *
+ * @param clazz
+ * The type of enum to retrieve.
+ * @param key
+ * A key string.
+ * @param defaultValue
+ * The default in case the value is not found
+ * @return The enum value associated with the key or defaultValue if the value
+ * is not found or cannot be assigned to <code>clazz</code>
+ */
+ public <E extends Enum<E>> E optEnum(Class<E> clazz, String key,
+ E defaultValue)
+ {
+ try
+ {
+ Object val = this.opt(key);
+ if (NULL.equals(val))
+ {
+ return defaultValue;
+ }
+ if (clazz.isAssignableFrom(val.getClass()))
+ {
+ // we just checked it!
+ @SuppressWarnings("unchecked")
+ E myE = (E) val;
+ return myE;
+ }
+ return Enum.valueOf(clazz, val.toString());
+ } catch (IllegalArgumentException e)
+ {
+ return defaultValue;
+ } catch (NullPointerException e)
+ {
+ return defaultValue;
+ }
+ }
+
+ /**
+ * Get an optional boolean associated with a key. It returns false if there is
+ * no such key, or if the value is not Boolean.TRUE or the String "true".
+ *
+ * @param key
+ * A key string.
+ * @return The truth.
+ */
+ public boolean optBoolean(String key)
+ {
+ return this.optBoolean(key, false);
+ }
+
+ /**
+ * Get an optional boolean associated with a key. It returns the defaultValue
+ * if there is no such key, or if it is not a Boolean or the String "true" or
+ * "false" (case insensitive).
+ *
+ * @param key
+ * A key string.
+ * @param defaultValue
+ * The default.
+ * @return The truth.
+ */
+ public boolean optBoolean(String key, boolean defaultValue)
+ {
+ Object val = this.opt(key);
+ if (NULL.equals(val))
+ {
+ return defaultValue;
+ }
+ if (val instanceof Boolean)
+ {
+ return ((Boolean) val).booleanValue();
+ }
+ try
+ {
+ // we'll use the get anyway because it does string conversion.
+ return this.getBoolean(key);
+ } catch (Exception e)
+ {
+ return defaultValue;
+ }
+ }
+
+ /**
+ * Get an optional BigDecimal associated with a key, or the defaultValue if
+ * there is no such key or if its value is not a number. If the value is a
+ * string, an attempt will be made to evaluate it as a number.
+ *
+ * @param key
+ * A key string.
+ * @param defaultValue
+ * The default.
+ * @return An object which is the value.
+ */
+ public BigDecimal optBigDecimal(String key, BigDecimal defaultValue)
+ {
+ Object val = this.opt(key);
+ if (NULL.equals(val))
+ {
+ return defaultValue;
+ }
+ if (val instanceof BigDecimal)
+ {
+ return (BigDecimal) val;
+ }
+ if (val instanceof BigInteger)
+ {
+ return new BigDecimal((BigInteger) val);
+ }
+ if (val instanceof Double || val instanceof Float)
+ {
+ return new BigDecimal(((Number) val).doubleValue());
+ }
+ if (val instanceof Long || val instanceof Integer
+ || val instanceof Short || val instanceof Byte)
+ {
+ return new BigDecimal(((Number) val).longValue());
+ }
+ // don't check if it's a string in case of unchecked Number subclasses
+ try
+ {
+ return new BigDecimal(val.toString());
+ } catch (Exception e)
+ {
+ return defaultValue;
+ }
+ }
+
+ /**
+ * Get an optional BigInteger associated with a key, or the defaultValue if
+ * there is no such key or if its value is not a number. If the value is a
+ * string, an attempt will be made to evaluate it as a number.
+ *
+ * @param key
+ * A key string.
+ * @param defaultValue
+ * The default.
+ * @return An object which is the value.
+ */
+ public BigInteger optBigInteger(String key, BigInteger defaultValue)
+ {
+ Object val = this.opt(key);
+ if (NULL.equals(val))
+ {
+ return defaultValue;
+ }
+ if (val instanceof BigInteger)
+ {
+ return (BigInteger) val;
+ }
+ if (val instanceof BigDecimal)
+ {
+ return ((BigDecimal) val).toBigInteger();
+ }
+ if (val instanceof Double || val instanceof Float)
+ {
+ return new BigDecimal(((Number) val).doubleValue()).toBigInteger();
+ }
+ if (val instanceof Long || val instanceof Integer
+ || val instanceof Short || val instanceof Byte)
+ {
+ return BigInteger.valueOf(((Number) val).longValue());
+ }
+ // don't check if it's a string in case of unchecked Number subclasses
+ try
+ {
+ // the other opt functions handle implicit conversions, i.e.
+ // jo.put("double",1.1d);
+ // jo.optInt("double"); -- will return 1, not an error
+ // this conversion to BigDecimal then to BigInteger is to maintain
+ // that type cast support that may truncate the decimal.
+ final String valStr = val.toString();
+ if (isDecimalNotation(valStr))
+ {
+ return new BigDecimal(valStr).toBigInteger();
+ }
+ return new BigInteger(valStr);
+ } catch (Exception e)
+ {
+ return defaultValue;
+ }
+ }
+
+ /**
+ * Get an optional double associated with a key, or NaN if there is no such
+ * key or if its value is not a number. If the value is a string, an attempt
+ * will be made to evaluate it as a number.
+ *
+ * @param key
+ * A string which is the key.
+ * @return An object which is the value.
+ */
+ public double optDouble(String key)
+ {
+ return this.optDouble(key, Double.NaN);
+ }
+
+ /**
+ * Get an optional double associated with a key, or the defaultValue if there
+ * is no such key or if its value is not a number. If the value is a string,
+ * an attempt will be made to evaluate it as a number.
+ *
+ * @param key
+ * A key string.
+ * @param defaultValue
+ * The default.
+ * @return An object which is the value.
+ */
+ public double optDouble(String key, double defaultValue)
+ {
+ Object val = this.opt(key);
+ if (NULL.equals(val))
+ {
+ return defaultValue;
+ }
+ if (val instanceof Number)
+ {
+ return ((Number) val).doubleValue();
+ }
+ if (val instanceof String)
+ {
+ try
+ {
+ return Double.parseDouble((String) val);
+ } catch (Exception e)
+ {
+ return defaultValue;
+ }
+ }
+ return defaultValue;
+ }
+
+ /**
+ * Get the optional double value associated with an index. NaN is returned if
+ * there is no value for the index, or if the value is not a number and cannot
+ * be converted to a number.
+ *
+ * @param key
+ * A key string.
+ * @return The value.
+ */
+ public float optFloat(String key)
+ {
+ return this.optFloat(key, Float.NaN);
+ }
+
+ /**
+ * Get the optional double value associated with an index. The defaultValue is
+ * returned if there is no value for the index, or if the value is not a
+ * number and cannot be converted to a number.
+ *
+ * @param key
+ * A key string.
+ * @param defaultValue
+ * The default value.
+ * @return The value.
+ */
+ public float optFloat(String key, float defaultValue)
+ {
+ Object val = this.opt(key);
+ if (JSONObject.NULL.equals(val))
+ {
+ return defaultValue;
+ }
+ if (val instanceof Number)
+ {
+ return ((Number) val).floatValue();
+ }
+ if (val instanceof String)
+ {
+ try
+ {
+ return Float.parseFloat((String) val);
+ } catch (Exception e)
+ {
+ return defaultValue;
+ }
+ }
+ return defaultValue;
+ }
+
+ /**
+ * Get an optional int value associated with a key, or zero if there is no
+ * such key or if the value is not a number. If the value is a string, an
+ * attempt will be made to evaluate it as a number.
+ *
+ * @param key
+ * A key string.
+ * @return An object which is the value.
+ */
+ public int optInt(String key)
+ {
+ return this.optInt(key, 0);
+ }
+
+ /**
+ * Get an optional int value associated with a key, or the default if there is
+ * no such key or if the value is not a number. If the value is a string, an
+ * attempt will be made to evaluate it as a number.
+ *
+ * @param key
+ * A key string.
+ * @param defaultValue
+ * The default.
+ * @return An object which is the value.
+ */
+ public int optInt(String key, int defaultValue)
+ {
+ Object val = this.opt(key);
+ if (NULL.equals(val))
+ {
+ return defaultValue;
+ }
+ if (val instanceof Number)
+ {
+ return ((Number) val).intValue();
+ }
+
+ if (val instanceof String)
+ {
+ try
+ {
+ return new BigDecimal((String) val).intValue();
+ } catch (Exception e)
+ {
+ return defaultValue;
+ }
+ }
+ return defaultValue;
+ }
+
+ /**
+ * Get an optional JSONArray associated with a key. It returns null if there
+ * is no such key, or if its value is not a JSONArray.
+ *
+ * @param key
+ * A key string.
+ * @return A JSONArray which is the value.
+ */
+ public JSONArray optJSONArray(String key)
+ {
+ Object o = this.opt(key);
+ return o instanceof JSONArray ? (JSONArray) o : null;
+ }
+
+ /**
+ * Get an optional JSONObject associated with a key. It returns null if there
+ * is no such key, or if its value is not a JSONObject.
+ *
+ * @param key
+ * A key string.
+ * @return A JSONObject which is the value.
+ */
+ public JSONObject optJSONObject(String key)
+ {
+ Object object = this.opt(key);
+ return object instanceof JSONObject ? (JSONObject) object : null;
+ }
+
+ /**
+ * Get an optional long value associated with a key, or zero if there is no
+ * such key or if the value is not a number. If the value is a string, an
+ * attempt will be made to evaluate it as a number.
+ *
+ * @param key
+ * A key string.
+ * @return An object which is the value.
+ */
+ public long optLong(String key)
+ {
+ return this.optLong(key, 0);
+ }
+
+ /**
+ * Get an optional long value associated with a key, or the default if there
+ * is no such key or if the value is not a number. If the value is a string,
+ * an attempt will be made to evaluate it as a number.
+ *
+ * @param key
+ * A key string.
+ * @param defaultValue
+ * The default.
+ * @return An object which is the value.
+ */
+ public long optLong(String key, long defaultValue)
+ {
+ Object val = this.opt(key);
+ if (NULL.equals(val))
+ {
+ return defaultValue;
+ }
+ if (val instanceof Number)
+ {
+ return ((Number) val).longValue();
+ }
+
+ if (val instanceof String)
+ {
+ try
+ {
+ return new BigDecimal((String) val).longValue();
+ } catch (Exception e)
+ {
+ return defaultValue;
+ }
+ }
+ return defaultValue;
+ }
+
+ /**
+ * Get an optional {@link Number} value associated with a key, or
+ * <code>null</code> if there is no such key or if the value is not a number.
+ * If the value is a string, an attempt will be made to evaluate it as a
+ * number ({@link BigDecimal}). This method would be used in cases where type
+ * coercion of the number value is unwanted.
+ *
+ * @param key
+ * A key string.
+ * @return An object which is the value.
+ */
+ public Number optNumber(String key)
+ {
+ return this.optNumber(key, null);
+ }
+
+ /**
+ * Get an optional {@link Number} value associated with a key, or the default
+ * if there is no such key or if the value is not a number. If the value is a
+ * string, an attempt will be made to evaluate it as a number. This method
+ * would be used in cases where type coercion of the number value is unwanted.
+ *
+ * @param key
+ * A key string.
+ * @param defaultValue
+ * The default.
+ * @return An object which is the value.
+ */
+ public Number optNumber(String key, Number defaultValue)
+ {
+ Object val = this.opt(key);
+ if (NULL.equals(val))
+ {
+ return defaultValue;
+ }
+ if (val instanceof Number)
+ {
+ return (Number) val;
+ }
+
+ if (val instanceof String)
+ {
+ try
+ {
+ return stringToNumber((String) val);
+ } catch (Exception e)
+ {
+ return defaultValue;
+ }
+ }
+ return defaultValue;
+ }
+
+ /**
+ * Get an optional string associated with a key. It returns an empty string if
+ * there is no such key. If the value is not a string and is not null, then it
+ * is converted to a string.
+ *
+ * @param key
+ * A key string.
+ * @return A string which is the value.
+ */
+ public String optString(String key)
+ {
+ return this.optString(key, "");
+ }
+
+ /**
+ * Get an optional string associated with a key. It returns the defaultValue
+ * if there is no such key.
+ *
+ * @param key
+ * A key string.
+ * @param defaultValue
+ * The default.
+ * @return A string which is the value.
+ */
+ public String optString(String key, String defaultValue)
+ {
+ Object object = this.opt(key);
+ return NULL.equals(object) ? defaultValue : object.toString();
+ }
+
+ /**
+ * Populates the internal map of the JSONObject with the bean properties. The
+ * bean can not be recursive.
+ *
+ * @see JSONObject#JSONObject(Object)
+ *
+ * @param bean
+ * the bean
+ */
+ private void populateMap(Object bean)
+ {
+ Class<?> klass = bean.getClass();
+
+ // If klass is a System class then set includeSuperClass to false.
+
+ boolean includeSuperClass = klass.getClassLoader() != null;
+
+ Method[] methods = includeSuperClass ? klass.getMethods()
+ : klass.getDeclaredMethods();
+ for (final Method method : methods)
+ {
+ final int modifiers = method.getModifiers();
+ if (Modifier.isPublic(modifiers) && !Modifier.isStatic(modifiers)
+ && method.getParameterTypes().length == 0
+ && !method.isBridge() && method.getReturnType() != Void.TYPE
+ && isValidMethodName(method.getName()))
+ {
+ final String key = getKeyNameFromMethod(method);
+ if (key != null && !key.isEmpty())
+ {
+ try
+ {
+ final Object result = method.invoke(bean);
+ if (result != null)
+ {
+ this.map.put(key, wrap(result));
+ // we don't use the result anywhere outside of wrap
+ // if it's a resource we should be sure to close it
+ // after calling toString
+ if (result instanceof Closeable)
+ {
+ try
+ {
+ ((Closeable) result).close();
+ } catch (IOException ignore)
+ {
+ }
+ }
+ }
+ } catch (IllegalAccessException ignore)
+ {
+ } catch (IllegalArgumentException ignore)
+ {
+ } catch (InvocationTargetException ignore)
+ {
+ }
+ }
+ }
+ }
+ }
+
+ private boolean isValidMethodName(String name)
+ {
+ return !"getClass".equals(name) && !"getDeclaringClass".equals(name);
+ }
+
+ private String getKeyNameFromMethod(Method method)
+ {
+ final int ignoreDepth = -1;// getAnnotationDepth(method,
+ // JSONPropertyIgnore.class);
+ // if (ignoreDepth > 0) {
+ // final int forcedNameDepth = getAnnotationDepth(method,
+ // JSONPropertyName.class);
+ // if (forcedNameDepth < 0 || ignoreDepth <= forcedNameDepth) {
+ // // the hierarchy asked to ignore, and the nearest name override
+ // // was higher or non-existent
+ // return null;
+ // }
+ // }
+ // JSONPropertyName annotation = getAnnotation(method,
+ // JSONPropertyName.class);
+ // if (annotation != null && annotation.value() != null &&
+ // !annotation.value().isEmpty()) {
+ // return annotation.value();
+ // }
+ String key;
+ final String name = method.getName();
+ if (name.startsWith("get") && name.length() > 3)
+ {
+ key = name.substring(3);
+ }
+ else if (name.startsWith("is") && name.length() > 2)
+ {
+ key = name.substring(2);
+ }
+ else
+ {
+ return null;
+ }
+ // if the first letter in the key is not uppercase, then skip.
+ // This is to maintain backwards compatibility before PR406
+ // (https://github.com/stleary/JSON-java/pull/406/)
+ if (Character.isLowerCase(key.charAt(0)))
+ {
+ return null;
+ }
+ if (key.length() == 1)
+ {
+ key = key.toLowerCase(Locale.ROOT);
+ }
+ else if (!Character.isUpperCase(key.charAt(1)))
+ {
+ key = key.substring(0, 1).toLowerCase(Locale.ROOT) + key.substring(1);
+ }
+ return (/** @j2sNative 1 ? key.split("$")[0] : */
+ key);
+ }
+
+ // /**
+ // * Searches the class hierarchy to see if the method or it's super
+ // * implementations and interfaces has the annotation.
+ // *
+ // * @param <A>
+ // * type of the annotation
+ // *
+ // * @param m
+ // * method to check
+ // * @param annotationClass
+ // * annotation to look for
+ // * @return the {@link Annotation} if the annotation exists on the current
+ // method
+ // * or one of it's super class definitions
+ // */
+ // private static <A extends Annotation> A getAnnotation(final Method m, final
+ // Class<A> annotationClass) {
+ // return null;
+ // // if we have invalid data the result is null
+ // if (true || m == null || annotationClass == null) {
+ // return null;
+ // }
+ //
+ // if (m.isAnnotationPresent(annotationClass)) {
+ // return m.getAnnotation(annotationClass);
+ // }
+ //
+ // // if we've already reached the Object class, return null;
+ // Class<?> c = m.getDeclaringClass();
+ // if (c.getSuperclass() == null) {
+ // return null;
+ // }
+ //
+ // // check directly implemented interfaces for the method being checked
+ // for (Class<?> i : c.getInterfaces()) {
+ // try {
+ // Method im = i.getMethod(m.getName(), m.getParameterTypes());
+ // return getAnnotation(im, annotationClass);
+ // } catch (final SecurityException ex) {
+ // continue;
+ // } catch (final NoSuchMethodException ex) {
+ // continue;
+ // }
+ // }
+ //
+ // try {
+ // return getAnnotation(
+ // c.getSuperclass().getMethod(m.getName(), m.getParameterTypes()),
+ // annotationClass);
+ // } catch (final SecurityException ex) {
+ // return null;
+ // } catch (final NoSuchMethodException ex) {
+ // return null;
+ // }
+ // }
+ //
+ // /**
+ // * Searches the class hierarchy to see if the method or it's super
+ // * implementations and interfaces has the annotation. Returns the depth of
+ // the
+ // * annotation in the hierarchy.
+ // *
+ // * @param <A>
+ // * type of the annotation
+ // *
+ // * @param m
+ // * method to check
+ // * @param annotationClass
+ // * annotation to look for
+ // * @return Depth of the annotation or -1 if the annotation is not on the
+ // method.
+ // */
+ // private static int getAnnotationDepth(final Method m, final Class<? extends
+ // Annotation> annotationClass) {
+ // // if we have invalid data the result is -1
+ // if (m == null || annotationClass == null) {
+ // return -1;
+ // }
+ // if (m.isAnnotationPresent(annotationClass)) {
+ // return 1;
+ // }
+ //
+ // // if we've already reached the Object class, return -1;
+ // Class<?> c = m.getDeclaringClass();
+ // if (c.getSuperclass() == null) {
+ // return -1;
+ // }
+ //
+ // // check directly implemented interfaces for the method being checked
+ // for (Class<?> i : c.getInterfaces()) {
+ // try {
+ // Method im = i.getMethod(m.getName(), m.getParameterTypes());
+ // int d = getAnnotationDepth(im, annotationClass);
+ // if (d > 0) {
+ // // since the annotation was on the interface, add 1
+ // return d + 1;
+ // }
+ // } catch (final SecurityException ex) {
+ // continue;
+ // } catch (final NoSuchMethodException ex) {
+ // continue;
+ // }
+ // }
+ //
+ // try {
+ // int d = getAnnotationDepth(
+ // c.getSuperclass().getMethod(m.getName(), m.getParameterTypes()),
+ // annotationClass);
+ // if (d > 0) {
+ // // since the annotation was on the superclass, add 1
+ // return d + 1;
+ // }
+ // return -1;
+ // } catch (final SecurityException ex) {
+ // return -1;
+ // } catch (final NoSuchMethodException ex) {
+ // return -1;
+ // }
+ // }
+
+ /**
+ * Put a key/boolean pair in the JSONObject.
+ *
+ * @param key
+ * A key string.
+ * @param value
+ * A boolean which is the value.
+ * @return this.
+ * @throws JSONException
+ * If the value is non-finite number.
+ * @throws NullPointerException
+ * If the key is <code>null</code>.
+ */
+ public JSONObject put(String key, boolean value) throws JSONException
+ {
+ return this.put(key, value ? Boolean.TRUE : Boolean.FALSE);
+ }
+
+ /**
+ * Put a key/value pair in the JSONObject, where the value will be a JSONArray
+ * which is produced from a Collection.
+ *
+ * @param key
+ * A key string.
+ * @param value
+ * A Collection value.
+ * @return this.
+ * @throws JSONException
+ * If the value is non-finite number.
+ * @throws NullPointerException
+ * If the key is <code>null</code>.
+ */
+ public JSONObject put(String key, Collection<?> value)
+ throws JSONException
+ {
+ return this.put(key, new JSONArray(value));
+ }
+
+ /**
+ * Put a key/double pair in the JSONObject.
+ *
+ * @param key
+ * A key string.
+ * @param value
+ * A double which is the value.
+ * @return this.
+ * @throws JSONException
+ * If the value is non-finite number.
+ * @throws NullPointerException
+ * If the key is <code>null</code>.
+ */
+ public JSONObject put(String key, double value) throws JSONException
+ {
+ return this.put(key, Double.valueOf(value));
+ }
+
+ /**
+ * Put a key/float pair in the JSONObject.
+ *
+ * @param key
+ * A key string.
+ * @param value
+ * A float which is the value.
+ * @return this.
+ * @throws JSONException
+ * If the value is non-finite number.
+ * @throws NullPointerException
+ * If the key is <code>null</code>.
+ */
+ public JSONObject put(String key, float value) throws JSONException
+ {
+ return this.put(key, Float.valueOf(value));
+ }
+
+ /**
+ * Put a key/int pair in the JSONObject.
+ *
+ * @param key
+ * A key string.
+ * @param value
+ * An int which is the value.
+ * @return this.
+ * @throws JSONException
+ * If the value is non-finite number.
+ * @throws NullPointerException
+ * If the key is <code>null</code>.
+ */
+ public JSONObject put(String key, int value) throws JSONException
+ {
+ return this.put(key, Integer.valueOf(value));
+ }
+
+ /**
+ * Put a key/long pair in the JSONObject.
+ *
+ * @param key
+ * A key string.
+ * @param value
+ * A long which is the value.
+ * @return this.
+ * @throws JSONException
+ * If the value is non-finite number.
+ * @throws NullPointerException
+ * If the key is <code>null</code>.
+ */
+ public JSONObject put(String key, long value) throws JSONException
+ {
+ return this.put(key, Long.valueOf(value));
+ }
+
+ /**
+ * Put a key/value pair in the JSONObject, where the value will be a
+ * JSONObject which is produced from a Map.
+ *
+ * @param key
+ * A key string.
+ * @param value
+ * A Map value.
+ * @return this.
+ * @throws JSONException
+ * If the value is non-finite number.
+ * @throws NullPointerException
+ * If the key is <code>null</code>.
+ */
+ public JSONObject put(String key, Map<?, ?> value) throws JSONException
+ {
+ return this.put(key, new JSONObject(value));
+ }
+
+ /**
+ * Put a key/value pair in the JSONObject. If the value is <code>null</code>,
+ * then the key will be removed from the JSONObject if it is present.
+ *
+ * @param key
+ * A key string.
+ * @param value
+ * An object which is the value. It should be of one of these types:
+ * Boolean, Double, Integer, JSONArray, JSONObject, Long, String, or
+ * the JSONObject.NULL object.
+ * @return this.
+ * @throws JSONException
+ * If the value is non-finite number.
+ * @throws NullPointerException
+ * If the key is <code>null</code>.
+ */
+ public JSONObject put(String key, Object value) throws JSONException
+ {
+ if (key == null)
+ {
+ throw new NullPointerException("Null key.");
+ }
+ if (value != null)
+ {
+ testValidity(value);
+ this.map.put(key, value);
+ }
+ else
+ {
+ this.remove(key);
+ }
+ return this;
+ }
+
+ /**
+ * Put a key/value pair in the JSONObject, but only if the key and the value
+ * are both non-null, and only if there is not already a member with that
+ * name.
+ *
+ * @param key
+ * string
+ * @param value
+ * object
+ * @return this.
+ * @throws JSONException
+ * if the key is a duplicate
+ */
+ public JSONObject putOnce(String key, Object value) throws JSONException
+ {
+ if (key != null && value != null)
+ {
+ if (this.opt(key) != null)
+ {
+ throw new JSONException("Duplicate key \"" + key + "\"");
+ }
+ return this.put(key, value);
+ }
+ return this;
+ }
+
+ /**
+ * Put a key/value pair in the JSONObject, but only if the key and the value
+ * are both non-null.
+ *
+ * @param key
+ * A key string.
+ * @param value
+ * An object which is the value. It should be of one of these types:
+ * Boolean, Double, Integer, JSONArray, JSONObject, Long, String, or
+ * the JSONObject.NULL object.
+ * @return this.
+ * @throws JSONException
+ * If the value is a non-finite number.
+ */
+ public JSONObject putOpt(String key, Object value) throws JSONException
+ {
+ if (key != null && value != null)
+ {
+ return this.put(key, value);
+ }
+ return this;
+ }
+
+ /**
+ * Creates a JSONPointer using an initialization string and tries to match it
+ * to an item within this JSONObject. For example, given a JSONObject
+ * initialized with this document:
+ *
+ * <pre>
+ * {
+ * "a":{"b":"c"}
+ * }
+ * </pre>
+ *
+ * and this JSONPointer string:
+ *
+ * <pre>
+ * "/a/b"
+ * </pre>
+ *
+ * Then this method will return the String "c". A JSONPointerException may be
+ * thrown from code called by this method.
+ *
+ * @param jsonPointer
+ * string that can be used to create a JSONPointer
+ * @return the item matched by the JSONPointer, otherwise null
+ */
+ public Object query(String jsonPointer)
+ {
+ return query(new JSONPointer(jsonPointer));
+ }
+
+ /**
+ * Uses a user initialized JSONPointer and tries to match it to an item within
+ * this JSONObject. For example, given a JSONObject initialized with this
+ * document:
+ *
+ * <pre>
+ * {
+ * "a":{"b":"c"}
+ * }
+ * </pre>
+ *
+ * and this JSONPointer:
+ *
+ * <pre>
+ * "/a/b"
+ * </pre>
+ *
+ * Then this method will return the String "c". A JSONPointerException may be
+ * thrown from code called by this method.
+ *
+ * @param jsonPointer
+ * string that can be used to create a JSONPointer
+ * @return the item matched by the JSONPointer, otherwise null
+ */
+ public Object query(JSONPointer jsonPointer)
+ {
+ return jsonPointer.queryFrom(this);
+ }
+
+ /**
+ * Queries and returns a value from this object using {@code jsonPointer}, or
+ * returns null if the query fails due to a missing key.
+ *
+ * @param jsonPointer
+ * the string representation of the JSON pointer
+ * @return the queried value or {@code null}
+ * @throws IllegalArgumentException
+ * if {@code jsonPointer} has invalid syntax
+ */
+ public Object optQuery(String jsonPointer)
+ {
+ return optQuery(new JSONPointer(jsonPointer));
+ }
+
+ /**
+ * Queries and returns a value from this object using {@code jsonPointer}, or
+ * returns null if the query fails due to a missing key.
+ *
+ * @param jsonPointer
+ * The JSON pointer
+ * @return the queried value or {@code null}
+ * @throws IllegalArgumentException
+ * if {@code jsonPointer} has invalid syntax
+ */
+ public Object optQuery(JSONPointer jsonPointer)
+ {
+ try
+ {
+ return jsonPointer.queryFrom(this);
+ } catch (JSONPointerException e)
+ {
+ return null;
+ }
+ }
+
+ /**
+ * Produce a string in double quotes with backslash sequences in all the right
+ * places. A backslash will be inserted within </, producing <\/, allowing
+ * JSON text to be delivered in HTML. In JSON text, a string cannot contain a
+ * control character or an unescaped quote or backslash.
+ *
+ * @param string
+ * A String
+ * @return A String correctly formatted for insertion in a JSON text.
+ */
+ public static String quote(String string)
+ {
+ StringWriter sw = new StringWriter();
+ synchronized (sw.getBuffer())
+ {
+ try
+ {
+ return quote(string, sw).toString();
+ } catch (IOException ignored)
+ {
+ // will never happen - we are writing to a string writer
+ return "";
+ }
+ }
+ }
+
+ public static Writer quote(String string, Writer w) throws IOException
+ {
+ if (string == null || string.isEmpty())
+ {
+ w.write("\"\"");
+ return w;
+ }
+
+ char b;
+ char c = 0;
+ String hhhh;
+ int i;
+ int len = string.length();
+
+ w.write('"');
+ for (i = 0; i < len; i += 1)
+ {
+ b = c;
+ c = string.charAt(i);
+ switch (c)
+ {
+ case '\\':
+ case '"':
+ w.write('\\');
+ w.write(c);
+ break;
+ case '/':
+ if (b == '<')
+ {
+ w.write('\\');
+ }
+ w.write(c);
+ break;
+ case '\b':
+ w.write("\\b");
+ break;
+ case '\t':
+ w.write("\\t");
+ break;
+ case '\n':
+ w.write("\\n");
+ break;
+ case '\f':
+ w.write("\\f");
+ break;
+ case '\r':
+ w.write("\\r");
+ break;
+ default:
+ if (c < ' ' || (c >= '\u0080' && c < '\u00a0')
+ || (c >= '\u2000' && c < '\u2100'))
+ {
+ w.write("\\u");
+ hhhh = Integer.toHexString(c);
+ w.write("0000", 0, 4 - hhhh.length());
+ w.write(hhhh);
+ }
+ else
+ {
+ w.write(c);
+ }
+ }
+ }
+ w.write('"');
+ return w;
+ }
+
+ /**
+ * Remove a name and its value, if present.
+ *
+ * @param key
+ * The name to be removed.
+ * @return The value that was associated with the name, or null if there was
+ * no value.
+ */
+ public Object remove(String key)
+ {
+ return this.map.remove(key);
+ }
+
+ /**
+ * Determine if two JSONObjects are similar. They must contain the same set of
+ * names which must be associated with similar values.
+ *
+ * @param other
+ * The other JSONObject
+ * @return true if they are equal
+ */
+ public boolean similar(Object other)
+ {
+ try
+ {
+ if (!(other instanceof JSONObject))
+ {
+ return false;
+ }
+ if (!this.keySet().equals(((JSONObject) other).keySet()))
+ {
+ return false;
+ }
+ for (final Entry<String, ?> entry : this.entrySet())
+ {
+ String name = entry.getKey();
+ Object valueThis = entry.getValue();
+ Object valueOther = ((JSONObject) other).get(name);
+ if (valueThis == valueOther)
+ {
+ continue;
+ }
+ if (valueThis == null)
+ {
+ return false;
+ }
+ if (valueThis instanceof JSONObject)
+ {
+ if (!((JSONObject) valueThis).similar(valueOther))
+ {
+ return false;
+ }
+ }
+ else if (valueThis instanceof JSONArray)
+ {
+ if (!((JSONArray) valueThis).similar(valueOther))
+ {
+ return false;
+ }
+ }
+ else if (!valueThis.equals(valueOther))
+ {
+ return false;
+ }
+ }
+ return true;
+ } catch (Throwable exception)
+ {
+ return false;
+ }
+ }
+
+ /**
+ * Tests if the value should be tried as a decimal. It makes no test if there
+ * are actual digits.
+ *
+ * @param val
+ * value to test
+ * @return true if the string is "-0" or if it contains '.', 'e', or 'E',
+ * false otherwise.
+ */
+ protected static boolean isDecimalNotation(final String val)
+ {
+ return val.indexOf('.') > -1 || val.indexOf('e') > -1
+ || val.indexOf('E') > -1 || "-0".equals(val);
+ }
+
+ /**
+ * Converts a string to a number using the narrowest possible type. Possible
+ * returns for this function are BigDecimal, Double, BigInteger, Long, and
+ * Integer. When a Double is returned, it should always be a valid Double and
+ * not NaN or +-infinity.
+ *
+ * @param val
+ * value to convert
+ * @return Number representation of the value.
+ * @throws NumberFormatException
+ * thrown if the value is not a valid number. A public caller should
+ * catch this and wrap it in a {@link JSONException} if applicable.
+ */
+ protected static Number stringToNumber(final String val)
+ throws NumberFormatException
+ {
+ char initial = val.charAt(0);
+ if ((initial >= '0' && initial <= '9') || initial == '-')
+ {
+ // decimal representation
+ if (isDecimalNotation(val))
+ {
+ // quick dirty way to see if we need a BigDecimal instead of a Double
+ // this only handles some cases of overflow or underflow
+ if (val.length() > 14)
+ {
+ return new BigDecimal(val);
+ }
+ final Double d = Double.valueOf(val);
+ if (d.isInfinite() || d.isNaN())
+ {
+ // if we can't parse it as a double, go up to BigDecimal
+ // this is probably due to underflow like 4.32e-678
+ // or overflow like 4.65e5324. The size of the string is small
+ // but can't be held in a Double.
+ return new BigDecimal(val);
+ }
+ return d;
+ }
+ // integer representation.
+ // This will narrow any values to the smallest reasonable Object
+ // representation
+ // (Integer, Long, or BigInteger)
+
+ // string version
+ // The compare string length method reduces GC,
+ // but leads to smaller integers being placed in larger wrappers even
+ // though not
+ // needed. i.e. 1,000,000,000 -> Long even though it's an Integer
+ // 1,000,000,000,000,000,000 -> BigInteger even though it's a Long
+ // if(val.length()<=9){
+ // return Integer.valueOf(val);
+ // }
+ // if(val.length()<=18){
+ // return Long.valueOf(val);
+ // }
+ // return new BigInteger(val);
+
+ // BigInteger version: We use a similar bitLenth compare as
+ // BigInteger#intValueExact uses. Increases GC, but objects hold
+ // only what they need. i.e. Less runtime overhead if the value is
+ // long lived. Which is the better tradeoff? This is closer to what's
+ // in stringToValue.
+ BigInteger bi = new BigInteger(val);
+ if (bi.bitLength() <= 31)
+ {
+ return Integer.valueOf(bi.intValue());
+ }
+ if (bi.bitLength() <= 63)
+ {
+ return Long.valueOf(bi.longValue());
+ }
+ return bi;
+ }
+ throw new NumberFormatException(
+ "val [" + val + "] is not a valid number.");
+ }
+
+ /**
+ * Try to convert a string into a number, boolean, or null. If the string
+ * can't be converted, return the string.
+ *
+ * @param string
+ * A String.
+ * @return A simple JSON value.
+ */
+ // Changes to this method must be copied to the corresponding method in
+ // the XML class to keep full support for Android
+ public static Object stringToValue(String string)
+ {
+ if (string.equals(""))
+ {
+ return string;
+ }
+ if (string.equalsIgnoreCase("true"))
+ {
+ return Boolean.TRUE;
+ }
+ if (string.equalsIgnoreCase("false"))
+ {
+ return Boolean.FALSE;
+ }
+ if (string.equalsIgnoreCase("null"))
+ {
+ return JSONObject.NULL;
+ }
+
+ /*
+ * If it might be a number, try converting it. If a number cannot be produced,
+ * then the value will just be a string.
+ */
+
+ char initial = string.charAt(0);
+ if ((initial >= '0' && initial <= '9') || initial == '-')
+ {
+ try
+ {
+ // if we want full Big Number support this block can be replaced with:
+ // return stringToNumber(string);
+ if (isDecimalNotation(string))
+ {
+ Double d = Double.valueOf(string);
+ if (!d.isInfinite() && !d.isNaN())
+ {
+ return d;
+ }
+ }
+ else
+ {
+ Long myLong = Long.valueOf(string);
+ if (string.equals(myLong.toString()))
+ {
+ if (myLong.longValue() == myLong.intValue())
+ {
+ return Integer.valueOf(myLong.intValue());
+ }
+ return myLong;
+ }
+ }
+ } catch (Exception ignore)
+ {
+ }
+ }
+ return string;
+ }
+
+ /**
+ * Throw an exception if the object is a NaN or infinite number.
+ *
+ * @param o
+ * The object to test.
+ * @throws JSONException
+ * If o is a non-finite number.
+ */
+ public static void testValidity(Object o) throws JSONException
+ {
+ if (o != null)
+ {
+ if (o instanceof Double)
+ {
+ if (((Double) o).isInfinite() || ((Double) o).isNaN())
+ {
+ throw new JSONException(
+ "JSON does not allow non-finite numbers.");
+ }
+ }
+ else if (o instanceof Float)
+ {
+ if (((Float) o).isInfinite() || ((Float) o).isNaN())
+ {
+ throw new JSONException(
+ "JSON does not allow non-finite numbers.");
+ }
+ }
+ }
+ }
+
+ /**
+ * Produce a JSONArray containing the values of the members of this
+ * JSONObject.
+ *
+ * @param names
+ * A JSONArray containing a list of key strings. This determines the
+ * sequence of the values in the result.
+ * @return A JSONArray of values.
+ * @throws JSONException
+ * If any of the values are non-finite numbers.
+ */
+ public JSONArray toJSONArray(JSONArray names) throws JSONException
+ {
+ if (names == null || names.isEmpty())
+ {
+ return null;
+ }
+ JSONArray ja = new JSONArray();
+ for (int i = 0; i < names.length(); i += 1)
+ {
+ ja.put(this.opt(names.getString(i)));
+ }
+ return ja;
+ }
+
+ /**
+ * Make a JSON text of this JSONObject. For compactness, no whitespace is
+ * added. If this would not result in a syntactically correct JSON text, then
+ * null will be returned instead.
+ * <p>
+ * <b> Warning: This method assumes that the data structure is acyclical. </b>
+ *
+ * @return a printable, displayable, portable, transmittable representation of
+ * the object, beginning with <code>{</code> <small>(left
+ * brace)</small> and ending with <code>}</code> <small>(right
+ * brace)</small>.
+ */
+ @Override
+ public String toString()
+ {
+ try
+ {
+ return this.toString(0);
+ } catch (Exception e)
+ {
+ return null;
+ }
+ }
+
+ /**
+ * Make a pretty-printed JSON text of this JSONObject.
+ *
+ * <p>
+ * If <code>indentFactor > 0</code> and the {@link JSONObject} has only one
+ * key, then the object will be output on a single line:
+ *
+ * <pre>
+ * {@code {"key": 1}}
+ * </pre>
+ *
+ * <p>
+ * If an object has 2 or more keys, then it will be output across multiple
+ * lines: <code><pre>{
+ * "key1": 1,
+ * "key2": "value 2",
+ * "key3": 3
+ * }</pre></code>
+ * <p>
+ * <b> Warning: This method assumes that the data structure is acyclical. </b>
+ *
+ * @param indentFactor
+ * The number of spaces to add to each level of indentation.
+ * @return a printable, displayable, portable, transmittable representation of
+ * the object, beginning with <code>{</code> <small>(left
+ * brace)</small> and ending with <code>}</code> <small>(right
+ * brace)</small>.
+ * @throws JSONException
+ * If the object contains an invalid number.
+ */
+ public String toString(int indentFactor) throws JSONException
+ {
+ StringWriter w = new StringWriter();
+ synchronized (w.getBuffer())
+ {
+ return this.write(w, indentFactor, 0).toString();
+ }
+ }
+
+ /**
+ * Make a JSON text of an Object value. If the object has an
+ * value.toJSONString() method, then that method will be used to produce the
+ * JSON text. The method is required to produce a strictly conforming text. If
+ * the object does not contain a toJSONString method (which is the most common
+ * case), then a text will be produced by other means. If the value is an
+ * array or Collection, then a JSONArray will be made from it and its
+ * toJSONString method will be called. If the value is a MAP, then a
+ * JSONObject will be made from it and its toJSONString method will be called.
+ * Otherwise, the value's toString method will be called, and the result will
+ * be quoted.
+ *
+ * <p>
+ * Warning: This method assumes that the data structure is acyclical.
+ *
+ * @param value
+ * The value to be serialized.
+ * @return a printable, displayable, transmittable representation of the
+ * object, beginning with <code>{</code> <small>(left
+ * brace)</small> and ending with <code>}</code> <small>(right
+ * brace)</small>.
+ * @throws JSONException
+ * If the value is or contains an invalid number.
+ */
+ public static String valueToString(Object value) throws JSONException
+ {
+ // moves the implementation to JSONWriter as:
+ // 1. It makes more sense to be part of the writer class
+ // 2. For Android support this method is not available. By implementing it
+ // in
+ // the Writer
+ // Android users can use the writer with the built in Android JSONObject
+ // implementation.
+ return JSONWriter.valueToString(value);
+ }
+
+ /**
+ * Wrap an object, if necessary. If the object is <code>null</code>, return
+ * the NULL object. If it is an array or collection, wrap it in a JSONArray.
+ * If it is a map, wrap it in a JSONObject. If it is a standard property
+ * (Double, String, et al) then it is already wrapped. Otherwise, if it comes
+ * from one of the java packages, turn it into a string. And if it doesn't,
+ * try to wrap it in a JSONObject. If the wrapping fails, then null is
+ * returned.
+ *
+ * @param object
+ * The object to wrap
+ * @return The wrapped value
+ */
+ public static Object wrap(Object object)
+ {
+ try
+ {
+ if (object == null)
+ {
+ return NULL;
+ }
+ if (object instanceof JSONObject || object instanceof JSONArray
+ || NULL.equals(object) || object instanceof JSONString
+ || object instanceof Byte || object instanceof Character
+ || object instanceof Short || object instanceof Integer
+ || object instanceof Long || object instanceof Boolean
+ || object instanceof Float || object instanceof Double
+ || object instanceof String || object instanceof BigInteger
+ || object instanceof BigDecimal || object instanceof Enum)
+ {
+ return object;
+ }
+
+ if (object instanceof Collection)
+ {
+ Collection<?> coll = (Collection<?>) object;
+ return new JSONArray(coll);
+ }
+ if (object.getClass().isArray())
+ {
+ return new JSONArray(object);
+ }
+ if (object instanceof Map)
+ {
+ Map<?, ?> map = (Map<?, ?>) object;
+ return new JSONObject(map);
+ }
+ Package objectPackage = object.getClass().getPackage();
+ String objectPackageName = objectPackage != null
+ ? objectPackage.getName()
+ : "";
+ if (objectPackageName.startsWith("java.")
+ || objectPackageName.startsWith("javax.")
+ || object.getClass().getClassLoader() == null)
+ {
+ return object.toString();
+ }
+ return new JSONObject(object);
+ } catch (Exception exception)
+ {
+ return null;
+ }
+ }
+
+ /**
+ * Write the contents of the JSONObject as JSON text to a writer. For
+ * compactness, no whitespace is added.
+ * <p>
+ * <b> Warning: This method assumes that the data structure is acyclical. </b>
+ *
+ * @return The writer.
+ * @throws JSONException
+ */
+ public Writer write(Writer writer) throws JSONException
+ {
+ return this.write(writer, 0, 0);
+ }
+
+ static final Writer writeValue(Writer writer, Object value,
+ int indentFactor, int indent) throws JSONException, IOException
+ {
+ if (value == null || value.equals(null))
+ {
+ writer.write("null");
+ }
+ else if (value instanceof JSONString)
+ {
+ Object o;
+ try
+ {
+ o = ((JSONString) value).toJSONString();
+ } catch (Exception e)
+ {
+ throw new JSONException(e);
+ }
+ writer.write(o != null ? o.toString() : quote(value.toString()));
+ }
+ else if (value instanceof Number)
+ {
+ // not all Numbers may match actual JSON Numbers. i.e. fractions or
+ // Imaginary
+ final String numberAsString = numberToString((Number) value);
+ try
+ {
+ // Use the BigDecimal constructor for its parser to validate the format.
+ @SuppressWarnings("unused")
+ BigDecimal testNum = new BigDecimal(numberAsString);
+ // Close enough to a JSON number that we will use it unquoted
+ writer.write(numberAsString);
+ } catch (NumberFormatException ex)
+ {
+ // The Number value is not a valid JSON number.
+ // Instead we will quote it as a string
+ quote(numberAsString, writer);
+ }
+ }
+ else if (value instanceof Boolean)
+ {
+ writer.write(value.toString());
+ }
+ else if (value instanceof Enum<?>)
+ {
+ writer.write(quote(((Enum<?>) value).name()));
+ }
+ else if (value instanceof JSONObject)
+ {
+ ((JSONObject) value).write(writer, indentFactor, indent);
+ }
+ else if (value instanceof JSONArray)
+ {
+ ((JSONArray) value).write(writer, indentFactor, indent);
+ }
+ else if (value instanceof Map)
+ {
+ Map<?, ?> map = (Map<?, ?>) value;
+ new JSONObject(map).write(writer, indentFactor, indent);
+ }
+ else if (value instanceof Collection)
+ {
+ Collection<?> coll = (Collection<?>) value;
+ new JSONArray(coll).write(writer, indentFactor, indent);
+ }
+ else if (value.getClass().isArray())
+ {
+ new JSONArray(value).write(writer, indentFactor, indent);
+ }
+ else
+ {
+ quote(value.toString(), writer);
+ }
+ return writer;
+ }
+
+ static final void indent(Writer writer, int indent) throws IOException
+ {
+ for (int i = 0; i < indent; i += 1)
+ {
+ writer.write(' ');
+ }
+ }
+
+ /**
+ * Write the contents of the JSONObject as JSON text to a writer.
+ *
+ * <p>
+ * If <code>indentFactor > 0</code> and the {@link JSONObject} has only one
+ * key, then the object will be output on a single line:
+ *
+ * <pre>
+ * {@code {"key": 1}}
+ * </pre>
+ *
+ * <p>
+ * If an object has 2 or more keys, then it will be output across multiple
+ * lines: <code><pre>{
+ * "key1": 1,
+ * "key2": "value 2",
+ * "key3": 3
+ * }</pre></code>
+ * <p>
+ * <b> Warning: This method assumes that the data structure is acyclical. </b>
+ *
+ * @param writer
+ * Writes the serialized JSON
+ * @param indentFactor
+ * The number of spaces to add to each level of indentation.
+ * @param indent
+ * The indentation of the top level.
+ * @return The writer.
+ * @throws JSONException
+ */
+ public Writer write(Writer writer, int indentFactor, int indent)
+ throws JSONException
+ {
+ try
+ {
+ boolean commanate = false;
+ final int length = this.length();
+ writer.write('{');
+
+ if (length == 1)
+ {
+ final Entry<String, ?> entry = this.entrySet().iterator().next();
+ final String key = entry.getKey();
+ writer.write(quote(key));
+ writer.write(':');
+ if (indentFactor > 0)
+ {
+ writer.write(' ');
+ }
+ try
+ {
+ writeValue(writer, entry.getValue(), indentFactor, indent);
+ } catch (Exception e)
+ {
+ throw new JSONException(
+ "Unable to write JSONObject value for key: " + key, e);
+ }
+ }
+ else if (length != 0)
+ {
+ final int newindent = indent + indentFactor;
+ for (final Entry<String, ?> entry : this.entrySet())
+ {
+ if (commanate)
+ {
+ writer.write(',');
+ }
+ if (indentFactor > 0)
+ {
+ writer.write('\n');
+ }
+ indent(writer, newindent);
+ final String key = entry.getKey();
+ writer.write(quote(key));
+ writer.write(':');
+ if (indentFactor > 0)
+ {
+ writer.write(' ');
+ }
+ try
+ {
+ writeValue(writer, entry.getValue(), indentFactor, newindent);
+ } catch (Exception e)
+ {
+ throw new JSONException(
+ "Unable to write JSONObject value for key: " + key, e);
+ }
+ commanate = true;
+ }
+ if (indentFactor > 0)
+ {
+ writer.write('\n');
+ }
+ indent(writer, indent);
+ }
+ writer.write('}');
+ return writer;
+ } catch (IOException exception)
+ {
+ throw new JSONException(exception);
+ }
+ }
+
+ /**
+ * Returns a java.util.Map containing all of the entries in this object. If an
+ * entry in the object is a JSONArray or JSONObject it will also be converted.
+ * <p>
+ * Warning: This method assumes that the data structure is acyclical.
+ *
+ * @return a java.util.Map containing the entries of this object
+ */
+ public Map<String, Object> toMap()
+ {
+ Map<String, Object> results = new HashMap<String, Object>();
+ for (Entry<String, Object> entry : this.entrySet())
+ {
+ Object value;
+ if (entry.getValue() == null || NULL.equals(entry.getValue()))
+ {
+ value = null;
+ }
+ else if (entry.getValue() instanceof JSONObject)
+ {
+ value = ((JSONObject) entry.getValue()).toMap();
+ }
+ else if (entry.getValue() instanceof JSONArray)
+ {
+ value = ((JSONArray) entry.getValue()).toList();
+ }
+ else
+ {
+ value = entry.getValue();
+ }
+ results.put(entry.getKey(), value);
+ }
+ return results;
+ }
}
*
* In a nutshell, JSONPointer allows the user to navigate into a JSON document
* using strings, and retrieve targeted objects, like a simple form of XPATH.
- * Path segments are separated by the '/' char, which signifies the root of
- * the document when it appears as the first char of the string. Array
- * elements are navigated using ordinals, counting from 0. JSONPointer strings
- * may be extended to any arbitrary number of segments. If the navigation
- * is successful, the matched item is returned. A matched item may be a
- * JSONObject, a JSONArray, or a JSON value. If the JSONPointer string building
- * fails, an appropriate exception is thrown. If the navigation fails to find
- * a match, a JSONPointerException is thrown.
+ * Path segments are separated by the '/' char, which signifies the root of the
+ * document when it appears as the first char of the string. Array elements are
+ * navigated using ordinals, counting from 0. JSONPointer strings may be
+ * extended to any arbitrary number of segments. If the navigation is
+ * successful, the matched item is returned. A matched item may be a JSONObject,
+ * a JSONArray, or a JSON value. If the JSONPointer string building fails, an
+ * appropriate exception is thrown. If the navigation fails to find a match, a
+ * JSONPointerException is thrown.
*
* @author JSON.org
* @version 2016-05-14
*/
-public class JSONPointer {
+public class JSONPointer
+{
- // used for URL encoding and decoding
- private static final String ENCODING = "utf-8";
+ // used for URL encoding and decoding
+ private static final String ENCODING = "utf-8";
- /**
- * This class allows the user to build a JSONPointer in steps, using
- * exactly one segment in each step.
- */
- public static class Builder {
-
- // Segments for the eventual JSONPointer string
- private final List<String> refTokens = new ArrayList<String>();
-
- /**
- * Creates a {@code JSONPointer} instance using the tokens previously set using the
- * {@link #append(String)} method calls.
- */
- public JSONPointer build() {
- return new JSONPointer(this.refTokens);
- }
+ /**
+ * This class allows the user to build a JSONPointer in steps, using exactly
+ * one segment in each step.
+ */
+ public static class Builder
+ {
- /**
- * Adds an arbitrary token to the list of reference tokens. It can be any non-null value.
- *
- * Unlike in the case of JSON string or URI fragment representation of JSON pointers, the
- * argument of this method MUST NOT be escaped. If you want to query the property called
- * {@code "a~b"} then you should simply pass the {@code "a~b"} string as-is, there is no
- * need to escape it as {@code "a~0b"}.
- *
- * @param token the new token to be appended to the list
- * @return {@code this}
- * @throws NullPointerException if {@code token} is null
- */
- public Builder append(String token) {
- if (token == null) {
- throw new NullPointerException("token cannot be null");
- }
- this.refTokens.add(token);
- return this;
- }
+ // Segments for the eventual JSONPointer string
+ private final List<String> refTokens = new ArrayList<String>();
- /**
- * Adds an integer to the reference token list. Although not necessarily, mostly this token will
- * denote an array index.
- *
- * @param arrayIndex the array index to be added to the token list
- * @return {@code this}
- */
- public Builder append(int arrayIndex) {
- this.refTokens.add(String.valueOf(arrayIndex));
- return this;
- }
+ /**
+ * Creates a {@code JSONPointer} instance using the tokens previously set
+ * using the {@link #append(String)} method calls.
+ */
+ public JSONPointer build()
+ {
+ return new JSONPointer(this.refTokens);
}
/**
- * Static factory method for {@link Builder}. Example usage:
+ * Adds an arbitrary token to the list of reference tokens. It can be any
+ * non-null value.
*
- * <pre><code>
- * JSONPointer pointer = JSONPointer.builder()
- * .append("obj")
- * .append("other~key").append("another/key")
- * .append("\"")
- * .append(0)
- * .build();
- * </code></pre>
+ * Unlike in the case of JSON string or URI fragment representation of JSON
+ * pointers, the argument of this method MUST NOT be escaped. If you want to
+ * query the property called {@code "a~b"} then you should simply pass the
+ * {@code "a~b"} string as-is, there is no need to escape it as
+ * {@code "a~0b"}.
*
- * @return a builder instance which can be used to construct a {@code JSONPointer} instance by chained
- * {@link Builder#append(String)} calls.
+ * @param token
+ * the new token to be appended to the list
+ * @return {@code this}
+ * @throws NullPointerException
+ * if {@code token} is null
*/
- public static Builder builder() {
- return new Builder();
+ public Builder append(String token)
+ {
+ if (token == null)
+ {
+ throw new NullPointerException("token cannot be null");
+ }
+ this.refTokens.add(token);
+ return this;
}
- // Segments for the JSONPointer string
- private final List<String> refTokens;
-
/**
- * Pre-parses and initializes a new {@code JSONPointer} instance. If you want to
- * evaluate the same JSON Pointer on different JSON documents then it is recommended
- * to keep the {@code JSONPointer} instances due to performance considerations.
+ * Adds an integer to the reference token list. Although not necessarily,
+ * mostly this token will denote an array index.
*
- * @param pointer the JSON String or URI Fragment representation of the JSON pointer.
- * @throws IllegalArgumentException if {@code pointer} is not a valid JSON pointer
+ * @param arrayIndex
+ * the array index to be added to the token list
+ * @return {@code this}
*/
- public JSONPointer(final String pointer) {
- if (pointer == null) {
- throw new NullPointerException("pointer cannot be null");
- }
- if (pointer.isEmpty() || pointer.equals("#")) {
- this.refTokens = Collections.emptyList();
- return;
- }
- String refs;
- if (pointer.startsWith("#/")) {
- refs = pointer.substring(2);
- try {
- refs = URLDecoder.decode(refs, ENCODING);
- } catch (UnsupportedEncodingException e) {
- throw new RuntimeException(e);
- }
- } else if (pointer.startsWith("/")) {
- refs = pointer.substring(1);
- } else {
- throw new IllegalArgumentException("a JSON pointer should start with '/' or '#/'");
- }
- this.refTokens = new ArrayList<String>();
- int slashIdx = -1;
- int prevSlashIdx = 0;
- do {
- prevSlashIdx = slashIdx + 1;
- slashIdx = refs.indexOf('/', prevSlashIdx);
- if(prevSlashIdx == slashIdx || prevSlashIdx == refs.length()) {
- // found 2 slashes in a row ( obj//next )
- // or single slash at the end of a string ( obj/test/ )
- this.refTokens.add("");
- } else if (slashIdx >= 0) {
- final String token = refs.substring(prevSlashIdx, slashIdx);
- this.refTokens.add(unescape(token));
- } else {
- // last item after separator, or no separator at all.
- final String token = refs.substring(prevSlashIdx);
- this.refTokens.add(unescape(token));
- }
- } while (slashIdx >= 0);
- // using split does not take into account consecutive separators or "ending nulls"
- //for (String token : refs.split("/")) {
- // this.refTokens.add(unescape(token));
- //}
+ public Builder append(int arrayIndex)
+ {
+ this.refTokens.add(String.valueOf(arrayIndex));
+ return this;
}
+ }
- public JSONPointer(List<String> refTokens) {
- this.refTokens = new ArrayList<String>(refTokens);
- }
+ /**
+ * Static factory method for {@link Builder}. Example usage:
+ *
+ * <pre>
+ * <code>
+ * JSONPointer pointer = JSONPointer.builder()
+ * .append("obj")
+ * .append("other~key").append("another/key")
+ * .append("\"")
+ * .append(0)
+ * .build();
+ * </code>
+ * </pre>
+ *
+ * @return a builder instance which can be used to construct a
+ * {@code JSONPointer} instance by chained
+ * {@link Builder#append(String)} calls.
+ */
+ public static Builder builder()
+ {
+ return new Builder();
+ }
- private String unescape(String token) {
- return token.replace("~1", "/").replace("~0", "~")
- .replace("\\\"", "\"")
- .replace("\\\\", "\\");
- }
+ // Segments for the JSONPointer string
+ private final List<String> refTokens;
- /**
- * Evaluates this JSON Pointer on the given {@code document}. The {@code document}
- * is usually a {@link JSONObject} or a {@link JSONArray} instance, but the empty
- * JSON Pointer ({@code ""}) can be evaluated on any JSON values and in such case the
- * returned value will be {@code document} itself.
- *
- * @param document the JSON document which should be the subject of querying.
- * @return the result of the evaluation
- * @throws JSONPointerException if an error occurs during evaluation
- */
- public Object queryFrom(Object document) throws JSONPointerException {
- if (this.refTokens.isEmpty()) {
- return document;
- }
- Object current = document;
- for (String token : this.refTokens) {
- if (current instanceof JSONObject) {
- current = ((JSONObject) current).opt(unescape(token));
- } else if (current instanceof JSONArray) {
- current = readByIndexToken(current, token);
- } else {
- throw new JSONPointerException(format(
- "value [%s] is not an array or object therefore its key %s cannot be resolved", current,
- token));
- }
- }
- return current;
+ /**
+ * Pre-parses and initializes a new {@code JSONPointer} instance. If you want
+ * to evaluate the same JSON Pointer on different JSON documents then it is
+ * recommended to keep the {@code JSONPointer} instances due to performance
+ * considerations.
+ *
+ * @param pointer
+ * the JSON String or URI Fragment representation of the JSON
+ * pointer.
+ * @throws IllegalArgumentException
+ * if {@code pointer} is not a valid JSON pointer
+ */
+ public JSONPointer(final String pointer)
+ {
+ if (pointer == null)
+ {
+ throw new NullPointerException("pointer cannot be null");
+ }
+ if (pointer.isEmpty() || pointer.equals("#"))
+ {
+ this.refTokens = Collections.emptyList();
+ return;
+ }
+ String refs;
+ if (pointer.startsWith("#/"))
+ {
+ refs = pointer.substring(2);
+ try
+ {
+ refs = URLDecoder.decode(refs, ENCODING);
+ } catch (UnsupportedEncodingException e)
+ {
+ throw new RuntimeException(e);
+ }
+ }
+ else if (pointer.startsWith("/"))
+ {
+ refs = pointer.substring(1);
}
+ else
+ {
+ throw new IllegalArgumentException(
+ "a JSON pointer should start with '/' or '#/'");
+ }
+ this.refTokens = new ArrayList<String>();
+ int slashIdx = -1;
+ int prevSlashIdx = 0;
+ do
+ {
+ prevSlashIdx = slashIdx + 1;
+ slashIdx = refs.indexOf('/', prevSlashIdx);
+ if (prevSlashIdx == slashIdx || prevSlashIdx == refs.length())
+ {
+ // found 2 slashes in a row ( obj//next )
+ // or single slash at the end of a string ( obj/test/ )
+ this.refTokens.add("");
+ }
+ else if (slashIdx >= 0)
+ {
+ final String token = refs.substring(prevSlashIdx, slashIdx);
+ this.refTokens.add(unescape(token));
+ }
+ else
+ {
+ // last item after separator, or no separator at all.
+ final String token = refs.substring(prevSlashIdx);
+ this.refTokens.add(unescape(token));
+ }
+ } while (slashIdx >= 0);
+ // using split does not take into account consecutive separators or "ending
+ // nulls"
+ // for (String token : refs.split("/")) {
+ // this.refTokens.add(unescape(token));
+ // }
+ }
- /**
- * Matches a JSONArray element by ordinal position
- * @param current the JSONArray to be evaluated
- * @param indexToken the array index in string form
- * @return the matched object. If no matching item is found a
- * @throws JSONPointerException is thrown if the index is out of bounds
- */
- private Object readByIndexToken(Object current, String indexToken) throws JSONPointerException {
- try {
- int index = Integer.parseInt(indexToken);
- JSONArray currentArr = (JSONArray) current;
- if (index >= currentArr.length()) {
- throw new JSONPointerException(format("index %d is out of bounds - the array has %d elements", index,
- currentArr.length()));
- }
- try {
- return currentArr.get(index);
- } catch (JSONException e) {
- throw new JSONPointerException("Error reading value at index position " + index, e);
- }
- } catch (NumberFormatException e) {
- throw new JSONPointerException(format("%s is not an array index", indexToken), e);
- }
+ public JSONPointer(List<String> refTokens)
+ {
+ this.refTokens = new ArrayList<String>(refTokens);
+ }
+
+ private String unescape(String token)
+ {
+ return token.replace("~1", "/").replace("~0", "~").replace("\\\"", "\"")
+ .replace("\\\\", "\\");
+ }
+
+ /**
+ * Evaluates this JSON Pointer on the given {@code document}. The
+ * {@code document} is usually a {@link JSONObject} or a {@link JSONArray}
+ * instance, but the empty JSON Pointer ({@code ""}) can be evaluated on any
+ * JSON values and in such case the returned value will be {@code document}
+ * itself.
+ *
+ * @param document
+ * the JSON document which should be the subject of querying.
+ * @return the result of the evaluation
+ * @throws JSONPointerException
+ * if an error occurs during evaluation
+ */
+ public Object queryFrom(Object document) throws JSONPointerException
+ {
+ if (this.refTokens.isEmpty())
+ {
+ return document;
+ }
+ Object current = document;
+ for (String token : this.refTokens)
+ {
+ if (current instanceof JSONObject)
+ {
+ current = ((JSONObject) current).opt(unescape(token));
+ }
+ else if (current instanceof JSONArray)
+ {
+ current = readByIndexToken(current, token);
+ }
+ else
+ {
+ throw new JSONPointerException(format(
+ "value [%s] is not an array or object therefore its key %s cannot be resolved",
+ current, token));
+ }
}
+ return current;
+ }
- /**
- * Returns a string representing the JSONPointer path value using string
- * representation
- */
- @Override
- public String toString() {
- StringBuilder rval = new StringBuilder("");
- for (String token: this.refTokens) {
- rval.append('/').append(escape(token));
- }
- return rval.toString();
+ /**
+ * Matches a JSONArray element by ordinal position
+ *
+ * @param current
+ * the JSONArray to be evaluated
+ * @param indexToken
+ * the array index in string form
+ * @return the matched object. If no matching item is found a
+ * @throws JSONPointerException
+ * is thrown if the index is out of bounds
+ */
+ private Object readByIndexToken(Object current, String indexToken)
+ throws JSONPointerException
+ {
+ try
+ {
+ int index = Integer.parseInt(indexToken);
+ JSONArray currentArr = (JSONArray) current;
+ if (index >= currentArr.length())
+ {
+ throw new JSONPointerException(format(
+ "index %d is out of bounds - the array has %d elements",
+ index, currentArr.length()));
+ }
+ try
+ {
+ return currentArr.get(index);
+ } catch (JSONException e)
+ {
+ throw new JSONPointerException(
+ "Error reading value at index position " + index, e);
+ }
+ } catch (NumberFormatException e)
+ {
+ throw new JSONPointerException(
+ format("%s is not an array index", indexToken), e);
}
+ }
- /**
- * Escapes path segment values to an unambiguous form.
- * The escape char to be inserted is '~'. The chars to be escaped
- * are ~, which maps to ~0, and /, which maps to ~1. Backslashes
- * and double quote chars are also escaped.
- * @param token the JSONPointer segment value to be escaped
- * @return the escaped value for the token
- */
- private String escape(String token) {
- return token.replace("~", "~0")
- .replace("/", "~1")
- .replace("\\", "\\\\")
- .replace("\"", "\\\"");
+ /**
+ * Returns a string representing the JSONPointer path value using string
+ * representation
+ */
+ @Override
+ public String toString()
+ {
+ StringBuilder rval = new StringBuilder("");
+ for (String token : this.refTokens)
+ {
+ rval.append('/').append(escape(token));
}
+ return rval.toString();
+ }
- /**
- * Returns a string representing the JSONPointer path value using URI
- * fragment identifier representation
- */
- public String toURIFragment() {
- try {
- StringBuilder rval = new StringBuilder("#");
- for (String token : this.refTokens) {
- rval.append('/').append(URLEncoder.encode(token, ENCODING));
- }
- return rval.toString();
- } catch (UnsupportedEncodingException e) {
- throw new RuntimeException(e);
- }
+ /**
+ * Escapes path segment values to an unambiguous form. The escape char to be
+ * inserted is '~'. The chars to be escaped are ~, which maps to ~0, and /,
+ * which maps to ~1. Backslashes and double quote chars are also escaped.
+ *
+ * @param token
+ * the JSONPointer segment value to be escaped
+ * @return the escaped value for the token
+ */
+ private String escape(String token)
+ {
+ return token.replace("~", "~0").replace("/", "~1").replace("\\", "\\\\")
+ .replace("\"", "\\\"");
+ }
+
+ /**
+ * Returns a string representing the JSONPointer path value using URI fragment
+ * identifier representation
+ */
+ public String toURIFragment()
+ {
+ try
+ {
+ StringBuilder rval = new StringBuilder("#");
+ for (String token : this.refTokens)
+ {
+ rval.append('/').append(URLEncoder.encode(token, ENCODING));
+ }
+ return rval.toString();
+ } catch (UnsupportedEncodingException e)
+ {
+ throw new RuntimeException(e);
}
-
+ }
+
}
* @author JSON.org
* @version 2016-05-13
*/
-public class JSONPointerException extends JSONException {
- private static final long serialVersionUID = 8872944667561856751L;
-
- public JSONPointerException(String message) {
- super(message);
- }
-
- public JSONPointerException(String message, Throwable cause) {
- super(message, cause);
- }
+public class JSONPointerException extends JSONException
+{
+ private static final long serialVersionUID = 8872944667561856751L;
+
+ public JSONPointerException(String message)
+ {
+ super(message);
+ }
+
+ public JSONPointerException(String message, Throwable cause)
+ {
+ super(message, cause);
+ }
}
@Documented
@Retention(RUNTIME)
-@Target({METHOD})
+@Target({ METHOD })
/**
- * Use this annotation on a getter method to override the Bean name
- * parser for Bean -> JSONObject mapping. If this annotation is
- * present at any level in the class hierarchy, then the method will
- * not be serialized from the bean into the JSONObject.
+ * Use this annotation on a getter method to override the Bean name parser for
+ * Bean -> JSONObject mapping. If this annotation is present at any level in
+ * the class hierarchy, then the method will not be serialized from the bean
+ * into the JSONObject.
*/
-public @interface JSONPropertyIgnore { }
+public @interface JSONPropertyIgnore
+{
+}
@Documented
@Retention(RUNTIME)
-@Target({METHOD})
+@Target({ METHOD })
/**
- * Use this annotation on a getter method to override the Bean name
- * parser for Bean -> JSONObject mapping. A value set to empty string <code>""</code>
+ * Use this annotation on a getter method to override the Bean name parser for
+ * Bean -> JSONObject mapping. A value set to empty string <code>""</code>
* will have the Bean parser fall back to the default field name processing.
*/
-public @interface JSONPropertyName {
- /**
- * @return The name of the property as to be used in the JSON Object.
- */
- String value();
+public @interface JSONPropertyName
+{
+ /**
+ * @return The name of the property as to be used in the JSON Object.
+ */
+ String value();
}
package org.json;
+
/**
* The <code>JSONString</code> interface allows a <code>toJSONString()</code>
* method so that a class can change the behavior of
- * <code>JSONObject.toString()</code>, <code>JSONArray.toString()</code>,
- * and <code>JSONWriter.value(</code>Object<code>)</code>. The
+ * <code>JSONObject.toString()</code>, <code>JSONArray.toString()</code>, and
+ * <code>JSONWriter.value(</code>Object<code>)</code>. The
* <code>toJSONString</code> method will be used instead of the default behavior
* of using the Object's <code>toString()</code> method and quoting the result.
*/
-public interface JSONString {
- /**
- * The <code>toJSONString</code> method allows a class to produce its own JSON
- * serialization.
- *
- * @return A strictly syntactically correct JSON text.
- */
- public String toJSONString();
+public interface JSONString
+{
+ /**
+ * The <code>toJSONString</code> method allows a class to produce its own JSON
+ * serialization.
+ *
+ * @return A strictly syntactically correct JSON text.
+ */
+ public String toJSONString();
}
import java.io.StringWriter;
/**
- * JSONStringer provides a quick and convenient way of producing JSON text.
- * The texts produced strictly conform to JSON syntax rules. No whitespace is
- * added, so the results are ready for transmission or storage. Each instance of
+ * JSONStringer provides a quick and convenient way of producing JSON text. The
+ * texts produced strictly conform to JSON syntax rules. No whitespace is added,
+ * so the results are ready for transmission or storage. Each instance of
* JSONStringer can produce one JSON text.
* <p>
* A JSONStringer instance provides a <code>value</code> method for appending
- * values to the
- * text, and a <code>key</code>
- * method for adding keys before values in objects. There are <code>array</code>
- * and <code>endArray</code> methods that make and bound array values, and
- * <code>object</code> and <code>endObject</code> methods which make and bound
- * object values. All of these methods return the JSONWriter instance,
- * permitting cascade style. For example, <pre>
- * myString = new JSONStringer()
- * .object()
- * .key("JSON")
- * .value("Hello, World!")
- * .endObject()
- * .toString();</pre> which produces the string <pre>
- * {"JSON":"Hello, World!"}</pre>
+ * values to the text, and a <code>key</code> method for adding keys before
+ * values in objects. There are <code>array</code> and <code>endArray</code>
+ * methods that make and bound array values, and <code>object</code> and
+ * <code>endObject</code> methods which make and bound object values. All of
+ * these methods return the JSONWriter instance, permitting cascade style. For
+ * example,
+ *
+ * <pre>
+ * myString = new JSONStringer().object().key("JSON").value("Hello, World!")
+ * .endObject().toString();
+ * </pre>
+ *
+ * which produces the string
+ *
+ * <pre>
+ * {"JSON":"Hello, World!"}
+ * </pre>
* <p>
* The first method called must be <code>array</code> or <code>object</code>.
* There are no methods for adding commas or colons. JSONStringer adds them for
* you. Objects and arrays can be nested up to 20 levels deep.
* <p>
* This can sometimes be easier than using a JSONObject to build a string.
+ *
* @author JSON.org
* @version 2015-12-09
*/
-public class JSONStringer extends JSONWriter {
- /**
- * Make a fresh JSONStringer. It can be used to build one JSON text.
- */
- public JSONStringer() {
- super(new StringWriter());
- }
+public class JSONStringer extends JSONWriter
+{
+ /**
+ * Make a fresh JSONStringer. It can be used to build one JSON text.
+ */
+ public JSONStringer()
+ {
+ super(new StringWriter());
+ }
- /**
- * Return the JSON text. This method is used to obtain the product of the
- * JSONStringer instance. It will return <code>null</code> if there was a
- * problem in the construction of the JSON text (such as the calls to
- * <code>array</code> were not properly balanced with calls to
- * <code>endArray</code>).
- * @return The JSON text.
- */
- @Override
- public String toString() {
- return this.mode == 'd' ? this.writer.toString() : null;
- }
+ /**
+ * Return the JSON text. This method is used to obtain the product of the
+ * JSONStringer instance. It will return <code>null</code> if there was a
+ * problem in the construction of the JSON text (such as the calls to
+ * <code>array</code> were not properly balanced with calls to
+ * <code>endArray</code>).
+ *
+ * @return The JSON text.
+ */
+ @Override
+ public String toString()
+ {
+ return this.mode == 'd' ? this.writer.toString() : null;
+ }
}
/**
* A JSONTokener takes a source string and extracts characters and tokens from
- * it. It is used by the JSONObject and JSONArray constructors to parse
- * JSON source strings.
+ * it. It is used by the JSONObject and JSONArray constructors to parse JSON
+ * source strings.
+ *
* @author JSON.org
* @version 2014-05-03
*/
-public class JSONTokener {
- /** current read character position on the current line. */
- private long character;
- /** flag to indicate if the end of the input has been found. */
- private boolean eof;
- /** current read index of the input. */
- private long index;
- /** current line of the input. */
- private long line;
- /** previous character read from the input. */
- private char previous;
- /** Reader for the input. */
- private final Reader reader;
- /** flag to indicate that a previous character was requested. */
- private boolean usePrevious;
- /** the number of characters read in the previous line. */
- private long characterPreviousLine;
-
-
- /**
- * Construct a JSONTokener from a Reader. The caller must close the Reader.
- *
- * @param reader A reader.
- */
- public JSONTokener(Reader reader) {
- this.reader = reader.markSupported()
- ? reader
- : new BufferedReader(reader);
- this.eof = false;
- this.usePrevious = false;
- this.previous = 0;
- this.index = 0;
- this.character = 1;
- this.characterPreviousLine = 0;
- this.line = 1;
+public class JSONTokener
+{
+ /** current read character position on the current line. */
+ private long character;
+
+ /** flag to indicate if the end of the input has been found. */
+ private boolean eof;
+
+ /** current read index of the input. */
+ private long index;
+
+ /** current line of the input. */
+ private long line;
+
+ /** previous character read from the input. */
+ private char previous;
+
+ /** Reader for the input. */
+ private final Reader reader;
+
+ /** flag to indicate that a previous character was requested. */
+ private boolean usePrevious;
+
+ /** the number of characters read in the previous line. */
+ private long characterPreviousLine;
+
+ /**
+ * Construct a JSONTokener from a Reader. The caller must close the Reader.
+ *
+ * @param reader
+ * A reader.
+ */
+ public JSONTokener(Reader reader)
+ {
+ this.reader = reader.markSupported() ? reader
+ : new BufferedReader(reader);
+ this.eof = false;
+ this.usePrevious = false;
+ this.previous = 0;
+ this.index = 0;
+ this.character = 1;
+ this.characterPreviousLine = 0;
+ this.line = 1;
+ }
+
+ /**
+ * Construct a JSONTokener from an InputStream. The caller must close the
+ * input stream.
+ *
+ * @param inputStream
+ * The source.
+ */
+ public JSONTokener(InputStream inputStream)
+ {
+ this(new InputStreamReader(inputStream));
+ }
+
+ /**
+ * Construct a JSONTokener from a string.
+ *
+ * @param s
+ * A source string.
+ */
+ public JSONTokener(String s)
+ {
+ this(new StringReader(s));
+ }
+
+ /**
+ * Back up one character. This provides a sort of lookahead capability, so
+ * that you can test for a digit or letter before attempting to parse the next
+ * number or identifier.
+ *
+ * @throws JSONException
+ * Thrown if trying to step back more than 1 step or if already at
+ * the start of the string
+ */
+ public void back() throws JSONException
+ {
+ if (this.usePrevious || this.index <= 0)
+ {
+ throw new JSONException("Stepping back two steps is not supported");
}
-
-
- /**
- * Construct a JSONTokener from an InputStream. The caller must close the input stream.
- * @param inputStream The source.
- */
- public JSONTokener(InputStream inputStream) {
- this(new InputStreamReader(inputStream));
+ this.decrementIndexes();
+ this.usePrevious = true;
+ this.eof = false;
+ }
+
+ /**
+ * Decrements the indexes for the {@link #back()} method based on the previous
+ * character read.
+ */
+ private void decrementIndexes()
+ {
+ this.index--;
+ if (this.previous == '\r' || this.previous == '\n')
+ {
+ this.line--;
+ this.character = this.characterPreviousLine;
}
-
-
- /**
- * Construct a JSONTokener from a string.
- *
- * @param s A source string.
- */
- public JSONTokener(String s) {
- this(new StringReader(s));
+ else if (this.character > 0)
+ {
+ this.character--;
}
-
-
- /**
- * Back up one character. This provides a sort of lookahead capability,
- * so that you can test for a digit or letter before attempting to parse
- * the next number or identifier.
- * @throws JSONException Thrown if trying to step back more than 1 step
- * or if already at the start of the string
- */
- public void back() throws JSONException {
- if (this.usePrevious || this.index <= 0) {
- throw new JSONException("Stepping back two steps is not supported");
- }
- this.decrementIndexes();
- this.usePrevious = true;
- this.eof = false;
+ }
+
+ /**
+ * Get the hex value of a character (base16).
+ *
+ * @param c
+ * A character between '0' and '9' or between 'A' and 'F' or between
+ * 'a' and 'f'.
+ * @return An int between 0 and 15, or -1 if c was not a hex digit.
+ */
+ public static int dehexchar(char c)
+ {
+ if (c >= '0' && c <= '9')
+ {
+ return c - '0';
}
-
- /**
- * Decrements the indexes for the {@link #back()} method based on the previous character read.
- */
- private void decrementIndexes() {
- this.index--;
- if(this.previous=='\r' || this.previous == '\n') {
- this.line--;
- this.character=this.characterPreviousLine ;
- } else if(this.character > 0){
- this.character--;
- }
+ if (c >= 'A' && c <= 'F')
+ {
+ return c - ('A' - 10);
}
-
- /**
- * Get the hex value of a character (base16).
- * @param c A character between '0' and '9' or between 'A' and 'F' or
- * between 'a' and 'f'.
- * @return An int between 0 and 15, or -1 if c was not a hex digit.
- */
- public static int dehexchar(char c) {
- if (c >= '0' && c <= '9') {
- return c - '0';
- }
- if (c >= 'A' && c <= 'F') {
- return c - ('A' - 10);
- }
- if (c >= 'a' && c <= 'f') {
- return c - ('a' - 10);
- }
- return -1;
+ if (c >= 'a' && c <= 'f')
+ {
+ return c - ('a' - 10);
}
-
- /**
- * Checks if the end of the input has been reached.
- *
- * @return true if at the end of the file and we didn't step back
- */
- public boolean end() {
- return this.eof && !this.usePrevious;
+ return -1;
+ }
+
+ /**
+ * Checks if the end of the input has been reached.
+ *
+ * @return true if at the end of the file and we didn't step back
+ */
+ public boolean end()
+ {
+ return this.eof && !this.usePrevious;
+ }
+
+ /**
+ * Determine if the source string still contains characters that next() can
+ * consume.
+ *
+ * @return true if not yet at the end of the source.
+ * @throws JSONException
+ * thrown if there is an error stepping forward or backward while
+ * checking for more data.
+ */
+ public boolean more() throws JSONException
+ {
+ if (this.usePrevious)
+ {
+ return true;
}
-
-
- /**
- * Determine if the source string still contains characters that next()
- * can consume.
- * @return true if not yet at the end of the source.
- * @throws JSONException thrown if there is an error stepping forward
- * or backward while checking for more data.
- */
- public boolean more() throws JSONException {
- if(this.usePrevious) {
- return true;
- }
- try {
- this.reader.mark(1);
- } catch (IOException e) {
- throw new JSONException("Unable to preserve stream position", e);
- }
- try {
- // -1 is EOF, but next() can not consume the null character '\0'
- if(this.reader.read() <= 0) {
- this.eof = true;
- return false;
- }
- this.reader.reset();
- } catch (IOException e) {
- throw new JSONException("Unable to read the next character from the stream", e);
- }
- return true;
+ try
+ {
+ this.reader.mark(1);
+ } catch (IOException e)
+ {
+ throw new JSONException("Unable to preserve stream position", e);
}
-
-
- /**
- * Get the next character in the source string.
- *
- * @return The next character, or 0 if past the end of the source string.
- * @throws JSONException Thrown if there is an error reading the source string.
- */
- public char next() throws JSONException {
- int c;
- if (this.usePrevious) {
- this.usePrevious = false;
- c = this.previous;
- } else {
- try {
- c = this.reader.read();
- } catch (IOException exception) {
- throw new JSONException(exception);
- }
- }
- if (c <= 0) { // End of stream
- this.eof = true;
- return 0;
- }
- this.incrementIndexes(c);
- this.previous = (char) c;
- return this.previous;
+ try
+ {
+ // -1 is EOF, but next() can not consume the null character '\0'
+ if (this.reader.read() <= 0)
+ {
+ this.eof = true;
+ return false;
+ }
+ this.reader.reset();
+ } catch (IOException e)
+ {
+ throw new JSONException(
+ "Unable to read the next character from the stream", e);
}
-
- /**
- * Increments the internal indexes according to the previous character
- * read and the character passed as the current character.
- * @param c the current character read.
- */
- private void incrementIndexes(int c) {
- if(c > 0) {
- this.index++;
- if(c=='\r') {
- this.line++;
- this.characterPreviousLine = this.character;
- this.character=0;
- }else if (c=='\n') {
- if(this.previous != '\r') {
- this.line++;
- this.characterPreviousLine = this.character;
- }
- this.character=0;
- } else {
- this.character++;
- }
- }
+ return true;
+ }
+
+ /**
+ * Get the next character in the source string.
+ *
+ * @return The next character, or 0 if past the end of the source string.
+ * @throws JSONException
+ * Thrown if there is an error reading the source string.
+ */
+ public char next() throws JSONException
+ {
+ int c;
+ if (this.usePrevious)
+ {
+ this.usePrevious = false;
+ c = this.previous;
}
-
- /**
- * Consume the next character, and check that it matches a specified
- * character.
- * @param c The character to match.
- * @return The character.
- * @throws JSONException if the character does not match.
- */
- public char next(char c) throws JSONException {
- char n = this.next();
- if (n != c) {
- if(n > 0) {
- throw this.syntaxError("Expected '" + c + "' and instead saw '" +
- n + "'");
- }
- throw this.syntaxError("Expected '" + c + "' and instead saw ''");
- }
- return n;
+ else
+ {
+ try
+ {
+ c = this.reader.read();
+ } catch (IOException exception)
+ {
+ throw new JSONException(exception);
+ }
}
-
-
- /**
- * Get the next n characters.
- *
- * @param n The number of characters to take.
- * @return A string of n characters.
- * @throws JSONException
- * Substring bounds error if there are not
- * n characters remaining in the source string.
- */
- public String next(int n) throws JSONException {
- if (n == 0) {
- return "";
- }
-
- char[] chars = new char[n];
- int pos = 0;
-
- while (pos < n) {
- chars[pos] = this.next();
- if (this.end()) {
- throw this.syntaxError("Substring bounds error");
- }
- pos += 1;
- }
- return new String(chars);
+ if (c <= 0)
+ { // End of stream
+ this.eof = true;
+ return 0;
}
-
-
- /**
- * Get the next char in the string, skipping whitespace.
- * @throws JSONException Thrown if there is an error reading the source string.
- * @return A character, or 0 if there are no more characters.
- */
- public char nextClean() throws JSONException {
- for (;;) {
- char c = this.next();
- if (c == 0 || c > ' ') {
- return c;
- }
+ this.incrementIndexes(c);
+ this.previous = (char) c;
+ return this.previous;
+ }
+
+ /**
+ * Increments the internal indexes according to the previous character read
+ * and the character passed as the current character.
+ *
+ * @param c
+ * the current character read.
+ */
+ private void incrementIndexes(int c)
+ {
+ if (c > 0)
+ {
+ this.index++;
+ if (c == '\r')
+ {
+ this.line++;
+ this.characterPreviousLine = this.character;
+ this.character = 0;
+ }
+ else if (c == '\n')
+ {
+ if (this.previous != '\r')
+ {
+ this.line++;
+ this.characterPreviousLine = this.character;
}
+ this.character = 0;
+ }
+ else
+ {
+ this.character++;
+ }
}
-
-
- /**
- * Return the characters up to the next close quote character.
- * Backslash processing is done. The formal JSON format does not
- * allow strings in single quotes, but an implementation is allowed to
- * accept them.
- * @param quote The quoting character, either
- * <code>"</code> <small>(double quote)</small> or
- * <code>'</code> <small>(single quote)</small>.
- * @return A String.
- * @throws JSONException Unterminated string.
- */
- public String nextString(char quote) throws JSONException {
- char c;
- StringBuilder sb = new StringBuilder();
- for (;;) {
- c = this.next();
- switch (c) {
- case 0:
- case '\n':
- case '\r':
- throw this.syntaxError("Unterminated string");
- case '\\':
- c = this.next();
- switch (c) {
- case 'b':
- sb.append('\b');
- break;
- case 't':
- sb.append('\t');
- break;
- case 'n':
- sb.append('\n');
- break;
- case 'f':
- sb.append('\f');
- break;
- case 'r':
- sb.append('\r');
- break;
- case 'u':
- try {
- sb.append((char)Integer.parseInt(this.next(4), 16));
- } catch (NumberFormatException e) {
- throw this.syntaxError("Illegal escape.", e);
- }
- break;
- case '"':
- case '\'':
- case '\\':
- case '/':
- sb.append(c);
- break;
- default:
- throw this.syntaxError("Illegal escape.");
- }
- break;
- default:
- if (c == quote) {
- return sb.toString();
- }
- sb.append(c);
- }
- }
+ }
+
+ /**
+ * Consume the next character, and check that it matches a specified
+ * character.
+ *
+ * @param c
+ * The character to match.
+ * @return The character.
+ * @throws JSONException
+ * if the character does not match.
+ */
+ public char next(char c) throws JSONException
+ {
+ char n = this.next();
+ if (n != c)
+ {
+ if (n > 0)
+ {
+ throw this.syntaxError(
+ "Expected '" + c + "' and instead saw '" + n + "'");
+ }
+ throw this.syntaxError("Expected '" + c + "' and instead saw ''");
}
-
-
- /**
- * Get the text up but not including the specified character or the
- * end of line, whichever comes first.
- * @param delimiter A delimiter character.
- * @return A string.
- * @throws JSONException Thrown if there is an error while searching
- * for the delimiter
- */
- public String nextTo(char delimiter) throws JSONException {
- StringBuilder sb = new StringBuilder();
- for (;;) {
- char c = this.next();
- if (c == delimiter || c == 0 || c == '\n' || c == '\r') {
- if (c != 0) {
- this.back();
- }
- return sb.toString().trim();
- }
- sb.append(c);
- }
+ return n;
+ }
+
+ /**
+ * Get the next n characters.
+ *
+ * @param n
+ * The number of characters to take.
+ * @return A string of n characters.
+ * @throws JSONException
+ * Substring bounds error if there are not n characters remaining in
+ * the source string.
+ */
+ public String next(int n) throws JSONException
+ {
+ if (n == 0)
+ {
+ return "";
}
-
- /**
- * Get the text up but not including one of the specified delimiter
- * characters or the end of line, whichever comes first.
- * @param delimiters A set of delimiter characters.
- * @return A string, trimmed.
- * @throws JSONException Thrown if there is an error while searching
- * for the delimiter
- */
- public String nextTo(String delimiters) throws JSONException {
- char c;
- StringBuilder sb = new StringBuilder();
- for (;;) {
- c = this.next();
- if (delimiters.indexOf(c) >= 0 || c == 0 ||
- c == '\n' || c == '\r') {
- if (c != 0) {
- this.back();
- }
- return sb.toString().trim();
- }
- sb.append(c);
- }
+ char[] chars = new char[n];
+ int pos = 0;
+
+ while (pos < n)
+ {
+ chars[pos] = this.next();
+ if (this.end())
+ {
+ throw this.syntaxError("Substring bounds error");
+ }
+ pos += 1;
}
-
-
- /**
- * Get the next value. The value can be a Boolean, Double, Integer,
- * JSONArray, JSONObject, Long, or String, or the JSONObject.NULL object.
- * @throws JSONException If syntax error.
- *
- * @return An object.
- */
- public Object nextValue() throws JSONException {
- char c = this.nextClean();
- String string;
-
- switch (c) {
+ return new String(chars);
+ }
+
+ /**
+ * Get the next char in the string, skipping whitespace.
+ *
+ * @throws JSONException
+ * Thrown if there is an error reading the source string.
+ * @return A character, or 0 if there are no more characters.
+ */
+ public char nextClean() throws JSONException
+ {
+ for (;;)
+ {
+ char c = this.next();
+ if (c == 0 || c > ' ')
+ {
+ return c;
+ }
+ }
+ }
+
+ /**
+ * Return the characters up to the next close quote character. Backslash
+ * processing is done. The formal JSON format does not allow strings in single
+ * quotes, but an implementation is allowed to accept them.
+ *
+ * @param quote
+ * The quoting character, either <code>"</code> <small>(double
+ * quote)</small> or <code>'</code> <small>(single
+ * quote)</small>.
+ * @return A String.
+ * @throws JSONException
+ * Unterminated string.
+ */
+ public String nextString(char quote) throws JSONException
+ {
+ char c;
+ StringBuilder sb = new StringBuilder();
+ for (;;)
+ {
+ c = this.next();
+ switch (c)
+ {
+ case 0:
+ case '\n':
+ case '\r':
+ throw this.syntaxError("Unterminated string");
+ case '\\':
+ c = this.next();
+ switch (c)
+ {
+ case 'b':
+ sb.append('\b');
+ break;
+ case 't':
+ sb.append('\t');
+ break;
+ case 'n':
+ sb.append('\n');
+ break;
+ case 'f':
+ sb.append('\f');
+ break;
+ case 'r':
+ sb.append('\r');
+ break;
+ case 'u':
+ try
+ {
+ sb.append((char) Integer.parseInt(this.next(4), 16));
+ } catch (NumberFormatException e)
+ {
+ throw this.syntaxError("Illegal escape.", e);
+ }
+ break;
case '"':
case '\'':
- return this.nextString(c);
- case '{':
- this.back();
- return new JSONObject(this);
- case '[':
- this.back();
- return new JSONArray(this);
+ case '\\':
+ case '/':
+ sb.append(c);
+ break;
+ default:
+ throw this.syntaxError("Illegal escape.");
}
-
- /*
- * Handle unquoted text. This could be the values true, false, or
- * null, or it can be a number. An implementation (such as this one)
- * is allowed to also accept non-standard forms.
- *
- * Accumulate characters until we reach the end of the text or a
- * formatting character.
- */
-
- StringBuilder sb = new StringBuilder();
- while (c >= ' ' && ",:]}/\\\"[{;=#".indexOf(c) < 0) {
- sb.append(c);
- c = this.next();
+ break;
+ default:
+ if (c == quote)
+ {
+ return sb.toString();
}
- this.back();
-
- string = sb.toString().trim();
- if ("".equals(string)) {
- throw this.syntaxError("Missing value");
+ sb.append(c);
+ }
+ }
+ }
+
+ /**
+ * Get the text up but not including the specified character or the end of
+ * line, whichever comes first.
+ *
+ * @param delimiter
+ * A delimiter character.
+ * @return A string.
+ * @throws JSONException
+ * Thrown if there is an error while searching for the delimiter
+ */
+ public String nextTo(char delimiter) throws JSONException
+ {
+ StringBuilder sb = new StringBuilder();
+ for (;;)
+ {
+ char c = this.next();
+ if (c == delimiter || c == 0 || c == '\n' || c == '\r')
+ {
+ if (c != 0)
+ {
+ this.back();
}
- return JSONObject.stringToValue(string);
+ return sb.toString().trim();
+ }
+ sb.append(c);
}
-
-
- /**
- * Skip characters until the next character is the requested character.
- * If the requested character is not found, no characters are skipped.
- * @param to A character to skip to.
- * @return The requested character, or zero if the requested character
- * is not found.
- * @throws JSONException Thrown if there is an error while searching
- * for the to character
- */
- public char skipTo(char to) throws JSONException {
- char c;
- try {
- long startIndex = this.index;
- long startCharacter = this.character;
- long startLine = this.line;
- this.reader.mark(1000000);
- do {
- c = this.next();
- if (c == 0) {
- // in some readers, reset() may throw an exception if
- // the remaining portion of the input is greater than
- // the mark size (1,000,000 above).
- this.reader.reset();
- this.index = startIndex;
- this.character = startCharacter;
- this.line = startLine;
- return 0;
- }
- } while (c != to);
- this.reader.mark(1);
- } catch (IOException exception) {
- throw new JSONException(exception);
+ }
+
+ /**
+ * Get the text up but not including one of the specified delimiter characters
+ * or the end of line, whichever comes first.
+ *
+ * @param delimiters
+ * A set of delimiter characters.
+ * @return A string, trimmed.
+ * @throws JSONException
+ * Thrown if there is an error while searching for the delimiter
+ */
+ public String nextTo(String delimiters) throws JSONException
+ {
+ char c;
+ StringBuilder sb = new StringBuilder();
+ for (;;)
+ {
+ c = this.next();
+ if (delimiters.indexOf(c) >= 0 || c == 0 || c == '\n' || c == '\r')
+ {
+ if (c != 0)
+ {
+ this.back();
}
- this.back();
- return c;
+ return sb.toString().trim();
+ }
+ sb.append(c);
}
-
- /**
- * Make a JSONException to signal a syntax error.
- *
- * @param message The error message.
- * @return A JSONException object, suitable for throwing
- */
- public JSONException syntaxError(String message) {
- return new JSONException(message + this.toString());
+ }
+
+ /**
+ * Get the next value. The value can be a Boolean, Double, Integer, JSONArray,
+ * JSONObject, Long, or String, or the JSONObject.NULL object.
+ *
+ * @throws JSONException
+ * If syntax error.
+ *
+ * @return An object.
+ */
+ public Object nextValue() throws JSONException
+ {
+ char c = this.nextClean();
+ String string;
+
+ switch (c)
+ {
+ case '"':
+ case '\'':
+ return this.nextString(c);
+ case '{':
+ this.back();
+ return new JSONObject(this);
+ case '[':
+ this.back();
+ return new JSONArray(this);
}
- /**
- * Make a JSONException to signal a syntax error.
+ /*
+ * Handle unquoted text. This could be the values true, false, or
+ * null, or it can be a number. An implementation (such as this one)
+ * is allowed to also accept non-standard forms.
*
- * @param message The error message.
- * @param causedBy The throwable that caused the error.
- * @return A JSONException object, suitable for throwing
+ * Accumulate characters until we reach the end of the text or a
+ * formatting character.
*/
- public JSONException syntaxError(String message, Throwable causedBy) {
- return new JSONException(message + this.toString(), causedBy);
+
+ StringBuilder sb = new StringBuilder();
+ while (c >= ' ' && ",:]}/\\\"[{;=#".indexOf(c) < 0)
+ {
+ sb.append(c);
+ c = this.next();
}
+ this.back();
- /**
- * Make a printable string of this JSONTokener.
- *
- * @return " at {index} [character {character} line {line}]"
- */
- @Override
- public String toString() {
- return " at " + this.index + " [character " + this.character + " line " +
- this.line + "]";
+ string = sb.toString().trim();
+ if ("".equals(string))
+ {
+ throw this.syntaxError("Missing value");
+ }
+ return JSONObject.stringToValue(string);
+ }
+
+ /**
+ * Skip characters until the next character is the requested character. If the
+ * requested character is not found, no characters are skipped.
+ *
+ * @param to
+ * A character to skip to.
+ * @return The requested character, or zero if the requested character is not
+ * found.
+ * @throws JSONException
+ * Thrown if there is an error while searching for the to character
+ */
+ public char skipTo(char to) throws JSONException
+ {
+ char c;
+ try
+ {
+ long startIndex = this.index;
+ long startCharacter = this.character;
+ long startLine = this.line;
+ this.reader.mark(1000000);
+ do
+ {
+ c = this.next();
+ if (c == 0)
+ {
+ // in some readers, reset() may throw an exception if
+ // the remaining portion of the input is greater than
+ // the mark size (1,000,000 above).
+ this.reader.reset();
+ this.index = startIndex;
+ this.character = startCharacter;
+ this.line = startLine;
+ return 0;
+ }
+ } while (c != to);
+ this.reader.mark(1);
+ } catch (IOException exception)
+ {
+ throw new JSONException(exception);
}
+ this.back();
+ return c;
+ }
+
+ /**
+ * Make a JSONException to signal a syntax error.
+ *
+ * @param message
+ * The error message.
+ * @return A JSONException object, suitable for throwing
+ */
+ public JSONException syntaxError(String message)
+ {
+ return new JSONException(message + this.toString());
+ }
+
+ /**
+ * Make a JSONException to signal a syntax error.
+ *
+ * @param message
+ * The error message.
+ * @param causedBy
+ * The throwable that caused the error.
+ * @return A JSONException object, suitable for throwing
+ */
+ public JSONException syntaxError(String message, Throwable causedBy)
+ {
+ return new JSONException(message + this.toString(), causedBy);
+ }
+
+ /**
+ * Make a printable string of this JSONTokener.
+ *
+ * @return " at {index} [character {character} line {line}]"
+ */
+ @Override
+ public String toString()
+ {
+ return " at " + this.index + " [character " + this.character + " line "
+ + this.line + "]";
+ }
}
*/
/**
- * JSONWriter provides a quick and convenient way of producing JSON text.
- * The texts produced strictly conform to JSON syntax rules. No whitespace is
- * added, so the results are ready for transmission or storage. Each instance of
+ * JSONWriter provides a quick and convenient way of producing JSON text. The
+ * texts produced strictly conform to JSON syntax rules. No whitespace is added,
+ * so the results are ready for transmission or storage. Each instance of
* JSONWriter can produce one JSON text.
* <p>
* A JSONWriter instance provides a <code>value</code> method for appending
- * values to the
- * text, and a <code>key</code>
- * method for adding keys before values in objects. There are <code>array</code>
- * and <code>endArray</code> methods that make and bound array values, and
- * <code>object</code> and <code>endObject</code> methods which make and bound
- * object values. All of these methods return the JSONWriter instance,
- * permitting a cascade style. For example, <pre>
- * new JSONWriter(myWriter)
- * .object()
- * .key("JSON")
- * .value("Hello, World!")
- * .endObject();</pre> which writes <pre>
- * {"JSON":"Hello, World!"}</pre>
+ * values to the text, and a <code>key</code> method for adding keys before
+ * values in objects. There are <code>array</code> and <code>endArray</code>
+ * methods that make and bound array values, and <code>object</code> and
+ * <code>endObject</code> methods which make and bound object values. All of
+ * these methods return the JSONWriter instance, permitting a cascade style. For
+ * example,
+ *
+ * <pre>
+ * new JSONWriter(myWriter).object().key("JSON").value("Hello, World!")
+ * .endObject();
+ * </pre>
+ *
+ * which writes
+ *
+ * <pre>
+ * {"JSON":"Hello, World!"}
+ * </pre>
* <p>
* The first method called must be <code>array</code> or <code>object</code>.
* There are no methods for adding commas or colons. JSONWriter adds them for
* you. Objects and arrays can be nested up to 200 levels deep.
* <p>
* This can sometimes be easier than using a JSONObject to build a string.
+ *
* @author JSON.org
* @version 2016-08-08
*/
-public class JSONWriter {
- private static final int maxdepth = 200;
+public class JSONWriter
+{
+ private static final int maxdepth = 200;
- /**
- * The comma flag determines if a comma should be output before the next
- * value.
- */
- private boolean comma;
+ /**
+ * The comma flag determines if a comma should be output before the next
+ * value.
+ */
+ private boolean comma;
- /**
- * The current mode. Values:
- * 'a' (array),
- * 'd' (done),
- * 'i' (initial),
- * 'k' (key),
- * 'o' (object).
- */
- protected char mode;
+ /**
+ * The current mode. Values: 'a' (array), 'd' (done), 'i' (initial), 'k'
+ * (key), 'o' (object).
+ */
+ protected char mode;
- /**
- * The object/array stack.
- */
- private final JSONObject stack[];
+ /**
+ * The object/array stack.
+ */
+ private final JSONObject stack[];
- /**
- * The stack top index. A value of 0 indicates that the stack is empty.
- */
- private int top;
+ /**
+ * The stack top index. A value of 0 indicates that the stack is empty.
+ */
+ private int top;
- /**
- * The writer that will receive the output.
- */
- protected Appendable writer;
+ /**
+ * The writer that will receive the output.
+ */
+ protected Appendable writer;
- /**
- * Make a fresh JSONWriter. It can be used to build one JSON text.
- */
- public JSONWriter(Appendable w) {
- this.comma = false;
- this.mode = 'i';
- this.stack = new JSONObject[maxdepth];
- this.top = 0;
- this.writer = w;
- }
+ /**
+ * Make a fresh JSONWriter. It can be used to build one JSON text.
+ */
+ public JSONWriter(Appendable w)
+ {
+ this.comma = false;
+ this.mode = 'i';
+ this.stack = new JSONObject[maxdepth];
+ this.top = 0;
+ this.writer = w;
+ }
- /**
- * Append a value.
- * @param string A string value.
- * @return this
- * @throws JSONException If the value is out of sequence.
- */
- private JSONWriter append(String string) throws JSONException {
- if (string == null) {
- throw new JSONException("Null pointer");
- }
- if (this.mode == 'o' || this.mode == 'a') {
- try {
- if (this.comma && this.mode == 'a') {
- this.writer.append(',');
- }
- this.writer.append(string);
- } catch (IOException e) {
- // Android as of API 25 does not support this exception constructor
- // however we won't worry about it. If an exception is happening here
- // it will just throw a "Method not found" exception instead.
- throw new JSONException(e);
- }
- if (this.mode == 'o') {
- this.mode = 'k';
- }
- this.comma = true;
- return this;
- }
- throw new JSONException("Value out of sequence.");
+ /**
+ * Append a value.
+ *
+ * @param string
+ * A string value.
+ * @return this
+ * @throws JSONException
+ * If the value is out of sequence.
+ */
+ private JSONWriter append(String string) throws JSONException
+ {
+ if (string == null)
+ {
+ throw new JSONException("Null pointer");
}
-
- /**
- * Begin appending a new array. All values until the balancing
- * <code>endArray</code> will be appended to this array. The
- * <code>endArray</code> method must be called to mark the array's end.
- * @return this
- * @throws JSONException If the nesting is too deep, or if the object is
- * started in the wrong place (for example as a key or after the end of the
- * outermost array or object).
- */
- public JSONWriter array() throws JSONException {
- if (this.mode == 'i' || this.mode == 'o' || this.mode == 'a') {
- this.push(null);
- this.append("[");
- this.comma = false;
- return this;
+ if (this.mode == 'o' || this.mode == 'a')
+ {
+ try
+ {
+ if (this.comma && this.mode == 'a')
+ {
+ this.writer.append(',');
}
- throw new JSONException("Misplaced array.");
+ this.writer.append(string);
+ } catch (IOException e)
+ {
+ // Android as of API 25 does not support this exception constructor
+ // however we won't worry about it. If an exception is happening here
+ // it will just throw a "Method not found" exception instead.
+ throw new JSONException(e);
+ }
+ if (this.mode == 'o')
+ {
+ this.mode = 'k';
+ }
+ this.comma = true;
+ return this;
}
+ throw new JSONException("Value out of sequence.");
+ }
- /**
- * End something.
- * @param m Mode
- * @param c Closing character
- * @return this
- * @throws JSONException If unbalanced.
- */
- private JSONWriter end(char m, char c) throws JSONException {
- if (this.mode != m) {
- throw new JSONException(m == 'a'
- ? "Misplaced endArray."
- : "Misplaced endObject.");
- }
- this.pop(m);
- try {
- this.writer.append(c);
- } catch (IOException e) {
- // Android as of API 25 does not support this exception constructor
- // however we won't worry about it. If an exception is happening here
- // it will just throw a "Method not found" exception instead.
- throw new JSONException(e);
- }
- this.comma = true;
- return this;
+ /**
+ * Begin appending a new array. All values until the balancing
+ * <code>endArray</code> will be appended to this array. The
+ * <code>endArray</code> method must be called to mark the array's end.
+ *
+ * @return this
+ * @throws JSONException
+ * If the nesting is too deep, or if the object is started in the
+ * wrong place (for example as a key or after the end of the
+ * outermost array or object).
+ */
+ public JSONWriter array() throws JSONException
+ {
+ if (this.mode == 'i' || this.mode == 'o' || this.mode == 'a')
+ {
+ this.push(null);
+ this.append("[");
+ this.comma = false;
+ return this;
}
+ throw new JSONException("Misplaced array.");
+ }
- /**
- * End an array. This method most be called to balance calls to
- * <code>array</code>.
- * @return this
- * @throws JSONException If incorrectly nested.
- */
- public JSONWriter endArray() throws JSONException {
- return this.end('a', ']');
+ /**
+ * End something.
+ *
+ * @param m
+ * Mode
+ * @param c
+ * Closing character
+ * @return this
+ * @throws JSONException
+ * If unbalanced.
+ */
+ private JSONWriter end(char m, char c) throws JSONException
+ {
+ if (this.mode != m)
+ {
+ throw new JSONException(
+ m == 'a' ? "Misplaced endArray." : "Misplaced endObject.");
}
-
- /**
- * End an object. This method most be called to balance calls to
- * <code>object</code>.
- * @return this
- * @throws JSONException If incorrectly nested.
- */
- public JSONWriter endObject() throws JSONException {
- return this.end('k', '}');
+ this.pop(m);
+ try
+ {
+ this.writer.append(c);
+ } catch (IOException e)
+ {
+ // Android as of API 25 does not support this exception constructor
+ // however we won't worry about it. If an exception is happening here
+ // it will just throw a "Method not found" exception instead.
+ throw new JSONException(e);
}
+ this.comma = true;
+ return this;
+ }
- /**
- * Append a key. The key will be associated with the next value. In an
- * object, every value must be preceded by a key.
- * @param string A key string.
- * @return this
- * @throws JSONException If the key is out of place. For example, keys
- * do not belong in arrays or if the key is null.
- */
- public JSONWriter key(String string) throws JSONException {
- if (string == null) {
- throw new JSONException("Null key.");
- }
- if (this.mode == 'k') {
- try {
- JSONObject topObject = this.stack[this.top - 1];
- // don't use the built in putOnce method to maintain Android support
- if(topObject.has(string)) {
- throw new JSONException("Duplicate key \"" + string + "\"");
- }
- topObject.put(string, true);
- if (this.comma) {
- this.writer.append(',');
- }
- this.writer.append(JSONObject.quote(string));
- this.writer.append(':');
- this.comma = false;
- this.mode = 'o';
- return this;
- } catch (IOException e) {
- // Android as of API 25 does not support this exception constructor
- // however we won't worry about it. If an exception is happening here
- // it will just throw a "Method not found" exception instead.
- throw new JSONException(e);
- }
- }
- throw new JSONException("Misplaced key.");
- }
+ /**
+ * End an array. This method most be called to balance calls to
+ * <code>array</code>.
+ *
+ * @return this
+ * @throws JSONException
+ * If incorrectly nested.
+ */
+ public JSONWriter endArray() throws JSONException
+ {
+ return this.end('a', ']');
+ }
+ /**
+ * End an object. This method most be called to balance calls to
+ * <code>object</code>.
+ *
+ * @return this
+ * @throws JSONException
+ * If incorrectly nested.
+ */
+ public JSONWriter endObject() throws JSONException
+ {
+ return this.end('k', '}');
+ }
- /**
- * Begin appending a new object. All keys and values until the balancing
- * <code>endObject</code> will be appended to this object. The
- * <code>endObject</code> method must be called to mark the object's end.
- * @return this
- * @throws JSONException If the nesting is too deep, or if the object is
- * started in the wrong place (for example as a key or after the end of the
- * outermost array or object).
- */
- public JSONWriter object() throws JSONException {
- if (this.mode == 'i') {
- this.mode = 'o';
+ /**
+ * Append a key. The key will be associated with the next value. In an object,
+ * every value must be preceded by a key.
+ *
+ * @param string
+ * A key string.
+ * @return this
+ * @throws JSONException
+ * If the key is out of place. For example, keys do not belong in
+ * arrays or if the key is null.
+ */
+ public JSONWriter key(String string) throws JSONException
+ {
+ if (string == null)
+ {
+ throw new JSONException("Null key.");
+ }
+ if (this.mode == 'k')
+ {
+ try
+ {
+ JSONObject topObject = this.stack[this.top - 1];
+ // don't use the built in putOnce method to maintain Android support
+ if (topObject.has(string))
+ {
+ throw new JSONException("Duplicate key \"" + string + "\"");
}
- if (this.mode == 'o' || this.mode == 'a') {
- this.append("{");
- this.push(new JSONObject());
- this.comma = false;
- return this;
+ topObject.put(string, true);
+ if (this.comma)
+ {
+ this.writer.append(',');
}
- throw new JSONException("Misplaced object.");
+ this.writer.append(JSONObject.quote(string));
+ this.writer.append(':');
+ this.comma = false;
+ this.mode = 'o';
+ return this;
+ } catch (IOException e)
+ {
+ // Android as of API 25 does not support this exception constructor
+ // however we won't worry about it. If an exception is happening here
+ // it will just throw a "Method not found" exception instead.
+ throw new JSONException(e);
+ }
+ }
+ throw new JSONException("Misplaced key.");
+ }
+ /**
+ * Begin appending a new object. All keys and values until the balancing
+ * <code>endObject</code> will be appended to this object. The
+ * <code>endObject</code> method must be called to mark the object's end.
+ *
+ * @return this
+ * @throws JSONException
+ * If the nesting is too deep, or if the object is started in the
+ * wrong place (for example as a key or after the end of the
+ * outermost array or object).
+ */
+ public JSONWriter object() throws JSONException
+ {
+ if (this.mode == 'i')
+ {
+ this.mode = 'o';
+ }
+ if (this.mode == 'o' || this.mode == 'a')
+ {
+ this.append("{");
+ this.push(new JSONObject());
+ this.comma = false;
+ return this;
}
+ throw new JSONException("Misplaced object.");
+ }
- /**
- * Pop an array or object scope.
- * @param c The scope to close.
- * @throws JSONException If nesting is wrong.
- */
- private void pop(char c) throws JSONException {
- if (this.top <= 0) {
- throw new JSONException("Nesting error.");
- }
- char m = this.stack[this.top - 1] == null ? 'a' : 'k';
- if (m != c) {
- throw new JSONException("Nesting error.");
- }
- this.top -= 1;
- this.mode = this.top == 0
- ? 'd'
- : this.stack[this.top - 1] == null
- ? 'a'
- : 'k';
+ /**
+ * Pop an array or object scope.
+ *
+ * @param c
+ * The scope to close.
+ * @throws JSONException
+ * If nesting is wrong.
+ */
+ private void pop(char c) throws JSONException
+ {
+ if (this.top <= 0)
+ {
+ throw new JSONException("Nesting error.");
}
-
- /**
- * Push an array or object scope.
- * @param jo The scope to open.
- * @throws JSONException If nesting is too deep.
- */
- private void push(JSONObject jo) throws JSONException {
- if (this.top >= maxdepth) {
- throw new JSONException("Nesting too deep.");
- }
- this.stack[this.top] = jo;
- this.mode = jo == null ? 'a' : 'k';
- this.top += 1;
+ char m = this.stack[this.top - 1] == null ? 'a' : 'k';
+ if (m != c)
+ {
+ throw new JSONException("Nesting error.");
}
+ this.top -= 1;
+ this.mode = this.top == 0 ? 'd'
+ : this.stack[this.top - 1] == null ? 'a' : 'k';
+ }
- /**
- * Make a JSON text of an Object value. If the object has an
- * value.toJSONString() method, then that method will be used to produce the
- * JSON text. The method is required to produce a strictly conforming text.
- * If the object does not contain a toJSONString method (which is the most
- * common case), then a text will be produced by other means. If the value
- * is an array or Collection, then a JSONArray will be made from it and its
- * toJSONString method will be called. If the value is a MAP, then a
- * JSONObject will be made from it and its toJSONString method will be
- * called. Otherwise, the value's toString method will be called, and the
- * result will be quoted.
- *
- * <p>
- * Warning: This method assumes that the data structure is acyclical.
- *
- * @param value
- * The value to be serialized.
- * @return a printable, displayable, transmittable representation of the
- * object, beginning with <code>{</code> <small>(left
- * brace)</small> and ending with <code>}</code> <small>(right
- * brace)</small>.
- * @throws JSONException
- * If the value is or contains an invalid number.
- */
- public static String valueToString(Object value) throws JSONException {
- if (value == null || value.equals(null)) {
- return "null";
- }
- if (value instanceof JSONString) {
- Object object;
- try {
- object = ((JSONString) value).toJSONString();
- } catch (Exception e) {
- throw new JSONException(e);
- }
- if (object instanceof String) {
- return (String) object;
- }
- throw new JSONException("Bad value from toJSONString: " + object);
- }
- if (value instanceof Number) {
- // not all Numbers may match actual JSON Numbers. i.e. Fractions or Complex
- final String numberAsString = JSONObject.numberToString((Number) value);
- try {
- // Use the BigDecimal constructor for it's parser to validate the format.
- @SuppressWarnings("unused")
- BigDecimal unused = new BigDecimal(numberAsString);
- // Close enough to a JSON number that we will return it unquoted
- return numberAsString;
- } catch (NumberFormatException ex){
- // The Number value is not a valid JSON number.
- // Instead we will quote it as a string
- return JSONObject.quote(numberAsString);
- }
- }
- if (value instanceof Boolean || value instanceof JSONObject
- || value instanceof JSONArray) {
- return value.toString();
- }
- if (value instanceof Map) {
- Map<?, ?> map = (Map<?, ?>) value;
- return new JSONObject(map).toString();
- }
- if (value instanceof Collection) {
- Collection<?> coll = (Collection<?>) value;
- return new JSONArray(coll).toString();
- }
- if (value.getClass().isArray()) {
- return new JSONArray(value).toString();
- }
- if(value instanceof Enum<?>){
- return JSONObject.quote(((Enum<?>)value).name());
- }
- return JSONObject.quote(value.toString());
+ /**
+ * Push an array or object scope.
+ *
+ * @param jo
+ * The scope to open.
+ * @throws JSONException
+ * If nesting is too deep.
+ */
+ private void push(JSONObject jo) throws JSONException
+ {
+ if (this.top >= maxdepth)
+ {
+ throw new JSONException("Nesting too deep.");
}
+ this.stack[this.top] = jo;
+ this.mode = jo == null ? 'a' : 'k';
+ this.top += 1;
+ }
- /**
- * Append either the value <code>true</code> or the value
- * <code>false</code>.
- * @param b A boolean.
- * @return this
- * @throws JSONException
- */
- public JSONWriter value(boolean b) throws JSONException {
- return this.append(b ? "true" : "false");
+ /**
+ * Make a JSON text of an Object value. If the object has an
+ * value.toJSONString() method, then that method will be used to produce the
+ * JSON text. The method is required to produce a strictly conforming text. If
+ * the object does not contain a toJSONString method (which is the most common
+ * case), then a text will be produced by other means. If the value is an
+ * array or Collection, then a JSONArray will be made from it and its
+ * toJSONString method will be called. If the value is a MAP, then a
+ * JSONObject will be made from it and its toJSONString method will be called.
+ * Otherwise, the value's toString method will be called, and the result will
+ * be quoted.
+ *
+ * <p>
+ * Warning: This method assumes that the data structure is acyclical.
+ *
+ * @param value
+ * The value to be serialized.
+ * @return a printable, displayable, transmittable representation of the
+ * object, beginning with <code>{</code> <small>(left
+ * brace)</small> and ending with <code>}</code> <small>(right
+ * brace)</small>.
+ * @throws JSONException
+ * If the value is or contains an invalid number.
+ */
+ public static String valueToString(Object value) throws JSONException
+ {
+ if (value == null || value.equals(null))
+ {
+ return "null";
}
-
- /**
- * Append a double value.
- * @param d A double.
- * @return this
- * @throws JSONException If the number is not finite.
- */
- public JSONWriter value(double d) throws JSONException {
- return this.value(Double.valueOf(d));
+ if (value instanceof JSONString)
+ {
+ Object object;
+ try
+ {
+ object = ((JSONString) value).toJSONString();
+ } catch (Exception e)
+ {
+ throw new JSONException(e);
+ }
+ if (object instanceof String)
+ {
+ return (String) object;
+ }
+ throw new JSONException("Bad value from toJSONString: " + object);
}
-
- /**
- * Append a long value.
- * @param l A long.
- * @return this
- * @throws JSONException
- */
- public JSONWriter value(long l) throws JSONException {
- return this.append(Long.toString(l));
+ if (value instanceof Number)
+ {
+ // not all Numbers may match actual JSON Numbers. i.e. Fractions or
+ // Complex
+ final String numberAsString = JSONObject
+ .numberToString((Number) value);
+ try
+ {
+ // Use the BigDecimal constructor for it's parser to validate the
+ // format.
+ @SuppressWarnings("unused")
+ BigDecimal unused = new BigDecimal(numberAsString);
+ // Close enough to a JSON number that we will return it unquoted
+ return numberAsString;
+ } catch (NumberFormatException ex)
+ {
+ // The Number value is not a valid JSON number.
+ // Instead we will quote it as a string
+ return JSONObject.quote(numberAsString);
+ }
+ }
+ if (value instanceof Boolean || value instanceof JSONObject
+ || value instanceof JSONArray)
+ {
+ return value.toString();
+ }
+ if (value instanceof Map)
+ {
+ Map<?, ?> map = (Map<?, ?>) value;
+ return new JSONObject(map).toString();
+ }
+ if (value instanceof Collection)
+ {
+ Collection<?> coll = (Collection<?>) value;
+ return new JSONArray(coll).toString();
+ }
+ if (value.getClass().isArray())
+ {
+ return new JSONArray(value).toString();
}
+ if (value instanceof Enum<?>)
+ {
+ return JSONObject.quote(((Enum<?>) value).name());
+ }
+ return JSONObject.quote(value.toString());
+ }
+ /**
+ * Append either the value <code>true</code> or the value <code>false</code>.
+ *
+ * @param b
+ * A boolean.
+ * @return this
+ * @throws JSONException
+ */
+ public JSONWriter value(boolean b) throws JSONException
+ {
+ return this.append(b ? "true" : "false");
+ }
- /**
- * Append an object value.
- * @param object The object to append. It can be null, or a Boolean, Number,
- * String, JSONObject, or JSONArray, or an object that implements JSONString.
- * @return this
- * @throws JSONException If the value is out of sequence.
- */
- public JSONWriter value(Object object) throws JSONException {
- return this.append(valueToString(object));
- }
+ /**
+ * Append a double value.
+ *
+ * @param d
+ * A double.
+ * @return this
+ * @throws JSONException
+ * If the number is not finite.
+ */
+ public JSONWriter value(double d) throws JSONException
+ {
+ return this.value(Double.valueOf(d));
+ }
+
+ /**
+ * Append a long value.
+ *
+ * @param l
+ * A long.
+ * @return this
+ * @throws JSONException
+ */
+ public JSONWriter value(long l) throws JSONException
+ {
+ return this.append(Long.toString(l));
+ }
+
+ /**
+ * Append an object value.
+ *
+ * @param object
+ * The object to append. It can be null, or a Boolean, Number,
+ * String, JSONObject, or JSONArray, or an object that implements
+ * JSONString.
+ * @return this
+ * @throws JSONException
+ * If the value is out of sequence.
+ */
+ public JSONWriter value(Object object) throws JSONException
+ {
+ return this.append(valueToString(object));
+ }
}
/**
* Converts a Property file data into JSONObject and back.
+ *
* @author JSON.org
* @version 2015-05-05
*/
-public class Property {
- /**
- * Converts a property file object into a JSONObject. The property file object is a table of name value pairs.
- * @param properties java.util.Properties
- * @return JSONObject
- * @throws JSONException
- */
- public static JSONObject toJSONObject(java.util.Properties properties) throws JSONException {
- // can't use the new constructor for Android support
- // JSONObject jo = new JSONObject(properties == null ? 0 : properties.size());
- JSONObject jo = new JSONObject();
- if (properties != null && !properties.isEmpty()) {
- Enumeration<?> enumProperties = properties.propertyNames();
- while(enumProperties.hasMoreElements()) {
- String name = (String)enumProperties.nextElement();
- jo.put(name, properties.getProperty(name));
- }
- }
- return jo;
+public class Property
+{
+ /**
+ * Converts a property file object into a JSONObject. The property file object
+ * is a table of name value pairs.
+ *
+ * @param properties
+ * java.util.Properties
+ * @return JSONObject
+ * @throws JSONException
+ */
+ public static JSONObject toJSONObject(java.util.Properties properties)
+ throws JSONException
+ {
+ // can't use the new constructor for Android support
+ // JSONObject jo = new JSONObject(properties == null ? 0 :
+ // properties.size());
+ JSONObject jo = new JSONObject();
+ if (properties != null && !properties.isEmpty())
+ {
+ Enumeration<?> enumProperties = properties.propertyNames();
+ while (enumProperties.hasMoreElements())
+ {
+ String name = (String) enumProperties.nextElement();
+ jo.put(name, properties.getProperty(name));
+ }
}
+ return jo;
+ }
- /**
- * Converts the JSONObject into a property file object.
- * @param jo JSONObject
- * @return java.util.Properties
- * @throws JSONException
- */
- public static Properties toProperties(JSONObject jo) throws JSONException {
- Properties properties = new Properties();
- if (jo != null) {
- // Don't use the new entrySet API to maintain Android support
- for (final String key : jo.keySet()) {
- Object value = jo.opt(key);
- if (!JSONObject.NULL.equals(value)) {
- properties.put(key, value.toString());
- }
- }
+ /**
+ * Converts the JSONObject into a property file object.
+ *
+ * @param jo
+ * JSONObject
+ * @return java.util.Properties
+ * @throws JSONException
+ */
+ public static Properties toProperties(JSONObject jo) throws JSONException
+ {
+ Properties properties = new Properties();
+ if (jo != null)
+ {
+ // Don't use the new entrySet API to maintain Android support
+ for (final String key : jo.keySet())
+ {
+ Object value = jo.opt(key);
+ if (!JSONObject.NULL.equals(value))
+ {
+ properties.put(key, value.toString());
}
- return properties;
+ }
}
+ return properties;
+ }
}
* @version 2016-08-10
*/
@SuppressWarnings("boxing")
-public class XML {
- /** The Character '&'. */
- public static final Character AMP = '&';
-
- /** The Character '''. */
- public static final Character APOS = '\'';
-
- /** The Character '!'. */
- public static final Character BANG = '!';
-
- /** The Character '='. */
- public static final Character EQ = '=';
-
- /** The Character '>'. */
- public static final Character GT = '>';
-
- /** The Character '<'. */
- public static final Character LT = '<';
-
- /** The Character '?'. */
- public static final Character QUEST = '?';
-
- /** The Character '"'. */
- public static final Character QUOT = '"';
-
- /** The Character '/'. */
- public static final Character SLASH = '/';
-
- /**
- * Creates an iterator for navigating Code Points in a string instead of
- * characters. Once Java7 support is dropped, this can be replaced with
- * <code>
- * string.codePoints()
- * </code>
- * which is available in Java8 and above.
- *
- * @see <a href=
- * "http://stackoverflow.com/a/21791059/6030888">http://stackoverflow.com/a/21791059/6030888</a>
- */
- private static Iterable<Integer> codePointIterator(final String string) {
- return new Iterable<Integer>() {
- @Override
- public Iterator<Integer> iterator() {
- return new Iterator<Integer>() {
- private int nextIndex = 0;
- private int length = string.length();
-
- @Override
- public boolean hasNext() {
- return this.nextIndex < this.length;
- }
-
- @Override
- public Integer next() {
- int result = string.codePointAt(this.nextIndex);
- this.nextIndex += Character.charCount(result);
- return result;
- }
-
- @Override
- public void remove() {
- throw new UnsupportedOperationException();
- }
- };
- }
+public class XML
+{
+ /** The Character '&'. */
+ public static final Character AMP = '&';
+
+ /** The Character '''. */
+ public static final Character APOS = '\'';
+
+ /** The Character '!'. */
+ public static final Character BANG = '!';
+
+ /** The Character '='. */
+ public static final Character EQ = '=';
+
+ /** The Character '>'. */
+ public static final Character GT = '>';
+
+ /** The Character '<'. */
+ public static final Character LT = '<';
+
+ /** The Character '?'. */
+ public static final Character QUEST = '?';
+
+ /** The Character '"'. */
+ public static final Character QUOT = '"';
+
+ /** The Character '/'. */
+ public static final Character SLASH = '/';
+
+ /**
+ * Creates an iterator for navigating Code Points in a string instead of
+ * characters. Once Java7 support is dropped, this can be replaced with <code>
+ * string.codePoints()
+ * </code> which is available in Java8 and above.
+ *
+ * @see <a href=
+ * "http://stackoverflow.com/a/21791059/6030888">http://stackoverflow.com/a/21791059/6030888</a>
+ */
+ private static Iterable<Integer> codePointIterator(final String string)
+ {
+ return new Iterable<Integer>()
+ {
+ @Override
+ public Iterator<Integer> iterator()
+ {
+ return new Iterator<Integer>()
+ {
+ private int nextIndex = 0;
+
+ private int length = string.length();
+
+ @Override
+ public boolean hasNext()
+ {
+ return this.nextIndex < this.length;
+ }
+
+ @Override
+ public Integer next()
+ {
+ int result = string.codePointAt(this.nextIndex);
+ this.nextIndex += Character.charCount(result);
+ return result;
+ }
+
+ @Override
+ public void remove()
+ {
+ throw new UnsupportedOperationException();
+ }
};
+ }
+ };
+ }
+
+ /**
+ * Replace special characters with XML escapes:
+ *
+ * <pre>
+ * & <small>(ampersand)</small> is replaced by &amp;
+ * < <small>(less than)</small> is replaced by &lt;
+ * > <small>(greater than)</small> is replaced by &gt;
+ * " <small>(double quote)</small> is replaced by &quot;
+ * ' <small>(single quote / apostrophe)</small> is replaced by &apos;
+ * </pre>
+ *
+ * @param string
+ * The string to be escaped.
+ * @return The escaped string.
+ */
+ public static String escape(String string)
+ {
+ StringBuilder sb = new StringBuilder(string.length());
+ for (final int cp : codePointIterator(string))
+ {
+ switch (cp)
+ {
+ case '&':
+ sb.append("&");
+ break;
+ case '<':
+ sb.append("<");
+ break;
+ case '>':
+ sb.append(">");
+ break;
+ case '"':
+ sb.append(""");
+ break;
+ case '\'':
+ sb.append("'");
+ break;
+ default:
+ if (mustEscape(cp))
+ {
+ sb.append("&#x");
+ sb.append(Integer.toHexString(cp));
+ sb.append(';');
+ }
+ else
+ {
+ sb.appendCodePoint(cp);
+ }
+ }
}
-
- /**
- * Replace special characters with XML escapes:
+ return sb.toString();
+ }
+
+ /**
+ * @param cp
+ * code point to test
+ * @return true if the code point is not valid for an XML
+ */
+ private static boolean mustEscape(int cp)
+ {
+ /* Valid range from https://www.w3.org/TR/REC-xml/#charsets
*
- * <pre>
- * & <small>(ampersand)</small> is replaced by &amp;
- * < <small>(less than)</small> is replaced by &lt;
- * > <small>(greater than)</small> is replaced by &gt;
- * " <small>(double quote)</small> is replaced by &quot;
- * ' <small>(single quote / apostrophe)</small> is replaced by &apos;
- * </pre>
+ * #x9 | #xA | #xD | [#x20-#xD7FF] | [#xE000-#xFFFD] | [#x10000-#x10FFFF]
*
- * @param string
- * The string to be escaped.
- * @return The escaped string.
+ * any Unicode character, excluding the surrogate blocks, FFFE, and FFFF.
*/
- public static String escape(String string) {
- StringBuilder sb = new StringBuilder(string.length());
- for (final int cp : codePointIterator(string)) {
- switch (cp) {
- case '&':
- sb.append("&");
- break;
- case '<':
- sb.append("<");
- break;
- case '>':
- sb.append(">");
- break;
- case '"':
- sb.append(""");
- break;
- case '\'':
- sb.append("'");
- break;
- default:
- if (mustEscape(cp)) {
- sb.append("&#x");
- sb.append(Integer.toHexString(cp));
- sb.append(';');
- } else {
- sb.appendCodePoint(cp);
- }
- }
+ // isISOControl is true when (cp >= 0 && cp <= 0x1F) || (cp >= 0x7F && cp <=
+ // 0x9F)
+ // all ISO control characters are out of range except tabs and new lines
+ return (Character.isISOControl(cp) && cp != 0x9 && cp != 0xA
+ && cp != 0xD) || !(
+ // valid the range of acceptable characters that aren't control
+ (cp >= 0x20 && cp <= 0xD7FF) || (cp >= 0xE000 && cp <= 0xFFFD)
+ || (cp >= 0x10000 && cp <= 0x10FFFF));
+ }
+
+ /**
+ * Removes XML escapes from the string.
+ *
+ * @param string
+ * string to remove escapes from
+ * @return string with converted entities
+ */
+ public static String unescape(String string)
+ {
+ StringBuilder sb = new StringBuilder(string.length());
+ for (int i = 0, length = string.length(); i < length; i++)
+ {
+ char c = string.charAt(i);
+ if (c == '&')
+ {
+ final int semic = string.indexOf(';', i);
+ if (semic > i)
+ {
+ final String entity = string.substring(i + 1, semic);
+ sb.append(XMLTokener.unescapeEntity(entity));
+ // skip past the entity we just parsed.
+ i += entity.length() + 1;
}
- return sb.toString();
+ else
+ {
+ // this shouldn't happen in most cases since the parser
+ // errors on unclosed entries.
+ sb.append(c);
+ }
+ }
+ else
+ {
+ // not part of an entity
+ sb.append(c);
+ }
}
-
- /**
- * @param cp code point to test
- * @return true if the code point is not valid for an XML
- */
- private static boolean mustEscape(int cp) {
- /* Valid range from https://www.w3.org/TR/REC-xml/#charsets
- *
- * #x9 | #xA | #xD | [#x20-#xD7FF] | [#xE000-#xFFFD] | [#x10000-#x10FFFF]
- *
- * any Unicode character, excluding the surrogate blocks, FFFE, and FFFF.
- */
- // isISOControl is true when (cp >= 0 && cp <= 0x1F) || (cp >= 0x7F && cp <= 0x9F)
- // all ISO control characters are out of range except tabs and new lines
- return (Character.isISOControl(cp)
- && cp != 0x9
- && cp != 0xA
- && cp != 0xD
- ) || !(
- // valid the range of acceptable characters that aren't control
- (cp >= 0x20 && cp <= 0xD7FF)
- || (cp >= 0xE000 && cp <= 0xFFFD)
- || (cp >= 0x10000 && cp <= 0x10FFFF)
- )
- ;
+ return sb.toString();
+ }
+
+ /**
+ * Throw an exception if the string contains whitespace. Whitespace is not
+ * allowed in tagNames and attributes.
+ *
+ * @param string
+ * A string.
+ * @throws JSONException
+ * Thrown if the string contains whitespace or is empty.
+ */
+ public static void noSpace(String string) throws JSONException
+ {
+ int i, length = string.length();
+ if (length == 0)
+ {
+ throw new JSONException("Empty string.");
}
-
- /**
- * Removes XML escapes from the string.
- *
- * @param string
- * string to remove escapes from
- * @return string with converted entities
- */
- public static String unescape(String string) {
- StringBuilder sb = new StringBuilder(string.length());
- for (int i = 0, length = string.length(); i < length; i++) {
- char c = string.charAt(i);
- if (c == '&') {
- final int semic = string.indexOf(';', i);
- if (semic > i) {
- final String entity = string.substring(i + 1, semic);
- sb.append(XMLTokener.unescapeEntity(entity));
- // skip past the entity we just parsed.
- i += entity.length() + 1;
- } else {
- // this shouldn't happen in most cases since the parser
- // errors on unclosed entries.
- sb.append(c);
- }
- } else {
- // not part of an entity
- sb.append(c);
- }
- }
- return sb.toString();
+ for (i = 0; i < length; i += 1)
+ {
+ if (Character.isWhitespace(string.charAt(i)))
+ {
+ throw new JSONException(
+ "'" + string + "' contains a space character.");
+ }
}
-
- /**
- * Throw an exception if the string contains whitespace. Whitespace is not
- * allowed in tagNames and attributes.
- *
- * @param string
- * A string.
- * @throws JSONException Thrown if the string contains whitespace or is empty.
- */
- public static void noSpace(String string) throws JSONException {
- int i, length = string.length();
- if (length == 0) {
- throw new JSONException("Empty string.");
+ }
+
+ /**
+ * Scan the content following the named tag, attaching it to the context.
+ *
+ * @param x
+ * The XMLTokener containing the source string.
+ * @param context
+ * The JSONObject that will include the new material.
+ * @param name
+ * The tag name.
+ * @return true if the close tag is processed.
+ * @throws JSONException
+ */
+ private static boolean parse(XMLTokener x, JSONObject context,
+ String name, boolean keepStrings) throws JSONException
+ {
+ char c;
+ int i;
+ JSONObject jsonobject = null;
+ String string;
+ String tagName;
+ Object token;
+
+ // Test for and skip past these forms:
+ // <!-- ... -->
+ // <! ... >
+ // <![ ... ]]>
+ // <? ... ?>
+ // Report errors for these forms:
+ // <>
+ // <=
+ // <<
+
+ token = x.nextToken();
+
+ // <!
+
+ if (token == BANG)
+ {
+ c = x.next();
+ if (c == '-')
+ {
+ if (x.next() == '-')
+ {
+ x.skipPast("-->");
+ return false;
}
- for (i = 0; i < length; i += 1) {
- if (Character.isWhitespace(string.charAt(i))) {
- throw new JSONException("'" + string
- + "' contains a space character.");
+ x.back();
+ }
+ else if (c == '[')
+ {
+ token = x.nextToken();
+ if ("CDATA".equals(token))
+ {
+ if (x.next() == '[')
+ {
+ string = x.nextCDATA();
+ if (string.length() > 0)
+ {
+ context.accumulate("content", string);
}
+ return false;
+ }
+ }
+ throw x.syntaxError("Expected 'CDATA['");
+ }
+ i = 1;
+ do
+ {
+ token = x.nextMeta();
+ if (token == null)
+ {
+ throw x.syntaxError("Missing '>' after '<!'.");
+ }
+ else if (token == LT)
+ {
+ i += 1;
}
+ else if (token == GT)
+ {
+ i -= 1;
+ }
+ } while (i > 0);
+ return false;
}
+ else if (token == QUEST)
+ {
- /**
- * Scan the content following the named tag, attaching it to the context.
- *
- * @param x
- * The XMLTokener containing the source string.
- * @param context
- * The JSONObject that will include the new material.
- * @param name
- * The tag name.
- * @return true if the close tag is processed.
- * @throws JSONException
- */
- private static boolean parse(XMLTokener x, JSONObject context, String name, boolean keepStrings)
- throws JSONException {
- char c;
- int i;
- JSONObject jsonobject = null;
- String string;
- String tagName;
- Object token;
-
- // Test for and skip past these forms:
- // <!-- ... -->
- // <! ... >
- // <![ ... ]]>
- // <? ... ?>
- // Report errors for these forms:
- // <>
- // <=
- // <<
-
- token = x.nextToken();
-
- // <!
-
- if (token == BANG) {
- c = x.next();
- if (c == '-') {
- if (x.next() == '-') {
- x.skipPast("-->");
- return false;
- }
- x.back();
- } else if (c == '[') {
- token = x.nextToken();
- if ("CDATA".equals(token)) {
- if (x.next() == '[') {
- string = x.nextCDATA();
- if (string.length() > 0) {
- context.accumulate("content", string);
- }
- return false;
- }
- }
- throw x.syntaxError("Expected 'CDATA['");
- }
- i = 1;
- do {
- token = x.nextMeta();
- if (token == null) {
- throw x.syntaxError("Missing '>' after '<!'.");
- } else if (token == LT) {
- i += 1;
- } else if (token == GT) {
- i -= 1;
- }
- } while (i > 0);
- return false;
- } else if (token == QUEST) {
+ // <?
+ x.skipPast("?>");
+ return false;
+ }
+ else if (token == SLASH)
+ {
+
+ // Close tag </
+
+ token = x.nextToken();
+ if (name == null)
+ {
+ throw x.syntaxError("Mismatched close tag " + token);
+ }
+ if (!token.equals(name))
+ {
+ throw x.syntaxError("Mismatched " + name + " and " + token);
+ }
+ if (x.nextToken() != GT)
+ {
+ throw x.syntaxError("Misshaped close tag");
+ }
+ return true;
- // <?
- x.skipPast("?>");
- return false;
- } else if (token == SLASH) {
+ }
+ else if (token instanceof Character)
+ {
+ throw x.syntaxError("Misshaped tag");
- // Close tag </
+ // Open tag <
+ }
+ else
+ {
+ tagName = (String) token;
+ token = null;
+ jsonobject = new JSONObject();
+ for (;;)
+ {
+ if (token == null)
+ {
+ token = x.nextToken();
+ }
+ // attribute = value
+ if (token instanceof String)
+ {
+ string = (String) token;
+ token = x.nextToken();
+ if (token == EQ)
+ {
token = x.nextToken();
- if (name == null) {
- throw x.syntaxError("Mismatched close tag " + token);
- }
- if (!token.equals(name)) {
- throw x.syntaxError("Mismatched " + name + " and " + token);
- }
- if (x.nextToken() != GT) {
- throw x.syntaxError("Misshaped close tag");
+ if (!(token instanceof String))
+ {
+ throw x.syntaxError("Missing value");
}
- return true;
+ jsonobject.accumulate(string, keepStrings ? ((String) token)
+ : stringToValue((String) token));
+ token = null;
+ }
+ else
+ {
+ jsonobject.accumulate(string, "");
+ }
- } else if (token instanceof Character) {
+ }
+ else if (token == SLASH)
+ {
+ // Empty tag <.../>
+ if (x.nextToken() != GT)
+ {
throw x.syntaxError("Misshaped tag");
+ }
+ if (jsonobject.length() > 0)
+ {
+ context.accumulate(tagName, jsonobject);
+ }
+ else
+ {
+ context.accumulate(tagName, "");
+ }
+ return false;
- // Open tag <
+ }
+ else if (token == GT)
+ {
+ // Content, between <...> and </...>
+ for (;;)
+ {
+ token = x.nextContent();
+ if (token == null)
+ {
+ if (tagName != null)
+ {
+ throw x.syntaxError("Unclosed tag " + tagName);
+ }
+ return false;
+ }
+ else if (token instanceof String)
+ {
+ string = (String) token;
+ if (string.length() > 0)
+ {
+ jsonobject.accumulate("content",
+ keepStrings ? string : stringToValue(string));
+ }
- } else {
- tagName = (String) token;
- token = null;
- jsonobject = new JSONObject();
- for (;;) {
- if (token == null) {
- token = x.nextToken();
+ }
+ else if (token == LT)
+ {
+ // Nested element
+ if (parse(x, jsonobject, tagName, keepStrings))
+ {
+ if (jsonobject.length() == 0)
+ {
+ context.accumulate(tagName, "");
}
- // attribute = value
- if (token instanceof String) {
- string = (String) token;
- token = x.nextToken();
- if (token == EQ) {
- token = x.nextToken();
- if (!(token instanceof String)) {
- throw x.syntaxError("Missing value");
- }
- jsonobject.accumulate(string,
- keepStrings ? ((String)token) : stringToValue((String) token));
- token = null;
- } else {
- jsonobject.accumulate(string, "");
- }
-
-
- } else if (token == SLASH) {
- // Empty tag <.../>
- if (x.nextToken() != GT) {
- throw x.syntaxError("Misshaped tag");
- }
- if (jsonobject.length() > 0) {
- context.accumulate(tagName, jsonobject);
- } else {
- context.accumulate(tagName, "");
- }
- return false;
-
- } else if (token == GT) {
- // Content, between <...> and </...>
- for (;;) {
- token = x.nextContent();
- if (token == null) {
- if (tagName != null) {
- throw x.syntaxError("Unclosed tag " + tagName);
- }
- return false;
- } else if (token instanceof String) {
- string = (String) token;
- if (string.length() > 0) {
- jsonobject.accumulate("content",
- keepStrings ? string : stringToValue(string));
- }
-
- } else if (token == LT) {
- // Nested element
- if (parse(x, jsonobject, tagName,keepStrings)) {
- if (jsonobject.length() == 0) {
- context.accumulate(tagName, "");
- } else if (jsonobject.length() == 1
- && jsonobject.opt("content") != null) {
- context.accumulate(tagName,
- jsonobject.opt("content"));
- } else {
- context.accumulate(tagName, jsonobject);
- }
- return false;
- }
- }
- }
- } else {
- throw x.syntaxError("Misshaped tag");
+ else if (jsonobject.length() == 1
+ && jsonobject.opt("content") != null)
+ {
+ context.accumulate(tagName, jsonobject.opt("content"));
}
- }
- }
- }
-
- /**
- * This method is the same as {@link JSONObject#stringToValue(String)}.
- *
- * @param string String to convert
- * @return JSON value of this string or the string
- */
- // To maintain compatibility with the Android API, this method is a direct copy of
- // the one in JSONObject. Changes made here should be reflected there.
- public static Object stringToValue(String string) {
- if (string.equals("")) {
- return string;
- }
- if (string.equalsIgnoreCase("true")) {
- return Boolean.TRUE;
- }
- if (string.equalsIgnoreCase("false")) {
- return Boolean.FALSE;
- }
- if (string.equalsIgnoreCase("null")) {
- return JSONObject.NULL;
- }
-
- /*
- * If it might be a number, try converting it. If a number cannot be
- * produced, then the value will just be a string.
- */
-
- char initial = string.charAt(0);
- if ((initial >= '0' && initial <= '9') || initial == '-') {
- try {
- // if we want full Big Number support this block can be replaced with:
- // return stringToNumber(string);
- if (string.indexOf('.') > -1 || string.indexOf('e') > -1
- || string.indexOf('E') > -1 || "-0".equals(string)) {
- Double d = Double.valueOf(string);
- if (!d.isInfinite() && !d.isNaN()) {
- return d;
- }
- } else {
- Long myLong = Long.valueOf(string);
- if (string.equals(myLong.toString())) {
- if (myLong.longValue() == myLong.intValue()) {
- return Integer.valueOf(myLong.intValue());
- }
- return myLong;
- }
+ else
+ {
+ context.accumulate(tagName, jsonobject);
}
- } catch (Exception ignore) {
+ return false;
+ }
}
+ }
}
- return string;
+ else
+ {
+ throw x.syntaxError("Misshaped tag");
+ }
+ }
}
-
- /**
- * Convert a well-formed (but not necessarily valid) XML string into a
- * JSONObject. Some information may be lost in this transformation because
- * JSON is a data format and XML is a document format. XML uses elements,
- * attributes, and content text, while JSON uses unordered collections of
- * name/value pairs and arrays of values. JSON does not does not like to
- * distinguish between elements and attributes. Sequences of similar
- * elements are represented as JSONArrays. Content text may be placed in a
- * "content" member. Comments, prologs, DTDs, and <code><[ [ ]]></code>
- * are ignored.
- *
- * @param string
- * The source string.
- * @return A JSONObject containing the structured data from the XML string.
- * @throws JSONException Thrown if there is an errors while parsing the string
- */
- public static JSONObject toJSONObject(String string) throws JSONException {
- return toJSONObject(string, false);
+ }
+
+ /**
+ * This method is the same as {@link JSONObject#stringToValue(String)}.
+ *
+ * @param string
+ * String to convert
+ * @return JSON value of this string or the string
+ */
+ // To maintain compatibility with the Android API, this method is a direct
+ // copy of
+ // the one in JSONObject. Changes made here should be reflected there.
+ public static Object stringToValue(String string)
+ {
+ if (string.equals(""))
+ {
+ return string;
}
-
- /**
- * Convert a well-formed (but not necessarily valid) XML into a
- * JSONObject. Some information may be lost in this transformation because
- * JSON is a data format and XML is a document format. XML uses elements,
- * attributes, and content text, while JSON uses unordered collections of
- * name/value pairs and arrays of values. JSON does not does not like to
- * distinguish between elements and attributes. Sequences of similar
- * elements are represented as JSONArrays. Content text may be placed in a
- * "content" member. Comments, prologs, DTDs, and <code><[ [ ]]></code>
- * are ignored.
- *
- * @param reader The XML source reader.
- * @return A JSONObject containing the structured data from the XML string.
- * @throws JSONException Thrown if there is an errors while parsing the string
- */
- public static JSONObject toJSONObject(Reader reader) throws JSONException {
- return toJSONObject(reader, false);
+ if (string.equalsIgnoreCase("true"))
+ {
+ return Boolean.TRUE;
+ }
+ if (string.equalsIgnoreCase("false"))
+ {
+ return Boolean.FALSE;
+ }
+ if (string.equalsIgnoreCase("null"))
+ {
+ return JSONObject.NULL;
}
- /**
- * Convert a well-formed (but not necessarily valid) XML into a
- * JSONObject. Some information may be lost in this transformation because
- * JSON is a data format and XML is a document format. XML uses elements,
- * attributes, and content text, while JSON uses unordered collections of
- * name/value pairs and arrays of values. JSON does not does not like to
- * distinguish between elements and attributes. Sequences of similar
- * elements are represented as JSONArrays. Content text may be placed in a
- * "content" member. Comments, prologs, DTDs, and <code><[ [ ]]></code>
- * are ignored.
- *
- * All values are converted as strings, for 1, 01, 29.0 will not be coerced to
- * numbers but will instead be the exact value as seen in the XML document.
- *
- * @param reader The XML source reader.
- * @param keepStrings If true, then values will not be coerced into boolean
- * or numeric values and will instead be left as strings
- * @return A JSONObject containing the structured data from the XML string.
- * @throws JSONException Thrown if there is an errors while parsing the string
+ /*
+ * If it might be a number, try converting it. If a number cannot be
+ * produced, then the value will just be a string.
*/
- public static JSONObject toJSONObject(Reader reader, boolean keepStrings) throws JSONException {
- JSONObject jo = new JSONObject();
- XMLTokener x = new XMLTokener(reader);
- while (x.more()) {
- x.skipPast("<");
- if(x.more()) {
- parse(x, jo, null, keepStrings);
+
+ char initial = string.charAt(0);
+ if ((initial >= '0' && initial <= '9') || initial == '-')
+ {
+ try
+ {
+ // if we want full Big Number support this block can be replaced with:
+ // return stringToNumber(string);
+ if (string.indexOf('.') > -1 || string.indexOf('e') > -1
+ || string.indexOf('E') > -1 || "-0".equals(string))
+ {
+ Double d = Double.valueOf(string);
+ if (!d.isInfinite() && !d.isNaN())
+ {
+ return d;
+ }
+ }
+ else
+ {
+ Long myLong = Long.valueOf(string);
+ if (string.equals(myLong.toString()))
+ {
+ if (myLong.longValue() == myLong.intValue())
+ {
+ return Integer.valueOf(myLong.intValue());
}
+ return myLong;
+ }
}
- return jo;
- }
-
- /**
- * Convert a well-formed (but not necessarily valid) XML string into a
- * JSONObject. Some information may be lost in this transformation because
- * JSON is a data format and XML is a document format. XML uses elements,
- * attributes, and content text, while JSON uses unordered collections of
- * name/value pairs and arrays of values. JSON does not does not like to
- * distinguish between elements and attributes. Sequences of similar
- * elements are represented as JSONArrays. Content text may be placed in a
- * "content" member. Comments, prologs, DTDs, and <code><[ [ ]]></code>
- * are ignored.
- *
- * All values are converted as strings, for 1, 01, 29.0 will not be coerced to
- * numbers but will instead be the exact value as seen in the XML document.
- *
- * @param string
- * The source string.
- * @param keepStrings If true, then values will not be coerced into boolean
- * or numeric values and will instead be left as strings
- * @return A JSONObject containing the structured data from the XML string.
- * @throws JSONException Thrown if there is an errors while parsing the string
- */
- public static JSONObject toJSONObject(String string, boolean keepStrings) throws JSONException {
- return toJSONObject(new StringReader(string), keepStrings);
+ } catch (Exception ignore)
+ {
+ }
}
-
- /**
- * Convert a JSONObject into a well-formed, element-normal XML string.
- *
- * @param object
- * A JSONObject.
- * @return A string.
- * @throws JSONException Thrown if there is an error parsing the string
- */
- public static String toString(Object object) throws JSONException {
- return toString(object, null);
+ return string;
+ }
+
+ /**
+ * Convert a well-formed (but not necessarily valid) XML string into a
+ * JSONObject. Some information may be lost in this transformation because
+ * JSON is a data format and XML is a document format. XML uses elements,
+ * attributes, and content text, while JSON uses unordered collections of
+ * name/value pairs and arrays of values. JSON does not does not like to
+ * distinguish between elements and attributes. Sequences of similar elements
+ * are represented as JSONArrays. Content text may be placed in a "content"
+ * member. Comments, prologs, DTDs, and <code><[ [ ]]></code> are ignored.
+ *
+ * @param string
+ * The source string.
+ * @return A JSONObject containing the structured data from the XML string.
+ * @throws JSONException
+ * Thrown if there is an errors while parsing the string
+ */
+ public static JSONObject toJSONObject(String string) throws JSONException
+ {
+ return toJSONObject(string, false);
+ }
+
+ /**
+ * Convert a well-formed (but not necessarily valid) XML into a JSONObject.
+ * Some information may be lost in this transformation because JSON is a data
+ * format and XML is a document format. XML uses elements, attributes, and
+ * content text, while JSON uses unordered collections of name/value pairs and
+ * arrays of values. JSON does not does not like to distinguish between
+ * elements and attributes. Sequences of similar elements are represented as
+ * JSONArrays. Content text may be placed in a "content" member. Comments,
+ * prologs, DTDs, and <code><[ [ ]]></code> are ignored.
+ *
+ * @param reader
+ * The XML source reader.
+ * @return A JSONObject containing the structured data from the XML string.
+ * @throws JSONException
+ * Thrown if there is an errors while parsing the string
+ */
+ public static JSONObject toJSONObject(Reader reader) throws JSONException
+ {
+ return toJSONObject(reader, false);
+ }
+
+ /**
+ * Convert a well-formed (but not necessarily valid) XML into a JSONObject.
+ * Some information may be lost in this transformation because JSON is a data
+ * format and XML is a document format. XML uses elements, attributes, and
+ * content text, while JSON uses unordered collections of name/value pairs and
+ * arrays of values. JSON does not does not like to distinguish between
+ * elements and attributes. Sequences of similar elements are represented as
+ * JSONArrays. Content text may be placed in a "content" member. Comments,
+ * prologs, DTDs, and <code><[ [ ]]></code> are ignored.
+ *
+ * All values are converted as strings, for 1, 01, 29.0 will not be coerced to
+ * numbers but will instead be the exact value as seen in the XML document.
+ *
+ * @param reader
+ * The XML source reader.
+ * @param keepStrings
+ * If true, then values will not be coerced into boolean or numeric
+ * values and will instead be left as strings
+ * @return A JSONObject containing the structured data from the XML string.
+ * @throws JSONException
+ * Thrown if there is an errors while parsing the string
+ */
+ public static JSONObject toJSONObject(Reader reader, boolean keepStrings)
+ throws JSONException
+ {
+ JSONObject jo = new JSONObject();
+ XMLTokener x = new XMLTokener(reader);
+ while (x.more())
+ {
+ x.skipPast("<");
+ if (x.more())
+ {
+ parse(x, jo, null, keepStrings);
+ }
}
+ return jo;
+ }
+
+ /**
+ * Convert a well-formed (but not necessarily valid) XML string into a
+ * JSONObject. Some information may be lost in this transformation because
+ * JSON is a data format and XML is a document format. XML uses elements,
+ * attributes, and content text, while JSON uses unordered collections of
+ * name/value pairs and arrays of values. JSON does not does not like to
+ * distinguish between elements and attributes. Sequences of similar elements
+ * are represented as JSONArrays. Content text may be placed in a "content"
+ * member. Comments, prologs, DTDs, and <code><[ [ ]]></code> are ignored.
+ *
+ * All values are converted as strings, for 1, 01, 29.0 will not be coerced to
+ * numbers but will instead be the exact value as seen in the XML document.
+ *
+ * @param string
+ * The source string.
+ * @param keepStrings
+ * If true, then values will not be coerced into boolean or numeric
+ * values and will instead be left as strings
+ * @return A JSONObject containing the structured data from the XML string.
+ * @throws JSONException
+ * Thrown if there is an errors while parsing the string
+ */
+ public static JSONObject toJSONObject(String string, boolean keepStrings)
+ throws JSONException
+ {
+ return toJSONObject(new StringReader(string), keepStrings);
+ }
+
+ /**
+ * Convert a JSONObject into a well-formed, element-normal XML string.
+ *
+ * @param object
+ * A JSONObject.
+ * @return A string.
+ * @throws JSONException
+ * Thrown if there is an error parsing the string
+ */
+ public static String toString(Object object) throws JSONException
+ {
+ return toString(object, null);
+ }
+
+ /**
+ * Convert a JSONObject into a well-formed, element-normal XML string.
+ *
+ * @param object
+ * A JSONObject.
+ * @param tagName
+ * The optional name of the enclosing tag.
+ * @return A string.
+ * @throws JSONException
+ * Thrown if there is an error parsing the string
+ */
+ public static String toString(final Object object, final String tagName)
+ throws JSONException
+ {
+ StringBuilder sb = new StringBuilder();
+ JSONArray ja;
+ JSONObject jo;
+ String string;
+
+ if (object instanceof JSONObject)
+ {
+
+ // Emit <tagName>
+ if (tagName != null)
+ {
+ sb.append('<');
+ sb.append(tagName);
+ sb.append('>');
+ }
+
+ // Loop thru the keys.
+ // don't use the new entrySet accessor to maintain Android Support
+ jo = (JSONObject) object;
+ for (final String key : jo.keySet())
+ {
+ Object value = jo.opt(key);
+ if (value == null)
+ {
+ value = "";
+ }
+ else if (value.getClass().isArray())
+ {
+ value = new JSONArray(value);
+ }
- /**
- * Convert a JSONObject into a well-formed, element-normal XML string.
- *
- * @param object
- * A JSONObject.
- * @param tagName
- * The optional name of the enclosing tag.
- * @return A string.
- * @throws JSONException Thrown if there is an error parsing the string
- */
- public static String toString(final Object object, final String tagName)
- throws JSONException {
- StringBuilder sb = new StringBuilder();
- JSONArray ja;
- JSONObject jo;
- String string;
-
- if (object instanceof JSONObject) {
-
- // Emit <tagName>
- if (tagName != null) {
- sb.append('<');
- sb.append(tagName);
- sb.append('>');
+ // Emit content in body
+ if ("content".equals(key))
+ {
+ if (value instanceof JSONArray)
+ {
+ ja = (JSONArray) value;
+ int jaLength = ja.length();
+ // don't use the new iterator API to maintain support for Android
+ for (int i = 0; i < jaLength; i++)
+ {
+ if (i > 0)
+ {
+ sb.append('\n');
+ }
+ Object val = ja.opt(i);
+ sb.append(escape(val.toString()));
}
+ }
+ else
+ {
+ sb.append(escape(value.toString()));
+ }
- // Loop thru the keys.
- // don't use the new entrySet accessor to maintain Android Support
- jo = (JSONObject) object;
- for (final String key : jo.keySet()) {
- Object value = jo.opt(key);
- if (value == null) {
- value = "";
- } else if (value.getClass().isArray()) {
- value = new JSONArray(value);
- }
+ // Emit an array of similar keys
- // Emit content in body
- if ("content".equals(key)) {
- if (value instanceof JSONArray) {
- ja = (JSONArray) value;
- int jaLength = ja.length();
- // don't use the new iterator API to maintain support for Android
- for (int i = 0; i < jaLength; i++) {
- if (i > 0) {
- sb.append('\n');
- }
- Object val = ja.opt(i);
- sb.append(escape(val.toString()));
- }
- } else {
- sb.append(escape(value.toString()));
- }
-
- // Emit an array of similar keys
-
- } else if (value instanceof JSONArray) {
- ja = (JSONArray) value;
- int jaLength = ja.length();
- // don't use the new iterator API to maintain support for Android
- for (int i = 0; i < jaLength; i++) {
- Object val = ja.opt(i);
- if (val instanceof JSONArray) {
- sb.append('<');
- sb.append(key);
- sb.append('>');
- sb.append(toString(val));
- sb.append("</");
- sb.append(key);
- sb.append('>');
- } else {
- sb.append(toString(val, key));
- }
- }
- } else if ("".equals(value)) {
- sb.append('<');
- sb.append(key);
- sb.append("/>");
-
- // Emit a new tag <k>
-
- } else {
- sb.append(toString(value, key));
- }
+ }
+ else if (value instanceof JSONArray)
+ {
+ ja = (JSONArray) value;
+ int jaLength = ja.length();
+ // don't use the new iterator API to maintain support for Android
+ for (int i = 0; i < jaLength; i++)
+ {
+ Object val = ja.opt(i);
+ if (val instanceof JSONArray)
+ {
+ sb.append('<');
+ sb.append(key);
+ sb.append('>');
+ sb.append(toString(val));
+ sb.append("</");
+ sb.append(key);
+ sb.append('>');
}
- if (tagName != null) {
-
- // Emit the </tagname> close tag
- sb.append("</");
- sb.append(tagName);
- sb.append('>');
+ else
+ {
+ sb.append(toString(val, key));
}
- return sb.toString();
-
+ }
}
+ else if ("".equals(value))
+ {
+ sb.append('<');
+ sb.append(key);
+ sb.append("/>");
- if (object != null && (object instanceof JSONArray || object.getClass().isArray())) {
- if(object.getClass().isArray()) {
- ja = new JSONArray(object);
- } else {
- ja = (JSONArray) object;
- }
- int jaLength = ja.length();
- // don't use the new iterator API to maintain support for Android
- for (int i = 0; i < jaLength; i++) {
- Object val = ja.opt(i);
- // XML does not have good support for arrays. If an array
- // appears in a place where XML is lacking, synthesize an
- // <array> element.
- sb.append(toString(val, tagName == null ? "array" : tagName));
- }
- return sb.toString();
+ // Emit a new tag <k>
+
+ }
+ else
+ {
+ sb.append(toString(value, key));
}
+ }
+ if (tagName != null)
+ {
+
+ // Emit the </tagname> close tag
+ sb.append("</");
+ sb.append(tagName);
+ sb.append('>');
+ }
+ return sb.toString();
- string = (object == null) ? "null" : escape(object.toString());
- return (tagName == null) ? "\"" + string + "\""
- : (string.length() == 0) ? "<" + tagName + "/>" : "<" + tagName
- + ">" + string + "</" + tagName + ">";
+ }
+ if (object != null
+ && (object instanceof JSONArray || object.getClass().isArray()))
+ {
+ if (object.getClass().isArray())
+ {
+ ja = new JSONArray(object);
+ }
+ else
+ {
+ ja = (JSONArray) object;
+ }
+ int jaLength = ja.length();
+ // don't use the new iterator API to maintain support for Android
+ for (int i = 0; i < jaLength; i++)
+ {
+ Object val = ja.opt(i);
+ // XML does not have good support for arrays. If an array
+ // appears in a place where XML is lacking, synthesize an
+ // <array> element.
+ sb.append(toString(val, tagName == null ? "array" : tagName));
+ }
+ return sb.toString();
}
+
+ string = (object == null) ? "null" : escape(object.toString());
+ return (tagName == null) ? "\"" + string + "\""
+ : (string.length() == 0) ? "<" + tagName + "/>"
+ : "<" + tagName + ">" + string + "</" + tagName + ">";
+
+ }
}
import java.io.Reader;
/**
- * The XMLTokener extends the JSONTokener to provide additional methods
- * for the parsing of XML texts.
+ * The XMLTokener extends the JSONTokener to provide additional methods for the
+ * parsing of XML texts.
+ *
* @author JSON.org
* @version 2015-12-09
*/
-public class XMLTokener extends JSONTokener {
-
-
- /** The table of entity values. It initially contains Character values for
- * amp, apos, gt, lt, quot.
- */
- public static final java.util.HashMap<String, Character> entity;
-
- static {
- entity = new java.util.HashMap<String, Character>(8);
- entity.put("amp", XML.AMP);
- entity.put("apos", XML.APOS);
- entity.put("gt", XML.GT);
- entity.put("lt", XML.LT);
- entity.put("quot", XML.QUOT);
- }
-
- /**
- * Construct an XMLTokener from a Reader.
- * @param r A source reader.
- */
- public XMLTokener(Reader r) {
- super(r);
+public class XMLTokener extends JSONTokener
+{
+
+ /**
+ * The table of entity values. It initially contains Character values for amp,
+ * apos, gt, lt, quot.
+ */
+ public static final java.util.HashMap<String, Character> entity;
+
+ static
+ {
+ entity = new java.util.HashMap<String, Character>(8);
+ entity.put("amp", XML.AMP);
+ entity.put("apos", XML.APOS);
+ entity.put("gt", XML.GT);
+ entity.put("lt", XML.LT);
+ entity.put("quot", XML.QUOT);
+ }
+
+ /**
+ * Construct an XMLTokener from a Reader.
+ *
+ * @param r
+ * A source reader.
+ */
+ public XMLTokener(Reader r)
+ {
+ super(r);
+ }
+
+ /**
+ * Construct an XMLTokener from a string.
+ *
+ * @param s
+ * A source string.
+ */
+ public XMLTokener(String s)
+ {
+ super(s);
+ }
+
+ /**
+ * Get the text in the CDATA block.
+ *
+ * @return The string up to the <code>]]></code>.
+ * @throws JSONException
+ * If the <code>]]></code> is not found.
+ */
+ public String nextCDATA() throws JSONException
+ {
+ char c;
+ int i;
+ StringBuilder sb = new StringBuilder();
+ while (more())
+ {
+ c = next();
+ sb.append(c);
+ i = sb.length() - 3;
+ if (i >= 0 && sb.charAt(i) == ']' && sb.charAt(i + 1) == ']'
+ && sb.charAt(i + 2) == '>')
+ {
+ sb.setLength(i);
+ return sb.toString();
+ }
}
-
- /**
- * Construct an XMLTokener from a string.
- * @param s A source string.
- */
- public XMLTokener(String s) {
- super(s);
+ throw syntaxError("Unclosed CDATA");
+ }
+
+ /**
+ * Get the next XML outer token, trimming whitespace. There are two kinds of
+ * tokens: the '<' character which begins a markup tag, and the content text
+ * between markup tags.
+ *
+ * @return A string, or a '<' Character, or null if there is no more source
+ * text.
+ * @throws JSONException
+ */
+ public Object nextContent() throws JSONException
+ {
+ char c;
+ StringBuilder sb;
+ do
+ {
+ c = next();
+ } while (Character.isWhitespace(c));
+ if (c == 0)
+ {
+ return null;
}
-
- /**
- * Get the text in the CDATA block.
- * @return The string up to the <code>]]></code>.
- * @throws JSONException If the <code>]]></code> is not found.
- */
- public String nextCDATA() throws JSONException {
- char c;
- int i;
- StringBuilder sb = new StringBuilder();
- while (more()) {
- c = next();
- sb.append(c);
- i = sb.length() - 3;
- if (i >= 0 && sb.charAt(i) == ']' &&
- sb.charAt(i + 1) == ']' && sb.charAt(i + 2) == '>') {
- sb.setLength(i);
- return sb.toString();
- }
- }
- throw syntaxError("Unclosed CDATA");
+ if (c == '<')
+ {
+ return XML.LT;
}
-
-
- /**
- * Get the next XML outer token, trimming whitespace. There are two kinds
- * of tokens: the '<' character which begins a markup tag, and the content
- * text between markup tags.
- *
- * @return A string, or a '<' Character, or null if there is no more
- * source text.
- * @throws JSONException
- */
- public Object nextContent() throws JSONException {
- char c;
- StringBuilder sb;
- do {
- c = next();
- } while (Character.isWhitespace(c));
- if (c == 0) {
- return null;
- }
- if (c == '<') {
- return XML.LT;
- }
- sb = new StringBuilder();
- for (;;) {
- if (c == 0) {
- return sb.toString().trim();
- }
- if (c == '<') {
- back();
- return sb.toString().trim();
- }
- if (c == '&') {
- sb.append(nextEntity(c));
- } else {
- sb.append(c);
- }
- c = next();
- }
+ sb = new StringBuilder();
+ for (;;)
+ {
+ if (c == 0)
+ {
+ return sb.toString().trim();
+ }
+ if (c == '<')
+ {
+ back();
+ return sb.toString().trim();
+ }
+ if (c == '&')
+ {
+ sb.append(nextEntity(c));
+ }
+ else
+ {
+ sb.append(c);
+ }
+ c = next();
}
-
-
- /**
- * Return the next entity. These entities are translated to Characters:
- * <code>& ' > < "</code>.
- * @param ampersand An ampersand character.
- * @return A Character or an entity String if the entity is not recognized.
- * @throws JSONException If missing ';' in XML entity.
- */
- public Object nextEntity(char ampersand) throws JSONException {
- StringBuilder sb = new StringBuilder();
- for (;;) {
- char c = next();
- if (Character.isLetterOrDigit(c) || c == '#') {
- sb.append(Character.toLowerCase(c));
- } else if (c == ';') {
- break;
- } else {
- throw syntaxError("Missing ';' in XML entity: &" + sb);
- }
- }
- String string = sb.toString();
- return unescapeEntity(string);
+ }
+
+ /**
+ * Return the next entity. These entities are translated to Characters:
+ * <code>& ' > < "</code>.
+ *
+ * @param ampersand
+ * An ampersand character.
+ * @return A Character or an entity String if the entity is not recognized.
+ * @throws JSONException
+ * If missing ';' in XML entity.
+ */
+ public Object nextEntity(char ampersand) throws JSONException
+ {
+ StringBuilder sb = new StringBuilder();
+ for (;;)
+ {
+ char c = next();
+ if (Character.isLetterOrDigit(c) || c == '#')
+ {
+ sb.append(Character.toLowerCase(c));
+ }
+ else if (c == ';')
+ {
+ break;
+ }
+ else
+ {
+ throw syntaxError("Missing ';' in XML entity: &" + sb);
+ }
}
-
- /**
- * Unescapes an XML entity encoding;
- * @param e entity (only the actual entity value, not the preceding & or ending ;
- * @return
- */
- static String unescapeEntity(String e) {
- // validate
- if (e == null || e.isEmpty()) {
- return "";
+ String string = sb.toString();
+ return unescapeEntity(string);
+ }
+
+ /**
+ * Unescapes an XML entity encoding;
+ *
+ * @param e
+ * entity (only the actual entity value, not the preceding & or
+ * ending ;
+ * @return
+ */
+ static String unescapeEntity(String e)
+ {
+ // validate
+ if (e == null || e.isEmpty())
+ {
+ return "";
+ }
+ // if our entity is an encoded unicode point, parse it.
+ if (e.charAt(0) == '#')
+ {
+ int cp;
+ if (e.charAt(1) == 'x')
+ {
+ // hex encoded unicode
+ cp = Integer.parseInt(e.substring(2), 16);
+ }
+ else
+ {
+ // decimal encoded unicode
+ cp = Integer.parseInt(e.substring(1));
+ }
+ return new String(new int[] { cp }, 0, 1);
+ }
+ Character knownEntity = entity.get(e);
+ if (knownEntity == null)
+ {
+ // we don't know the entity so keep it encoded
+ return '&' + e + ';';
+ }
+ return knownEntity.toString();
+ }
+
+ /**
+ * Returns the next XML meta token. This is used for skipping over <!...> and
+ * <?...?> structures.
+ *
+ * @return Syntax characters (<code>< > / = ! ?</code>) are returned as
+ * Character, and strings and names are returned as Boolean. We don't
+ * care what the values actually are.
+ * @throws JSONException
+ * If a string is not properly closed or if the XML is badly
+ * structured.
+ */
+ public Object nextMeta() throws JSONException
+ {
+ char c;
+ char q;
+ do
+ {
+ c = next();
+ } while (Character.isWhitespace(c));
+ switch (c)
+ {
+ case 0:
+ throw syntaxError("Misshaped meta tag");
+ case '<':
+ return XML.LT;
+ case '>':
+ return XML.GT;
+ case '/':
+ return XML.SLASH;
+ case '=':
+ return XML.EQ;
+ case '!':
+ return XML.BANG;
+ case '?':
+ return XML.QUEST;
+ case '"':
+ case '\'':
+ q = c;
+ for (;;)
+ {
+ c = next();
+ if (c == 0)
+ {
+ throw syntaxError("Unterminated string");
}
- // if our entity is an encoded unicode point, parse it.
- if (e.charAt(0) == '#') {
- int cp;
- if (e.charAt(1) == 'x') {
- // hex encoded unicode
- cp = Integer.parseInt(e.substring(2), 16);
- } else {
- // decimal encoded unicode
- cp = Integer.parseInt(e.substring(1));
- }
- return new String(new int[] {cp},0,1);
- }
- Character knownEntity = entity.get(e);
- if(knownEntity==null) {
- // we don't know the entity so keep it encoded
- return '&' + e + ';';
+ if (c == q)
+ {
+ return Boolean.TRUE;
}
- return knownEntity.toString();
- }
-
-
- /**
- * Returns the next XML meta token. This is used for skipping over <!...>
- * and <?...?> structures.
- * @return Syntax characters (<code>< > / = ! ?</code>) are returned as
- * Character, and strings and names are returned as Boolean. We don't care
- * what the values actually are.
- * @throws JSONException If a string is not properly closed or if the XML
- * is badly structured.
- */
- public Object nextMeta() throws JSONException {
- char c;
- char q;
- do {
- c = next();
- } while (Character.isWhitespace(c));
- switch (c) {
+ }
+ default:
+ for (;;)
+ {
+ c = next();
+ if (Character.isWhitespace(c))
+ {
+ return Boolean.TRUE;
+ }
+ switch (c)
+ {
case 0:
- throw syntaxError("Misshaped meta tag");
case '<':
- return XML.LT;
case '>':
- return XML.GT;
case '/':
- return XML.SLASH;
case '=':
- return XML.EQ;
case '!':
- return XML.BANG;
case '?':
- return XML.QUEST;
case '"':
case '\'':
- q = c;
- for (;;) {
- c = next();
- if (c == 0) {
- throw syntaxError("Unterminated string");
- }
- if (c == q) {
- return Boolean.TRUE;
- }
- }
- default:
- for (;;) {
- c = next();
- if (Character.isWhitespace(c)) {
- return Boolean.TRUE;
- }
- switch (c) {
- case 0:
- case '<':
- case '>':
- case '/':
- case '=':
- case '!':
- case '?':
- case '"':
- case '\'':
- back();
- return Boolean.TRUE;
- }
- }
+ back();
+ return Boolean.TRUE;
}
+ }
}
-
-
- /**
- * Get the next XML Token. These tokens are found inside of angle
- * brackets. It may be one of these characters: <code>/ > = ! ?</code> or it
- * may be a string wrapped in single quotes or double quotes, or it may be a
- * name.
- * @return a String or a Character.
- * @throws JSONException If the XML is not well formed.
- */
- public Object nextToken() throws JSONException {
- char c;
- char q;
- StringBuilder sb;
- do {
- c = next();
- } while (Character.isWhitespace(c));
- switch (c) {
+ }
+
+ /**
+ * Get the next XML Token. These tokens are found inside of angle brackets. It
+ * may be one of these characters: <code>/ > = ! ?</code> or it may be a
+ * string wrapped in single quotes or double quotes, or it may be a name.
+ *
+ * @return a String or a Character.
+ * @throws JSONException
+ * If the XML is not well formed.
+ */
+ public Object nextToken() throws JSONException
+ {
+ char c;
+ char q;
+ StringBuilder sb;
+ do
+ {
+ c = next();
+ } while (Character.isWhitespace(c));
+ switch (c)
+ {
+ case 0:
+ throw syntaxError("Misshaped element");
+ case '<':
+ throw syntaxError("Misplaced '<'");
+ case '>':
+ return XML.GT;
+ case '/':
+ return XML.SLASH;
+ case '=':
+ return XML.EQ;
+ case '!':
+ return XML.BANG;
+ case '?':
+ return XML.QUEST;
+
+ // Quoted string
+
+ case '"':
+ case '\'':
+ q = c;
+ sb = new StringBuilder();
+ for (;;)
+ {
+ c = next();
+ if (c == 0)
+ {
+ throw syntaxError("Unterminated string");
+ }
+ if (c == q)
+ {
+ return sb.toString();
+ }
+ if (c == '&')
+ {
+ sb.append(nextEntity(c));
+ }
+ else
+ {
+ sb.append(c);
+ }
+ }
+ default:
+
+ // Name
+
+ sb = new StringBuilder();
+ for (;;)
+ {
+ sb.append(c);
+ c = next();
+ if (Character.isWhitespace(c))
+ {
+ return sb.toString();
+ }
+ switch (c)
+ {
case 0:
- throw syntaxError("Misshaped element");
- case '<':
- throw syntaxError("Misplaced '<'");
+ return sb.toString();
case '>':
- return XML.GT;
case '/':
- return XML.SLASH;
case '=':
- return XML.EQ;
case '!':
- return XML.BANG;
case '?':
- return XML.QUEST;
-
-// Quoted string
-
+ case '[':
+ case ']':
+ back();
+ return sb.toString();
+ case '<':
case '"':
case '\'':
- q = c;
- sb = new StringBuilder();
- for (;;) {
- c = next();
- if (c == 0) {
- throw syntaxError("Unterminated string");
- }
- if (c == q) {
- return sb.toString();
- }
- if (c == '&') {
- sb.append(nextEntity(c));
- } else {
- sb.append(c);
- }
- }
- default:
-
-// Name
-
- sb = new StringBuilder();
- for (;;) {
- sb.append(c);
- c = next();
- if (Character.isWhitespace(c)) {
- return sb.toString();
- }
- switch (c) {
- case 0:
- return sb.toString();
- case '>':
- case '/':
- case '=':
- case '!':
- case '?':
- case '[':
- case ']':
- back();
- return sb.toString();
- case '<':
- case '"':
- case '\'':
- throw syntaxError("Bad character in a name");
- }
- }
+ throw syntaxError("Bad character in a name");
}
+ }
}
+ }
+
+ /**
+ * Skip characters until past the requested string. If it is not found, we are
+ * left at the end of the source with a result of false.
+ *
+ * @param to
+ * A string to skip past.
+ */
+ // The Android implementation of JSONTokener has a public method of public
+ // void skipPast(String to)
+ // even though ours does not have that method, to have API compatibility, our
+ // method in the subclass
+ // should match.
+ public void skipPast(String to)
+ {
+ boolean b;
+ char c;
+ int i;
+ int j;
+ int offset = 0;
+ int length = to.length();
+ char[] circle = new char[length];
+
+ /*
+ * First fill the circle buffer with as many characters as are in the
+ * to string. If we reach an early end, bail.
+ */
+ for (i = 0; i < length; i += 1)
+ {
+ c = next();
+ if (c == 0)
+ {
+ return;
+ }
+ circle[i] = c;
+ }
- /**
- * Skip characters until past the requested string.
- * If it is not found, we are left at the end of the source with a result of false.
- * @param to A string to skip past.
- */
- // The Android implementation of JSONTokener has a public method of public void skipPast(String to)
- // even though ours does not have that method, to have API compatibility, our method in the subclass
- // should match.
- public void skipPast(String to) {
- boolean b;
- char c;
- int i;
- int j;
- int offset = 0;
- int length = to.length();
- char[] circle = new char[length];
-
- /*
- * First fill the circle buffer with as many characters as are in the
- * to string. If we reach an early end, bail.
- */
-
- for (i = 0; i < length; i += 1) {
- c = next();
- if (c == 0) {
- return;
- }
- circle[i] = c;
- }
+ /* We will loop, possibly for all of the remaining characters. */
+
+ for (;;)
+ {
+ j = offset;
+ b = true;
- /* We will loop, possibly for all of the remaining characters. */
-
- for (;;) {
- j = offset;
- b = true;
-
- /* Compare the circle buffer with the to string. */
-
- for (i = 0; i < length; i += 1) {
- if (circle[j] != to.charAt(i)) {
- b = false;
- break;
- }
- j += 1;
- if (j >= length) {
- j -= length;
- }
- }
-
- /* If we exit the loop with b intact, then victory is ours. */
-
- if (b) {
- return;
- }
-
- /* Get the next character. If there isn't one, then defeat is ours. */
-
- c = next();
- if (c == 0) {
- return;
- }
- /*
- * Shove the character in the circle buffer and advance the
- * circle offset. The offset is mod n.
- */
- circle[offset] = c;
- offset += 1;
- if (offset >= length) {
- offset -= length;
- }
+ /* Compare the circle buffer with the to string. */
+
+ for (i = 0; i < length; i += 1)
+ {
+ if (circle[j] != to.charAt(i))
+ {
+ b = false;
+ break;
+ }
+ j += 1;
+ if (j >= length)
+ {
+ j -= length;
}
+ }
+
+ /* If we exit the loop with b intact, then victory is ours. */
+
+ if (b)
+ {
+ return;
+ }
+
+ /* Get the next character. If there isn't one, then defeat is ours. */
+
+ c = next();
+ if (c == 0)
+ {
+ return;
+ }
+ /*
+ * Shove the character in the circle buffer and advance the
+ * circle offset. The offset is mod n.
+ */
+ circle[offset] = c;
+ offset += 1;
+ if (offset >= length)
+ {
+ offset -= length;
+ }
}
+ }
}
import java.util.StringTokenizer;
/**
- * |a:b:c| => |a|,|b|,|c|
- * |:| => ||,||
- * |a:| => |a|,||
+ * |a:b:c| => |a|,|b|,|c| |:| => ||,|| |a:| => |a|,||
+ *
* @author FangYidong<fangyidong@yahoo.com.cn>
*/
-public class ItemList {
- private String sp=",";
- List items=new ArrayList();
-
-
- public ItemList(){}
-
-
- public ItemList(String s){
- this.split(s,sp,items);
- }
-
- public ItemList(String s,String sp){
- this.sp=s;
- this.split(s,sp,items);
- }
-
- public ItemList(String s,String sp,boolean isMultiToken){
- split(s,sp,items,isMultiToken);
- }
-
- public List getItems(){
- return this.items;
- }
-
- public String[] getArray(){
- return (String[])this.items.toArray();
- }
-
- public void split(String s,String sp,List append,boolean isMultiToken){
- if(s==null || sp==null)
- return;
- if(isMultiToken){
- StringTokenizer tokens=new StringTokenizer(s,sp);
- while(tokens.hasMoreTokens()){
- append.add(tokens.nextToken().trim());
- }
- }
- else{
- this.split(s,sp,append);
- }
- }
-
- public void split(String s,String sp,List append){
- if(s==null || sp==null)
- return;
- int pos=0;
- int prevPos=0;
- do{
- prevPos=pos;
- pos=s.indexOf(sp,pos);
- if(pos==-1)
- break;
- append.add(s.substring(prevPos,pos).trim());
- pos+=sp.length();
- }while(pos!=-1);
- append.add(s.substring(prevPos).trim());
- }
-
- public void setSP(String sp){
- this.sp=sp;
- }
-
- public void add(int i,String item){
- if(item==null)
- return;
- items.add(i,item.trim());
- }
-
- public void add(String item){
- if(item==null)
- return;
- items.add(item.trim());
- }
-
- public void addAll(ItemList list){
- items.addAll(list.items);
- }
-
- public void addAll(String s){
- this.split(s,sp,items);
- }
-
- public void addAll(String s,String sp){
- this.split(s,sp,items);
- }
-
- public void addAll(String s,String sp,boolean isMultiToken){
- this.split(s,sp,items,isMultiToken);
- }
-
- /**
- * @param i 0-based
- * @return
- */
- public String get(int i){
- return (String)items.get(i);
- }
-
- public int size(){
- return items.size();
- }
-
- public String toString(){
- return toString(sp);
- }
-
- public String toString(String sp){
- StringBuffer sb=new StringBuffer();
-
- for(int i=0;i<items.size();i++){
- if(i==0)
- sb.append(items.get(i));
- else{
- sb.append(sp);
- sb.append(items.get(i));
- }
- }
- return sb.toString();
-
- }
-
- public void clear(){
- items.clear();
- }
-
- public void reset(){
- sp=",";
- items.clear();
- }
+public class ItemList
+{
+ private String sp = ",";
+
+ List items = new ArrayList();
+
+ public ItemList()
+ {
+ }
+
+ public ItemList(String s)
+ {
+ this.split(s, sp, items);
+ }
+
+ public ItemList(String s, String sp)
+ {
+ this.sp = s;
+ this.split(s, sp, items);
+ }
+
+ public ItemList(String s, String sp, boolean isMultiToken)
+ {
+ split(s, sp, items, isMultiToken);
+ }
+
+ public List getItems()
+ {
+ return this.items;
+ }
+
+ public String[] getArray()
+ {
+ return (String[]) this.items.toArray();
+ }
+
+ public void split(String s, String sp, List append, boolean isMultiToken)
+ {
+ if (s == null || sp == null)
+ return;
+ if (isMultiToken)
+ {
+ StringTokenizer tokens = new StringTokenizer(s, sp);
+ while (tokens.hasMoreTokens())
+ {
+ append.add(tokens.nextToken().trim());
+ }
+ }
+ else
+ {
+ this.split(s, sp, append);
+ }
+ }
+
+ public void split(String s, String sp, List append)
+ {
+ if (s == null || sp == null)
+ return;
+ int pos = 0;
+ int prevPos = 0;
+ do
+ {
+ prevPos = pos;
+ pos = s.indexOf(sp, pos);
+ if (pos == -1)
+ break;
+ append.add(s.substring(prevPos, pos).trim());
+ pos += sp.length();
+ } while (pos != -1);
+ append.add(s.substring(prevPos).trim());
+ }
+
+ public void setSP(String sp)
+ {
+ this.sp = sp;
+ }
+
+ public void add(int i, String item)
+ {
+ if (item == null)
+ return;
+ items.add(i, item.trim());
+ }
+
+ public void add(String item)
+ {
+ if (item == null)
+ return;
+ items.add(item.trim());
+ }
+
+ public void addAll(ItemList list)
+ {
+ items.addAll(list.items);
+ }
+
+ public void addAll(String s)
+ {
+ this.split(s, sp, items);
+ }
+
+ public void addAll(String s, String sp)
+ {
+ this.split(s, sp, items);
+ }
+
+ public void addAll(String s, String sp, boolean isMultiToken)
+ {
+ this.split(s, sp, items, isMultiToken);
+ }
+
+ /**
+ * @param i
+ * 0-based
+ * @return
+ */
+ public String get(int i)
+ {
+ return (String) items.get(i);
+ }
+
+ public int size()
+ {
+ return items.size();
+ }
+
+ public String toString()
+ {
+ return toString(sp);
+ }
+
+ public String toString(String sp)
+ {
+ StringBuffer sb = new StringBuffer();
+
+ for (int i = 0; i < items.size(); i++)
+ {
+ if (i == 0)
+ sb.append(items.get(i));
+ else
+ {
+ sb.append(sp);
+ sb.append(items.get(i));
+ }
+ }
+ return sb.toString();
+
+ }
+
+ public void clear()
+ {
+ items.clear();
+ }
+
+ public void reset()
+ {
+ sp = ",";
+ items.clear();
+ }
}
*
* @author FangYidong<fangyidong@yahoo.com.cn>
*/
-public class JSONArray extends ArrayList implements JSONAware, JSONStreamAware {
- private static final long serialVersionUID = 3957988303675231981L;
-
- /**
- * Constructs an empty JSONArray.
- */
- public JSONArray(){
- super();
- }
-
- /**
- * Constructs a JSONArray containing the elements of the specified
- * collection, in the order they are returned by the collection's iterator.
- *
- * @param c the collection whose elements are to be placed into this JSONArray
- */
- public JSONArray(Collection c){
- super(c);
- }
-
- /**
- * Encode a list into JSON text and write it to out.
- * If this list is also a JSONStreamAware or a JSONAware, JSONStreamAware and JSONAware specific behaviours will be ignored at this top level.
- *
- * @see org.json.simple.JSONValue#writeJSONString(Object, Writer)
- *
- * @param collection
- * @param out
- */
- public static void writeJSONString(Collection collection, Writer out) throws IOException{
- if(collection == null){
- out.write("null");
- return;
- }
-
- boolean first = true;
- Iterator iter=collection.iterator();
-
- out.write('[');
- while(iter.hasNext()){
- if(first)
- first = false;
- else
- out.write(',');
-
- Object value=iter.next();
- if(value == null){
- out.write("null");
- continue;
- }
-
- JSONValue.writeJSONString(value, out);
- }
- out.write(']');
- }
-
- public void writeJSONString(Writer out) throws IOException{
- writeJSONString(this, out);
- }
-
- /**
- * Convert a list to JSON text. The result is a JSON array.
- * If this list is also a JSONAware, JSONAware specific behaviours will be omitted at this top level.
- *
- * @see org.json.simple.JSONValue#toJSONString(Object)
- *
- * @param collection
- * @return JSON text, or "null" if list is null.
- */
- public static String toJSONString(Collection collection){
- final StringWriter writer = new StringWriter();
-
- try {
- writeJSONString(collection, writer);
- return writer.toString();
- } catch(IOException e){
- // This should never happen for a StringWriter
- throw new RuntimeException(e);
- }
- }
-
- public static void writeJSONString(byte[] array, Writer out) throws IOException{
- if(array == null){
- out.write("null");
- } else if(array.length == 0) {
- out.write("[]");
- } else {
- out.write("[");
- out.write(String.valueOf(array[0]));
-
- for(int i = 1; i < array.length; i++){
- out.write(",");
- out.write(String.valueOf(array[i]));
- }
-
- out.write("]");
- }
- }
-
- public static String toJSONString(byte[] array){
- final StringWriter writer = new StringWriter();
-
- try {
- writeJSONString(array, writer);
- return writer.toString();
- } catch(IOException e){
- // This should never happen for a StringWriter
- throw new RuntimeException(e);
- }
- }
-
- public static void writeJSONString(short[] array, Writer out) throws IOException{
- if(array == null){
- out.write("null");
- } else if(array.length == 0) {
- out.write("[]");
- } else {
- out.write("[");
- out.write(String.valueOf(array[0]));
-
- for(int i = 1; i < array.length; i++){
- out.write(",");
- out.write(String.valueOf(array[i]));
- }
-
- out.write("]");
- }
- }
-
- public static String toJSONString(short[] array){
- final StringWriter writer = new StringWriter();
-
- try {
- writeJSONString(array, writer);
- return writer.toString();
- } catch(IOException e){
- // This should never happen for a StringWriter
- throw new RuntimeException(e);
- }
- }
-
- public static void writeJSONString(int[] array, Writer out) throws IOException{
- if(array == null){
- out.write("null");
- } else if(array.length == 0) {
- out.write("[]");
- } else {
- out.write("[");
- out.write(String.valueOf(array[0]));
-
- for(int i = 1; i < array.length; i++){
- out.write(",");
- out.write(String.valueOf(array[i]));
- }
-
- out.write("]");
- }
- }
-
- public static String toJSONString(int[] array){
- final StringWriter writer = new StringWriter();
-
- try {
- writeJSONString(array, writer);
- return writer.toString();
- } catch(IOException e){
- // This should never happen for a StringWriter
- throw new RuntimeException(e);
- }
- }
-
- public static void writeJSONString(long[] array, Writer out) throws IOException{
- if(array == null){
- out.write("null");
- } else if(array.length == 0) {
- out.write("[]");
- } else {
- out.write("[");
- out.write(String.valueOf(array[0]));
-
- for(int i = 1; i < array.length; i++){
- out.write(",");
- out.write(String.valueOf(array[i]));
- }
-
- out.write("]");
- }
- }
-
- public static String toJSONString(long[] array){
- final StringWriter writer = new StringWriter();
-
- try {
- writeJSONString(array, writer);
- return writer.toString();
- } catch(IOException e){
- // This should never happen for a StringWriter
- throw new RuntimeException(e);
- }
- }
-
- public static void writeJSONString(float[] array, Writer out) throws IOException{
- if(array == null){
- out.write("null");
- } else if(array.length == 0) {
- out.write("[]");
- } else {
- out.write("[");
- out.write(String.valueOf(array[0]));
-
- for(int i = 1; i < array.length; i++){
- out.write(",");
- out.write(String.valueOf(array[i]));
- }
-
- out.write("]");
- }
- }
-
- public static String toJSONString(float[] array){
- final StringWriter writer = new StringWriter();
-
- try {
- writeJSONString(array, writer);
- return writer.toString();
- } catch(IOException e){
- // This should never happen for a StringWriter
- throw new RuntimeException(e);
- }
- }
-
- public static void writeJSONString(double[] array, Writer out) throws IOException{
- if(array == null){
- out.write("null");
- } else if(array.length == 0) {
- out.write("[]");
- } else {
- out.write("[");
- out.write(String.valueOf(array[0]));
-
- for(int i = 1; i < array.length; i++){
- out.write(",");
- out.write(String.valueOf(array[i]));
- }
-
- out.write("]");
- }
- }
-
- public static String toJSONString(double[] array){
- final StringWriter writer = new StringWriter();
-
- try {
- writeJSONString(array, writer);
- return writer.toString();
- } catch(IOException e){
- // This should never happen for a StringWriter
- throw new RuntimeException(e);
- }
- }
-
- public static void writeJSONString(boolean[] array, Writer out) throws IOException{
- if(array == null){
- out.write("null");
- } else if(array.length == 0) {
- out.write("[]");
- } else {
- out.write("[");
- out.write(String.valueOf(array[0]));
-
- for(int i = 1; i < array.length; i++){
- out.write(",");
- out.write(String.valueOf(array[i]));
- }
-
- out.write("]");
- }
- }
-
- public static String toJSONString(boolean[] array){
- final StringWriter writer = new StringWriter();
-
- try {
- writeJSONString(array, writer);
- return writer.toString();
- } catch(IOException e){
- // This should never happen for a StringWriter
- throw new RuntimeException(e);
- }
- }
-
- public static void writeJSONString(char[] array, Writer out) throws IOException{
- if(array == null){
- out.write("null");
- } else if(array.length == 0) {
- out.write("[]");
- } else {
- out.write("[\"");
- out.write(String.valueOf(array[0]));
-
- for(int i = 1; i < array.length; i++){
- out.write("\",\"");
- out.write(String.valueOf(array[i]));
- }
-
- out.write("\"]");
- }
- }
-
- public static String toJSONString(char[] array){
- final StringWriter writer = new StringWriter();
-
- try {
- writeJSONString(array, writer);
- return writer.toString();
- } catch(IOException e){
- // This should never happen for a StringWriter
- throw new RuntimeException(e);
- }
- }
-
- public static void writeJSONString(Object[] array, Writer out) throws IOException{
- if(array == null){
- out.write("null");
- } else if(array.length == 0) {
- out.write("[]");
- } else {
- out.write("[");
- JSONValue.writeJSONString(array[0], out);
-
- for(int i = 1; i < array.length; i++){
- out.write(",");
- JSONValue.writeJSONString(array[i], out);
- }
-
- out.write("]");
- }
- }
-
- public static String toJSONString(Object[] array){
- final StringWriter writer = new StringWriter();
-
- try {
- writeJSONString(array, writer);
- return writer.toString();
- } catch(IOException e){
- // This should never happen for a StringWriter
- throw new RuntimeException(e);
- }
- }
-
- public String toJSONString(){
- return toJSONString(this);
- }
-
- /**
- * Returns a string representation of this array. This is equivalent to
- * calling {@link JSONArray#toJSONString()}.
- */
- public String toString() {
- return toJSONString();
- }
+public class JSONArray extends ArrayList
+ implements JSONAware, JSONStreamAware
+{
+ private static final long serialVersionUID = 3957988303675231981L;
+
+ /**
+ * Constructs an empty JSONArray.
+ */
+ public JSONArray()
+ {
+ super();
+ }
+
+ /**
+ * Constructs a JSONArray containing the elements of the specified collection,
+ * in the order they are returned by the collection's iterator.
+ *
+ * @param c
+ * the collection whose elements are to be placed into this JSONArray
+ */
+ public JSONArray(Collection c)
+ {
+ super(c);
+ }
+
+ /**
+ * Encode a list into JSON text and write it to out. If this list is also a
+ * JSONStreamAware or a JSONAware, JSONStreamAware and JSONAware specific
+ * behaviours will be ignored at this top level.
+ *
+ * @see org.json.simple.JSONValue#writeJSONString(Object, Writer)
+ *
+ * @param collection
+ * @param out
+ */
+ public static void writeJSONString(Collection collection, Writer out)
+ throws IOException
+ {
+ if (collection == null)
+ {
+ out.write("null");
+ return;
+ }
+
+ boolean first = true;
+ Iterator iter = collection.iterator();
+
+ out.write('[');
+ while (iter.hasNext())
+ {
+ if (first)
+ first = false;
+ else
+ out.write(',');
+
+ Object value = iter.next();
+ if (value == null)
+ {
+ out.write("null");
+ continue;
+ }
+
+ JSONValue.writeJSONString(value, out);
+ }
+ out.write(']');
+ }
+
+ public void writeJSONString(Writer out) throws IOException
+ {
+ writeJSONString(this, out);
+ }
+
+ /**
+ * Convert a list to JSON text. The result is a JSON array. If this list is
+ * also a JSONAware, JSONAware specific behaviours will be omitted at this top
+ * level.
+ *
+ * @see org.json.simple.JSONValue#toJSONString(Object)
+ *
+ * @param collection
+ * @return JSON text, or "null" if list is null.
+ */
+ public static String toJSONString(Collection collection)
+ {
+ final StringWriter writer = new StringWriter();
+
+ try
+ {
+ writeJSONString(collection, writer);
+ return writer.toString();
+ } catch (IOException e)
+ {
+ // This should never happen for a StringWriter
+ throw new RuntimeException(e);
+ }
+ }
+
+ public static void writeJSONString(byte[] array, Writer out)
+ throws IOException
+ {
+ if (array == null)
+ {
+ out.write("null");
+ }
+ else if (array.length == 0)
+ {
+ out.write("[]");
+ }
+ else
+ {
+ out.write("[");
+ out.write(String.valueOf(array[0]));
+
+ for (int i = 1; i < array.length; i++)
+ {
+ out.write(",");
+ out.write(String.valueOf(array[i]));
+ }
+
+ out.write("]");
+ }
+ }
+
+ public static String toJSONString(byte[] array)
+ {
+ final StringWriter writer = new StringWriter();
+
+ try
+ {
+ writeJSONString(array, writer);
+ return writer.toString();
+ } catch (IOException e)
+ {
+ // This should never happen for a StringWriter
+ throw new RuntimeException(e);
+ }
+ }
+
+ public static void writeJSONString(short[] array, Writer out)
+ throws IOException
+ {
+ if (array == null)
+ {
+ out.write("null");
+ }
+ else if (array.length == 0)
+ {
+ out.write("[]");
+ }
+ else
+ {
+ out.write("[");
+ out.write(String.valueOf(array[0]));
+
+ for (int i = 1; i < array.length; i++)
+ {
+ out.write(",");
+ out.write(String.valueOf(array[i]));
+ }
+
+ out.write("]");
+ }
+ }
+
+ public static String toJSONString(short[] array)
+ {
+ final StringWriter writer = new StringWriter();
+
+ try
+ {
+ writeJSONString(array, writer);
+ return writer.toString();
+ } catch (IOException e)
+ {
+ // This should never happen for a StringWriter
+ throw new RuntimeException(e);
+ }
+ }
+
+ public static void writeJSONString(int[] array, Writer out)
+ throws IOException
+ {
+ if (array == null)
+ {
+ out.write("null");
+ }
+ else if (array.length == 0)
+ {
+ out.write("[]");
+ }
+ else
+ {
+ out.write("[");
+ out.write(String.valueOf(array[0]));
+
+ for (int i = 1; i < array.length; i++)
+ {
+ out.write(",");
+ out.write(String.valueOf(array[i]));
+ }
+
+ out.write("]");
+ }
+ }
+
+ public static String toJSONString(int[] array)
+ {
+ final StringWriter writer = new StringWriter();
+
+ try
+ {
+ writeJSONString(array, writer);
+ return writer.toString();
+ } catch (IOException e)
+ {
+ // This should never happen for a StringWriter
+ throw new RuntimeException(e);
+ }
+ }
+
+ public static void writeJSONString(long[] array, Writer out)
+ throws IOException
+ {
+ if (array == null)
+ {
+ out.write("null");
+ }
+ else if (array.length == 0)
+ {
+ out.write("[]");
+ }
+ else
+ {
+ out.write("[");
+ out.write(String.valueOf(array[0]));
+
+ for (int i = 1; i < array.length; i++)
+ {
+ out.write(",");
+ out.write(String.valueOf(array[i]));
+ }
+
+ out.write("]");
+ }
+ }
+
+ public static String toJSONString(long[] array)
+ {
+ final StringWriter writer = new StringWriter();
+
+ try
+ {
+ writeJSONString(array, writer);
+ return writer.toString();
+ } catch (IOException e)
+ {
+ // This should never happen for a StringWriter
+ throw new RuntimeException(e);
+ }
+ }
+
+ public static void writeJSONString(float[] array, Writer out)
+ throws IOException
+ {
+ if (array == null)
+ {
+ out.write("null");
+ }
+ else if (array.length == 0)
+ {
+ out.write("[]");
+ }
+ else
+ {
+ out.write("[");
+ out.write(String.valueOf(array[0]));
+
+ for (int i = 1; i < array.length; i++)
+ {
+ out.write(",");
+ out.write(String.valueOf(array[i]));
+ }
+
+ out.write("]");
+ }
+ }
+
+ public static String toJSONString(float[] array)
+ {
+ final StringWriter writer = new StringWriter();
+
+ try
+ {
+ writeJSONString(array, writer);
+ return writer.toString();
+ } catch (IOException e)
+ {
+ // This should never happen for a StringWriter
+ throw new RuntimeException(e);
+ }
+ }
+
+ public static void writeJSONString(double[] array, Writer out)
+ throws IOException
+ {
+ if (array == null)
+ {
+ out.write("null");
+ }
+ else if (array.length == 0)
+ {
+ out.write("[]");
+ }
+ else
+ {
+ out.write("[");
+ out.write(String.valueOf(array[0]));
+
+ for (int i = 1; i < array.length; i++)
+ {
+ out.write(",");
+ out.write(String.valueOf(array[i]));
+ }
+
+ out.write("]");
+ }
+ }
+
+ public static String toJSONString(double[] array)
+ {
+ final StringWriter writer = new StringWriter();
+
+ try
+ {
+ writeJSONString(array, writer);
+ return writer.toString();
+ } catch (IOException e)
+ {
+ // This should never happen for a StringWriter
+ throw new RuntimeException(e);
+ }
+ }
+
+ public static void writeJSONString(boolean[] array, Writer out)
+ throws IOException
+ {
+ if (array == null)
+ {
+ out.write("null");
+ }
+ else if (array.length == 0)
+ {
+ out.write("[]");
+ }
+ else
+ {
+ out.write("[");
+ out.write(String.valueOf(array[0]));
+
+ for (int i = 1; i < array.length; i++)
+ {
+ out.write(",");
+ out.write(String.valueOf(array[i]));
+ }
+
+ out.write("]");
+ }
+ }
+
+ public static String toJSONString(boolean[] array)
+ {
+ final StringWriter writer = new StringWriter();
+
+ try
+ {
+ writeJSONString(array, writer);
+ return writer.toString();
+ } catch (IOException e)
+ {
+ // This should never happen for a StringWriter
+ throw new RuntimeException(e);
+ }
+ }
+
+ public static void writeJSONString(char[] array, Writer out)
+ throws IOException
+ {
+ if (array == null)
+ {
+ out.write("null");
+ }
+ else if (array.length == 0)
+ {
+ out.write("[]");
+ }
+ else
+ {
+ out.write("[\"");
+ out.write(String.valueOf(array[0]));
+
+ for (int i = 1; i < array.length; i++)
+ {
+ out.write("\",\"");
+ out.write(String.valueOf(array[i]));
+ }
+
+ out.write("\"]");
+ }
+ }
+
+ public static String toJSONString(char[] array)
+ {
+ final StringWriter writer = new StringWriter();
+
+ try
+ {
+ writeJSONString(array, writer);
+ return writer.toString();
+ } catch (IOException e)
+ {
+ // This should never happen for a StringWriter
+ throw new RuntimeException(e);
+ }
+ }
+
+ public static void writeJSONString(Object[] array, Writer out)
+ throws IOException
+ {
+ if (array == null)
+ {
+ out.write("null");
+ }
+ else if (array.length == 0)
+ {
+ out.write("[]");
+ }
+ else
+ {
+ out.write("[");
+ JSONValue.writeJSONString(array[0], out);
+
+ for (int i = 1; i < array.length; i++)
+ {
+ out.write(",");
+ JSONValue.writeJSONString(array[i], out);
+ }
+
+ out.write("]");
+ }
+ }
+
+ public static String toJSONString(Object[] array)
+ {
+ final StringWriter writer = new StringWriter();
+
+ try
+ {
+ writeJSONString(array, writer);
+ return writer.toString();
+ } catch (IOException e)
+ {
+ // This should never happen for a StringWriter
+ throw new RuntimeException(e);
+ }
+ }
+
+ public String toJSONString()
+ {
+ return toJSONString(this);
+ }
+
+ /**
+ * Returns a string representation of this array. This is equivalent to
+ * calling {@link JSONArray#toJSONString()}.
+ */
+ public String toString()
+ {
+ return toJSONString();
+ }
}
package org.json.simple;
/**
- * Beans that support customized output of JSON text shall implement this interface.
+ * Beans that support customized output of JSON text shall implement this
+ * interface.
+ *
* @author FangYidong<fangyidong@yahoo.com.cn>
*/
-public interface JSONAware {
- /**
- * @return JSON text
- */
- String toJSONString();
+public interface JSONAware
+{
+ /**
+ * @return JSON text
+ */
+ String toJSONString();
}
import java.util.Map;
/**
- * A JSON object. Key value pairs are unordered. JSONObject supports java.util.Map interface.
+ * A JSON object. Key value pairs are unordered. JSONObject supports
+ * java.util.Map interface.
*
* @author FangYidong<fangyidong@yahoo.com.cn>
*/
-public class JSONObject extends HashMap implements Map, JSONAware, JSONStreamAware{
-
- private static final long serialVersionUID = -503443796854799292L;
-
-
- public JSONObject() {
- super();
- }
-
- /**
- * Allows creation of a JSONObject from a Map. After that, both the
- * generated JSONObject and the Map can be modified independently.
- *
- * @param map
- */
- public JSONObject(Map map) {
- super(map);
- }
-
-
- /**
- * Encode a map into JSON text and write it to out.
- * If this map is also a JSONAware or JSONStreamAware, JSONAware or JSONStreamAware specific behaviours will be ignored at this top level.
- *
- * @see org.json.simple.JSONValue#writeJSONString(Object, Writer)
- *
- * @param map
- * @param out
- */
- public static void writeJSONString(Map map, Writer out) throws IOException {
- if(map == null){
- out.write("null");
- return;
- }
-
- boolean first = true;
- Iterator iter=map.entrySet().iterator();
-
- out.write('{');
- while(iter.hasNext()){
- if(first)
- first = false;
- else
- out.write(',');
- Map.Entry entry=(Map.Entry)iter.next();
- out.write('\"');
- out.write(escape(String.valueOf(entry.getKey())));
- out.write('\"');
- out.write(':');
- JSONValue.writeJSONString(entry.getValue(), out);
- }
- out.write('}');
- }
-
- public void writeJSONString(Writer out) throws IOException{
- writeJSONString(this, out);
- }
-
- /**
- * Convert a map to JSON text. The result is a JSON object.
- * If this map is also a JSONAware, JSONAware specific behaviours will be omitted at this top level.
- *
- * @see org.json.simple.JSONValue#toJSONString(Object)
- *
- * @param map
- * @return JSON text, or "null" if map is null.
- */
- public static String toJSONString(Map map){
- final StringWriter writer = new StringWriter();
-
- try {
- writeJSONString(map, writer);
- return writer.toString();
- } catch (IOException e) {
- // This should never happen with a StringWriter
- throw new RuntimeException(e);
- }
- }
-
- public String toJSONString(){
- return toJSONString(this);
- }
-
- public String toString(){
- return toJSONString();
- }
-
- public static String toString(String key,Object value){
- StringBuffer sb = new StringBuffer();
- sb.append('\"');
- if(key == null)
- sb.append("null");
- else
- JSONValue.escape(key, sb);
- sb.append('\"').append(':');
-
- sb.append(JSONValue.toJSONString(value));
-
- return sb.toString();
- }
-
- /**
- * Escape quotes, \, /, \r, \n, \b, \f, \t and other control characters (U+0000 through U+001F).
- * It's the same as JSONValue.escape() only for compatibility here.
- *
- * @see org.json.simple.JSONValue#escape(String)
- *
- * @param s
- * @return
- */
- public static String escape(String s){
- return JSONValue.escape(s);
- }
+public class JSONObject extends HashMap
+ implements Map, JSONAware, JSONStreamAware
+{
+
+ private static final long serialVersionUID = -503443796854799292L;
+
+ public JSONObject()
+ {
+ super();
+ }
+
+ /**
+ * Allows creation of a JSONObject from a Map. After that, both the generated
+ * JSONObject and the Map can be modified independently.
+ *
+ * @param map
+ */
+ public JSONObject(Map map)
+ {
+ super(map);
+ }
+
+ /**
+ * Encode a map into JSON text and write it to out. If this map is also a
+ * JSONAware or JSONStreamAware, JSONAware or JSONStreamAware specific
+ * behaviours will be ignored at this top level.
+ *
+ * @see org.json.simple.JSONValue#writeJSONString(Object, Writer)
+ *
+ * @param map
+ * @param out
+ */
+ public static void writeJSONString(Map map, Writer out) throws IOException
+ {
+ if (map == null)
+ {
+ out.write("null");
+ return;
+ }
+
+ boolean first = true;
+ Iterator iter = map.entrySet().iterator();
+
+ out.write('{');
+ while (iter.hasNext())
+ {
+ if (first)
+ first = false;
+ else
+ out.write(',');
+ Map.Entry entry = (Map.Entry) iter.next();
+ out.write('\"');
+ out.write(escape(String.valueOf(entry.getKey())));
+ out.write('\"');
+ out.write(':');
+ JSONValue.writeJSONString(entry.getValue(), out);
+ }
+ out.write('}');
+ }
+
+ public void writeJSONString(Writer out) throws IOException
+ {
+ writeJSONString(this, out);
+ }
+
+ /**
+ * Convert a map to JSON text. The result is a JSON object. If this map is
+ * also a JSONAware, JSONAware specific behaviours will be omitted at this top
+ * level.
+ *
+ * @see org.json.simple.JSONValue#toJSONString(Object)
+ *
+ * @param map
+ * @return JSON text, or "null" if map is null.
+ */
+ public static String toJSONString(Map map)
+ {
+ final StringWriter writer = new StringWriter();
+
+ try
+ {
+ writeJSONString(map, writer);
+ return writer.toString();
+ } catch (IOException e)
+ {
+ // This should never happen with a StringWriter
+ throw new RuntimeException(e);
+ }
+ }
+
+ public String toJSONString()
+ {
+ return toJSONString(this);
+ }
+
+ public String toString()
+ {
+ return toJSONString();
+ }
+
+ public static String toString(String key, Object value)
+ {
+ StringBuffer sb = new StringBuffer();
+ sb.append('\"');
+ if (key == null)
+ sb.append("null");
+ else
+ JSONValue.escape(key, sb);
+ sb.append('\"').append(':');
+
+ sb.append(JSONValue.toJSONString(value));
+
+ return sb.toString();
+ }
+
+ /**
+ * Escape quotes, \, /, \r, \n, \b, \f, \t and other control characters
+ * (U+0000 through U+001F). It's the same as JSONValue.escape() only for
+ * compatibility here.
+ *
+ * @see org.json.simple.JSONValue#escape(String)
+ *
+ * @param s
+ * @return
+ */
+ public static String escape(String s)
+ {
+ return JSONValue.escape(s);
+ }
}
import java.io.Writer;
/**
- * Beans that support customized output of JSON text to a writer shall implement this interface.
+ * Beans that support customized output of JSON text to a writer shall implement
+ * this interface.
+ *
* @author FangYidong<fangyidong@yahoo.com.cn>
*/
-public interface JSONStreamAware {
- /**
- * write JSON string to out.
- */
- void writeJSONString(Writer out) throws IOException;
+public interface JSONStreamAware
+{
+ /**
+ * write JSON string to out.
+ */
+ void writeJSONString(Writer out) throws IOException;
}
import org.json.simple.parser.JSONParser;
import org.json.simple.parser.ParseException;
-
/**
* @author FangYidong<fangyidong@yahoo.com.cn>
*/
-public class JSONValue {
- /**
- * Parse JSON text into java object from the input source.
- * Please use parseWithException() if you don't want to ignore the exception.
- *
- * @see org.json.simple.parser.JSONParser#parse(Reader)
- * @see #parseWithException(Reader)
- *
- * @param in
- * @return Instance of the following:
- * org.json.simple.JSONObject,
- * org.json.simple.JSONArray,
- * java.lang.String,
- * java.lang.Number,
- * java.lang.Boolean,
- * null
- *
- * @deprecated this method may throw an {@code Error} instead of returning
- * {@code null}; please use {@link JSONValue#parseWithException(Reader)}
- * instead
- */
+public class JSONValue
+{
+ /**
+ * Parse JSON text into java object from the input source. Please use
+ * parseWithException() if you don't want to ignore the exception.
+ *
+ * @see org.json.simple.parser.JSONParser#parse(Reader)
+ * @see #parseWithException(Reader)
+ *
+ * @param in
+ * @return Instance of the following: org.json.simple.JSONObject,
+ * org.json.simple.JSONArray, java.lang.String, java.lang.Number,
+ * java.lang.Boolean, null
+ *
+ * @deprecated this method may throw an {@code Error} instead of returning
+ * {@code null}; please use
+ * {@link JSONValue#parseWithException(Reader)} instead
+ */
@Deprecated
- public static Object parse(Reader in){
- try{
- JSONParser parser=new JSONParser();
- return parser.parse(in);
- }
- catch(Exception e){
- return null;
- }
- }
-
- /**
- * Parse JSON text into java object from the given string.
- * Please use parseWithException() if you don't want to ignore the exception.
- *
- * @see org.json.simple.parser.JSONParser#parse(Reader)
- * @see #parseWithException(Reader)
- *
- * @param s
- * @return Instance of the following:
- * org.json.simple.JSONObject,
- * org.json.simple.JSONArray,
- * java.lang.String,
- * java.lang.Number,
- * java.lang.Boolean,
- * null
- *
- * @deprecated this method may throw an {@code Error} instead of returning
- * {@code null}; please use {@link JSONValue#parseWithException(String)}
- * instead
- */
+ public static Object parse(Reader in)
+ {
+ try
+ {
+ JSONParser parser = new JSONParser();
+ return parser.parse(in);
+ } catch (Exception e)
+ {
+ return null;
+ }
+ }
+
+ /**
+ * Parse JSON text into java object from the given string. Please use
+ * parseWithException() if you don't want to ignore the exception.
+ *
+ * @see org.json.simple.parser.JSONParser#parse(Reader)
+ * @see #parseWithException(Reader)
+ *
+ * @param s
+ * @return Instance of the following: org.json.simple.JSONObject,
+ * org.json.simple.JSONArray, java.lang.String, java.lang.Number,
+ * java.lang.Boolean, null
+ *
+ * @deprecated this method may throw an {@code Error} instead of returning
+ * {@code null}; please use
+ * {@link JSONValue#parseWithException(String)} instead
+ */
@Deprecated
- public static Object parse(String s){
- StringReader in=new StringReader(s);
- return parse(in);
- }
-
- /**
- * Parse JSON text into java object from the input source.
- *
- * @see org.json.simple.parser.JSONParser
- *
- * @param in
- * @return Instance of the following:
- * org.json.simple.JSONObject,
- * org.json.simple.JSONArray,
- * java.lang.String,
- * java.lang.Number,
- * java.lang.Boolean,
- * null
- *
- * @throws IOException
- * @throws ParseException
- */
- public static Object parseWithException(Reader in) throws IOException, ParseException{
- JSONParser parser=new JSONParser();
- return parser.parse(in);
- }
-
- public static Object parseWithException(String s) throws ParseException{
- JSONParser parser=new JSONParser();
- return parser.parse(s);
- }
-
- /**
- * Encode an object into JSON text and write it to out.
- * <p>
- * If this object is a Map or a List, and it's also a JSONStreamAware or a JSONAware, JSONStreamAware or JSONAware will be considered firstly.
- * <p>
- * DO NOT call this method from writeJSONString(Writer) of a class that implements both JSONStreamAware and (Map or List) with
- * "this" as the first parameter, use JSONObject.writeJSONString(Map, Writer) or JSONArray.writeJSONString(List, Writer) instead.
- *
- * @see org.json.simple.JSONObject#writeJSONString(Map, Writer)
- * @see org.json.simple.JSONArray#writeJSONString(List, Writer)
- *
- * @param value
- * @param writer
- */
- public static void writeJSONString(Object value, Writer out) throws IOException {
- if(value == null){
- out.write("null");
- return;
- }
-
- if(value instanceof String){
- out.write('\"');
- out.write(escape((String)value));
- out.write('\"');
- return;
- }
-
- if(value instanceof Double){
- if(((Double)value).isInfinite() || ((Double)value).isNaN())
- out.write("null");
- else
- out.write(value.toString());
- return;
- }
-
- if(value instanceof Float){
- if(((Float)value).isInfinite() || ((Float)value).isNaN())
- out.write("null");
- else
- out.write(value.toString());
- return;
- }
-
- if(value instanceof Number){
- out.write(value.toString());
- return;
- }
-
- if(value instanceof Boolean){
- out.write(value.toString());
- return;
- }
-
- if((value instanceof JSONStreamAware)){
- ((JSONStreamAware)value).writeJSONString(out);
- return;
- }
-
- if((value instanceof JSONAware)){
- out.write(((JSONAware)value).toJSONString());
- return;
- }
-
- if(value instanceof Map){
- JSONObject.writeJSONString((Map)value, out);
- return;
- }
-
- if(value instanceof Collection){
- JSONArray.writeJSONString((Collection)value, out);
- return;
- }
-
- if(value instanceof byte[]){
- JSONArray.writeJSONString((byte[])value, out);
- return;
- }
-
- if(value instanceof short[]){
- JSONArray.writeJSONString((short[])value, out);
- return;
- }
-
- if(value instanceof int[]){
- JSONArray.writeJSONString((int[])value, out);
- return;
- }
-
- if(value instanceof long[]){
- JSONArray.writeJSONString((long[])value, out);
- return;
- }
-
- if(value instanceof float[]){
- JSONArray.writeJSONString((float[])value, out);
- return;
- }
-
- if(value instanceof double[]){
- JSONArray.writeJSONString((double[])value, out);
- return;
- }
-
- if(value instanceof boolean[]){
- JSONArray.writeJSONString((boolean[])value, out);
- return;
- }
-
- if(value instanceof char[]){
- JSONArray.writeJSONString((char[])value, out);
- return;
- }
-
- if(value instanceof Object[]){
- JSONArray.writeJSONString((Object[])value, out);
- return;
- }
-
- out.write(value.toString());
- }
+ public static Object parse(String s)
+ {
+ StringReader in = new StringReader(s);
+ return parse(in);
+ }
+
+ /**
+ * Parse JSON text into java object from the input source.
+ *
+ * @see org.json.simple.parser.JSONParser
+ *
+ * @param in
+ * @return Instance of the following: org.json.simple.JSONObject,
+ * org.json.simple.JSONArray, java.lang.String, java.lang.Number,
+ * java.lang.Boolean, null
+ *
+ * @throws IOException
+ * @throws ParseException
+ */
+ public static Object parseWithException(Reader in)
+ throws IOException, ParseException
+ {
+ JSONParser parser = new JSONParser();
+ return parser.parse(in);
+ }
+
+ public static Object parseWithException(String s) throws ParseException
+ {
+ JSONParser parser = new JSONParser();
+ return parser.parse(s);
+ }
+
+ /**
+ * Encode an object into JSON text and write it to out.
+ * <p>
+ * If this object is a Map or a List, and it's also a JSONStreamAware or a
+ * JSONAware, JSONStreamAware or JSONAware will be considered firstly.
+ * <p>
+ * DO NOT call this method from writeJSONString(Writer) of a class that
+ * implements both JSONStreamAware and (Map or List) with "this" as the first
+ * parameter, use JSONObject.writeJSONString(Map, Writer) or
+ * JSONArray.writeJSONString(List, Writer) instead.
+ *
+ * @see org.json.simple.JSONObject#writeJSONString(Map, Writer)
+ * @see org.json.simple.JSONArray#writeJSONString(List, Writer)
+ *
+ * @param value
+ * @param writer
+ */
+ public static void writeJSONString(Object value, Writer out)
+ throws IOException
+ {
+ if (value == null)
+ {
+ out.write("null");
+ return;
+ }
+
+ if (value instanceof String)
+ {
+ out.write('\"');
+ out.write(escape((String) value));
+ out.write('\"');
+ return;
+ }
- /**
- * Convert an object to JSON text.
- * <p>
- * If this object is a Map or a List, and it's also a JSONAware, JSONAware will be considered firstly.
- * <p>
- * DO NOT call this method from toJSONString() of a class that implements both JSONAware and Map or List with
- * "this" as the parameter, use JSONObject.toJSONString(Map) or JSONArray.toJSONString(List) instead.
- *
- * @see org.json.simple.JSONObject#toJSONString(Map)
- * @see org.json.simple.JSONArray#toJSONString(List)
- *
- * @param value
- * @return JSON text, or "null" if value is null or it's an NaN or an INF number.
- */
- public static String toJSONString(Object value){
- final StringWriter writer = new StringWriter();
-
- try{
- writeJSONString(value, writer);
- return writer.toString();
- } catch(IOException e){
- // This should never happen for a StringWriter
- throw new RuntimeException(e);
- }
- }
+ if (value instanceof Double)
+ {
+ if (((Double) value).isInfinite() || ((Double) value).isNaN())
+ out.write("null");
+ else
+ out.write(value.toString());
+ return;
+ }
+
+ if (value instanceof Float)
+ {
+ if (((Float) value).isInfinite() || ((Float) value).isNaN())
+ out.write("null");
+ else
+ out.write(value.toString());
+ return;
+ }
- /**
- * Escape quotes, \, /, \r, \n, \b, \f, \t and other control characters (U+0000 through U+001F).
- * @param s
- * @return
- */
- public static String escape(String s){
- if(s==null)
- return null;
- StringBuffer sb = new StringBuffer();
- escape(s, sb);
- return sb.toString();
+ if (value instanceof Number)
+ {
+ out.write(value.toString());
+ return;
}
- /**
- * @param s - Must not be null.
- * @param sb
- */
- static void escape(String s, StringBuffer sb) {
- final int len = s.length();
- for(int i=0;i<len;i++){
- char ch=s.charAt(i);
- switch(ch){
- case '"':
- sb.append("\\\"");
- break;
- case '\\':
- sb.append("\\\\");
- break;
- case '\b':
- sb.append("\\b");
- break;
- case '\f':
- sb.append("\\f");
- break;
- case '\n':
- sb.append("\\n");
- break;
- case '\r':
- sb.append("\\r");
- break;
- case '\t':
- sb.append("\\t");
- break;
- case '/':
- sb.append("\\/");
- break;
- default:
- //Reference: http://www.unicode.org/versions/Unicode5.1.0/
- if((ch>='\u0000' && ch<='\u001F') || (ch>='\u007F' && ch<='\u009F') || (ch>='\u2000' && ch<='\u20FF')){
- String ss=Integer.toHexString(ch);
- sb.append("\\u");
- for(int k=0;k<4-ss.length();k++){
- sb.append('0');
- }
- sb.append(ss.toUpperCase(Locale.ROOT));
- }
- else{
- sb.append(ch);
- }
- }
- }//for
- }
+ if (value instanceof Boolean)
+ {
+ out.write(value.toString());
+ return;
+ }
+
+ if ((value instanceof JSONStreamAware))
+ {
+ ((JSONStreamAware) value).writeJSONString(out);
+ return;
+ }
+
+ if ((value instanceof JSONAware))
+ {
+ out.write(((JSONAware) value).toJSONString());
+ return;
+ }
+
+ if (value instanceof Map)
+ {
+ JSONObject.writeJSONString((Map) value, out);
+ return;
+ }
+
+ if (value instanceof Collection)
+ {
+ JSONArray.writeJSONString((Collection) value, out);
+ return;
+ }
+
+ if (value instanceof byte[])
+ {
+ JSONArray.writeJSONString((byte[]) value, out);
+ return;
+ }
+
+ if (value instanceof short[])
+ {
+ JSONArray.writeJSONString((short[]) value, out);
+ return;
+ }
+
+ if (value instanceof int[])
+ {
+ JSONArray.writeJSONString((int[]) value, out);
+ return;
+ }
+
+ if (value instanceof long[])
+ {
+ JSONArray.writeJSONString((long[]) value, out);
+ return;
+ }
+
+ if (value instanceof float[])
+ {
+ JSONArray.writeJSONString((float[]) value, out);
+ return;
+ }
+
+ if (value instanceof double[])
+ {
+ JSONArray.writeJSONString((double[]) value, out);
+ return;
+ }
+
+ if (value instanceof boolean[])
+ {
+ JSONArray.writeJSONString((boolean[]) value, out);
+ return;
+ }
+
+ if (value instanceof char[])
+ {
+ JSONArray.writeJSONString((char[]) value, out);
+ return;
+ }
+
+ if (value instanceof Object[])
+ {
+ JSONArray.writeJSONString((Object[]) value, out);
+ return;
+ }
+
+ out.write(value.toString());
+ }
+
+ /**
+ * Convert an object to JSON text.
+ * <p>
+ * If this object is a Map or a List, and it's also a JSONAware, JSONAware
+ * will be considered firstly.
+ * <p>
+ * DO NOT call this method from toJSONString() of a class that implements both
+ * JSONAware and Map or List with "this" as the parameter, use
+ * JSONObject.toJSONString(Map) or JSONArray.toJSONString(List) instead.
+ *
+ * @see org.json.simple.JSONObject#toJSONString(Map)
+ * @see org.json.simple.JSONArray#toJSONString(List)
+ *
+ * @param value
+ * @return JSON text, or "null" if value is null or it's an NaN or an INF
+ * number.
+ */
+ public static String toJSONString(Object value)
+ {
+ final StringWriter writer = new StringWriter();
+
+ try
+ {
+ writeJSONString(value, writer);
+ return writer.toString();
+ } catch (IOException e)
+ {
+ // This should never happen for a StringWriter
+ throw new RuntimeException(e);
+ }
+ }
+
+ /**
+ * Escape quotes, \, /, \r, \n, \b, \f, \t and other control characters
+ * (U+0000 through U+001F).
+ *
+ * @param s
+ * @return
+ */
+ public static String escape(String s)
+ {
+ if (s == null)
+ return null;
+ StringBuffer sb = new StringBuffer();
+ escape(s, sb);
+ return sb.toString();
+ }
+
+ /**
+ * @param s
+ * - Must not be null.
+ * @param sb
+ */
+ static void escape(String s, StringBuffer sb)
+ {
+ final int len = s.length();
+ for (int i = 0; i < len; i++)
+ {
+ char ch = s.charAt(i);
+ switch (ch)
+ {
+ case '"':
+ sb.append("\\\"");
+ break;
+ case '\\':
+ sb.append("\\\\");
+ break;
+ case '\b':
+ sb.append("\\b");
+ break;
+ case '\f':
+ sb.append("\\f");
+ break;
+ case '\n':
+ sb.append("\\n");
+ break;
+ case '\r':
+ sb.append("\\r");
+ break;
+ case '\t':
+ sb.append("\\t");
+ break;
+ case '/':
+ sb.append("\\/");
+ break;
+ default:
+ // Reference: http://www.unicode.org/versions/Unicode5.1.0/
+ if ((ch >= '\u0000' && ch <= '\u001F')
+ || (ch >= '\u007F' && ch <= '\u009F')
+ || (ch >= '\u2000' && ch <= '\u20FF'))
+ {
+ String ss = Integer.toHexString(ch);
+ sb.append("\\u");
+ for (int k = 0; k < 4 - ss.length(); k++)
+ {
+ sb.append('0');
+ }
+ sb.append(ss.toUpperCase(Locale.ROOT));
+ }
+ else
+ {
+ sb.append(ch);
+ }
+ }
+ } // for
+ }
}
/**
* Container factory for creating containers for JSON object and JSON array.
*
- * @see org.json.simple.parser.JSONParser#parse(java.io.Reader, ContainerFactory)
+ * @see org.json.simple.parser.JSONParser#parse(java.io.Reader,
+ * ContainerFactory)
*
* @author FangYidong<fangyidong@yahoo.com.cn>
*/
-public interface ContainerFactory {
- /**
- * @return A Map instance to store JSON object, or null if you want to use org.json.simple.JSONObject.
- */
- Map createObjectContainer();
-
- /**
- * @return A List instance to store JSON array, or null if you want to use org.json.simple.JSONArray.
- */
- List creatArrayContainer();
+public interface ContainerFactory
+{
+ /**
+ * @return A Map instance to store JSON object, or null if you want to use
+ * org.json.simple.JSONObject.
+ */
+ Map createObjectContainer();
+
+ /**
+ * @return A List instance to store JSON array, or null if you want to use
+ * org.json.simple.JSONArray.
+ */
+ List creatArrayContainer();
}
import java.io.IOException;
/**
- * A simplified and stoppable SAX-like content handler for stream processing of JSON text.
+ * A simplified and stoppable SAX-like content handler for stream processing of
+ * JSON text.
*
* @see org.xml.sax.ContentHandler
- * @see org.json.simple.parser.JSONParser#parse(java.io.Reader, ContentHandler, boolean)
+ * @see org.json.simple.parser.JSONParser#parse(java.io.Reader, ContentHandler,
+ * boolean)
*
* @author FangYidong<fangyidong@yahoo.com.cn>
*/
-public interface ContentHandler {
- /**
- * Receive notification of the beginning of JSON processing.
- * The parser will invoke this method only once.
- *
- * @throws ParseException
- * - JSONParser will stop and throw the same exception to the caller when receiving this exception.
- */
- void startJSON() throws ParseException, IOException;
-
- /**
- * Receive notification of the end of JSON processing.
- *
- * @throws ParseException
- */
- void endJSON() throws ParseException, IOException;
-
- /**
- * Receive notification of the beginning of a JSON object.
- *
- * @return false if the handler wants to stop parsing after return.
- * @throws ParseException
- * - JSONParser will stop and throw the same exception to the caller when receiving this exception.
- * @see #endJSON
- */
- boolean startObject() throws ParseException, IOException;
-
- /**
- * Receive notification of the end of a JSON object.
- *
- * @return false if the handler wants to stop parsing after return.
- * @throws ParseException
- *
- * @see #startObject
- */
- boolean endObject() throws ParseException, IOException;
-
- /**
- * Receive notification of the beginning of a JSON object entry.
- *
- * @param key - Key of a JSON object entry.
- *
- * @return false if the handler wants to stop parsing after return.
- * @throws ParseException
- *
- * @see #endObjectEntry
- */
- boolean startObjectEntry(String key) throws ParseException, IOException;
-
- /**
- * Receive notification of the end of the value of previous object entry.
- *
- * @return false if the handler wants to stop parsing after return.
- * @throws ParseException
- *
- * @see #startObjectEntry
- */
- boolean endObjectEntry() throws ParseException, IOException;
-
- /**
- * Receive notification of the beginning of a JSON array.
- *
- * @return false if the handler wants to stop parsing after return.
- * @throws ParseException
- *
- * @see #endArray
- */
- boolean startArray() throws ParseException, IOException;
-
- /**
- * Receive notification of the end of a JSON array.
- *
- * @return false if the handler wants to stop parsing after return.
- * @throws ParseException
- *
- * @see #startArray
- */
- boolean endArray() throws ParseException, IOException;
-
- /**
- * Receive notification of the JSON primitive values:
- * java.lang.String,
- * java.lang.Number,
- * java.lang.Boolean
- * null
- *
- * @param value - Instance of the following:
- * java.lang.String,
- * java.lang.Number,
- * java.lang.Boolean
- * null
- *
- * @return false if the handler wants to stop parsing after return.
- * @throws ParseException
- */
- boolean primitive(Object value) throws ParseException, IOException;
-
+public interface ContentHandler
+{
+ /**
+ * Receive notification of the beginning of JSON processing. The parser will
+ * invoke this method only once.
+ *
+ * @throws ParseException
+ * - JSONParser will stop and throw the same exception to the caller
+ * when receiving this exception.
+ */
+ void startJSON() throws ParseException, IOException;
+
+ /**
+ * Receive notification of the end of JSON processing.
+ *
+ * @throws ParseException
+ */
+ void endJSON() throws ParseException, IOException;
+
+ /**
+ * Receive notification of the beginning of a JSON object.
+ *
+ * @return false if the handler wants to stop parsing after return.
+ * @throws ParseException
+ * - JSONParser will stop and throw the same exception to the caller
+ * when receiving this exception.
+ * @see #endJSON
+ */
+ boolean startObject() throws ParseException, IOException;
+
+ /**
+ * Receive notification of the end of a JSON object.
+ *
+ * @return false if the handler wants to stop parsing after return.
+ * @throws ParseException
+ *
+ * @see #startObject
+ */
+ boolean endObject() throws ParseException, IOException;
+
+ /**
+ * Receive notification of the beginning of a JSON object entry.
+ *
+ * @param key
+ * - Key of a JSON object entry.
+ *
+ * @return false if the handler wants to stop parsing after return.
+ * @throws ParseException
+ *
+ * @see #endObjectEntry
+ */
+ boolean startObjectEntry(String key) throws ParseException, IOException;
+
+ /**
+ * Receive notification of the end of the value of previous object entry.
+ *
+ * @return false if the handler wants to stop parsing after return.
+ * @throws ParseException
+ *
+ * @see #startObjectEntry
+ */
+ boolean endObjectEntry() throws ParseException, IOException;
+
+ /**
+ * Receive notification of the beginning of a JSON array.
+ *
+ * @return false if the handler wants to stop parsing after return.
+ * @throws ParseException
+ *
+ * @see #endArray
+ */
+ boolean startArray() throws ParseException, IOException;
+
+ /**
+ * Receive notification of the end of a JSON array.
+ *
+ * @return false if the handler wants to stop parsing after return.
+ * @throws ParseException
+ *
+ * @see #startArray
+ */
+ boolean endArray() throws ParseException, IOException;
+
+ /**
+ * Receive notification of the JSON primitive values: java.lang.String,
+ * java.lang.Number, java.lang.Boolean null
+ *
+ * @param value
+ * - Instance of the following: java.lang.String, java.lang.Number,
+ * java.lang.Boolean null
+ *
+ * @return false if the handler wants to stop parsing after return.
+ * @throws ParseException
+ */
+ boolean primitive(Object value) throws ParseException, IOException;
+
}
* @author FangYidong<fangyidong@yahoo.com.cn>
*
*/
-public class ParseException extends Exception {
- private static final long serialVersionUID = -7880698968187728547L;
-
- public static final int ERROR_UNEXPECTED_CHAR = 0;
- public static final int ERROR_UNEXPECTED_TOKEN = 1;
- public static final int ERROR_UNEXPECTED_EXCEPTION = 2;
-
- private int errorType;
- private Object unexpectedObject;
- private int position;
-
- public ParseException(int errorType){
- this(-1, errorType, null);
- }
-
- public ParseException(int errorType, Object unexpectedObject){
- this(-1, errorType, unexpectedObject);
- }
-
- public ParseException(int position, int errorType, Object unexpectedObject){
- this.position = position;
- this.errorType = errorType;
- this.unexpectedObject = unexpectedObject;
- }
-
- public int getErrorType() {
- return errorType;
- }
-
- public void setErrorType(int errorType) {
- this.errorType = errorType;
- }
-
- /**
- * @see org.json.simple.parser.JSONParser#getPosition()
- *
- * @return The character position (starting with 0) of the input where the error occurs.
- */
- public int getPosition() {
- return position;
- }
-
- public void setPosition(int position) {
- this.position = position;
- }
-
- /**
- * @see org.json.simple.parser.Yytoken
- *
- * @return One of the following base on the value of errorType:
- * ERROR_UNEXPECTED_CHAR java.lang.Character
- * ERROR_UNEXPECTED_TOKEN org.json.simple.parser.Yytoken
- * ERROR_UNEXPECTED_EXCEPTION java.lang.Exception
- */
- public Object getUnexpectedObject() {
- return unexpectedObject;
- }
-
- public void setUnexpectedObject(Object unexpectedObject) {
- this.unexpectedObject = unexpectedObject;
- }
-
- public String getMessage() {
- StringBuffer sb = new StringBuffer();
-
- switch(errorType){
- case ERROR_UNEXPECTED_CHAR:
- sb.append("Unexpected character (").append(unexpectedObject).append(") at position ").append(position).append(".");
- break;
- case ERROR_UNEXPECTED_TOKEN:
- sb.append("Unexpected token ").append(unexpectedObject).append(" at position ").append(position).append(".");
- break;
- case ERROR_UNEXPECTED_EXCEPTION:
- sb.append("Unexpected exception at position ").append(position).append(": ").append(unexpectedObject);
- break;
- default:
- sb.append("Unkown error at position ").append(position).append(".");
- break;
- }
- return sb.toString();
- }
+public class ParseException extends Exception
+{
+ private static final long serialVersionUID = -7880698968187728547L;
+
+ public static final int ERROR_UNEXPECTED_CHAR = 0;
+
+ public static final int ERROR_UNEXPECTED_TOKEN = 1;
+
+ public static final int ERROR_UNEXPECTED_EXCEPTION = 2;
+
+ private int errorType;
+
+ private Object unexpectedObject;
+
+ private int position;
+
+ public ParseException(int errorType)
+ {
+ this(-1, errorType, null);
+ }
+
+ public ParseException(int errorType, Object unexpectedObject)
+ {
+ this(-1, errorType, unexpectedObject);
+ }
+
+ public ParseException(int position, int errorType,
+ Object unexpectedObject)
+ {
+ this.position = position;
+ this.errorType = errorType;
+ this.unexpectedObject = unexpectedObject;
+ }
+
+ public int getErrorType()
+ {
+ return errorType;
+ }
+
+ public void setErrorType(int errorType)
+ {
+ this.errorType = errorType;
+ }
+
+ /**
+ * @see org.json.simple.parser.JSONParser#getPosition()
+ *
+ * @return The character position (starting with 0) of the input where the
+ * error occurs.
+ */
+ public int getPosition()
+ {
+ return position;
+ }
+
+ public void setPosition(int position)
+ {
+ this.position = position;
+ }
+
+ /**
+ * @see org.json.simple.parser.Yytoken
+ *
+ * @return One of the following base on the value of errorType:
+ * ERROR_UNEXPECTED_CHAR java.lang.Character ERROR_UNEXPECTED_TOKEN
+ * org.json.simple.parser.Yytoken ERROR_UNEXPECTED_EXCEPTION
+ * java.lang.Exception
+ */
+ public Object getUnexpectedObject()
+ {
+ return unexpectedObject;
+ }
+
+ public void setUnexpectedObject(Object unexpectedObject)
+ {
+ this.unexpectedObject = unexpectedObject;
+ }
+
+ public String getMessage()
+ {
+ StringBuffer sb = new StringBuffer();
+
+ switch (errorType)
+ {
+ case ERROR_UNEXPECTED_CHAR:
+ sb.append("Unexpected character (").append(unexpectedObject)
+ .append(") at position ").append(position).append(".");
+ break;
+ case ERROR_UNEXPECTED_TOKEN:
+ sb.append("Unexpected token ").append(unexpectedObject)
+ .append(" at position ").append(position).append(".");
+ break;
+ case ERROR_UNEXPECTED_EXCEPTION:
+ sb.append("Unexpected exception at position ").append(position)
+ .append(": ").append(unexpectedObject);
+ break;
+ default:
+ sb.append("Unkown error at position ").append(position).append(".");
+ break;
+ }
+ return sb.toString();
+ }
}
package org.json.simple.parser;
-class Yylex {
+class Yylex
+{
/** This character denotes the end of file */
public static final int YYEOF = -1;
/** lexical states */
public static final int YYINITIAL = 0;
+
public static final int STRING_BEGIN = 2;
/**
* ZZ_LEXSTATE[l] is the state in the DFA for the lexical state l
- * ZZ_LEXSTATE[l+1] is the state in the DFA for the lexical state l
- * at the beginning of a line
- * l is of the form l = 2*k, k a non negative integer
+ * ZZ_LEXSTATE[l+1] is the state in the DFA for the lexical state l at the
+ * beginning of a line l is of the form l = 2*k, k a non negative integer
*/
- private static final int ZZ_LEXSTATE[] = {
- 0, 0, 1, 1
- };
+ private static final int ZZ_LEXSTATE[] = { 0, 0, 1, 1 };
- /**
+ /**
* Translates characters to character classes
*/
- private static final String ZZ_CMAP_PACKED =
- "\11\0\1\7\1\7\2\0\1\7\22\0\1\7\1\0\1\11\10\0"+
- "\1\6\1\31\1\2\1\4\1\12\12\3\1\32\6\0\4\1\1\5"+
- "\1\1\24\0\1\27\1\10\1\30\3\0\1\22\1\13\2\1\1\21"+
- "\1\14\5\0\1\23\1\0\1\15\3\0\1\16\1\24\1\17\1\20"+
- "\5\0\1\25\1\0\1\26\uff82\0";
-
- /**
+ private static final String ZZ_CMAP_PACKED = "\11\0\1\7\1\7\2\0\1\7\22\0\1\7\1\0\1\11\10\0"
+ + "\1\6\1\31\1\2\1\4\1\12\12\3\1\32\6\0\4\1\1\5"
+ + "\1\1\24\0\1\27\1\10\1\30\3\0\1\22\1\13\2\1\1\21"
+ + "\1\14\5\0\1\23\1\0\1\15\3\0\1\16\1\24\1\17\1\20"
+ + "\5\0\1\25\1\0\1\26\uff82\0";
+
+ /**
* Translates characters to character classes
*/
- private static final char [] ZZ_CMAP = zzUnpackCMap(ZZ_CMAP_PACKED);
+ private static final char[] ZZ_CMAP = zzUnpackCMap(ZZ_CMAP_PACKED);
- /**
+ /**
* Translates DFA states to action switch labels.
*/
- private static final int [] ZZ_ACTION = zzUnpackAction();
+ private static final int[] ZZ_ACTION = zzUnpackAction();
- private static final String ZZ_ACTION_PACKED_0 =
- "\2\0\2\1\1\2\1\3\1\4\3\1\1\5\1\6"+
- "\1\7\1\10\1\11\1\12\1\13\1\14\1\15\5\0"+
- "\1\14\1\16\1\17\1\20\1\21\1\22\1\23\1\24"+
- "\1\0\1\25\1\0\1\25\4\0\1\26\1\27\2\0"+
- "\1\30";
+ private static final String ZZ_ACTION_PACKED_0 = "\2\0\2\1\1\2\1\3\1\4\3\1\1\5\1\6"
+ + "\1\7\1\10\1\11\1\12\1\13\1\14\1\15\5\0"
+ + "\1\14\1\16\1\17\1\20\1\21\1\22\1\23\1\24"
+ + "\1\0\1\25\1\0\1\25\4\0\1\26\1\27\2\0" + "\1\30";
- private static int [] zzUnpackAction() {
- int [] result = new int[45];
+ private static int[] zzUnpackAction()
+ {
+ int[] result = new int[45];
int offset = 0;
offset = zzUnpackAction(ZZ_ACTION_PACKED_0, offset, result);
return result;
}
- private static int zzUnpackAction(String packed, int offset, int [] result) {
- int i = 0; /* index in packed string */
- int j = offset; /* index in unpacked array */
+ private static int zzUnpackAction(String packed, int offset, int[] result)
+ {
+ int i = 0; /* index in packed string */
+ int j = offset; /* index in unpacked array */
int l = packed.length();
- while (i < l) {
+ while (i < l)
+ {
int count = packed.charAt(i++);
int value = packed.charAt(i++);
- do result[j++] = value; while (--count > 0);
+ do
+ result[j++] = value;
+ while (--count > 0);
}
return j;
}
-
- /**
+ /**
* Translates a state to a row index in the transition table
*/
- private static final int [] ZZ_ROWMAP = zzUnpackRowMap();
-
- private static final String ZZ_ROWMAP_PACKED_0 =
- "\0\0\0\33\0\66\0\121\0\154\0\207\0\66\0\242"+
- "\0\275\0\330\0\66\0\66\0\66\0\66\0\66\0\66"+
- "\0\363\0\u010e\0\66\0\u0129\0\u0144\0\u015f\0\u017a\0\u0195"+
- "\0\66\0\66\0\66\0\66\0\66\0\66\0\66\0\66"+
- "\0\u01b0\0\u01cb\0\u01e6\0\u01e6\0\u0201\0\u021c\0\u0237\0\u0252"+
- "\0\66\0\66\0\u026d\0\u0288\0\66";
-
- private static int [] zzUnpackRowMap() {
- int [] result = new int[45];
+ private static final int[] ZZ_ROWMAP = zzUnpackRowMap();
+
+ private static final String ZZ_ROWMAP_PACKED_0 = "\0\0\0\33\0\66\0\121\0\154\0\207\0\66\0\242"
+ + "\0\275\0\330\0\66\0\66\0\66\0\66\0\66\0\66"
+ + "\0\363\0\u010e\0\66\0\u0129\0\u0144\0\u015f\0\u017a\0\u0195"
+ + "\0\66\0\66\0\66\0\66\0\66\0\66\0\66\0\66"
+ + "\0\u01b0\0\u01cb\0\u01e6\0\u01e6\0\u0201\0\u021c\0\u0237\0\u0252"
+ + "\0\66\0\66\0\u026d\0\u0288\0\66";
+
+ private static int[] zzUnpackRowMap()
+ {
+ int[] result = new int[45];
int offset = 0;
offset = zzUnpackRowMap(ZZ_ROWMAP_PACKED_0, offset, result);
return result;
}
- private static int zzUnpackRowMap(String packed, int offset, int [] result) {
- int i = 0; /* index in packed string */
- int j = offset; /* index in unpacked array */
+ private static int zzUnpackRowMap(String packed, int offset, int[] result)
+ {
+ int i = 0; /* index in packed string */
+ int j = offset; /* index in unpacked array */
int l = packed.length();
- while (i < l) {
+ while (i < l)
+ {
int high = packed.codePointAt(i++) << 16;
result[j++] = high | packed.codePointAt(i++);
}
return j;
}
- /**
+ /**
* The transition table of the DFA
*/
- private static final int ZZ_TRANS [] = {
- 2, 2, 3, 4, 2, 2, 2, 5, 2, 6,
- 2, 2, 7, 8, 2, 9, 2, 2, 2, 2,
- 2, 10, 11, 12, 13, 14, 15, 16, 16, 16,
- 16, 16, 16, 16, 16, 17, 18, 16, 16, 16,
- 16, 16, 16, 16, 16, 16, 16, 16, 16, 16,
- 16, 16, 16, 16, -1, -1, -1, -1, -1, -1,
- -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
- -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
- -1, -1, -1, -1, 4, -1, -1, -1, -1, -1,
- -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
- -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
- -1, 4, 19, 20, -1, -1, -1, -1, -1, -1,
- -1, -1, -1, -1, -1, 20, -1, -1, -1, -1,
- -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
- -1, -1, 5, -1, -1, -1, -1, -1, -1, -1,
- -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
- -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
- -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
- 21, -1, -1, -1, -1, -1, -1, -1, -1, -1,
- -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
- -1, -1, -1, -1, -1, 22, -1, -1, -1, -1,
- -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
- -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
- 23, -1, -1, -1, -1, -1, -1, -1, -1, -1,
- -1, -1, -1, 16, 16, 16, 16, 16, 16, 16,
- 16, -1, -1, 16, 16, 16, 16, 16, 16, 16,
- 16, 16, 16, 16, 16, 16, 16, 16, 16, 16,
- -1, -1, -1, -1, -1, -1, -1, -1, 24, 25,
- 26, 27, 28, 29, 30, 31, 32, -1, -1, -1,
- -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
- 33, -1, -1, -1, -1, -1, -1, -1, -1, -1,
- -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
- -1, -1, -1, -1, -1, -1, 34, 35, -1, -1,
- 34, -1, -1, -1, -1, -1, -1, -1, -1, -1,
- -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
- -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
- -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
- 36, -1, -1, -1, -1, -1, -1, -1, -1, -1,
- -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
- -1, -1, -1, -1, -1, -1, -1, 37, -1, -1,
- -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
- -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
- -1, 38, -1, -1, -1, -1, -1, -1, -1, -1,
- -1, -1, -1, 39, -1, 39, -1, 39, -1, -1,
- -1, -1, -1, 39, 39, -1, -1, -1, -1, 39,
- 39, -1, -1, -1, -1, -1, -1, -1, -1, -1,
- -1, -1, 33, -1, 20, -1, -1, -1, -1, -1,
- -1, -1, -1, -1, -1, -1, 20, -1, -1, -1,
- -1, -1, -1, -1, -1, -1, -1, -1, -1, 35,
- -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
- -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
- -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
- -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
- -1, -1, -1, 38, -1, -1, -1, -1, -1, -1,
- -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
- -1, -1, -1, -1, -1, -1, -1, -1, -1, 40,
- -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
- -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
- -1, -1, -1, -1, 41, -1, -1, -1, -1, -1,
- -1, -1, -1, -1, -1, 42, -1, 42, -1, 42,
- -1, -1, -1, -1, -1, 42, 42, -1, -1, -1,
- -1, 42, 42, -1, -1, -1, -1, -1, -1, -1,
- -1, -1, 43, -1, 43, -1, 43, -1, -1, -1,
- -1, -1, 43, 43, -1, -1, -1, -1, 43, 43,
- -1, -1, -1, -1, -1, -1, -1, -1, -1, 44,
- -1, 44, -1, 44, -1, -1, -1, -1, -1, 44,
- 44, -1, -1, -1, -1, 44, 44, -1, -1, -1,
- -1, -1, -1, -1, -1,
- };
+ private static final int ZZ_TRANS[] = { 2, 2, 3, 4, 2, 2, 2, 5, 2, 6, 2,
+ 2, 7, 8, 2, 9, 2, 2, 2, 2, 2, 10, 11, 12, 13, 14, 15, 16, 16, 16, 16,
+ 16, 16, 16, 16, 17, 18, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16,
+ 16, 16, 16, 16, 16, 16, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+ -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+ -1, -1, 4, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+ -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 4, 19, 20, -1, -1, -1, -1,
+ -1, -1, -1, -1, -1, -1, -1, 20, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+ -1, -1, -1, -1, -1, -1, -1, 5, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+ -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+ -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 21, -1, -1, -1, -1, -1, -1,
+ -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+ -1, 22, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+ -1, -1, -1, -1, -1, -1, -1, -1, -1, 23, -1, -1, -1, -1, -1, -1, -1,
+ -1, -1, -1, -1, -1, 16, 16, 16, 16, 16, 16, 16, 16, -1, -1, 16, 16,
+ 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, -1, -1,
+ -1, -1, -1, -1, -1, -1, 24, 25, 26, 27, 28, 29, 30, 31, 32, -1, -1,
+ -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 33, -1, -1, -1, -1, -1,
+ -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+ -1, -1, -1, 34, 35, -1, -1, 34, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+ -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+ -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 36, -1, -1, -1,
+ -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+ -1, -1, -1, -1, -1, -1, 37, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+ -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 38, -1, -1, -1,
+ -1, -1, -1, -1, -1, -1, -1, -1, 39, -1, 39, -1, 39, -1, -1, -1, -1,
+ -1, 39, 39, -1, -1, -1, -1, 39, 39, -1, -1, -1, -1, -1, -1, -1, -1,
+ -1, -1, -1, 33, -1, 20, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+ 20, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 35, -1, -1, -1,
+ -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+ -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+ -1, -1, -1, -1, -1, -1, 38, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+ -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 40, -1,
+ -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+ -1, -1, -1, -1, -1, -1, 41, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1,
+ 42, -1, 42, -1, 42, -1, -1, -1, -1, -1, 42, 42, -1, -1, -1, -1, 42,
+ 42, -1, -1, -1, -1, -1, -1, -1, -1, -1, 43, -1, 43, -1, 43, -1, -1,
+ -1, -1, -1, 43, 43, -1, -1, -1, -1, 43, 43, -1, -1, -1, -1, -1, -1,
+ -1, -1, -1, 44, -1, 44, -1, 44, -1, -1, -1, -1, -1, 44, 44, -1, -1,
+ -1, -1, 44, 44, -1, -1, -1, -1, -1, -1, -1, -1, };
/* error codes */
private static final int ZZ_UNKNOWN_ERROR = 0;
+
private static final int ZZ_NO_MATCH = 1;
+
private static final int ZZ_PUSHBACK_2BIG = 2;
/* error messages for the codes above */
private static final String ZZ_ERROR_MSG[] = {
- "Unkown internal scanner error",
- "Error: could not match input",
- "Error: pushback value was too large"
- };
+ "Unkown internal scanner error", "Error: could not match input",
+ "Error: pushback value was too large" };
/**
* ZZ_ATTRIBUTE[aState] contains the attributes of state <code>aState</code>
*/
- private static final int [] ZZ_ATTRIBUTE = zzUnpackAttribute();
+ private static final int[] ZZ_ATTRIBUTE = zzUnpackAttribute();
- private static final String ZZ_ATTRIBUTE_PACKED_0 =
- "\2\0\1\11\3\1\1\11\3\1\6\11\2\1\1\11"+
- "\5\0\10\11\1\0\1\1\1\0\1\1\4\0\2\11"+
- "\2\0\1\11";
+ private static final String ZZ_ATTRIBUTE_PACKED_0 = "\2\0\1\11\3\1\1\11\3\1\6\11\2\1\1\11"
+ + "\5\0\10\11\1\0\1\1\1\0\1\1\4\0\2\11" + "\2\0\1\11";
- private static int [] zzUnpackAttribute() {
- int [] result = new int[45];
+ private static int[] zzUnpackAttribute()
+ {
+ int[] result = new int[45];
int offset = 0;
offset = zzUnpackAttribute(ZZ_ATTRIBUTE_PACKED_0, offset, result);
return result;
}
- private static int zzUnpackAttribute(String packed, int offset, int [] result) {
- int i = 0; /* index in packed string */
- int j = offset; /* index in unpacked array */
+ private static int zzUnpackAttribute(String packed, int offset,
+ int[] result)
+ {
+ int i = 0; /* index in packed string */
+ int j = offset; /* index in unpacked array */
int l = packed.length();
- while (i < l) {
+ while (i < l)
+ {
int count = packed.charAt(i++);
int value = packed.charAt(i++);
- do result[j++] = value; while (--count > 0);
+ do
+ result[j++] = value;
+ while (--count > 0);
}
return j;
}
/** the current lexical state */
private int zzLexicalState = YYINITIAL;
- /** this buffer contains the current text to be matched and is
- the source of the yytext() string */
+ /**
+ * this buffer contains the current text to be matched and is the source of
+ * the yytext() string
+ */
private char zzBuffer[] = new char[ZZ_BUFFERSIZE];
/** the textposition at the last accepting state */
/** startRead marks the beginning of the yytext() string in the buffer */
private int zzStartRead;
- /** endRead marks the last character in the buffer, that has been read
- from input */
+ /**
+ * endRead marks the last character in the buffer, that has been read from
+ * input
+ */
private int zzEndRead;
/** number of newlines encountered up to the start of the matched text */
private int yychar;
/**
- * the number of characters from the last newline up to the start of the
+ * the number of characters from the last newline up to the start of the
* matched text
*/
private int yycolumn;
- /**
+ /**
* zzAtBOL == true <=> the scanner is currently at the beginning of a line
*/
private boolean zzAtBOL = true;
private boolean zzAtEOF;
/* user code: */
-private StringBuffer sb=new StringBuffer();
-
-int getPosition(){
- return yychar;
-}
-
+ private StringBuffer sb = new StringBuffer();
+ int getPosition()
+ {
+ return yychar;
+ }
/**
- * Creates a new scanner
- * There is also a java.io.InputStream version of this constructor.
+ * Creates a new scanner There is also a java.io.InputStream version of this
+ * constructor.
*
- * @param in the java.io.Reader to read input from.
+ * @param in
+ * the java.io.Reader to read input from.
*/
- Yylex(java.io.Reader in) {
+ Yylex(java.io.Reader in)
+ {
this.zzReader = in;
}
/**
- * Creates a new scanner.
- * There is also java.io.Reader version of this constructor.
+ * Creates a new scanner. There is also java.io.Reader version of this
+ * constructor.
*
- * @param in the java.io.Inputstream to read input from.
+ * @param in
+ * the java.io.Inputstream to read input from.
*/
- Yylex(java.io.InputStream in) {
+ Yylex(java.io.InputStream in)
+ {
this(new java.io.InputStreamReader(in));
}
- /**
+ /**
* Unpacks the compressed character translation table.
*
- * @param packed the packed character translation table
- * @return the unpacked character translation table
+ * @param packed
+ * the packed character translation table
+ * @return the unpacked character translation table
*/
- private static char [] zzUnpackCMap(String packed) {
- char [] map = new char[0x10000];
- int i = 0; /* index in packed string */
- int j = 0; /* index in unpacked array */
- while (i < 90) {
- int count = packed.charAt(i++);
+ private static char[] zzUnpackCMap(String packed)
+ {
+ char[] map = new char[0x10000];
+ int i = 0; /* index in packed string */
+ int j = 0; /* index in unpacked array */
+ while (i < 90)
+ {
+ int count = packed.charAt(i++);
char value = packed.charAt(i++);
- do map[j++] = value; while (--count > 0);
+ do
+ map[j++] = value;
+ while (--count > 0);
}
return map;
}
-
/**
* Refills the input buffer.
*
- * @return <code>false</code>, iff there was new input.
+ * @return <code>false</code>, iff there was new input.
*
- * @exception java.io.IOException if any I/O-Error occurs
+ * @exception java.io.IOException
+ * if any I/O-Error occurs
*/
- private boolean zzRefill() throws java.io.IOException {
+ private boolean zzRefill() throws java.io.IOException
+ {
/* first: make room (if you can) */
- if (zzStartRead > 0) {
- System.arraycopy(zzBuffer, zzStartRead,
- zzBuffer, 0,
- zzEndRead-zzStartRead);
+ if (zzStartRead > 0)
+ {
+ System.arraycopy(zzBuffer, zzStartRead, zzBuffer, 0,
+ zzEndRead - zzStartRead);
/* translate stored positions */
- zzEndRead-= zzStartRead;
- zzCurrentPos-= zzStartRead;
- zzMarkedPos-= zzStartRead;
+ zzEndRead -= zzStartRead;
+ zzCurrentPos -= zzStartRead;
+ zzMarkedPos -= zzStartRead;
zzStartRead = 0;
}
/* is the buffer big enough? */
- if (zzCurrentPos >= zzBuffer.length) {
+ if (zzCurrentPos >= zzBuffer.length)
+ {
/* if not: blow it up */
- char newBuffer[] = new char[zzCurrentPos*2];
+ char newBuffer[] = new char[zzCurrentPos * 2];
System.arraycopy(zzBuffer, 0, newBuffer, 0, zzBuffer.length);
zzBuffer = newBuffer;
}
/* finally: fill the buffer with new input */
int numRead = zzReader.read(zzBuffer, zzEndRead,
- zzBuffer.length-zzEndRead);
+ zzBuffer.length - zzEndRead);
- if (numRead > 0) {
- zzEndRead+= numRead;
+ if (numRead > 0)
+ {
+ zzEndRead += numRead;
return false;
}
- // unlikely but not impossible: read 0 characters, but not at end of stream
- if (numRead == 0) {
+ // unlikely but not impossible: read 0 characters, but not at end of stream
+ if (numRead == 0)
+ {
int c = zzReader.read();
- if (c == -1) {
+ if (c == -1)
+ {
return true;
- } else {
+ }
+ else
+ {
zzBuffer[zzEndRead++] = (char) c;
return false;
- }
+ }
}
- // numRead < 0
+ // numRead < 0
return true;
}
-
/**
* Closes the input stream.
*/
- public final void yyclose() throws java.io.IOException {
- zzAtEOF = true; /* indicate end of file */
- zzEndRead = zzStartRead; /* invalidate buffer */
+ public final void yyclose() throws java.io.IOException
+ {
+ zzAtEOF = true; /* indicate end of file */
+ zzEndRead = zzStartRead; /* invalidate buffer */
if (zzReader != null)
zzReader.close();
}
-
/**
- * Resets the scanner to read from a new input stream.
- * Does not close the old reader.
+ * Resets the scanner to read from a new input stream. Does not close the old
+ * reader.
*
- * All internal variables are reset, the old input stream
- * <b>cannot</b> be reused (internal buffer is discarded and lost).
- * Lexical state is set to <tt>ZZ_INITIAL</tt>.
+ * All internal variables are reset, the old input stream <b>cannot</b> be
+ * reused (internal buffer is discarded and lost). Lexical state is set to
+ * <tt>ZZ_INITIAL</tt>.
*
- * @param reader the new input stream
+ * @param reader
+ * the new input stream
*/
- public final void yyreset(java.io.Reader reader) {
+ public final void yyreset(java.io.Reader reader)
+ {
zzReader = reader;
- zzAtBOL = true;
- zzAtEOF = false;
+ zzAtBOL = true;
+ zzAtEOF = false;
zzEndRead = zzStartRead = 0;
zzCurrentPos = zzMarkedPos = 0;
yyline = yychar = yycolumn = 0;
zzLexicalState = YYINITIAL;
}
-
/**
* Returns the current lexical state.
*/
- public final int yystate() {
+ public final int yystate()
+ {
return zzLexicalState;
}
-
/**
* Enters a new lexical state
*
- * @param newState the new lexical state
+ * @param newState
+ * the new lexical state
*/
- public final void yybegin(int newState) {
+ public final void yybegin(int newState)
+ {
zzLexicalState = newState;
}
-
/**
* Returns the text matched by the current regular expression.
*/
- public final String yytext() {
- return new String( zzBuffer, zzStartRead, zzMarkedPos-zzStartRead );
+ public final String yytext()
+ {
+ return new String(zzBuffer, zzStartRead, zzMarkedPos - zzStartRead);
}
-
/**
- * Returns the character at position <tt>pos</tt> from the
- * matched text.
+ * Returns the character at position <tt>pos</tt> from the matched text.
*
* It is equivalent to yytext().charAt(pos), but faster
*
- * @param pos the position of the character to fetch.
- * A value from 0 to yylength()-1.
+ * @param pos
+ * the position of the character to fetch. A value from 0 to
+ * yylength()-1.
*
* @return the character at position pos
*/
- public final char yycharat(int pos) {
- return zzBuffer[zzStartRead+pos];
+ public final char yycharat(int pos)
+ {
+ return zzBuffer[zzStartRead + pos];
}
-
/**
* Returns the length of the matched text region.
*/
- public final int yylength() {
- return zzMarkedPos-zzStartRead;
+ public final int yylength()
+ {
+ return zzMarkedPos - zzStartRead;
}
-
/**
* Reports an error that occured while scanning.
*
- * In a wellformed scanner (no or only correct usage of
- * yypushback(int) and a match-all fallback rule) this method
- * will only be called with things that "Can't Possibly Happen".
- * If this method is called, something is seriously wrong
- * (e.g. a JFlex bug producing a faulty scanner etc.).
+ * In a wellformed scanner (no or only correct usage of yypushback(int) and a
+ * match-all fallback rule) this method will only be called with things that
+ * "Can't Possibly Happen". If this method is called, something is seriously
+ * wrong (e.g. a JFlex bug producing a faulty scanner etc.).
*
- * Usual syntax/scanner level error handling should be done
- * in error fallback rules.
+ * Usual syntax/scanner level error handling should be done in error fallback
+ * rules.
*
- * @param errorCode the code of the errormessage to display
+ * @param errorCode
+ * the code of the errormessage to display
*/
- private void zzScanError(int errorCode) {
+ private void zzScanError(int errorCode)
+ {
String message;
- try {
+ try
+ {
message = ZZ_ERROR_MSG[errorCode];
- }
- catch (ArrayIndexOutOfBoundsException e) {
+ } catch (ArrayIndexOutOfBoundsException e)
+ {
message = ZZ_ERROR_MSG[ZZ_UNKNOWN_ERROR];
}
throw new Error(message);
- }
-
+ }
/**
* Pushes the specified amount of characters back into the input stream.
*
* They will be read again by then next call of the scanning method
*
- * @param number the number of characters to be read again.
- * This number must not be greater than yylength()!
+ * @param number
+ * the number of characters to be read again. This number must not be
+ * greater than yylength()!
*/
- public void yypushback(int number) {
- if ( number > yylength() )
+ public void yypushback(int number)
+ {
+ if (number > yylength())
zzScanError(ZZ_PUSHBACK_2BIG);
zzMarkedPos -= number;
}
-
/**
* Resumes scanning until the next regular expression is matched, the end of
* input is encountered or an I/O-Error occurs.
}
}
-
}
/**
* @author FangYidong<fangyidong@yahoo.com.cn>
*/
-public class Yytoken {
- public static final int TYPE_VALUE=0;//JSON primitive value: string,number,boolean,null
- public static final int TYPE_LEFT_BRACE=1;
- public static final int TYPE_RIGHT_BRACE=2;
- public static final int TYPE_LEFT_SQUARE=3;
- public static final int TYPE_RIGHT_SQUARE=4;
- public static final int TYPE_COMMA=5;
- public static final int TYPE_COLON=6;
- public static final int TYPE_EOF=-1;//end of file
-
- public int type=0;
- public Object value=null;
-
- public Yytoken(int type,Object value){
- this.type=type;
- this.value=value;
- }
-
- public String toString(){
- StringBuffer sb = new StringBuffer();
- switch(type){
- case TYPE_VALUE:
- sb.append("VALUE(").append(value).append(")");
- break;
- case TYPE_LEFT_BRACE:
- sb.append("LEFT BRACE({)");
- break;
- case TYPE_RIGHT_BRACE:
- sb.append("RIGHT BRACE(})");
- break;
- case TYPE_LEFT_SQUARE:
- sb.append("LEFT SQUARE([)");
- break;
- case TYPE_RIGHT_SQUARE:
- sb.append("RIGHT SQUARE(])");
- break;
- case TYPE_COMMA:
- sb.append("COMMA(,)");
- break;
- case TYPE_COLON:
- sb.append("COLON(:)");
- break;
- case TYPE_EOF:
- sb.append("END OF FILE");
- break;
- }
- return sb.toString();
- }
+public class Yytoken
+{
+ public static final int TYPE_VALUE = 0;// JSON primitive value:
+ // string,number,boolean,null
+
+ public static final int TYPE_LEFT_BRACE = 1;
+
+ public static final int TYPE_RIGHT_BRACE = 2;
+
+ public static final int TYPE_LEFT_SQUARE = 3;
+
+ public static final int TYPE_RIGHT_SQUARE = 4;
+
+ public static final int TYPE_COMMA = 5;
+
+ public static final int TYPE_COLON = 6;
+
+ public static final int TYPE_EOF = -1;// end of file
+
+ public int type = 0;
+
+ public Object value = null;
+
+ public Yytoken(int type, Object value)
+ {
+ this.type = type;
+ this.value = value;
+ }
+
+ public String toString()
+ {
+ StringBuffer sb = new StringBuffer();
+ switch (type)
+ {
+ case TYPE_VALUE:
+ sb.append("VALUE(").append(value).append(")");
+ break;
+ case TYPE_LEFT_BRACE:
+ sb.append("LEFT BRACE({)");
+ break;
+ case TYPE_RIGHT_BRACE:
+ sb.append("RIGHT BRACE(})");
+ break;
+ case TYPE_LEFT_SQUARE:
+ sb.append("LEFT SQUARE([)");
+ break;
+ case TYPE_RIGHT_SQUARE:
+ sb.append("RIGHT SQUARE(])");
+ break;
+ case TYPE_COMMA:
+ sb.append("COMMA(,)");
+ break;
+ case TYPE_COLON:
+ sb.append("COLON(:)");
+ break;
+ case TYPE_EOF:
+ sb.append("END OF FILE");
+ break;
+ }
+ return sb.toString();
+ }
}
import java.util.Locale;
/**
- * Represents a Windows shortcut (typically visible to Java only as a '.lnk' file).
+ * Represents a Windows shortcut (typically visible to Java only as a '.lnk'
+ * file).
*
- * Retrieved 2011-09-23 from http://stackoverflow.com/questions/309495/windows-shortcut-lnk-parser-in-java/672775#672775
+ * Retrieved 2011-09-23 from
+ * http://stackoverflow.com/questions/309495/windows-shortcut-lnk-parser-in-java/672775#672775
* Originally called LnkParser
*
- * Written by: (the stack overflow users, obviously!)
- * Apache Commons VFS dependency removed by crysxd (why were we using that!?) https://github.com/crysxd
- * Headerified, refactored and commented by Code Bling http://stackoverflow.com/users/675721/code-bling
- * Network file support added by Stefan Cordes http://stackoverflow.com/users/81330/stefan-cordes
- * Adapted by Sam Brightman http://stackoverflow.com/users/2492/sam-brightman
- * Based on information in 'The Windows Shortcut File Format' by Jesse Hager <jessehager@iname.com>
- * And somewhat based on code from the book 'Swing Hacks: Tips and Tools for Killer GUIs'
- * by Joshua Marinacci and Chris Adamson
- * ISBN: 0-596-00907-0
- * http://www.oreilly.com/catalog/swinghks/
+ * Written by: (the stack overflow users, obviously!) Apache Commons VFS
+ * dependency removed by crysxd (why were we using that!?)
+ * https://github.com/crysxd Headerified, refactored and commented by Code Bling
+ * http://stackoverflow.com/users/675721/code-bling Network file support added
+ * by Stefan Cordes http://stackoverflow.com/users/81330/stefan-cordes Adapted
+ * by Sam Brightman http://stackoverflow.com/users/2492/sam-brightman Based on
+ * information in 'The Windows Shortcut File Format' by Jesse Hager
+ * <jessehager@iname.com> And somewhat based on code from the book 'Swing
+ * Hacks: Tips and Tools for Killer GUIs' by Joshua Marinacci and Chris Adamson
+ * ISBN: 0-596-00907-0 http://www.oreilly.com/catalog/swinghks/
*/
public class WindowsShortcut
{
- private boolean isDirectory;
- private boolean isLocal;
- private String real_file;
-
- /**
- * Provides a quick test to see if this could be a valid link !
- * If you try to instantiate a new WindowShortcut and the link is not valid,
- * Exceptions may be thrown and Exceptions are extremely slow to generate,
- * therefore any code needing to loop through several files should first check this.
- *
- * @param file the potential link
- * @return true if may be a link, false otherwise
- * @throws IOException if an IOException is thrown while reading from the file
- */
- public static boolean isPotentialValidLink(File file) throws IOException {
- final int minimum_length = 0x64;
- InputStream fis = new FileInputStream(file);
- boolean isPotentiallyValid = false;
- try {
- isPotentiallyValid = file.isFile()
- && file.getName().toLowerCase(Locale.ROOT).endsWith(".lnk")
- && fis.available() >= minimum_length
- && isMagicPresent(getBytes(fis, 32));
- } finally {
- fis.close();
- }
- return isPotentiallyValid;
- }
+ private boolean isDirectory;
- public WindowsShortcut(File file) throws IOException, ParseException {
- InputStream in = new FileInputStream(file);
- try {
- parseLink(getBytes(in));
- } finally {
- in.close();
- }
- }
+ private boolean isLocal;
- /**
- * @return the name of the filesystem object pointed to by this shortcut
- */
- public String getRealFilename() {
- return real_file;
- }
+ private String real_file;
- /**
- * Tests if the shortcut points to a local resource.
- * @return true if the 'local' bit is set in this shortcut, false otherwise
- */
- public boolean isLocal() {
- return isLocal;
+ /**
+ * Provides a quick test to see if this could be a valid link ! If you try to
+ * instantiate a new WindowShortcut and the link is not valid, Exceptions may
+ * be thrown and Exceptions are extremely slow to generate, therefore any code
+ * needing to loop through several files should first check this.
+ *
+ * @param file
+ * the potential link
+ * @return true if may be a link, false otherwise
+ * @throws IOException
+ * if an IOException is thrown while reading from the file
+ */
+ public static boolean isPotentialValidLink(File file) throws IOException
+ {
+ final int minimum_length = 0x64;
+ InputStream fis = new FileInputStream(file);
+ boolean isPotentiallyValid = false;
+ try
+ {
+ isPotentiallyValid = file.isFile()
+ && file.getName().toLowerCase(Locale.ROOT).endsWith(".lnk")
+ && fis.available() >= minimum_length
+ && isMagicPresent(getBytes(fis, 32));
+ } finally
+ {
+ fis.close();
}
+ return isPotentiallyValid;
+ }
- /**
- * Tests if the shortcut points to a directory.
- * @return true if the 'directory' bit is set in this shortcut, false otherwise
- */
- public boolean isDirectory() {
- return isDirectory;
+ public WindowsShortcut(File file) throws IOException, ParseException
+ {
+ InputStream in = new FileInputStream(file);
+ try
+ {
+ parseLink(getBytes(in));
+ } finally
+ {
+ in.close();
}
+ }
- /**
- * Gets all the bytes from an InputStream
- * @param in the InputStream from which to read bytes
- * @return array of all the bytes contained in 'in'
- * @throws IOException if an IOException is encountered while reading the data from the InputStream
- */
- private static byte[] getBytes(InputStream in) throws IOException {
- return getBytes(in, null);
- }
-
- /**
- * Gets up to max bytes from an InputStream
- * @param in the InputStream from which to read bytes
- * @param max maximum number of bytes to read
- * @return array of all the bytes contained in 'in'
- * @throws IOException if an IOException is encountered while reading the data from the InputStream
- */
- private static byte[] getBytes(InputStream in, Integer max) throws IOException {
- // read the entire file into a byte buffer
- ByteArrayOutputStream bout = new ByteArrayOutputStream();
- byte[] buff = new byte[256];
- while (max == null || max > 0) {
- int n = in.read(buff);
- if (n == -1) {
- break;
- }
- bout.write(buff, 0, n);
- if (max != null)
- max -= n;
- }
- in.close();
- return bout.toByteArray();
- }
+ /**
+ * @return the name of the filesystem object pointed to by this shortcut
+ */
+ public String getRealFilename()
+ {
+ return real_file;
+ }
- private static boolean isMagicPresent(byte[] link) {
- final int magic = 0x0000004C;
- final int magic_offset = 0x00;
- return link.length >= 32 && bytesToDword(link, magic_offset) == magic;
- }
+ /**
+ * Tests if the shortcut points to a local resource.
+ *
+ * @return true if the 'local' bit is set in this shortcut, false otherwise
+ */
+ public boolean isLocal()
+ {
+ return isLocal;
+ }
- /**
- * Gobbles up link data by parsing it and storing info in member fields
- * @param link all the bytes from the .lnk file
- */
- private void parseLink(byte[] link) throws ParseException {
- try {
- if (!isMagicPresent(link))
- throw new ParseException("Invalid shortcut; magic is missing", 0);
-
- // get the flags byte
- byte flags = link[0x14];
-
- // get the file attributes byte
- final int file_atts_offset = 0x18;
- byte file_atts = link[file_atts_offset];
- byte is_dir_mask = (byte)0x10;
- if ((file_atts & is_dir_mask) > 0) {
- isDirectory = true;
- } else {
- isDirectory = false;
- }
-
- // if the shell settings are present, skip them
- final int shell_offset = 0x4c;
- final byte has_shell_mask = (byte)0x01;
- int shell_len = 0;
- if ((flags & has_shell_mask) > 0) {
- // the plus 2 accounts for the length marker itself
- shell_len = bytesToWord(link, shell_offset) + 2;
- }
-
- // get to the file settings
- int file_start = 0x4c + shell_len;
-
- final int file_location_info_flag_offset_offset = 0x08;
- int file_location_info_flag = link[file_start + file_location_info_flag_offset_offset];
- isLocal = (file_location_info_flag & 2) == 0;
- // get the local volume and local system values
- //final int localVolumeTable_offset_offset = 0x0C;
- final int basename_offset_offset = 0x10;
- final int networkVolumeTable_offset_offset = 0x14;
- final int finalname_offset_offset = 0x18;
- int finalname_offset = link[file_start + finalname_offset_offset] + file_start;
- String finalname = getNullDelimitedString(link, finalname_offset);
- if (isLocal) {
- int basename_offset = link[file_start + basename_offset_offset] + file_start;
- String basename = getNullDelimitedString(link, basename_offset);
- real_file = basename + finalname;
- } else {
- int networkVolumeTable_offset = link[file_start + networkVolumeTable_offset_offset] + file_start;
- int shareName_offset_offset = 0x08;
- int shareName_offset = link[networkVolumeTable_offset + shareName_offset_offset]
- + networkVolumeTable_offset;
- String shareName = getNullDelimitedString(link, shareName_offset);
- real_file = shareName + "\\" + finalname;
- }
- } catch (ArrayIndexOutOfBoundsException e) {
- throw new ParseException("Could not be parsed, probably not a valid WindowsShortcut", 0);
- }
- }
+ /**
+ * Tests if the shortcut points to a directory.
+ *
+ * @return true if the 'directory' bit is set in this shortcut, false
+ * otherwise
+ */
+ public boolean isDirectory()
+ {
+ return isDirectory;
+ }
+
+ /**
+ * Gets all the bytes from an InputStream
+ *
+ * @param in
+ * the InputStream from which to read bytes
+ * @return array of all the bytes contained in 'in'
+ * @throws IOException
+ * if an IOException is encountered while reading the data from the
+ * InputStream
+ */
+ private static byte[] getBytes(InputStream in) throws IOException
+ {
+ return getBytes(in, null);
+ }
- private static String getNullDelimitedString(byte[] bytes, int off) {
- int len = 0;
- // count bytes until the null character (0)
- while (true) {
- if (bytes[off + len] == 0) {
- break;
- }
- len++;
- }
- return new String(bytes, off, len);
+ /**
+ * Gets up to max bytes from an InputStream
+ *
+ * @param in
+ * the InputStream from which to read bytes
+ * @param max
+ * maximum number of bytes to read
+ * @return array of all the bytes contained in 'in'
+ * @throws IOException
+ * if an IOException is encountered while reading the data from the
+ * InputStream
+ */
+ private static byte[] getBytes(InputStream in, Integer max)
+ throws IOException
+ {
+ // read the entire file into a byte buffer
+ ByteArrayOutputStream bout = new ByteArrayOutputStream();
+ byte[] buff = new byte[256];
+ while (max == null || max > 0)
+ {
+ int n = in.read(buff);
+ if (n == -1)
+ {
+ break;
+ }
+ bout.write(buff, 0, n);
+ if (max != null)
+ max -= n;
}
+ in.close();
+ return bout.toByteArray();
+ }
- /*
- * convert two bytes into a short note, this is little endian because it's
- * for an Intel only OS.
- */
- private static int bytesToWord(byte[] bytes, int off) {
- return ((bytes[off + 1] & 0xff) << 8) | (bytes[off] & 0xff);
+ private static boolean isMagicPresent(byte[] link)
+ {
+ final int magic = 0x0000004C;
+ final int magic_offset = 0x00;
+ return link.length >= 32 && bytesToDword(link, magic_offset) == magic;
+ }
+
+ /**
+ * Gobbles up link data by parsing it and storing info in member fields
+ *
+ * @param link
+ * all the bytes from the .lnk file
+ */
+ private void parseLink(byte[] link) throws ParseException
+ {
+ try
+ {
+ if (!isMagicPresent(link))
+ throw new ParseException("Invalid shortcut; magic is missing", 0);
+
+ // get the flags byte
+ byte flags = link[0x14];
+
+ // get the file attributes byte
+ final int file_atts_offset = 0x18;
+ byte file_atts = link[file_atts_offset];
+ byte is_dir_mask = (byte) 0x10;
+ if ((file_atts & is_dir_mask) > 0)
+ {
+ isDirectory = true;
+ }
+ else
+ {
+ isDirectory = false;
+ }
+
+ // if the shell settings are present, skip them
+ final int shell_offset = 0x4c;
+ final byte has_shell_mask = (byte) 0x01;
+ int shell_len = 0;
+ if ((flags & has_shell_mask) > 0)
+ {
+ // the plus 2 accounts for the length marker itself
+ shell_len = bytesToWord(link, shell_offset) + 2;
+ }
+
+ // get to the file settings
+ int file_start = 0x4c + shell_len;
+
+ final int file_location_info_flag_offset_offset = 0x08;
+ int file_location_info_flag = link[file_start
+ + file_location_info_flag_offset_offset];
+ isLocal = (file_location_info_flag & 2) == 0;
+ // get the local volume and local system values
+ // final int localVolumeTable_offset_offset = 0x0C;
+ final int basename_offset_offset = 0x10;
+ final int networkVolumeTable_offset_offset = 0x14;
+ final int finalname_offset_offset = 0x18;
+ int finalname_offset = link[file_start + finalname_offset_offset]
+ + file_start;
+ String finalname = getNullDelimitedString(link, finalname_offset);
+ if (isLocal)
+ {
+ int basename_offset = link[file_start + basename_offset_offset]
+ + file_start;
+ String basename = getNullDelimitedString(link, basename_offset);
+ real_file = basename + finalname;
+ }
+ else
+ {
+ int networkVolumeTable_offset = link[file_start
+ + networkVolumeTable_offset_offset] + file_start;
+ int shareName_offset_offset = 0x08;
+ int shareName_offset = link[networkVolumeTable_offset
+ + shareName_offset_offset] + networkVolumeTable_offset;
+ String shareName = getNullDelimitedString(link, shareName_offset);
+ real_file = shareName + "\\" + finalname;
+ }
+ } catch (ArrayIndexOutOfBoundsException e)
+ {
+ throw new ParseException(
+ "Could not be parsed, probably not a valid WindowsShortcut",
+ 0);
}
+ }
- private static int bytesToDword(byte[] bytes, int off) {
- return (bytesToWord(bytes, off + 2) << 16) | bytesToWord(bytes, off);
+ private static String getNullDelimitedString(byte[] bytes, int off)
+ {
+ int len = 0;
+ // count bytes until the null character (0)
+ while (true)
+ {
+ if (bytes[off + len] == 0)
+ {
+ break;
+ }
+ len++;
}
+ return new String(bytes, off, len);
+ }
+
+ /*
+ * convert two bytes into a short note, this is little endian because it's
+ * for an Intel only OS.
+ */
+ private static int bytesToWord(byte[] bytes, int off)
+ {
+ return ((bytes[off + 1] & 0xff) << 8) | (bytes[off] & 0xff);
+ }
+
+ private static int bytesToDword(byte[] bytes, int off)
+ {
+ return (bytesToWord(bytes, off + 2) << 16) | bytesToWord(bytes, off);
+ }
}
import swingjs.api.js.HTML5Applet;
-public interface JSUtilI {
+public interface JSUtilI
+{
/**
* Indicate to SwingJS that the given file type is binary.
package swingjs.api.js;
-public interface HTML5Applet {
+public interface HTML5Applet
+{
- /**
- * The canvas that is being used by the HTML5 applet
- *
- * @return
- */
- Object _getHtml5Canvas();
+ /**
+ * The canvas that is being used by the HTML5 applet
+ *
+ * @return
+ */
+ Object _getHtml5Canvas();
- int _getHeight();
+ int _getHeight();
- int _getWidth();
+ int _getWidth();
- /**
- * The div associated with the HTML5 applet
- *
- * @return
- */
- Object _getContentLayer();
+ /**
+ * The div associated with the HTML5 applet
+ *
+ * @return
+ */
+ Object _getContentLayer();
- /**
- * Simple resizing for an inline applet
- *
- * @param widthHeight
- */
- void _resizeApplet(int[] widthHeight);
+ /**
+ * Simple resizing for an inline applet
+ *
+ * @param widthHeight
+ */
+ void _resizeApplet(int[] widthHeight);
- void _show(boolean b);
-
- String _getID();
+ void _show(boolean b);
+ String _getID();
}
__equalsCalc = obj;
boolean _equals;
_equals = true
- && ((this.accession == null && other.getAccession() == null) || (this.accession != null && this.accession
- .equals(other.getAccession())))
- && ((this.accessionVersion == null && other
- .getAccessionVersion() == null) || (this.accessionVersion != null && this.accessionVersion
- .equals(other.getAccessionVersion())))
- && ((this.databaseDescription == null && other
- .getDatabaseDescription() == null) || (this.databaseDescription != null && this.databaseDescription
- .equals(other.getDatabaseDescription())))
- && ((this.databaseName == null && other.getDatabaseName() == null) || (this.databaseName != null && this.databaseName
- .equals(other.getDatabaseName())))
- && ((this.dateAdded == null && other.getDateAdded() == null) || (this.dateAdded != null && this.dateAdded
- .equals(other.getDateAdded())))
- && ((this.dateDeleted == null && other.getDateDeleted() == null) || (this.dateDeleted != null && this.dateDeleted
- .equals(other.getDateDeleted())))
+ && ((this.accession == null && other.getAccession() == null)
+ || (this.accession != null
+ && this.accession.equals(other.getAccession())))
+ && ((this.accessionVersion == null
+ && other.getAccessionVersion() == null)
+ || (this.accessionVersion != null
+ && this.accessionVersion
+ .equals(other.getAccessionVersion())))
+ && ((this.databaseDescription == null
+ && other.getDatabaseDescription() == null)
+ || (this.databaseDescription != null
+ && this.databaseDescription.equals(
+ other.getDatabaseDescription())))
+ && ((this.databaseName == null
+ && other.getDatabaseName() == null)
+ || (this.databaseName != null && this.databaseName
+ .equals(other.getDatabaseName())))
+ && ((this.dateAdded == null && other.getDateAdded() == null)
+ || (this.dateAdded != null
+ && this.dateAdded.equals(other.getDateAdded())))
+ && ((this.dateDeleted == null && other.getDateDeleted() == null)
+ || (this.dateDeleted != null && this.dateDeleted
+ .equals(other.getDateDeleted())))
&& this.deleted == other.isDeleted()
- && ((this.gi == null && other.getGi() == null) || (this.gi != null && this.gi
- .equals(other.getGi())))
- && ((this.taxonId == null && other.getTaxonId() == null) || (this.taxonId != null && this.taxonId
- .equals(other.getTaxonId())));
+ && ((this.gi == null && other.getGi() == null)
+ || (this.gi != null && this.gi.equals(other.getGi())))
+ && ((this.taxonId == null && other.getTaxonId() == null)
+ || (this.taxonId != null
+ && this.taxonId.equals(other.getTaxonId())));
__equalsCalc = null;
return _equals;
}
this.logicalCrossReferences = logicalCrossReferences;
}
- public uk.ac.ebi.picr.model.CrossReference getLogicalCrossReferences(int i)
+ public uk.ac.ebi.picr.model.CrossReference getLogicalCrossReferences(
+ int i)
{
return this.logicalCrossReferences[i];
}
}
__equalsCalc = obj;
boolean _equals;
- _equals = true
- && ((this.CRC64 == null && other.getCRC64() == null) || (this.CRC64 != null && this.CRC64
- .equals(other.getCRC64())))
- && ((this.UPI == null && other.getUPI() == null) || (this.UPI != null && this.UPI
- .equals(other.getUPI())))
- && ((this.identicalCrossReferences == null && other
- .getIdenticalCrossReferences() == null) || (this.identicalCrossReferences != null && java.util.Arrays
- .equals(this.identicalCrossReferences,
- other.getIdenticalCrossReferences())))
- && ((this.logicalCrossReferences == null && other
- .getLogicalCrossReferences() == null) || (this.logicalCrossReferences != null && java.util.Arrays
- .equals(this.logicalCrossReferences,
- other.getLogicalCrossReferences())))
- && ((this.sequence == null && other.getSequence() == null) || (this.sequence != null && this.sequence
- .equals(other.getSequence())))
- && ((this.timestamp == null && other.getTimestamp() == null) || (this.timestamp != null && this.timestamp
- .equals(other.getTimestamp())));
+ _equals = true && ((this.CRC64 == null && other.getCRC64() == null)
+ || (this.CRC64 != null && this.CRC64.equals(other.getCRC64())))
+ && ((this.UPI == null && other.getUPI() == null)
+ || (this.UPI != null
+ && this.UPI.equals(other.getUPI())))
+ && ((this.identicalCrossReferences == null
+ && other.getIdenticalCrossReferences() == null)
+ || (this.identicalCrossReferences != null
+ && java.util.Arrays.equals(
+ this.identicalCrossReferences,
+ other.getIdenticalCrossReferences())))
+ && ((this.logicalCrossReferences == null
+ && other.getLogicalCrossReferences() == null)
+ || (this.logicalCrossReferences != null
+ && java.util.Arrays.equals(
+ this.logicalCrossReferences,
+ other.getLogicalCrossReferences())))
+ && ((this.sequence == null && other.getSequence() == null)
+ || (this.sequence != null
+ && this.sequence.equals(other.getSequence())))
+ && ((this.timestamp == null && other.getTimestamp() == null)
+ || (this.timestamp != null && this.timestamp
+ .equals(other.getTimestamp())));
__equalsCalc = null;
return _equals;
}
for (int i = 0; i < java.lang.reflect.Array
.getLength(getIdenticalCrossReferences()); i++)
{
- java.lang.Object obj = java.lang.reflect.Array.get(
- getIdenticalCrossReferences(), i);
+ java.lang.Object obj = java.lang.reflect.Array
+ .get(getIdenticalCrossReferences(), i);
if (obj != null && !obj.getClass().isArray())
{
_hashCode += obj.hashCode();
for (int i = 0; i < java.lang.reflect.Array
.getLength(getLogicalCrossReferences()); i++)
{
- java.lang.Object obj = java.lang.reflect.Array.get(
- getLogicalCrossReferences(), i);
+ java.lang.Object obj = java.lang.reflect.Array
+ .get(getLogicalCrossReferences(), i);
if (obj != null && !obj.getClass().isArray())
{
_hashCode += obj.hashCode();
__equalsCalc = obj;
boolean _equals;
_equals = true
- && ((type == null && other.getType() == null) || (type != null && type
- .equals(other.getType())))
- && ((content == null && other.getContent() == null) || (content != null && content
- .equals(other.getContent())));
+ && ((type == null && other.getType() == null)
+ || (type != null && type.equals(other.getType())))
+ && ((content == null && other.getContent() == null)
+ || (content != null
+ && content.equals(other.getContent())));
__equalsCalc = null;
return _equals;
}
}
__equalsCalc = obj;
boolean _equals;
- _equals = true
- && ((program == null && other.getProgram() == null) || (program != null && program
- .equals(other.getProgram())))
- && ((database == null && other.getDatabase() == null) || (database != null && database
- .equals(other.getDatabase())))
- && ((matrix == null && other.getMatrix() == null) || (matrix != null && matrix
- .equals(other.getMatrix())))
- && exp == other.getExp()
- && echofilter == other.isEchofilter()
- && ((filter == null && other.getFilter() == null) || (filter != null && filter
- .equals(other.getFilter())))
- && numal == other.getNumal()
- && scores == other.getScores()
- && ((sensitivity == null && other.getSensitivity() == null) || (sensitivity != null && sensitivity
- .equals(other.getSensitivity())))
- && ((sort == null && other.getSort() == null) || (sort != null && sort
- .equals(other.getSort())))
- && ((stats == null && other.getStats() == null) || (stats != null && stats
- .equals(other.getStats())))
- && ((strand == null && other.getStrand() == null) || (strand != null && strand
- .equals(other.getStrand())))
- && ((outformat == null && other.getOutformat() == null) || (outformat != null && outformat
- .equals(other.getOutformat())))
- && topcombon == other.getTopcombon()
- && async == other.isAsync()
- && ((email == null && other.getEmail() == null) || (email != null && email
- .equals(other.getEmail())));
+ _equals = true && ((program == null && other.getProgram() == null)
+ || (program != null && program.equals(other.getProgram())))
+ && ((database == null && other.getDatabase() == null)
+ || (database != null
+ && database.equals(other.getDatabase())))
+ && ((matrix == null && other.getMatrix() == null)
+ || (matrix != null && matrix.equals(other.getMatrix())))
+ && exp == other.getExp() && echofilter == other.isEchofilter()
+ && ((filter == null && other.getFilter() == null)
+ || (filter != null && filter.equals(other.getFilter())))
+ && numal == other.getNumal() && scores == other.getScores()
+ && ((sensitivity == null && other.getSensitivity() == null)
+ || (sensitivity != null
+ && sensitivity.equals(other.getSensitivity())))
+ && ((sort == null && other.getSort() == null)
+ || (sort != null && sort.equals(other.getSort())))
+ && ((stats == null && other.getStats() == null)
+ || (stats != null && stats.equals(other.getStats())))
+ && ((strand == null && other.getStrand() == null)
+ || (strand != null && strand.equals(other.getStrand())))
+ && ((outformat == null && other.getOutformat() == null)
+ || (outformat != null
+ && outformat.equals(other.getOutformat())))
+ && topcombon == other.getTopcombon() && async == other.isAsync()
+ && ((email == null && other.getEmail() == null)
+ || (email != null && email.equals(other.getEmail())));
__equalsCalc = null;
return _equals;
}
__equalsCalc = obj;
boolean _equals;
_equals = true
- && ((type == null && other.getType() == null) || (type != null && type
- .equals(other.getType())))
- && ((ext == null && other.getExt() == null) || (ext != null && ext
- .equals(other.getExt())));
+ && ((type == null && other.getType() == null)
+ || (type != null && type.equals(other.getType())))
+ && ((ext == null && other.getExt() == null)
+ || (ext != null && ext.equals(other.getExt())));
__equalsCalc = null;
return _equals;
}
throw new javax.xml.rpc.ServiceException(t);
}
throw new javax.xml.rpc.ServiceException(MessageManager.formatMessage(
- "exception.no_stub_implementation_for_interface",
- new String[] { (serviceEndpointInterface == null ? "null"
+ "exception.no_stub_implementation_for_interface", new String[]
+ { (serviceEndpointInterface == null ? "null"
: serviceEndpointInterface.getName()) }));
}
new javax.xml.namespace.QName(
"http://www.w3.org/2001/XMLSchema", "string"),
java.lang.String.class, javax.xml.rpc.ParameterMode.IN);
- _call.setReturnType(new javax.xml.namespace.QName(
- "http://www.w3.org/2001/XMLSchema", "base64Binary"),
+ _call.setReturnType(
+ new javax.xml.namespace.QName(
+ "http://www.w3.org/2001/XMLSchema", "base64Binary"),
byte[].class);
_call.setUseSOAPAction(true);
_call.setSOAPActionURI("http://www.ebi.ac.uk/WSWUBlast#poll");
_call.setOperationName(new javax.xml.namespace.QName(
"http://www.ebi.ac.uk/WSWUBlast", "poll"));
- java.lang.Object _resp = _call.invoke(new java.lang.Object[] { jobid,
- type });
+ java.lang.Object _resp = _call
+ .invoke(new java.lang.Object[]
+ { jobid, type });
if (_resp instanceof java.rmi.RemoteException)
{
org.apache.axis.client.Call _call = createCall();
_call.addParameter(new javax.xml.namespace.QName("", "params"),
new javax.xml.namespace.QName("http://www.ebi.ac.uk/WSWUBlast",
- "inputParams"), uk.ac.ebi.www.InputParams.class,
+ "inputParams"),
+ uk.ac.ebi.www.InputParams.class,
javax.xml.rpc.ParameterMode.IN);
_call.addParameter(new javax.xml.namespace.QName("", "content"),
new javax.xml.namespace.QName("http://www.ebi.ac.uk/WSWUBlast",
- "WSArrayofData"), uk.ac.ebi.www.Data[].class,
- javax.xml.rpc.ParameterMode.IN);
- _call.setReturnType(new javax.xml.namespace.QName(
- "http://www.w3.org/2001/XMLSchema", "string"),
+ "WSArrayofData"),
+ uk.ac.ebi.www.Data[].class, javax.xml.rpc.ParameterMode.IN);
+ _call.setReturnType(
+ new javax.xml.namespace.QName(
+ "http://www.w3.org/2001/XMLSchema", "string"),
java.lang.String.class);
_call.setUseSOAPAction(true);
_call.setSOAPActionURI("http://www.ebi.ac.uk/WSWUBlast#runWUBlast");
_call.setOperationName(new javax.xml.namespace.QName(
"http://www.ebi.ac.uk/WSWUBlast", "runWUBlast"));
- java.lang.Object _resp = _call.invoke(new java.lang.Object[] { params,
- content });
+ java.lang.Object _resp = _call
+ .invoke(new java.lang.Object[]
+ { params, content });
if (_resp instanceof java.rmi.RemoteException)
{
return (java.lang.String) _resp;
} catch (java.lang.Exception _exception)
{
- return (java.lang.String) org.apache.axis.utils.JavaUtils.convert(
- _resp, java.lang.String.class);
+ return (java.lang.String) org.apache.axis.utils.JavaUtils
+ .convert(_resp, java.lang.String.class);
}
}
}
new javax.xml.namespace.QName(
"http://www.w3.org/2001/XMLSchema", "string"),
java.lang.String.class, javax.xml.rpc.ParameterMode.IN);
- _call.setReturnType(new javax.xml.namespace.QName(
- "http://www.w3.org/2001/XMLSchema", "base64Binary"),
+ _call.setReturnType(
+ new javax.xml.namespace.QName(
+ "http://www.w3.org/2001/XMLSchema", "base64Binary"),
byte[].class);
_call.setUseSOAPAction(true);
_call.setSOAPActionURI("http://www.ebi.ac.uk/WSWUBlast#test");
_call.setOperationName(new javax.xml.namespace.QName(
"http://www.ebi.ac.uk/WSWUBlast", "test"));
- java.lang.Object _resp = _call.invoke(new java.lang.Object[] { jobid,
- type });
+ java.lang.Object _resp = _call
+ .invoke(new java.lang.Object[]
+ { jobid, type });
if (_resp instanceof java.rmi.RemoteException)
{
new javax.xml.namespace.QName(
"http://www.w3.org/2001/XMLSchema", "string"),
java.lang.String.class, javax.xml.rpc.ParameterMode.IN);
- _call.setReturnType(new javax.xml.namespace.QName(
- "http://www.w3.org/2001/XMLSchema", "string"),
+ _call.setReturnType(
+ new javax.xml.namespace.QName(
+ "http://www.w3.org/2001/XMLSchema", "string"),
java.lang.String.class);
_call.setUseSOAPAction(true);
_call.setSOAPActionURI("http://www.ebi.ac.uk/WSWUBlast#checkStatus");
return (java.lang.String) _resp;
} catch (java.lang.Exception _exception)
{
- return (java.lang.String) org.apache.axis.utils.JavaUtils.convert(
- _resp, java.lang.String.class);
+ return (java.lang.String) org.apache.axis.utils.JavaUtils
+ .convert(_resp, java.lang.String.class);
}
}
}
new javax.xml.namespace.QName(
"http://www.w3.org/2001/XMLSchema", "string"),
java.lang.String.class, javax.xml.rpc.ParameterMode.IN);
- _call.setReturnType(new javax.xml.namespace.QName(
- "http://www.ebi.ac.uk/WSWUBlast", "WSArrayofFile"),
+ _call.setReturnType(
+ new javax.xml.namespace.QName("http://www.ebi.ac.uk/WSWUBlast",
+ "WSArrayofFile"),
uk.ac.ebi.www.WSFile[].class);
_call.setUseSOAPAction(true);
_call.setSOAPActionURI("http://www.ebi.ac.uk/WSWUBlast#getResults");
new javax.xml.namespace.QName(
"http://www.w3.org/2001/XMLSchema", "string"),
java.lang.String.class, javax.xml.rpc.ParameterMode.IN);
- _call.setReturnType(new javax.xml.namespace.QName(
- "http://www.w3.org/2001/XMLSchema", "base64Binary"),
+ _call.setReturnType(
+ new javax.xml.namespace.QName(
+ "http://www.w3.org/2001/XMLSchema", "base64Binary"),
byte[].class);
_call.setUseSOAPAction(true);
_call.setSOAPActionURI("http://www.ebi.ac.uk/WSWUBlast#polljob");
_call.setOperationName(new javax.xml.namespace.QName(
"http://www.ebi.ac.uk/WSWUBlast", "polljob"));
- java.lang.Object _resp = _call.invoke(new java.lang.Object[] { jobid,
- outformat });
+ java.lang.Object _resp = _call
+ .invoke(new java.lang.Object[]
+ { jobid, outformat });
if (_resp instanceof java.rmi.RemoteException)
{
org.apache.axis.client.Call _call = createCall();
_call.addParameter(new javax.xml.namespace.QName("", "params"),
new javax.xml.namespace.QName("http://www.ebi.ac.uk/WSWUBlast",
- "inputParams"), uk.ac.ebi.www.InputParams.class,
+ "inputParams"),
+ uk.ac.ebi.www.InputParams.class,
javax.xml.rpc.ParameterMode.IN);
_call.addParameter(new javax.xml.namespace.QName("", "content"),
new javax.xml.namespace.QName(
"http://www.w3.org/2001/XMLSchema", "base64Binary"),
byte[].class, javax.xml.rpc.ParameterMode.IN);
- _call.setReturnType(new javax.xml.namespace.QName(
- "http://www.w3.org/2001/XMLSchema", "base64Binary"),
+ _call.setReturnType(
+ new javax.xml.namespace.QName(
+ "http://www.w3.org/2001/XMLSchema", "base64Binary"),
byte[].class);
_call.setUseSOAPAction(true);
_call.setSOAPActionURI("http://www.ebi.ac.uk/WSWUBlast#doWUBlast");
_call.setOperationName(new javax.xml.namespace.QName(
"http://www.ebi.ac.uk/WSWUBlast", "doWUBlast"));
- java.lang.Object _resp = _call.invoke(new java.lang.Object[] { params,
- content });
+ java.lang.Object _resp = _call
+ .invoke(new java.lang.Object[]
+ { params, content });
if (_resp instanceof java.rmi.RemoteException)
{
oper.addParameter(
new javax.xml.namespace.QName(
"http://www.ebi.ac.uk/picr/AccessionMappingService",
- "sequence"), new javax.xml.namespace.QName(
+ "sequence"),
+ new javax.xml.namespace.QName(
"http://www.w3.org/2001/XMLSchema", "string"),
java.lang.String.class,
org.apache.axis.description.ParameterDesc.IN, false, false);
- oper.addParameter(new javax.xml.namespace.QName(
- "http://www.ebi.ac.uk/picr/AccessionMappingService",
- "searchDatabases"), new javax.xml.namespace.QName(
- "http://www.w3.org/2001/XMLSchema", "string"),
- java.lang.String[].class,
- org.apache.axis.description.ParameterDesc.IN, false, false);
oper.addParameter(
new javax.xml.namespace.QName(
"http://www.ebi.ac.uk/picr/AccessionMappingService",
- "taxonId"), new javax.xml.namespace.QName(
+ "searchDatabases"),
+ new javax.xml.namespace.QName(
"http://www.w3.org/2001/XMLSchema", "string"),
- java.lang.String.class,
+ java.lang.String[].class,
org.apache.axis.description.ParameterDesc.IN, false, false);
oper.addParameter(new javax.xml.namespace.QName(
- "http://www.ebi.ac.uk/picr/AccessionMappingService",
- "onlyActive"), new javax.xml.namespace.QName(
- "http://www.w3.org/2001/XMLSchema", "boolean"), boolean.class,
+ "http://www.ebi.ac.uk/picr/AccessionMappingService", "taxonId"),
+ new javax.xml.namespace.QName(
+ "http://www.w3.org/2001/XMLSchema", "string"),
+ java.lang.String.class,
org.apache.axis.description.ParameterDesc.IN, false, false);
+ oper.addParameter(
+ new javax.xml.namespace.QName(
+ "http://www.ebi.ac.uk/picr/AccessionMappingService",
+ "onlyActive"),
+ new javax.xml.namespace.QName(
+ "http://www.w3.org/2001/XMLSchema", "boolean"),
+ boolean.class, org.apache.axis.description.ParameterDesc.IN,
+ false, false);
oper.setReturnType(new javax.xml.namespace.QName(
"http://model.picr.ebi.ac.uk", "UPEntry"));
oper.setReturnClass(uk.ac.ebi.picr.model.UPEntry.class);
oper = new org.apache.axis.description.OperationDesc();
oper.setName("getUPIForAccession");
- oper.addParameter(new javax.xml.namespace.QName(
- "http://www.ebi.ac.uk/picr/AccessionMappingService",
- "accession"), new javax.xml.namespace.QName(
- "http://www.w3.org/2001/XMLSchema", "string"),
+ oper.addParameter(
+ new javax.xml.namespace.QName(
+ "http://www.ebi.ac.uk/picr/AccessionMappingService",
+ "accession"),
+ new javax.xml.namespace.QName(
+ "http://www.w3.org/2001/XMLSchema", "string"),
java.lang.String.class,
org.apache.axis.description.ParameterDesc.IN, false, false);
- oper.addParameter(new javax.xml.namespace.QName(
- "http://www.ebi.ac.uk/picr/AccessionMappingService",
- "ac_version"), new javax.xml.namespace.QName(
- "http://www.w3.org/2001/XMLSchema", "string"),
+ oper.addParameter(
+ new javax.xml.namespace.QName(
+ "http://www.ebi.ac.uk/picr/AccessionMappingService",
+ "ac_version"),
+ new javax.xml.namespace.QName(
+ "http://www.w3.org/2001/XMLSchema", "string"),
java.lang.String.class,
org.apache.axis.description.ParameterDesc.IN, false, false);
- oper.addParameter(new javax.xml.namespace.QName(
- "http://www.ebi.ac.uk/picr/AccessionMappingService",
- "searchDatabases"), new javax.xml.namespace.QName(
- "http://www.w3.org/2001/XMLSchema", "string"),
- java.lang.String[].class,
- org.apache.axis.description.ParameterDesc.IN, false, false);
oper.addParameter(
new javax.xml.namespace.QName(
"http://www.ebi.ac.uk/picr/AccessionMappingService",
- "taxonId"), new javax.xml.namespace.QName(
+ "searchDatabases"),
+ new javax.xml.namespace.QName(
"http://www.w3.org/2001/XMLSchema", "string"),
- java.lang.String.class,
+ java.lang.String[].class,
org.apache.axis.description.ParameterDesc.IN, false, false);
oper.addParameter(new javax.xml.namespace.QName(
- "http://www.ebi.ac.uk/picr/AccessionMappingService",
- "onlyActive"), new javax.xml.namespace.QName(
- "http://www.w3.org/2001/XMLSchema", "boolean"), boolean.class,
+ "http://www.ebi.ac.uk/picr/AccessionMappingService", "taxonId"),
+ new javax.xml.namespace.QName(
+ "http://www.w3.org/2001/XMLSchema", "string"),
+ java.lang.String.class,
org.apache.axis.description.ParameterDesc.IN, false, false);
+ oper.addParameter(
+ new javax.xml.namespace.QName(
+ "http://www.ebi.ac.uk/picr/AccessionMappingService",
+ "onlyActive"),
+ new javax.xml.namespace.QName(
+ "http://www.w3.org/2001/XMLSchema", "boolean"),
+ boolean.class, org.apache.axis.description.ParameterDesc.IN,
+ false, false);
oper.setReturnType(new javax.xml.namespace.QName(
"http://model.picr.ebi.ac.uk", "UPEntry"));
oper.setReturnClass(uk.ac.ebi.picr.model.UPEntry[].class);
Boolean.FALSE);
_call.setProperty(org.apache.axis.AxisEngine.PROP_DOMULTIREFS,
Boolean.FALSE);
- _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
+ _call.setSOAPVersion(
+ org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
_call.setOperationName(new javax.xml.namespace.QName(
"http://www.ebi.ac.uk/picr/AccessionMappingService",
"getUPIForSequence"));
setRequestHeaders(_call);
setAttachments(_call);
- java.lang.Object _resp = _call.invoke(new java.lang.Object[] {
- sequence, searchDatabases, taxonId,
- java.lang.Boolean.valueOf(onlyActive) });
+ java.lang.Object _resp = _call
+ .invoke(new java.lang.Object[]
+ { sequence, searchDatabases, taxonId,
+ java.lang.Boolean.valueOf(onlyActive) });
if (_resp instanceof java.rmi.RemoteException)
{
Boolean.FALSE);
_call.setProperty(org.apache.axis.AxisEngine.PROP_DOMULTIREFS,
Boolean.FALSE);
- _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
+ _call.setSOAPVersion(
+ org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
_call.setOperationName(new javax.xml.namespace.QName(
"http://www.ebi.ac.uk/picr/AccessionMappingService",
"getUPIForAccession"));
setRequestHeaders(_call);
setAttachments(_call);
- java.lang.Object _resp = _call.invoke(new java.lang.Object[] {
- accession, ac_version, searchDatabases, taxonId,
- java.lang.Boolean.valueOf(onlyActive) });
+ java.lang.Object _resp = _call
+ .invoke(new java.lang.Object[]
+ { accession, ac_version, searchDatabases, taxonId,
+ java.lang.Boolean.valueOf(onlyActive) });
if (_resp instanceof java.rmi.RemoteException)
{
Boolean.FALSE);
_call.setProperty(org.apache.axis.AxisEngine.PROP_DOMULTIREFS,
Boolean.FALSE);
- _call.setSOAPVersion(org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
+ _call.setSOAPVersion(
+ org.apache.axis.soap.SOAPConstants.SOAP11_CONSTANTS);
_call.setOperationName(new javax.xml.namespace.QName(
"http://www.ebi.ac.uk/picr/AccessionMappingService",
"getMappedDatabaseNames"));
import jalview.util.MessageManager;
-public class AccessionMapperServiceLocator extends
- org.apache.axis.client.Service implements
+public class AccessionMapperServiceLocator
+ extends org.apache.axis.client.Service implements
uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperService
{
}
}
- public void setAccessionMapperPortEndpointAddress(java.lang.String address)
+ public void setAccessionMapperPortEndpointAddress(
+ java.lang.String address)
{
AccessionMapperPort_address = address;
}
throw new javax.xml.rpc.ServiceException(t);
}
throw new javax.xml.rpc.ServiceException(MessageManager.formatMessage(
- "exception.no_stub_implementation_for_interface",
- new String[] { (serviceEndpointInterface == null ? "null"
+ "exception.no_stub_implementation_for_interface", new String[]
+ { (serviceEndpointInterface == null ? "null"
: serviceEndpointInterface.getName()) }));
}
}
else
{ // Unknown Port Name
- throw new javax.xml.rpc.ServiceException(
- MessageManager.formatMessage(
- "exception.cannot_set_endpoint_address_unknown_port",
- new String[] { portName }));
+ throw new javax.xml.rpc.ServiceException(MessageManager.formatMessage(
+ "exception.cannot_set_endpoint_address_unknown_port",
+ new String[]
+ { portName }));
}
}
*/
package vamsas.objects.simple;
-public class Alignment extends vamsas.objects.simple.Object implements
- java.io.Serializable
+public class Alignment extends vamsas.objects.simple.Object
+ implements java.io.Serializable
{
private java.lang.String gapchar;
__equalsCalc = obj;
boolean _equals;
_equals = super.equals(obj)
- && ((this.gapchar == null && other.getGapchar() == null) || (this.gapchar != null && this.gapchar
- .equals(other.getGapchar())))
- && ((this.method == null && other.getMethod() == null) || (this.method != null && java.util.Arrays
- .equals(this.method, other.getMethod())))
- && ((this.seqs == null && other.getSeqs() == null) || (this.seqs != null && this.seqs
- .equals(other.getSeqs())));
+ && ((this.gapchar == null && other.getGapchar() == null)
+ || (this.gapchar != null
+ && this.gapchar.equals(other.getGapchar())))
+ && ((this.method == null && other.getMethod() == null)
+ || (this.method != null && java.util.Arrays
+ .equals(this.method, other.getMethod())))
+ && ((this.seqs == null && other.getSeqs() == null)
+ || (this.seqs != null
+ && this.seqs.equals(other.getSeqs())));
__equalsCalc = null;
return _equals;
}
}
if (getMethod() != null)
{
- for (int i = 0; i < java.lang.reflect.Array.getLength(getMethod()); i++)
+ for (int i = 0; i < java.lang.reflect.Array
+ .getLength(getMethod()); i++)
{
java.lang.Object obj = java.lang.reflect.Array.get(getMethod(), i);
if (obj != null && !obj.getClass().isArray())
*/
package vamsas.objects.simple;
-public class JpredResult extends vamsas.objects.simple.Result implements
- java.io.Serializable
+public class JpredResult extends vamsas.objects.simple.Result
+ implements java.io.Serializable
{
private java.lang.String aligfile;
__equalsCalc = obj;
boolean _equals;
_equals = super.equals(obj)
- && ((this.aligfile == null && other.getAligfile() == null) || (this.aligfile != null && this.aligfile
- .equals(other.getAligfile())))
- && ((this.predfile == null && other.getPredfile() == null) || (this.predfile != null && this.predfile
- .equals(other.getPredfile())));
+ && ((this.aligfile == null && other.getAligfile() == null)
+ || (this.aligfile != null
+ && this.aligfile.equals(other.getAligfile())))
+ && ((this.predfile == null && other.getPredfile() == null)
+ || (this.predfile != null
+ && this.predfile.equals(other.getPredfile())));
__equalsCalc = null;
return _equals;
}
*/
package vamsas.objects.simple;
-public class MsaResult extends vamsas.objects.simple.Result implements
- java.io.Serializable
+public class MsaResult extends vamsas.objects.simple.Result
+ implements java.io.Serializable
{
private vamsas.objects.simple.Alignment msa;
__equalsCalc = obj;
boolean _equals;
- _equals = super.equals(obj)
- && (((this.msa == null) && (other.getMsa() == null)) || ((this.msa != null) && this.msa
- .equals(other.getMsa())));
+ _equals = super.equals(obj) && (((this.msa == null)
+ && (other.getMsa() == null))
+ || ((this.msa != null) && this.msa.equals(other.getMsa())));
__equalsCalc = null;
return _equals;
}
__equalsCalc = obj;
boolean _equals;
- _equals = true
- && ((this.msf == null && other.getMsf() == null) || (this.msf != null && this.msf
- .equals(other.getMsf())))
- && ((this.notes == null && other.getNotes() == null) || (this.notes != null && this.notes
- .equals(other.getNotes())));
+ _equals = true && ((this.msf == null && other.getMsf() == null)
+ || (this.msf != null && this.msf.equals(other.getMsf())))
+ && ((this.notes == null && other.getNotes() == null)
+ || (this.notes != null
+ && this.notes.equals(other.getNotes())));
__equalsCalc = null;
return _equals;
}
}
__equalsCalc = obj;
boolean _equals;
- _equals = true
- && this.broken == other.isBroken()
+ _equals = true && this.broken == other.isBroken()
&& this.failed == other.isFailed()
&& this.finished == other.isFinished()
&& this.invalid == other.isInvalid()
&& this.running == other.isRunning()
&& this.serverError == other.isServerError()
&& this.state == other.getState()
- && ((this.status == null && other.getStatus() == null) || (this.status != null && this.status
- .equals(other.getStatus())))
+ && ((this.status == null && other.getStatus() == null)
+ || (this.status != null
+ && this.status.equals(other.getStatus())))
&& this.suspended == other.isSuspended();
__equalsCalc = null;
return _equals;
}
__equalsCalc = obj;
boolean _equals;
- _equals = true && ((this.output == null && other.getOutput() == null) || (this.output != null && this.output
- .equals(other.getOutput())));
+ _equals = true && ((this.output == null && other.getOutput() == null)
+ || (this.output != null
+ && this.output.equals(other.getOutput())));
__equalsCalc = null;
return _equals;
}
*/
package vamsas.objects.simple;
-public class SeqSearchResult extends vamsas.objects.simple.Result implements
- java.io.Serializable
+public class SeqSearchResult extends vamsas.objects.simple.Result
+ implements java.io.Serializable
{
private vamsas.objects.simple.Alignment alignment;
__equalsCalc = obj;
boolean _equals;
_equals = super.equals(obj)
- && ((this.alignment == null && other.getAlignment() == null) || (this.alignment != null && this.alignment
- .equals(other.getAlignment())))
- && ((this.annotation == null && other.getAnnotation() == null) || (this.annotation != null && this.annotation
- .equals(other.getAnnotation())))
- && ((this.features == null && other.getFeatures() == null) || (this.features != null && this.features
- .equals(other.getFeatures())))
- && ((this.newickTree == null && other.getNewickTree() == null) || (this.newickTree != null && this.newickTree
- .equals(other.getNewickTree())));
+ && ((this.alignment == null && other.getAlignment() == null)
+ || (this.alignment != null
+ && this.alignment.equals(other.getAlignment())))
+ && ((this.annotation == null && other.getAnnotation() == null)
+ || (this.annotation != null && this.annotation
+ .equals(other.getAnnotation())))
+ && ((this.features == null && other.getFeatures() == null)
+ || (this.features != null
+ && this.features.equals(other.getFeatures())))
+ && ((this.newickTree == null && other.getNewickTree() == null)
+ || (this.newickTree != null && this.newickTree
+ .equals(other.getNewickTree())));
__equalsCalc = null;
return _equals;
}
__equalsCalc = obj;
boolean _equals;
_equals = true
- && ((this.id == null && other.getId() == null) || (this.id != null && this.id
- .equals(other.getId())))
- && ((this.seq == null && other.getSeq() == null) || (this.seq != null && this.seq
- .equals(other.getSeq())));
+ && ((this.id == null && other.getId() == null)
+ || (this.id != null && this.id.equals(other.getId())))
+ && ((this.seq == null && other.getSeq() == null)
+ || (this.seq != null
+ && this.seq.equals(other.getSeq())));
__equalsCalc = null;
return _equals;
}
}
__equalsCalc = obj;
boolean _equals;
- _equals = true && ((this.seqs == null && other.getSeqs() == null) || (this.seqs != null && java.util.Arrays
- .equals(this.seqs, other.getSeqs())));
+ _equals = true && ((this.seqs == null && other.getSeqs() == null)
+ || (this.seqs != null && java.util.Arrays.equals(this.seqs,
+ other.getSeqs())));
__equalsCalc = null;
return _equals;
}
}
__equalsCalc = obj;
boolean _equals;
- _equals = true
- && ((this.jobId == null && other.getJobId() == null) || (this.jobId != null && this.jobId
- .equals(other.getJobId())))
+ _equals = true && ((this.jobId == null && other.getJobId() == null)
+ || (this.jobId != null && this.jobId.equals(other.getJobId())))
&& this.status == other.getStatus();
__equalsCalc = null;
return _equals;
SequenceI seq4 = new Sequence("Seq4", "CA--t");
SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 };
int width = seq1.getLength();
- ProfilesI result = AAFrequency.calculate(seqs, width, 0, width,
- false);
+ ProfilesI result = AAFrequency.calculate(seqs, width, 0, width, false);
// col 0 is 100% C
ProfileI col = result.get(0);
SequenceI seq4 = new Sequence("Seq4", "CA-t");
SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 };
int width = seq1.getLength();
- ProfilesI result = AAFrequency.calculate(seqs, width, 0, width,
- true);
+ ProfilesI result = AAFrequency.calculate(seqs, width, 0, width, true);
ProfileI profile = result.get(0);
assertEquals(4, profile.getCounts().getCount('C'));
AlignmentAnnotation consensus = new AlignmentAnnotation("Consensus",
"PID", new Annotation[width]);
- AAFrequency
- .completeConsensus(consensus, profiles, 0, 5, false, true, 4);
+ AAFrequency.completeConsensus(consensus, profiles, 0, 5, false, true,
+ 4);
Annotation ann = consensus.annotations[0];
assertEquals("C 100%", ann.description);
SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 };
int width = seq1.getLength();
ProfilesI profiles = AAFrequency.calculate(seqs, width, 0, width, true);
-
+
AlignmentAnnotation consensus = new AlignmentAnnotation("Consensus",
"PID", new Annotation[width]);
- AAFrequency
- .completeConsensus(consensus, profiles, 0, 5, true, false, 4);
-
+ AAFrequency.completeConsensus(consensus, profiles, 0, 5, true, false,
+ 4);
+
Annotation ann = consensus.annotations[0];
assertEquals("C 100%", ann.description);
assertEquals("C", ann.displayCharacter);
counts.put('L', 38);
counts.put('H', 2);
profile.setCounts(counts);
-
+
/*
* [0, noOfValues, totalPercent, char1, count1, ...]
* G: 70/200 = 35%
*/
int[] extracted = AAFrequency.extractProfile(profile, false);
int[] expected = new int[] { AlignmentAnnotation.SEQUENCE_PROFILE, 4,
- 85, 'G', 35, 'R', 30, 'L', 19, 'H',
- 1 };
+ 85, 'G', 35, 'R', 30, 'L', 19, 'H', 1 };
org.testng.Assert.assertEquals(extracted, expected);
-
+
/*
* add some counts of 1; these round down to 0% and should be discarded
*/
expected = new int[] { AlignmentAnnotation.SEQUENCE_PROFILE, 4, 84, 'G',
34, 'R', 30, 'L', 19, 'H', 1 };
org.testng.Assert.assertEquals(extracted, expected);
-
+
}
@Test(groups = { "Functional" })
codonCounts[0] = 120;
codonCounts[1] = 110;
profile.put(AAFrequency.PROFILE, codonCounts);
-
+
/*
* [0, noOfValues, totalPercent, char1, count1, ...]
* codon1: 30/110 = 27.2 = 27%
* max count 70 for modal residue 'G'
*/
Hashtable profile = new Hashtable();
-
+
/*
* cdna profile is {seqCount, ungappedCount, codonCount1, ...codonCount64}
* where 1..64 positions correspond to encoded codons
codonCounts[0] = 120;
codonCounts[1] = 110;
profile.put(AAFrequency.PROFILE, codonCounts);
-
+
/*
* [0, noOfValues, totalPercent, char1, count1, ...]
* codon1: 30/120 = 25%
@Test(groups = { "Functional" })
public void testIndexEncode_nucleotide()
{
- AlignSeq as = new AlignSeq(new Sequence("s1", "TTAG"), new Sequence(
- "s2", "ACGT"), AlignSeq.DNA);
+ AlignSeq as = new AlignSeq(new Sequence("s1", "TTAG"),
+ new Sequence("s2", "ACGT"), AlignSeq.DNA);
int[] expected = new int[] { 0, 0, 1, 1, 2, 2, 3, 3, 4, 4, 5, 5, 6, 6,
7, 7, 8, 8, 9, 9, -1, -1, 10, -1 };
String s = "aAcCgGtTuUiIxXrRyYnN .-?";
@Test(groups = { "Functional" })
public void testIndexEncode_peptide()
{
- AlignSeq as = new AlignSeq(new Sequence("s1", "PFY"), new Sequence(
- "s2", "RQW"), AlignSeq.PEP);
+ AlignSeq as = new AlignSeq(new Sequence("s1", "PFY"),
+ new Sequence("s2", "RQW"), AlignSeq.PEP);
int[] expected = new int[] { 0, 0, 1, 1, 2, 2, 21, 21, 22, 22, -1, 23,
-1, -1, -1 };
String s = "aArRnNzZxX *.-?";
anns[4].graphGroup = -1;
anns[4].visible = true;
- BitSet result = AlignmentAnnotationUtils
- .getVisibleLineGraphGroups(AlignmentAnnotationUtils
- .asList(anns));
+ BitSet result = AlignmentAnnotationUtils.getVisibleLineGraphGroups(
+ AlignmentAnnotationUtils.asList(anns));
assertTrue(result.get(5));
assertFalse(result.get(0));
assertFalse(result.get(1));
import org.testng.annotations.BeforeClass;
/**
- * Generates, and outputs in Fasta format, a random peptide or nucleotide alignment for given
- * sequence length and count. Will regenerate the same alignment each time if
- * the same random seed is used (so may be used for reproducible unit tests).
- * Not guaranteed to reproduce the same results between versions, as the rules
- * may get tweaked to produce more 'realistic' results.
+ * Generates, and outputs in Fasta format, a random peptide or nucleotide
+ * alignment for given sequence length and count. Will regenerate the same
+ * alignment each time if the same random seed is used (so may be used for
+ * reproducible unit tests). Not guaranteed to reproduce the same results
+ * between versions, as the rules may get tweaked to produce more 'realistic'
+ * results.
*
* @author gmcarstairs
*/
int gapPercentage = Integer.valueOf(args[4]);
int changePercentage = Integer.valueOf(args[5]);
- ps.println("; " + height + " sequences of " + width
- + " bases with " + gapPercentage + "% gaps and "
- + changePercentage + "% mutations (random seed = " + randomSeed
- + ")");
+ ps.println("; " + height + " sequences of " + width + " bases with "
+ + gapPercentage + "% gaps and " + changePercentage
+ + "% mutations (random seed = " + randomSeed + ")");
new AlignmentGenerator(nucleotide, ps).generate(width, height,
randomSeed, gapPercentage, changePercentage);
System.out.println("arg0: n (for nucleotide) or p (for peptide)");
System.out.println("arg1: number of (non-gap) bases per sequence");
System.out.println("arg2: number of sequences");
- System.out
- .println("arg3: an integer as random seed (same seed = same results)");
+ System.out.println(
+ "arg3: an integer as random seed (same seed = same results)");
System.out.println("arg4: percentage of gaps to (randomly) generate");
- System.out
- .println("arg5: percentage of 'mutations' to (randomly) generate");
- System.out
- .println("arg6: (optional) path to output file (default is sysout)");
+ System.out.println(
+ "arg5: percentage of 'mutations' to (randomly) generate");
+ System.out.println(
+ "arg6: (optional) path to output file (default is sysout)");
System.out.println("Example: AlignmentGenerator n 12 15 387 10 5");
- System.out
- .println("- 15 nucleotide sequences of 12 bases each, approx 10% gaps and 5% mutations, random seed = 387");
+ System.out.println(
+ "- 15 nucleotide sequences of 12 bases each, approx 10% gaps and 5% mutations, random seed = 387");
}
for (int count = 0; count < length;)
{
boolean addGap = random.nextInt(100) < gapPercentage;
- char c = addGap ? GAP : BASES[random.nextInt(Integer.MAX_VALUE)
- % BASES.length];
+ char c = addGap ? GAP
+ : BASES[random.nextInt(Integer.MAX_VALUE) % BASES.length];
seq.append(c);
if (!addGap)
{
* @param changePercentage
* @return
*/
- private SequenceI generateAnotherSequence(char[] ds, int seqno,
- int width, int changePercentage)
+ private SequenceI generateAnotherSequence(char[] ds, int seqno, int width,
+ int changePercentage)
{
int length = ds.length;
char[] seq = new char[length];
* seq3 KD(-4), KD(3.0) average -0.5
* seq4 Helix(NaN) - should sort as if largest score
*/
- seq1.addSequenceFeature(new SequenceFeature("Cath", "", 2, 3, 2.0f,
- "g1"));
- seq1.addSequenceFeature(new SequenceFeature("Pfam", "", 4, 5, 4.0f,
- "g2"));
- seq2.addSequenceFeature(new SequenceFeature("Cath", "", 2, 3, 2.5f,
- "g3"));
- seq2.addSequenceFeature(new SequenceFeature("Metal", "", 2, 3,
- Float.NaN, "g4"));
+ seq1.addSequenceFeature(
+ new SequenceFeature("Cath", "", 2, 3, 2.0f, "g1"));
+ seq1.addSequenceFeature(
+ new SequenceFeature("Pfam", "", 4, 5, 4.0f, "g2"));
+ seq2.addSequenceFeature(
+ new SequenceFeature("Cath", "", 2, 3, 2.5f, "g3"));
+ seq2.addSequenceFeature(
+ new SequenceFeature("Metal", "", 2, 3, Float.NaN, "g4"));
seq3.addSequenceFeature(new SequenceFeature("kD", "", 2, 3, -4f, "g5"));
- seq3.addSequenceFeature(new SequenceFeature("kD", "", 5, 6, 3.0f, "g6"));
- seq4.addSequenceFeature(new SequenceFeature("Helix", "", 2, 3,
- Float.NaN, "g7"));
+ seq3.addSequenceFeature(
+ new SequenceFeature("kD", "", 5, 6, 3.0f, "g6"));
+ seq4.addSequenceFeature(
+ new SequenceFeature("Helix", "", 2, 3, Float.NaN, "g7"));
/*
* sort by ascending score, no filter on feature type or group
* seq3 average is now 3.0
* next sort is ascending (not toggled) as for a different group spec
*/
- List<String> groups = Arrays.asList(new String[] { "g1", "g2", "g3",
- "g6" });
+ List<String> groups = Arrays
+ .asList(new String[]
+ { "g1", "g2", "g3", "g6" });
AlignmentSorter.sortByFeature(types, groups, 0, al.getWidth(), al,
AlignmentSorter.FEATURE_SCORE);
assertSame(al.getSequenceAt(0), seq1); // 2.0
SequenceI s1 = ts.deriveSequence().getSubSequence(i, i + 7);
al.addSequence(s1);
}
- System.out.println(new AppletFormatAdapter().formatSequences(
- FileFormat.Clustal,
- al, true));
+ System.out.println(new AppletFormatAdapter()
+ .formatSequences(FileFormat.Clustal, al, true));
for (int flnk = -1; flnk < 25; flnk++)
{
AlignmentI exp = AlignmentUtils.expandContext(al, flnk);
System.out.println("\nFlank size: " + flnk);
- System.out.println(new AppletFormatAdapter().formatSequences(
- FileFormat.Clustal, exp, true));
+ System.out.println(new AppletFormatAdapter()
+ .formatSequences(FileFormat.Clustal, exp, true));
if (flnk == -1)
{
/*
{
String ung = sq.getSequenceAsString().replaceAll("-+", "");
final String errorMsg = "Flanking sequence not the same as original dataset sequence.\n"
- + ung
- + "\n"
+ + ung + "\n"
+ sq.getDatasetSequence().getSequenceAsString();
- assertTrue(errorMsg, ung.equalsIgnoreCase(sq.getDatasetSequence()
- .getSequenceAsString()));
+ assertTrue(errorMsg, ung.equalsIgnoreCase(
+ sq.getDatasetSequence().getSequenceAsString()));
}
}
else if (flnk == 24)
* Expand the subsequence to the full sequence abcDEFghi
*/
AlignmentI expanded = AlignmentUtils.expandContext(al, -1);
- assertEquals("abcDEFghi", expanded.getSequenceAt(0)
- .getSequenceAsString());
+ assertEquals("abcDEFghi",
+ expanded.getSequenceAt(0).getSequenceAsString());
/*
* Confirm the alignment and sequence have the same SS annotation,
protected AlignmentI loadAlignment(final String data, FileFormatI format)
throws IOException
{
- AlignmentI a = new FormatAdapter().readFile(data,
- DataSourceType.PASTE, format);
+ AlignmentI a = new FormatAdapter().readFile(data, DataSourceType.PASTE,
+ format);
a.setDataset(null);
return a;
}
MapList mapList = protMappings[0].getMap();
assertEquals(3, mapList.getFromRatio());
assertEquals(1, mapList.getToRatio());
- assertTrue(Arrays.equals(new int[] { 1, 9 }, mapList.getFromRanges()
- .get(0)));
+ assertTrue(
+ Arrays.equals(new int[]
+ { 1, 9 }, mapList.getFromRanges().get(0)));
assertEquals(1, mapList.getFromRanges().size());
- assertTrue(Arrays.equals(new int[] { 1, 3 },
- mapList.getToRanges().get(0)));
+ assertTrue(
+ Arrays.equals(new int[]
+ { 1, 3 }, mapList.getToRanges().get(0)));
assertEquals(1, mapList.getToRanges().size());
// V12346 mapped to A33333
* Exons at codon 2 (AAA) and 4 (TTT)
*/
MapList map = new MapList(new int[] { 4, 6, 10, 12 },
- new int[] { 1, 2 }, 3, 1);
+ new int[]
+ { 1, 2 }, 3, 1);
/*
* Simple case: no gaps in dna
/*
* Add gaps to dna - but ignore when realigning.
*/
- checkAlignSequenceAs("-G-G-G--A--A---AC-CC-T-TT-GG-G-", "--A-L-",
- false, false, map, "GGG---AAACCCTTTGGG");
+ checkAlignSequenceAs("-G-G-G--A--A---AC-CC-T-TT-GG-G-", "--A-L-", false,
+ false, map, "GGG---AAACCCTTTGGG");
/*
* Add gaps to dna - include within exons only when realigning.
*/
- checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-",
- true, false, map, "GGG---A--A---ACCCT-TTGGG");
+ checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-", true,
+ false, map, "GGG---A--A---ACCCT-TTGGG");
/*
* Include gaps outside exons only when realigning.
/*
* Include gaps following first intron if we are 'preserving mapped gaps'
*/
- checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-",
- true, true, map, "-G-G-G--A--A---A-C-CC-T-TT-GG-G-");
+ checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-", true,
+ true, map, "-G-G-G--A--A---A-C-CC-T-TT-GG-G-");
/*
* Include all gaps in dna when realigning.
*/
- checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-",
- true, true, map, "-G-G-G--A--A---A-C-CC-T-TT-GG-G-");
+ checkAlignSequenceAs("-G-G-G--A--A---A-C-CC-T-TT-GG-G-", "--A-L-", true,
+ true, map, "-G-G-G--A--A---A-C-CC-T-TT-GG-G-");
}
/**
/*
* Exons at codon 2 (AAA) and 4 (TTT) mapped to A and P
*/
- final MapList map = new MapList(new int[] { 4, 6, 10, 12 }, new int[] {
- 1, 1, 3, 3 }, 3, 1);
+ final MapList map = new MapList(new int[] { 4, 6, 10, 12 },
+ new int[]
+ { 1, 1, 3, 3 }, 3, 1);
/*
* -L- 'aligns' ccc------
SequenceI alignFrom = new Sequence("Seq2", alignModel);
alignFrom.createDatasetSequence();
AlignedCodonFrame acf = new AlignedCodonFrame();
- acf.addMap(alignMe.getDatasetSequence(),
- alignFrom.getDatasetSequence(), map);
+ acf.addMap(alignMe.getDatasetSequence(), alignFrom.getDatasetSequence(),
+ map);
AlignmentUtils.alignSequenceAs(alignMe, alignFrom, acf, "---", '-',
preserveMappedGaps, preserveUnmappedGaps);
/*
* Intron GGGAAA followed by exon CCCTTT
*/
- MapList map = new MapList(new int[] { 7, 12 }, new int[] { 1, 2 }, 3, 1);
+ MapList map = new MapList(new int[] { 7, 12 }, new int[] { 1, 2 }, 3,
+ 1);
checkAlignSequenceAs("GG-G-AA-A-C-CC-T-TT", "AL", false, true, map,
"GG-G-AA-ACCCTTT");
SequenceI prot2 = new Sequence("Seq2", "CHYQ");
SequenceI prot3 = new Sequence("Seq3", "CHYQ");
SequenceI prot4 = new Sequence("Seq4", "R-QSV"); // unmapped, unchanged
- AlignmentI protein = new Alignment(new SequenceI[] { prot1, prot2,
- prot3, prot4 });
+ AlignmentI protein = new Alignment(
+ new SequenceI[]
+ { prot1, prot2, prot3, prot4 });
protein.setDataset(null);
- MapList map = new MapList(new int[] { 1, 12 }, new int[] { 1, 4 }, 3, 1);
+ MapList map = new MapList(new int[] { 1, 12 }, new int[] { 1, 4 }, 3,
+ 1);
AlignedCodonFrame acf = new AlignedCodonFrame();
acf.addMap(dna1.getDatasetSequence(), prot1.getDatasetSequence(), map);
acf.addMap(dna2.getDatasetSequence(), prot2.getDatasetSequence(), map);
"F*PK*G".toCharArray()));
// wrong protein
- assertFalse(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(),
- 0, "FPMG".toCharArray()));
+ assertFalse(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(), 0,
+ "FPMG".toCharArray()));
// truncated dna
assertFalse(AlignmentUtils.translatesAs("tttcccaaagg".toCharArray(), 0,
"FPKG".toCharArray()));
// truncated protein
- assertFalse(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(),
- 0, "FPK".toCharArray()));
+ assertFalse(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(), 0,
+ "FPK".toCharArray()));
// overlong dna (doesn't end in stop codon)
- assertFalse(AlignmentUtils.translatesAs(
- "tttcccaaagggttt".toCharArray(), 0, "FPKG".toCharArray()));
+ assertFalse(AlignmentUtils.translatesAs("tttcccaaagggttt".toCharArray(),
+ 0, "FPKG".toCharArray()));
// dna + stop codon + more
assertFalse(AlignmentUtils.translatesAs(
"tttcccaaagggttaga".toCharArray(), 0, "FPKG".toCharArray()));
// overlong protein
- assertFalse(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(),
- 0, "FPKGQ".toCharArray()));
+ assertFalse(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(), 0,
+ "FPKGQ".toCharArray()));
}
/**
MapList mapList = protMappings[0].getMap();
assertEquals(3, mapList.getFromRatio());
assertEquals(1, mapList.getToRatio());
- assertTrue(Arrays.equals(new int[] { 1, 9 }, mapList.getFromRanges()
- .get(0)));
+ assertTrue(
+ Arrays.equals(new int[]
+ { 1, 9 }, mapList.getFromRanges().get(0)));
assertEquals(1, mapList.getFromRanges().size());
- assertTrue(Arrays.equals(new int[] { 1, 3 },
- mapList.getToRanges().get(0)));
+ assertTrue(
+ Arrays.equals(new int[]
+ { 1, 3 }, mapList.getToRanges().get(0)));
assertEquals(1, mapList.getToRanges().size());
// V12346 mapped from A33333 starting position 4
mapList = protMappings[0].getMap();
assertEquals(3, mapList.getFromRatio());
assertEquals(1, mapList.getToRatio());
- assertTrue(Arrays.equals(new int[] { 4, 12 }, mapList.getFromRanges()
- .get(0)));
+ assertTrue(
+ Arrays.equals(new int[]
+ { 4, 12 }, mapList.getFromRanges().get(0)));
assertEquals(1, mapList.getFromRanges().size());
- assertTrue(Arrays.equals(new int[] { 1, 3 },
- mapList.getToRanges().get(0)));
+ assertTrue(
+ Arrays.equals(new int[]
+ { 1, 3 }, mapList.getToRanges().get(0)));
assertEquals(1, mapList.getToRanges().size());
// V12347 mapped to A11111 starting position 4
mapList = protMappings[0].getMap();
assertEquals(3, mapList.getFromRatio());
assertEquals(1, mapList.getToRatio());
- assertTrue(Arrays.equals(new int[] { 4, 12 }, mapList.getFromRanges()
- .get(0)));
+ assertTrue(
+ Arrays.equals(new int[]
+ { 4, 12 }, mapList.getFromRanges().get(0)));
assertEquals(1, mapList.getFromRanges().size());
- assertTrue(Arrays.equals(new int[] { 1, 3 },
- mapList.getToRanges().get(0)));
+ assertTrue(
+ Arrays.equals(new int[]
+ { 1, 3 }, mapList.getToRanges().get(0)));
assertEquals(1, mapList.getToRanges().size());
// no mapping involving the 'extra' A44444
List<SequenceI> dnaseqs = new ArrayList<>();
dnaseqs.add(new Sequence("EMBL|A11111", "GAAATCCAG")); // = EIQ
dnaseqs.add(new Sequence("EMBL|A22222", "GAAATTCAG")); // = EIQ
- AlignmentI cdna = new Alignment(dnaseqs.toArray(new SequenceI[dnaseqs
- .size()]));
+ AlignmentI cdna = new Alignment(
+ dnaseqs.toArray(new SequenceI[dnaseqs.size()]));
cdna.setDataset(null);
// Xref A22222 to V12345 (should get mapped)
ann2.setSequenceRef(seq2);
AlignmentAnnotation ann3 = new AlignmentAnnotation("Structure", "ann3",
anns);
- AlignmentAnnotation ann4 = new AlignmentAnnotation("Temp", "ann4", anns);
+ AlignmentAnnotation ann4 = new AlignmentAnnotation("Temp", "ann4",
+ anns);
ann4.setSequenceRef(seq1);
- AlignmentAnnotation ann5 = new AlignmentAnnotation("Temp", "ann5", anns);
+ AlignmentAnnotation ann5 = new AlignmentAnnotation("Temp", "ann5",
+ anns);
ann5.setSequenceRef(seq2);
- AlignmentAnnotation ann6 = new AlignmentAnnotation("Temp", "ann6", anns);
+ AlignmentAnnotation ann6 = new AlignmentAnnotation("Temp", "ann6",
+ anns);
AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2, seq3 });
al.addAnnotation(ann1); // Structure for Seq1
al.addAnnotation(ann2); // Structure for Seq2
assertTrue(AlignmentUtils.haveCrossRef(seq2, seq1));
// now the other way round
- seq1.setDBRefs(null);
+ seq1.setDBRefs(null);
seq2.addDBRef(new DBRefEntry("EMBL", "1", "A12345"));
assertTrue(AlignmentUtils.haveCrossRef(seq1, seq2));
assertTrue(AlignmentUtils.haveCrossRef(seq2, seq1));
* put a variant feature on dna2 base 8
* - should transfer to cds2 base 5
*/
- dna2.addSequenceFeature(new SequenceFeature("variant", "hgmd", 8, 8,
- 0f, null));
+ dna2.addSequenceFeature(
+ new SequenceFeature("variant", "hgmd", 8, 8, 0f, null));
/*
* need a sourceDbRef if we are to construct dbrefs to the CDS
* CDS sequences are 'discovered' from dna-to-protein mappings on the alignment
* dataset (e.g. added from dbrefs by CrossRef.findXrefSequences)
*/
- MapList mapfordna1 = new MapList(new int[] { 4, 6, 10, 12 }, new int[] {
- 1, 2 }, 3, 1);
+ MapList mapfordna1 = new MapList(new int[] { 4, 6, 10, 12 },
+ new int[]
+ { 1, 2 }, 3, 1);
AlignedCodonFrame acf = new AlignedCodonFrame();
acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(),
mapfordna1);
dna.addCodonFrame(acf);
MapList mapfordna2 = new MapList(new int[] { 1, 3, 7, 9, 13, 15 },
- new int[] { 1, 3 }, 3, 1);
+ new int[]
+ { 1, 3 }, 3, 1);
acf = new AlignedCodonFrame();
acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(),
mapfordna2);
/*
* execute method under test:
*/
- AlignmentI cds = AlignmentUtils.makeCdsAlignment(new SequenceI[] {
- dna1, dna2 }, dna.getDataset(), null);
+ AlignmentI cds = AlignmentUtils
+ .makeCdsAlignment(new SequenceI[]
+ { dna1, dna2 }, dna.getDataset(), null);
/*
* verify cds sequences
assertEquals(dna1xref.getAccessionId(), dbref.getAccessionId());
assertNotNull(dbref.getMap());
assertSame(pep1.getDatasetSequence(), dbref.getMap().getTo());
- MapList cdsMapping = new MapList(new int[] { 1, 6 },
- new int[] { 1, 2 }, 3, 1);
+ MapList cdsMapping = new MapList(new int[] { 1, 6 }, new int[] { 1, 2 },
+ 3, 1);
assertEquals(cdsMapping, dbref.getMap().getMap());
/*
DBRefEntry dbRefEntry = dna1.getDBRefs().get(2);
assertSame(cds1Dss, dbRefEntry.getMap().getTo());
MapList dnaToCdsMapping = new MapList(new int[] { 4, 6, 10, 12 },
- new int[] { 1, 6 }, 1, 1);
+ new int[]
+ { 1, 6 }, 1, 1);
assertEquals(dnaToCdsMapping, dbRefEntry.getMap().getMap());
assertEquals(3, dna2.getDBRefs().size());
dbRefEntry = dna2.getDBRefs().get(2);
assertSame(cds2Dss, dbRefEntry.getMap().getTo());
dnaToCdsMapping = new MapList(new int[] { 1, 3, 7, 9, 13, 15 },
- new int[] { 1, 9 }, 1, 1);
+ new int[]
+ { 1, 9 }, 1, 1);
assertEquals(dnaToCdsMapping, dbRefEntry.getMap().getMap());
/*
assertEquals(2, cds1Dss.getDBRefs().size());
dbRefEntry = cds1Dss.getDBRefs().get(1);
assertSame(dna1.getDatasetSequence(), dbRefEntry.getMap().getTo());
- MapList cdsToDnaMapping = new MapList(new int[] { 1, 6 }, new int[] {
- 4, 6, 10, 12 }, 1, 1);
+ MapList cdsToDnaMapping = new MapList(new int[] { 1, 6 },
+ new int[]
+ { 4, 6, 10, 12 }, 1, 1);
assertEquals(cdsToDnaMapping, dbRefEntry.getMap().getMap());
assertEquals(2, cds2Dss.getDBRefs().size());
dbRefEntry = cds2Dss.getDBRefs().get(1);
assertSame(dna2.getDatasetSequence(), dbRefEntry.getMap().getTo());
- cdsToDnaMapping = new MapList(new int[] { 1, 9 }, new int[] { 1, 3, 7,
- 9, 13, 15 }, 1, 1);
+ cdsToDnaMapping = new MapList(new int[] { 1, 9 },
+ new int[]
+ { 1, 3, 7, 9, 13, 15 }, 1, 1);
assertEquals(cdsToDnaMapping, dbRefEntry.getMap().getMap());
/*
pep1.createDatasetSequence();
pep2.createDatasetSequence();
pep3.createDatasetSequence();
- pep1.getDatasetSequence().addDBRef(
- new DBRefEntry("EMBLCDS", "2", "A12345"));
- pep2.getDatasetSequence().addDBRef(
- new DBRefEntry("EMBLCDS", "3", "A12346"));
- pep3.getDatasetSequence().addDBRef(
- new DBRefEntry("EMBLCDS", "4", "A12347"));
+ pep1.getDatasetSequence()
+ .addDBRef(new DBRefEntry("EMBLCDS", "2", "A12345"));
+ pep2.getDatasetSequence()
+ .addDBRef(new DBRefEntry("EMBLCDS", "3", "A12346"));
+ pep3.getDatasetSequence()
+ .addDBRef(new DBRefEntry("EMBLCDS", "4", "A12347"));
/*
* Create the CDS alignment
*/
// map ...GGG...TTT to GF
MapList map = new MapList(new int[] { 4, 6, 10, 12 },
- new int[] { 1, 2 }, 3, 1);
+ new int[]
+ { 1, 2 }, 3, 1);
AlignedCodonFrame acf = new AlignedCodonFrame();
acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map);
dna.addCodonFrame(acf);
/*
* execute method under test
*/
- AlignmentI cdsal = AlignmentUtils.makeCdsAlignment(
- new SequenceI[] { dna1 }, dna.getDataset(), null);
+ AlignmentI cdsal = AlignmentUtils
+ .makeCdsAlignment(new SequenceI[]
+ { dna1 }, dna.getDataset(), null);
/*
* Verify we have 3 cds sequences, mapped to pep1/2/3 respectively
.findMappingsForSequence(pep1, dnaMappings);
assertEquals(1, mappings.size());
assertEquals(1, mappings.get(0).getMappings().size());
- assertSame(pep1.getDatasetSequence(), mappings.get(0).getMappings()
- .get(0).getMapping().getTo());
+ assertSame(pep1.getDatasetSequence(),
+ mappings.get(0).getMappings().get(0).getMapping().getTo());
/*
* dna1 to cds1
Mapping mapping = dnaToCds1Mappings.get(0).getMappings().get(0)
.getMapping();
assertSame(cds.get(0).getDatasetSequence(), mapping.getTo());
- assertEquals("G(1) in CDS should map to G(4) in DNA", 4, mapping
- .getMap().getToPosition(1));
+ assertEquals("G(1) in CDS should map to G(4) in DNA", 4,
+ mapping.getMap().getToPosition(1));
/*
* dna1 to pep2
mappings = MappingUtils.findMappingsForSequence(pep2, dnaMappings);
assertEquals(1, mappings.size());
assertEquals(1, mappings.get(0).getMappings().size());
- assertSame(pep2.getDatasetSequence(), mappings.get(0).getMappings()
- .get(0).getMapping().getTo());
+ assertSame(pep2.getDatasetSequence(),
+ mappings.get(0).getMappings().get(0).getMapping().getTo());
/*
* dna1 to cds2
.findMappingsForSequence(cds.get(1), dnaMappings);
mapping = dnaToCds2Mappings.get(0).getMappings().get(0).getMapping();
assertSame(cds.get(1).getDatasetSequence(), mapping.getTo());
- assertEquals("c(4) in CDS should map to c(7) in DNA", 7, mapping
- .getMap().getToPosition(4));
+ assertEquals("c(4) in CDS should map to c(7) in DNA", 7,
+ mapping.getMap().getToPosition(4));
/*
* dna1 to pep3
mappings = MappingUtils.findMappingsForSequence(pep3, dnaMappings);
assertEquals(1, mappings.size());
assertEquals(1, mappings.get(0).getMappings().size());
- assertSame(pep3.getDatasetSequence(), mappings.get(0).getMappings()
- .get(0).getMapping().getTo());
+ assertSame(pep3.getDatasetSequence(),
+ mappings.get(0).getMappings().get(0).getMapping().getTo());
/*
* dna1 to cds3
.findMappingsForSequence(cds.get(2), dnaMappings);
mapping = dnaToCds3Mappings.get(0).getMappings().get(0).getMapping();
assertSame(cds.get(2).getDatasetSequence(), mapping.getTo());
- assertEquals("T(4) in CDS should map to T(10) in DNA", 10, mapping
- .getMap().getToPosition(4));
+ assertEquals("T(4) in CDS should map to T(10) in DNA", 10,
+ mapping.getMap().getToPosition(4));
}
@Test(groups = { "Functional" })
AlignedCodonFrame acf = new AlignedCodonFrame();
// this is like a domain or motif match of part of a peptide sequence
- MapList map = new MapList(new int[] { 6, 12 }, new int[] { 1, 7 }, 1, 1);
- acf.addMap(alignFrom.getDatasetSequence(),
- alignMe.getDatasetSequence(), map);
+ MapList map = new MapList(new int[] { 6, 12 }, new int[] { 1, 7 }, 1,
+ 1);
+ acf.addMap(alignFrom.getDatasetSequence(), alignMe.getDatasetSequence(),
+ map);
AlignmentUtils.alignSequenceAs(alignMe, alignFrom, acf, "-", '-', true,
true);
SequenceI cds = new Sequence("cds/10-15", "TAGGCC");
// no overlap
- dna.addSequenceFeature(new SequenceFeature("type1", "desc1", 1, 2, 1f,
- null));
+ dna.addSequenceFeature(
+ new SequenceFeature("type1", "desc1", 1, 2, 1f, null));
// partial overlap - to [1, 1]
- dna.addSequenceFeature(new SequenceFeature("type2", "desc2", 3, 4, 2f,
- null));
+ dna.addSequenceFeature(
+ new SequenceFeature("type2", "desc2", 3, 4, 2f, null));
// exact overlap - to [1, 3]
- dna.addSequenceFeature(new SequenceFeature("type3", "desc3", 4, 6, 3f,
- null));
+ dna.addSequenceFeature(
+ new SequenceFeature("type3", "desc3", 4, 6, 3f, null));
// spanning overlap - to [2, 5]
- dna.addSequenceFeature(new SequenceFeature("type4", "desc4", 5, 11, 4f,
- null));
+ dna.addSequenceFeature(
+ new SequenceFeature("type4", "desc4", 5, 11, 4f, null));
// exactly overlaps whole mapped range [1, 6]
- dna.addSequenceFeature(new SequenceFeature("type5", "desc5", 4, 12, 5f,
- null));
+ dna.addSequenceFeature(
+ new SequenceFeature("type5", "desc5", 4, 12, 5f, null));
// no overlap (internal)
- dna.addSequenceFeature(new SequenceFeature("type6", "desc6", 7, 9, 6f,
- null));
+ dna.addSequenceFeature(
+ new SequenceFeature("type6", "desc6", 7, 9, 6f, null));
// no overlap (3' end)
- dna.addSequenceFeature(new SequenceFeature("type7", "desc7", 13, 15,
- 7f, null));
+ dna.addSequenceFeature(
+ new SequenceFeature("type7", "desc7", 13, 15, 7f, null));
// overlap (3' end) - to [6, 6]
- dna.addSequenceFeature(new SequenceFeature("type8", "desc8", 12, 12,
- 8f, null));
+ dna.addSequenceFeature(
+ new SequenceFeature("type8", "desc8", 12, 12, 8f, null));
// extended overlap - to [6, +]
- dna.addSequenceFeature(new SequenceFeature("type9", "desc9", 12, 13,
- 9f, null));
+ dna.addSequenceFeature(
+ new SequenceFeature("type9", "desc9", 12, 13, 9f, null));
MapList map = new MapList(new int[] { 4, 6, 10, 12 },
- new int[] { 1, 6 }, 1, 1);
+ new int[]
+ { 1, 6 }, 1, 1);
/*
* transferFeatures() will build 'partial overlap' for regions
SequenceI cds = new Sequence("cds/10-15", "TAGGCC");
MapList map = new MapList(new int[] { 4, 6, 10, 12 },
- new int[] { 1, 6 }, 1, 1);
+ new int[]
+ { 1, 6 }, 1, 1);
// [5, 11] maps to [2, 5]
- dna.addSequenceFeature(new SequenceFeature("type4", "desc4", 5, 11, 4f,
- null));
+ dna.addSequenceFeature(
+ new SequenceFeature("type4", "desc4", 5, 11, 4f, null));
// [4, 12] maps to [1, 6]
- dna.addSequenceFeature(new SequenceFeature("type5", "desc5", 4, 12, 5f,
- null));
+ dna.addSequenceFeature(
+ new SequenceFeature("type5", "desc5", 4, 12, 5f, null));
// [12, 12] maps to [6, 6]
- dna.addSequenceFeature(new SequenceFeature("type8", "desc8", 12, 12,
- 8f, null));
+ dna.addSequenceFeature(
+ new SequenceFeature("type8", "desc8", 12, 12, 8f, null));
// desc4 and desc8 are the 'omit these' varargs
AlignmentUtils.transferFeatures(dna, cds, map, null, "type4", "type8");
SequenceI cds = new Sequence("cds/10-15", "TAGGCC");
MapList map = new MapList(new int[] { 4, 6, 10, 12 },
- new int[] { 1, 6 }, 1, 1);
+ new int[]
+ { 1, 6 }, 1, 1);
// [5, 11] maps to [2, 5]
- dna.addSequenceFeature(new SequenceFeature("type4", "desc4", 5, 11, 4f,
- null));
+ dna.addSequenceFeature(
+ new SequenceFeature("type4", "desc4", 5, 11, 4f, null));
// [4, 12] maps to [1, 6]
- dna.addSequenceFeature(new SequenceFeature("type5", "desc5", 4, 12, 5f,
- null));
+ dna.addSequenceFeature(
+ new SequenceFeature("type5", "desc5", 4, 12, 5f, null));
// [12, 12] maps to [6, 6]
- dna.addSequenceFeature(new SequenceFeature("type8", "desc8", 12, 12,
- 8f, null));
+ dna.addSequenceFeature(
+ new SequenceFeature("type8", "desc8", 12, 12, 8f, null));
// "type5" is the 'select this type' argument
AlignmentUtils.transferFeatures(dna, cds, map, "type5");
dna.setDataset(null);
MapList map = new MapList(new int[] { 4, 12, 16, 18 },
- new int[] { 1, 4 }, 3, 1);
+ new int[]
+ { 1, 4 }, 3, 1);
AlignedCodonFrame acf = new AlignedCodonFrame();
acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map);
dna.addCodonFrame(acf);
map = new MapList(new int[] { 4, 8, 12, 12, 16, 18 },
- new int[] { 1, 3 }, 3, 1);
+ new int[]
+ { 1, 3 }, 3, 1);
acf = new AlignedCodonFrame();
acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(), map);
dna.addCodonFrame(acf);
- AlignmentI cds = AlignmentUtils.makeCdsAlignment(new SequenceI[] {
- dna1, dna2, dna3 }, dna.getDataset(), null);
+ AlignmentI cds = AlignmentUtils
+ .makeCdsAlignment(new SequenceI[]
+ { dna1, dna2, dna3 }, dna.getDataset(), null);
List<SequenceI> cdsSeqs = cds.getSequences();
assertEquals(2, cdsSeqs.size());
assertEquals("GGGCCCTTTGGG", cdsSeqs.get(0).getSequenceAsString());
pep1CdsMappings);
assertEquals(1, sr.getResults().size());
SearchResultMatchI m = sr.getResults().get(0);
- assertEquals(cds.getSequenceAt(0).getDatasetSequence(), m.getSequence());
+ assertEquals(cds.getSequenceAt(0).getDatasetSequence(),
+ m.getSequence());
assertEquals(1, m.getStart());
assertEquals(3, m.getEnd());
sr = MappingUtils.buildSearchResults(pep1, 2, pep1CdsMappings);
sr = MappingUtils.buildSearchResults(pep2, 1, pep2CdsMappings);
assertEquals(1, sr.getResults().size());
m = sr.getResults().get(0);
- assertEquals(cds.getSequenceAt(1).getDatasetSequence(), m.getSequence());
+ assertEquals(cds.getSequenceAt(1).getDatasetSequence(),
+ m.getSequence());
assertEquals(1, m.getStart());
assertEquals(3, m.getEnd());
sr = MappingUtils.buildSearchResults(pep2, 2, pep2CdsMappings);
SequenceI prot1 = new Sequence("Seq1", "XKFG"); // X for incomplete start
SequenceI prot2 = new Sequence("Seq2", "NG");
SequenceI prot3 = new Sequence("Seq3", "XG"); // X for incomplete start
- AlignmentI protein = new Alignment(new SequenceI[] { prot1, prot2,
- prot3 });
+ AlignmentI protein = new Alignment(
+ new SequenceI[]
+ { prot1, prot2, prot3 });
protein.setDataset(null);
// map dna1 [3, 11] to prot1 [2, 4] KFG
- MapList map = new MapList(new int[] { 3, 11 }, new int[] { 2, 4 }, 3, 1);
+ MapList map = new MapList(new int[] { 3, 11 }, new int[] { 2, 4 }, 3,
+ 1);
AlignedCodonFrame acf = new AlignedCodonFrame();
acf.addMap(dna1.getDatasetSequence(), prot1.getDatasetSequence(), map);
dna.addCodonFrame(acf);
AlignmentUtils.alignAs(cds, dna);
assertEquals("---GGGTTT", cds.getSequenceAt(0).getSequenceAsString());
- assertEquals("CCC------AAA", cds.getSequenceAt(1).getSequenceAsString());
+ assertEquals("CCC------AAA",
+ cds.getSequenceAt(1).getSequenceAsString());
}
@Test(groups = { "Functional" })
SequenceI seq1 = new Sequence("cds", "AAATTT");
from.createDatasetSequence();
seq1.createDatasetSequence();
- Mapping mapping = new Mapping(seq1, new MapList(
- new int[] { 3, 6, 9, 10 }, new int[] { 1, 6 }, 1, 1));
+ Mapping mapping = new Mapping(seq1,
+ new MapList(new int[]
+ { 3, 6, 9, 10 }, new int[] { 1, 6 }, 1, 1));
Map<Integer, Map<SequenceI, Character>> map = new TreeMap<>();
AlignmentUtils.addMappedPositions(seq1, from, mapping, map);
SequenceI seq1 = new Sequence("cds", "AAATTT");
from.createDatasetSequence();
seq1.createDatasetSequence();
- Mapping mapping = new Mapping(seq1, new MapList(
- new int[] { 3, 6, 9, 10 }, new int[] { 1, 6 }, 1, 1));
+ Mapping mapping = new Mapping(seq1,
+ new MapList(new int[]
+ { 3, 6, 9, 10 }, new int[] { 1, 6 }, 1, 1));
Map<Integer, Map<SequenceI, Character>> map = new TreeMap<>();
AlignmentUtils.addMappedPositions(seq1, from, mapping, map);
AlignedCodonFrame acf = new AlignedCodonFrame();
MapList map = new MapList(new int[] { 4, 6, 10, 12 },
- new int[] { 1, 2 }, 3, 1);
+ new int[]
+ { 1, 2 }, 3, 1);
acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map);
acf.addMap(dna1.getDatasetSequence(), pep3.getDatasetSequence(), map);
dna.addCodonFrame(acf);
/*
* execute method under test to find CDS for EMBL peptides only
*/
- AlignmentI cds = AlignmentUtils.makeCdsAlignment(new SequenceI[] {
- dna1, dna2 }, dna.getDataset(), emblPeptides.getSequencesArray());
+ AlignmentI cds = AlignmentUtils
+ .makeCdsAlignment(new SequenceI[]
+ { dna1, dna2 }, dna.getDataset(),
+ emblPeptides.getSequencesArray());
assertEquals(2, cds.getSequences().size());
assertEquals("GGGTTT", cds.getSequenceAt(0).getSequenceAsString());
*/
assertTrue(AlignmentUtils.alignAsSameSequences(al1, al2));
String aligned1 = "-cc-GG-GTTT-aaa";
- assertEquals(aligned1,
- al1.getSequenceAt(0).getSequenceAsString());
+ assertEquals(aligned1, al1.getSequenceAt(0).getSequenceAsString());
String aligned2 = "C--C-Cgg-gtttAAA";
- assertEquals(aligned2,
- al1.getSequenceAt(1).getSequenceAsString());
+ assertEquals(aligned2, al1.getSequenceAt(1).getSequenceAsString());
/*
* add another sequence to 'aligned' - should still succeed, since
SequenceI uas1 = dna1.deriveSequence();
SequenceI uas2 = dna1.deriveSequence().getSubSequence(3, 7);
SequenceI uas3 = dna2.deriveSequence();
- AlignmentI tobealigned = new Alignment(new SequenceI[] { uas1, uas2,
- uas3 });
+ AlignmentI tobealigned = new Alignment(
+ new SequenceI[]
+ { uas1, uas2, uas3 });
((Alignment) tobealigned).createDatasetAlignment();
/*
SequenceI pep1 = new Sequence("pep1", "MLS");
pep1.createDatasetSequence();
List<AlignedCodonFrame> seqMappings = new ArrayList<>();
- MapList mapList = new MapList(
+ MapList mapList = new MapList(new int[] { 5, 6, 9, 15 },
new int[]
- { 5, 6, 9, 15 }, new int[] { 1, 3 }, 3, 1);
+ { 1, 3 }, 3, 1);
Mapping dnaToPeptide = new Mapping(pep1.getDatasetSequence(), mapList);
-
+
// add dna to peptide mapping
seqMappings.add(acf1);
acf1.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(),
// need to tidy up use of lists of mappings in AlignedCodonFrame
AlignedCodonFrame acf2 = new AlignedCodonFrame();
mappings.add(acf2);
- MapList cdsToPeptideMapping = new MapList(new int[]
- { 1, 9 }, new int[] { 1, 3 }, 3, 1);
+ MapList cdsToPeptideMapping = new MapList(new int[] { 1, 9 },
+ new int[]
+ { 1, 3 }, 3, 1);
acf2.addMap(cds1.getDatasetSequence(), pep1.getDatasetSequence(),
cdsToPeptideMapping);
assertNull(AlignmentUtils.findCdsForProtein(mappings, dna1, seqMappings,
List<AlignedCodonFrame> mappings = new ArrayList<>();
AlignedCodonFrame acf1 = new AlignedCodonFrame();
mappings.add(acf1);
-
+
SequenceI dna1 = new Sequence("dna1", "ATGCTATCTTAA");
dna1.createDatasetSequence();
-
+
// NB we currently exclude STOP codon from CDS sequences
// the test would need to change if this changes in future
SequenceI cds1 = new Sequence("cds1", "ATGCTATCT");
cds1.createDatasetSequence();
-
+
SequenceI pep1 = new Sequence("pep1", "MLS");
pep1.createDatasetSequence();
List<AlignedCodonFrame> seqMappings = new ArrayList<>();
- MapList mapList = new MapList(
- new int[]
- { 1, 9 }, new int[] { 1, 3 }, 3, 1);
+ MapList mapList = new MapList(new int[] { 1, 9 }, new int[] { 1, 3 }, 3,
+ 1);
Mapping dnaToPeptide = new Mapping(pep1.getDatasetSequence(), mapList);
-
+
// add dna to peptide mapping
seqMappings.add(acf1);
acf1.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(),
mapList);
-
+
/*
* first case - transcript lacks CDS features - it appears to be
* the CDS sequence and is returned
SequenceI seq = AlignmentUtils.findCdsForProtein(mappings, dna1,
seqMappings, dnaToPeptide);
assertSame(seq, dna1.getDatasetSequence());
-
+
/*
* second case - transcript has CDS feature - this means it is
* not returned as a match for CDS (CDS sequences don't have CDS features)
// need to tidy up use of lists of mappings in AlignedCodonFrame
AlignedCodonFrame acf2 = new AlignedCodonFrame();
mappings.add(acf2);
- MapList cdsToPeptideMapping = new MapList(new int[]
- { 1, 9 }, new int[] { 1, 3 }, 3, 1);
+ MapList cdsToPeptideMapping = new MapList(new int[] { 1, 9 },
+ new int[]
+ { 1, 3 }, 3, 1);
acf2.addMap(cds1.getDatasetSequence(), pep1.getDatasetSequence(),
cdsToPeptideMapping);
assertNull(AlignmentUtils.findCdsForProtein(mappings, dna1, seqMappings,
dnaToPeptide));
-
+
/*
* fourth case - add dna-to-CDS mapping - CDS is now found!
*/
testee.sort(annotations, SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
long endTime = System.currentTimeMillis();
final long elapsed = endTime - startTime;
- System.out.println("Timing test for presorted " + numSeqs
- + " sequences and " + numAnns + " annotations took " + elapsed
- + "ms");
+ System.out.println(
+ "Timing test for presorted " + numSeqs + " sequences and "
+ + numAnns + " annotations took " + elapsed + "ms");
}
/**
testee.sort(annotations, SequenceAnnotationOrder.SEQUENCE_AND_LABEL);
long endTime = System.currentTimeMillis();
final long elapsed = endTime - startTime;
- System.out.println("Timing test for unsorted " + numSeqs
- + " sequences and " + numAnns + " annotations took " + elapsed
- + "ms");
+ System.out.println(
+ "Timing test for unsorted " + numSeqs + " sequences and "
+ + numAnns + " annotations took " + elapsed + "ms");
}
/**
Alignment alignment = buildAlignment(numSeqs);
AlignmentAnnotation[] annotations = buildAnnotations(numAnns);
- String[] labels = new String[] { "label1", "label2", "label3",
- "label4", "label5", "label6" };
+ String[] labels = new String[] { "label1", "label2", "label3", "label4",
+ "label5", "label6" };
/*
* Set the annotations in sequence order with randomly assigned labels.
testee.sort(annotations, SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
long endTime = System.currentTimeMillis();
long elapsed = endTime - startTime;
- System.out.println("Sort by label for semisorted " + numSeqs
- + " sequences and " + numAnns + " annotations took " + elapsed
- + "ms");
+ System.out.println(
+ "Sort by label for semisorted " + numSeqs + " sequences and "
+ + numAnns + " annotations took " + elapsed + "ms");
// now resort by sequence
startTime = System.currentTimeMillis();
testee.sort(annotations, SequenceAnnotationOrder.LABEL_AND_SEQUENCE);
endTime = System.currentTimeMillis();
elapsed = endTime - startTime;
- System.out.println("Resort by label for semisorted " + numSeqs
- + " sequences and " + numAnns + " annotations took " + elapsed
- + "ms");
+ System.out.println(
+ "Resort by label for semisorted " + numSeqs + " sequences and "
+ + numAnns + " annotations took " + elapsed + "ms");
}
}
@Test(groups = { "Functional" })
public void testDecodeCodon()
{
- assertTrue(Arrays.equals(new char[] { 'A', 'A', 'A' },
- CodingUtils.decodeCodon(0)));
- assertTrue(Arrays.equals(new char[] { 'A', 'A', 'C' },
- CodingUtils.decodeCodon(1)));
- assertTrue(Arrays.equals(new char[] { 'A', 'A', 'G' },
- CodingUtils.decodeCodon(2)));
- assertTrue(Arrays.equals(new char[] { 'A', 'A', 'T' },
- CodingUtils.decodeCodon(3)));
- assertTrue(Arrays.equals(new char[] { 'A', 'C', 'A' },
- CodingUtils.decodeCodon(4)));
- assertTrue(Arrays.equals(new char[] { 'C', 'A', 'A' },
- CodingUtils.decodeCodon(16)));
- assertTrue(Arrays.equals(new char[] { 'G', 'G', 'G' },
- CodingUtils.decodeCodon(42)));
- assertTrue(Arrays.equals(new char[] { 'T', 'T', 'T' },
- CodingUtils.decodeCodon(63)));
+ assertTrue(
+ Arrays.equals(new char[]
+ { 'A', 'A', 'A' }, CodingUtils.decodeCodon(0)));
+ assertTrue(
+ Arrays.equals(new char[]
+ { 'A', 'A', 'C' }, CodingUtils.decodeCodon(1)));
+ assertTrue(
+ Arrays.equals(new char[]
+ { 'A', 'A', 'G' }, CodingUtils.decodeCodon(2)));
+ assertTrue(
+ Arrays.equals(new char[]
+ { 'A', 'A', 'T' }, CodingUtils.decodeCodon(3)));
+ assertTrue(
+ Arrays.equals(new char[]
+ { 'A', 'C', 'A' }, CodingUtils.decodeCodon(4)));
+ assertTrue(
+ Arrays.equals(new char[]
+ { 'C', 'A', 'A' }, CodingUtils.decodeCodon(16)));
+ assertTrue(
+ Arrays.equals(new char[]
+ { 'G', 'G', 'G' }, CodingUtils.decodeCodon(42)));
+ assertTrue(
+ Arrays.equals(new char[]
+ { 'T', 'T', 'T' }, CodingUtils.decodeCodon(63)));
}
@Test(groups = { "Functional" })
seqs.add(new Sequence("seq3", "V-IW-"));
seqs.add(new Sequence("seq4", "VGLH-"));
seqs.add(new Sequence("seq5", "VGLH-"));
-
+
/*
* threshold 50% means a residue has to occur 3 or more times
* in a column to be counted for conservation
// but it is treated as percentage threshold in calculate() ?
Conservation cons = new Conservation("", 50, seqs, 0, 4);
cons.calculate();
-
+
/*
* column 0: all V (hydrophobic/aliphatic/small)
*/
assertEquals(colCons.get("polar").intValue(), 0);
assertEquals(colCons.get("positive").intValue(), 0);
assertEquals(colCons.get("aromatic").intValue(), 0);
-
+
/*
* column 1: all G (hydrophobic/small/tiny)
* gaps are ignored as not above threshold
assertEquals(colCons.get("polar").intValue(), 0);
assertEquals(colCons.get("positive").intValue(), 0);
assertEquals(colCons.get("aromatic").intValue(), 0);
-
+
/*
* column 2: I/L (aliphatic/hydrophobic), all others negatively conserved
*/
assertEquals(colCons.get("polar").intValue(), 0);
assertEquals(colCons.get("positive").intValue(), 0);
assertEquals(colCons.get("aromatic").intValue(), 0);
-
+
/*
* column 3: nothing above threshold
*/
colCons = cons.total[3];
assertTrue(colCons.isEmpty());
-
+
/*
* column 4: all gaps - counted as having all properties
*/
* verify tooltips; conserved properties are sorted alphabetically within
* positive followed by negative
*/
- assertEquals(
- cons.getTooltip(0),
+ assertEquals(cons.getTooltip(0),
"aliphatic hydrophobic small !aromatic !charged !negative !polar !positive !proline !tiny");
- assertEquals(
- cons.getTooltip(1),
+ assertEquals(cons.getTooltip(1),
"hydrophobic small tiny !aliphatic !aromatic !charged !negative !polar !positive !proline");
- assertEquals(
- cons.getTooltip(2),
+ assertEquals(cons.getTooltip(2),
"aliphatic hydrophobic !aromatic !charged !negative !polar !positive !proline !small !tiny");
- assertEquals(cons.getTooltip(3), "hydrophobic !negative !proline !tiny");
+ assertEquals(cons.getTooltip(3),
+ "hydrophobic !negative !proline !tiny");
assertEquals(cons.getTooltip(4), "hydrophobic");
assertEquals(cons.getTooltip(5), "");
assertEquals(cons.getTooltip(6), "");
DBRefEntry ref8 = new DBRefEntry("PFAM", "1", "A123");
// ENSEMBL is a source of either dna or protein sequence data
DBRefEntry ref9 = new DBRefEntry("ENSEMBL", "1", "A123");
- List<DBRefEntry> refs = Arrays.asList(new DBRefEntry[] { ref1, ref2, ref3, ref4, ref5,
- ref6, ref7, ref8, ref9 });
+ List<DBRefEntry> refs = Arrays
+ .asList(new DBRefEntry[]
+ { ref1, ref2, ref3, ref4, ref5, ref6, ref7, ref8, ref9 });
/*
* Just the DNA refs:
* and others to dna coding databases
*/
sources.clear();
- seq.setDBRefs(null);
+ seq.setDBRefs(null);
seq.addDBRef(new DBRefEntry("UNIPROT", "0", "A1234"));
seq.addDBRef(new DBRefEntry("EMBLCDS", "0", "E2347"));
SequenceI seq2 = new Sequence("Seq2", "MGKYQARLSS");
* peptide sequence with UNIPROT dbref
*/
SequenceI dna1 = new Sequence("AF039662", "GGGGCAGCACAAGAAC");
- Mapping map = new Mapping(new Sequence("pep2", "MLAVSRG"), new MapList(
- new int[] { 1, 21 }, new int[] { 1, 7 }, 3, 1));
+ Mapping map = new Mapping(new Sequence("pep2", "MLAVSRG"),
+ new MapList(new int[]
+ { 1, 21 }, new int[] { 1, 7 }, 3, 1));
DBRefEntry dbref = new DBRefEntry("UNIPROT", "0", "Q9ZTS2", map);
dna1.addDBRef(dbref);
dna1.addDBRef(new DBRefEntry("EMBL", "0", "AF039662"));
acf = new AlignedCodonFrame();
dbref = new DBRefEntry("UNIPROT", "0", "Q9ZTS2");
found = testee.searchDataset(!dna1.isProtein(), dna1, dbref, result,
- acf, false, DBRefUtils.SEARCH_MODE_FULL); // search dataset with a protein xref from a dna
- // sequence to locate the protein product
+ acf, false, DBRefUtils.SEARCH_MODE_FULL); // search dataset with a
+ // protein xref from a dna
+ // sequence to locate the protein product
assertTrue(found);
assertEquals(1, result.size());
assertSame(pep1, result.get(0));
acf = new AlignedCodonFrame();
dbref = new DBRefEntry("UNIPROT", "0", "Q9ZTS2");
found = testee.searchDataset(!pep1.isProtein(), pep1, dbref, result,
- acf, false, DBRefUtils.SEARCH_MODE_FULL); // search dataset with a protein's direct dbref to
- // locate dna sequences with matching xref
+ acf, false, DBRefUtils.SEARCH_MODE_FULL); // search dataset with a
+ // protein's direct dbref
+ // to
+ // locate dna sequences with matching xref
assertTrue(found);
assertEquals(1, result.size());
assertSame(dna1, result.get(0));
pep1.createDatasetSequence();
pep2.createDatasetSequence();
- pep1.getDatasetSequence().addDBRef(
- new DBRefEntry("Pfam", "0", "PF00111"));
- pep1.addSequenceFeature(new SequenceFeature("type", "desc", 12, 14, 1f,
- "group"));
+ pep1.getDatasetSequence()
+ .addDBRef(new DBRefEntry("Pfam", "0", "PF00111"));
+ pep1.addSequenceFeature(
+ new SequenceFeature("type", "desc", 12, 14, 1f, "group"));
pep2.getDatasetSequence().addDBRef(new DBRefEntry("PDB", "0", "3JTK"));
- pep2.addSequenceFeature(new SequenceFeature("type2", "desc2", 13, 15,
- 12f, "group2"));
+ pep2.addSequenceFeature(
+ new SequenceFeature("type2", "desc2", 13, 15, 12f, "group2"));
MapList mapList = new MapList(new int[] { 1, 24 }, new int[] { 1, 3 },
3, 1);
assertEquals(copy.getName(), original.getName());
assertEquals(copy.getStart(), original.getStart());
assertEquals(copy.getEnd(), original.getEnd());
- assertEquals(copy.getSequenceAsString(), original.getSequenceAsString());
+ assertEquals(copy.getSequenceAsString(),
+ original.getSequenceAsString());
}
/**
@Test(groups = { "Functional_Failing" })
public void testFindXrefSequences_withFetch()
{
- // JBPNote: this fails because pep1 and pep2 do not have DbRefEntrys with mappings
- // Fix#1 would be to revise the test data so it fits with 2.11.2+ Jalview assumptions
+ // JBPNote: this fails because pep1 and pep2 do not have DbRefEntrys with
+ // mappings
+ // Fix#1 would be to revise the test data so it fits with 2.11.2+ Jalview
+ // assumptions
// that ENA retrievals yield dbrefs with Mappings
-
+
SequenceI dna1 = new Sequence("AF039662", "GGGGCAGCACAAGAAC");
dna1.addDBRef(new DBRefEntry("UNIPROT", "ENA:0", "Q9ZTS2"));
dna1.addDBRef(new DBRefEntry("UNIPROT", "ENA:0", "P30419"));
dna1.addDBRef(new DBRefEntry("UNIPROT", "ENA:0", "P00314"));
final SequenceI pep1 = new Sequence("Q9ZTS2", "MYQLIRSSW");
- pep1.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2",null,true));
+ pep1.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2", null, true));
final SequenceI pep2 = new Sequence("P00314", "MRKLLAASG");
- pep2.addDBRef(new DBRefEntry("UNIPROT", "0", "P00314",null,true));
+ pep2.addDBRef(new DBRefEntry("UNIPROT", "0", "P00314", null, true));
/*
* argument false suppresses adding DAS sources
/*
* 'transcript' with CDS feature (supports mapping to protein)
*/
- SequenceI braf001 = new Sequence("ENST00000288602", "taagATGGCGGCGCTGa");
+ SequenceI braf001 = new Sequence("ENST00000288602",
+ "taagATGGCGGCGCTGa");
braf001.addDBRef(new DBRefEntry("UNIPROT", "0", "P15056"));
- braf001.addSequenceFeature(new SequenceFeature("CDS", "", 5, 16, 0f,
- null));
+ braf001.addSequenceFeature(
+ new SequenceFeature("CDS", "", 5, 16, 0f, null));
/*
* 'spliced transcript' with CDS ranges
*/
- SequenceI braf002 = new Sequence("ENST00000497784", "gCAGGCtaTCTGTTCaa");
+ SequenceI braf002 = new Sequence("ENST00000497784",
+ "gCAGGCtaTCTGTTCaa");
braf002.addDBRef(new DBRefEntry("UNIPROT", "ENSEMBL|0", "H7C5K3"));
- braf002.addSequenceFeature(new SequenceFeature("CDS", "", 2, 6, 0f,
- null));
- braf002.addSequenceFeature(new SequenceFeature("CDS", "", 9, 15, 0f,
- null));
+ braf002.addSequenceFeature(
+ new SequenceFeature("CDS", "", 2, 6, 0f, null));
+ braf002.addSequenceFeature(
+ new SequenceFeature("CDS", "", 9, 15, 0f, null));
/*
* TODO code is fragile - use of SequenceIdMatcher depends on fetched
/*
* J03321 with mappings to P0CE19 and P0CE20
*/
- final SequenceI j03321 = new Sequence("EMBL|J03321", "AAACCCTTTGGGAAAA");
+ final SequenceI j03321 = new Sequence("EMBL|J03321",
+ "AAACCCTTTGGGAAAA");
DBRefEntry dbref1 = new DBRefEntry("UNIPROT", "0", "P0CE19");
MapList mapList = new MapList(new int[] { 1, 12 }, new int[] { 1, 4 },
3, 1);
DBRefEntry dbref3 = new DBRefEntry("UNIPROT", "0", "P0CE19");
MapList map2 = new MapList(new int[] { 4, 15 }, new int[] { 1, 4 }, 3,
1);
- dbref3.setMap(new Mapping(new Sequence("UNIPROT|P0CE19", "KPFG"), map2));
+ dbref3.setMap(
+ new Mapping(new Sequence("UNIPROT|P0CE19", "KPFG"), map2));
x06707.addDBRef(dbref3);
DBRefEntry dbref4 = new DBRefEntry("UNIPROT", "0", "P0CE20");
MapList map3 = new MapList(new int[] { 4, 15 }, new int[] { 1, 4 }, 3,
1);
- dbref4.setMap(new Mapping(new Sequence("UNIPROT|P0CE20", "PFGK"), map3));
+ dbref4.setMap(
+ new Mapping(new Sequence("UNIPROT|P0CE20", "PFGK"), map3));
x06707.addDBRef(dbref4);
/*
/*
* verify dbrefs on EMBL are mapped to alignment seqs
*/
-
+
assertSame(p0ce19, j03321.getDBRefs().get(0).getMap().getTo());
assertSame(p0ce20, j03321.getDBRefs().get(1).getMap().getTo());
assertSame(p0ce19, x06707.getDBRefs().get(0).getMap().getTo());
assertFalse(CrossRef.sameSequence(null, seq1));
assertTrue(CrossRef.sameSequence(seq1, new Sequence("seq2", "ABCDEF")));
assertTrue(CrossRef.sameSequence(seq1, new Sequence("seq2", "abcdef")));
- assertFalse(CrossRef
- .sameSequence(seq1, new Sequence("seq2", "ABCDE-F")));
+ assertFalse(
+ CrossRef.sameSequence(seq1, new Sequence("seq2", "ABCDE-F")));
assertFalse(CrossRef.sameSequence(seq1, new Sequence("seq2", "BCDEF")));
}
}
Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
false);
Dna dna = new Dna(av, contigs);
- AlignmentI translated = dna.translateCdna(GeneticCodes.getInstance()
- .getStandardCodeTable());
+ AlignmentI translated = dna.translateCdna(
+ GeneticCodes.getInstance().getStandardCodeTable());
assertNotNull("Couldn't do a full width translation of test data.",
translated);
}
cs.hideColumns(0, ipos - 1);
}
cs.hideColumns(ipos + vwidth, alf.getWidth());
- Iterator<int[]> vcontigs = cs.getVisContigsIterator(0,
- alf.getWidth(), false);
+ Iterator<int[]> vcontigs = cs.getVisContigsIterator(0, alf.getWidth(),
+ false);
AlignViewportI av = new AlignViewport(alf, cs);
Dna dna = new Dna(av, vcontigs);
- AlignmentI transAlf = dna.translateCdna(GeneticCodes.getInstance()
- .getStandardCodeTable());
+ AlignmentI transAlf = dna.translateCdna(
+ GeneticCodes.getInstance().getStandardCodeTable());
- assertTrue("Translation failed (ipos=" + ipos
- + ") No alignment data.", transAlf != null);
+ assertTrue(
+ "Translation failed (ipos=" + ipos + ") No alignment data.",
+ transAlf != null);
assertTrue("Translation failed (ipos=" + ipos + ") Empty alignment.",
transAlf.getHeight() > 0);
- assertTrue("Translation failed (ipos=" + ipos + ") Translated "
- + transAlf.getHeight() + " sequences from " + alf.getHeight()
- + " sequences", alf.getHeight() == transAlf.getHeight());
+ assertTrue(
+ "Translation failed (ipos=" + ipos + ") Translated "
+ + transAlf.getHeight() + " sequences from "
+ + alf.getHeight() + " sequences",
+ alf.getHeight() == transAlf.getHeight());
}
}
Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
false);
Dna dna = new Dna(av, contigs);
- AlignmentI translated = dna.translateCdna(GeneticCodes.getInstance()
- .getStandardCodeTable());
+ AlignmentI translated = dna.translateCdna(
+ GeneticCodes.getInstance().getStandardCodeTable());
String aa = translated.getSequenceAt(0).getSequenceAsString();
assertEquals(
"AAAACCDDEEFFGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVWYY***",
Iterator<int[]> contigs = cs.getVisContigsIterator(0, alf.getWidth(),
false);
Dna dna = new Dna(av, contigs);
- AlignmentI translated = dna.translateCdna(GeneticCodes.getInstance()
- .getStandardCodeTable());
+ AlignmentI translated = dna.translateCdna(
+ GeneticCodes.getInstance().getStandardCodeTable());
String aa = translated.getSequenceAt(0).getSequenceAsString();
- assertEquals("AACDDGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVW", aa);
+ assertEquals("AACDDGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVW",
+ aa);
}
/**
/*
* Generate cDNA - 8 sequences of 12 bases each.
*/
- AlignmentI cdna = new AlignmentGenerator(true)
- .generate(12, 8, 97, 5, 5);
+ AlignmentI cdna = new AlignmentGenerator(true).generate(12, 8, 97, 5,
+ 5);
HiddenColumns cs = new HiddenColumns();
AlignViewportI av = new AlignViewport(cdna, cs);
Iterator<int[]> contigs = cs.getVisContigsIterator(0, cdna.getWidth(),
false);
Dna dna = new Dna(av, contigs);
- AlignmentI translated = dna.translateCdna(GeneticCodes.getInstance()
- .getStandardCodeTable());
+ AlignmentI translated = dna.translateCdna(
+ GeneticCodes.getInstance().getStandardCodeTable());
/*
* Jumble the cDNA sequences and translate.
av = new AlignViewport(cdnaReordered, cs);
contigs = cs.getVisContigsIterator(0, cdna.getWidth(), false);
dna = new Dna(av, contigs);
- AlignmentI translated2 = dna.translateCdna(GeneticCodes.getInstance()
- .getStandardCodeTable());
+ AlignmentI translated2 = dna.translateCdna(
+ GeneticCodes.getInstance().getStandardCodeTable());
/*
* Check translated sequences are the same in both alignments.
int sortedSequenceIndex = 0;
for (int originalSequenceIndex : jumbler)
{
- final String translation1 = translated.getSequenceAt(
- originalSequenceIndex).getSequenceAsString();
- final String translation2 = translated2.getSequenceAt(
- sortedSequenceIndex).getSequenceAsString();
+ final String translation1 = translated
+ .getSequenceAt(originalSequenceIndex).getSequenceAsString();
+ final String translation2 = translated2
+ .getSequenceAt(sortedSequenceIndex).getSequenceAsString();
assertEquals(translation2, translation1);
sortedSequenceIndex++;
}
private void assertSymmetric(String codon1, String codon2)
{
- assertEquals("Comparison of '" + codon1 + "' and '" + codon2
- + " not symmetric", Integer.signum(compare(codon1, codon2)),
+ assertEquals(
+ "Comparison of '" + codon1 + "' and '" + codon2
+ + " not symmetric",
+ Integer.signum(compare(codon1, codon2)),
-Integer.signum(compare(codon2, codon1)));
}
*/
private void assertPrecedes(String codon1, String codon2)
{
- assertEquals("Expected '" + codon1 + "' precedes '" + codon2 + "'",
- -1, compare(codon1, codon2));
+ assertEquals("Expected '" + codon1 + "' precedes '" + codon2 + "'", -1,
+ compare(codon1, codon2));
}
/**
SequenceI dna = new Sequence("Seq1", seq);
Alignment al = new Alignment(new SequenceI[] { dna });
al.createDatasetAlignment();
- assertEquals(seqDs, al.getSequenceAt(0).getDatasetSequence()
- .getSequenceAsString());
+ assertEquals(seqDs,
+ al.getSequenceAt(0).getDatasetSequence().getSequenceAsString());
HiddenColumns cs = new HiddenColumns();
AlignViewportI av = new AlignViewport(al, cs);
* single symbol should find *all* matching symbols
*/
Finder f = new Finder(av);
- f.findAll("M", false,false,false);
+ f.findAll("M", false, false, false);
SearchResultsI sr = f.getSearchResults();
- assertEquals(sr.getCount(),5);
-
+ assertEquals(sr.getCount(), 5);
+
}
+
/**
* Test for (undocumented) find residue by position
*/
sg.addSequence(al.getSequenceAt(1), false);
sg.addSequence(al.getSequenceAt(2), false);
av.setSelectionGroup(sg);
-
+
/*
* search for 'e' should match two sequence ids and one residue
*/
}
/**
- * Test that find does not report hidden positions, but does report matches that
- * span hidden gaps
+ * Test that find does not report hidden positions, but does report matches
+ * that span hidden gaps
*/
@Test(groups = "Functional")
public void testFind_withHiddenColumns()
* --bcdEFH
* aa---aMMMMMaaa
*/
-
+
/*
* hide columns 2-4 and 6-7
*/
hc.hideColumns(2, 4);
hc.hideColumns(6, 7);
al.setHiddenColumns(hc);
-
+
/*
* select rows 2-3
*/
Sequence s5 = new Sequence("s5", "AAAADDEDTTEE");
- SequenceGroup sg_12 = new SequenceGroup(Arrays.asList(new SequenceI[] {
- s1, s2 }), "Group1", null, false, false, false, 0, 5);
+ SequenceGroup sg_12 = new SequenceGroup(
+ Arrays.asList(new SequenceI[]
+ { s1, s2 }), "Group1", null, false, false, false, 0, 5);
- SequenceGroup sg_345 = new SequenceGroup(Arrays.asList(new SequenceI[] {
- s3, s4, s5 }), "Group2", null, false, false, false, 0, 5);
+ SequenceGroup sg_345 = new SequenceGroup(
+ Arrays.asList(new SequenceI[]
+ { s3, s4, s5 }), "Group2", null, false, false, false, 0, 5);
AlignmentI alignment = new Alignment(
- new SequenceI[] { s1, s2, s3, s4, s5 });
+ new SequenceI[]
+ { s1, s2, s3, s4, s5 });
/*
* test for the case where column selections are not added in
}
SequenceGroup[] seqgroupsString = Grouping.makeGroupsFrom(
alignment.getSequencesArray(), str,
- Arrays.asList(new SequenceGroup[] { sg_12, sg_345 }));
+ Arrays.asList(new SequenceGroup[]
+ { sg_12, sg_345 }));
ColumnSelection cs = new ColumnSelection();
for (int p : positions)
}
SequenceGroup[] seqgroupsColSel = Grouping.makeGroupsFromCols(
alignment.getSequencesArray(), cs,
- Arrays.asList(new SequenceGroup[] { sg_12, sg_345 }));
- AssertJUnit
- .assertEquals(seqgroupsString.length, seqgroupsColSel.length);
+ Arrays.asList(new SequenceGroup[]
+ { sg_12, sg_345 }));
+ AssertJUnit.assertEquals(seqgroupsString.length,
+ seqgroupsColSel.length);
for (int p = 0; p < seqgroupsString.length; p++)
{
AssertJUnit.assertEquals(seqgroupsString[p].getName(),
for (int i = 0; i <= 255; i++)
{
boolean isClosingChar = Rna.isClosingParenthesis((char) i);
- boolean isClosingString = Rna.isClosingParenthesis(String
- .valueOf((char) i));
+ boolean isClosingString = Rna
+ .isClosingParenthesis(String.valueOf((char) i));
if ((i >= 'a' && i <= 'z') || i == ')' || i == '}' || i == ']'
|| i == '>')
{
else
{
assertFalse(String.format("close base pair %c", i), isClosingChar);
- assertFalse(String.format("close base pair %c", i), isClosingString);
+ assertFalse(String.format("close base pair %c", i),
+ isClosingString);
}
assertFalse(Rna.isClosingParenthesis(String.valueOf((char) i) + " "));
}
for (int i = 0; i <= 255; i++)
{
boolean isOpeningChar = Rna.isOpeningParenthesis((char) i);
- boolean isOpeningString = Rna.isOpeningParenthesis(String
- .valueOf((char) i));
+ boolean isOpeningString = Rna
+ .isOpeningParenthesis(String.valueOf((char) i));
if ((i >= 'A' && i <= 'Z') || i == '(' || i == '{' || i == '['
|| i == '<')
{
for (int i = 0; i <= 255; i++)
{
boolean isValidChar = Rna.isRnaSecondaryStructureSymbol((char) i);
- boolean isValidString = Rna.isRnaSecondaryStructureSymbol(String
- .valueOf((char) i));
+ boolean isValidString = Rna
+ .isRnaSecondaryStructureSymbol(String.valueOf((char) i));
if ((i >= 'A' && i <= 'Z') || (i >= 'a' && i <= 'z') || i == '('
|| i == ')' || i == '{' || i == '}' || i == '[' || i == ']'
|| i == '<' || i == '>')
assertFalse(String.format("close base pair %c", i), isValidChar);
assertFalse(String.format("close base pair %c", i), isValidString);
}
- assertFalse(Rna.isRnaSecondaryStructureSymbol(String
- .valueOf((char) i) + " "));
+ assertFalse(Rna.isRnaSecondaryStructureSymbol(
+ String.valueOf((char) i) + " "));
}
}
String rna = ".([.)]..{.<}.>";
SequenceFeature[] sfs = Rna.getHelixMap(rna);
assertEquals(4, sfs.length);
-
+
/*
* pairs are added in the order in which the closing bracket is found
* (see testGetSimpleBPs)
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
-
/**
* test for JAL-2046 bug - duplication of sequence features on reconstructed
* alignment
@Test(groups = { "Functional" })
public void testSeqFeatureAddition()
{
- SequenceI[] sqset = new SequenceI[] {
- new Sequence("Aseq1", "AREALSEQ"),
+ SequenceI[] sqset = new SequenceI[] { new Sequence("Aseq1", "AREALSEQ"),
new Sequence("Aseq2", "AREALSEQ") };
AlignmentI al = new Alignment(sqset);
// are on the shared dataset sequence
Assert.assertEquals(sqset[0].getSequenceFeatures().size(), 2);
Assert.assertEquals(sqset2[0].getSequenceFeatures().size(), 2);
- Assert.assertSame(sqset[0].getSequenceFeatures().get(0), sqset2[0]
- .getSequenceFeatures().get(0));
- Assert.assertSame(sqset[0].getSequenceFeatures().get(1), sqset2[0]
- .getSequenceFeatures().get(1));
+ Assert.assertSame(sqset[0].getSequenceFeatures().get(0),
+ sqset2[0].getSequenceFeatures().get(0));
+ Assert.assertSame(sqset[0].getSequenceFeatures().get(1),
+ sqset2[0].getSequenceFeatures().get(1));
}
}
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
-
/**
* Test the method that checks for one sequence id starting with the other,
* followed by an 'allowed' separator character
as.printAlignment(ps);
String expected = "Score = 320.0\nLength of alignment = 10\nSequence Seq1/4-13 (Sequence length = 14)\nSequence Seq3/1-10 (Sequence length = 10)\n\n"
- + "Seq1/4-13 SDFAQQQRRR\n"
- + " ||||||| \n"
+ + "Seq1/4-13 SDFAQQQRRR\n" + " ||||||| \n"
+ "Seq3/1-10 SDFAQQQSSS\n\n" + "Percentage ID = 70.00\n\n";
assertEquals(expected, baos.toString());
}
*/
public AlignFrame getTestAlignmentFrame()
{
- AlignFrame alf = new FileLoader(false).LoadFileWaitTillLoaded(
- alntestFile, DataSourceType.PASTE);
+ AlignFrame alf = new FileLoader(false)
+ .LoadFileWaitTillLoaded(alntestFile, DataSourceType.PASTE);
AlignmentI al = alf.getViewport().getAlignment();
Assert.assertEquals(al.getHeight(), 4);
Assert.assertEquals(al.getWidth(), 5);
alf.getFeatureRenderer().setVisible("sf2");
alf.getFeatureRenderer().setVisible("sf3");
alf.getFeatureRenderer().findAllFeatures(true);
- Assert.assertEquals(alf.getFeatureRenderer().getDisplayedFeatureTypes()
- .size(), 3, "Number of feature types");
+ Assert.assertEquals(
+ alf.getFeatureRenderer().getDisplayedFeatureTypes().size(), 3,
+ "Number of feature types");
assertTrue(alf.getCurrentView().areFeaturesDisplayed());
return alf;
}
alf.getCurrentView().getAlignPanel());
alf.selectAllSequenceMenuItem_actionPerformed(null);
- MatrixI dm = sm.findDistances(
- alf.getViewport().getAlignmentView(true),
+ MatrixI dm = sm.findDistances(alf.getViewport().getAlignmentView(true),
SimilarityParams.Jalview);
assertEquals(dm.getValue(0, 2), 0d,
"FER1_MESCR (0) should be identical with RAPSA (2)");
sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
alf.getCurrentView().getAlignPanel());
alf.selectAllSequenceMenuItem_actionPerformed(null);
- MatrixI dm = sm.findDistances(
- alf.getViewport().getAlignmentView(true),
+ MatrixI dm = sm.findDistances(alf.getViewport().getAlignmentView(true),
SimilarityParams.Jalview);
assertEquals(dm.getValue(0, 2), 0d,
"FER1_MESCR (0) should be identical with RAPSA (2)");
sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
alf.getCurrentView().getAlignPanel());
alf.selectAllSequenceMenuItem_actionPerformed(null);
- MatrixI dm = sm.findDistances(
- alf.getViewport().getAlignmentView(true),
+ MatrixI dm = sm.findDistances(alf.getViewport().getAlignmentView(true),
SimilarityParams.Jalview);
- assertEquals(
- dm.getValue(0, 2),
- 0d,
+ assertEquals(dm.getValue(0, 2), 0d,
"After hiding last two columns FER1_MESCR (0) should still be identical with RAPSA (2)");
- assertEquals(
- dm.getValue(0, 1),
- 0d,
+ assertEquals(dm.getValue(0, 1), 0d,
"After hiding last two columns FER1_MESCR (0) should now also be identical with SPIOL (1)");
for (int s = 0; s < 3; s++)
{
- assertTrue(dm.getValue(s, 3) > 0d, "After hiding last two columns "
- + alf.getViewport().getAlignment().getSequenceAt(s).getName()
- + "(" + s + ") should still be distinct from FER1_MAIZE (3)");
+ assertTrue(dm.getValue(s, 3) > 0d,
+ "After hiding last two columns "
+ + alf.getViewport().getAlignment().getSequenceAt(s)
+ .getName()
+ + "(" + s
+ + ") should still be distinct from FER1_MAIZE (3)");
}
}
assertTrue(sf.isContactFeature());
af.refreshFeatureUI(true);
af.getFeatureRenderer().setAllVisible(Arrays.asList("disulphide bond"));
- Assert.assertEquals(af.getFeatureRenderer().getDisplayedFeatureTypes()
- .size(), 1, "Should be just one feature type displayed");
+ Assert.assertEquals(
+ af.getFeatureRenderer().getDisplayedFeatureTypes().size(), 1,
+ "Should be just one feature type displayed");
// step through and check for pointwise feature presence/absence
- Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtColumn(aseq, 1)
- .size(), 0);
+ Assert.assertEquals(
+ af.getFeatureRenderer().findFeaturesAtColumn(aseq, 1).size(),
+ 0);
// step through and check for pointwise feature presence/absence
- Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtColumn(aseq, 2)
- .size(), 1);
+ Assert.assertEquals(
+ af.getFeatureRenderer().findFeaturesAtColumn(aseq, 2).size(),
+ 1);
// step through and check for pointwise feature presence/absence
- Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtColumn(aseq, 3)
- .size(), 0);
+ Assert.assertEquals(
+ af.getFeatureRenderer().findFeaturesAtColumn(aseq, 3).size(),
+ 0);
// step through and check for pointwise feature presence/absence
- Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtColumn(aseq, 4)
- .size(), 0);
+ Assert.assertEquals(
+ af.getFeatureRenderer().findFeaturesAtColumn(aseq, 4).size(),
+ 0);
// step through and check for pointwise feature presence/absence
- Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtColumn(aseq, 5)
- .size(), 1);
+ Assert.assertEquals(
+ af.getFeatureRenderer().findFeaturesAtColumn(aseq, 5).size(),
+ 1);
// step through and check for pointwise feature presence/absence
- Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtColumn(aseq, 6)
- .size(), 0);
+ Assert.assertEquals(
+ af.getFeatureRenderer().findFeaturesAtColumn(aseq, 6).size(),
+ 0);
}
@Test(groups = { "Functional" })
* 20120 (two features of the same type doesn't affect score)
* giving an average (pairwise distance) of 5/5 or 1.0
*/
- s1.addSequenceFeature(new SequenceFeature("domain", null, 1, 3, 0f,
- null));
- s1.addSequenceFeature(new SequenceFeature("variant", null, 2, 4, 0f,
- null));
- s1.addSequenceFeature(new SequenceFeature("variant", null, 3, 5, 0f,
- null));
- s2.addSequenceFeature(new SequenceFeature("domain", null, 2, 4, 0f,
- null));
- s2.addSequenceFeature(new SequenceFeature("variant", null, 1, 2, 0f,
- null));
- s2.addSequenceFeature(new SequenceFeature("variant", null, 5, 5, 0f,
- null));
+ s1.addSequenceFeature(
+ new SequenceFeature("domain", null, 1, 3, 0f, null));
+ s1.addSequenceFeature(
+ new SequenceFeature("variant", null, 2, 4, 0f, null));
+ s1.addSequenceFeature(
+ new SequenceFeature("variant", null, 3, 5, 0f, null));
+ s2.addSequenceFeature(
+ new SequenceFeature("domain", null, 2, 4, 0f, null));
+ s2.addSequenceFeature(
+ new SequenceFeature("variant", null, 1, 2, 0f, null));
+ s2.addSequenceFeature(
+ new SequenceFeature("variant", null, 5, 5, 0f, null));
alf.setShowSeqFeatures(true);
alf.getFeatureRenderer().findAllFeatures(true);
alf.getCurrentView().getAlignPanel());
alf.selectAllSequenceMenuItem_actionPerformed(null);
- AlignmentView alignmentView = alf.getViewport()
- .getAlignmentView(true);
+ AlignmentView alignmentView = alf.getViewport().getAlignmentView(true);
MatrixI distances = sm.findDistances(alignmentView,
SimilarityParams.Jalview);
assertEquals(distances.width(), 2);
assertEquals(distances.getValue(1, 1), 0d);
assertEquals(distances.getValue(0, 1), 13d / 6); // should be 13d/6
assertEquals(distances.getValue(1, 0), 13d / 6);
-
+
/*
* exclude gaps
* score = 3 + 3 + 0 + 0 + 0 + 0 = 6/6
SequenceI s1 = new Sequence("s1", "FR K S");
SequenceI s2 = new Sequence("s2", "FS L");
- s1.addSequenceFeature(new SequenceFeature("chain", null, 1, 4, 0f, null));
- s1.addSequenceFeature(new SequenceFeature("domain", null, 1, 4, 0f,
- null));
- s2.addSequenceFeature(new SequenceFeature("chain", null, 1, 3, 0f, null));
- s2.addSequenceFeature(new SequenceFeature("metal", null, 1, 3, 0f, null));
- s2.addSequenceFeature(new SequenceFeature("Pfam", null, 1, 3, 0f, null));
+ s1.addSequenceFeature(
+ new SequenceFeature("chain", null, 1, 4, 0f, null));
+ s1.addSequenceFeature(
+ new SequenceFeature("domain", null, 1, 4, 0f, null));
+ s2.addSequenceFeature(
+ new SequenceFeature("chain", null, 1, 3, 0f, null));
+ s2.addSequenceFeature(
+ new SequenceFeature("metal", null, 1, 3, 0f, null));
+ s2.addSequenceFeature(
+ new SequenceFeature("Pfam", null, 1, 3, 0f, null));
AlignmentI al = new Alignment(new SequenceI[] { s1, s2 });
AlignFrame af = new AlignFrame(al, 300, 300);
af.setShowSeqFeatures(true);
{
String s1 = "FR-K-S";
String s2 = "FS--L";
-
+
/*
* match gap-gap and gap-char
* shorter sequence treated as if with trailing gaps
* PID = 5/6 = 83.333...%
*/
- SimilarityParamsI params = new SimilarityParams(true, true, true, false);
+ SimilarityParamsI params = new SimilarityParams(true, true, true,
+ false);
assertEquals(PIDModel.computePID(s1, s2, params), 500d / 6);
assertEquals(PIDModel.computePID(s2, s1, params), 500d / 6);
-
+
/*
* match gap-char but not gap-gap
* PID = 4/5 = 80%
params = new SimilarityParams(false, true, true, false);
assertEquals(PIDModel.computePID(s1, s2, params), 80d);
assertEquals(PIDModel.computePID(s2, s1, params), 80d);
-
+
/*
* include gaps but don't match them
* include gap-gap, counted as identity
params = new SimilarityParams(true, false, true, false);
assertEquals(PIDModel.computePID(s1, s2, params), 100d / 3);
assertEquals(PIDModel.computePID(s2, s1, params), 100d / 3);
-
+
/*
* include gaps but don't match them
* exclude gap-gap
String[] seqs2 = new String[] { seq2, seq1 };
MatrixI res2 = sm.findSimilarities(seqs2, params);
assertFalse(res1.equals(res2));
- assertTrue(res2.equals(new Matrix(new double[][]
+ assertTrue(
+ res2.equals(new Matrix(new double[][]
{ { 16d, 3d }, { 3d, 14d } }), delta));
/*
sm = new ScoreMatrix("Test", "AB".toCharArray(), scores);
assertFalse(sm.isSymmetric()); // [0, 1] != [1, 0]
res1 = sm.findSimilarities(seqs1, params);
- assertTrue(res1.equals(new Matrix(new double[][]
+ assertTrue(
+ res1.equals(new Matrix(new double[][]
{ { 14d, 7d }, { 11d, 16d } }), delta));
/*
assertTrue(sm instanceof PairwiseScoreModelI);
assertFalse(sm instanceof DistanceScoreModel);
assertEquals(sm.getName(), "BLOSUM62");
- assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('I', 'R'), -3f);
+ assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('I', 'R'),
+ -3f);
sm = models.next();
assertTrue(sm instanceof SimilarityScoreModel);
assertTrue(sm instanceof PairwiseScoreModelI);
assertFalse(sm instanceof DistanceScoreModel);
assertEquals(sm.getName(), "PAM250");
- assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('R', 'C'), -4f);
+ assertEquals(((PairwiseScoreModelI) sm).getPairwiseScore('R', 'C'),
+ -4f);
sm = models.next();
assertTrue(sm instanceof SimilarityScoreModel);
@Test(groups = "Functional")
public void testGetValue()
{
- ArgsParser ap = new ArgsParser(new String[] { "-name", "Henry", "-job",
- "Tester" });
+ ArgsParser ap = new ArgsParser(
+ new String[]
+ { "-name", "Henry", "-job", "Tester" });
assertEquals(4, ap.getSize());
assertNull(ap.getValue("rubbish"));
assertEquals("Tester", ap.getValue("job"));
@Test(groups = "Functional")
public void testGetValue_decoded()
{
- ArgsParser ap = new ArgsParser(new String[] { "-name%241", "Henry",
- "-job", "Test%203%2a" });
+ ArgsParser ap = new ArgsParser(
+ new String[]
+ { "-name%241", "Henry", "-job", "Test%203%2a" });
// parameter value is decoded
assertEquals("Test 3*", ap.getValue("job", true));
// parameter name is not decoded
@Test(groups = "Functional")
public void testNextValue()
{
- ArgsParser ap = new ArgsParser(new String[] { "-name", "Henry", "-job",
- "Tester" });
+ ArgsParser ap = new ArgsParser(
+ new String[]
+ { "-name", "Henry", "-job", "Tester" });
assertEquals("name", ap.nextValue());
assertEquals("Henry", ap.nextValue());
assertEquals("job", ap.nextValue());
@Test(groups = "Functional")
public void testContains()
{
- ArgsParser ap = new ArgsParser(new String[] { "-name", "Henry", "-job",
- "Tester" });
+ ArgsParser ap = new ArgsParser(
+ new String[]
+ { "-name", "Henry", "-job", "Tester" });
assertFalse(ap.contains("Susan"));
assertFalse(ap.contains("-name"));
assertTrue(ap.contains("name"));
}
private static final int TEST_TIMEOUT = 12500; // Note longer timeout needed
- // on
- // full test run than on
- // individual tests
+ // on
+ // full test run than on
+ // individual tests
private static final int SETUP_TIMEOUT = 9000;
// not expanded by the shell
String classpath = getClassPath();
String _cmd = java_exe + " "
- + (withAwt ? "-Djava.awt.headless=true" : "")
- + " -classpath " + classpath
+ + (withAwt ? "-Djava.awt.headless=true" : "") + " -classpath "
+ + classpath
+ (modules.length() > 2 ? "--add-modules=\"" + modules + "\""
: "")
+ " jalview.bin.Jalview ";
String cmds = "-open examples/uniref50.fa -noquestionnaire -nousagestats";
final Worker worker = getJalviewDesktopRunner(false, cmds,
SETUP_TIMEOUT);
-
-
+
// number of lines expected on STDERR when Jalview starts up normally
// may need to adjust this if Jalview is excessively noisy ?
- final int STDERR_SETUPLINES=30;
-
+ final int STDERR_SETUPLINES = 30;
+
// thread monitors stderr - bails after SETUP_TIMEOUT or when
// STDERR_SETUPLINES have been read
Thread runner = new Thread(new Runnable()
" -eps", workingDir + "test_uniref50_out.eps", true,
MINFILESIZE_BIG, TEST_TIMEOUT },
{ "nodisplay -open examples/uniref50.fa", " -eps",
- workingDir + "test_uniref50_out.eps", false,
- MINFILESIZE_BIG, TEST_TIMEOUT },
+ workingDir + "test_uniref50_out.eps", false, MINFILESIZE_BIG,
+ TEST_TIMEOUT },
{ "nogui -open examples/uniref50.fa", " -eps",
workingDir + "test_uniref50_out.eps", true, MINFILESIZE_BIG,
TEST_TIMEOUT },
{ "nogui -open examples/uniref50.fa", " -eps",
- workingDir + "test_uniref50_out.eps", false,
- MINFILESIZE_BIG, TEST_TIMEOUT },
+ workingDir + "test_uniref50_out.eps", false, MINFILESIZE_BIG,
+ TEST_TIMEOUT },
{ "headless -open examples/uniref50.fa", " -eps",
workingDir + "test_uniref50_out.eps", true, MINFILESIZE_BIG,
TEST_TIMEOUT },
{ "headless -open examples/uniref50.fa", " -svg",
- workingDir + "test_uniref50_out.svg", false,
- MINFILESIZE_BIG, TEST_TIMEOUT },
+ workingDir + "test_uniref50_out.svg", false, MINFILESIZE_BIG,
+ TEST_TIMEOUT },
{ "headless -open examples/uniref50.fa", " -png",
workingDir + "test_uniref50_out.png", true, MINFILESIZE_BIG,
TEST_TIMEOUT },
{ "headless -open examples/uniref50.fa", " -html",
- workingDir + "test_uniref50_out.html", true,
- MINFILESIZE_BIG, TEST_TIMEOUT },
+ workingDir + "test_uniref50_out.html", true, MINFILESIZE_BIG,
+ TEST_TIMEOUT },
{ "headless -open examples/uniref50.fa", " -fasta",
workingDir + "test_uniref50_out.mfa", true, MINFILESIZE_SMALL,
TEST_TIMEOUT },
assertEquals("[abc]",
Arrays.toString(JalviewLite.separatorListToArray("abc|", "|")));
- assertEquals("[abc]", Arrays.toString(JalviewLite.separatorListToArray(
- "abcxy", "xy")));
+ assertEquals("[abc]", Arrays
+ .toString(JalviewLite.separatorListToArray("abcxy", "xy")));
// these fail:
// assertEquals("[abc]",
*/
EditCommand edit = new EditCommand("", Action.REPLACE, "xyZ",
new SequenceI[]
- { seq }, 2,
- 4, al);
+ { seq }, 2, 4, al);
assertEquals("ABxyZ-DEF", seq.getSequenceAsString());
assertEquals(1, seq.getStart());
assertEquals(8, seq.getEnd());
/*
* undo the edit
*/
- AlignmentI[] views = new AlignmentI[]
- { new Alignment(new SequenceI[] { seq }) };
+ AlignmentI[] views = new AlignmentI[] {
+ new Alignment(new SequenceI[]
+ { seq }) };
edit.undoCommand(views);
assertEquals("ABC--DEF", seq.getSequenceAsString());
// and ds is preserved
assertTrue(dsseq == seqs[1].getDatasetSequence());
// and it is unchanged and UPPERCASE !
- assertEquals("fghjklmnopq".toUpperCase(Locale.ROOT), dsseq.getSequenceAsString());
+ assertEquals("fghjklmnopq".toUpperCase(Locale.ROOT),
+ dsseq.getSequenceAsString());
// and that alignment sequence start has been adjusted
assertEquals(5, seqs[1].getStart());
assertEquals(11, seqs[1].getEnd());
// and ds is preserved
assertTrue(dsseq == seqs[1].getDatasetSequence());
// and it is unchanged AND UPPERCASE !
- assertEquals("fghjklmnopq".toUpperCase(Locale.ROOT), dsseq.getSequenceAsString());
+ assertEquals("fghjklmnopq".toUpperCase(Locale.ROOT),
+ dsseq.getSequenceAsString());
// and that alignment sequence start has been adjusted
assertEquals(5, seqs[1].getStart());
assertEquals(11, seqs[1].getEnd());
* 3 insert gap in a row (aka mouse drag right):
*/
Edit e = new EditCommand().new Edit(Action.INSERT_GAP,
- new SequenceI[] { seqs[0] }, 1, 1, al);
+ new SequenceI[]
+ { seqs[0] }, 1, 1, al);
testee.addEdit(e);
SequenceI edited = new Sequence("seq0", "a?bcdefghjk");
edited.setDatasetSequence(seqs[0].getDatasetSequence());
e = new EditCommand().new Edit(Action.INSERT_GAP,
- new SequenceI[] { edited }, 2, 1, al);
+ new SequenceI[]
+ { edited }, 2, 1, al);
testee.addEdit(e);
edited = new Sequence("seq0", "a??bcdefghjk");
edited.setDatasetSequence(seqs[0].getDatasetSequence());
e = new EditCommand().new Edit(Action.INSERT_GAP,
- new SequenceI[] { edited }, 3, 1, al);
+ new SequenceI[]
+ { edited }, 3, 1, al);
testee.addEdit(e);
assertEquals(1, testee.getSize());
assertEquals(Action.INSERT_GAP, testee.getEdit(0).getAction());
* Add a non-contiguous edit - should not be merged.
*/
e = new EditCommand().new Edit(Action.INSERT_GAP,
- new SequenceI[] { edited }, 5, 2, al);
+ new SequenceI[]
+ { edited }, 5, 2, al);
testee.addEdit(e);
assertEquals(2, testee.getSize());
assertEquals(5, testee.getEdit(1).getPosition());
* Add a Delete after the Insert - should not be merged.
*/
e = new EditCommand().new Edit(Action.DELETE_GAP,
- new SequenceI[] { edited }, 6, 2, al);
+ new SequenceI[]
+ { edited }, 6, 2, al);
testee.addEdit(e);
assertEquals(3, testee.getSize());
assertEquals(Action.DELETE_GAP, testee.getEdit(2).getAction());
*/
seqs[0].setSequence("a???bcdefghjk");
Edit e = new EditCommand().new Edit(Action.DELETE_GAP,
- new SequenceI[] { seqs[0] }, 4, 1, al);
+ new SequenceI[]
+ { seqs[0] }, 4, 1, al);
testee.addEdit(e);
assertEquals(1, testee.getSize());
SequenceI edited = new Sequence("seq0", "a??bcdefghjk");
edited.setDatasetSequence(seqs[0].getDatasetSequence());
e = new EditCommand().new Edit(Action.DELETE_GAP,
- new SequenceI[] { edited }, 3, 1, al);
+ new SequenceI[]
+ { edited }, 3, 1, al);
testee.addEdit(e);
assertEquals(1, testee.getSize());
edited = new Sequence("seq0", "a?bcdefghjk");
edited.setDatasetSequence(seqs[0].getDatasetSequence());
e = new EditCommand().new Edit(Action.DELETE_GAP,
- new SequenceI[] { edited }, 2, 1, al);
+ new SequenceI[]
+ { edited }, 2, 1, al);
testee.addEdit(e);
assertEquals(1, testee.getSize());
assertEquals(Action.DELETE_GAP, testee.getEdit(0).getAction());
* Add a non-contiguous edit - should not be merged.
*/
e = new EditCommand().new Edit(Action.DELETE_GAP,
- new SequenceI[] { edited }, 2, 1, al);
+ new SequenceI[]
+ { edited }, 2, 1, al);
testee.addEdit(e);
assertEquals(2, testee.getSize());
assertEquals(Action.DELETE_GAP, testee.getEdit(0).getAction());
* Add an Insert after the Delete - should not be merged.
*/
e = new EditCommand().new Edit(Action.INSERT_GAP,
- new SequenceI[] { edited }, 1, 1, al);
+ new SequenceI[]
+ { edited }, 1, 1, al);
testee.addEdit(e);
assertEquals(3, testee.getSize());
assertEquals(Action.INSERT_GAP, testee.getEdit(2).getAction());
{
seqs[0].setSequence("a???bcdefghjk");
Edit e = new EditCommand().new Edit(Action.DELETE_GAP,
- new SequenceI[] { seqs[0] }, 4, 1, al);
+ new SequenceI[]
+ { seqs[0] }, 4, 1, al);
testee.addEdit(e);
seqs[1].setSequence("f??ghjklmnopq");
- Edit e2 = new EditCommand().new Edit(Action.DELETE_GAP, new SequenceI[]
- { seqs[1] }, 3, 1, al);
+ Edit e2 = new EditCommand().new Edit(Action.DELETE_GAP,
+ new SequenceI[]
+ { seqs[1] }, 3, 1, al);
testee.addEdit(e2);
assertEquals(2, testee.getSize());
assertSame(e, testee.getEdit(0));
/*
* 2 insert gap in a row (aka mouse drag right), on two sequences:
*/
- Edit e = new EditCommand().new Edit(Action.INSERT_GAP, new SequenceI[] {
- seqs[0], seqs[1] }, 1, 1, al);
+ Edit e = new EditCommand().new Edit(Action.INSERT_GAP,
+ new SequenceI[]
+ { seqs[0], seqs[1] }, 1, 1, al);
testee.addEdit(e);
SequenceI seq1edited = new Sequence("seq0", "a?bcdefghjk");
seq1edited.setDatasetSequence(seqs[0].getDatasetSequence());
SequenceI seq2edited = new Sequence("seq1", "f?ghjklmnopq");
seq2edited.setDatasetSequence(seqs[1].getDatasetSequence());
- e = new EditCommand().new Edit(Action.INSERT_GAP, new SequenceI[] {
- seq1edited, seq2edited }, 2, 1, al);
+ e = new EditCommand().new Edit(Action.INSERT_GAP,
+ new SequenceI[]
+ { seq1edited, seq2edited }, 2, 1, al);
testee.addEdit(e);
assertEquals(1, testee.getSize());
assertEquals(Action.INSERT_GAP, testee.getEdit(0).getAction());
assertEquals(1, testee.getEdit(0).getPosition());
assertEquals(2, testee.getEdit(0).getNumber());
- assertEquals(seqs[0].getDatasetSequence(), testee.getEdit(0)
- .getSequences()[0].getDatasetSequence());
- assertEquals(seqs[1].getDatasetSequence(), testee.getEdit(0)
- .getSequences()[1].getDatasetSequence());
+ assertEquals(seqs[0].getDatasetSequence(),
+ testee.getEdit(0).getSequences()[0].getDatasetSequence());
+ assertEquals(seqs[1].getDatasetSequence(),
+ testee.getEdit(0).getSequences()[1].getDatasetSequence());
}
/**
* a cut of columns/residues 4-7
*/
SequenceI seq0 = seqs[0]; // abcdefghjk/1-10
- seq0.addSequenceFeature(new SequenceFeature("before", "", 1, 3, 0f,
- null));
- seq0.addSequenceFeature(new SequenceFeature("overlap left", "", 2, 6,
- 0f, null));
- seq0.addSequenceFeature(new SequenceFeature("internal", "", 5, 6, 0f,
- null));
- seq0.addSequenceFeature(new SequenceFeature("overlap right", "", 7, 8,
- 0f, null));
- seq0.addSequenceFeature(new SequenceFeature("after", "", 8, 10, 0f,
- null));
+ seq0.addSequenceFeature(
+ new SequenceFeature("before", "", 1, 3, 0f, null));
+ seq0.addSequenceFeature(
+ new SequenceFeature("overlap left", "", 2, 6, 0f, null));
+ seq0.addSequenceFeature(
+ new SequenceFeature("internal", "", 5, 6, 0f, null));
+ seq0.addSequenceFeature(
+ new SequenceFeature("overlap right", "", 7, 8, 0f, null));
+ seq0.addSequenceFeature(
+ new SequenceFeature("after", "", 8, 10, 0f, null));
/*
* add some contact features
*/
- SequenceFeature internalContact = new SequenceFeature("disulphide bond", "", 5,
- 6, 0f, null);
+ SequenceFeature internalContact = new SequenceFeature("disulphide bond",
+ "", 5, 6, 0f, null);
seq0.addSequenceFeature(internalContact); // should get deleted
SequenceFeature overlapLeftContact = new SequenceFeature(
"disulphide bond", "", 2, 6, 0f, null);
SequenceFeature overlapRightContact = new SequenceFeature(
"disulphide bond", "", 5, 8, 0f, null);
seq0.addSequenceFeature(overlapRightContact); // should get deleted
- SequenceFeature spanningContact = new SequenceFeature(
- "disulphide bond", "", 2, 9, 0f, null);
+ SequenceFeature spanningContact = new SequenceFeature("disulphide bond",
+ "", 2, 9, 0f, null);
seq0.addSequenceFeature(spanningContact); // should get shortened 3'
/*
for (int to = from; to <= end; to++)
{
String desc = String.format("%d-%d", from, to);
- SequenceFeature sf = new SequenceFeature("test", desc, from, to,
- 0f, null);
+ SequenceFeature sf = new SequenceFeature("test", desc, from, to, 0f,
+ null);
sf.setValue("from", Integer.valueOf(from));
sf.setValue("to", Integer.valueOf(to));
seq0.addSequenceFeature(sf);
{
for (int to = from; to < seq0.getLength(); to++)
{
- EditCommand ec = new EditCommand("Cut", Action.CUT, sqs, from, (to
- - from + 1), alignment);
+ EditCommand ec = new EditCommand("Cut", Action.CUT, sqs, from,
+ (to - from + 1), alignment);
final String msg = String.format("Cut %d-%d ", from + 1, to + 1);
boolean newDatasetSequence = copySeq0.getDatasetSequence() != seq0
.getDatasetSequence();
else
{
// failure in checkFeatureRelocation is more informative!
- assertEquals(msg + "wrong number of features left", func(5)
- - func(to - from + 1), sfs.size());
+ assertEquals(msg + "wrong number of features left",
+ func(5) - func(to - from + 1), sfs.size());
}
/*
{
final int oldFrom = ((Integer) sf.getValue("from")).intValue();
final int oldTo = ((Integer) sf.getValue("to")).intValue();
- String msg = String.format(
- "Undo cut of [%d-%d], feature at [%d-%d] ", from + 1, to + 1,
- oldFrom, oldTo);
+ String msg = String.format("Undo cut of [%d-%d], feature at [%d-%d] ",
+ from + 1, to + 1, oldFrom, oldTo);
assertEquals(msg + "start", oldFrom, sf.getBegin());
assertEquals(msg + "end", oldTo, sf.getEnd());
}
* @param seqStart
*/
private void verifyFeatureRelocation(SequenceFeature sf, int from, int to,
- boolean newDataset, int seqStart)
+ boolean newDataset, int seqStart)
{
// TODO handle the gapped sequence case as well
int cutSize = to - from + 1;
SequenceI seq0 = new Sequence("seq/8-11", "A-BCC");
seq0.createDatasetSequence();
assertEquals(8, seq0.getStart());
- seq0.addSequenceFeature(new SequenceFeature("", "", 10, 11, 0f,
- null));
+ seq0.addSequenceFeature(new SequenceFeature("", "", 10, 11, 0f, null));
SequenceI[] seqsArray = new SequenceI[] { seq0 };
AlignmentI alignment = new Alignment(seqsArray);
*/
Edit ec = testee.new Edit(Action.CUT, seqsArray, 0, 3, alignment);
EditCommand.cut(ec, new AlignmentI[] { alignment });
-
+
/*
* feature on CC(10-11) should still be on CC(10-11)
*/
/*
* features start/end are base 1
*/
- seq1.addSequenceFeature(new SequenceFeature("Metal", "desc", 2, 4, 0f,
- null));
- seq1.addSequenceFeature(new SequenceFeature("Helix", "desc", 1, 15, 0f,
- null));
- seq2.addSequenceFeature(new SequenceFeature("Metal", "desc", 4, 10,
- 10f,
- null));
- seq3.addSequenceFeature(new SequenceFeature("Metal", "desc", 11, 15,
- 10f, null));
+ seq1.addSequenceFeature(
+ new SequenceFeature("Metal", "desc", 2, 4, 0f, null));
+ seq1.addSequenceFeature(
+ new SequenceFeature("Helix", "desc", 1, 15, 0f, null));
+ seq2.addSequenceFeature(
+ new SequenceFeature("Metal", "desc", 4, 10, 10f, null));
+ seq3.addSequenceFeature(
+ new SequenceFeature("Metal", "desc", 11, 15, 10f, null));
// disulfide bond is a 'contact feature' - only select its 'start' and 'end'
- seq3.addSequenceFeature(new SequenceFeature("disulfide bond", "desc",
- 8, 12, 0f, null));
+ seq3.addSequenceFeature(
+ new SequenceFeature("disulfide bond", "desc", 8, 12, 0f, null));
/*
* select the first five columns --> Metal in seq1 cols 4-5
/*
* set features visible on a viewport as only visible features are selected
*/
- AlignFrame af = new AlignFrame(new Alignment(new SequenceI[] { seq1,
- seq2, seq3, seq4 }), 100, 100);
+ AlignFrame af = new AlignFrame(
+ new Alignment(new SequenceI[]
+ { seq1, seq2, seq3, seq4 }), 100, 100);
af.getFeatureRenderer().findAllFeatures(true);
AlignViewController avc = new AlignViewController(af, af.getViewport(),
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
"seq1 aMMMaaaaaaaaaaaaaaaa\n" + "seq2 aaaMMMMMMMaaaaaaaaaa\n"
+ "seq3 aaaaaaaaaaMMMMMaaaaa\n"
- + "seq4 aaaaaaaaaaaaaaaaaaaa\n", DataSourceType.PASTE);
+ + "seq4 aaaaaaaaaaaaaaaaaaaa\n",
+ DataSourceType.PASTE);
SearchResultsI sr = new SearchResults();
SequenceI[] sqs = af.getViewport().getAlignment().getSequencesArray();
AlignViewControllerI avc = af.avc;
avc.markHighlightedColumns(false, false, false);
- assertTrue("Didn't select highlighted columns", Arrays.deepEquals(af
- .getViewport().getColumnSelection().getSelectedRanges()
- .toArray(), new int[][] { { 1, 14 } }));
+ assertTrue("Didn't select highlighted columns",
+ Arrays.deepEquals(af.getViewport().getColumnSelection()
+ .getSelectedRanges().toArray(), new int[][]
+ { { 1, 14 } }));
}
}
/*
* DNA seq1 maps to AA seq2
*/
- assertEquals(aa.getSequenceAt(1), acf.findAlignedSequence(cdna
- .getSequenceAt(0).getDatasetSequence(), aa));
+ assertEquals(aa.getSequenceAt(1), acf.findAlignedSequence(
+ cdna.getSequenceAt(0).getDatasetSequence(), aa));
// can also find this from the dna aligned sequence
assertEquals(aa.getSequenceAt(1),
acf.findAlignedSequence(cdna.getSequenceAt(0), aa));
- assertEquals(cdna.getSequenceAt(0), acf.findAlignedSequence(aa
- .getSequenceAt(1).getDatasetSequence(), cdna));
+ assertEquals(cdna.getSequenceAt(0), acf.findAlignedSequence(
+ aa.getSequenceAt(1).getDatasetSequence(), cdna));
}
/**
* Set up the mappings for the exons (upper-case bases)
* Note residue Q is unmapped
*/
- MapList map1 = new MapList(new int[] { 11, 13, 15, 15, 17, 18 }, new int[] {
- 3, 4 }, 3, 1);
+ MapList map1 = new MapList(new int[] { 11, 13, 15, 15, 17, 18 },
+ new int[]
+ { 3, 4 }, 3, 1);
acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map1);
- MapList map2 = new MapList(new int[] { 20, 21, 23, 24, 26, 27 }, new int[] { 7, 9 },
- 3, 1);
+ MapList map2 = new MapList(new int[] { 20, 21, 23, 24, 26, 27 },
+ new int[]
+ { 7, 9 }, 3, 1);
acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(), map2);
/*
* No mapping from dna1 to pep2
*/
assertNull(acf.getMappedRegion(dna1, pep2, 7));
-
+
/*
* get peptide position for codon position
*/
/*
* Set up the mappings for the exons (upper-case bases)
*/
- MapList map = new MapList(new int[] { 2, 4, 6, 6, 8, 9 }, new int[] {
- 1, 2 }, 3, 1);
+ MapList map = new MapList(new int[] { 2, 4, 6, 6, 8, 9 },
+ new int[]
+ { 1, 2 }, 3, 1);
acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
- assertEquals(1, acf.getMappedCodons(aseq1.getDatasetSequence(), 1)
- .size());
- assertEquals(
- "[G, T, A]",
- Arrays.toString(acf.getMappedCodons(aseq1.getDatasetSequence(),
- 1).get(0)));
- assertEquals(
- "[C, T, T]",
- Arrays.toString(acf.getMappedCodons(aseq1.getDatasetSequence(),
- 2).get(0)));
+ assertEquals(1,
+ acf.getMappedCodons(aseq1.getDatasetSequence(), 1).size());
+ assertEquals("[G, T, A]", Arrays.toString(
+ acf.getMappedCodons(aseq1.getDatasetSequence(), 1).get(0)));
+ assertEquals("[C, T, T]", Arrays.toString(
+ acf.getMappedCodons(aseq1.getDatasetSequence(), 2).get(0)));
}
/**
/*
* Set up the mappings for the exons (upper-case bases)
*/
- MapList map = new MapList(new int[] { 2, 4, 6, 6, 8, 9 }, new int[] {
- 1, 2 }, 3, 1);
+ MapList map = new MapList(new int[] { 2, 4, 6, 6, 8, 9 },
+ new int[]
+ { 1, 2 }, 3, 1);
acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
acf.addMap(seq2.getDatasetSequence(), aseq1.getDatasetSequence(), map);
- assertEquals(2, acf.getMappedCodons(aseq1.getDatasetSequence(), 1)
- .size());
- List<char[]> codonsForV = acf.getMappedCodons(
- aseq1.getDatasetSequence(), 1);
+ assertEquals(2,
+ acf.getMappedCodons(aseq1.getDatasetSequence(), 1).size());
+ List<char[]> codonsForV = acf
+ .getMappedCodons(aseq1.getDatasetSequence(), 1);
assertEquals("[G, T, A]", Arrays.toString(codonsForV.get(0)));
assertEquals("[G, T, T]", Arrays.toString(codonsForV.get(1)));
- List<char[]> codonsForL = acf.getMappedCodons(
- aseq1.getDatasetSequence(), 2);
+ List<char[]> codonsForL = acf
+ .getMappedCodons(aseq1.getDatasetSequence(), 2);
assertEquals("[C, T, T]", Arrays.toString(codonsForL.get(0)));
assertEquals("[T, T, A]", Arrays.toString(codonsForL.get(1)));
}
*/
AlignedCodonFrame acf = new AlignedCodonFrame();
MapList map = new MapList(new int[] { 28, 30, 32, 32, 34, 35 },
- new int[] { 12, 13 }, 3, 1);
+ new int[]
+ { 12, 13 }, 3, 1);
acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
- assertEquals(
- "[G, T, A]",
- Arrays.toString(acf.getMappedCodons(aseq1.getDatasetSequence(),
- 12).get(0)));
- assertEquals(
- "[C, T, T]",
- Arrays.toString(acf.getMappedCodons(aseq1.getDatasetSequence(),
- 13).get(0)));
+ assertEquals("[G, T, A]", Arrays.toString(
+ acf.getMappedCodons(aseq1.getDatasetSequence(), 12).get(0)));
+ assertEquals("[C, T, T]", Arrays.toString(
+ acf.getMappedCodons(aseq1.getDatasetSequence(), 13).get(0)));
}
@Test(groups = { "Functional" })
assertTrue(AlignedCodonFrame.couldRealiseSequence(seq1proxy, seq1, 12,
17));
// map to region overlapping sequence is ok
- assertTrue(AlignedCodonFrame.couldRealiseSequence(seq1proxy, seq1, 5,
- 10));
+ assertTrue(
+ AlignedCodonFrame.couldRealiseSequence(seq1proxy, seq1, 5, 10));
assertTrue(AlignedCodonFrame.couldRealiseSequence(seq1proxy, seq1, 21,
26));
// map to region before sequence is not ok
- assertFalse(AlignedCodonFrame.couldRealiseSequence(seq1proxy, seq1, 4,
- 9));
+ assertFalse(
+ AlignedCodonFrame.couldRealiseSequence(seq1proxy, seq1, 4, 9));
// map to region after sequence is not ok
assertFalse(AlignedCodonFrame.couldRealiseSequence(seq1proxy, seq1, 22,
27));
* a real sequence can't replace a real one
*/
SequenceI seq1a = new Sequence("Seq1/10-21", "aaacccgggttt");
- assertFalse(AlignedCodonFrame.couldRealiseSequence(seq1, seq1a, 12, 17));
+ assertFalse(
+ AlignedCodonFrame.couldRealiseSequence(seq1, seq1a, 12, 17));
}
/**
* map Seq1 to all of Seq2 and part of Seq3
*/
AlignedCodonFrame acf = new AlignedCodonFrame();
- MapList map = new MapList(new int[] { 1, 12 }, new int[] { 1, 4 }, 3, 1);
+ MapList map = new MapList(new int[] { 1, 12 }, new int[] { 1, 4 }, 3,
+ 1);
acf.addMap(seq1.getDatasetSequence(), seq2.getDatasetSequence(), map);
map = new MapList(new int[] { 1, 12 }, new int[] { 3, 6 }, 3, 1);
acf.addMap(seq1.getDatasetSequence(), seq3.getDatasetSequence(), map);
aseq1.createDatasetSequence();
AlignedCodonFrame acf = new AlignedCodonFrame();
- MapList map = new MapList(new int[] { 2, 4, 6, 6, 8, 9 }, new int[] {
- 1, 2 }, 3, 1);
+ MapList map = new MapList(new int[] { 2, 4, 6, 6, 8, 9 },
+ new int[]
+ { 1, 2 }, 3, 1);
acf.addMap(seq1.getDatasetSequence(), aseq1.getDatasetSequence(), map);
assertEquals(1, acf.getMappingsFromSequence(seq1).size());
Mapping before = acf.getMappingsFromSequence(seq1).get(0);
assertEquals(1, acf.getMappingsFromSequence(seq1).size());
assertSame(before, acf.getMappingsFromSequence(seq1).get(0));
}
-
+
@Test(groups = { "Functional" })
public void testGetCoveringMapping()
{
SequenceI cds = new Sequence("cds/7-15", "ATGGCGGAC");
cds.setDatasetSequence(dna);
SequenceI pep = new Sequence("pep", "MAD");
-
+
/*
* with null argument or no mappings
*/
AlignedCodonFrame acf = new AlignedCodonFrame();
- assertNull(acf.getCoveringMapping(null, null));
- assertNull(acf.getCoveringMapping(dna, null));
- assertNull(acf.getCoveringMapping(null, pep));
- assertNull(acf.getCoveringMapping(dna, pep));
+ assertNull(acf.getCoveringMapping(null, null));
+ assertNull(acf.getCoveringMapping(dna, null));
+ assertNull(acf.getCoveringMapping(null, pep));
+ assertNull(acf.getCoveringMapping(dna, pep));
/*
* with a non-covering mapping e.g. overlapping exon
*/
- MapList map = new MapList(new int[] { 7, 9 }, new int[] {
- 1, 1 }, 3, 1);
+ MapList map = new MapList(new int[] { 7, 9 }, new int[] { 1, 1 }, 3, 1);
acf.addMap(dna, pep, map);
- assertNull(acf.getCoveringMapping(dna, pep));
-
+ assertNull(acf.getCoveringMapping(dna, pep));
+
acf = new AlignedCodonFrame();
- MapList map2 = new MapList(new int[] { 13, 18 }, new int[] {
- 2, 2 }, 3, 1);
+ MapList map2 = new MapList(new int[] { 13, 18 }, new int[] { 2, 2 }, 3,
+ 1);
acf.addMap(dna, pep, map2);
- assertNull(acf.getCoveringMapping(dna, pep));
-
+ assertNull(acf.getCoveringMapping(dna, pep));
+
/*
* with a covering mapping from CDS (dataset) to protein
*/
acf = new AlignedCodonFrame();
- MapList map3 = new MapList(new int[] { 7, 15 }, new int[] {
- 1, 3 }, 3, 1);
+ MapList map3 = new MapList(new int[] { 7, 15 }, new int[] { 1, 3 }, 3,
+ 1);
acf.addMap(dna, pep, map3);
- assertNull(acf.getCoveringMapping(dna, pep));
- SequenceToSequenceMapping mapping = acf.getCoveringMapping(cds, pep);
+ assertNull(acf.getCoveringMapping(dna, pep));
+ SequenceToSequenceMapping mapping = acf.getCoveringMapping(cds, pep);
assertNotNull(mapping);
-
+
/*
* with a mapping that extends to stop codon
*/
acf = new AlignedCodonFrame();
- MapList map4 = new MapList(new int[] { 7, 18 }, new int[] {
- 1, 3 }, 3, 1);
+ MapList map4 = new MapList(new int[] { 7, 18 }, new int[] { 1, 3 }, 3,
+ 1);
acf.addMap(dna, pep, map4);
- assertNull(acf.getCoveringMapping(dna, pep));
- assertNull(acf.getCoveringMapping(cds, pep));
+ assertNull(acf.getCoveringMapping(dna, pep));
+ assertNull(acf.getCoveringMapping(cds, pep));
SequenceI cds2 = new Sequence("cds/7-18", "ATGGCGGACtaa");
cds2.setDatasetSequence(dna);
- mapping = acf.getCoveringMapping(cds2, pep);
+ mapping = acf.getCoveringMapping(cds2, pep);
assertNotNull(mapping);
}
dna1.createDatasetSequence();
final Sequence dna2 = new Sequence("Seq2/20-28", "-TA-gG-Gg-CG-a");
dna2.createDatasetSequence();
-
+
final Sequence pep1 = new Sequence("Seq1/3-4", "-P-R");
pep1.createDatasetSequence();
final Sequence pep2 = new Sequence("Seq2/7-9", "-LY-Q");
pep2.createDatasetSequence();
-
+
/*
* First with no mappings
*/
SearchResults sr = new SearchResults();
acf.markMappedRegion(dna1, 12, sr);
assertTrue(sr.isEmpty());
-
+
/*
* Set up the mappings for the exons (upper-case bases)
* Note residue Q is unmapped
*/
- MapList map1 = new MapList(new int[] { 11, 13, 15, 15, 17, 18 }, new int[] {
- 3, 4 }, 3, 1);
+ MapList map1 = new MapList(new int[] { 11, 13, 15, 15, 17, 18 },
+ new int[]
+ { 3, 4 }, 3, 1);
acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map1);
- MapList map2 = new MapList(new int[] { 20, 21, 23, 24, 26, 27 }, new int[] { 7, 8 },
- 3, 1);
+ MapList map2 = new MapList(new int[] { 20, 21, 23, 24, 26, 27 },
+ new int[]
+ { 7, 8 }, 3, 1);
acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(), map2);
-
+
/*
* intron bases are not mapped
*/
acf.markMappedRegion(dna1, 10, sr);
assertTrue(sr.isEmpty());
-
+
/*
* Q is not mapped
*/
*/
acf.markMappedRegion(dna1, 11, sr);
SearchResults expected = new SearchResults();
- expected.addResult(pep1.getDatasetSequence(), 3, 3);
+ expected.addResult(pep1.getDatasetSequence(), 3, 3);
assertEquals(sr, expected);
/*
sr = new SearchResults();
acf.markMappedRegion(dna1.getDatasetSequence(), 11, sr);
assertEquals(sr, expected);
-
+
/*
* marking the same position a second time should not create a duplicate match
*/
acf.markMappedRegion(dna1.getDatasetSequence(), 12, sr);
assertEquals(sr, expected);
-
+
/*
* mark exon positions for peptide position (of aligned sequence)
*/
sr = new SearchResults();
acf.markMappedRegion(pep2, 7, sr); // codon positions 20, 21, 23
expected = new SearchResults();
- expected.addResult(dna2.getDatasetSequence(), 20, 21);
- expected.addResult(dna2.getDatasetSequence(), 23, 23);
+ expected.addResult(dna2.getDatasetSequence(), 20, 21);
+ expected.addResult(dna2.getDatasetSequence(), 23, 23);
assertEquals(sr, expected);
-
+
/*
* add another codon to the same SearchResults
*/
- acf.markMappedRegion(pep1.getDatasetSequence(), 4, sr); // codon positions 15, 17, 18
- expected.addResult(dna1.getDatasetSequence(), 15, 15);
- expected.addResult(dna1.getDatasetSequence(), 17, 18);
+ acf.markMappedRegion(pep1.getDatasetSequence(), 4, sr); // codon positions
+ // 15, 17, 18
+ expected.addResult(dna1.getDatasetSequence(), 15, 15);
+ expected.addResult(dna1.getDatasetSequence(), 17, 18);
assertEquals(sr, expected);
}
SequenceI cds = new Sequence("cds/1-9", "-A--TGGC-GGAC");
cds.createDatasetSequence();
SequenceI pep = new Sequence("pep/1-3", "MAD");
-
+
/*
* with null argument or no mappings
*/
assertNull(acf.getCoveringCodonMapping(null));
assertNull(acf.getCoveringCodonMapping(dna));
assertNull(acf.getCoveringCodonMapping(pep));
-
+
/*
* with a non-covering mapping e.g. overlapping exon
*/
- MapList map = new MapList(new int[] { 16, 18 }, new int[] {
- 1, 1 }, 3, 1);
+ MapList map = new MapList(new int[] { 16, 18 }, new int[] { 1, 1 }, 3,
+ 1);
acf.addMap(dna, pep, map);
assertNull(acf.getCoveringCodonMapping(dna));
assertNull(acf.getCoveringCodonMapping(pep));
-
+
acf = new AlignedCodonFrame();
- MapList map2 = new MapList(new int[] { 13, 18 }, new int[] {
- 2, 2 }, 3, 1);
+ MapList map2 = new MapList(new int[] { 13, 18 }, new int[] { 2, 2 }, 3,
+ 1);
acf.addMap(dna, pep, map2);
assertNull(acf.getCoveringCodonMapping(dna));
assertNull(acf.getCoveringCodonMapping(pep));
-
+
/*
* with a covering mapping from CDS (dataset) to protein
*/
acf = new AlignedCodonFrame();
- MapList map3 = new MapList(new int[] { 1, 9 }, new int[] {
- 1, 3 }, 3, 1);
+ MapList map3 = new MapList(new int[] { 1, 9 }, new int[] { 1, 3 }, 3,
+ 1);
acf.addMap(cds.getDatasetSequence(), pep, map3);
assertNull(acf.getCoveringCodonMapping(dna));
SequenceToSequenceMapping mapping = acf.getCoveringCodonMapping(pep);
assertNotNull(mapping);
- SequenceToSequenceMapping mapping2 = acf.getCoveringCodonMapping(cds.getDatasetSequence());
+ SequenceToSequenceMapping mapping2 = acf
+ .getCoveringCodonMapping(cds.getDatasetSequence());
assertSame(mapping, mapping2);
-
+
/*
* with a mapping that extends to stop codon
* (EMBL CDS location often includes the stop codon)
SequenceI cds2 = new Sequence("cds/1-12", "-A--TGGC-GGACTAA");
cds2.createDatasetSequence();
acf = new AlignedCodonFrame();
- MapList map4 = new MapList(new int[] { 1, 12 }, new int[] {
- 1, 3 }, 3, 1);
+ MapList map4 = new MapList(new int[] { 1, 12 }, new int[] { 1, 3 }, 3,
+ 1);
acf.addMap(cds2, pep, map4);
mapping = acf.getCoveringCodonMapping(cds2.getDatasetSequence());
assertNotNull(mapping);
from.createDatasetSequence();
SequenceI to = new Sequence("Seq1", "-PQ-R-");
to.createDatasetSequence();
- MapList map = new MapList(
- new int[] { 1, 1, 3, 4, 6, 6, 8, 10, 12, 13 },
- new int[] { 1, 3 }, 3, 1);
+ MapList map = new MapList(new int[] { 1, 1, 3, 4, 6, 6, 8, 10, 12, 13 },
+ new int[]
+ { 1, 3 }, 3, 1);
Mapping m = new Mapping(to.getDatasetSequence(), map);
Iterator<AlignedCodon> codons = m.getCodonIterator(from, '-');
from.createDatasetSequence();
SequenceI to = new Sequence("Seq1", "-PQ-TR-");
to.createDatasetSequence();
- MapList map = new MapList(
- new int[] { 1, 1, 3, 4, 6, 6, 8, 10, 12, 13 }, new int[] { 1,
- 2, 4, 4 }, 3, 1);
+ MapList map = new MapList(new int[] { 1, 1, 3, 4, 6, 6, 8, 10, 12, 13 },
+ new int[]
+ { 1, 2, 4, 4 }, 3, 1);
Mapping m = new Mapping(to.getDatasetSequence(), map);
Iterator<AlignedCodon> codons = m.getCodonIterator(from, '-');
SequenceI to = new Sequence("Seq1", "-PQ-R-");
to.createDatasetSequence();
MapList map = new MapList(new int[] { 1, 1, 3, 4, 6, 6, 8, 8 },
- new int[] { 1, 3 }, 3, 1);
+ new int[]
+ { 1, 3 }, 3, 1);
Mapping m = new Mapping(to.getDatasetSequence(), map);
Iterator<AlignedCodon> codons = m.getCodonIterator(from, '-');
from.createDatasetSequence();
SequenceI to = new Sequence("Seq1", "CHYQ");
to.createDatasetSequence();
- MapList map = new MapList(new int[] { 1, 12 }, new int[] { 1, 4 }, 3, 1);
+ MapList map = new MapList(new int[] { 1, 12 }, new int[] { 1, 4 }, 3,
+ 1);
Mapping m = new Mapping(to.getDatasetSequence(), map);
Iterator<AlignedCodon> codons = m.getCodonIterator(from, '-');
from.createDatasetSequence();
SequenceI to = new Sequence("Seq1/10-12", "-PQ-R-");
to.createDatasetSequence();
- MapList map = new MapList(new int[] { 7, 7, 9, 10, 12, 12, 14, 16, 18,
- 19 }, new int[] { 10, 12 }, 3, 1);
+ MapList map = new MapList(
+ new int[]
+ { 7, 7, 9, 10, 12, 12, 14, 16, 18, 19 }, new int[] { 10, 12 },
+ 3, 1);
Mapping m = new Mapping(to.getDatasetSequence(), map);
Iterator<AlignedCodon> codons = m.getCodonIterator(from, '-');
al[i] = new Annotation(new Annotation("" + sq.getCharAt(i), "",
(char) 0, sq.findPosition(i)));
}
- AlignmentAnnotation alan = new AlignmentAnnotation("For "
- + sq.getName(), "Fake alignment annot", al);
+ AlignmentAnnotation alan = new AlignmentAnnotation(
+ "For " + sq.getName(), "Fake alignment annot", al);
// create a sequence mapping for the annotation vector in its current state
alan.createSequenceMapping(sq, sq.getStart(), false);
alan.setProperty("CreatedBy", "createAnnotation");
{
if (ala.annotations[p] != null)
{
- assertEquals("Mismatch at position " + p
- + " between annotation position value and sequence"
- + ala.annotations[p], (int) ala.annotations[p].value,
+ assertEquals(
+ "Mismatch at position " + p
+ + " between annotation position value and sequence"
+ + ala.annotations[p],
+ (int) ala.annotations[p].value,
ala.sequenceRef.findPosition(p));
}
}
alSeq2.setStart(sqTo.getStart() + align.getSeq2Start() - 1);
alSeq2.setEnd(sqTo.getStart() + align.getSeq2End() - 1);
alSeq2.setDatasetSequence(sqTo);
- System.out.println(new AppletFormatAdapter()
-.formatSequences(
- FileFormat.Stockholm, new Alignment(new SequenceI[] { sqFrom,
- alSeq1, sqTo, alSeq2 }), true));
+ System.out.println(new AppletFormatAdapter().formatSequences(
+ FileFormat.Stockholm, new Alignment(new SequenceI[]
+ { sqFrom, alSeq1, sqTo, alSeq2 }), true));
Mapping mp = align.getMappingFromS1(false);
AlignmentI all = new Alignment(new SequenceI[] { alSeq1, alSeq2 });
all.addAnnotation(almap1);
all.addAnnotation(almap2);
- System.out.println(new AppletFormatAdapter().formatSequences(
- FileFormat.Stockholm,
- all, true));
+ System.out.println(new AppletFormatAdapter()
+ .formatSequences(FileFormat.Stockholm, all, true));
for (int p = 0; p < alSeq1.getLength(); p++)
{
"Mismatch on Original To and transferred annotation on 1",
(orig1 != null) ? orig1.toString() : null,
(trans1 != null) ? trans1.toString() : null);
- String alm1 = ""
- + (almap1.annotations.length > p ? almap1.annotations[p].displayCharacter
- : "Out of range");
- String alm2 = ""
- + (almap2.annotations.length > p ? almap2.annotations[p].displayCharacter
- : "Out of range");
+ String alm1 = "" + (almap1.annotations.length > p
+ ? almap1.annotations[p].displayCharacter
+ : "Out of range");
+ String alm2 = "" + (almap2.annotations.length > p
+ ? almap2.annotations[p].displayCharacter
+ : "Out of range");
assertEquals("Position " + p + " " + alm1 + " " + alm2, alm1, alm2);
}
}
Assert.assertFalse(ann.isQuantitative(),
"Empty annotation set should not be quantitative.");
- ann = new AlignmentAnnotation("an", "some an", new Annotation[] {
- newAnnotation("4"), newAnnotation("1"), newAnnotation("1"),
- newAnnotation("0.1"), newAnnotation("0.3") });
+ ann = new AlignmentAnnotation("an", "some an",
+ new Annotation[]
+ { newAnnotation("4"), newAnnotation("1"), newAnnotation("1"),
+ newAnnotation("0.1"), newAnnotation("0.3") });
Assert.assertTrue(ann.isQuantitative(),
"All numbers annotation set should be quantitative.");
- ann = new AlignmentAnnotation("an", "some an", new Annotation[] {
- newAnnotation("E"), newAnnotation("E"), newAnnotation("E"),
- newAnnotation("E"), newAnnotation("E") });
+ ann = new AlignmentAnnotation("an", "some an",
+ new Annotation[]
+ { newAnnotation("E"), newAnnotation("E"), newAnnotation("E"),
+ newAnnotation("E"), newAnnotation("E") });
Assert.assertFalse(ann.isQuantitative(),
"All 'E' annotation set should not be quantitative.");
- ann = new AlignmentAnnotation("an", "some an", new Annotation[] {
- newAnnotation("E"), newAnnotation("1"), newAnnotation("2"),
- newAnnotation("3"), newAnnotation("E") });
+ ann = new AlignmentAnnotation("an", "some an",
+ new Annotation[]
+ { newAnnotation("E"), newAnnotation("1"), newAnnotation("2"),
+ newAnnotation("3"), newAnnotation("E") });
Assert.assertTrue(ann.isQuantitative(),
"Mixed 'E' annotation set should be quantitative.");
}
return false;
}
}
- return verifyAlignmentDatasetRefs(alignment.getDataset(),
- raiseAssert, message);
+ return verifyAlignmentDatasetRefs(alignment.getDataset(), raiseAssert,
+ message);
}
else
{
{
if (raiseAssert)
{
- Assert.fail(message
- + " DBRefEntry " + dbr + " for sequence "
- + seqds
+ Assert.fail(message + " DBRefEntry " + dbr
+ + " for sequence " + seqds
+ " in alignment has map to sequence not in dataset");
}
return false;
ae.printStackTrace();
Assert.fail(
"Valid test alignment raised assertion errors when raiseAsserts enabled: "
- + msg, ae);
+ + msg,
+ ae);
}
// also check validation passes with asserts disabled
Assert.assertTrue(verifyAlignmentDatasetRefs(al, false, null),
}
if (!assertRaised)
{
- Assert.fail("Invalid test alignment passed when raiseAsserts enabled:"
- + msg);
+ Assert.fail(
+ "Invalid test alignment passed when raiseAsserts enabled:"
+ + msg);
}
// also check validation passes with asserts disabled
Assert.assertFalse(verifyAlignmentDatasetRefs(al, false, null),
@Test(groups = { "Functional" })
public void testVerifyAlignmentDatasetRefs()
{
- SequenceI sq1 = new Sequence("sq1", "ASFDD"), sq2 = new Sequence("sq2",
- "TTTTTT");
+ SequenceI sq1 = new Sequence("sq1", "ASFDD"),
+ sq2 = new Sequence("sq2", "TTTTTT");
// construct simple valid alignment dataset
Alignment al = new Alignment(new SequenceI[] { sq1, sq2 });
"didn't detect dataset sequence with a dataset sequence reference.");
sq1.setDatasetSequence(null);
- assertVerifyAlignment(
- al,
- true,
+ assertVerifyAlignment(al, true,
"didn't reinstate validity after nulling dataset sequence dataset reference");
// now create dataset and check again
// create a dbref on sq1 with a sequence ref to sq2
DBRefEntry dbrs1tos2 = new DBRefEntry("UNIPROT", "1", "Q111111");
- dbrs1tos2.setMap(new Mapping(sq2.getDatasetSequence(),
- new int[] { 1, 5 }, new int[] { 2, 6 }, 1, 1));
+ dbrs1tos2
+ .setMap(new Mapping(sq2.getDatasetSequence(), new int[]
+ { 1, 5 }, new int[] { 2, 6 }, 1, 1));
sq1.getDatasetSequence().addDBRef(dbrs1tos2);
assertVerifyAlignment(al, true,
"verify failed after addition of valid DBRefEntry/map");
// now create a dbref on a new sequence which maps to another sequence
// outside of the dataset
- SequenceI sqout = new Sequence("sqout", "ututututucagcagcag"), sqnew = new Sequence(
- "sqnew", "EEERRR");
+ SequenceI sqout = new Sequence("sqout", "ututututucagcagcag"),
+ sqnew = new Sequence("sqnew", "EEERRR");
DBRefEntry sqnewsqout = new DBRefEntry("ENAFOO", "1", "R000001");
- sqnewsqout.setMap(new Mapping(sqout, new int[] { 1, 6 }, new int[] { 1,
- 18 }, 1, 3));
+ sqnewsqout
+ .setMap(new Mapping(sqout, new int[]
+ { 1, 6 }, new int[] { 1, 18 }, 1, 3));
al.getDataset().addSequence(sqnew);
assertVerifyAlignment(al, true,
"verify failed after addition of new sequence to dataset");
// now start checking exception conditions
sqnew.addDBRef(sqnewsqout);
- assertVerifyAlignment(
- al,
- false,
+ assertVerifyAlignment(al, false,
"verify passed when a dbref with map to sequence outside of dataset was added");
// make the verify pass by adding the outsider back in
al.getDataset().addSequence(sqout);
"aggtutaggcagcagcag");
AlignedCodonFrame alc = new AlignedCodonFrame();
- alc.addMap(sqanotherout, sqnew, new MapList(new int[] { 1, 6 },
- new int[] { 1, 18 }, 3, 1));
+ alc.addMap(sqanotherout, sqnew,
+ new MapList(new int[]
+ { 1, 6 }, new int[] { 1, 18 }, 3, 1));
al.addCodonFrame(alc);
Assert.assertEquals(al.getDataset().getCodonFrames().size(), 1);
- assertVerifyAlignment(
- al,
- false,
+ assertVerifyAlignment(al, false,
"verify passed when alCodonFrame mapping to sequence outside of dataset was added");
// make the verify pass by adding the outsider back in
al.getDataset().addSequence(sqanotherout);
- assertVerifyAlignment(
- al,
- true,
+ assertVerifyAlignment(al, true,
"verify should have passed once all sequences involved in alCodonFrame were added to dataset");
al.getDataset().addSequence(sqanotherout);
assertVerifyAlignment(al, false,
* @param message
* - null or message prepended to exception message.
*/
- public static void assertDatasetIsNormalised(AlignmentI al, String message)
+ public static void assertDatasetIsNormalised(AlignmentI al,
+ String message)
{
if (al.getDataset() != null)
{
assertDatasetIsNormalised(al);
} catch (AssertionError ae)
{
- Assert.fail("Two different sequences should be valid normalised dataset.");
+ Assert.fail(
+ "Two different sequences should be valid normalised dataset.");
}
/*
* now change sq2's name in the alignment. should still be valid
assertDatasetIsNormalised(al);
} catch (AssertionError ae)
{
- Assert.fail("Two different sequences in dataset, but same name in alignment, should be valid normalised dataset.");
+ Assert.fail(
+ "Two different sequences in dataset, but same name in alignment, should be valid normalised dataset.");
}
al.addSequence(sq1seqd);
assertDatasetIsNormalised(al);
} catch (AssertionError ae)
{
- Assert.fail("sq1 and sq1 with different sequence should be distinct.");
+ Assert.fail(
+ "sq1 and sq1 with different sequence should be distinct.");
}
al.addSequence(sq1shift);
assertDatasetIsNormalised(al);
} catch (AssertionError ae)
{
- Assert.fail("sq1 and sq1 with different start/end should be distinct.");
+ Assert.fail(
+ "sq1 and sq1 with different start/end should be distinct.");
}
/*
* finally, the failure case
makeMappings(al1, al2);
((Alignment) al2).alignAs(al1, false, true);
- assertEquals("GC-TC--GUC-GTACT", al2.getSequenceAt(0)
- .getSequenceAsString());
- assertEquals("-GG-GTC--AGG--CAGT", al2.getSequenceAt(1)
- .getSequenceAsString());
+ assertEquals("GC-TC--GUC-GTACT",
+ al2.getSequenceAt(0).getSequenceAsString());
+ assertEquals("-GG-GTC--AGG--CAGT",
+ al2.getSequenceAt(1).getSequenceAsString());
}
/**
* Realign DNA; currently keeping existing gaps in introns only
*/
((Alignment) al1).alignAs(al2, false, true);
- assertEquals("ACG---GCUCCA------ACT---", al1.getSequenceAt(0)
- .getSequenceAsString());
- assertEquals("---CGT---TAACGA---AGT---", al1.getSequenceAt(1)
- .getSequenceAsString());
+ assertEquals("ACG---GCUCCA------ACT---",
+ al1.getSequenceAt(0).getSequenceAsString());
+ assertEquals("---CGT---TAACGA---AGT---",
+ al1.getSequenceAt(1).getSequenceAsString());
}
/**
{
SequenceI seqFrom = alFrom.getSequenceAt(i);
SequenceI seqTo = alTo.getSequenceAt(i);
- MapList ml = new MapList(new int[] { seqFrom.getStart(),
- seqFrom.getEnd() },
- new int[] { seqTo.getStart(), seqTo.getEnd() }, ratio, 1);
+ MapList ml = new MapList(
+ new int[]
+ { seqFrom.getStart(), seqFrom.getEnd() },
+ new int[]
+ { seqTo.getStart(), seqTo.getEnd() }, ratio, 1);
acf.addMap(seqFrom, seqTo, ml);
}
*/
String dna1 = "A-Aa-gG-GCC-cT-TT";
String dna2 = "c--CCGgg-TT--T-AA-A";
- AlignmentI al1 = loadAlignment(">Dna1/6-17\n" + dna1
- + "\n>Dna2/20-31\n" + dna2 + "\n", FileFormat.Fasta);
+ AlignmentI al1 = loadAlignment(
+ ">Dna1/6-17\n" + dna1 + "\n>Dna2/20-31\n" + dna2 + "\n",
+ FileFormat.Fasta);
AlignmentI al2 = loadAlignment(
">Pep1/7-9\n-P--YK\n>Pep2/11-13\nG-T--F\n", FileFormat.Fasta);
AlignedCodonFrame acf = new AlignedCodonFrame();
// Seq1 has intron at dna positions 3,4,9 so splice is AAG GCC TTT
// Seq2 has intron at dna positions 1,5,6 so splice is CCG TTT AAA
- MapList ml1 = new MapList(new int[] { 6, 7, 10, 13, 15, 17 }, new int[]
- { 7, 9 }, 3, 1);
+ MapList ml1 = new MapList(new int[] { 6, 7, 10, 13, 15, 17 },
+ new int[]
+ { 7, 9 }, 3, 1);
acf.addMap(al1.getSequenceAt(0), al2.getSequenceAt(0), ml1);
- MapList ml2 = new MapList(new int[] { 21, 23, 26, 31 }, new int[] { 11,
- 13 }, 3, 1);
+ MapList ml2 = new MapList(new int[] { 21, 23, 26, 31 },
+ new int[]
+ { 11, 13 }, 3, 1);
acf.addMap(al1.getSequenceAt(1), al2.getSequenceAt(1), ml2);
al2.addCodonFrame(acf);
* Align ignoring gaps in dna introns and exons
*/
((Alignment) al1).alignAs(al2, false, false);
- assertEquals("---AAagG------GCCcTTT", al1.getSequenceAt(0)
- .getSequenceAsString());
+ assertEquals("---AAagG------GCCcTTT",
+ al1.getSequenceAt(0).getSequenceAsString());
// note 1 gap in protein corresponds to 'gg-' in DNA (3 positions)
- assertEquals("cCCGgg-TTT------AAA", al1.getSequenceAt(1)
- .getSequenceAsString());
+ assertEquals("cCCGgg-TTT------AAA",
+ al1.getSequenceAt(1).getSequenceAsString());
/*
* Reset and realign, preserving gaps in dna introns and exons
// String dna1 = "A-Aa-gG-GCC-cT-TT";
// String dna2 = "c--CCGgg-TT--T-AA-A";
// assumption: we include 'the greater of' protein/dna gap lengths, not both
- assertEquals("---A-Aa-gG------GCC-cT-TT", al1.getSequenceAt(0)
- .getSequenceAsString());
- assertEquals("c--CCGgg-TT--T------AA-A", al1.getSequenceAt(1)
- .getSequenceAsString());
+ assertEquals("---A-Aa-gG------GCC-cT-TT",
+ al1.getSequenceAt(0).getSequenceAsString());
+ assertEquals("c--CCGgg-TT--T------AA-A",
+ al1.getSequenceAt(1).getSequenceAsString());
}
@Test(groups = "Functional")
// create sequence and alignment datasets
protein.setDataset(null);
AlignedCodonFrame acf = new AlignedCodonFrame();
- List<AlignedCodonFrame> acfList = Arrays.asList(new AlignedCodonFrame[]
- { acf });
+ List<AlignedCodonFrame> acfList = Arrays
+ .asList(new AlignedCodonFrame[]
+ { acf });
protein.getDataset().setCodonFrames(acfList);
AlignmentI copy = new Alignment(protein);
*/
assertFalse(copy.getSequenceAt(0) == protein.getSequenceAt(0));
assertFalse(copy.getSequenceAt(1) == protein.getSequenceAt(1));
- assertSame(copy.getSequenceAt(0).getDatasetSequence(), protein
- .getSequenceAt(0).getDatasetSequence());
- assertSame(copy.getSequenceAt(1).getDatasetSequence(), protein
- .getSequenceAt(1).getDatasetSequence());
+ assertSame(copy.getSequenceAt(0).getDatasetSequence(),
+ protein.getSequenceAt(0).getDatasetSequence());
+ assertSame(copy.getSequenceAt(1).getDatasetSequence(),
+ protein.getSequenceAt(1).getDatasetSequence());
// TODO should the copy constructor copy the dataset?
// or make a new one referring to the same dataset sequences??
// side-effect: dataset created on second sequence
assertNotNull(protein.getSequenceAt(1).getDatasetSequence());
// dataset alignment has references to dataset sequences
- assertEquals(ds.getSequenceAt(0), protein.getSequenceAt(0)
- .getDatasetSequence());
- assertEquals(ds.getSequenceAt(1), protein.getSequenceAt(1)
- .getDatasetSequence());
+ assertEquals(ds.getSequenceAt(0),
+ protein.getSequenceAt(0).getDatasetSequence());
+ assertEquals(ds.getSequenceAt(1),
+ protein.getSequenceAt(1).getDatasetSequence());
// codon frames should have been moved to the dataset
// getCodonFrames() should delegate to the dataset:
// cross-references to two more sequences.
DBRefEntry dbr = new DBRefEntry("SQ1", "", "sq3");
SequenceI sq3 = new Sequence("sq3", "VWANG");
- dbr.setMap(new Mapping(sq3, new MapList(new int[] { 1, 4 }, new int[] {
- 2, 5 }, 1, 1)));
+ dbr.setMap(
+ new Mapping(sq3, new MapList(new int[]
+ { 1, 4 }, new int[] { 2, 5 }, 1, 1)));
sq1.addDBRef(dbr);
SequenceI sq4 = new Sequence("sq4", "ERKWI");
DBRefEntry dbr2 = new DBRefEntry("SQ2", "", "sq4");
- dbr2.setMap(new Mapping(sq4, new MapList(new int[] { 1, 4 }, new int[] {
- 2, 5 }, 1, 1)));
+ dbr2.setMap(
+ new Mapping(sq4, new MapList(new int[]
+ { 1, 4 }, new int[] { 2, 5 }, 1, 1)));
sq2.addDBRef(dbr2);
// and a 1:1 codonframe mapping between them.
AlignedCodonFrame alc = new AlignedCodonFrame();
- alc.addMap(sq1, sq2, new MapList(new int[] { 1, 4 },
- new int[] { 1, 4 }, 1, 1));
+ alc.addMap(sq1, sq2,
+ new MapList(new int[]
+ { 1, 4 }, new int[] { 1, 4 }, 1, 1));
AlignmentI protein = new Alignment(new SequenceI[] { sq1, sq2 });
Assert.assertEquals(align.getDataset().getHeight(), 1,
"Dataset shouldn't have more than one sequence.");
- Sequence seq2 = new Sequence("newtestSeq", "ABCDEFGHIJKLMNOPQRSTUVWXYZ");
+ Sequence seq2 = new Sequence("newtestSeq",
+ "ABCDEFGHIJKLMNOPQRSTUVWXYZ");
align.addSequence(seq2);
Assert.assertEquals(align.getDataset().getHeight(), 2,
"Dataset should now have two sequences.");
// add dbref from dna to peptide
DBRefEntry dbr = new DBRefEntry("UNIPROT", "", "pep");
- dbr.setMap(new Mapping(pep, new MapList(new int[] { 4, 15 }, new int[] {
- 1, 4 }, 3, 1)));
+ dbr.setMap(
+ new Mapping(pep, new MapList(new int[]
+ { 4, 15 }, new int[] { 1, 4 }, 3, 1)));
dna.addDBRef(dbr);
// add dbref from dna to peptide
DBRefEntry dbr2 = new DBRefEntry("UNIPROT", "", "pep");
- dbr2.setMap(new Mapping(pep, new MapList(new int[] { 1, 12 }, new int[]
- { 1, 4 }, 3, 1)));
+ dbr2.setMap(
+ new Mapping(pep, new MapList(new int[]
+ { 1, 12 }, new int[] { 1, 4 }, 3, 1)));
cds.addDBRef(dbr2);
// add dbref from peptide to dna
DBRefEntry dbr3 = new DBRefEntry("EMBL", "", "dna");
- dbr3.setMap(new Mapping(dna, new MapList(new int[] { 1, 4 }, new int[] {
- 4, 15 }, 1, 3)));
+ dbr3.setMap(
+ new Mapping(dna, new MapList(new int[]
+ { 1, 4 }, new int[] { 4, 15 }, 1, 3)));
pep.addDBRef(dbr3);
// add dbref from peptide to cds
DBRefEntry dbr4 = new DBRefEntry("EMBLCDS", "", "cds");
- dbr4.setMap(new Mapping(cds, new MapList(new int[] { 1, 4 }, new int[] {
- 1, 12 }, 1, 3)));
+ dbr4.setMap(
+ new Mapping(cds, new MapList(new int[]
+ { 1, 4 }, new int[] { 1, 12 }, 1, 3)));
pep.addDBRef(dbr4);
AlignmentI protein = new Alignment(new SequenceI[] { pep });
@Test(
groups = "Functional",
- expectedExceptions = { IllegalArgumentException.class })
+ expectedExceptions =
+ { IllegalArgumentException.class })
public void testSetDataset_selfReference()
{
SequenceI seq = new Sequence("a", "a");
assertEquals('-', alignment.getGapCharacter());
assertSame(seq, alignment.getSequenceAt(0));
- assertEquals("KP--L-FQII-", alignment.getSequenceAt(1)
- .getSequenceAsString());
+ assertEquals("KP--L-FQII-",
+ alignment.getSequenceAt(1).getSequenceAsString());
// todo test coverage for annotations, mappings, groups,
// hidden sequences, properties
public class AllColsIteratorTest
{
HiddenColumns hiddenCols;
-
+
@BeforeClass(alwaysRun = true)
public void setup()
{
hiddenCols = new HiddenColumns();
hiddenCols.hideColumns(2, 4);
}
-
/*
* Test iterator iterates through collection correctly
* Test iterator throws NoSuchElementException at end of iteration
*/
@Test(
- groups = { "Functional" },
- expectedExceptions = { NoSuchElementException.class })
+ groups =
+ { "Functional" },
+ expectedExceptions =
+ { NoSuchElementException.class })
public void testLastNext() throws NoSuchElementException
{
AllColsIterator it = new AllColsIterator(0, 3, hiddenCols);
* Test iterator throws UnsupportedOperationException on call to remove
*/
@Test(
- groups = { "Functional" },
- expectedExceptions = { UnsupportedOperationException.class })
+ groups =
+ { "Functional" },
+ expectedExceptions =
+ { UnsupportedOperationException.class })
public void testRemove() throws UnsupportedOperationException
{
AllColsIterator it = new AllColsIterator(0, 3, hiddenCols);
* Test iterator throws NoSuchElementException at end of iteration
*/
@Test(
- groups = { "Functional" },
- expectedExceptions = { NoSuchElementException.class })
+ groups =
+ { "Functional" },
+ expectedExceptions =
+ { NoSuchElementException.class })
public void testLastNext() throws NoSuchElementException
{
AllRowsIterator it = new AllRowsIterator(0, 3, al);
* Test iterator throws UnsupportedOperationException on call to remove
*/
@Test(
- groups = { "Functional" },
- expectedExceptions = { UnsupportedOperationException.class })
+ groups =
+ { "Functional" },
+ expectedExceptions =
+ { UnsupportedOperationException.class })
public void testRemove() throws UnsupportedOperationException
{
AllRowsIterator it = new AllRowsIterator(0, 3, al);
it.remove();
}
-
/*
* Hide sequences between start and end
*/
*/
@Test(
groups = "Functional",
- expectedExceptions = { ConcurrentModificationException.class })
+ expectedExceptions =
+ { ConcurrentModificationException.class })
public void testGetSelected_concurrentModification()
{
ColumnSelection cs = new ColumnSelection();
assertEquals("[3, 1]", cs2.getSelected().toString());
}
-
@Test(groups = { "Functional" })
public void testStretchGroup_expand()
{
Annotation ann4 = new Annotation("x", "desc", 'Y', 3f);
added = cs
.filterAnnotations(new Annotation[]
- { null, helix, sheet, turn, ann4 },
- filter);
+ { null, helix, sheet, turn, ann4 }, filter);
assertEquals(1, added);
assertTrue(cs.contains(1));
assertFalse(ref1.equalRef(new DBRefEntry("UNIPROT", "1", "V71632")));
// presence of or differences in mappings are ignored
- ref1.setMap(new Mapping(new MapList(new int[] { 1, 3 }, new int[] { 1,
- 1 }, 3, 1)));
+ ref1.setMap(
+ new Mapping(new MapList(new int[]
+ { 1, 3 }, new int[] { 1, 1 }, 3, 1)));
assertTrue(ref1.equalRef(ref2));
assertTrue(ref2.equalRef(ref1));
- ref1.setMap(new Mapping(new MapList(new int[] { 1, 6 }, new int[] { 1,
- 2 }, 3, 1)));
+ ref1.setMap(
+ new Mapping(new MapList(new int[]
+ { 1, 6 }, new int[] { 1, 2 }, 3, 1)));
assertTrue(ref1.equalRef(ref2));
assertTrue(ref2.equalRef(ref1));
}
/*
* ref1 has no mapping, acquires mapping from ref2
*/
- Mapping map = new Mapping(new MapList(new int[] { 1, 3 }, new int[] {
- 1, 1 }, 3, 1));
+ Mapping map = new Mapping(
+ new MapList(new int[]
+ { 1, 3 }, new int[] { 1, 1 }, 3, 1));
ref2.setMap(map);
assertTrue(ref1.updateFrom(ref2));
assertSame(map, ref1.getMap()); // null mapping updated
/*
* 1:1 mapping - ok
*/
- dbr.setMap(new Mapping(null, new int[] { 1, 3 }, new int[] { 1, 3 }, 1,
- 1));
+ dbr.setMap(
+ new Mapping(null, new int[]
+ { 1, 3 }, new int[] { 1, 3 }, 1, 1));
assertTrue(dbr.isPrimaryCandidate());
/*
* 1:1 mapping of identical split ranges - not ok
*/
- dbr.setMap(new Mapping(null, new int[] { 1, 3, 6, 9 }, new int[] { 1,
- 3, 6, 9 }, 1, 1));
+ dbr.setMap(
+ new Mapping(null, new int[]
+ { 1, 3, 6, 9 }, new int[] { 1, 3, 6, 9 }, 1, 1));
assertFalse(dbr.isPrimaryCandidate());
/*
* 1:1 mapping of different ranges - not ok
*/
- dbr.setMap(new Mapping(null, new int[] { 1, 4 }, new int[] { 2, 5 }, 1,
- 1));
+ dbr.setMap(
+ new Mapping(null, new int[]
+ { 1, 4 }, new int[] { 2, 5 }, 1, 1));
assertFalse(dbr.isPrimaryCandidate());
/*
* 1:1 mapping of 'isoform' ranges - not ok
*/
- dbr.setMap(new Mapping(null, new int[] { 1, 2, 6, 9 }, new int[] { 1,
- 3, 7, 9 }, 1, 1));
+ dbr.setMap(
+ new Mapping(null, new int[]
+ { 1, 2, 6, 9 }, new int[] { 1, 3, 7, 9 }, 1, 1));
assertFalse(dbr.isPrimaryCandidate());
dbr.setMap(null);
assertTrue(dbr.isPrimaryCandidate());
/*
* 1:1 mapping and sequenceRef (fail)
*/
- dbr.setMap(new Mapping(new Sequence("foo", "ASDF"), new int[] { 1, 3 },
- new int[] { 1, 3 }, 1, 1));
+ dbr.setMap(
+ new Mapping(new Sequence("foo", "ASDF"), new int[]
+ { 1, 3 }, new int[] { 1, 3 }, 1, 1));
assertFalse(dbr.isPrimaryCandidate());
/*
* 1:3 mapping (fail)
*/
- dbr.setMap(new Mapping(null, new int[] { 1, 3 }, new int[] { 1, 3 }, 1,
- 3));
+ dbr.setMap(
+ new Mapping(null, new int[]
+ { 1, 3 }, new int[] { 1, 3 }, 1, 3));
assertFalse(dbr.isPrimaryCandidate());
/*
* 2:2 mapping with shift (expected fail, but maybe use case for a pass)
*/
- dbr.setMap(new Mapping(null, new int[] { 1, 4 }, new int[] { 1, 4 }, 2,
- 2));
+ dbr.setMap(
+ new Mapping(null, new int[]
+ { 1, 4 }, new int[] { 1, 4 }, 2, 2));
assertFalse(dbr.isPrimaryCandidate());
}
}
public void testFindRegionForColumn()
{
HiddenColumnsCursor cursor = new HiddenColumnsCursor();
-
+
HiddenCursorPosition pos = cursor.findRegionForColumn(20, false);
assertNull(pos);
-
+
List<int[]> hidden = new ArrayList<>();
hidden.add(new int[] { 53, 76 });
hidden.add(new int[] { 104, 125 });
cursor = new HiddenColumnsCursor(hidden);
- int regionIndex = cursor.findRegionForColumn(126, false).getRegionIndex();
+ int regionIndex = cursor.findRegionForColumn(126, false)
+ .getRegionIndex();
assertEquals(2, regionIndex);
regionIndex = cursor.findRegionForColumn(125, false).getRegionIndex();
cs.hideColumns(10, 11);
cs.hideColumns(5, 7);
Iterator<int[]> regions = cs.iterator();
- assertEquals("[5, 7]",
- Arrays.toString(regions.next()));
+ assertEquals("[5, 7]", Arrays.toString(regions.next()));
HiddenColumns cs2 = new HiddenColumns(cs);
regions = cs2.iterator();
assertTrue(cs2.hasHiddenColumns());
assertEquals(2, cs2.getNumberOfRegions());
// hidden columns are held in column order
- assertEquals("[5, 7]",
- Arrays.toString(regions.next()));
- assertEquals("[10, 11]",
- Arrays.toString(regions.next()));
+ assertEquals("[5, 7]", Arrays.toString(regions.next()));
+ assertEquals("[10, 11]", Arrays.toString(regions.next()));
}
@Test(groups = "Functional")
Iterator<int[]> regions = cs2.iterator();
// only [5,7] returned, offset by 1
- assertEquals("[4, 6]",
- Arrays.toString(regions.next()));
+ assertEquals("[4, 6]", Arrays.toString(regions.next()));
assertEquals(3, cs2.getSize());
cs2 = new HiddenColumns(cs, 8, 15, 4);
assertTrue(cs2.hasHiddenColumns());
// only [10,11] returned, offset by 4
- assertEquals("[6, 7]",
- Arrays.toString(regions.next()));
+ assertEquals("[6, 7]", Arrays.toString(regions.next()));
assertEquals(2, cs2.getSize());
cs2 = new HiddenColumns(cs, 6, 10, 4);
assertFalse(cs2.hasHiddenColumns());
}
-
@Test(groups = { "Functional" })
public void testHideColumns()
{
cs.hideColumns(4, 5);
regions = cs.iterator();
assertEquals(1, cs.getNumberOfRegions());
- assertEquals("[3, 6]",
- Arrays.toString(regions.next()));
+ assertEquals("[3, 6]", Arrays.toString(regions.next()));
assertEquals(cs.getSize(), 4);
cs.hideColumns(3, 5);
regions = cs.iterator();
assertEquals(1, cs.getNumberOfRegions());
- assertEquals("[3, 6]",
- Arrays.toString(regions.next()));
+ assertEquals("[3, 6]", Arrays.toString(regions.next()));
assertEquals(cs.getSize(), 4);
cs.hideColumns(4, 6);
regions = cs.iterator();
assertEquals(1, cs.getNumberOfRegions());
- assertEquals("[3, 6]",
- Arrays.toString(regions.next()));
+ assertEquals("[3, 6]", Arrays.toString(regions.next()));
assertEquals(cs.getSize(), 4);
cs.hideColumns(3, 6);
regions = cs.iterator();
assertEquals(1, cs.getNumberOfRegions());
- assertEquals("[3, 6]",
- Arrays.toString(regions.next()));
+ assertEquals("[3, 6]", Arrays.toString(regions.next()));
assertEquals(cs.getSize(), 4);
cs.revealAllHiddenColumns(colsel);
* T>C at dna13, consequence CGT>CGC synonymous
*/
List<SequenceFeature> features = new ArrayList<>();
- SequenceFeature sf1 = new SequenceFeature("sequence_variant", "C,T",
- 11, 11, null);
+ SequenceFeature sf1 = new SequenceFeature("sequence_variant", "C,T", 11,
+ 11, null);
sf1.setValue("alleles", "C,T");
features.add(sf1);
SequenceFeature sf2 = new SequenceFeature("sequence_variant", "T,C", 13,
/*
* missense variant in first codon
*/
- MappedFeatures mf = new MappedFeatures(mapping, from, 1, 'R',
- features);
+ MappedFeatures mf = new MappedFeatures(mapping, from, 1, 'R', features);
String variant = mf.findProteinVariants(sf1);
assertEquals(variant, "p.Arg1Cys");
@Test(groups = { "Functional" })
public void testIntersectVisContigs()
{
- MapList fk = new MapList(new int[] { 1, 6, 8, 13, 15, 23 }, new int[] {
- 1, 7 }, 3, 1);
+ MapList fk = new MapList(new int[] { 1, 6, 8, 13, 15, 23 },
+ new int[]
+ { 1, 7 }, 3, 1);
Mapping m = new Mapping(fk);
- Mapping m_1 = m.intersectVisContigs(new int[] { fk.getFromLowest(),
- fk.getFromHighest() });
+ Mapping m_1 = m
+ .intersectVisContigs(new int[]
+ { fk.getFromLowest(), fk.getFromHighest() });
Mapping m_2 = m.intersectVisContigs(new int[] { 1, 7, 11, 20 });
// assertions from output values 'as is', not checked for correctness
PDBEntry case9 = new PDBEntry("1xyz", "A", null, "x/y/z/File");
// different file only
PDBEntry case10 = new PDBEntry("1xyz", "A", null, "a/b/c/File");
-
+
/*
* assertEquals will invoke PDBEntry.equals()
*/
assertTrue(pdb1.updateFrom(pdb2));
assertEquals(pdb1.getFile(), "filePath");
assertEquals(pdb1.getType(), Type.FILE.toString());
- assertEquals(pdb1.getChainCode(),"B");
+ assertEquals(pdb1.getChainCode(), "B");
/*
* change of file is not allowed
*/
pdb2.setProperty("hello", "moon");
assertTrue(pdb1.updateFrom(pdb2));
assertEquals(pdb1.getProperty("hello"), "moon");
-
+
/*
* different id but authoritative
*/
// can update pdb1 (authoritative) from pdb2 (non-authoritative)
assertTrue(pdb1.updateFrom(pdb2));
// but the ID must remain the same
- assertEquals(pdb1.getId(),"af:1xyz");
-
+ assertEquals(pdb1.getId(), "af:1xyz");
+
}
@Test(groups = { "Functional" })
* when alignment has hidden cols
*/
@Test(
- groups = { "Functional" },
- expectedExceptions = { NoSuchElementException.class })
+ groups =
+ { "Functional" },
+ expectedExceptions =
+ { NoSuchElementException.class })
public void testLastNextWithHidden() throws NoSuchElementException
{
Iterator<Integer> it = hiddenCols.getVisibleColsIterator(0, 3);
* when alignment has no hidden cols
*/
@Test(
- groups = { "Functional" },
- expectedExceptions = { NoSuchElementException.class })
+ groups =
+ { "Functional" },
+ expectedExceptions =
+ { NoSuchElementException.class })
public void testLastNextNoHidden() throws NoSuchElementException
{
HiddenColumns test = new HiddenColumns();
* when alignment has hidden cols at start
*/
@Test(
- groups = { "Functional" },
- expectedExceptions = { NoSuchElementException.class })
+ groups =
+ { "Functional" },
+ expectedExceptions =
+ { NoSuchElementException.class })
public void testLastNextStartHidden() throws NoSuchElementException
{
Iterator<Integer> it3 = hiddenColsAtStart.getVisibleColsIterator(0, 6);
* when alignment has hidden cols at end
*/
@Test(
- groups = { "Functional" },
- expectedExceptions = { NoSuchElementException.class })
+ groups =
+ { "Functional" },
+ expectedExceptions =
+ { NoSuchElementException.class })
public void testLastNextEndHidden() throws NoSuchElementException
{
Iterator<Integer> it4 = hiddenCols.getVisibleColsIterator(0, 4);
* Test calls to remove throw UnsupportedOperationException
*/
@Test(
- groups = { "Functional" },
- expectedExceptions = { UnsupportedOperationException.class })
+ groups =
+ { "Functional" },
+ expectedExceptions =
+ { UnsupportedOperationException.class })
public void testRemove() throws UnsupportedOperationException
{
Iterator<Integer> it = hiddenCols.getVisibleColsIterator(0, 3);
rc.add('-');
rc.add('.');
rc.add(' ');
-
+
assertEquals(rc.getGapCount(), 4);
assertEquals(rc.getCount(' '), 4);
assertEquals(rc.getCount('-'), 4);
assertEquals(rc.getCount('.'), 4);
assertFalse(rc.isUsingOtherData());
assertFalse(rc.isCountingInts());
-
- rc.set(ResidueCount.GAP_COUNT, Short.MAX_VALUE-2);
- assertEquals(rc.getGapCount(), Short.MAX_VALUE-2);
+
+ rc.set(ResidueCount.GAP_COUNT, Short.MAX_VALUE - 2);
+ assertEquals(rc.getGapCount(), Short.MAX_VALUE - 2);
assertFalse(rc.isCountingInts());
rc.addGap();
- assertEquals(rc.getGapCount(), Short.MAX_VALUE-1);
+ assertEquals(rc.getGapCount(), Short.MAX_VALUE - 1);
assertFalse(rc.isCountingInts());
rc.addGap();
assertEquals(rc.getGapCount(), Short.MAX_VALUE);
rc.addGap();
assertTrue(rc.isCountingInts());
- assertEquals(rc.getGapCount(), Short.MAX_VALUE+1);
+ assertEquals(rc.getGapCount(), Short.MAX_VALUE + 1);
}
@Test(groups = "Functional")
rc.add('P');
assertEquals(rc.getResiduesForCount(Short.MAX_VALUE + 1), "P");
assertEquals(rc.getResiduesForCount(1), "C");
-
+
// modal count is in the 'other data' counts
rc = new ResidueCount();
rc.add('Q');
rc.add('K');
}
rc.add('F');
-
+
/*
* percentages are rounded (0.5 rounded up)
* 10/40 9/40 7/40 6/40 1/40
int marked = 0;
SequenceI seq1 = new Sequence("", "abcdefghijklm");
SequenceI seq2 = new Sequence("", "abcdefghijklm");
- SequenceGroup s1g=new SequenceGroup(), s2g=new SequenceGroup(), sallg=new SequenceGroup();
+ SequenceGroup s1g = new SequenceGroup(), s2g = new SequenceGroup(),
+ sallg = new SequenceGroup();
s1g.addSequence(seq1, false);
s2g.addSequence(seq2, false);
sallg.addSequence(seq1, false);
sallg.addSequence(seq2, false);
-
+
SearchResultsI sr = new SearchResults();
BitSet bs = new BitSet();
-
+
SearchResultMatchI srm = null;
srm = sr.addResult(seq1, 1, 1);
Assert.assertNotNull("addResult didn't return Match", srm);
assertEquals("Sequence reference not set", seq2, srm.getSequence());
assertEquals("match start incorrect", 1, srm.getStart());
assertEquals("match end incorrect", 2, srm.getEnd());
-
+
// set start/end range for groups to cover matches
s1g.setStartRes(0);
assertTrue("Didn't mark expected position", bs.get(0));
// now check return value for marking the same again
assertEquals(
- "Didn't count number of bits marked for existing marked set",
- 0,
+ "Didn't count number of bits marked for existing marked set", 0,
sr.markColumns(s1g, bs));
bs.clear();
-
+
/*
* just seq2
*/
assertEquals("Didn't return count of number of bits marked", 2, marked);
assertTrue("Didn't mark expected position (1)", bs.get(0));
assertTrue("Didn't mark expected position (2)", bs.get(1));
-
+
/*
* both seq1 and seq2
* should be same as seq2
s2g.setEndRes(1);
sallg.setEndRes(0);
BitSet tbs = new BitSet();
- assertEquals("Group start/end didn't select columns to mark",1, sr.markColumns(s2g, tbs));
- assertEquals("Group start/end didn't select columns to mark", 1, sr.markColumns(sallg, tbs));
+ assertEquals("Group start/end didn't select columns to mark", 1,
+ sr.markColumns(s2g, tbs));
+ assertEquals("Group start/end didn't select columns to mark", 1,
+ sr.markColumns(sallg, tbs));
assertEquals(
"Didn't set expected number of columns in total for two successive marks",
2, tbs.cardinality());
SequenceI gen_sgapped_s = gen_sgapped.getSeq('-');
// assertEquals("Couldn't reconstruct sequence", s_gapped.getSequence(),
// gen_sgapped_s);
- if (!gen_sgapped_s.getSequenceAsString().equals(
- s_gapped.getSequenceAsString()))
+ if (!gen_sgapped_s.getSequenceAsString()
+ .equals(s_gapped.getSequenceAsString()))
{
// TODO: investigate errors reported here, to allow full conversion to
// passing JUnit assertion form
+ "<tr><td>Type</td><td>variant</td><td></td></tr>"
+ "<tr><td>Description</td><td>G,C</td><td></td></tr>"
+ "<tr><td>Consequence</td><td><i>Translated by Jalview</i></td><td>p.Leu9Phe</td></tr>"
- + "<tr><td>alleles</td><td></td><td>G,C</td></tr>"
- + "</table>";
+ + "<tr><td>alleles</td><td></td><td>G,C</td></tr>" + "</table>";
assertEquals(expected, sf.getDetailsReport(seq.getName(), mf));
-
/*
* exon feature extending beyond mapped range; mapped location should be
* restricted to peptide mapped range limit i.e. 10-13
*/
- SequenceFeature sf2 = new SequenceFeature("exon", "exon 1", 109, 230, null);
+ SequenceFeature sf2 = new SequenceFeature("exon", "exon 1", 109, 230,
+ null);
features.add(sf2);
expected = "<br><table><tr><td>Location</td><td>Cds</td><td>109-230</td></tr>"
+ "<tr><td>Peptide Location</td><td>TestSeq</td><td>10-13</td></tr>"
public class SequenceGroupTest
{
- @Test(groups={"Functional"})
+ @Test(groups = { "Functional" })
public void testAddSequence()
{
SequenceGroup sg = new SequenceGroup();
assertTrue(sg.getSequences().contains(seq3));
}
- @Test(groups={"Functional"})
+ @Test(groups = { "Functional" })
public void testAddOrRemove()
{
SequenceGroup sg = new SequenceGroup();
assertTrue(sg.getSequences().isEmpty());
-
+
SequenceI seq1 = new Sequence("seq1", "abc");
SequenceI seq2 = new Sequence("seq2", "abc");
SequenceI seq3 = new Sequence(seq1);
-
+
sg.addOrRemove(seq1, false);
assertEquals(sg.getSequences().size(), 1);
sg.addOrRemove(seq2, false);
assertFalse(sg.getSequences().contains(seq1));
}
- @Test(groups={"Functional"})
+ @Test(groups = { "Functional" })
public void testGetColourScheme()
{
SequenceGroup sg = new SequenceGroup();
assertSame(scheme, sg.getColourScheme());
}
- @Test(groups={"Functional"})
+ @Test(groups = { "Functional" })
public void testSetContext()
{
SequenceGroup sg1 = new SequenceGroup();
assertEquals("getInsertionsAsBits didn't mark expected number of gaps",
6, gapfield.cardinality());
- assertEquals("getInsertionsAsBits not correct.", expectedgaps, gapfield);
+ assertEquals("getInsertionsAsBits not correct.", expectedgaps,
+ gapfield);
}
@Test(groups = ("Functional"))
@Test(groups = ("Functional"))
public void testIsProteinWithXorNAmbiguityCodes()
{
- // test Protein with N - poly asparagine
+ // test Protein with N - poly asparagine
assertTrue(new Sequence("prot", "ASDFASDFASDFNNNNNNNNN").isProtein());
assertTrue(new Sequence("prot", "NNNNNNNNNNNNNNNNNNNNN").isProtein());
// test Protein with X
assertTrue(seq.getAlignmentAnnotations(null, null).isEmpty());
}
-
@Test(groups = { "Functional" })
public void testGetAlignmentAnnotations_forCalcIdLabelAndDescription()
{
/**
* null matching should fail
*/
- assertTrue(seq.getAlignmentAnnotations("calcId3", "label2",null).isEmpty());
-
- assertTrue(seq.getAlignmentAnnotations("calcId2", "label3",null).isEmpty());
- assertTrue(seq.getAlignmentAnnotations("calcId3", "label5",null).isEmpty());
- assertTrue(seq.getAlignmentAnnotations("calcId2", null,null).isEmpty());
- assertTrue(seq.getAlignmentAnnotations(null, "label3",null).isEmpty());
- assertTrue(seq.getAlignmentAnnotations(null, null,null).isEmpty());
+ assertTrue(seq.getAlignmentAnnotations("calcId3", "label2", null)
+ .isEmpty());
+
+ assertTrue(seq.getAlignmentAnnotations("calcId2", "label3", null)
+ .isEmpty());
+ assertTrue(seq.getAlignmentAnnotations("calcId3", "label5", null)
+ .isEmpty());
+ assertTrue(
+ seq.getAlignmentAnnotations("calcId2", null, null).isEmpty());
+ assertTrue(seq.getAlignmentAnnotations(null, "label3", null).isEmpty());
+ assertTrue(seq.getAlignmentAnnotations(null, null, null).isEmpty());
}
/**
public void testAddAlignmentAnnotation()
{
assertNull(seq.getAnnotation());
- final AlignmentAnnotation annotation = new AlignmentAnnotation("a",
- "b", 2d);
+ final AlignmentAnnotation annotation = new AlignmentAnnotation("a", "b",
+ 2d);
assertNull(annotation.sequenceRef);
seq.addAlignmentAnnotation(annotation);
assertSame(seq, annotation.sequenceRef);
/*
* SequenceFeature on sequence
*/
- SequenceFeature sf = new SequenceFeature("Cath", "desc", 2, 4, 2f, null);
+ SequenceFeature sf = new SequenceFeature("Cath", "desc", 2, 4, 2f,
+ null);
sq.addSequenceFeature(sf);
List<SequenceFeature> sfs = sq.getSequenceFeatures();
assertEquals(1, sfs.size());
try
{
sq.getDatasetSequence().setDatasetSequence(sq); // loop!
- Assert.fail("Expected Error to be raised when calling setDatasetSequence with self reference");
+ Assert.fail(
+ "Expected Error to be raised when calling setDatasetSequence with self reference");
} catch (IllegalArgumentException e)
{
// TODO Jalview error/exception class for raising implementation errors
public void testCreateDatasetSequence()
{
SequenceI sq = new Sequence("my", "ASDASD");
- sq.addSequenceFeature(new SequenceFeature("type", "desc", 1, 10, 1f,
- "group"));
+ sq.addSequenceFeature(
+ new SequenceFeature("type", "desc", 1, 10, 1f, "group"));
sq.addDBRef(new DBRefEntry("source", "version", "accession"));
assertNull(sq.getDatasetSequence());
assertNotNull(PA.getValue(sq, "sequenceFeatureStore"));
DBRefEntry pdb1pdb = new DBRefEntry("PDB", "version1", "1PDB");
DBRefEntry pdb2pdb = new DBRefEntry("PDB", "version2", "2PDB");
- List<DBRefEntry> primRefs = Arrays.asList(new DBRefEntry[] { pdb1pdb,
- pdb2pdb });
+ List<DBRefEntry> primRefs = Arrays
+ .asList(new DBRefEntry[]
+ { pdb1pdb, pdb2pdb });
sq.getDatasetSequence().addDBRef(pdb1pdb); // should do nothing
sq.getDatasetSequence().addDBRef(pdb2pdb); // should do nothing
- sq.getDatasetSequence().addDBRef(
- new DBRefEntry("PDB", "version3", "3PDB")); // should do nothing
- sq.getDatasetSequence().addDBRef(
- new DBRefEntry("PDB", "version4", "4PDB")); // should do nothing
+ sq.getDatasetSequence()
+ .addDBRef(new DBRefEntry("PDB", "version3", "3PDB")); // should do
+ // nothing
+ sq.getDatasetSequence()
+ .addDBRef(new DBRefEntry("PDB", "version4", "4PDB")); // should do
+ // nothing
PDBEntry pdbe1a = new PDBEntry("1PDB", "A", Type.PDB, "filePath/test1");
PDBEntry pdbe1b = new PDBEntry("1PDB", "B", Type.PDB, "filePath/test1");
/*
* test we added pdb entries to the dataset sequence
*/
- Assert.assertEquals(sq.getDatasetSequence().getAllPDBEntries(), Arrays
- .asList(new PDBEntry[] { pdbe1a, pdbe1b, pdbe2a, pdbe2b }),
+ Assert.assertEquals(sq.getDatasetSequence().getAllPDBEntries(),
+ Arrays.asList(new PDBEntry[]
+ { pdbe1a, pdbe1b, pdbe2a, pdbe2b }),
"PDB Entries were not found on dataset sequence.");
/*
* we should recover a pdb entry that is on the dataset sequence via PDBEntry
*/
- Assert.assertEquals(pdbe1a,
- sq.getDatasetSequence().getPDBEntry("1PDB"),
+ Assert.assertEquals(pdbe1a, sq.getDatasetSequence().getPDBEntry("1PDB"),
"PDB Entry '1PDB' not found on dataset sequence via getPDBEntry.");
ArrayList<Annotation> annotsList = new ArrayList<>();
System.out.println(">>>>>> " + sq.getSequenceAsString().length());
Annotation[] annots = annotsList.toArray(new Annotation[0]);
sq.addAlignmentAnnotation(new AlignmentAnnotation("Test annot",
"Test annot description", annots));
- sq.getDatasetSequence().addAlignmentAnnotation(
- new AlignmentAnnotation("Test annot", "Test annot description",
- annots));
+ sq.getDatasetSequence().addAlignmentAnnotation(new AlignmentAnnotation(
+ "Test annot", "Test annot description", annots));
Assert.assertEquals(sq.getDescription(), "Test sequence description..");
Assert.assertEquals(sq.getDBRefs().size(), 5); // DBRefs are on dataset
// sequence
Assert.assertNotNull(derived.getAnnotation());
Assert.assertEquals(derived.getAnnotation()[0].annotations.length, 2);
Assert.assertEquals(derived.getDatasetSequence().getDBRefs().size(), 5);
- Assert.assertEquals(derived.getDatasetSequence().getAllPDBEntries()
- .size(), 4);
+ Assert.assertEquals(
+ derived.getDatasetSequence().getAllPDBEntries().size(), 4);
Assert.assertNotNull(derived.getDatasetSequence().getAnnotation());
assertEquals("CD", derived.getSequenceAsString());
assertEquals(6, sq.getEnd());
SequenceI derived = sq.deriveSequence();
assertEquals("ABCDEF", derived.getSequenceAsString());
- assertEquals("ABCDEF", derived.getDatasetSequence()
- .getSequenceAsString());
+ assertEquals("ABCDEF",
+ derived.getDatasetSequence().getSequenceAsString());
}
/**
assertNull(sq.getDatasetSequence());
SequenceI derived = sq.deriveSequence();
assertEquals("AB-C.D EF", derived.getSequenceAsString());
- assertEquals("ABCDEF", derived.getDatasetSequence()
- .getSequenceAsString());
+ assertEquals("ABCDEF",
+ derived.getDatasetSequence().getSequenceAsString());
}
@Test(groups = { "Functional" })
{
SequenceI seq1 = new Sequence("Seq1", "AB-C.D EF");
seq1.setDescription("description");
- seq1.addAlignmentAnnotation(new AlignmentAnnotation("label", "desc",
- 1.3d));
- seq1.addSequenceFeature(new SequenceFeature("type", "desc", 22, 33,
- 12.4f, "group"));
+ seq1.addAlignmentAnnotation(
+ new AlignmentAnnotation("label", "desc", 1.3d));
+ seq1.addSequenceFeature(
+ new SequenceFeature("type", "desc", 22, 33, 12.4f, "group"));
seq1.addPDBId(new PDBEntry("1A70", "B", Type.PDB, "File"));
seq1.addDBRef(new DBRefEntry("EMBL", "1.2", "AZ12345"));
SequenceI seq1 = new Sequence("Seq1", "AB-C.D EF");
seq1.createDatasetSequence();
seq1.setDescription("description");
- seq1.addAlignmentAnnotation(new AlignmentAnnotation("label", "desc",
- 1.3d));
+ seq1.addAlignmentAnnotation(
+ new AlignmentAnnotation("label", "desc", 1.3d));
// JAL-2046 - what is the contract for using a derived sequence's
// addSequenceFeature ?
- seq1.addSequenceFeature(new SequenceFeature("type", "desc", 22, 33,
- 12.4f, "group"));
+ seq1.addSequenceFeature(
+ new SequenceFeature("type", "desc", 22, 33, 12.4f, "group"));
seq1.addPDBId(new PDBEntry("1A70", "B", Type.PDB, "File"));
// here we add DBRef to the dataset sequence:
- seq1.getDatasetSequence().addDBRef(
- new DBRefEntry("EMBL", "1.2", "AZ12345"));
+ seq1.getDatasetSequence()
+ .addDBRef(new DBRefEntry("EMBL", "1.2", "AZ12345"));
SequenceI copy = new Sequence(seq1);
{
SequenceI sq = new Sequence("", "abcde");
// type may not be null
- assertFalse(sq.addSequenceFeature(new SequenceFeature(null, "desc", 4,
- 8, 0f, null)));
- assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 4,
- 8, 0f, null)));
+ assertFalse(sq.addSequenceFeature(
+ new SequenceFeature(null, "desc", 4, 8, 0f, null)));
+ assertTrue(sq.addSequenceFeature(
+ new SequenceFeature("Cath", "desc", 4, 8, 0f, null)));
// can't add a duplicate feature
- assertFalse(sq.addSequenceFeature(new SequenceFeature("Cath", "desc",
- 4, 8, 0f, null)));
+ assertFalse(sq.addSequenceFeature(
+ new SequenceFeature("Cath", "desc", 4, 8, 0f, null)));
// can add a different feature
- assertTrue(sq.addSequenceFeature(new SequenceFeature("Scop", "desc", 4,
- 8, 0f, null))); // different type
- assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath",
- "description", 4, 8, 0f, null)));// different description
- assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 3,
- 8, 0f, null))); // different start position
- assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 4,
- 9, 0f, null))); // different end position
- assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 4,
- 8, 1f, null))); // different score
- assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 4,
- 8, Float.NaN, null))); // score NaN
- assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 4,
- 8, 0f, "Metal"))); // different group
+ assertTrue(sq.addSequenceFeature(
+ new SequenceFeature("Scop", "desc", 4, 8, 0f, null))); // different
+ // type
+ assertTrue(sq.addSequenceFeature(
+ new SequenceFeature("Cath", "description", 4, 8, 0f, null)));// different
+ // description
+ assertTrue(sq.addSequenceFeature(
+ new SequenceFeature("Cath", "desc", 3, 8, 0f, null))); // different
+ // start
+ // position
+ assertTrue(sq.addSequenceFeature(
+ new SequenceFeature("Cath", "desc", 4, 9, 0f, null))); // different
+ // end
+ // position
+ assertTrue(sq.addSequenceFeature(
+ new SequenceFeature("Cath", "desc", 4, 8, 1f, null))); // different
+ // score
+ assertTrue(sq.addSequenceFeature(
+ new SequenceFeature("Cath", "desc", 4, 8, Float.NaN, null))); // score
+ // NaN
+ assertTrue(sq.addSequenceFeature(
+ new SequenceFeature("Cath", "desc", 4, 8, 0f, "Metal"))); // different
+ // group
assertEquals(8, sq.getFeatures().getAllFeatures().size());
}
* matching ref with a mapping - map updated
*/
DBRefEntry dbref5 = new DBRefEntry("UniRef", "1", "p00341");
- Mapping map = new Mapping(new MapList(new int[] { 1, 3 }, new int[] {
- 1, 1 }, 3, 1));
+ Mapping map = new Mapping(
+ new MapList(new int[]
+ { 1, 3 }, new int[] { 1, 1 }, 3, 1));
dbref5.setMap(map);
sq.addDBRef(dbref5);
assertEquals(4, sq.getDBRefs().size());
assertTrue(primaryDBRefs.isEmpty());
// empty dbrefs
- sq.setDBRefs(null);
+ sq.setDBRefs(null);
primaryDBRefs = sq.getPrimaryDBRefs();
assertTrue(primaryDBRefs.isEmpty());
// primary - uniprot with congruent map
DBRefEntry upentry2 = new DBRefEntry("UNIPROT", "0", "Q04762");
- upentry2.setMap(new Mapping(null, new MapList(new int[] { 10, 22 },
- new int[] { 10, 22 }, 1, 1)));
+ upentry2.setMap(
+ new Mapping(null, new MapList(new int[]
+ { 10, 22 }, new int[] { 10, 22 }, 1, 1)));
sq.addDBRef(upentry2);
// primary - uniprot with map of enclosing sequence
DBRefEntry upentry3 = new DBRefEntry("UNIPROT", "0", "Q04763");
- upentry3.setMap(new Mapping(null, new MapList(new int[] { 8, 24 },
- new int[] { 8, 24 }, 1, 1)));
+ upentry3.setMap(
+ new Mapping(null, new MapList(new int[]
+ { 8, 24 }, new int[] { 8, 24 }, 1, 1)));
sq.addDBRef(upentry3);
// not primary - uniprot with map of sub-sequence (5')
DBRefEntry upentry4 = new DBRefEntry("UNIPROT", "0", "Q04764");
- upentry4.setMap(new Mapping(null, new MapList(new int[] { 10, 18 },
- new int[] { 10, 18 }, 1, 1)));
+ upentry4.setMap(
+ new Mapping(null, new MapList(new int[]
+ { 10, 18 }, new int[] { 10, 18 }, 1, 1)));
sq.addDBRef(upentry4);
// not primary - uniprot with map that overlaps 3'
DBRefEntry upentry5 = new DBRefEntry("UNIPROT", "0", "Q04765");
- upentry5.setMap(new Mapping(null, new MapList(new int[] { 12, 22 },
- new int[] { 12, 22 }, 1, 1)));
+ upentry5.setMap(
+ new Mapping(null, new MapList(new int[]
+ { 12, 22 }, new int[] { 12, 22 }, 1, 1)));
sq.addDBRef(upentry5);
// not primary - uniprot with map to different coordinates frame
DBRefEntry upentry6 = new DBRefEntry("UNIPROT", "0", "Q04766");
- upentry6.setMap(new Mapping(null, new MapList(new int[] { 12, 18 },
- new int[] { 112, 118 }, 1, 1)));
+ upentry6.setMap(
+ new Mapping(null, new MapList(new int[]
+ { 12, 18 }, new int[] { 112, 118 }, 1, 1)));
sq.addDBRef(upentry6);
// not primary - dbref to 'non-core' database
// add corroborating PDB entry for primary DBref -
// needs to have a file as well as matching ID
// note PDB ID is not treated as case sensitive
- sq.addPDBId(new PDBEntry("1QIP", null, Type.PDB, new File("/blah")
- .toString()));
+ sq.addPDBId(new PDBEntry("1QIP", null, Type.PDB,
+ new File("/blah").toString()));
// not valid DBRef - no file..
sq.addPDBId(new PDBEntry("1AAA", null, null, null));
@Test(groups = { "Functional" })
public void testGetPrimaryDBRefs_nucleotide()
{
- SequenceI sq = new Sequence("aseq", "TGATCACTCGACTAGCATCAGCATA", 10, 34);
+ SequenceI sq = new Sequence("aseq", "TGATCACTCGACTAGCATCAGCATA", 10,
+ 34);
// primary - Ensembl
DBRefEntry dbr1 = new DBRefEntry("ENSEMBL", "0", "ENSG1234");
// not primary - Ensembl 'transcript' mapping of sub-sequence
DBRefEntry dbr2 = new DBRefEntry("ENSEMBL", "0", "ENST1234");
- dbr2.setMap(new Mapping(null, new MapList(new int[] { 15, 25 },
- new int[] { 1, 11 }, 1, 1)));
+ dbr2.setMap(
+ new Mapping(null, new MapList(new int[]
+ { 15, 25 }, new int[] { 1, 11 }, 1, 1)));
sq.addDBRef(dbr2);
// primary - EMBL with congruent map
DBRefEntry dbr3 = new DBRefEntry("EMBL", "0", "J1234");
- dbr3.setMap(new Mapping(null, new MapList(new int[] { 10, 34 },
- new int[] { 10, 34 }, 1, 1)));
+ dbr3.setMap(
+ new Mapping(null, new MapList(new int[]
+ { 10, 34 }, new int[] { 10, 34 }, 1, 1)));
sq.addDBRef(dbr3);
// not primary - to non-core database
seq.addPDBId(pdbe5);
assertEquals(4, seq.getAllPDBEntries().size());
assertSame(pdbe5, seq.getAllPDBEntries().get(3));
-
- // add with a fake pdbid
+
+ // add with a fake pdbid
// (models don't have an embedded ID)
String realId = "RealIDQ";
- PDBEntry pdbe6 = new PDBEntry(realId,null,Type.PDB,"real/localpath");
- PDBEntry pdbe7 = new PDBEntry("RealID/real/localpath","C",Type.MMCIF,"real/localpath");
+ PDBEntry pdbe6 = new PDBEntry(realId, null, Type.PDB, "real/localpath");
+ PDBEntry pdbe7 = new PDBEntry("RealID/real/localpath", "C", Type.MMCIF,
+ "real/localpath");
pdbe7.setFakedPDBId(true);
seq.addPDBId(pdbe6);
- assertEquals(5,seq.getAllPDBEntries().size());
+ assertEquals(5, seq.getAllPDBEntries().size());
seq.addPDBId(pdbe7);
- assertEquals(5,seq.getAllPDBEntries().size());
+ assertEquals(5, seq.getAllPDBEntries().size());
assertFalse(pdbe6.fakedPDBId());
- assertSame(pdbe6,seq.getAllPDBEntries().get(4));
- assertEquals("C",pdbe6.getChainCode());
+ assertSame(pdbe6, seq.getAllPDBEntries().get(4));
+ assertEquals("C", pdbe6.getChainCode());
assertEquals(realId, pdbe6.getId());
}
@Test(
- groups = { "Functional" },
- expectedExceptions = { IllegalArgumentException.class })
+ groups =
+ { "Functional" },
+ expectedExceptions =
+ { IllegalArgumentException.class })
public void testSetDatasetSequence_toSelf()
{
seq.setDatasetSequence(seq);
}
@Test(
- groups = { "Functional" },
- expectedExceptions = { IllegalArgumentException.class })
+ groups =
+ { "Functional" },
+ expectedExceptions =
+ { IllegalArgumentException.class })
public void testSetDatasetSequence_cascading()
{
SequenceI seq2 = new Sequence("Seq2", "xyz");
"desc", 13, 14, 2f, null);
sq.addSequenceFeature(sfContactFG);
// add single position feature at [I]
- SequenceFeature sfI = new SequenceFeature("Disulfide Bond",
- "desc", 16, 16, null);
+ SequenceFeature sfI = new SequenceFeature("Disulfide Bond", "desc", 16,
+ 16, null);
sq.addSequenceFeature(sfI);
// no features in columns 1-2 (-A)
Sequence sq = new Sequence("test/8-13", "-A--BCD-EF--");
final int tok = (int) PA.getValue(sq, "changeCount");
assertEquals(1, tok);
-
+
// find F pos given A - lastCol gets set in cursor
assertEquals(13,
sq.findPosition(10, new SequenceCursor(sq, 8, 2, tok)));
sq.findPosition(2, new SequenceCursor(sq, 13, 10, tok)));
assertEquals("test:Pos8:Col2:startCol2:endCol10:tok1",
PA.getValue(sq, "cursor").toString());
-
+
// find C pos given C (neither startCol nor endCol is set)
assertEquals(10,
sq.findPosition(6, new SequenceCursor(sq, 10, 6, tok)));
public void testFindPosition_withCursorAndEdits()
{
Sequence sq = new Sequence("test/8-13", "-A--BCD-EF--");
-
+
// find F pos given A
assertEquals(13, sq.findPosition(10, new SequenceCursor(sq, 8, 2, 0)));
int token = (int) PA.getValue(sq, "changeCount"); // 0
*/
SequenceI sq = new Sequence("test", "-ABC--DEF--", 1, 20);
sq.createDatasetSequence();
-
+
assertTrue(sq.findFeatures(1, 9).isEmpty());
// should be no array bounds exception - JAL-2772
assertTrue(sq.findFeatures(1, 15).isEmpty());
-
+
// add feature on BCD
SequenceFeature sfBCD = new SequenceFeature("Cath", "desc", 2, 4, 2f,
null);
sq.addSequenceFeature(sfBCD);
-
+
// no features in columns 1-2 (-A)
List<SequenceFeature> found = sq.findFeatures(1, 2);
assertTrue(found.isEmpty());
-
+
// columns 1-6 (-ABC--) includes BCD
found = sq.findFeatures(1, 6);
assertEquals(1, found.size());
assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator()));
}
- @Test(groups= {"Functional"})
- public void testTransferAnnotation() {
- Sequence origSeq = new Sequence("MYSEQ","THISISASEQ");
- Sequence toSeq = new Sequence("MYSEQ","THISISASEQ");
+
+ @Test(groups = { "Functional" })
+ public void testTransferAnnotation()
+ {
+ Sequence origSeq = new Sequence("MYSEQ", "THISISASEQ");
+ Sequence toSeq = new Sequence("MYSEQ", "THISISASEQ");
origSeq.addDBRef(new DBRefEntry("UNIPROT", "0", "Q12345", null, true));
toSeq.transferAnnotation(origSeq, null);
- assertTrue(toSeq.getDBRefs().size()==1);
-
+ assertTrue(toSeq.getDBRefs().size() == 1);
+
assertTrue(toSeq.getDBRefs().get(0).isCanonical());
-
- // check for promotion of non-canonical
+
+ // check for promotion of non-canonical
// to canonical (e.g. fetch-db-refs on a jalview project pre 2.11.2)
toSeq.setDBRefs(null);
toSeq.addDBRef(new DBRefEntry("UNIPROT", "0", "Q12345", null, false));
toSeq.transferAnnotation(origSeq, null);
- assertTrue(toSeq.getDBRefs().size()==1);
-
- assertTrue("Promotion of non-canonical DBRefEntry failed",toSeq.getDBRefs().get(0).isCanonical());
-
-
+ assertTrue(toSeq.getDBRefs().size() == 1);
+
+ assertTrue("Promotion of non-canonical DBRefEntry failed",
+ toSeq.getDBRefs().get(0).isCanonical());
+
}
}
List<int[]> hiddenColumns = null;
// null hidden columns
- Iterator<Integer> it = new StartRegionIterator(3, 10,
- hiddenColumns);
+ Iterator<Integer> it = new StartRegionIterator(3, 10, hiddenColumns);
assertFalse(it.hasNext());
hiddenColumns = new ArrayList<>();
hiddenColumns = new ArrayList<>();
// no hidden columns
- it = new VisibleContigsIterator(3, 10,
- hiddenColumns);
+ it = new VisibleContigsIterator(3, 10, hiddenColumns);
assertTrue(it.hasNext());
assertFalse(it.endsAtHidden());
result = it.next();
* when alignment has hidden rows
*/
@Test(
- groups = { "Functional" },
- expectedExceptions = { NoSuchElementException.class })
+ groups =
+ { "Functional" },
+ expectedExceptions =
+ { NoSuchElementException.class })
public void testLastNextWithHidden() throws NoSuchElementException
{
VisibleRowsIterator it = new VisibleRowsIterator(0, 3, al);
* when alignment has no hidden rows
*/
@Test(
- groups = { "Functional" },
- expectedExceptions = { NoSuchElementException.class })
+ groups =
+ { "Functional" },
+ expectedExceptions =
+ { NoSuchElementException.class })
public void testLastNextNoHidden() throws NoSuchElementException
{
VisibleRowsIterator it = new VisibleRowsIterator(0, 3, al3);
* when alignment has hidden rows at start
*/
@Test(
- groups = { "Functional" },
- expectedExceptions = { NoSuchElementException.class })
+ groups =
+ { "Functional" },
+ expectedExceptions =
+ { NoSuchElementException.class })
public void testLastNextStartHidden() throws NoSuchElementException
{
VisibleRowsIterator it = new VisibleRowsIterator(0, 3, al2);
* when alignment has hidden rows at end
*/
@Test(
- groups = { "Functional" },
- expectedExceptions = { NoSuchElementException.class })
+ groups =
+ { "Functional" },
+ expectedExceptions =
+ { NoSuchElementException.class })
public void testLastNextEndHidden() throws NoSuchElementException
{
VisibleRowsIterator it = new VisibleRowsIterator(0, 4, al);
* Test calls to remove throw UnsupportedOperationException
*/
@Test(
- groups = { "Functional" },
- expectedExceptions = { UnsupportedOperationException.class })
+ groups =
+ { "Functional" },
+ expectedExceptions =
+ { UnsupportedOperationException.class })
public void testRemove() throws UnsupportedOperationException
{
VisibleRowsIterator it = new VisibleRowsIterator(0, 3, al);
* Test the method that keeps attribute names in non-case-sensitive order,
* including handling of 'compound' names
*/
- @Test(groups="Functional")
+ @Test(groups = "Functional")
public void testAttributeNameComparator()
{
FeatureAttributes fa = FeatureAttributes.getInstance();
"comparator");
assertEquals(
- comp.compare(new String[] { "CSQ" }, new String[] { "csq" }), 0);
+ comp.compare(new String[]
+ { "CSQ" }, new String[] { "csq" }), 0);
- assertTrue(comp.compare(new String[] { "CSQ", "a" },
- new String[] { "csq" }) > 0);
+ assertTrue(
+ comp.compare(new String[]
+ { "CSQ", "a" }, new String[] { "csq" }) > 0);
- assertTrue(comp.compare(new String[] { "CSQ" }, new String[] { "csq",
- "b" }) < 0);
+ assertTrue(
+ comp.compare(new String[]
+ { "CSQ" }, new String[] { "csq", "b" }) < 0);
- assertTrue(comp.compare(new String[] { "CSQ", "AF" }, new String[] {
- "csq", "ac" }) > 0);
+ assertTrue(
+ comp.compare(new String[]
+ { "CSQ", "AF" }, new String[] { "csq", "ac" }) > 0);
- assertTrue(comp.compare(new String[] { "CSQ", "ac" }, new String[] {
- "csq", "AF" }) < 0);
+ assertTrue(
+ comp.compare(new String[]
+ { "CSQ", "ac" }, new String[] { "csq", "AF" }) < 0);
}
@Test(groups = "Functional")
}
/**
- * Tests for the 'compound attribute' key i.e. where first key's value is a map
- * from which we take the value for the second key, e.g. CSQ : Consequence
+ * Tests for the 'compound attribute' key i.e. where first key's value is a
+ * map from which we take the value for the second key, e.g. CSQ : Consequence
*/
@Test(groups = "Functional")
public void testMatches_compoundKey()
FeatureMatcherI fm1 = FeatureMatcher.byAttribute(Condition.LT, "1.2",
"AF");
assertEquals(fm1.toStableString(), "AF LT 1.2");
-
+
FeatureMatcher fm2 = FeatureMatcher.byAttribute(Condition.NotContains,
"path", "CLIN_SIG");
assertEquals(fm2.toStableString(), "CLIN_SIG NotContains path");
-
+
/*
* AND them
*/
fms.and(fm2);
assertEquals(fms.toStableString(),
"(AF LT 1.2) AND (CLIN_SIG NotContains path)");
-
+
/*
* OR them
*/
fms.or(fm2);
assertEquals(fms.toStableString(),
"(AF LT 1.2) OR (CLIN_SIG NotContains path)");
-
+
/*
* attribute or value including space is quoted
*/
fms = FeatureMatcherSet
.fromString("(AF LT 1.2) and (CLIN_SIG NotContains path)");
assertEquals(fms.toStableString(), descriptor);
-
+
descriptor = "(AF LT 1.2) OR (CLIN_SIG NotContains path)";
fms = FeatureMatcherSet.fromString(descriptor);
assertEquals(fms.toStableString(), descriptor);
fms = FeatureMatcherSet
.fromString("(AF LT 1.2) or CLIN_SIG NotContains path");
assertEquals(fms.toStableString(), descriptor);
-
+
descriptor = "(AF LT 1.2) OR (CLIN_SIG NotContains path) OR ('CSQ:Poly Phen' NotMatches 'foo bar')";
fms = FeatureMatcherSet.fromString(descriptor);
assertEquals(fms.toStableString(), descriptor);
/*
* a numeric matcher - MatcherTest covers more conditions
*/
- FeatureMatcherI fm = FeatureMatcher
- .byAttribute(Condition.GE, "-2", "AF");
+ FeatureMatcherI fm = FeatureMatcher.byAttribute(Condition.GE, "-2",
+ "AF");
SequenceFeature sf = new SequenceFeature("Cath", "desc", 11, 12, "grp");
assertFalse(fm.matches(sf));
sf.setValue("AF", "foobar");
public void testFindFeatures_nonNested()
{
FeatureStore fs = new FeatureStore();
- fs.addFeature(new SequenceFeature("", "", 10, 20, Float.NaN,
- null));
+ fs.addFeature(new SequenceFeature("", "", 10, 20, Float.NaN, null));
// same range different description
fs.addFeature(new SequenceFeature("", "desc", 10, 20, Float.NaN, null));
fs.addFeature(new SequenceFeature("", "", 15, 25, Float.NaN, null));
Float.NaN, null);
store.addFeature(sf6);
// contact feature
- SequenceFeature sf7 = new SequenceFeature("Disulphide bond", "desc",
- 18, 45, Float.NaN, null);
+ SequenceFeature sf7 = new SequenceFeature("Disulphide bond", "desc", 18,
+ 45, Float.NaN, null);
store.addFeature(sf7);
List<SequenceFeature> features = store.getPositionalFeatures();
/*
* contact feature deletion
*/
- SequenceFeature sf3 = new SequenceFeature("", "Disulphide Bond", 11,
- 23, Float.NaN, null);
+ SequenceFeature sf3 = new SequenceFeature("", "Disulphide Bond", 11, 23,
+ Float.NaN, null);
store.addFeature(sf3);
assertEquals(store.getPositionalFeatures().size(), 1);
assertTrue(store.getPositionalFeatures().contains(sf3));
{
FeatureStore fs = new FeatureStore();
- SequenceFeature sf1 = new SequenceFeature("Cath", "", 10, 20,
- Float.NaN, null);
- SequenceFeature sf2 = new SequenceFeature("Cath", "", 10, 20,
- Float.NaN, null);
+ SequenceFeature sf1 = new SequenceFeature("Cath", "", 10, 20, Float.NaN,
+ null);
+ SequenceFeature sf2 = new SequenceFeature("Cath", "", 10, 20, Float.NaN,
+ null);
assertTrue(fs.addFeature(sf1));
assertEquals(fs.getFeatureCount(true), 1); // positional
/*
* non-nested feature
*/
- SequenceFeature sf1 = new SequenceFeature("Cath", "", 10, 20,
- Float.NaN, null);
+ SequenceFeature sf1 = new SequenceFeature("Cath", "", 10, 20, Float.NaN,
+ null);
fs.addFeature(sf1);
assertFalse(fs.isEmpty());
assertEquals(fs.getFeatureCount(true), 1);
/*
* contact feature
*/
- sf1 = new SequenceFeature("Disulfide bond", "", 19, 49, Float.NaN, null);
+ sf1 = new SequenceFeature("Disulfide bond", "", 19, 49, Float.NaN,
+ null);
fs.addFeature(sf1);
assertFalse(fs.isEmpty());
assertEquals(fs.getFeatureCount(true), 1);
* sf2, sf3 added as nested features
*/
sf1 = new SequenceFeature("Cath", "", 19, 49, Float.NaN, null);
- SequenceFeature sf2 = new SequenceFeature("Cath", "", 20, 40,
- Float.NaN, null);
- SequenceFeature sf3 = new SequenceFeature("Cath", "", 25, 35,
- Float.NaN, null);
+ SequenceFeature sf2 = new SequenceFeature("Cath", "", 20, 40, Float.NaN,
+ null);
+ SequenceFeature sf3 = new SequenceFeature("Cath", "", 25, 35, Float.NaN,
+ null);
fs.addFeature(sf1);
fs.addFeature(sf2);
fs.addFeature(sf3);
assertTrue(fs.getFeatureGroups(true).isEmpty());
assertTrue(fs.getFeatureGroups(false).isEmpty());
- SequenceFeature sf1 = new SequenceFeature("Cath", "desc", 10, 20, 1f, "group1");
+ SequenceFeature sf1 = new SequenceFeature("Cath", "desc", 10, 20, 1f,
+ "group1");
fs.addFeature(sf1);
Set<String> groups = fs.getFeatureGroups(true);
assertEquals(groups.size(), 1);
/*
* add another feature of the same group, delete one, delete both
*/
- SequenceFeature sf2 = new SequenceFeature("Cath", "desc", 20, 30, 1f, "group1");
+ SequenceFeature sf2 = new SequenceFeature("Cath", "desc", 20, 30, 1f,
+ "group1");
fs.addFeature(sf2);
groups = fs.getFeatureGroups(true);
assertEquals(groups.size(), 1);
groups = fs.getFeatureGroups(true);
assertTrue(fs.getFeatureGroups(true).isEmpty());
- SequenceFeature sf3 = new SequenceFeature("Cath", "desc", 20, 30, 1f, "group2");
+ SequenceFeature sf3 = new SequenceFeature("Cath", "desc", 20, 30, 1f,
+ "group2");
fs.addFeature(sf3);
- SequenceFeature sf4 = new SequenceFeature("Cath", "desc", 20, 30, 1f, "Group2");
+ SequenceFeature sf4 = new SequenceFeature("Cath", "desc", 20, 30, 1f,
+ "Group2");
fs.addFeature(sf4);
- SequenceFeature sf5 = new SequenceFeature("Cath", "desc", 20, 30, 1f, null);
+ SequenceFeature sf5 = new SequenceFeature("Cath", "desc", 20, 30, 1f,
+ null);
fs.addFeature(sf5);
groups = fs.getFeatureGroups(true);
assertEquals(groups.size(), 3);
assertEquals(fs.getTotalFeatureLength(), 93);
// contact features count 1
- SequenceFeature sf3 = new SequenceFeature("disulphide bond", "desc",
- 15, 35, 1f, "group1");
+ SequenceFeature sf3 = new SequenceFeature("disulphide bond", "desc", 15,
+ 35, 1f, "group1");
fs.addFeature(sf3);
assertEquals(fs.getTotalFeatureLength(), 94);
/*
* positional feature
*/
- SequenceFeature sf1 = new SequenceFeature("Cath", "desc", 10, 20, 1f, "group1");
+ SequenceFeature sf1 = new SequenceFeature("Cath", "desc", 10, 20, 1f,
+ "group1");
assertEquals(FeatureStore.getFeatureLength(sf1), 11);
-
+
/*
* non-positional feature
*/
/*
* contact feature counts 1
*/
- SequenceFeature sf3 = new SequenceFeature("Disulphide Bond", "desc",
- 14, 28, 1f, "AGroup");
+ SequenceFeature sf3 = new SequenceFeature("Disulphide Bond", "desc", 14,
+ 28, 1f, "AGroup");
assertEquals(FeatureStore.getFeatureLength(sf3), 1);
}
assertTrue(features.contains(sf2));
assertTrue(store.features.contains(sf1));
assertTrue(store.features.contains(sf2));
-
+
/*
* delete the first feature
*/
public void testContains()
{
FeatureStore fs = new FeatureStore();
- SequenceFeature sf1 = new SequenceFeature("Cath", "", 10, 20,
- Float.NaN, "group1");
- SequenceFeature sf2 = new SequenceFeature("Cath", "", 10, 20,
- Float.NaN, "group2");
+ SequenceFeature sf1 = new SequenceFeature("Cath", "", 10, 20, Float.NaN,
+ "group1");
+ SequenceFeature sf2 = new SequenceFeature("Cath", "", 10, 20, Float.NaN,
+ "group2");
SequenceFeature sf3 = new SequenceFeature("Cath", "", 0, 0, Float.NaN,
"group1");
SequenceFeature sf4 = new SequenceFeature("Cath", "", 0, 0, 0f,
/*
* add a nested feature
*/
- SequenceFeature sf7 = new SequenceFeature("Cath", "", 12, 16,
- Float.NaN, "group1");
+ SequenceFeature sf7 = new SequenceFeature("Cath", "", 12, 16, Float.NaN,
+ "group1");
fs.addFeature(sf7);
assertTrue(fs.contains(sf7));
assertTrue(fs.contains(new SequenceFeature(sf7)));
Float.NaN, null);
store.add(sf6);
// contact feature
- SequenceFeature sf7 = new SequenceFeature("Disulphide bond", "desc",
- 18, 45, Float.NaN, null);
+ SequenceFeature sf7 = new SequenceFeature("Disulphide bond", "desc", 18,
+ 45, Float.NaN, null);
store.add(sf7);
// different feature type
SequenceFeature sf8 = new SequenceFeature("Pfam", "desc", 30, 40,
Float.NaN, null);
store.add(sf2);
// contact feature
- SequenceFeature sf3 = new SequenceFeature("Disulphide bond", "desc",
- 18, 45, Float.NaN, null);
+ SequenceFeature sf3 = new SequenceFeature("Disulphide bond", "desc", 18,
+ 45, Float.NaN, null);
store.add(sf3);
// repeat for different feature type
SequenceFeature sf4 = new SequenceFeature("Pfam", "desc", 10, 20,
SequenceFeature sf6 = new SequenceFeature("Disulfide bond", "desc", 18,
45, Float.NaN, null);
store.add(sf6);
-
+
/*
* get all contact features
*/
assertEquals(features.size(), 2);
assertTrue(features.contains(sf3));
assertTrue(features.contains(sf6));
-
+
/*
* get contact features by type
*/
assertTrue(store.getContactFeatures("Cath").isEmpty());
assertTrue(store.getContactFeatures("Pfam").isEmpty());
assertTrue(store.getContactFeatures("DISULPHIDE BOND").isEmpty());
-
+
features = store.getContactFeatures("Disulphide bond");
assertEquals(features.size(), 1);
assertTrue(features.contains(sf3));
-
+
features = store.getContactFeatures("Disulfide bond");
assertEquals(features.size(), 1);
assertTrue(features.contains(sf6));
Float.NaN, null);
store.add(sf2);
// contact feature
- SequenceFeature sf3 = new SequenceFeature("Disulphide bond", "desc",
- 18, 45, Float.NaN, null);
+ SequenceFeature sf3 = new SequenceFeature("Disulphide bond", "desc", 18,
+ 45, Float.NaN, null);
store.add(sf3);
// repeat for different feature type
SequenceFeature sf4 = new SequenceFeature("Pfam", "desc", 10, 20,
SequenceFeature sf7 = new SequenceFeature("Pfam", "desc2", 0, 0,
Float.NaN, null);
store.add(sf7);
-
+
/*
* get all non-positional features
*/
assertTrue(features.contains(sf2));
assertTrue(features.contains(sf5));
assertTrue(features.contains(sf7));
-
+
/*
* get non-positional features by type
*/
assertTrue(store.getNonPositionalFeatures((String) null).isEmpty());
assertTrue(store.getNonPositionalFeatures("Cath").isEmpty());
assertTrue(store.getNonPositionalFeatures("PFAM").isEmpty());
-
+
features = store.getNonPositionalFeatures("Metal");
assertEquals(features.size(), 1);
assertTrue(features.contains(sf2));
-
+
features = store.getNonPositionalFeatures("Pfam");
assertEquals(features.size(), 2);
assertTrue(features.contains(sf5));
SequenceFeature addFeature(SequenceFeaturesI sf, String type, int from,
int to)
{
- SequenceFeature sf1 = new SequenceFeature(type, "", from, to,
- Float.NaN,
+ SequenceFeature sf1 = new SequenceFeature(type, "", from, to, Float.NaN,
null);
sf.add(sf1);
return sf1;
SequenceFeature sf10 = addFeature(sf, "Cath", 40, 100);
SequenceFeature sf11 = addFeature(sf, "Cath", 60, 100);
SequenceFeature sf12 = addFeature(sf, "Cath", 70, 70);
-
+
List<SequenceFeature> overlaps = sf.findFeatures(200, 200, "Pfam");
assertTrue(overlaps.isEmpty());
-
- overlaps = sf.findFeatures( 1, 9, "Pfam");
+
+ overlaps = sf.findFeatures(1, 9, "Pfam");
assertEquals(overlaps.size(), 1);
assertTrue(overlaps.contains(sf2));
-
- overlaps = sf.findFeatures( 5, 18, "Pfam");
+
+ overlaps = sf.findFeatures(5, 18, "Pfam");
assertEquals(overlaps.size(), 2);
assertTrue(overlaps.contains(sf1));
assertTrue(overlaps.contains(sf2));
-
+
overlaps = sf.findFeatures(30, 40, "Pfam");
assertEquals(overlaps.size(), 3);
assertTrue(overlaps.contains(sf1));
assertTrue(overlaps.contains(sf3));
assertTrue(overlaps.contains(sf4));
-
- overlaps = sf.findFeatures( 80, 90, "Pfam");
+
+ overlaps = sf.findFeatures(80, 90, "Pfam");
assertEquals(overlaps.size(), 2);
assertTrue(overlaps.contains(sf4));
assertTrue(overlaps.contains(sf5));
-
- overlaps = sf.findFeatures( 68, 70, "Pfam");
+
+ overlaps = sf.findFeatures(68, 70, "Pfam");
assertEquals(overlaps.size(), 3);
assertTrue(overlaps.contains(sf4));
assertTrue(overlaps.contains(sf5));
* add, then delete, more non-positional features of different types
*/
SequenceFeature sfy = new SequenceFeature("AnotherType", "Desc", 0, 0,
- 0f,
- "AnotherGroup");
+ 0f, "AnotherGroup");
sf.add(sfy);
SequenceFeature sfz = new SequenceFeature("AThirdType", "Desc", 0, 0,
- 0f,
- null);
+ 0f, null);
sf.add(sfz);
groups = sf.getFeatureGroups(false);
assertEquals(groups.size(), 3);
{
SequenceFeaturesI sf = new SequenceFeatures();
assertTrue(sf.getFeatureTypesForGroups(true, (String) null).isEmpty());
-
+
/*
* add feature with group = "Uniprot", type = "helix"
*/
assertEquals(groups.size(), 1);
assertTrue(groups.contains("helix"));
assertTrue(sf.getFeatureTypesForGroups(true, (String) null).isEmpty());
-
+
/*
* add feature with group = "Uniprot", type = "strand"
*/
assertTrue(groups.contains("turn"));
assertTrue(groups.contains("strand"));
// alternative vararg syntax
- groups = sf.getFeatureTypesForGroups(true, new String[] { "Cath",
- "Scop" });
+ groups = sf.getFeatureTypesForGroups(true,
+ new String[]
+ { "Cath", "Scop" });
assertEquals(groups.size(), 2);
assertTrue(groups.contains("turn"));
assertTrue(groups.contains("strand"));
/*
* add contact feature
*/
- SequenceFeature sf4 = new SequenceFeature("Disulphide Bond", "desc",
- 10, 20, Float.NaN, null);
+ SequenceFeature sf4 = new SequenceFeature("Disulphide Bond", "desc", 10,
+ 20, Float.NaN, null);
store.add(sf4);
types = store.getFeatureTypes();
assertEquals(types.size(), 3);
SequenceFeaturesI store = new SequenceFeatures();
assertEquals(store.getFeatureCount(true), 0);
assertEquals(store.getFeatureCount(false), 0);
-
+
/*
* add positional
*/
assertFalse(store.add(sf2));
assertEquals(store.getFeatureCount(true), 1);
assertEquals(store.getFeatureCount(false), 0);
-
+
/*
* add non-positional feature
*/
store.add(sf3);
assertEquals(store.getFeatureCount(true), 1);
assertEquals(store.getFeatureCount(false), 1);
-
+
/*
* add contact feature (counts as 1)
*/
- SequenceFeature sf4 = new SequenceFeature("Disulphide Bond", "desc",
- 10, 20, Float.NaN, null);
+ SequenceFeature sf4 = new SequenceFeature("Disulphide Bond", "desc", 10,
+ 20, Float.NaN, null);
store.add(sf4);
assertEquals(store.getFeatureCount(true), 2);
assertEquals(store.getFeatureCount(false), 1);
-
+
/*
* add another Pfam but this time as a positional feature
*/
assertTrue(store.delete(sf3));
assertEquals(store.getFeatureCount(true), 3);
assertEquals(store.getFeatureCount(false), 0);
-
+
/*
* delete second Pfam (positional)
*/
SequenceFeaturesI store = new SequenceFeatures();
List<SequenceFeature> features = store.getAllFeatures();
assertTrue(features.isEmpty());
-
+
SequenceFeature sf1 = new SequenceFeature("Metal", "desc", 10, 20,
Float.NaN, null);
store.add(sf1);
features = store.getAllFeatures();
assertEquals(features.size(), 1);
assertTrue(features.contains(sf1));
-
+
SequenceFeature sf2 = new SequenceFeature("Metallic", "desc", 10, 20,
Float.NaN, null);
store.add(sf2);
features = store.getAllFeatures();
assertEquals(features.size(), 2);
assertTrue(features.contains(sf2));
-
+
/*
* add non-positional feature
*/
features = store.getAllFeatures();
assertEquals(features.size(), 3);
assertTrue(features.contains(sf3));
-
+
/*
* add contact feature
*/
- SequenceFeature sf4 = new SequenceFeature("Disulphide Bond", "desc",
- 10, 20, Float.NaN, null);
+ SequenceFeature sf4 = new SequenceFeature("Disulphide Bond", "desc", 10,
+ 20, Float.NaN, null);
store.add(sf4);
features = store.getAllFeatures();
assertEquals(features.size(), 4);
assertTrue(features.contains(sf4));
-
+
/*
* add another Pfam
*/
assertTrue(features.contains(sf1));
assertTrue(features.contains(sf3));
assertTrue(features.contains(sf5));
-
+
/*
* delete first Pfam
*/
features = store.getAllFeatures();
assertEquals(features.size(), 4);
assertFalse(features.contains(sf3));
-
+
/*
* delete second Pfam
*/
/*
* add contact feature - counts 1 to feature length
*/
- SequenceFeature sf4 = new SequenceFeature("Disulphide Bond", "desc",
- 10, 20, Float.NaN, null);
+ SequenceFeature sf4 = new SequenceFeature("Disulphide Bond", "desc", 10,
+ 20, Float.NaN, null);
store.add(sf4);
assertEquals(store.getTotalFeatureLength(), 12);
public void testGetFeatureTypes_byOntology()
{
SequenceFeaturesI store = new SequenceFeatures();
-
+
SequenceFeature sf1 = new SequenceFeature("transcript", "desc", 10, 20,
Float.NaN, null);
store.add(sf1);
assertTrue(features.isEmpty());
assertTrue(store.getFeaturesByOntology(new String[] {}).isEmpty());
assertTrue(store.getFeaturesByOntology((String[]) null).isEmpty());
-
- SequenceFeature transcriptFeature = new SequenceFeature("transcript", "desc", 10, 20,
- Float.NaN, null);
+
+ SequenceFeature transcriptFeature = new SequenceFeature("transcript",
+ "desc", 10, 20, Float.NaN, null);
store.add(transcriptFeature);
/*
Float.NaN, null);
store.add(mrnaFeature);
- SequenceFeature pfamFeature = new SequenceFeature("Pfam", "desc", 30, 40,
- Float.NaN, null);
+ SequenceFeature pfamFeature = new SequenceFeature("Pfam", "desc", 30,
+ 40, Float.NaN, null);
store.add(pfamFeature);
/*
public void testSortFeatures()
{
List<SequenceFeature> sfs = new ArrayList<>();
- SequenceFeature sf1 = new SequenceFeature("Pfam", "desc", 30,
- 60,
+ SequenceFeature sf1 = new SequenceFeature("Pfam", "desc", 30, 60,
Float.NaN, null);
sfs.add(sf1);
SequenceFeature sf2 = new SequenceFeature("Rfam", "desc", 40, 50,
SequenceFeature sf3 = new SequenceFeature("Rfam", "desc", 50, 60,
Float.NaN, null);
sfs.add(sf3);
- SequenceFeature sf4 = new SequenceFeature("Xfam", "desc", 30,
- 80,
+ SequenceFeature sf4 = new SequenceFeature("Xfam", "desc", 30, 80,
Float.NaN, null);
sfs.add(sf4);
- SequenceFeature sf5 = new SequenceFeature("Xfam", "desc", 30,
- 90,
+ SequenceFeature sf5 = new SequenceFeature("Xfam", "desc", 30, 90,
Float.NaN, null);
sfs.add(sf5);
assertTrue(features.contains(sf5));
// positional features for null group, specified type
- features = store.getFeaturesForGroup(true, null, new String[] { "Pfam",
- "Xfam" });
+ features = store.getFeaturesForGroup(true, null,
+ new String[]
+ { "Pfam", "Xfam" });
assertEquals(features.size(), 1);
assertTrue(features.contains(sf1));
- features = store.getFeaturesForGroup(true, null, new String[] { "Pfam",
- "Xfam", "Cath" });
+ features = store.getFeaturesForGroup(true, null,
+ new String[]
+ { "Pfam", "Xfam", "Cath" });
assertEquals(features.size(), 2);
assertTrue(features.contains(sf1));
assertTrue(features.contains(sf5));
"Rfam");
assertEquals(features.size(), 1);
assertTrue(features.contains(sf3));
- assertTrue(store.getFeaturesForGroup(true, "Uniprot", "Cath").isEmpty());
+ assertTrue(
+ store.getFeaturesForGroup(true, "Uniprot", "Cath").isEmpty());
// non-positional features for null group, any type
features = store.getFeaturesForGroup(false, null);
// non-positional feature:
SequenceFeature sf4 = new SequenceFeature("Pfam", "", 0, 0, 0f, null);
store.add(sf4);
-
+
/*
* shift features right by 5
*/
assertTrue(store.shiftFeatures(0, 5));
-
+
// non-positional features untouched:
List<SequenceFeature> nonPos = store.getNonPositionalFeatures();
assertEquals(nonPos.size(), 1);
assertTrue(nonPos.contains(sf4));
-
+
// positional features are replaced
List<SequenceFeature> pos = store.getPositionalFeatures();
assertEquals(pos.size(), 3);
assertEquals(pos.get(2).getBegin(), 28);
assertEquals(pos.get(2).getEnd(), 37);
assertEquals(pos.get(2).getType(), "Disulfide bond");
-
+
/*
* now shift left by 15
* feature at [7-10] should be removed
public void testAdd()
{
SparseIntArray counter = new SparseIntArray();
-
+
assertEquals(counter.add('P', 2), 2);
assertEquals(counter.add('P', 3), 5);
counter.put('Q', 7);
{
// expected
}
-
+
counter.put('y', Integer.MIN_VALUE);
try
{
public void testAdd()
{
SparseShortArray counter = new SparseShortArray();
-
+
assertEquals(counter.add('P', 2), 2);
assertEquals(counter.add('P', 3), 5);
counter.put('Q', 7);
{
// expected;
}
-
+
// decrement giving underflow
counter.put('y', Short.MIN_VALUE);
try
String accId = "ABC123";
EnsemblCdna testee = new EnsemblCdna();
- SequenceFeature sf = new SequenceFeature("transcript", "", 20000,
- 20500, 0f, null);
+ SequenceFeature sf = new SequenceFeature("transcript", "", 20000, 20500,
+ 0f, null);
assertFalse(testee.retainFeature(sf, accId));
sf = new SequenceFeature("aberrant_processed_transcript", "", 20000,
20500, 0f, null);
assertFalse(testee.retainFeature(sf, accId));
- sf = new SequenceFeature("NMD_transcript_variant", "", 20000, 20500,
- 0f, null);
+ sf = new SequenceFeature("NMD_transcript_variant", "", 20000, 20500, 0f,
+ null);
assertFalse(testee.retainFeature(sf, accId));
// other feature with no parent is retained
- sf = new SequenceFeature("sequence_variant", "", 20000, 20500, 0f, null);
+ sf = new SequenceFeature("sequence_variant", "", 20000, 20500, 0f,
+ null);
assertTrue(testee.retainFeature(sf, accId));
// other feature with desired parent is retained
assertFalse(testee.retainFeature(sf, accId));
// other feature with no parent is retained
- sf = new SequenceFeature("anotherType", "", 20000,
- 20500, 0f, null);
+ sf = new SequenceFeature("anotherType", "", 20000, 20500, 0f, null);
assertTrue(testee.retainFeature(sf, accId));
// other feature with desired parent is retained
genomic.addSequenceFeature(sf1);
// transcript sub-type feature
- SequenceFeature sf2 = new SequenceFeature("snRNA", "", 21000, 21500,
- 0f, null);
+ SequenceFeature sf2 = new SequenceFeature("snRNA", "", 21000, 21500, 0f,
+ null);
sf2.setValue("Parent", geneId);
sf2.setValue("id", "transcript2");
genomic.addSequenceFeature(sf2);
genomic.addSequenceFeature(sf3);
// transcript for a different gene - ignored
- SequenceFeature sf4 = new SequenceFeature("snRNA", "", 23000, 23500,
- 0f, null);
+ SequenceFeature sf4 = new SequenceFeature("snRNA", "", 23000, 23500, 0f,
+ null);
sf4.setValue("Parent", "XYZ");
sf4.setValue("id", "transcript4");
genomic.addSequenceFeature(sf4);
sf.setValue("Parent", geneId);
assertTrue(testee.retainFeature(sf, geneId));
- sf = new SequenceFeature("NMD_transcript_variant", "", 20000, 20500,
- 0f, null);
+ sf = new SequenceFeature("NMD_transcript_variant", "", 20000, 20500, 0f,
+ null);
sf.setValue("Parent", geneId);
assertTrue(testee.retainFeature(sf, geneId));
seq.addSequenceFeature(sf3);
// gene sub-type with right ID is valid
- SequenceFeature sf4 = new SequenceFeature("snRNA_gene", "", 1, 2, 0f, null);
+ SequenceFeature sf4 = new SequenceFeature("snRNA_gene", "", 1, 2, 0f,
+ null);
sf4.setValue("id", accId);
seq.addSequenceFeature(sf4);
// transcript not valid:
- SequenceFeature sf5 = new SequenceFeature("transcript", "", 1, 2, 0f, null);
+ SequenceFeature sf5 = new SequenceFeature("transcript", "", 1, 2, 0f,
+ null);
sf5.setValue("id", accId);
seq.addSequenceFeature(sf5);
SequenceFeature sf6 = new SequenceFeature("exon", "", 1, 2, 0f, null);
sf6.setValue("id", accId);
seq.addSequenceFeature(sf6);
-
+
List<SequenceFeature> sfs = new EnsemblGene()
.getIdentifyingFeatures(seq, accId);
assertFalse(sfs.contains(sf1));
assertTrue(fc.isFeatureHidden("transcript"));
assertTrue(fc.isFeatureHidden("CDS"));
- assertEquals(Color.RED, fc.getFeatureColour("sequence_variant")
- .getColour());
- assertEquals(Color.RED, fc.getFeatureColour("feature_variant")
- .getColour());
+ assertEquals(Color.RED,
+ fc.getFeatureColour("sequence_variant").getColour());
+ assertEquals(Color.RED,
+ fc.getFeatureColour("feature_variant").getColour());
assertTrue(fc.getFeatureColour("exon").isColourByLabel());
assertTrue(fc.getFeatureColour("coding_exon").isColourByLabel());
assertEquals(1, fc.compare("sequence_variant", "exon"));
assertTrue(geneIds.contains("ENSDARG00000017661")); // zebrafish
assertTrue(geneIds.contains("ENSGALG00000012865")); // chicken
assertEquals(8, geneIds.size());
-
+
}
}
String transcriptId = "ABC123";
// transcript at (start+10000) length 501
- SequenceFeature sf = new SequenceFeature("transcript", "", 20000,
- 20500, 0f, null);
+ SequenceFeature sf = new SequenceFeature("transcript", "", 20000, 20500,
+ 0f, null);
sf.setValue("id", transcriptId);
sf.setStrand("+");
genomic.addSequenceFeature(sf);
// Ensembl treats NMD_transcript_variant as if transcript
// although strictly it is a sequence_variant in SO
- sf = new SequenceFeature("NMD_transcript_variant", "", 11000, 12000,
- 0f, null);
+ sf = new SequenceFeature("NMD_transcript_variant", "", 11000, 12000, 0f,
+ null);
sf.setValue("id", transcriptId);
sf.setStrand("+");
genomic.addSequenceFeature(sf);
String accId = "ABC123";
EnsemblGenome testee = new EnsemblGenome();
- SequenceFeature sf = new SequenceFeature("transcript", "", 20000,
- 20500, 0f, null);
+ SequenceFeature sf = new SequenceFeature("transcript", "", 20000, 20500,
+ 0f, null);
assertFalse(testee.retainFeature(sf, accId));
sf = new SequenceFeature("mature_transcript", "", 20000, 20500, 0f,
null);
assertFalse(testee.retainFeature(sf, accId));
- sf = new SequenceFeature("NMD_transcript_variant", "", 20000, 20500,
- 0f, null);
+ sf = new SequenceFeature("NMD_transcript_variant", "", 20000, 20500, 0f,
+ null);
assertFalse(testee.retainFeature(sf, accId));
// other feature with no parent is kept
}
else
{
- System.err
- .println("Ensembl is DOWN or unreachable ******************* BAD!");
+ System.err.println(
+ "Ensembl is DOWN or unreachable ******************* BAD!");
}
}
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
- private static final Object[][] allSeqs = new Object[][] {
- {
- new EnsemblProtein(),
- "CCDS5863.1",
- ">CCDS5863.1\n"
- + "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEH\n"
- + "IEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSSASMDTV\n"
- + "TSSSSSSLSVLPSSLSVFQNPTDVARSNPKSPQKPIVRVFLPNKQRTVVPARCGVTVRDS\n"
- + "LKKALMMRGLIPECCAVYRIQDGEKKPIGWDTDISWLTGEELHVEVLENVPLTTHNFVRK\n"
- + "TFFTLAFCDFCRKLLFQGFRCQTCGYKFHQRCSTEVPLMCVNYDQLDLLFVSKFFEHHPI\n"
- + "PQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSKSIPIPQPFRPADEDHRNQFGQR\n"
- + "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDGGSTTGLSATPPASLPGSLTNVKALQKSP\n"
- + "GPQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDV\n"
- + "AVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHH\n"
- + "LHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATV\n"
- + "KSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNIN\n"
- + "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
- + "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH\n" },
- {
- new EnsemblCdna(),
- "CCDS5863.1",
- ">CCDS5863.1\n"
- + "ATGGCGGCGCTGAGCGGTGGCGGTGGTGGCGGCGCGGAGCCGGGCCAGGCTCTGTTCAAC\n"
- + "GGGGACATGGAGCCCGAGGCCGGCGCCGGCGCCGGCGCCGCGGCCTCTTCGGCTGCGGAC\n"
- + "CCTGCCATTCCGGAGGAGGTGTGGAATATCAAACAAATGATTAAGTTGACACAGGAACAT\n"
- + "ATAGAGGCCCTATTGGACAAATTTGGTGGGGAGCATAATCCACCATCAATATATCTGGAG\n"
- + "GCCTATGAAGAATACACCAGCAAGCTAGATGCACTCCAACAAAGAGAACAACAGTTATTG\n"
- + "GAATCTCTGGGGAACGGAACTGATTTTTCTGTTTCTAGCTCTGCATCAATGGATACCGTT\n"
- + "ACATCTTCTTCCTCTTCTAGCCTTTCAGTGCTACCTTCATCTCTTTCAGTTTTTCAAAAT\n"
- + "CCCACAGATGTGGCACGGAGCAACCCCAAGTCACCACAAAAACCTATCGTTAGAGTCTTC\n"
- + "CTGCCCAACAAACAGAGGACAGTGGTACCTGCAAGGTGTGGAGTTACAGTCCGAGACAGT\n"
- + "CTAAAGAAAGCACTGATGATGAGAGGTCTAATCCCAGAGTGCTGTGCTGTTTACAGAATT\n"
- + "CAGGATGGAGAGAAGAAACCAATTGGTTGGGACACTGATATTTCCTGGCTTACTGGAGAA\n"
- + "GAATTGCATGTGGAAGTGTTGGAGAATGTTCCACTTACAACACACAACTTTGTACGAAAA\n"
- + "ACGTTTTTCACCTTAGCATTTTGTGACTTTTGTCGAAAGCTGCTTTTCCAGGGTTTCCGC\n"
- + "TGTCAAACATGTGGTTATAAATTTCACCAGCGTTGTAGTACAGAAGTTCCACTGATGTGT\n"
- + "GTTAATTATGACCAACTTGATTTGCTGTTTGTCTCCAAGTTCTTTGAACACCACCCAATA\n"
- + "CCACAGGAAGAGGCGTCCTTAGCAGAGACTGCCCTAACATCTGGATCATCCCCTTCCGCA\n"
- + "CCCGCCTCGGACTCTATTGGGCCCCAAATTCTCACCAGTCCGTCTCCTTCAAAATCCATT\n"
- + "CCAATTCCACAGCCCTTCCGACCAGCAGATGAAGATCATCGAAATCAATTTGGGCAACGA\n"
- + "GACCGATCCTCATCAGCTCCCAATGTGCATATAAACACAATAGAACCTGTCAATATTGAT\n"
- + "GACTTGATTAGAGACCAAGGATTTCGTGGTGATGGAGGATCAACCACAGGTTTGTCTGCT\n"
- + "ACCCCCCCTGCCTCATTACCTGGCTCACTAACTAACGTGAAAGCCTTACAGAAATCTCCA\n"
- + "GGACCTCAGCGAGAAAGGAAGTCATCTTCATCCTCAGAAGACAGGAATCGAATGAAAACA\n"
- + "CTTGGTAGACGGGACTCGAGTGATGATTGGGAGATTCCTGATGGGCAGATTACAGTGGGA\n"
- + "CAAAGAATTGGATCTGGATCATTTGGAACAGTCTACAAGGGAAAGTGGCATGGTGATGTG\n"
- + "GCAGTGAAAATGTTGAATGTGACAGCACCTACACCTCAGCAGTTACAAGCCTTCAAAAAT\n"
- + "GAAGTAGGAGTACTCAGGAAAACACGACATGTGAATATCCTACTCTTCATGGGCTATTCC\n"
- + "ACAAAGCCACAACTGGCTATTGTTACCCAGTGGTGTGAGGGCTCCAGCTTGTATCACCAT\n"
- + "CTCCATATCATTGAGACCAAATTTGAGATGATCAAACTTATAGATATTGCACGACAGACT\n"
- + "GCACAGGGCATGGATTACTTACACGCCAAGTCAATCATCCACAGAGACCTCAAGAGTAAT\n"
- + "AATATATTTCTTCATGAAGACCTCACAGTAAAAATAGGTGATTTTGGTCTAGCTACAGTG\n"
- + "AAATCTCGATGGAGTGGGTCCCATCAGTTTGAACAGTTGTCTGGATCCATTTTGTGGATG\n"
- + "GCACCAGAAGTCATCAGAATGCAAGATAAAAATCCATACAGCTTTCAGTCAGATGTATAT\n"
- + "GCATTTGGAATTGTTCTGTATGAATTGATGACTGGACAGTTACCTTATTCAAACATCAAC\n"
- + "AACAGGGACCAGATAATTTTTATGGTGGGACGAGGATACCTGTCTCCAGATCTCAGTAAG\n"
- + "GTACGGAGTAACTGTCCAAAAGCCATGAAGAGATTAATGGCAGAGTGCCTCAAAAAGAAA\n"
- + "AGAGATGAGAGACCACTCTTTCCCCAAATTCTCGCCTCTATTGAGCTGCTGGCCCGCTCA\n"
- + "TTGCCAAAAATTCACCGCAGTGCATCAGAACCCTCCTTGAATCGGGCTGGTTTCCAAACA\n"
- + "GAGGATTTTAGTCTATATGCTTGTGCTTCTCCAAAAACACCCATCCAGGCAGGGGGATAT\n"
- + "GGTGCGTTTCCTGTCCACTGA\n" },
- {
- new EnsemblProtein(),
- "ENSP00000288602",
- ">ENSP00000288602\n"
- + "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEH\n"
- + "IEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSSASMDTV\n"
- + "TSSSSSSLSVLPSSLSVFQNPTDVARSNPKSPQKPIVRVFLPNKQRTVVPARCGVTVRDS\n"
- + "LKKALMMRGLIPECCAVYRIQDGEKKPIGWDTDISWLTGEELHVEVLENVPLTTHNFVRK\n"
- + "TFFTLAFCDFCRKLLFQGFRCQTCGYKFHQRCSTEVPLMCVNYDQLDLLFVSKFFEHHPI\n"
- + "PQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSKSIPIPQPFRPADEDHRNQFGQR\n"
- + "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDG\n"
- // ? insertion added in ENSP00000288602.11, not in P15056
- + "APLNQLMRCLRKYQSRTPSPLLHSVPSEIVFDFEPGPVFR\n"
- // end insertion
- + "GSTTGLSATPPASLPGSLTNVKALQKSP\n"
- + "GPQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDV\n"
- + "AVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHH\n"
- + "LHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATV\n"
- + "KSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNIN\n"
- + "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
- + "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH" } };
+ private static final Object[][] allSeqs = new Object[][] { {
+ new EnsemblProtein(), "CCDS5863.1",
+ ">CCDS5863.1\n"
+ + "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEH\n"
+ + "IEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSSASMDTV\n"
+ + "TSSSSSSLSVLPSSLSVFQNPTDVARSNPKSPQKPIVRVFLPNKQRTVVPARCGVTVRDS\n"
+ + "LKKALMMRGLIPECCAVYRIQDGEKKPIGWDTDISWLTGEELHVEVLENVPLTTHNFVRK\n"
+ + "TFFTLAFCDFCRKLLFQGFRCQTCGYKFHQRCSTEVPLMCVNYDQLDLLFVSKFFEHHPI\n"
+ + "PQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSKSIPIPQPFRPADEDHRNQFGQR\n"
+ + "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDGGSTTGLSATPPASLPGSLTNVKALQKSP\n"
+ + "GPQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDV\n"
+ + "AVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHH\n"
+ + "LHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATV\n"
+ + "KSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNIN\n"
+ + "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
+ + "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH\n" },
+ { new EnsemblCdna(), "CCDS5863.1", ">CCDS5863.1\n"
+ + "ATGGCGGCGCTGAGCGGTGGCGGTGGTGGCGGCGCGGAGCCGGGCCAGGCTCTGTTCAAC\n"
+ + "GGGGACATGGAGCCCGAGGCCGGCGCCGGCGCCGGCGCCGCGGCCTCTTCGGCTGCGGAC\n"
+ + "CCTGCCATTCCGGAGGAGGTGTGGAATATCAAACAAATGATTAAGTTGACACAGGAACAT\n"
+ + "ATAGAGGCCCTATTGGACAAATTTGGTGGGGAGCATAATCCACCATCAATATATCTGGAG\n"
+ + "GCCTATGAAGAATACACCAGCAAGCTAGATGCACTCCAACAAAGAGAACAACAGTTATTG\n"
+ + "GAATCTCTGGGGAACGGAACTGATTTTTCTGTTTCTAGCTCTGCATCAATGGATACCGTT\n"
+ + "ACATCTTCTTCCTCTTCTAGCCTTTCAGTGCTACCTTCATCTCTTTCAGTTTTTCAAAAT\n"
+ + "CCCACAGATGTGGCACGGAGCAACCCCAAGTCACCACAAAAACCTATCGTTAGAGTCTTC\n"
+ + "CTGCCCAACAAACAGAGGACAGTGGTACCTGCAAGGTGTGGAGTTACAGTCCGAGACAGT\n"
+ + "CTAAAGAAAGCACTGATGATGAGAGGTCTAATCCCAGAGTGCTGTGCTGTTTACAGAATT\n"
+ + "CAGGATGGAGAGAAGAAACCAATTGGTTGGGACACTGATATTTCCTGGCTTACTGGAGAA\n"
+ + "GAATTGCATGTGGAAGTGTTGGAGAATGTTCCACTTACAACACACAACTTTGTACGAAAA\n"
+ + "ACGTTTTTCACCTTAGCATTTTGTGACTTTTGTCGAAAGCTGCTTTTCCAGGGTTTCCGC\n"
+ + "TGTCAAACATGTGGTTATAAATTTCACCAGCGTTGTAGTACAGAAGTTCCACTGATGTGT\n"
+ + "GTTAATTATGACCAACTTGATTTGCTGTTTGTCTCCAAGTTCTTTGAACACCACCCAATA\n"
+ + "CCACAGGAAGAGGCGTCCTTAGCAGAGACTGCCCTAACATCTGGATCATCCCCTTCCGCA\n"
+ + "CCCGCCTCGGACTCTATTGGGCCCCAAATTCTCACCAGTCCGTCTCCTTCAAAATCCATT\n"
+ + "CCAATTCCACAGCCCTTCCGACCAGCAGATGAAGATCATCGAAATCAATTTGGGCAACGA\n"
+ + "GACCGATCCTCATCAGCTCCCAATGTGCATATAAACACAATAGAACCTGTCAATATTGAT\n"
+ + "GACTTGATTAGAGACCAAGGATTTCGTGGTGATGGAGGATCAACCACAGGTTTGTCTGCT\n"
+ + "ACCCCCCCTGCCTCATTACCTGGCTCACTAACTAACGTGAAAGCCTTACAGAAATCTCCA\n"
+ + "GGACCTCAGCGAGAAAGGAAGTCATCTTCATCCTCAGAAGACAGGAATCGAATGAAAACA\n"
+ + "CTTGGTAGACGGGACTCGAGTGATGATTGGGAGATTCCTGATGGGCAGATTACAGTGGGA\n"
+ + "CAAAGAATTGGATCTGGATCATTTGGAACAGTCTACAAGGGAAAGTGGCATGGTGATGTG\n"
+ + "GCAGTGAAAATGTTGAATGTGACAGCACCTACACCTCAGCAGTTACAAGCCTTCAAAAAT\n"
+ + "GAAGTAGGAGTACTCAGGAAAACACGACATGTGAATATCCTACTCTTCATGGGCTATTCC\n"
+ + "ACAAAGCCACAACTGGCTATTGTTACCCAGTGGTGTGAGGGCTCCAGCTTGTATCACCAT\n"
+ + "CTCCATATCATTGAGACCAAATTTGAGATGATCAAACTTATAGATATTGCACGACAGACT\n"
+ + "GCACAGGGCATGGATTACTTACACGCCAAGTCAATCATCCACAGAGACCTCAAGAGTAAT\n"
+ + "AATATATTTCTTCATGAAGACCTCACAGTAAAAATAGGTGATTTTGGTCTAGCTACAGTG\n"
+ + "AAATCTCGATGGAGTGGGTCCCATCAGTTTGAACAGTTGTCTGGATCCATTTTGTGGATG\n"
+ + "GCACCAGAAGTCATCAGAATGCAAGATAAAAATCCATACAGCTTTCAGTCAGATGTATAT\n"
+ + "GCATTTGGAATTGTTCTGTATGAATTGATGACTGGACAGTTACCTTATTCAAACATCAAC\n"
+ + "AACAGGGACCAGATAATTTTTATGGTGGGACGAGGATACCTGTCTCCAGATCTCAGTAAG\n"
+ + "GTACGGAGTAACTGTCCAAAAGCCATGAAGAGATTAATGGCAGAGTGCCTCAAAAAGAAA\n"
+ + "AGAGATGAGAGACCACTCTTTCCCCAAATTCTCGCCTCTATTGAGCTGCTGGCCCGCTCA\n"
+ + "TTGCCAAAAATTCACCGCAGTGCATCAGAACCCTCCTTGAATCGGGCTGGTTTCCAAACA\n"
+ + "GAGGATTTTAGTCTATATGCTTGTGCTTCTCCAAAAACACCCATCCAGGCAGGGGGATAT\n"
+ + "GGTGCGTTTCCTGTCCACTGA\n" },
+ { new EnsemblProtein(), "ENSP00000288602", ">ENSP00000288602\n"
+ + "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEH\n"
+ + "IEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSSASMDTV\n"
+ + "TSSSSSSLSVLPSSLSVFQNPTDVARSNPKSPQKPIVRVFLPNKQRTVVPARCGVTVRDS\n"
+ + "LKKALMMRGLIPECCAVYRIQDGEKKPIGWDTDISWLTGEELHVEVLENVPLTTHNFVRK\n"
+ + "TFFTLAFCDFCRKLLFQGFRCQTCGYKFHQRCSTEVPLMCVNYDQLDLLFVSKFFEHHPI\n"
+ + "PQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSKSIPIPQPFRPADEDHRNQFGQR\n"
+ + "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDG\n"
+ // ? insertion added in ENSP00000288602.11, not in P15056
+ + "APLNQLMRCLRKYQSRTPSPLLHSVPSEIVFDFEPGPVFR\n"
+ // end insertion
+ + "GSTTGLSATPPASLPGSLTNVKALQKSP\n"
+ + "GPQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDV\n"
+ + "AVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHH\n"
+ + "LHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATV\n"
+ + "KSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNIN\n"
+ + "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
+ + "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH" } };
@BeforeClass(alwaysRun = true)
public void setUp()
for (SequenceI tr : expected)
{
SequenceI[] rseq;
- Assert.assertNotNull(
- rseq = retrieved.findSequenceMatch(tr.getName()),
+ Assert.assertNotNull(rseq = retrieved.findSequenceMatch(tr.getName()),
"Couldn't find sequences matching expected sequence "
+ tr.getName());
Assert.assertEquals(rseq.length, 1,
"Expected only one sequence for sequence ID " + tr.getName());
- Assert.assertEquals(
- rseq[0].getSequenceAsString(),
+ Assert.assertEquals(rseq[0].getSequenceAsString(),
tr.getSequenceAsString(),
"Sequences differ for " + tr.getName() + "\n" + "Exp:"
+ tr.getSequenceAsString() + "\n" + "Got:"
public void testReverseComplementAlleles()
{
String alleles = "C,G,-TAC,HGMD_MUTATION,gac";
- SequenceFeature sf = new SequenceFeature("sequence_variant", alleles,
- 1, 2, 0f, null);
+ SequenceFeature sf = new SequenceFeature("sequence_variant", alleles, 1,
+ 2, 0f, null);
sf.setValue("alleles", alleles);
EnsemblSeqProxy.reverseComplementAlleles(sf);
dbVers)
{
@SuppressWarnings("unchecked")
- @Override
- protected Object getJSON(URL url, List<String> ids, int msDelay, int mode, String mapKey) throws IOException, ParseException
- {
- return ((List<Object>)JSONUtils.parse(JSON)).iterator();
- }
+ @Override
+ protected Object getJSON(URL url, List<String> ids, int msDelay,
+ int mode, String mapKey) throws IOException, ParseException
+ {
+ return ((List<Object>) JSONUtils.parse(JSON)).iterator();
+ }
};
public class VCFReaderTest
{
- private static final String[] VCF = new String[] {
- "##fileformat=VCFv4.2",
+ private static final String[] VCF = new String[] { "##fileformat=VCFv4.2",
"#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO",
"20\t3\t.\tC\tG\t.\tPASS\tDP=100", // SNP C/G
"20\t7\t.\tG\tGA\t.\tPASS\tDP=100", // insertion G/GA
File f = File.createTempFile("Test", "vcf");
f.deleteOnExit();
PrintWriter pw = new PrintWriter(f);
- for (String vcfLine : VCF) {
+ for (String vcfLine : VCF)
+ {
pw.println(vcfLine);
}
pw.close();
return f;
}
-
+
/**
* A 'test' that demonstrates querying an indexed VCF file for features in a
* specified interval
* if not specified, assumes index file is filename.tbi
*/
VCFReader reader = new VCFReader(VCF_PATH);
-
+
/*
* gene NMT1 (human) is on chromosome 17
* GCHR38 (Ensembl): 45051610-45109016
}
// "https://storage.cloud.google.com/gnomad-public/release/2.0.1/vcf/exomes/gnomad.exomes.r2.0.1.sites.vcf.gz";
-
+
/**
* Test the query method that wraps a non-indexed VCF file
*
* query for overlap of 5-8 - should find variant at 7
*/
CloseableIterator<VariantContext> variants = reader.query("20", 5, 8);
-
+
/*
* INDEL G/GA variant
*/
"B", map, null);
ssm.addStructureMapping(sm2);
- String[] commands = testee.colourBySequence(ssm,
- files,
- seqs, sr, af.alignPanel);
+ String[] commands = testee.colourBySequence(ssm, files, seqs, sr,
+ af.alignPanel);
assertEquals(commands.length, 2);
String chainACommand = commands[0];
AtomSpecModel model = new AtomSpecModel();
assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "");
model.addRange("1", 2, 4, "A");
- assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "2-4:A/1.1");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
+ "2-4:A/1.1");
model.addRange("1", 8, 8, "A");
- assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "2-4:A/1.1|8:A/1.1");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
+ "2-4:A/1.1|8:A/1.1");
model.addRange("1", 5, 7, "B");
assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"2-4:A/1.1|8:A/1.1|5-7:B/1.1");
toAlign.addRange("2", 20, 21, "B");
toAlign.addRange("2", 22, 22, "C");
List<StructureCommandI> command = testee.superposeStructures(ref,
- toAlign, AtomSpecType.ALPHA); // doesn't matter for Jmol whether nuc or protein
+ toAlign, AtomSpecType.ALPHA); // doesn't matter for Jmol whether nuc
+ // or protein
assertEquals(command.size(), 1);
String refSpec = "12-14:A/1.1|18:B/1.1|22-23:B/1.1";
String toAlignSpec = "15-17:B/2.1|20-21:B/2.1|22:C/2.1";
/*
* local structures have a fake ID
*/
- assertTrue(structureData.getSeqs().get(0).getAllPDBEntries().get(0).fakedPDBId());
+ assertTrue(structureData.getSeqs().get(0).getAllPDBEntries().get(0)
+ .fakedPDBId());
/*
* the ID is also the group for features derived from structure data
*/
{
if (args == null || args[0] == null)
{
- System.err
- .println("You must provide a PDB directory in the launch argument");
+ System.err.println(
+ "You must provide a PDB directory in the launch argument");
return;
}
JmolParser jtest = null;
try
{
- mctest = new PDBfile(false, false, false, testFile, DataSourceType.FILE);
+ mctest = new PDBfile(false, false, false, testFile,
+ DataSourceType.FILE);
jtest = new JmolParser(testFile, DataSourceType.FILE);
} catch (IOException e)
{
int count = 0;
System.out.println("\n\nTotal sequence Scanned : " + totalSeqScanned);
- System.out.println("Total sequence passed : "
- + (totalSeqScanned - totalFail));
+ System.out.println(
+ "Total sequence passed : " + (totalSeqScanned - totalFail));
System.out.println("Total sequence failed : " + totalFail);
- System.out
- .println("Success rate: "
- + ((totalSeqScanned - totalFail) * 100)
- / totalSeqScanned + "%");
+ System.out.println("Success rate: "
+ + ((totalSeqScanned - totalFail) * 100) / totalSeqScanned
+ + "%");
System.out.println("\nList of " + failedFiles.size()
+ " file(s) with sequence diffs:");
for (String problemFile : failedFiles)
{
Iterator<Reader> ids = Annotate3D.getRNAMLForPDBId("2GIS");
assertTrue("Didn't retrieve 2GIS by id.", ids != null);
- Iterator<Reader> files = Annotate3D.getRNAMLForPDBFileAsString(FileUtil
- .readFileToString(new File("examples/2GIS.pdb")));
+ Iterator<Reader> files = Annotate3D.getRNAMLForPDBFileAsString(
+ FileUtil.readFileToString(new File("examples/2GIS.pdb")));
assertTrue("Didn't retrieve using examples/2GIS.pdb.", files != null);
int i = 0;
while (ids.hasNext() && files.hasNext())
{
- BufferedReader file = new BufferedReader(files.next()), id = new BufferedReader(
- ids.next());
+ BufferedReader file = new BufferedReader(files.next()),
+ id = new BufferedReader(ids.next());
String iline, fline;
do
{
Assert.assertTrue(pdbf.isValid());
// Comment - should add new FileParse constructor like new FileParse(Reader
// ..). for direct reading
- Iterator<Reader> readers = Annotate3D
- .getRNAMLForPDBFileAsString(FileUtil.readFileToString(new File(
- "examples/2GIS.pdb")));
+ Iterator<Reader> readers = Annotate3D.getRNAMLForPDBFileAsString(
+ FileUtil.readFileToString(new File("examples/2GIS.pdb")));
testRNAMLcontent(readers, pdbf);
}
}
if (struseq == null)
{
- AssertJUnit
- .fail("Couldn't find this sequence in original input:\n"
- + new FastaFile().print(
- new SequenceI[] { sq }, true)
- + "\n\nOriginal input:\n"
- + new FastaFile().print(
- pdbf.getSeqsAsArray(), true) + "\n");
+ AssertJUnit.fail(
+ "Couldn't find this sequence in original input:\n"
+ + new FastaFile().print(new SequenceI[]
+ { sq }, true) + "\n\nOriginal input:\n"
+ + new FastaFile().print(pdbf.getSeqsAsArray(),
+ true)
+ + "\n");
}
}
}
assertEquals(commands.size(), 3);
assertEquals(commands.get(0), new StructureCommand("color", "0x0000ff",
"0//A/2-5+9-23/ 0//B/7/ 1//A/1/ 1//B/4-7/"));
- assertEquals(commands.get(
- 1),
+ assertEquals(commands.get(1),
new StructureCommand("color", "0xffff00", "1//A/3-5+8/"));
- assertEquals(commands.get(
- 2),
+ assertEquals(commands.get(2),
new StructureCommand("color", "0xff0000", "0//A/3-9/"));
}
AtomSpecModel model = new AtomSpecModel();
assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "");
model.addRange("1", 2, 4, "A");
- assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "1//A/2-4/");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
+ "1//A/2-4/");
model.addRange("1", 8, 8, "A");
- assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "1//A/2-4+8/");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
+ "1//A/2-4+8/");
model.addRange("1", 5, 7, "B");
- assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "1//A/2-4+8/ 1//B/5-7/");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
+ "1//A/2-4+8/ 1//B/5-7/");
model.addRange("1", 3, 5, "A");
- assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "1//A/2-5+8/ 1//B/5-7/");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
+ "1//A/2-5+8/ 1//B/5-7/");
model.addRange("0", 1, 4, "B");
assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"0//B/1-4/ 1//A/2-5+8/ 1//B/5-7/");
String toAlignSpecCA = "(2//B/15-17+20-21/CA 2//C/22/CA";
String refSpec = "1//A/12-14/ 1//B/18+22-23/";
String toAlignSpec = "2//B/15-17+20-21/ 2//C/22/";
- String altLoc = " and (altloc '' or altloc 'a'))";
+ String altLoc = " and (altloc '' or altloc 'a'))";
// super command: separate arguments for regions to align
- assertEquals(commands.get(1),
- new StructureCommand("pair_fit", toAlignSpecCA+altLoc, refSpecCA+altLoc));
+ assertEquals(commands.get(1), new StructureCommand("pair_fit",
+ toAlignSpecCA + altLoc, refSpecCA + altLoc));
// show aligned regions: one argument for combined atom specs
assertEquals(commands.get(3), new StructureCommand("show", "cartoon",
refSpec + " " + toAlignSpec));
AtomSpecModel model = new AtomSpecModel();
assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "");
model.addRange("1", 2, 4, "A");
- assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "1//A/2-4/CA");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
+ "1//A/2-4/CA");
model.addRange("1", 8, 8, "A");
- assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "1//A/2-4+8/CA");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
+ "1//A/2-4+8/CA");
model.addRange("1", 5, 7, "B");
assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"1//A/2-4+8/CA 1//B/5-7/CA");
@Test(groups = "Functional")
public void testColourResidues()
{
- assertEquals(testee.colourResidues("something",
- Color.MAGENTA),
+ assertEquals(testee.colourResidues("something", Color.MAGENTA),
new StructureCommand("color", "0xff00ff", "something"));
}
@Test(groups = "Functional")
public void testSetBackgroundColour()
{
- assertEquals(testee.setBackgroundColour(
- Color.PINK),
+ assertEquals(testee.setBackgroundColour(Color.PINK),
new StructureCommand("bg_color", "0xffafaf"));
}
req = PymolManager
.getPostRequest(new StructureCommand("foobar", "blue", "all"));
- assertEquals(req, "<methodCall><methodName>foobar</methodName><params>"
- + "<parameter><value>blue</value></parameter>"
- + "<parameter><value>all</value></parameter>"
- + "</params></methodCall>");
+ assertEquals(req,
+ "<methodCall><methodName>foobar</methodName><params>"
+ + "<parameter><value>blue</value></parameter>"
+ + "<parameter><value>all</value></parameter>"
+ + "</params></methodCall>");
}
@Test(groups = "Functional")
assertEquals(testee.makeAttributeName(null), "jv_");
assertEquals(testee.makeAttributeName(""), "jv_");
assertEquals(testee.makeAttributeName("helix"), "jv_helix");
- assertEquals(testee.makeAttributeName(
- "Hello World 24"),
+ assertEquals(testee.makeAttributeName("Hello World 24"),
"jv_Hello_World_24");
- assertEquals(testee.makeAttributeName(
- "!this is-a_very*{odd(name"),
+ assertEquals(testee.makeAttributeName("!this is-a_very*{odd(name"),
"jv__this_is_a_very__odd_name");
// name ending in color gets underscore appended
assertEquals(testee.makeAttributeName("helixColor"), "jv_helixColor_");
AtomSpecModel model = new AtomSpecModel();
assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "");
model.addRange("1", 2, 4, "A");
- assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "#1:2-4.A");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
+ "#1:2-4.A");
model.addRange("1", 8, 8, "A");
- assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "#1:2-4.A,8.A");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
+ "#1:2-4.A,8.A");
model.addRange("1", 5, 7, "B");
- assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "#1:2-4.A,8.A,5-7.B");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
+ "#1:2-4.A,8.A,5-7.B");
model.addRange("1", 3, 5, "A");
- assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "#1:2-5.A,8.A,5-7.B");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
+ "#1:2-5.A,8.A,5-7.B");
model.addRange("0", 1, 4, "B");
assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"#0:1-4.B|#1:2-5.A,8.A,5-7.B");
{
List<StructureCommandI> cmds = testee.colourByCharge();
assertEquals(cmds.size(), 1);
- assertEquals(cmds.get(0)
- .getCommand(),
+ assertEquals(cmds.get(0).getCommand(),
"color white;color red ::ASP,GLU;color blue ::LYS,ARG;color yellow ::CYS");
}
@Test(groups = "Functional")
public void testGetColourCommand()
{
- assertEquals(testee.colourResidues("something", Color.MAGENTA)
- .getCommand(),
+ assertEquals(
+ testee.colourResidues("something", Color.MAGENTA).getCommand(),
"color #ff00ff something");
}
{
List<StructureCommandI> cmds = testee.startNotifications("to here");
assertEquals(cmds.size(), 2);
- assertEquals(cmds.get(0), new StructureCommand("listen start models url to here"));
- assertEquals(cmds.get(1), new StructureCommand("listen start select prefix SelectionChanged url to here"));
+ assertEquals(cmds.get(0),
+ new StructureCommand("listen start models url to here"));
+ assertEquals(cmds.get(1), new StructureCommand(
+ "listen start select prefix SelectionChanged url to here"));
}
@Test(groups = "Functional")
List<StructureCommandI> cmds = testee.stopNotifications();
assertEquals(cmds.size(), 2);
assertEquals(cmds.get(0), new StructureCommand("listen stop models"));
- assertEquals(cmds.get(1), new StructureCommand("listen stop selection"));
+ assertEquals(cmds.get(1),
+ new StructureCommand("listen stop selection"));
}
}
toAlign.addRange("2", 20, 21, "B");
toAlign.addRange("2", 22, 22, "C");
List<StructureCommandI> command = testee.superposeStructures(ref,
- toAlign,AtomSpecType.ALPHA);
+ toAlign, AtomSpecType.ALPHA);
assertEquals(command.size(), 1);
String cmd = command.get(0).getCommand();
String refSpec = "#1/A:12-14/B:18,22-23";
public void testGetAtomSpec()
{
AtomSpecModel model = new AtomSpecModel();
- assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY
- ), "");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "");
model.addRange("1", 2, 4, "A");
- assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "#1/A:2-4");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
+ "#1/A:2-4");
model.addRange("1", 8, 8, "A");
- assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "#1/A:2-4,8");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
+ "#1/A:2-4,8");
model.addRange("1", 5, 7, "B");
- assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "#1/A:2-4,8/B:5-7");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
+ "#1/A:2-4,8/B:5-7");
model.addRange("1", 3, 5, "A");
- assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "#1/A:2-5,8/B:5-7");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
+ "#1/A:2-5,8/B:5-7");
model.addRange("0", 1, 4, "B");
assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"#0/B:1-4|#1/A:2-5,8/B:5-7");
AtomSpecModel model = new AtomSpecModel();
assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "");
model.addRange("1", 2, 4, "A");
- assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "#1/A:2-4@CA");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
+ "#1/A:2-4@CA");
model.addRange("1", 8, 8, "A");
- assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "#1/A:2-4,8@CA");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
+ "#1/A:2-4,8@CA");
model.addRange("1", 5, 7, "B");
- assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "#1/A:2-4,8/B:5-7@CA");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
+ "#1/A:2-4,8/B:5-7@CA");
model.addRange("1", 3, 5, "A");
- assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "#1/A:2-5,8/B:5-7@CA");
+ assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
+ "#1/A:2-5,8/B:5-7@CA");
model.addRange("0", 1, 4, "B");
assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"#0/B:1-4@CA|#1/A:2-5,8/B:5-7@CA");
@Test(groups = "Functional")
public void testGetColourCommand()
{
- assertEquals(testee.colourResidues("something", Color.MAGENTA)
- .getCommand(),
+ assertEquals(
+ testee.colourResidues("something", Color.MAGENTA).getCommand(),
"color something #ff00ff");
}
model.addRange("1", 89, 92, "A");
model.addRange("2", 12, 20, "B");
model.addRange("2", 8, 9, "B");
- assertEquals(testee.setAttribute("jv_kd", "27.3", model)
- .getCommand(),
+ assertEquals(testee.setAttribute("jv_kd", "27.3", model).getCommand(),
"setattr #1/A:89-92|#2/B:8-9,12-20 res jv_kd '27.3' create true");
}
{
List<StructureCommandI> cmds = testee.startNotifications("to here");
assertEquals(cmds.size(), 2);
- assertEquals(cmds.get(0), new StructureCommand("info notify start models jalview prefix ModelChanged url to here"));
- assertEquals(cmds.get(1), new StructureCommand("info notify start selection jalview prefix SelectionChanged url to here"));
+ assertEquals(cmds.get(0), new StructureCommand(
+ "info notify start models jalview prefix ModelChanged url to here"));
+ assertEquals(cmds.get(1), new StructureCommand(
+ "info notify start selection jalview prefix SelectionChanged url to here"));
}
@Test(groups = "Functional")
{
List<StructureCommandI> cmds = testee.stopNotifications();
assertEquals(cmds.size(), 2);
- assertEquals(cmds.get(0), new StructureCommand("info notify stop models jalview"));
- assertEquals(cmds.get(1), new StructureCommand("info notify stop selection jalview"));
+ assertEquals(cmds.get(0),
+ new StructureCommand("info notify stop models jalview"));
+ assertEquals(cmds.get(1),
+ new StructureCommand("info notify stop selection jalview"));
}
@Test(groups = "Functional")
@BeforeClass(alwaysRun = true)
public static void setUpBeforeClass() throws Exception
{
- Jalview.main(new String[] { "-noquestionnaire", "-nonews", "-props",
- "test/jalview/ext/rbvi/chimera/testProps.jvprops" });
+ Jalview.main(
+ new String[]
+ { "-noquestionnaire", "-nonews", "-props",
+ "test/jalview/ext/rbvi/chimera/testProps.jvprops" });
Cache.setProperty(Preferences.STRUCTURE_DISPLAY,
ViewerType.CHIMERA.name());
Cache.setProperty("SHOW_ANNOTATIONS", "false");
assertEquals(pdbIds.size(), 1);
PDBEntry pdbEntry = pdbIds.get(0);
assertEquals(pdbEntry.getId(), "1GAQ");
- StructureViewer structureViewer = new StructureViewer(af.getViewport()
- .getStructureSelectionManager());
+ StructureViewer structureViewer = new StructureViewer(
+ af.getViewport().getStructureSelectionManager());
chimeraViewer = structureViewer.viewStructures(pdbEntry,
- new SequenceI[] { sq }, af.getCurrentView().getAlignPanel());
+ new SequenceI[]
+ { sq }, af.getCurrentView().getAlignPanel());
JalviewChimeraBinding binding = (JalviewChimeraBinding) chimeraViewer
.getBinding();
} catch (InterruptedException e)
{
}
- } while (!binding.isFinishedInit() || !chimeraViewer.isVisible());
+ } while (!binding.isFinishedInit() || !chimeraViewer.isVisible());
assertTrue(binding.isViewerRunning(), "Failed to start Chimera");
assertTrue(chimeraViewer.hasViewerActionsMenu());
// now add another sequence and bind to view
- //
+ //
AlignmentI al = af.getViewport().getAlignment();
PDBEntry xpdb = al.getSequenceAt(0).getPDBEntry("1GAQ");
- sq = new Sequence("1GAQ", al.getSequenceAt(0).getSequence(25, 95).toString());
+ sq = new Sequence("1GAQ",
+ al.getSequenceAt(0).getSequence(25, 95).toString());
al.addSequence(sq);
- structureViewer.viewStructures(new PDBEntry[] { xpdb }, new SequenceI[] { sq }, af.getCurrentView().getAlignPanel());
+ structureViewer.viewStructures(new PDBEntry[] { xpdb },
+ new SequenceI[]
+ { sq }, af.getCurrentView().getAlignPanel());
/*
* Wait for viewer load thread to complete
*/
- do
+ do
{
- try {
+ try
+ {
Thread.sleep(1500);
- } catch (InterruptedException q) {};
+ } catch (InterruptedException q)
+ {
+ }
+ ;
} while (!binding.isLoadingFinished());
-
+
// still just one PDB structure shown
assertEquals(chimeraViewer.getBinding().getPdbCount(), 1);
// and the viewer action menu should still be visible
/*
* use local test PDB and SIFTS files
*/
- String pdbFilePath = new File(
- "test/jalview/ext/rbvi/chimera/4zho.pdb").getPath();
+ String pdbFilePath = new File("test/jalview/ext/rbvi/chimera/4zho.pdb")
+ .getPath();
PDBEntry pdbEntry = new PDBEntry("4ZHO", null, null, pdbFilePath);
String siftsFilePath = new File(
- "test/jalview/ext/rbvi/chimera/4zho.xml.gz")
- .getPath();
+ "test/jalview/ext/rbvi/chimera/4zho.xml.gz").getPath();
SiftsClient.setMockSiftsFile(new File(siftsFilePath));
- StructureViewer structureViewer = new StructureViewer(af.getViewport()
- .getStructureSelectionManager());
+ StructureViewer structureViewer = new StructureViewer(
+ af.getViewport().getStructureSelectionManager());
chimeraViewer = structureViewer.viewStructures(pdbEntry,
- new SequenceI[] { sq }, af.getCurrentView().getAlignPanel());
+ new SequenceI[]
+ { sq }, af.getCurrentView().getAlignPanel());
JalviewChimeraBinding binding = (JalviewChimeraBinding) chimeraViewer
.getBinding();
sq.addSequenceFeature(new SequenceFeature("metal ion-binding site",
"Iron-Sulfur (2Fe-2S)", 96, 96, Float.NaN, null));
// on a sequence region that is partially mapped to structure:
- sq.addSequenceFeature(new SequenceFeature("helix", null, 50, 60,
- Float.NaN, null));
+ sq.addSequenceFeature(
+ new SequenceFeature("helix", null, 50, 60, Float.NaN, null));
// and again:
- sq.addSequenceFeature(new SequenceFeature("chain", null, 50, 70,
- Float.NaN, null));
+ sq.addSequenceFeature(
+ new SequenceFeature("chain", null, 50, 70, Float.NaN, null));
// add numeric valued features - score is set as attribute value
sq.addSequenceFeature(new SequenceFeature("kd", "hydrophobicity", 62,
62, -2.1f, null));
new StructureCommand("list resi att jv_metal_ion_binding_site"),
true);
assertEquals(reply.size(), 4);
- assertTrue(reply
- .contains("residue id #0:40.A jv_metal_ion_binding_site \"Iron-Sulfur (2Fe-2S)\" index 40"));
- assertTrue(reply
- .contains("residue id #0:45.A jv_metal_ion_binding_site \"Iron-Sulfur (2Fe-2S)\" index 45"));
- assertTrue(reply
- .contains("residue id #0:40.B jv_metal_ion_binding_site \"Iron-Sulfur (2Fe-2S)\" index 40"));
- assertTrue(reply
- .contains("residue id #0:45.B jv_metal_ion_binding_site \"Iron-Sulfur (2Fe-2S)\" index 45"));
+ assertTrue(reply.contains(
+ "residue id #0:40.A jv_metal_ion_binding_site \"Iron-Sulfur (2Fe-2S)\" index 40"));
+ assertTrue(reply.contains(
+ "residue id #0:45.A jv_metal_ion_binding_site \"Iron-Sulfur (2Fe-2S)\" index 45"));
+ assertTrue(reply.contains(
+ "residue id #0:40.B jv_metal_ion_binding_site \"Iron-Sulfur (2Fe-2S)\" index 40"));
+ assertTrue(reply.contains(
+ "residue id #0:45.B jv_metal_ion_binding_site \"Iron-Sulfur (2Fe-2S)\" index 45"));
/*
* check attributes with score values
SequenceI fer2Arath = af.getViewport().getAlignment()
.findName("FER2_ARATH");
assertNotNull(fer2Arath, "Didn't find FER2_ARATH");
-
+
/*
* need a Uniprot dbref for SIFTS mapping to work!!
*/
fer2Arath.addDBRef(new DBRefEntry("UNIPROT", "0", "P16972", null));
-
+
/*
* use local test PDB and SIFTS files
*/
- String pdbFilePath = new File(
- "test/jalview/ext/rbvi/chimera/4zho.pdb").getPath();
+ String pdbFilePath = new File("test/jalview/ext/rbvi/chimera/4zho.pdb")
+ .getPath();
PDBEntry pdbEntry = new PDBEntry("4ZHO", null, null, pdbFilePath);
String siftsFilePath = new File(
- "test/jalview/ext/rbvi/chimera/4zho.xml.gz")
- .getPath();
+ "test/jalview/ext/rbvi/chimera/4zho.xml.gz").getPath();
SiftsClient.setMockSiftsFile(new File(siftsFilePath));
-
- StructureViewer structureViewer = new StructureViewer(af.getViewport()
- .getStructureSelectionManager());
+
+ StructureViewer structureViewer = new StructureViewer(
+ af.getViewport().getStructureSelectionManager());
chimeraViewer = structureViewer.viewStructures(pdbEntry,
- new SequenceI[] { fer2Arath }, af.getCurrentView()
- .getAlignPanel());
-
+ new SequenceI[]
+ { fer2Arath }, af.getCurrentView().getAlignPanel());
+
JalviewChimeraBinding binding = (JalviewChimeraBinding) chimeraViewer
.getBinding();
do
{
}
} while (!binding.isFinishedInit());
-
+
assertTrue(binding.isViewerRunning(), "Failed to launch Chimera");
-
+
assertEquals(binding.getPdbCount(), 1);
-
+
/*
* 'perform' menu action to copy Chimera attributes
* to features in Jalview
*/
// TODO rename and pull up method to binding interface
// once functionality is added for Jmol as well
- binding.copyStructureAttributesToFeatures("isHelix", af.getViewport()
- .getAlignPanel());
+ binding.copyStructureAttributesToFeatures("isHelix",
+ af.getViewport().getAlignPanel());
/*
* verify 22 residues have isHelix feature
/*
* fetch a numeric valued attribute
*/
- binding.copyStructureAttributesToFeatures("phi", af.getViewport()
- .getAlignPanel());
+ binding.copyStructureAttributesToFeatures("phi",
+ af.getViewport().getAlignPanel());
fr.setVisible("phi");
List<SequenceFeature> fs = fer2Arath.getFeatures().findFeatures(54, 54,
"phi");
t.printStackTrace(System.err);
}
long elapsed = System.currentTimeMillis() - now;
- System.out.println("Load and cache of Sequence Ontology took "
- + elapsed + "ms");
+ System.out.println(
+ "Load and cache of Sequence Ontology took " + elapsed + "ms");
}
@Test(groups = "Functional")
foundIndex = ftsRestClient.getPrimaryKeyColumIndex(wantedFields,
false);
Assert.assertEquals(foundIndex, 0);
- foundIndex = ftsRestClient
- .getPrimaryKeyColumIndex(wantedFields, true);
+ foundIndex = ftsRestClient.getPrimaryKeyColumIndex(wantedFields,
+ true);
Assert.assertEquals(foundIndex, 1);
} catch (Exception e)
{
@Test(groups = { "Functional" })
public void getAllDefaulDisplayedDataColumns()
{
- Assert.assertNotNull(ftsRestClient
- .getAllDefaultDisplayedFTSDataColumns());
+ Assert.assertNotNull(
+ ftsRestClient.getAllDefaultDisplayedFTSDataColumns());
Assert.assertTrue(!ftsRestClient.getAllDefaultDisplayedFTSDataColumns()
.isEmpty());
- Assert.assertEquals(ftsRestClient
- .getAllDefaultDisplayedFTSDataColumns().size(), 7);
+ Assert.assertEquals(
+ ftsRestClient.getAllDefaultDisplayedFTSDataColumns().size(), 7);
}
@Test(groups = { "Functional" })
actualGroupStr = ftsRestClient.getDataColumnGroupById("g4")
.toString();
Assert.assertEquals(actualGroupStr, "Procedures & Softwares");
- actualGroupStr = ftsRestClient.getDataColumnGroupById(
- "unavailable group").toString();
+ actualGroupStr = ftsRestClient
+ .getDataColumnGroupById("unavailable group").toString();
} catch (Exception e)
{
Assert.assertTrue(true);
{
PDBFTSPanel searchPanel = new PDBFTSPanel(null);
JInternalFrame mainFrame = searchPanel.getMainFrame();
-// JComboBox<String> txt_search = PA.gsearchPanel.getTxtSearch();
+ // JComboBox<String> txt_search = PA.gsearchPanel.getTxtSearch();
assertTrue(mainFrame.getTitle().length() == 20);
- assertTrue(mainFrame.getTitle()
- .equalsIgnoreCase("PDB Sequence Fetcher"));
- PA.invokeMethod(PA.getValue(searchPanel, "txt_search"), "setSelectedItem(java.lang.String)", "ABC");
- // txt_search.setSelectedItem("ABC");
+ assertTrue(
+ mainFrame.getTitle().equalsIgnoreCase("PDB Sequence Fetcher"));
+ PA.invokeMethod(PA.getValue(searchPanel, "txt_search"),
+ "setSelectedItem(java.lang.String)", "ABC");
+ // txt_search.setSelectedItem("ABC");
try
{
// wait for web-service to handle response
e.printStackTrace();
}
assertTrue(mainFrame.getTitle().length() > 20);
- assertTrue(!mainFrame.getTitle().equalsIgnoreCase(
- "PDB Sequence Fetcher"));
+ assertTrue(
+ !mainFrame.getTitle().equalsIgnoreCase("PDB Sequence Fetcher"));
}
-
+
@Test
- public void getFTSframeTitleTest() {
+ public void getFTSframeTitleTest()
+ {
PDBFTSPanel searchPanel = new PDBFTSPanel(null);
String outcome = searchPanel.getFTSFrameTitle();
- //System.out.println("FTS Frame title :" + outcome);
+ // System.out.println("FTS Frame title :" + outcome);
assertEquals(outcome, "PDB Sequence Fetcher");
}
}
System.out.println("wantedFields >>" + wantedFields);
-
FTSRestRequest request = new FTSRestRequest();
request.setAllowEmptySeq(false);
request.setResponseSize(100);
String jsonErrorResponse = "";
try
{
- jsonErrorResponse = readJsonStringFromFile("test/jalview/io/pdb_request_json_error.txt");
+ jsonErrorResponse = readJsonStringFromFile(
+ "test/jalview/io/pdb_request_json_error.txt");
} catch (IOException e)
{
e.printStackTrace();
assertEquals(expectedErrorMsg, parsedErrorResponse);
}
- @Test(groups = { "External" }, enabled = false, expectedExceptions = Exception.class)
+ @Test(
+ groups =
+ { "External" },
+ enabled = false,
+ expectedExceptions = Exception.class)
public void testForExpectedRuntimeException() throws Exception
{
- // FIXME JBPNote: looks like this test fails for no good reason - what exception was supposed to be raised ?
+ // FIXME JBPNote: looks like this test fails for no good reason - what
+ // exception was supposed to be raised ?
List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
wantedFields.add(PDBFTSRestClient.getInstance()
.getDataColumnByNameOrCode("pdb_id"));
String jsonString = "";
try
{
- jsonString = readJsonStringFromFile("test/jalview/io/pdb_response_json.txt");
+ jsonString = readJsonStringFromFile(
+ "test/jalview/io/pdb_response_json.txt");
} catch (IOException e)
{
e.printStackTrace();
}
- FTSRestResponse response = PDBFTSRestClient.parsePDBJsonResponse(
- jsonString, request);
+ FTSRestResponse response = PDBFTSRestClient
+ .parsePDBJsonResponse(jsonString, request);
assertTrue(response.getSearchSummary() != null);
assertTrue(response.getNumberOfItemsFound() == 931);
assertTrue(response.getSearchSummary().size() == 14);
.queryParam("q", "text:abc AND molecule_sequence:['' TO *]");
// Execute the REST request
- ClientResponse clientResponse = webResource.accept(
- MediaType.APPLICATION_JSON).get(ClientResponse.class);
+ ClientResponse clientResponse = webResource
+ .accept(MediaType.APPLICATION_JSON).get(ClientResponse.class);
// Get the JSON string from the response object
String pdbJsonResponseString = clientResponse.getEntity(String.class);
pdbResponse != null);
assertTrue("Couldn't Retrieve 'QTime' value", queryTime != null);
assertTrue("Couldn't Retrieve 'numFound' value", numFound != null);
- assertTrue("Couldn't Retrieve 'docs' object", docs != null
- || !docIter.hasNext());
+ assertTrue("Couldn't Retrieve 'docs' object",
+ docs != null || !docIter.hasNext());
JSONObject pdbJsonDoc = docIter.next();
if (pdbJsonDoc.get(field.getCode()) == null)
{
// System.out.println(">>>\t" + field.getCode());
- assertTrue(field.getCode()
- + " has been removed from PDB doc Entity",
+ assertTrue(
+ field.getCode()
+ + " has been removed from PDB doc Entity",
!pdbJsonResponseString.contains(field.getCode()));
}
}
} catch (ParseException e)
{
- Assert.fail(">>> Test failed due to exception while parsing pdb response json !!!");
+ Assert.fail(
+ ">>> Test failed due to exception while parsing pdb response json !!!");
e.printStackTrace();
}
}
/**
* reads any string from filePath
+ *
* @param filePath
* @return
* @throws IOException
*/
- public static String readJsonStringFromFile(String filePath) throws IOException
+ public static String readJsonStringFromFile(String filePath)
+ throws IOException
{
String fileContent;
BufferedReader br = new BufferedReader(new FileReader(filePath));
public static void setMock()
{
String[][] mocks = new String[2][];
- mocks[0] = new String[] {"https://www.ebi.ac.uk/pdbe/search/pdb/select?wt=json&fl=pdb_id,title,experimental_method,resolution&rows=500&start=0&q=(4igk+OR+7lyb+OR+3k0h+OR+3k0k+OR+1t15+OR+3pxc+OR+3pxd+OR+3pxe+OR+1jm7+OR+7jzv+OR+3pxa+OR+3pxb+OR+1y98+OR+1n5o+OR+4ifi+OR+4y2g+OR+3k15+OR+3k16+OR+4jlu+OR+2ing+OR+4ofb+OR+6g2i+OR+3coj+OR+1jnx+OR+4y18+OR+4u4a+OR+1oqa+OR+1t29+OR+1t2u+OR+1t2v)+AND+molecule_sequence:%5B''+TO+*%5D+AND+status:REL&sort=",
- "{\n"
- + " \"responseHeader\":{\n"
- + " \"status\":0,\n"
- + " \"QTime\":0,\n"
- + " \"params\":{\n"
- + " \"q\":\"(4igk OR 7lyb OR 3k0h OR 3k0k OR 1t15 OR 3pxc OR 3pxd OR 3pxe OR 1jm7 OR 7jzv OR 3pxa OR 3pxb OR 1y98 OR 1n5o OR 4ifi OR 4y2g OR 3k15 OR 3k16 OR 4jlu OR 2ing OR 4ofb OR 6g2i OR 3coj OR 1jnx OR 4y18 OR 4u4a OR 1oqa OR 1t29 OR 1t2u OR 1t2v) AND molecule_sequence:['' TO *] AND status:REL\",\n"
- + " \"fl\":\"pdb_id,title,experimental_method,resolution\",\n"
- + " \"start\":\"0\",\n"
- + " \"sort\":\"\",\n"
- + " \"rows\":\"500\",\n"
- + " \"wt\":\"json\"}},\n"
- + " \"response\":{\"numFound\":64,\"start\":0,\"docs\":[\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"4ofb\",\n"
- + " \"resolution\":3.05,\n"
- + " \"title\":\"Crystal structure of human BRCA1 BRCT in complex with nonphosphopeptide inhibitor\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"3pxe\",\n"
- + " \"resolution\":2.85,\n"
- + " \"title\":\"Impact of BRCA1 BRCT domain missense substitutions on phospho-peptide recognition: E1836K\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"4jlu\",\n"
- + " \"resolution\":3.5,\n"
- + " \"title\":\"Crystal structure of BRCA1 BRCT with doubly phosphorylated Abraxas\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"4y2g\",\n"
- + " \"resolution\":2.5,\n"
- + " \"title\":\"Structure of BRCA1 BRCT domains in complex with Abraxas single phosphorylated peptide\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"Solution NMR\"],\n"
- + " \"pdb_id\":\"1oqa\",\n"
- + " \"title\":\"Solution structure of the BRCT-c domain from human BRCA1\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"4u4a\",\n"
- + " \"resolution\":3.51,\n"
- + " \"title\":\"Complex Structure of BRCA1 BRCT with singly phospho Abraxas\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"3k16\",\n"
- + " \"resolution\":3.0,\n"
- + " \"title\":\"Crystal Structure of BRCA1 BRCT D1840T in complex with a minimal recognition tetrapeptide with a free carboxy C-terminus\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"1t15\",\n"
- + " \"resolution\":1.85,\n"
- + " \"title\":\"Crystal Structure of the Brca1 BRCT Domains in Complex with the Phosphorylated Interacting Region from Bach1 Helicase\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"3k15\",\n"
- + " \"resolution\":2.8,\n"
- + " \"title\":\"Crystal Structure of BRCA1 BRCT D1840T in complex with a minimal recognition tetrapeptide with an amidated C-terminus\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"1t2v\",\n"
- + " \"resolution\":3.3,\n"
- + " \"title\":\"Structural basis of phospho-peptide recognition by the BRCT domain of BRCA1, structure with phosphopeptide\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"1y98\",\n"
- + " \"resolution\":2.5,\n"
- + " \"title\":\"Structure of the BRCT repeats of BRCA1 bound to a CtIP phosphopeptide.\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"1t29\",\n"
- + " \"resolution\":2.3,\n"
- + " \"title\":\"Crystal structure of the BRCA1 BRCT repeats bound to a phosphorylated BACH1 peptide\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"3k0k\",\n"
- + " \"resolution\":2.7,\n"
- + " \"title\":\"Crystal Structure of BRCA1 BRCT in complex with a minimal recognition tetrapeptide with a free carboxy C-terminus.\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"3k0h\",\n"
- + " \"resolution\":2.7,\n"
- + " \"title\":\"The crystal structure of BRCA1 BRCT in complex with a minimal recognition tetrapeptide with an amidated C-terminus\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"4ifi\",\n"
- + " \"resolution\":2.2,\n"
- + " \"title\":\"Structure of human BRCA1 BRCT in complex with BAAT peptide\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"3pxd\",\n"
- + " \"resolution\":2.8,\n"
- + " \"title\":\"Impact of BRCA1 BRCT domain missense substitutions on phospho-peptide recognition: R1835P\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"3pxc\",\n"
- + " \"resolution\":2.8,\n"
- + " \"title\":\"Impact of BRCA1 BRCT domain missense substitutions on phospho-peptide recognition: R1699Q\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"1jnx\",\n"
- + " \"resolution\":2.5,\n"
- + " \"title\":\"Crystal structure of the BRCT repeat region from the breast cancer associated protein, BRCA1\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"3pxa\",\n"
- + " \"resolution\":2.55,\n"
- + " \"title\":\"Impact of BRCA1 BRCT domain missense substitutions on phospho-peptide recognition: G1656D\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"Solution NMR\"],\n"
- + " \"pdb_id\":\"1jm7\",\n"
- + " \"title\":\"Solution structure of the BRCA1/BARD1 RING-domain heterodimer\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"4igk\",\n"
- + " \"resolution\":1.75,\n"
- + " \"title\":\"Structure of human BRCA1 BRCT in complex with ATRIP peptide\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"1t2u\",\n"
- + " \"resolution\":2.8,\n"
- + " \"title\":\"Structural basis of phosphopeptide recognition by the BRCT domain of BRCA1: structure of BRCA1 missense variant V1809F\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"3pxb\",\n"
- + " \"resolution\":2.5,\n"
- + " \"title\":\"Impact of BRCA1 BRCT domain missense substitutions on phospho-peptide recognition: T1700A\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"1n5o\",\n"
- + " \"resolution\":2.8,\n"
- + " \"title\":\"Structural consequences of a cancer-causing BRCA1-BRCT missense mutation\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"3coj\",\n"
- + " \"resolution\":3.21,\n"
- + " \"title\":\"Crystal Structure of the BRCT Domains of Human BRCA1 in Complex with a Phosphorylated Peptide from Human Acetyl-CoA Carboxylase 1\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"Electron Microscopy\"],\n"
- + " \"pdb_id\":\"6g2i\",\n"
- + " \"resolution\":5.9,\n"
- + " \"title\":\"Filament of acetyl-CoA carboxylase and BRCT domains of BRCA1 (ACC-BRCT) at 5.9 A resolution\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"4jlu\",\n"
- + " \"resolution\":3.5,\n"
- + " \"title\":\"Crystal structure of BRCA1 BRCT with doubly phosphorylated Abraxas\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"4ofb\",\n"
- + " \"resolution\":3.05,\n"
- + " \"title\":\"Crystal structure of human BRCA1 BRCT in complex with nonphosphopeptide inhibitor\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"3pxe\",\n"
- + " \"resolution\":2.85,\n"
- + " \"title\":\"Impact of BRCA1 BRCT domain missense substitutions on phospho-peptide recognition: E1836K\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"4u4a\",\n"
- + " \"resolution\":3.51,\n"
- + " \"title\":\"Complex Structure of BRCA1 BRCT with singly phospho Abraxas\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"4y2g\",\n"
- + " \"resolution\":2.5,\n"
- + " \"title\":\"Structure of BRCA1 BRCT domains in complex with Abraxas single phosphorylated peptide\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"4y18\",\n"
- + " \"resolution\":3.5,\n"
- + " \"title\":\"Structure of BRCA1 BRCT domains in complex with Abraxas double phosphorylated peptide\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"2ing\",\n"
- + " \"resolution\":3.6,\n"
- + " \"title\":\"X-ray Structure of the BRCA1 BRCT mutant M1775K\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"1t15\",\n"
- + " \"resolution\":1.85,\n"
- + " \"title\":\"Crystal Structure of the Brca1 BRCT Domains in Complex with the Phosphorylated Interacting Region from Bach1 Helicase\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"1t29\",\n"
- + " \"resolution\":2.3,\n"
- + " \"title\":\"Crystal structure of the BRCA1 BRCT repeats bound to a phosphorylated BACH1 peptide\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"Solution NMR\"],\n"
- + " \"pdb_id\":\"1jm7\",\n"
- + " \"title\":\"Solution structure of the BRCA1/BARD1 RING-domain heterodimer\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"1t2v\",\n"
- + " \"resolution\":3.3,\n"
- + " \"title\":\"Structural basis of phospho-peptide recognition by the BRCT domain of BRCA1, structure with phosphopeptide\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"4ifi\",\n"
- + " \"resolution\":2.2,\n"
- + " \"title\":\"Structure of human BRCA1 BRCT in complex with BAAT peptide\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"4igk\",\n"
- + " \"resolution\":1.75,\n"
- + " \"title\":\"Structure of human BRCA1 BRCT in complex with ATRIP peptide\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"3k0k\",\n"
- + " \"resolution\":2.7,\n"
- + " \"title\":\"Crystal Structure of BRCA1 BRCT in complex with a minimal recognition tetrapeptide with a free carboxy C-terminus.\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"3k16\",\n"
- + " \"resolution\":3.0,\n"
- + " \"title\":\"Crystal Structure of BRCA1 BRCT D1840T in complex with a minimal recognition tetrapeptide with a free carboxy C-terminus\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"3k15\",\n"
- + " \"resolution\":2.8,\n"
- + " \"title\":\"Crystal Structure of BRCA1 BRCT D1840T in complex with a minimal recognition tetrapeptide with an amidated C-terminus\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"3k0h\",\n"
- + " \"resolution\":2.7,\n"
- + " \"title\":\"The crystal structure of BRCA1 BRCT in complex with a minimal recognition tetrapeptide with an amidated C-terminus\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"1y98\",\n"
- + " \"resolution\":2.5,\n"
- + " \"title\":\"Structure of the BRCT repeats of BRCA1 bound to a CtIP phosphopeptide.\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"3coj\",\n"
- + " \"resolution\":3.21,\n"
- + " \"title\":\"Crystal Structure of the BRCT Domains of Human BRCA1 in Complex with a Phosphorylated Peptide from Human Acetyl-CoA Carboxylase 1\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"X-ray diffraction\"],\n"
- + " \"pdb_id\":\"4y18\",\n"
- + " \"resolution\":3.5,\n"
- + " \"title\":\"Structure of BRCA1 BRCT domains in complex with Abraxas double phosphorylated peptide\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"Electron Microscopy\"],\n"
- + " \"pdb_id\":\"7jzv\",\n"
- + " \"resolution\":3.9,\n"
- + " \"title\":\"Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"Electron Microscopy\"],\n"
- + " \"pdb_id\":\"7jzv\",\n"
- + " \"resolution\":3.9,\n"
- + " \"title\":\"Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"Electron Microscopy\"],\n"
- + " \"pdb_id\":\"7lyb\",\n"
- + " \"resolution\":3.28,\n"
- + " \"title\":\"Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"Electron Microscopy\"],\n"
- + " \"pdb_id\":\"7lyb\",\n"
- + " \"resolution\":3.28,\n"
- + " \"title\":\"Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"Electron Microscopy\"],\n"
- + " \"pdb_id\":\"7lyb\",\n"
- + " \"resolution\":3.28,\n"
- + " \"title\":\"Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"Electron Microscopy\"],\n"
- + " \"pdb_id\":\"7jzv\",\n"
- + " \"resolution\":3.9,\n"
- + " \"title\":\"Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"Electron Microscopy\"],\n"
- + " \"pdb_id\":\"7lyb\",\n"
- + " \"resolution\":3.28,\n"
- + " \"title\":\"Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"Electron Microscopy\"],\n"
- + " \"pdb_id\":\"7jzv\",\n"
- + " \"resolution\":3.9,\n"
- + " \"title\":\"Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"Electron Microscopy\"],\n"
- + " \"pdb_id\":\"7lyb\",\n"
- + " \"resolution\":3.28,\n"
- + " \"title\":\"Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"Electron Microscopy\"],\n"
- + " \"pdb_id\":\"7jzv\",\n"
- + " \"resolution\":3.9,\n"
- + " \"title\":\"Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"Electron Microscopy\"],\n"
- + " \"pdb_id\":\"7lyb\",\n"
- + " \"resolution\":3.28,\n"
- + " \"title\":\"Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"Electron Microscopy\"],\n"
- + " \"pdb_id\":\"7lyb\",\n"
- + " \"resolution\":3.28,\n"
- + " \"title\":\"Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"Electron Microscopy\"],\n"
- + " \"pdb_id\":\"7lyb\",\n"
- + " \"resolution\":3.28,\n"
- + " \"title\":\"Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"Electron Microscopy\"],\n"
- + " \"pdb_id\":\"7jzv\",\n"
- + " \"resolution\":3.9,\n"
- + " \"title\":\"Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"Electron Microscopy\"],\n"
- + " \"pdb_id\":\"6g2i\",\n"
- + " \"resolution\":5.9,\n"
- + " \"title\":\"Filament of acetyl-CoA carboxylase and BRCT domains of BRCA1 (ACC-BRCT) at 5.9 A resolution\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"Electron Microscopy\"],\n"
- + " \"pdb_id\":\"7jzv\",\n"
- + " \"resolution\":3.9,\n"
- + " \"title\":\"Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"Electron Microscopy\"],\n"
- + " \"pdb_id\":\"7lyb\",\n"
- + " \"resolution\":3.28,\n"
- + " \"title\":\"Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c\"},\n"
- + " {\n"
- + " \"experimental_method\":[\"Electron Microscopy\"],\n"
- + " \"pdb_id\":\"7jzv\",\n"
- + " \"resolution\":3.9,\n"
- + " \"title\":\"Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome\"}]\n"
- + " }}" };
-
+ mocks[0] = new String[] {
+ "https://www.ebi.ac.uk/pdbe/search/pdb/select?wt=json&fl=pdb_id,title,experimental_method,resolution&rows=500&start=0&q=(4igk+OR+7lyb+OR+3k0h+OR+3k0k+OR+1t15+OR+3pxc+OR+3pxd+OR+3pxe+OR+1jm7+OR+7jzv+OR+3pxa+OR+3pxb+OR+1y98+OR+1n5o+OR+4ifi+OR+4y2g+OR+3k15+OR+3k16+OR+4jlu+OR+2ing+OR+4ofb+OR+6g2i+OR+3coj+OR+1jnx+OR+4y18+OR+4u4a+OR+1oqa+OR+1t29+OR+1t2u+OR+1t2v)+AND+molecule_sequence:%5B''+TO+*%5D+AND+status:REL&sort=",
+ "{\n" + " \"responseHeader\":{\n" + " \"status\":0,\n"
+ + " \"QTime\":0,\n" + " \"params\":{\n"
+ + " \"q\":\"(4igk OR 7lyb OR 3k0h OR 3k0k OR 1t15 OR 3pxc OR 3pxd OR 3pxe OR 1jm7 OR 7jzv OR 3pxa OR 3pxb OR 1y98 OR 1n5o OR 4ifi OR 4y2g OR 3k15 OR 3k16 OR 4jlu OR 2ing OR 4ofb OR 6g2i OR 3coj OR 1jnx OR 4y18 OR 4u4a OR 1oqa OR 1t29 OR 1t2u OR 1t2v) AND molecule_sequence:['' TO *] AND status:REL\",\n"
+ + " \"fl\":\"pdb_id,title,experimental_method,resolution\",\n"
+ + " \"start\":\"0\",\n" + " \"sort\":\"\",\n"
+ + " \"rows\":\"500\",\n" + " \"wt\":\"json\"}},\n"
+ + " \"response\":{\"numFound\":64,\"start\":0,\"docs\":[\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"4ofb\",\n"
+ + " \"resolution\":3.05,\n"
+ + " \"title\":\"Crystal structure of human BRCA1 BRCT in complex with nonphosphopeptide inhibitor\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"3pxe\",\n"
+ + " \"resolution\":2.85,\n"
+ + " \"title\":\"Impact of BRCA1 BRCT domain missense substitutions on phospho-peptide recognition: E1836K\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"4jlu\",\n"
+ + " \"resolution\":3.5,\n"
+ + " \"title\":\"Crystal structure of BRCA1 BRCT with doubly phosphorylated Abraxas\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"4y2g\",\n"
+ + " \"resolution\":2.5,\n"
+ + " \"title\":\"Structure of BRCA1 BRCT domains in complex with Abraxas single phosphorylated peptide\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Solution NMR\"],\n"
+ + " \"pdb_id\":\"1oqa\",\n"
+ + " \"title\":\"Solution structure of the BRCT-c domain from human BRCA1\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"4u4a\",\n"
+ + " \"resolution\":3.51,\n"
+ + " \"title\":\"Complex Structure of BRCA1 BRCT with singly phospho Abraxas\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"3k16\",\n"
+ + " \"resolution\":3.0,\n"
+ + " \"title\":\"Crystal Structure of BRCA1 BRCT D1840T in complex with a minimal recognition tetrapeptide with a free carboxy C-terminus\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"1t15\",\n"
+ + " \"resolution\":1.85,\n"
+ + " \"title\":\"Crystal Structure of the Brca1 BRCT Domains in Complex with the Phosphorylated Interacting Region from Bach1 Helicase\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"3k15\",\n"
+ + " \"resolution\":2.8,\n"
+ + " \"title\":\"Crystal Structure of BRCA1 BRCT D1840T in complex with a minimal recognition tetrapeptide with an amidated C-terminus\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"1t2v\",\n"
+ + " \"resolution\":3.3,\n"
+ + " \"title\":\"Structural basis of phospho-peptide recognition by the BRCT domain of BRCA1, structure with phosphopeptide\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"1y98\",\n"
+ + " \"resolution\":2.5,\n"
+ + " \"title\":\"Structure of the BRCT repeats of BRCA1 bound to a CtIP phosphopeptide.\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"1t29\",\n"
+ + " \"resolution\":2.3,\n"
+ + " \"title\":\"Crystal structure of the BRCA1 BRCT repeats bound to a phosphorylated BACH1 peptide\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"3k0k\",\n"
+ + " \"resolution\":2.7,\n"
+ + " \"title\":\"Crystal Structure of BRCA1 BRCT in complex with a minimal recognition tetrapeptide with a free carboxy C-terminus.\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"3k0h\",\n"
+ + " \"resolution\":2.7,\n"
+ + " \"title\":\"The crystal structure of BRCA1 BRCT in complex with a minimal recognition tetrapeptide with an amidated C-terminus\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"4ifi\",\n"
+ + " \"resolution\":2.2,\n"
+ + " \"title\":\"Structure of human BRCA1 BRCT in complex with BAAT peptide\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"3pxd\",\n"
+ + " \"resolution\":2.8,\n"
+ + " \"title\":\"Impact of BRCA1 BRCT domain missense substitutions on phospho-peptide recognition: R1835P\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"3pxc\",\n"
+ + " \"resolution\":2.8,\n"
+ + " \"title\":\"Impact of BRCA1 BRCT domain missense substitutions on phospho-peptide recognition: R1699Q\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"1jnx\",\n"
+ + " \"resolution\":2.5,\n"
+ + " \"title\":\"Crystal structure of the BRCT repeat region from the breast cancer associated protein, BRCA1\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"3pxa\",\n"
+ + " \"resolution\":2.55,\n"
+ + " \"title\":\"Impact of BRCA1 BRCT domain missense substitutions on phospho-peptide recognition: G1656D\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Solution NMR\"],\n"
+ + " \"pdb_id\":\"1jm7\",\n"
+ + " \"title\":\"Solution structure of the BRCA1/BARD1 RING-domain heterodimer\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"4igk\",\n"
+ + " \"resolution\":1.75,\n"
+ + " \"title\":\"Structure of human BRCA1 BRCT in complex with ATRIP peptide\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"1t2u\",\n"
+ + " \"resolution\":2.8,\n"
+ + " \"title\":\"Structural basis of phosphopeptide recognition by the BRCT domain of BRCA1: structure of BRCA1 missense variant V1809F\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"3pxb\",\n"
+ + " \"resolution\":2.5,\n"
+ + " \"title\":\"Impact of BRCA1 BRCT domain missense substitutions on phospho-peptide recognition: T1700A\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"1n5o\",\n"
+ + " \"resolution\":2.8,\n"
+ + " \"title\":\"Structural consequences of a cancer-causing BRCA1-BRCT missense mutation\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"3coj\",\n"
+ + " \"resolution\":3.21,\n"
+ + " \"title\":\"Crystal Structure of the BRCT Domains of Human BRCA1 in Complex with a Phosphorylated Peptide from Human Acetyl-CoA Carboxylase 1\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Electron Microscopy\"],\n"
+ + " \"pdb_id\":\"6g2i\",\n"
+ + " \"resolution\":5.9,\n"
+ + " \"title\":\"Filament of acetyl-CoA carboxylase and BRCT domains of BRCA1 (ACC-BRCT) at 5.9 A resolution\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"4jlu\",\n"
+ + " \"resolution\":3.5,\n"
+ + " \"title\":\"Crystal structure of BRCA1 BRCT with doubly phosphorylated Abraxas\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"4ofb\",\n"
+ + " \"resolution\":3.05,\n"
+ + " \"title\":\"Crystal structure of human BRCA1 BRCT in complex with nonphosphopeptide inhibitor\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"3pxe\",\n"
+ + " \"resolution\":2.85,\n"
+ + " \"title\":\"Impact of BRCA1 BRCT domain missense substitutions on phospho-peptide recognition: E1836K\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"4u4a\",\n"
+ + " \"resolution\":3.51,\n"
+ + " \"title\":\"Complex Structure of BRCA1 BRCT with singly phospho Abraxas\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"4y2g\",\n"
+ + " \"resolution\":2.5,\n"
+ + " \"title\":\"Structure of BRCA1 BRCT domains in complex with Abraxas single phosphorylated peptide\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"4y18\",\n"
+ + " \"resolution\":3.5,\n"
+ + " \"title\":\"Structure of BRCA1 BRCT domains in complex with Abraxas double phosphorylated peptide\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"2ing\",\n"
+ + " \"resolution\":3.6,\n"
+ + " \"title\":\"X-ray Structure of the BRCA1 BRCT mutant M1775K\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"1t15\",\n"
+ + " \"resolution\":1.85,\n"
+ + " \"title\":\"Crystal Structure of the Brca1 BRCT Domains in Complex with the Phosphorylated Interacting Region from Bach1 Helicase\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"1t29\",\n"
+ + " \"resolution\":2.3,\n"
+ + " \"title\":\"Crystal structure of the BRCA1 BRCT repeats bound to a phosphorylated BACH1 peptide\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Solution NMR\"],\n"
+ + " \"pdb_id\":\"1jm7\",\n"
+ + " \"title\":\"Solution structure of the BRCA1/BARD1 RING-domain heterodimer\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"1t2v\",\n"
+ + " \"resolution\":3.3,\n"
+ + " \"title\":\"Structural basis of phospho-peptide recognition by the BRCT domain of BRCA1, structure with phosphopeptide\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"4ifi\",\n"
+ + " \"resolution\":2.2,\n"
+ + " \"title\":\"Structure of human BRCA1 BRCT in complex with BAAT peptide\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"4igk\",\n"
+ + " \"resolution\":1.75,\n"
+ + " \"title\":\"Structure of human BRCA1 BRCT in complex with ATRIP peptide\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"3k0k\",\n"
+ + " \"resolution\":2.7,\n"
+ + " \"title\":\"Crystal Structure of BRCA1 BRCT in complex with a minimal recognition tetrapeptide with a free carboxy C-terminus.\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"3k16\",\n"
+ + " \"resolution\":3.0,\n"
+ + " \"title\":\"Crystal Structure of BRCA1 BRCT D1840T in complex with a minimal recognition tetrapeptide with a free carboxy C-terminus\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"3k15\",\n"
+ + " \"resolution\":2.8,\n"
+ + " \"title\":\"Crystal Structure of BRCA1 BRCT D1840T in complex with a minimal recognition tetrapeptide with an amidated C-terminus\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"3k0h\",\n"
+ + " \"resolution\":2.7,\n"
+ + " \"title\":\"The crystal structure of BRCA1 BRCT in complex with a minimal recognition tetrapeptide with an amidated C-terminus\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"1y98\",\n"
+ + " \"resolution\":2.5,\n"
+ + " \"title\":\"Structure of the BRCT repeats of BRCA1 bound to a CtIP phosphopeptide.\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"3coj\",\n"
+ + " \"resolution\":3.21,\n"
+ + " \"title\":\"Crystal Structure of the BRCT Domains of Human BRCA1 in Complex with a Phosphorylated Peptide from Human Acetyl-CoA Carboxylase 1\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"X-ray diffraction\"],\n"
+ + " \"pdb_id\":\"4y18\",\n"
+ + " \"resolution\":3.5,\n"
+ + " \"title\":\"Structure of BRCA1 BRCT domains in complex with Abraxas double phosphorylated peptide\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Electron Microscopy\"],\n"
+ + " \"pdb_id\":\"7jzv\",\n"
+ + " \"resolution\":3.9,\n"
+ + " \"title\":\"Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Electron Microscopy\"],\n"
+ + " \"pdb_id\":\"7jzv\",\n"
+ + " \"resolution\":3.9,\n"
+ + " \"title\":\"Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Electron Microscopy\"],\n"
+ + " \"pdb_id\":\"7lyb\",\n"
+ + " \"resolution\":3.28,\n"
+ + " \"title\":\"Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Electron Microscopy\"],\n"
+ + " \"pdb_id\":\"7lyb\",\n"
+ + " \"resolution\":3.28,\n"
+ + " \"title\":\"Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Electron Microscopy\"],\n"
+ + " \"pdb_id\":\"7lyb\",\n"
+ + " \"resolution\":3.28,\n"
+ + " \"title\":\"Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Electron Microscopy\"],\n"
+ + " \"pdb_id\":\"7jzv\",\n"
+ + " \"resolution\":3.9,\n"
+ + " \"title\":\"Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Electron Microscopy\"],\n"
+ + " \"pdb_id\":\"7lyb\",\n"
+ + " \"resolution\":3.28,\n"
+ + " \"title\":\"Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Electron Microscopy\"],\n"
+ + " \"pdb_id\":\"7jzv\",\n"
+ + " \"resolution\":3.9,\n"
+ + " \"title\":\"Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Electron Microscopy\"],\n"
+ + " \"pdb_id\":\"7lyb\",\n"
+ + " \"resolution\":3.28,\n"
+ + " \"title\":\"Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Electron Microscopy\"],\n"
+ + " \"pdb_id\":\"7jzv\",\n"
+ + " \"resolution\":3.9,\n"
+ + " \"title\":\"Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Electron Microscopy\"],\n"
+ + " \"pdb_id\":\"7lyb\",\n"
+ + " \"resolution\":3.28,\n"
+ + " \"title\":\"Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Electron Microscopy\"],\n"
+ + " \"pdb_id\":\"7lyb\",\n"
+ + " \"resolution\":3.28,\n"
+ + " \"title\":\"Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Electron Microscopy\"],\n"
+ + " \"pdb_id\":\"7lyb\",\n"
+ + " \"resolution\":3.28,\n"
+ + " \"title\":\"Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Electron Microscopy\"],\n"
+ + " \"pdb_id\":\"7jzv\",\n"
+ + " \"resolution\":3.9,\n"
+ + " \"title\":\"Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Electron Microscopy\"],\n"
+ + " \"pdb_id\":\"6g2i\",\n"
+ + " \"resolution\":5.9,\n"
+ + " \"title\":\"Filament of acetyl-CoA carboxylase and BRCT domains of BRCA1 (ACC-BRCT) at 5.9 A resolution\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Electron Microscopy\"],\n"
+ + " \"pdb_id\":\"7jzv\",\n"
+ + " \"resolution\":3.9,\n"
+ + " \"title\":\"Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Electron Microscopy\"],\n"
+ + " \"pdb_id\":\"7lyb\",\n"
+ + " \"resolution\":3.28,\n"
+ + " \"title\":\"Cryo-EM structure of the human nucleosome core particle in complex with BRCA1-BARD1-UbcH5c\"},\n"
+ + " {\n"
+ + " \"experimental_method\":[\"Electron Microscopy\"],\n"
+ + " \"pdb_id\":\"7jzv\",\n"
+ + " \"resolution\":3.9,\n"
+ + " \"title\":\"Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome\"}]\n"
+ + " }}" };
+
mocks[1] = new String[2];
- try {
- mocks[1][0] = readJsonStringFromFile("test/jalview/fts/threedbeacons/p01308_pdbfts_query.txt").trim();
- mocks[1][1] = readJsonStringFromFile("test/jalview/fts/threedbeacons/p01308_pdbfts_resp.txt").trim();
+ try
+ {
+ mocks[1][0] = readJsonStringFromFile(
+ "test/jalview/fts/threedbeacons/p01308_pdbfts_query.txt")
+ .trim();
+ mocks[1][1] = readJsonStringFromFile(
+ "test/jalview/fts/threedbeacons/p01308_pdbfts_resp.txt")
+ .trim();
} catch (Throwable e)
{
- Assert.fail("Couldn't read mock data.",e);
+ Assert.fail("Couldn't read mock data.", e);
}
-
- FTSRestClient.createMockFTSRestClient((FTSRestClient) PDBFTSRestClient.getInstance(), mocks);
+
+ FTSRestClient.createMockFTSRestClient(
+ (FTSRestClient) PDBFTSRestClient.getInstance(), mocks);
}
}
private static String[][] mocks = { { "P38398.json",
"{\"uniprot_entry\":{\"sequence_length\":1863,\"ac\":\"P38398\",\"id\":\"BRCA1_HUMAN\"},\"structures\":[{\"model_identifier\":\"4igk\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2012-12-17\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":1.75,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/4igk_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/4igk\"},{\"model_identifier\":\"1t15\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2004-04-15\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":1.85,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1t15_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/1t15\"},{\"model_identifier\":\"4ifi\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2012-12-14\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.2,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/4ifi_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/4ifi\"},{\"model_identifier\":\"1t29\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2004-04-20\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.3,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1t29_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/1t29\"},{\"model_identifier\":\"3pxb\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2010-12-09\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.5,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3pxb_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/3pxb\"},{\"model_identifier\":\"4y2g\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2015-02-09\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.5,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/4y2g_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/4y2g\"},{\"model_identifier\":\"1y98\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2004-12-14\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.5,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1y98_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/1y98\"},{\"model_identifier\":\"1jnx\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2001-07-26\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.5,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1jnx_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/1jnx\"},{\"model_identifier\":\"3pxa\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2010-12-09\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.55,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3pxa_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/3pxa\"},{\"model_identifier\":\"3k0h\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2009-09-24\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.7,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3k0h_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/3k0h\"},{\"model_identifier\":\"3k0k\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2009-09-24\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.7,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3k0k_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/3k0k\"},{\"model_identifier\":\"1n5o\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2002-11-06\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.8,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1n5o_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/1n5o\"},{\"model_identifier\":\"3pxc\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2010-12-09\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.8,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3pxc_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/3pxc\"},{\"model_identifier\":\"3pxd\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2010-12-09\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.8,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3pxd_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/3pxd\"},{\"model_identifier\":\"1t2u\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2004-04-22\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.8,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1t2u_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/1t2u\"},{\"model_identifier\":\"3k15\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2009-09-25\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.8,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3k15_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/3k15\"},{\"model_identifier\":\"3pxe\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2010-12-09\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.85,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3pxe_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/3pxe\"},{\"model_identifier\":\"3k16\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2009-09-25\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":3.0,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3k16_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/3k16\"},{\"model_identifier\":\"4ofb\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2014-01-14\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":3.05,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/4ofb_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/4ofb\"},{\"model_identifier\":\"3coj\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2008-03-28\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":3.21,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3coj_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/3coj\"},{\"model_identifier\":\"7lyb\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2021-03-06\",\"sequence_identity\":100.0,\"uniprot_start\":1,\"uniprot_end\":100,\"resolution\":3.28,\"coverage\":5.37,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/7lyb_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"ELECTRON MICROSCOPY\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/7lyb\"},{\"model_identifier\":\"1t2v\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2004-04-22\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":3.3,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1t2v_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/1t2v\"},{\"model_identifier\":\"4y18\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2015-02-06\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":3.5,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/4y18_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/4y18\"},{\"model_identifier\":\"4jlu\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2013-03-13\",\"sequence_identity\":100.0,\"uniprot_start\":1649,\"uniprot_end\":1859,\"resolution\":3.5,\"coverage\":11.33,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/4jlu_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/4jlu\"},{\"model_identifier\":\"4u4a\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2014-07-23\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":3.51,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/4u4a_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/4u4a\"},{\"model_identifier\":\"2ing\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2006-10-07\",\"sequence_identity\":100.0,\"uniprot_start\":1649,\"uniprot_end\":1859,\"resolution\":3.6,\"coverage\":11.33,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/2ing_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"X-RAY DIFFRACTION\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/2ing\"},{\"model_identifier\":\"7jzv\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2020-09-02\",\"sequence_identity\":99.0,\"uniprot_start\":2,\"uniprot_end\":104,\"resolution\":3.9,\"coverage\":5.53,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/7jzv_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"ELECTRON MICROSCOPY\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/7jzv\"},{\"model_identifier\":\"6g2i\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2018-03-23\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":5.9,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/6g2i_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"ELECTRON MICROSCOPY\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/6g2i\"},{\"model_identifier\":\"1jm7\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2001-07-17\",\"sequence_identity\":100.0,\"uniprot_start\":1,\"uniprot_end\":110,\"resolution\":null,\"coverage\":5.9,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1jm7_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"SOLUTION NMR\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/1jm7\"},{\"model_identifier\":\"1oqa\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBe\",\"created\":\"2003-03-07\",\"sequence_identity\":100.0,\"uniprot_start\":1755,\"uniprot_end\":1863,\"resolution\":null,\"coverage\":5.85,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1oqa_updated.cif\",\"model_format\":\"MMCIF\",\"experimental_method\":\"SOLUTION NMR\",\"model_page_url\":\"https://www.ebi.ac.uk/pdbe/entry/pdb/1oqa\"},{\"model_identifier\":\"P38398_1646-1859:6g2i.1.K\",\"model_category\":\"TEMPLATE-BASED\",\"provider\":\"SWISS-MODEL\",\"created\":\"2021-11-05\",\"sequence_identity\":1.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"coverage\":0.115,\"confidence_version\":\"4.2.0\",\"confidence_avg_local_score\":0.776,\"model_url\":\"https://swissmodel.expasy.org/3d-beacons/uniprot/P38398.pdb?range=1646-1859&template=6g2i.1.K&provider=swissmodel\",\"model_format\":\"PDB\",\"model_page_url\":\"https://swissmodel.expasy.org/repository/uniprot/P38398?range=1646-1859&template=6g2i.1.K\",\"confidence_type\":\"QMEANDisCo\"},{\"model_identifier\":\"P38398_1-103:1jm7.1.A\",\"model_category\":\"TEMPLATE-BASED\",\"provider\":\"SWISS-MODEL\",\"created\":\"2021-11-05\",\"sequence_identity\":1.0,\"uniprot_start\":1,\"uniprot_end\":103,\"coverage\":0.055,\"confidence_version\":\"4.2.0\",\"confidence_avg_local_score\":0.655,\"model_url\":\"https://swissmodel.expasy.org/3d-beacons/uniprot/P38398.pdb?range=1-103&template=1jm7.1.A&provider=swissmodel\",\"model_format\":\"PDB\",\"model_page_url\":\"https://swissmodel.expasy.org/repository/uniprot/P38398?range=1-103&template=1jm7.1.A\",\"confidence_type\":\"QMEANDisCo\"},{\"model_identifier\":\"AF-P38398-F1\",\"model_category\":\"DEEP-LEARNING\",\"provider\":\"AlphaFold DB\",\"created\":\"2021-07-01\",\"sequence_identity\":1.0,\"uniprot_start\":1,\"uniprot_end\":1863,\"coverage\":100.0,\"model_url\":\"https://alphafold.ebi.ac.uk/files/AF-P38398-F1-model_v1.cif\",\"model_format\":\"MMCIF\",\"model_page_url\":\"https://alphafold.ebi.ac.uk/entry/P38398\"}]}" },
- { "P01308.json",null}};
+ { "P01308.json", null } };
private static void setMockData()
{
try
{
- mocks[1][1]= PDBFTSRestClientTest.readJsonStringFromFile("test/jalview/fts/threedbeacons/p01308_tdb_resp.txt");
+ mocks[1][1] = PDBFTSRestClientTest.readJsonStringFromFile(
+ "test/jalview/fts/threedbeacons/p01308_tdb_resp.txt");
} catch (IOException e)
{
- Assert.fail("Couldn't read mock response data",e);
+ Assert.fail("Couldn't read mock response data", e);
}
}
-
+
public static void setMock()
{
setMockData();
FTSRestClient.createMockFTSRestClient(
- (FTSRestClient) TDBeaconsFTSRestClient.getInstance(),
- mocks);
+ (FTSRestClient) TDBeaconsFTSRestClient.getInstance(), mocks);
}
private static String dev_url = "https://wwwdev.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/";
+
private static String prod_url = "https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/";
/**
* check that the mock request and response are the same as the response from
* a live 3D-beacons endpoint
*
- * Note - servers often have rapidly changing ids / URIs so this might fail, but the overall structure will remain.
+ * Note - servers often have rapidly changing ids / URIs so this might fail,
+ * but the overall structure will remain.
*
* @throws Exception
*/
public void verifyMockTDBRequest() throws Exception
{
setMockData();
- for (String[] otherMock:mocks)
+ for (String[] otherMock : mocks)
{
- verifyMockTDBRequest(otherMock[0],otherMock[1]);
+ verifyMockTDBRequest(otherMock[0], otherMock[1]);
}
}
- private void verifyMockTDBRequest(String mockRequest, String _mockResponse) throws Exception
+
+ private void verifyMockTDBRequest(String mockRequest,
+ String _mockResponse) throws Exception
{
URL tdb_req = new URL(prod_url + mockRequest);
byte[] resp = tdb_req.openStream().readAllBytes();
package jalview.fts.threedbeacons;
-
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertTrue;
import junit.extensions.PA;
-
public class TDBeaconsPanelTest
{
@BeforeClass(alwaysRun = true)
assertTrue(searchPanel.getCmbSearchTarget().getItemCount() > 0);
searchPanel.populateCmbSearchTargetOptions();
}
-
+
@Test
- public void getFTSframeTitleTest() {
+ public void getFTSframeTitleTest()
+ {
TDBeaconsFTSPanel searchPanel = new TDBeaconsFTSPanel(null);
System.out.println(searchPanel.getFTSFrameTitle());
}
-
+
@Test
- public void testgetUNIPROTid() {
+ public void testgetUNIPROTid()
+ {
String outcome = TDBeaconsFTSPanel.decodeSearchTerm("P01308");
System.out.println(outcome);
}
-//
-// @Test
-// public void queryTest() {
-// int outcome = TDBeaconsFTSPanel.executeParse("P01308");
-// //System.out.println("query outcome :" + outcome);
-// int expected_length = 110;
-// assertEquals(outcome, expected_length);
-// }
+ //
+ // @Test
+ // public void queryTest() {
+ // int outcome = TDBeaconsFTSPanel.executeParse("P01308");
+ // //System.out.println("query outcome :" + outcome);
+ // int expected_length = 110;
+ // assertEquals(outcome, expected_length);
+ // }
}
}
/**
- * configure (read-only) properties for test to ensure Consensus is computed for
- * colour Above PID testing
+ * configure (read-only) properties for test to ensure Consensus is computed
+ * for colour Above PID testing
*/
@BeforeMethod(alwaysRun = true)
public void setUp()
{
SequenceI seq1 = new Sequence("Seq1", "ABCDEFGHIJ");
SequenceI seq2 = new Sequence("Seq2", "ABCDEFGHIJ");
- seq1.addSequenceFeature(new SequenceFeature("Metal", "", 1, 5, 0f, null));
- seq2.addSequenceFeature(new SequenceFeature("Metal", "", 6, 10, 10f,
- null));
- seq1.addSequenceFeature(new SequenceFeature("Turn", "", 2, 4,
- Float.NaN, null));
- seq2.addSequenceFeature(new SequenceFeature("Turn", "", 7, 9,
- Float.NaN, null));
+ seq1.addSequenceFeature(
+ new SequenceFeature("Metal", "", 1, 5, 0f, null));
+ seq2.addSequenceFeature(
+ new SequenceFeature("Metal", "", 6, 10, 10f, null));
+ seq1.addSequenceFeature(
+ new SequenceFeature("Turn", "", 2, 4, Float.NaN, null));
+ seq2.addSequenceFeature(
+ new SequenceFeature("Turn", "", 7, 9, Float.NaN, null));
AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
AlignFrame alignFrame = new AlignFrame(al, al.getWidth(),
al.getHeight());
assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
.getNumberOfRegions(), 0);
-
/*
* threshold Metal to hide features where score < 5
* seq1 feature in columns 1-5 is hidden
fc.setThreshold(5f);
alignFrame.getFeatureRenderer().setColour("Metal", fc);
assertTrue(alignFrame.hideFeatureColumns("Metal", true));
- HiddenColumns hidden = alignFrame.getViewport().getAlignment().getHiddenColumns();
+ HiddenColumns hidden = alignFrame.getViewport().getAlignment()
+ .getHiddenColumns();
assertEquals(hidden.getNumberOfRegions(), 1);
Iterator<int[]> regions = hidden.iterator();
int[] next = regions.next();
*/
alignFrame.getViewport().showAllHiddenColumns();
assertTrue(alignFrame.hideFeatureColumns("Turn", true));
- regions = alignFrame.getViewport().getAlignment()
- .getHiddenColumns().iterator();
+ regions = alignFrame.getViewport().getAlignment().getHiddenColumns()
+ .iterator();
assertEquals(alignFrame.getViewport().getAlignment().getHiddenColumns()
.getNumberOfRegions(), 2);
next = regions.next();
* <ul>
* <li>with Apply Colour to All Groups not selected, does not change group
* colours</li>
- * <li>with Apply Colour to All Groups selected, does change group colours</li>
+ * <li>with Apply Colour to All Groups selected, does change group
+ * colours</li>
* <li>in neither case, changes alignment or group colour thresholds (PID or
* Conservation)</li>
* </ul>
af.conservationMenuItem_actionPerformed(true);
SliderPanel sp = SliderPanel.getSliderPanel();
assertEquals(sp.getTitle(), MessageManager.formatMessage(
- "label.conservation_colour_increment",
- new String[] { "Background" }));
+ "label.conservation_colour_increment", new String[]
+ { "Background" }));
assertTrue(sp.isForConservation());
sp.valueChanged(20);
assertTrue(av.getResidueShading().conservationApplied());
sp = SliderPanel.getSliderPanel();
assertFalse(sp.isForConservation());
assertEquals(sp.getTitle(), MessageManager.formatMessage(
- "label.percentage_identity_threshold",
- new String[] { "Background" }));
+ "label.percentage_identity_threshold", new String[]
+ { "Background" }));
sp.valueChanged(10);
assertEquals(av.getResidueShading().getThreshold(), 10);
assertTrue(av.getResidueShading().conservationApplied());
*/
PopupMenu popupMenu = new PopupMenu(af.alignPanel, al.getSequenceAt(2),
null);
- popupMenu.changeColour_actionPerformed(JalviewColourScheme.Strand
- .toString());
+ popupMenu.changeColour_actionPerformed(
+ JalviewColourScheme.Strand.toString());
assertTrue(sg.getColourScheme() instanceof StrandColourScheme);
assertEquals(al.getGroups().size(), 1);
assertSame(al.getGroups().get(0), sg);
sp = SliderPanel.getSliderPanel();
assertTrue(sp.isForConservation());
assertEquals(sp.getTitle(), MessageManager.formatMessage(
- "label.conservation_colour_increment",
- new String[] { sg.getName() }));
+ "label.conservation_colour_increment", new String[]
+ { sg.getName() }));
sp.valueChanged(30);
assertTrue(sg.getGroupColourScheme().conservationApplied());
assertEquals(sg.getGroupColourScheme().getConservationInc(), 30);
sp = SliderPanel.getSliderPanel();
assertFalse(sp.isForConservation());
assertEquals(sp.getTitle(), MessageManager.formatMessage(
- "label.percentage_identity_threshold",
- new String[] { sg.getName() }));
+ "label.percentage_identity_threshold", new String[]
+ { sg.getName() }));
sp.valueChanged(40);
assertEquals(sg.getGroupColourScheme().getThreshold(), 40);
// conservation threshold is unchanged:
av.setSelectionGroup(sg);
PopupMenu popupMenu = new PopupMenu(af.alignPanel, al.getSequenceAt(0),
null);
- popupMenu.changeColour_actionPerformed(JalviewColourScheme.Strand
- .toString());
+ popupMenu.changeColour_actionPerformed(
+ JalviewColourScheme.Strand.toString());
assertTrue(sg.getColourScheme() instanceof StrandColourScheme);
assertEquals(al.getGroups().size(), 1);
assertSame(al.getGroups().get(0), sg);
sp = SliderPanel.getSliderPanel();
assertTrue(sp.isForConservation());
assertEquals(sp.getTitle(), MessageManager.formatMessage(
- "label.conservation_colour_increment",
- new String[] { "Background" }));
+ "label.conservation_colour_increment", new String[]
+ { "Background" }));
/*
* make a new View, verify alignment and group colour schemes
sp = SliderPanel.getSliderPanel();
assertTrue(sp.isForConservation());
assertEquals(sp.getTitle(), MessageManager.formatMessage(
- "label.conservation_colour_increment",
- new String[] { "View 1" }));
+ "label.conservation_colour_increment", new String[]
+ { "View 1" }));
sp.valueChanged(22);
assertEquals(av2.getResidueShading().getConservationInc(), 22);
}
@BeforeClass(alwaysRun = true)
public static void setUpBeforeClass() throws Exception
{
- Jalview.main(new String[] { "-nonews", "-props",
- "test/jalview/testProps.jvprops" });
+ Jalview.main(
+ new String[]
+ { "-nonews", "-props", "test/jalview/testProps.jvprops" });
/*
* remove any sequence mappings left lying around by other tests
/*
* alignment with reference to mappings
*/
- AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
- ">Seq1\nCAGT\n", DataSourceType.PASTE);
+ AlignFrame af1 = new FileLoader()
+ .LoadFileWaitTillLoaded(">Seq1\nCAGT\n", DataSourceType.PASTE);
SequenceI s1 = af1.getViewport().getAlignment().getSequenceAt(0);
AlignedCodonFrame acf1 = new AlignedCodonFrame();
- acf1.addMap(s1, s1, new MapList(new int[] { 1, 4 }, new int[] { 1, 4 },
- 1, 1));
+ acf1.addMap(s1, s1,
+ new MapList(new int[]
+ { 1, 4 }, new int[] { 1, 4 }, 1, 1));
AlignedCodonFrame acf2 = new AlignedCodonFrame();
- acf2.addMap(s1, s1, new MapList(new int[] { 1, 4 }, new int[] { 4, 1 },
- 1, 1));
+ acf2.addMap(s1, s1,
+ new MapList(new int[]
+ { 1, 4 }, new int[] { 4, 1 }, 1, 1));
List<AlignedCodonFrame> mappings = new ArrayList<>();
mappings.add(acf1);
.getStructureSelectionManager(Desktop.instance);
ssm.resetAll();
- AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
- ">Seq1\nRSVQ\n", DataSourceType.PASTE);
- AlignFrame af2 = new FileLoader().LoadFileWaitTillLoaded(
- ">Seq2\nDGEL\n", DataSourceType.PASTE);
+ AlignFrame af1 = new FileLoader()
+ .LoadFileWaitTillLoaded(">Seq1\nRSVQ\n", DataSourceType.PASTE);
+ AlignFrame af2 = new FileLoader()
+ .LoadFileWaitTillLoaded(">Seq2\nDGEL\n", DataSourceType.PASTE);
SequenceI cs1 = new Sequence("cseq1", "CCCGGGTTTAAA");
SequenceI cs2 = new Sequence("cseq2", "CTTGAGTCTAGA");
SequenceI s1 = af1.getViewport().getAlignment().getSequenceAt(0);
SequenceI s2 = af2.getViewport().getAlignment().getSequenceAt(0);
// need to be distinct
AlignedCodonFrame acf1 = new AlignedCodonFrame();
- acf1.addMap(cs1, s1, new MapList(new int[] { 1, 4 },
- new int[] { 1, 12 }, 1, 3));
+ acf1.addMap(cs1, s1,
+ new MapList(new int[]
+ { 1, 4 }, new int[] { 1, 12 }, 1, 3));
AlignedCodonFrame acf2 = new AlignedCodonFrame();
- acf2.addMap(cs2, s2, new MapList(new int[] { 1, 4 },
- new int[] { 1, 12 }, 1, 3));
+ acf2.addMap(cs2, s2,
+ new MapList(new int[]
+ { 1, 4 }, new int[] { 1, 12 }, 1, 3));
AlignedCodonFrame acf3 = new AlignedCodonFrame();
- acf3.addMap(cs2, cs2, new MapList(new int[] { 1, 12 }, new int[] { 1,
- 12 }, 1, 1));
+ acf3.addMap(cs2, cs2,
+ new MapList(new int[]
+ { 1, 12 }, new int[] { 1, 12 }, 1, 1));
List<AlignedCodonFrame> mappings1 = new ArrayList<>();
mappings1.add(acf1);
.getStructureSelectionManager(Desktop.instance);
ssm.resetAll();
- AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
- ">Seq1\nRSVQ\n", DataSourceType.PASTE);
- AlignFrame af2 = new FileLoader().LoadFileWaitTillLoaded(
- ">Seq2\nDGEL\n", DataSourceType.PASTE);
+ AlignFrame af1 = new FileLoader()
+ .LoadFileWaitTillLoaded(">Seq1\nRSVQ\n", DataSourceType.PASTE);
+ AlignFrame af2 = new FileLoader()
+ .LoadFileWaitTillLoaded(">Seq2\nDGEL\n", DataSourceType.PASTE);
SequenceI cs1 = new Sequence("cseq1", "CCCGGGTTTAAA");
SequenceI cs2 = new Sequence("cseq2", "CTTGAGTCTAGA");
SequenceI s1 = af1.getViewport().getAlignment().getSequenceAt(0);
SequenceI s2 = af2.getViewport().getAlignment().getSequenceAt(0);
// need to be distinct
AlignedCodonFrame acf1 = new AlignedCodonFrame();
- acf1.addMap(cs1, s1, new MapList(new int[] { 1, 4 },
- new int[] { 1, 12 }, 1, 3));
+ acf1.addMap(cs1, s1,
+ new MapList(new int[]
+ { 1, 4 }, new int[] { 1, 12 }, 1, 3));
AlignedCodonFrame acf2 = new AlignedCodonFrame();
- acf2.addMap(cs2, s2, new MapList(new int[] { 1, 4 },
- new int[] { 1, 12 }, 1, 3));
+ acf2.addMap(cs2, s2,
+ new MapList(new int[]
+ { 1, 4 }, new int[] { 1, 12 }, 1, 3));
AlignedCodonFrame acf3 = new AlignedCodonFrame();
- acf3.addMap(cs2, cs2, new MapList(new int[] { 1, 12 }, new int[] { 1,
- 12 }, 1, 1));
+ acf3.addMap(cs2, cs2,
+ new MapList(new int[]
+ { 1, 12 }, new int[] { 1, 12 }, 1, 1));
List<AlignedCodonFrame> mappings1 = new ArrayList<>();
mappings1.add(acf1);
* Test for JAL-1306 - conservation thread should run even when only Quality
* (and not Conservation) is enabled in Preferences
*/
- @Test(groups = { "Functional" }, timeOut=2000)
+ @Test(groups = { "Functional" }, timeOut = 2000)
public void testUpdateConservation_qualityOnly()
{
Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
ColourSchemeI cs = new PIDColourScheme();
AlignViewport viewport = af.getViewport();
viewport.setGlobalColourScheme(cs);
- assertFalse(viewport.getResidueShading()
- .conservationApplied());
+ assertFalse(viewport.getResidueShading().conservationApplied());
/*
* JAL-3201 groups have their own ColourSchemeI instances
av.setSelectionGroup(sg3);
assertTrue(sg3.isDefined()); // unchanged
}
+
/**
- * Verify that setting/clearing SHOW_OCCUPANCY preference adds or omits occupancy row from viewport
+ * Verify that setting/clearing SHOW_OCCUPANCY preference adds or omits
+ * occupancy row from viewport
*/
@Test(groups = { "Functional" })
public void testShowOrDontShowOccupancy()
{
// disable occupancy
- jalview.bin.Cache.setProperty("SHOW_OCCUPANCY", Boolean.FALSE.toString());
+ jalview.bin.Cache.setProperty("SHOW_OCCUPANCY",
+ Boolean.FALSE.toString());
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
"examples/uniref50.fa", DataSourceType.FILE);
AlignViewport av = af.getViewport();
- Assert.assertNull(av.getAlignmentGapAnnotation(), "Preference did not disable occupancy row.");
+ Assert.assertNull(av.getAlignmentGapAnnotation(),
+ "Preference did not disable occupancy row.");
int c = 0;
for (AlignmentAnnotation aa : av.getAlignment().findAnnotations(null,
null, "Occupancy"))
c++;
}
Assert.assertEquals(c, 0, "Expected zero occupancy rows.");
-
+
// enable occupancy
- jalview.bin.Cache.setProperty("SHOW_OCCUPANCY", Boolean.TRUE.toString());
- af = new FileLoader().LoadFileWaitTillLoaded(
- "examples/uniref50.fa", DataSourceType.FILE);
+ jalview.bin.Cache.setProperty("SHOW_OCCUPANCY",
+ Boolean.TRUE.toString());
+ af = new FileLoader().LoadFileWaitTillLoaded("examples/uniref50.fa",
+ DataSourceType.FILE);
av = af.getViewport();
- Assert.assertNotNull(av.getAlignmentGapAnnotation(), "Preference did not enable occupancy row.");
+ Assert.assertNotNull(av.getAlignmentGapAnnotation(),
+ "Preference did not enable occupancy row.");
c = 0;
for (AlignmentAnnotation aa : av.getAlignment().findAnnotations(null,
null, av.getAlignmentGapAnnotation().label))
/*
* hide first and third sequences
*/
- testee.hideSequence(new SequenceI[] { al.getSequenceAt(0),
- al.getSequenceAt(2) });
+ testee.hideSequence(
+ new SequenceI[]
+ { al.getSequenceAt(0), al.getSequenceAt(2) });
assertEquals(1, al.getHeight());
assertEquals(0, ranges.getStartSeq());
assertEquals(0, ranges.getEndSeq());
@BeforeMethod(alwaysRun = true)
public void setUp() throws InvocationTargetException, InterruptedException
{
- Jalview.main(new String[] { "-nonews", "-props",
- "test/jalview/testProps.jvprops" });
+ Jalview.main(
+ new String[]
+ { "-nonews", "-props", "test/jalview/testProps.jvprops" });
Cache.applicationProperties.setProperty("SHOW_IDENTITY",
Boolean.TRUE.toString());
af = new FileLoader().LoadFileWaitTillLoaded("examples/uniref50.fa",
DataSourceType.FILE);
-
+
/*
* ensure the panel has been repainted and so ViewportRanges set
*/
- SwingUtilities.invokeAndWait(new Runnable() {
- @Override
- public void run() {
- af.repaint();
- }});
+ SwingUtilities.invokeAndWait(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ af.repaint();
+ }
+ });
/*
* wait for Consensus thread to complete
scrollpos = 130;
af.getViewport().showAllHiddenColumns();
af.alignPanel.setScrollValues(scrollpos, 5);
- assertEquals(ranges.getEndRes(), af.getViewport()
- .getAlignment().getWidth() - 1);
+ assertEquals(ranges.getEndRes(),
+ af.getViewport().getAlignment().getWidth() - 1);
// now hide some columns, and scroll to position within <width>
// distance of the end of the alignment
// columns
af.getViewport().hideColumns(30, 50);
af.alignPanel.setScrollValues(scrollpos, 5);
- assertEquals(ranges.getEndRes(), af.getViewport()
- .getAlignment().getWidth() - 1 - 21); // 21 is the number of hidden
- // columns
+ assertEquals(ranges.getEndRes(),
+ af.getViewport().getAlignment().getWidth() - 1 - 21); // 21 is the
+ // number of
+ // hidden
+ // columns
}
/**
}
/**
- * Test the variant of calculateIdWidth that only recomputes the width if it is
- * not already saved in the viewport (initial value is -1)
+ * Test the variant of calculateIdWidth that only recomputes the width if it
+ * is not already saved in the viewport (initial value is -1)
*/
@Test(groups = "Functional")
public void testCalculateIdWidth_noArgs()
// Assumption ID_WIDTH_PADDING == 4
int expwidth = 4 + fmfor.stringWidth(aa.label);
d = af.alignPanel.calculateIdWidth(2000);
- assertEquals(d.width, expwidth); // 228 == ID_WIDTH_PADDING + pixel width of "THIS IS A VERY LONG LABEL INDEED"
+ assertEquals(d.width, expwidth); // 228 == ID_WIDTH_PADDING + pixel width of
+ // "THIS IS A VERY LONG LABEL INDEED"
assertEquals(d.height, 12);
/*
Cache.applicationProperties.setProperty(Preferences.SORT_ANNOTATIONS,
SequenceAnnotationOrder.NONE.name());
final String TRUE = Boolean.TRUE.toString();
- Cache.applicationProperties.setProperty(
- Preferences.SHOW_AUTOCALC_ABOVE, TRUE);
+ Cache.applicationProperties.setProperty(Preferences.SHOW_AUTOCALC_ABOVE,
+ TRUE);
Cache.applicationProperties.setProperty("SHOW_QUALITY", TRUE);
Cache.applicationProperties.setProperty("SHOW_CONSERVATION", TRUE);
Cache.applicationProperties.setProperty("SHOW_IDENTITY", TRUE);
* Add 4 annotations, 3 of them sequence-specific.
*
* <PRE>
- * ann1 - for sequence 0 - label 'IUPRED'
- * ann2 - not sequence related - label 'Beauty'
- * ann3 - for sequence 3 - label 'JMol'
- * ann4 - for sequence 2 - label 'IUPRED'
- * ann5 - for sequence 1 - label 'JMol'
+ * ann1 - for sequence 0 - label 'IUPRED' ann2 - not sequence related - label
+ * 'Beauty' ann3 - for sequence 3 - label 'JMol' ann4 - for sequence 2 - label
+ * 'IUPRED' ann5 - for sequence 1 - label 'JMol'
*/
private void addAnnotations()
{
assertTrue("Not enabled", cb1.isEnabled());
assertTrue("Not enabled", cb2.isEnabled());
assertTrue("Not enabled", cb3.isEnabled());
- assertEquals("Option not selected", cb2, cb2.getCheckboxGroup()
- .getSelectedCheckbox());
+ assertEquals("Option not selected", cb2,
+ cb2.getCheckboxGroup().getSelectedCheckbox());
// check state variables match checkbox selection
assertTrue(testee.isApplyToSelectedSequences());
assertTrue("Not enabled", cb1.isEnabled());
assertFalse("Enabled", cb2.isEnabled());
assertFalse("Enabled", cb3.isEnabled());
- assertEquals("Not selected", cb1, cb1.getCheckboxGroup()
- .getSelectedCheckbox());
+ assertEquals("Not selected", cb1,
+ cb1.getCheckboxGroup().getSelectedCheckbox());
// check state variables match checkbox selection
assertTrue(testee.isApplyToSelectedSequences());
assertTrue(testee.isApplyToUnselectedSequences());
assertEquals("Wrong text",
- MessageManager.getString("label.all_sequences"), cb1.getLabel());
+ MessageManager.getString("label.all_sequences"),
+ cb1.getLabel());
assertEquals("Wrong text",
MessageManager.getString("label.selected_sequences"),
cb2.getLabel());
assertTrue("Hide not enabled", cb2.isEnabled());
// Hide (button 2) selected; note this may change to none (null)
- assertEquals("Not selected", cb2, cb2.getCheckboxGroup()
- .getSelectedCheckbox());
+ assertEquals("Not selected", cb2,
+ cb2.getCheckboxGroup().getSelectedCheckbox());
assertTrue("Show is flagged", !testee.isShowSelected());
// selection group should make no difference to the result
// as all annotation types for the alignment are considered
- List<String> types = AnnotationChooser.getAnnotationTypes(
- parentPanel.getAlignment(), true);
+ List<String> types = AnnotationChooser
+ .getAnnotationTypes(parentPanel.getAlignment(), true);
assertEquals("Not two annotation types", 2, types.size());
assertTrue("IUPRED missing", types.contains("IUPRED"));
assertTrue("JMol missing", types.contains("JMol"));
- types = AnnotationChooser.getAnnotationTypes(
- parentPanel.getAlignment(), false);
+ types = AnnotationChooser.getAnnotationTypes(parentPanel.getAlignment(),
+ false);
assertEquals("Not six annotation types", 7, types.size());
assertTrue("IUPRED missing", types.contains("IUPRED"));
assertTrue("JMol missing", types.contains("JMol"));
final Checkbox hideCheckbox = (Checkbox) getComponent(testee, 1, 0, 1);
setSelected(hideCheckbox, true);
- final Checkbox allSequencesCheckbox = (Checkbox) getComponent(testee,
- 1, 1, 0);
+ final Checkbox allSequencesCheckbox = (Checkbox) getComponent(testee, 1,
+ 1, 0);
setSelected(allSequencesCheckbox, true);
AlignmentAnnotation[] anns = parentPanel.getAlignment()
final Checkbox hideCheckbox = (Checkbox) getComponent(testee, 1, 0, 1);
setSelected(hideCheckbox, true);
- final Checkbox allSequencesCheckbox = (Checkbox) getComponent(testee,
- 1, 1, 0);
+ final Checkbox allSequencesCheckbox = (Checkbox) getComponent(testee, 1,
+ 1, 0);
setSelected(allSequencesCheckbox, true);
AlignmentAnnotation[] anns = parentPanel.getAlignment()
final Checkbox showCheckbox = (Checkbox) getComponent(testee, 1, 0, 0);
final Checkbox hideCheckbox = (Checkbox) getComponent(testee, 1, 0, 1);
- final Checkbox allSequencesCheckbox = (Checkbox) getComponent(testee,
- 1, 1, 0);
+ final Checkbox allSequencesCheckbox = (Checkbox) getComponent(testee, 1,
+ 1, 0);
AlignmentAnnotation[] anns = parentPanel.getAlignment()
.getAlignmentAnnotation();
final Checkbox showCheckbox = (Checkbox) getComponent(testee, 1, 0, 0);
setSelected(showCheckbox, true);
- final Checkbox allSequencesCheckbox = (Checkbox) getComponent(testee,
- 1, 1, 0);
+ final Checkbox allSequencesCheckbox = (Checkbox) getComponent(testee, 1,
+ 1, 0);
setSelected(allSequencesCheckbox, true);
AlignmentAnnotation[] anns = parentPanel.getAlignment()
// TODO refactor to a test utility class
cb.setState(select);
// have to manually fire the action listener
- cb.getItemListeners()[0].itemStateChanged(new ItemEvent(cb,
- ItemEvent.ITEM_STATE_CHANGED, cb, select ? ItemEvent.SELECTED
- : ItemEvent.DESELECTED));
+ cb.getItemListeners()[0].itemStateChanged(
+ new ItemEvent(cb, ItemEvent.ITEM_STATE_CHANGED, cb,
+ select ? ItemEvent.SELECTED : ItemEvent.DESELECTED));
}
/**
final Checkbox hideCheckbox = (Checkbox) getComponent(testee, 1, 0, 1);
setSelected(hideCheckbox, true);
- final Checkbox allSequencesCheckbox = (Checkbox) getComponent(testee,
- 1, 1, 0);
+ final Checkbox allSequencesCheckbox = (Checkbox) getComponent(testee, 1,
+ 1, 0);
setSelected(allSequencesCheckbox, true);
setSelected(getTypeCheckbox("JMol"), true);
ann.description = null;
assertEquals(AnnotationLabels.getTooltip(ann),
"<html> Score: 2.34</html>");
-
+
/*
* sequenceref, simple description
*/
Cache.loadProperties("test/jalview/io/testProps.jvprops");
Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
Boolean.TRUE.toString());
- Cache.applicationProperties.setProperty(
- Preferences.SHOW_AUTOCALC_ABOVE, Boolean.TRUE.toString());
+ Cache.applicationProperties.setProperty(Preferences.SHOW_AUTOCALC_ABOVE,
+ Boolean.TRUE.toString());
af = new FileLoader().LoadFileWaitTillLoaded("examples/uniref50.fa",
DataSourceType.FILE);
testee = new AnnotationRowFilter(af.viewport, af.alignPanel)
null);
ann4.setSequenceRef(seq2);
al.addAnnotation(ann4);
- AlignmentAnnotation ann5 = new AlignmentAnnotation("Jnet", "Jnet", null);
+ AlignmentAnnotation ann5 = new AlignmentAnnotation("Jnet", "Jnet",
+ null);
ann5.setSequenceRef(seq2);
al.addAnnotation(ann5);
/*
* a second Jnet annotation for FER_BRANA
*/
- AlignmentAnnotation ann6 = new AlignmentAnnotation("Jnet", "Jnet", null);
+ AlignmentAnnotation ann6 = new AlignmentAnnotation("Jnet", "Jnet",
+ null);
ann6.setSequenceRef(seq2);
al.addAnnotation(ann6);
* drop-down items with 'Per-sequence only' not checked
*/
Vector<String> items = testee.getAnnotationItems(false);
- assertEquals(
- items.toString(),
+ assertEquals(items.toString(),
"[Conservation, Quality, Consensus, Occupancy, ann1Label, Significance, Significance_1, Jronn_FER_CAPAA, Jronn_FER_BRANA, Jnet_FER_BRANA, Jnet_FER_BRANA_2]");
assertEquals(testee.getAnnotationMenuLabel(ann1), "ann1Label");
assertEquals(testee.getAnnotationMenuLabel(ann2), "Significance");
PopupMenu popup = new PopupMenu(af.alignPanel, s1, null);
ButtonGroup bg = ColourMenuHelper.addMenuItems(menu, popup, al, false);
Enumeration<AbstractButton> bgElements = bg.getElements();
-
+
/*
* first entry is 'No Colour' option
*/
assertEquals(item.getText(), MessageManager.getString("label.none"));
AbstractButton bgItem = bgElements.nextElement();
assertSame(bgItem, item);
-
+
/*
* check that each registered colour scheme is in the menu,
* and in the button group;
{
assertTrue(enabled);
}
-
+
/*
* check i18n for display name
*/
name);
assertEquals(item.getText(), label);
}
-
+
/*
* check nothing left over
*/
SequenceI s1 = new Sequence("s1", "KFRQSILM");
AlignmentI al = new Alignment(new SequenceI[] { s1 });
JMenu menu = new JMenu();
-
+
ButtonGroup bg = ColourMenuHelper.addMenuItems(menu, null, al, true);
Enumeration<AbstractButton> bgElements = bg.getElements();
-
+
/*
* check that only 'simple' colour schemes are included
*/
AbstractButton bgItem = bgElements.nextElement();
assertSame(bgItem, item);
}
-
+
/*
* check nothing left over
*/
AlignmentI al = new Alignment(new SequenceI[] { s1 });
AlignFrame af = new AlignFrame(al, 500, 500);
JMenu menu = new JMenu();
-
+
ButtonGroup bg = ColourMenuHelper.addMenuItems(menu, af, al, false);
Enumeration<AbstractButton> bgElements = bg.getElements();
-
+
/*
* check that each registered colour scheme is in the menu,
* (skipping over No Colour which is the first menu item),
ColourSchemeI cs = colourSchemes.next();
assertEquals(item.getName(), cs.getSchemeName());
}
-
+
/*
* check menu also has User Defined Colour
*/
assertTrue(fc.isBelowThreshold());
assertEquals(fc.getThreshold(), 3f);
- assertEquals(fr.getFeatureFilter("type1").toStableString(), "Label Contains x");
+ assertEquals(fr.getFeatureFilter("type1").toStableString(),
+ "Label Contains x");
assertEquals(fr.getFeatureFilter("type2").toStableString(),
"(Score LE 2.4) AND (Score GT 1.1)");
assertEquals(fr.getFeatureFilter("type3").toStableString(),
// oo.setVisible(true);
// parent.setVisible(true);
EditNameDialog end = new EditNameDialog("Sequence Name",
- "Try and drag between the two text fields", "label 1", "Label 2");// );cont.getRootPane());
+ "Try and drag between the two text fields", "label 1",
+ "Label 2");// );cont.getRootPane());
assert (end != null);
finish = true;
}
Object[] selectionValues = null;
-
@Test(groups = { "Functional" })
public void showConfirmDialogFamilyTest()
{
tip = "0123456789012345678901234567890123456789012345678901234567890"; // 61
assertFalse(tip.equals(JvSwingUtils.wrapTooltip(false, tip)));
- assertFalse(("<html>" + tip + "</html>").equals(JvSwingUtils
- .wrapTooltip(true, tip)));
+ assertFalse(("<html>" + tip + "</html>")
+ .equals(JvSwingUtils.wrapTooltip(true, tip)));
}
/**
textArea = new JTextArea();
textArea.setEditable(false);
JScrollPane scrollPane = new JScrollPane(textArea);
- scrollPane
- .setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_ALWAYS);
+ scrollPane.setVerticalScrollBarPolicy(
+ JScrollPane.VERTICAL_SCROLLBAR_ALWAYS);
scrollPane.setPreferredSize(new Dimension(400, 75));
blankArea = new BlankArea(Color.YELLOW);
AlignmentViewport av = new AlignViewport(al);
AlignFrame af = new AlignFrame(al, 4, 1);
AlignmentPanel ap1 = af.alignPanel;
- AlignmentPanel[] panels = PaintRefresher.getAssociatedPanels(av
- .getSequenceSetId());
+ AlignmentPanel[] panels = PaintRefresher
+ .getAssociatedPanels(av.getSequenceSetId());
assertEquals(1, panels.length);
assertSame(ap1, panels[0]);
Console.initLogger();
String inMenuString = ("EMBL-EBI Search | http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$"
- + SEQUENCE_ID
- + "$"
- + "|"
- + "UNIPROT | http://www.uniprot.org/uniprot/$" + DB_ACCESSION + "$")
- + "|"
+ + SEQUENCE_ID + "$" + "|"
+ + "UNIPROT | http://www.uniprot.org/uniprot/$" + DB_ACCESSION
+ + "$") + "|"
+ ("INTERPRO | http://www.ebi.ac.uk/interpro/entry/$"
+ DB_ACCESSION + "$")
- + "|"
- +
+ + "|" +
// Gene3D entry tests for case (in)sensitivity
("Gene3D | http://gene3d.biochem.ucl.ac.uk/Gene3D/search?sterm=$"
+ DB_ACCESSION + "$&mode=protein");
seq0.addDBRef(new DBRefEntry("INTERPRO", "1", "IPR006058"));
seq1.addDBRef(new DBRefEntry(DBRefSource.UNIPROT, "1", "Q9ZTS2"));
seq1.addDBRef(new DBRefEntry("GENE3D", "1", "3.10.20.30"));
-
+
/*
* check the Link Menu for the first sequence
*/
JMenu linkMenu = PopupMenu.buildLinkMenu(seq0, noFeatures);
assertEquals(linkText, linkMenu.getText());
Component[] linkItems = linkMenu.getMenuComponents();
-
+
/*
* menu items are ordered: SEQUENCE_ID search first, then dbrefs in order
* of database name (and within that by order of dbref addition)
{
// get sequences from the alignment
List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
-
+
// add our own seqs to avoid problems with changes to existing sequences
// (gap at end of sequences varies depending on how tests are run!)
Sequence seqGap1 = new Sequence("GappySeq",
// get the Popup Menu for 7th sequence - no insertions
testee = new PopupMenu(parentPanel, seqs.get(7), null);
testee.hideInsertions_actionPerformed(null);
-
+
HiddenColumns hidden = parentPanel.av.getAlignment().getHiddenColumns();
Iterator<int[]> it = hidden.iterator();
assertFalse(it.hasNext());
/*
* long feature descriptions are truncated to 40 characters
*/
- sf1.setDescription(
- "this is a quite extraordinarily long description");
+ sf1.setDescription("this is a quite extraordinarily long description");
testee.remove(menu); // don't create the sub-menu twice
testee.addFeatureDetails(features, seq, 10);
menu = findMenu(testee, menuText);
{
try
{
- SwingUtilities.invokeAndWait(new Runnable()
- {
- @Override
- public void run()
+ SwingUtilities.invokeAndWait(new Runnable()
{
- int msgCount = msgs.length;
- assertEquals(1 + msgCount, layout.getRows());
- assertEquals(msgCount, statusPanel.getComponentCount());
- int i = 0;
- for (Component c : statusPanel.getComponents())
- {
- assertTrue(c instanceof JPanel);
- assertTrue(((JPanel) c).getComponent(0) instanceof JLabel);
- assertEquals(msgs[i++],
- ((JLabel) ((JPanel) c).getComponent(0)).getText());
- }
- }
- });
+ @Override
+ public void run()
+ {
+ int msgCount = msgs.length;
+ assertEquals(1 + msgCount, layout.getRows());
+ assertEquals(msgCount, statusPanel.getComponentCount());
+ int i = 0;
+ for (Component c : statusPanel.getComponents())
+ {
+ assertTrue(c instanceof JPanel);
+ assertTrue(((JPanel) c).getComponent(0) instanceof JLabel);
+ assertEquals(msgs[i++],
+ ((JLabel) ((JPanel) c).getComponent(0)).getText());
+ }
+ }
+ });
} catch (Exception e)
{
throw new AssertionError(
alignFrame.alignPanel.updateLayout();
assertEquals(ranges.getStartRes(), 0);
assertEquals(ranges.getEndRes(), 22);
-
+
int cw = viewport.getCharWidth();
int xPos = 9 * cw + 2;
MouseEvent mouse = new MouseEvent(scalePanel, 0, 1, 0, xPos, 0, 1,
import static org.testng.Assert.assertNull;
import static org.testng.Assert.assertTrue;
-
import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SearchResults;
int canvasWidth = 400;
int canvasHeight = 300;
int residueColumns = (canvasWidth - 2 * labelWidth) / charWidth;
- int wrappedWidth = testee.calculateWrappedGeometry(canvasWidth, canvasHeight);
+ int wrappedWidth = testee.calculateWrappedGeometry(canvasWidth,
+ canvasHeight);
assertEquals(wrappedWidth, residueColumns);
assertEquals(PA.getValue(testee, "labelWidthWest"), labelWidth);
assertEquals(PA.getValue(testee, "labelWidthEast"), labelWidth);
assertEquals(PA.getValue(testee, "wrappedSpaceAboveAlignment"),
2 * charHeight);
- int repeatingHeight = (int) PA.getValue(testee, "wrappedRepeatHeightPx");
+ int repeatingHeight = (int) PA.getValue(testee,
+ "wrappedRepeatHeightPx");
assertEquals(repeatingHeight, charHeight * (2 + al.getHeight()));
assertEquals(PA.getValue(testee, "wrappedVisibleWidths"), 1);
AlignmentI al = av.getAlignment();
assertEquals(al.getWidth(), 157);
assertEquals(al.getHeight(), 15);
-
+
av.setWrapAlignment(true);
av.getRanges().setStartEndSeq(0, 14);
av.setFont(new Font("SansSerif", Font.PLAIN, 14), true);
int charWidth = av.getCharWidth();
assertEquals(charHeight, 17);
assertEquals(charWidth, 12);
-
+
SeqCanvas testee = af.alignPanel.getSeqPanel().seqCanvas;
-
+
/*
* first with scales above, left, right
*/
int canvasWidth = 400;
int canvasHeight = 300;
int residueColumns = (canvasWidth - 2 * labelWidth) / charWidth;
- int wrappedWidth = testee.calculateWrappedGeometry(canvasWidth, canvasHeight);
+ int wrappedWidth = testee.calculateWrappedGeometry(canvasWidth,
+ canvasHeight);
assertEquals(wrappedWidth, residueColumns);
assertEquals(PA.getValue(testee, "labelWidthWest"), labelWidth);
assertEquals(PA.getValue(testee, "labelWidthEast"), labelWidth);
assertEquals(PA.getValue(testee, "wrappedSpaceAboveAlignment"),
2 * charHeight);
- int repeatingHeight = (int) PA.getValue(testee, "wrappedRepeatHeightPx");
+ int repeatingHeight = (int) PA.getValue(testee,
+ "wrappedRepeatHeightPx");
assertEquals(repeatingHeight, charHeight * (2 + al.getHeight())
+ SeqCanvas.SEQS_ANNOTATION_GAP + annotationHeight);
assertEquals(PA.getValue(testee, "wrappedVisibleWidths"), 1);
-
+
/*
* repeat height is 17 * (2 + 15) = 289 + 3 + annotationHeight = 510
* make canvas height 2 of these plus 3 charHeights
+ 2 * (annotationHeight + SeqCanvas.SEQS_ANNOTATION_GAP);
testee.calculateWrappedGeometry(canvasWidth, canvasHeight);
assertEquals(PA.getValue(testee, "wrappedVisibleWidths"), 3);
-
+
/*
* reduce canvas height by 1 pixel - should not be enough height
* to draw 3 widths
canvasHeight -= 1;
testee.calculateWrappedGeometry(canvasWidth, canvasHeight);
assertEquals(PA.getValue(testee, "wrappedVisibleWidths"), 2);
-
+
/*
* turn off scale above - can now fit in 2 and a bit widths
*/
av.setScaleAboveWrapped(false);
testee.calculateWrappedGeometry(canvasWidth, canvasHeight);
assertEquals(PA.getValue(testee, "wrappedVisibleWidths"), 3);
-
+
/*
* reduce height to enough for 2 widths and not quite a third
* i.e. two repeating heights + spacer + sequence - 1 pixel
Boolean.TRUE.toString());
af = new FileLoader().LoadFileWaitTillLoaded("examples/uniref50.fa",
DataSourceType.FILE);
-
+
/*
* wait for Consensus thread to complete
*/
}
} while (af.getViewport().getCalcManager().isWorking());
}
+
@Test(groups = "Functional")
public void testClear_HighlightAndSelection()
{
JvOptionPane.setInteractiveMode(false);
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
+
@Test(groups = "Functional")
public void testSetStatusReturnsNearestResiduePosition()
{
AlignmentI visAl = alignFrame.getViewport().getAlignment();
// Test either side of gap
- assertEquals(
- alignFrame.alignPanel.getSeqPanel().setStatusMessage(
- visAl.getSequenceAt(1), 1, 1), 2);
+ assertEquals(alignFrame.alignPanel.getSeqPanel()
+ .setStatusMessage(visAl.getSequenceAt(1), 1, 1), 2);
assertEquals(((JLabel) PA.getValue(alignFrame, "statusBar")).getText(),
"Sequence 2 ID: Seq2 Residue: ALA (2)");
- assertEquals(
- alignFrame.alignPanel.getSeqPanel().setStatusMessage(
- visAl.getSequenceAt(1), 4, 1), 3);
+ assertEquals(alignFrame.alignPanel.getSeqPanel()
+ .setStatusMessage(visAl.getSequenceAt(1), 4, 1), 3);
assertEquals(((JLabel) PA.getValue(alignFrame, "statusBar")).getText(),
"Sequence 2 ID: Seq2 Residue: GLU (3)");
// no status message at a gap, returns next residue position to the right
- assertEquals(
- alignFrame.alignPanel.getSeqPanel().setStatusMessage(
- visAl.getSequenceAt(1), 2, 1), 3);
+ assertEquals(alignFrame.alignPanel.getSeqPanel()
+ .setStatusMessage(visAl.getSequenceAt(1), 2, 1), 3);
assertEquals(((JLabel) PA.getValue(alignFrame, "statusBar")).getText(),
"Sequence 2 ID: Seq2");
- assertEquals(
- alignFrame.alignPanel.getSeqPanel().setStatusMessage(
- visAl.getSequenceAt(1), 3, 1), 3);
+ assertEquals(alignFrame.alignPanel.getSeqPanel()
+ .setStatusMessage(visAl.getSequenceAt(1), 3, 1), 3);
assertEquals(((JLabel) PA.getValue(alignFrame, "statusBar")).getText(),
"Sequence 2 ID: Seq2");
}
al.getHeight());
AlignmentI visAl = alignFrame.getViewport().getAlignment();
- assertEquals(
- alignFrame.alignPanel.getSeqPanel().setStatusMessage(
- visAl.getSequenceAt(1), 1, 1), 2);
+ assertEquals(alignFrame.alignPanel.getSeqPanel()
+ .setStatusMessage(visAl.getSequenceAt(1), 1, 1), 2);
assertEquals(((JLabel) PA.getValue(alignFrame, "statusBar")).getText(),
"Sequence 2 ID: Seq2 Residue: B (2)");
}
assertNull(SeqPanel.getEditStatusMessage(edit));
SequenceI[] seqs = new SequenceI[] { new Sequence("a", "b") };
-
+
// 1 gap
edit.addEdit(edit.new Edit(Action.INSERT_GAP, seqs, 1, 1, '-'));
String expected = MessageManager.formatMessage("label.insert_gap", "1");
{
EditCommand edit = new EditCommand(); // empty
SequenceI[] seqs = new SequenceI[] { new Sequence("a", "b") };
-
+
// 1 gap inserted, balanced by 1 delete
Edit e1 = edit.new Edit(Action.INSERT_GAP, seqs, 1, 1, '-');
edit.addEdit(e1);
edit.addEdit(e2);
String expected = MessageManager.formatMessage("label.insert_gap", "1");
assertEquals(SeqPanel.getEditStatusMessage(edit), expected);
-
+
// 2 more gaps makes +3
Edit e3 = edit.new Edit(Action.INSERT_GAP, seqs, 1, 2, '-');
edit.addEdit(e3);
edit.addEdit(e4);
expected = MessageManager.formatMessage("label.insert_gaps", "3");
assertEquals(SeqPanel.getEditStatusMessage(edit), expected);
-
+
// 2 deletes makes + 1
Edit e5 = edit.new Edit(Action.DELETE_GAP, seqs, 1, 2, '-');
edit.addEdit(e5);
edit.addEdit(e6);
expected = MessageManager.formatMessage("label.insert_gap", "1");
assertEquals(SeqPanel.getEditStatusMessage(edit), expected);
-
+
// 1 more delete makes 0 - no text
Edit e7 = edit.new Edit(Action.DELETE_GAP, seqs, 1, 1, '-');
edit.addEdit(e7);
edit.addEdit(e8);
expected = MessageManager.formatMessage("label.insert_gaps", "2");
assertNull(SeqPanel.getEditStatusMessage(edit));
-
+
// 1 more delete makes 1 delete
Edit e9 = edit.new Edit(Action.DELETE_GAP, seqs, 1, 1, '-');
edit.addEdit(e9);
edit.addEdit(e10);
expected = MessageManager.formatMessage("label.delete_gap", "1");
assertEquals(SeqPanel.getEditStatusMessage(edit), expected);
-
+
// 2 more deletes makes 3 deletes
Edit e11 = edit.new Edit(Action.DELETE_GAP, seqs, 1, 2, '-');
edit.addEdit(e11);
/*
* mouse at top left of unwrapped panel
*/
- MouseEvent evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y,
- 0, 0, 0, false, 0);
+ MouseEvent evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0,
+ x, y, 0, 0, 0, false, 0);
MousePos pos = testee.findMousePosition(evt);
assertEquals(pos.column, 0);
assertEquals(pos.seqIndex, 0);
final int charHeight = av.getCharHeight();
final int charWidth = av.getCharWidth();
final int alignmentHeight = av.getAlignment().getHeight();
-
+
// sanity checks:
assertTrue(charHeight > 0);
assertTrue(charWidth > 0);
assertTrue(alignFrame.alignPanel.getSeqPanel().getWidth() > 0);
-
+
SeqPanel testee = alignFrame.alignPanel.getSeqPanel();
int x = 0;
int y = 0;
-
+
/*
* mouse at top left of wrapped panel; there is a gap of charHeight
* above the alignment
*/
- MouseEvent evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y,
- 0, 0, 0, false, 0);
+ MouseEvent evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0,
+ x, y, 0, 0, 0, false, 0);
MousePos pos = testee.findMousePosition(evt);
assertEquals(pos.column, 0);
assertEquals(pos.seqIndex, -1); // above sequences
* cursor at bottom of gap above
*/
y = charHeight - 1;
- evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0,
- false, 0);
+ evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
+ 0, false, 0);
pos = testee.findMousePosition(evt);
assertEquals(pos.seqIndex, -1);
assertEquals(pos.annotationIndex, -1);
* cursor over top of first sequence
*/
y = charHeight;
- evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0,
- false, 0);
+ evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
+ 0, false, 0);
pos = testee.findMousePosition(evt);
assertEquals(pos.seqIndex, 0);
assertEquals(pos.annotationIndex, -1);
* cursor at bottom of first sequence
*/
y = 2 * charHeight - 1;
- evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0,
- false, 0);
+ evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
+ 0, false, 0);
pos = testee.findMousePosition(evt);
assertEquals(pos.seqIndex, 0);
assertEquals(pos.annotationIndex, -1);
* cursor at top of second sequence
*/
y = 2 * charHeight;
- evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0,
- false, 0);
+ evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
+ 0, false, 0);
pos = testee.findMousePosition(evt);
assertEquals(pos.seqIndex, 1);
assertEquals(pos.annotationIndex, -1);
* cursor at bottom of second sequence
*/
y = 3 * charHeight - 1;
- evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0,
- false, 0);
+ evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
+ 0, false, 0);
pos = testee.findMousePosition(evt);
assertEquals(pos.seqIndex, 1);
assertEquals(pos.annotationIndex, -1);
* cursor at bottom of last sequence
*/
y = charHeight * (1 + alignmentHeight) - 1;
- evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0,
- false, 0);
+ evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
+ 0, false, 0);
pos = testee.findMousePosition(evt);
assertEquals(pos.seqIndex, alignmentHeight - 1);
assertEquals(pos.annotationIndex, -1);
* method reports index of nearest sequence above
*/
y += 1;
- evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0,
- false, 0);
+ evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
+ 0, false, 0);
pos = testee.findMousePosition(evt);
assertEquals(pos.seqIndex, alignmentHeight - 1);
assertEquals(pos.annotationIndex, -1);
* cursor still in the gap above annotations, now at the bottom of it
*/
y += SeqCanvas.SEQS_ANNOTATION_GAP - 1; // 3-1 = 2
- evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0,
- false, 0);
+ evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
+ 0, false, 0);
pos = testee.findMousePosition(evt);
assertEquals(pos.seqIndex, alignmentHeight - 1);
assertEquals(pos.annotationIndex, -1);
* cursor at the top of the n'th annotation
*/
y += 1;
- evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0,
- false, 0);
+ evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0,
+ 0, 0, false, 0);
pos = testee.findMousePosition(evt);
assertEquals(pos.seqIndex, alignmentHeight - 1);
assertEquals(pos.annotationIndex, n); // over n'th annotation
* cursor at the bottom of the n'th annotation
*/
y += annotationRows[n].height - 1;
- evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0,
- false, 0);
+ evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0,
+ 0, 0, false, 0);
pos = testee.findMousePosition(evt);
assertEquals(pos.seqIndex, alignmentHeight - 1);
assertEquals(pos.annotationIndex, n);
* cursor in gap between wrapped widths
*/
y += 1;
- evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0,
- false, 0);
+ evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
+ 0, false, 0);
pos = testee.findMousePosition(evt);
assertEquals(pos.seqIndex, -1);
assertEquals(pos.annotationIndex, -1);
* cursor at bottom of gap between wrapped widths
*/
y += charHeight - 1;
- evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0,
- false, 0);
+ evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
+ 0, false, 0);
pos = testee.findMousePosition(evt);
assertEquals(pos.seqIndex, -1);
assertEquals(pos.annotationIndex, -1);
* cursor at top of first sequence, second wrapped width
*/
y += 1;
- evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0,
- false, 0);
+ evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
+ 0, false, 0);
pos = testee.findMousePosition(evt);
assertEquals(pos.seqIndex, 0);
assertEquals(pos.annotationIndex, -1);
final int charHeight = av.getCharHeight();
final int charWidth = av.getCharWidth();
final int alignmentHeight = av.getAlignment().getHeight();
-
+
// sanity checks:
assertTrue(charHeight > 0);
assertTrue(charWidth > 0);
assertTrue(alignFrame.alignPanel.getSeqPanel().getWidth() > 0);
-
+
SeqPanel testee = alignFrame.alignPanel.getSeqPanel();
int x = 0;
int y = 0;
-
+
/*
* mouse at top left of wrapped panel; there is a gap of charHeight
* above the alignment
*/
- MouseEvent evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y,
- 0, 0, 0, false, 0);
+ MouseEvent evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0,
+ x, y, 0, 0, 0, false, 0);
MousePos pos = testee.findMousePosition(evt);
assertEquals(pos.column, 0);
assertEquals(pos.seqIndex, -1); // above sequences
assertEquals(pos.annotationIndex, -1);
-
+
/*
* cursor at bottom of gap above
* two charHeights including scale panel
*/
y = 2 * charHeight - 1;
- evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0,
- false, 0);
+ evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
+ 0, false, 0);
pos = testee.findMousePosition(evt);
assertEquals(pos.seqIndex, -1);
assertEquals(pos.annotationIndex, -1);
-
+
/*
* cursor over top of first sequence
*/
y += 1;
- evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0,
- false, 0);
+ evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
+ 0, false, 0);
pos = testee.findMousePosition(evt);
assertEquals(pos.seqIndex, 0);
assertEquals(pos.annotationIndex, -1);
-
+
/*
* cursor at bottom of first sequence
*/
y += charHeight - 1;
- evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0,
- false, 0);
+ evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
+ 0, false, 0);
pos = testee.findMousePosition(evt);
assertEquals(pos.seqIndex, 0);
assertEquals(pos.annotationIndex, -1);
-
+
/*
* cursor at top of second sequence
*/
y += 1;
- evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0,
- false, 0);
+ evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
+ 0, false, 0);
pos = testee.findMousePosition(evt);
assertEquals(pos.seqIndex, 1);
assertEquals(pos.annotationIndex, -1);
-
+
/*
* cursor at bottom of second sequence
*/
y += charHeight - 1;
- evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0,
- false, 0);
+ evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
+ 0, false, 0);
pos = testee.findMousePosition(evt);
assertEquals(pos.seqIndex, 1);
assertEquals(pos.annotationIndex, -1);
-
+
/*
* cursor at bottom of last sequence
* (scale + gap + sequences)
*/
y = charHeight * (2 + alignmentHeight) - 1;
- evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0,
- false, 0);
+ evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
+ 0, false, 0);
pos = testee.findMousePosition(evt);
assertEquals(pos.seqIndex, alignmentHeight - 1);
assertEquals(pos.annotationIndex, -1);
-
+
/*
* cursor below sequences, in 3-pixel gap above annotations
*/
y += 1;
- evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0,
- false, 0);
+ evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
+ 0, false, 0);
pos = testee.findMousePosition(evt);
assertEquals(pos.seqIndex, alignmentHeight - 1);
assertEquals(pos.annotationIndex, -1);
-
+
/*
* cursor still in the gap above annotations, now at the bottom of it
* method reports index of nearest sequence above
*/
y += SeqCanvas.SEQS_ANNOTATION_GAP - 1; // 3-1 = 2
- evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0,
- false, 0);
+ evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
+ 0, false, 0);
pos = testee.findMousePosition(evt);
assertEquals(pos.seqIndex, alignmentHeight - 1);
assertEquals(pos.annotationIndex, -1);
-
- AlignmentAnnotation[] annotationRows = av.getAlignment().getAlignmentAnnotation();
+
+ AlignmentAnnotation[] annotationRows = av.getAlignment()
+ .getAlignmentAnnotation();
for (int n = 0; n < annotationRows.length; n++)
{
/*
* cursor at the top of the n'th annotation
*/
y += 1;
- evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0,
- false, 0);
+ evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0,
+ 0, 0, false, 0);
pos = testee.findMousePosition(evt);
assertEquals(pos.seqIndex, alignmentHeight - 1);
assertEquals(pos.annotationIndex, n); // over n'th annotation
* cursor at the bottom of the n'th annotation
*/
y += annotationRows[n].height - 1;
- evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0,
- false, 0);
+ evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0,
+ 0, 0, false, 0);
pos = testee.findMousePosition(evt);
SeqCanvas sc = testee.seqCanvas;
assertEquals(pos.seqIndex, alignmentHeight - 1,
sc.wrappedSpaceAboveAlignment));
assertEquals(pos.annotationIndex, n);
}
-
+
/*
* cursor in gap between wrapped widths
*/
y += 1;
- evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0,
- false, 0);
+ evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
+ 0, false, 0);
pos = testee.findMousePosition(evt);
assertEquals(pos.seqIndex, -1);
assertEquals(pos.annotationIndex, -1);
-
+
/*
* cursor at bottom of gap between wrapped widths
*/
y += charHeight - 1;
- evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0,
- false, 0);
+ evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
+ 0, false, 0);
pos = testee.findMousePosition(evt);
assertEquals(pos.seqIndex, -1);
assertEquals(pos.annotationIndex, -1);
-
+
/*
* cursor at top of scale, second wrapped width
*/
y += 1;
- evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0,
- false, 0);
+ evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
+ 0, false, 0);
pos = testee.findMousePosition(evt);
assertEquals(pos.seqIndex, -1);
assertEquals(pos.annotationIndex, -1);
* cursor at bottom of scale, second wrapped width
*/
y += charHeight - 1;
- evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0,
- false, 0);
+ evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
+ 0, false, 0);
pos = testee.findMousePosition(evt);
assertEquals(pos.seqIndex, -1);
assertEquals(pos.annotationIndex, -1);
* cursor at top of first sequence, second wrapped width
*/
y += 1;
- evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0,
- false, 0);
+ evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
+ 0, false, 0);
pos = testee.findMousePosition(evt);
assertEquals(pos.seqIndex, 0);
assertEquals(pos.annotationIndex, -1);
final int charHeight = av.getCharHeight();
final int charWidth = av.getCharWidth();
final int alignmentHeight = av.getAlignment().getHeight();
-
+
// sanity checks:
assertTrue(charHeight > 0);
assertTrue(charWidth > 0);
assertTrue(alignFrame.alignPanel.getSeqPanel().getWidth() > 0);
-
+
SeqPanel testee = alignFrame.alignPanel.getSeqPanel();
int x = 0;
int y = 0;
-
+
/*
* mouse at top left of wrapped panel; there is a gap of charHeight
* above the alignment
*/
- MouseEvent evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y,
- 0, 0, 0, false, 0);
+ MouseEvent evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0,
+ x, y, 0, 0, 0, false, 0);
MousePos pos = testee.findMousePosition(evt);
assertEquals(pos.column, 0);
assertEquals(pos.seqIndex, -1); // above sequences
assertEquals(pos.annotationIndex, -1);
-
+
/*
* cursor over top of first sequence
*/
y = charHeight;
- evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0,
- false, 0);
+ evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
+ 0, false, 0);
pos = testee.findMousePosition(evt);
assertEquals(pos.seqIndex, 0);
assertEquals(pos.annotationIndex, -1);
* cursor at bottom of last sequence
*/
y = charHeight * (1 + alignmentHeight) - 1;
- evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0,
- false, 0);
+ evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
+ 0, false, 0);
pos = testee.findMousePosition(evt);
assertEquals(pos.seqIndex, alignmentHeight - 1);
assertEquals(pos.annotationIndex, -1);
-
+
/*
* cursor below sequences, at top of charHeight gap between widths
*/
y += 1;
- evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0,
- false, 0);
+ evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
+ 0, false, 0);
pos = testee.findMousePosition(evt);
assertEquals(pos.seqIndex, -1);
assertEquals(pos.annotationIndex, -1);
-
+
/*
* cursor below sequences, at top of charHeight gap between widths
*/
y += charHeight - 1;
- evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0,
- false, 0);
+ evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
+ 0, false, 0);
pos = testee.findMousePosition(evt);
assertEquals(pos.seqIndex, -1);
assertEquals(pos.annotationIndex, -1);
-
+
/*
* cursor at the top of the first sequence, second width
*/
y += 1;
- evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0,
- false, 0);
+ evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
+ 0, false, 0);
pos = testee.findMousePosition(evt);
assertEquals(pos.seqIndex, 0);
assertEquals(pos.annotationIndex, -1);
/*
* mouse at top left of unwrapped panel
*/
- MouseEvent evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0,
- 0, 0, 0, false, 0);
+ MouseEvent evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0,
+ x, 0, 0, 0, 0, false, 0);
assertEquals(testee.findColumn(evt), 0);
-
+
/*
* not quite one charWidth across
*/
- x = charWidth-1;
- evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0,
- 0, 0, 0, false, 0);
+ x = charWidth - 1;
+ evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0, 0, 0,
+ 0, false, 0);
assertEquals(testee.findColumn(evt), 0);
/*
* one charWidth across
*/
x = charWidth;
- evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0, 0, 0, 0,
- false, 0);
+ evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0, 0, 0,
+ 0, false, 0);
assertEquals(testee.findColumn(evt), 1);
/*
* two charWidths across
*/
x = 2 * charWidth;
- evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0, 0, 0, 0,
- false, 0);
+ evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0, 0, 0,
+ 0, false, 0);
assertEquals(testee.findColumn(evt), 2);
/*
* limited to last column of seqcanvas
*/
x = 20000;
- evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0, 0, 0, 0,
- false, 0);
+ evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0, 0, 0,
+ 0, false, 0);
SeqCanvas seqCanvas = alignFrame.alignPanel.getSeqPanel().seqCanvas;
int w = seqCanvas.getWidth();
// limited to number of whole columns, base 0,
alignFrame.getViewport().hideColumns(4, 9);
x = 5 * charWidth + 2;
// x is in 6th visible column, absolute column 12, or 11 base 0
- evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0, 0, 0, 0,
- false, 0);
+ evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0, 0, 0,
+ 0, false, 0);
assertEquals(testee.findColumn(evt), 11);
}
final int charWidth = av.getCharWidth();
assertTrue(charWidth > 0); // sanity check
assertEquals(av.getRanges().getStartRes(), 0);
-
+
/*
* mouse at top left of wrapped panel, no West (left) scale
*/
- MouseEvent evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0,
- 0, 0, 0, false, 0);
+ MouseEvent evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0,
+ x, 0, 0, 0, 0, false, 0);
assertEquals(testee.findColumn(evt), 0);
-
+
/*
* not quite one charWidth across
*/
- x = charWidth-1;
- evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0,
- 0, 0, 0, false, 0);
+ x = charWidth - 1;
+ evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0, 0, 0,
+ 0, false, 0);
assertEquals(testee.findColumn(evt), 0);
-
+
/*
* one charWidth across
*/
x = charWidth;
- evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0, 0, 0, 0,
- false, 0);
+ evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0, 0, 0,
+ 0, false, 0);
assertEquals(testee.findColumn(evt), 1);
/*
int labelWidth = (int) PA.getValue(seqCanvas, "labelWidthWest");
assertTrue(labelWidth > 0);
x = labelWidth - 1;
- evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0, 0, 0, 0,
- false, 0);
+ evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0, 0, 0,
+ 0, false, 0);
assertEquals(testee.findColumn(evt), -1);
x = labelWidth;
- evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0, 0, 0, 0,
- false, 0);
+ evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0, 0, 0,
+ 0, false, 0);
assertEquals(testee.findColumn(evt), 0);
/*
int residuesWide = av.getRanges().getViewportWidth();
assertTrue(residuesWide > 0);
x = labelWidth + charWidth * residuesWide - 1;
- evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0, 0, 0, 0,
- false, 0);
+ evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0, 0, 0,
+ 0, false, 0);
assertEquals(testee.findColumn(evt), residuesWide - 1);
/*
assertTrue(residuesWide2 > 0);
assertTrue(residuesWide2 < residuesWide); // available width reduced
x += 1; // just over left edge of scale right
- evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0, 0, 0, 0,
- false, 0);
+ evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, 0, 0, 0,
+ 0, false, 0);
assertEquals(testee.findColumn(evt), -1);
-
+
// todo add startRes offset, hidden columns
}
+
@BeforeClass(alwaysRun = true)
public static void setUpBeforeClass() throws Exception
{
e.printStackTrace();
}
}
+
@Test(groups = "Functional")
public void testFindMousePosition_wrapped_scales_longSequence()
{
Cache.applicationProperties.setProperty("FONT_STYLE", "0");
// sequence of 50 bases, doubled 10 times, = 51200 bases
String dna = "ATGGCCATTGGGCCCAAATTTCCCAAAGGGTTTCCCTGAGGTCAGTCAGA";
- for (int i = 0 ; i < 10 ; i++)
+ for (int i = 0; i < 10; i++)
{
dna += dna;
}
assertEquals(dna.length(), 51200);
- AlignFrame alignFrame = new FileLoader()
- .LoadFileWaitTillLoaded(dna, DataSourceType.PASTE);
+ AlignFrame alignFrame = new FileLoader().LoadFileWaitTillLoaded(dna,
+ DataSourceType.PASTE);
SeqPanel testee = alignFrame.alignPanel.getSeqPanel();
AlignViewport av = alignFrame.getViewport();
av.setScaleAboveWrapped(true);
} catch (InterruptedException e)
{
}
-
+
final int charHeight = av.getCharHeight();
final int charWidth = av.getCharWidth();
assertEquals(charHeight, 17);
assertEquals(charWidth, 12);
-
+
FontMetrics fm = testee.getFontMetrics(av.getFont());
int labelWidth = fm.stringWidth("00000") + charWidth;
assertEquals(labelWidth, 57); // 5 x 9 + charWidth
int x = 0;
int y = 0;
-
+
/*
* mouse at top left of wrapped panel; there is a gap of 2 * charHeight
* above the alignment
*/
- MouseEvent evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y,
- 0, 0, 0, false, 0);
+ MouseEvent evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0,
+ x, y, 0, 0, 0, false, 0);
MousePos pos = testee.findMousePosition(evt);
assertEquals(pos.column, -1); // over scale left, not an alignment column
assertEquals(pos.seqIndex, -1); // above sequences
*/
y += charHeight;
x = labelWidth;
- evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0,
- false, 0);
+ evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
+ 0, false, 0);
pos = testee.findMousePosition(evt);
assertEquals(pos.seqIndex, -1);
assertEquals(pos.column, 0);
assertEquals(pos.annotationIndex, -1);
-
+
/*
* cursor over scale left of first sequence
*/
y += charHeight;
x = 0;
- evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0,
- false, 0);
+ evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
+ 0, false, 0);
pos = testee.findMousePosition(evt);
assertEquals(pos.seqIndex, 0);
assertEquals(pos.column, -1);
assertEquals(pos.annotationIndex, -1);
-
+
/*
* cursor over start of first sequence
*/
x = labelWidth;
- evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0,
- false, 0);
+ evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
+ 0, false, 0);
pos = testee.findMousePosition(evt);
assertEquals(pos.seqIndex, 0);
assertEquals(pos.column, 0);
assertEquals(pos.annotationIndex, -1);
-
+
/*
* move one character right, to bottom pixel of same row
*/
x += charWidth;
y += charHeight - 1;
- evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0,
- false, 0);
+ evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
+ 0, false, 0);
pos = testee.findMousePosition(evt);
assertEquals(pos.seqIndex, 0);
assertEquals(pos.column, 1);
-
+
/*
* move down one pixel - now in the no man's land between rows
*/
y += 1;
- evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0,
- false, 0);
+ evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
+ 0, false, 0);
pos = testee.findMousePosition(evt);
assertEquals(pos.seqIndex, -1);
assertEquals(pos.column, 1);
-
+
/*
* move down two char heights less one pixel - still in the no man's land
* (scale above + spacer line)
*/
y += (2 * charHeight - 1);
- evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0,
- false, 0);
+ evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
+ 0, false, 0);
pos = testee.findMousePosition(evt);
assertEquals(pos.seqIndex, -1);
assertEquals(pos.column, 1);
-
+
/*
* move down one more pixel - now on the next row of the sequence
*/
y += 1;
- evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0,
- false, 0);
+ evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
+ 0, false, 0);
pos = testee.findMousePosition(evt);
assertEquals(pos.seqIndex, 0);
assertEquals(pos.column, 1 + av.getWrappedWidth());
-
+
/*
* scroll to near the end of the sequence
*/
SearchResultsI sr = new SearchResults();
int scrollTo = dna.length() - 1000;
- sr.addResult(av.getAlignment().getSequenceAt(0), scrollTo, scrollTo);
+ sr.addResult(av.getAlignment().getSequenceAt(0), scrollTo, scrollTo);
alignFrame.alignPanel.scrollToPosition(sr);
-
+
/*
* place the mouse on the first column of the 6th sequence, and
* verify that (computed) findMousePosition matches (actual) ViewportRanges
*/
x = labelWidth;
y = 17 * charHeight; // 17 = 6 times two header rows and 5 sequence rows
- evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0, 0,
- false, 0);
+ evt = new MouseEvent(testee, MouseEvent.MOUSE_MOVED, 0L, 0, x, y, 0, 0,
+ 0, false, 0);
pos = testee.findMousePosition(evt);
assertEquals(pos.seqIndex, 0);
int expected = av.getRanges().getStartRes() + 5 * av.getWrappedWidth();
public class SequenceRendererTest
{
AlignmentI al;
+
AlignViewport av;
SequenceI seq1;
{
Jalview.main(
new String[]
- { "-nonews", "-props", "test/jalview/testProps.jvprops" });
+ { "-nonews", "-props", "test/jalview/testProps.jvprops" });
}
@BeforeMethod(alwaysRun = true)
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
- Sequence seq,upSeq,upSeq_nocanonical;
+ Sequence seq, upSeq, upSeq_nocanonical;
@BeforeMethod(alwaysRun = true)
public void setUp() throws Exception
pdbIds.add(dbRef);
seq.setPDBId(pdbIds);
-
+
// Uniprot sequence for 3D-Beacons mocks
- upSeq = new Sequence("P38398",
+ upSeq = new Sequence("P38398",
"MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRS\n"
- + "LQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNRAKRLLQSEPEN\n"
- + "PSLQETSLSVQLSNLGTVRTLRTKQRIQPQKTSVYIELGSDSSEDTVNKATYCSVGDQELLQITPQGTRDEI\n"
- + "SLDSAKKAACEFSETDVTNTEHHQPSNNDLNTTEKRAAERHPEKYQGSSVSNLHVEPCGTNTHASSLQHENS\n"
- + "SLLLTKDRMNVEKAEFCNKSKQPGLARSQHNRWAGSKETCNDRRTPSTEKKVDLNADPLCERKEWNKQKLPC\n"
- + "SENPRDTEDVPWITLNSSIQKVNEWFSRSDELLGSDDSHDGESESNAKVADVLDVLNEVDEYSGSSEKIDLL\n"
- + "ASDPHEALICKSERVHSKSVESNIEDKIFGKTYRKKASLPNLSHVTENLIIGAFVTEPQIIQERPLTNKLKR\n"
- + "KRRPTSGLHPEDFIKKADLAVQKTPEMINQGTNQTEQNGQVMNITNSGHENKTKGDSIQNEKNPNPIESLEK\n"
- + "ESAFKTKAEPISSSISNMELELNIHNSKAPKKNRLRRKSSTRHIHALELVVSRNLSPPNCTELQIDSCSSSE\n"
- + "EIKKKKYNQMPVRHSRNLQLMEGKEPATGAKKSNKPNEQTSKRHDSDTFPELKLTNAPGSFTKCSNTSELKE\n"
- + "FVNPSLPREEKEEKLETVKVSNNAEDPKDLMLSGERVLQTERSVESSSISLVPGTDYGTQESISLLEVSTLG\n"
- + "KAKTEPNKCVSQCAAFENPKGLIHGCSKDNRNDTEGFKYPLGHEVNHSRETSIEMEESELDAQYLQNTFKVS\n"
- + "KRQSFAPFSNPGNAEEECATFSAHSGSLKKQSPKVTFECEQKEENQGKNESNIKPVQTVNITAGFPVVGQKD\n"
- + "KPVDNAKCSIKGGSRFCLSSQFRGNETGLITPNKHGLLQNPYRIPPLFPIKSFVKTKCKKNLLEENFEEHSM\n"
- + "SPEREMGNENIPSTVSTISRNNIRENVFKEASSSNINEVGSSTNEVGSSINEIGSSDENIQAELGRNRGPKL\n"
- + "NAMLRLGVLQPEVYKQSLPGSNCKHPEIKKQEYEEVVQTVNTDFSPYLISDNLEQPMGSSHASQVCSETPDD\n"
- + "LLDDGEIKEDTSFAENDIKESSAVFSKSVQKGELSRSPSPFTHTHLAQGYRRGAKKLESSEENLSSEDEELP\n"
- + "CFQHLLFGKVNNIPSQSTRHSTVATECLSKNTEENLLSLKNSLNDCSNQVILAKASQEHHLSEETKCSASLF\n"
- + "SSQCSELEDLTANTNTQDPFLIGSSKQMRHQSESQGVGLSDKELVSDDEERGTGLEENNQEEQSMDSNLGEA\n"
- + "ASGCESETSVSEDCSGLSSQSDILTTQQRDTMQHNLIKLQQEMAELEAVLEQHGSQPSNSYPSIISDSSALE\n"
- + "DLRNPEQSTSEKAVLTSQKSSEYPISQNPEGLSADKFEVSADSSTSKNKEPGVERSSPSKCPSLDDRWYMHS\n"
- + "CSGSLQNRNYPSQEELIKVVDVEEQQLEESGPHDLTETSYLPRQDLEGTPYLESGISLFSDDPESDPSEDRA\n"
- + "PESARVGNIPSSTSALKVPQLKVAESAQSPAAAHTTDTAGYNAMEESVSREKPELTASTERVNKRMSMVVSG\n"
- + "LTPEEFMLVYKFARKHHITLTNLITEETTHVVMKTDAEFVCERTLKYFLGIAGGKWVVSYFWVTQSIKERKM\n"
- + "LNEHDFEVRGDVVNGRNHQGPKRARESQDRKIFRGLEICCYGPFTNMPTDQLEWMVQLCGASVVKELSSFTL\n"
- + "GTGVHPIVVVQPDAWTEDNGFHAIGQMCEAPVVTREWVLDSVALYQCQELDTYLIPQIPHSHY\n"
- + "", 1,
-1863);
+ + "LQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNRAKRLLQSEPEN\n"
+ + "PSLQETSLSVQLSNLGTVRTLRTKQRIQPQKTSVYIELGSDSSEDTVNKATYCSVGDQELLQITPQGTRDEI\n"
+ + "SLDSAKKAACEFSETDVTNTEHHQPSNNDLNTTEKRAAERHPEKYQGSSVSNLHVEPCGTNTHASSLQHENS\n"
+ + "SLLLTKDRMNVEKAEFCNKSKQPGLARSQHNRWAGSKETCNDRRTPSTEKKVDLNADPLCERKEWNKQKLPC\n"
+ + "SENPRDTEDVPWITLNSSIQKVNEWFSRSDELLGSDDSHDGESESNAKVADVLDVLNEVDEYSGSSEKIDLL\n"
+ + "ASDPHEALICKSERVHSKSVESNIEDKIFGKTYRKKASLPNLSHVTENLIIGAFVTEPQIIQERPLTNKLKR\n"
+ + "KRRPTSGLHPEDFIKKADLAVQKTPEMINQGTNQTEQNGQVMNITNSGHENKTKGDSIQNEKNPNPIESLEK\n"
+ + "ESAFKTKAEPISSSISNMELELNIHNSKAPKKNRLRRKSSTRHIHALELVVSRNLSPPNCTELQIDSCSSSE\n"
+ + "EIKKKKYNQMPVRHSRNLQLMEGKEPATGAKKSNKPNEQTSKRHDSDTFPELKLTNAPGSFTKCSNTSELKE\n"
+ + "FVNPSLPREEKEEKLETVKVSNNAEDPKDLMLSGERVLQTERSVESSSISLVPGTDYGTQESISLLEVSTLG\n"
+ + "KAKTEPNKCVSQCAAFENPKGLIHGCSKDNRNDTEGFKYPLGHEVNHSRETSIEMEESELDAQYLQNTFKVS\n"
+ + "KRQSFAPFSNPGNAEEECATFSAHSGSLKKQSPKVTFECEQKEENQGKNESNIKPVQTVNITAGFPVVGQKD\n"
+ + "KPVDNAKCSIKGGSRFCLSSQFRGNETGLITPNKHGLLQNPYRIPPLFPIKSFVKTKCKKNLLEENFEEHSM\n"
+ + "SPEREMGNENIPSTVSTISRNNIRENVFKEASSSNINEVGSSTNEVGSSINEIGSSDENIQAELGRNRGPKL\n"
+ + "NAMLRLGVLQPEVYKQSLPGSNCKHPEIKKQEYEEVVQTVNTDFSPYLISDNLEQPMGSSHASQVCSETPDD\n"
+ + "LLDDGEIKEDTSFAENDIKESSAVFSKSVQKGELSRSPSPFTHTHLAQGYRRGAKKLESSEENLSSEDEELP\n"
+ + "CFQHLLFGKVNNIPSQSTRHSTVATECLSKNTEENLLSLKNSLNDCSNQVILAKASQEHHLSEETKCSASLF\n"
+ + "SSQCSELEDLTANTNTQDPFLIGSSKQMRHQSESQGVGLSDKELVSDDEERGTGLEENNQEEQSMDSNLGEA\n"
+ + "ASGCESETSVSEDCSGLSSQSDILTTQQRDTMQHNLIKLQQEMAELEAVLEQHGSQPSNSYPSIISDSSALE\n"
+ + "DLRNPEQSTSEKAVLTSQKSSEYPISQNPEGLSADKFEVSADSSTSKNKEPGVERSSPSKCPSLDDRWYMHS\n"
+ + "CSGSLQNRNYPSQEELIKVVDVEEQQLEESGPHDLTETSYLPRQDLEGTPYLESGISLFSDDPESDPSEDRA\n"
+ + "PESARVGNIPSSTSALKVPQLKVAESAQSPAAAHTTDTAGYNAMEESVSREKPELTASTERVNKRMSMVVSG\n"
+ + "LTPEEFMLVYKFARKHHITLTNLITEETTHVVMKTDAEFVCERTLKYFLGIAGGKWVVSYFWVTQSIKERKM\n"
+ + "LNEHDFEVRGDVVNGRNHQGPKRARESQDRKIFRGLEICCYGPFTNMPTDQLEWMVQLCGASVVKELSSFTL\n"
+ + "GTGVHPIVVVQPDAWTEDNGFHAIGQMCEAPVVTREWVLDSVALYQCQELDTYLIPQIPHSHY\n"
+ + "",
+ 1, 1863);
upSeq.setDescription("Breast cancer type 1 susceptibility protein");
upSeq_nocanonical = new Sequence(upSeq);
upSeq.createDatasetSequence();
- upSeq.addDBRef(new DBRefEntry("UNIPROT","0","P38398",null,true));
-
+ upSeq.addDBRef(new DBRefEntry("UNIPROT", "0", "P38398", null, true));
+
upSeq_nocanonical.createDatasetSequence();
// not a canonical reference
- upSeq_nocanonical.addDBRef(new DBRefEntry("UNIPROT","0","P38398",null,false));
+ upSeq_nocanonical.addDBRef(
+ new DBRefEntry("UNIPROT", "0", "P38398", null, false));
}
public void tearDown() throws Exception
{
seq = null;
- upSeq=null;
- upSeq_nocanonical=null;
+ upSeq = null;
+ upSeq_nocanonical = null;
}
@Test(groups = { "Functional" })
SequenceI[] selectedSeqs = new SequenceI[] { seq };
StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
ThreadwaitFor(200, sc);
-
+
// if structures are not discovered then don't
// populate filter options
sc.populateFilterComboBox(false, false);
int optionsSize = sc.getCmbFilterOption().getItemCount();
System.out.println("Items (no data, no cache): ");
StringBuilder items = new StringBuilder();
- for (int p=0;p<optionsSize;p++)
+ for (int p = 0; p < optionsSize; p++)
{
- items.append
- ("- ").append(sc.getCmbFilterOption().getItemAt(p).getName()).append("\n");
+ items.append("- ")
+ .append(sc.getCmbFilterOption().getItemAt(p).getName())
+ .append("\n");
}
// report items when this fails - seems to be a race condition
- Assert.assertEquals(items.toString(),optionsSize,2);
+ Assert.assertEquals(items.toString(), optionsSize, 2);
sc.populateFilterComboBox(true, false);
optionsSize = sc.getCmbFilterOption().getItemCount();
FilterOption filterOpt = (FilterOption) sc.getCmbFilterOption()
.getSelectedItem();
assertEquals("Cached Structures", filterOpt.getName());
- FTSRestClient.unMock((FTSRestClient) TDBeaconsFTSRestClient.getInstance());
+ FTSRestClient
+ .unMock((FTSRestClient) TDBeaconsFTSRestClient.getInstance());
FTSRestClient.unMock((FTSRestClient) PDBFTSRestClient.getInstance());
}
PDBFTSRestClientTest.setMock();
SequenceI[] selectedSeqs = new SequenceI[] { upSeq_nocanonical };
- StructureChooser sc = new StructureChooser(selectedSeqs, upSeq_nocanonical, null);
+ StructureChooser sc = new StructureChooser(selectedSeqs,
+ upSeq_nocanonical, null);
// mock so should be quick. Exceptions from mocked PDBFTS are expected too
ThreadwaitFor(500, sc);
-
+
assertTrue(sc.isCanQueryTDB() && sc.isNotQueriedTDBYet());
}
@Test(groups = { "Network" })
public void fetchStructuresInfoTest()
{
- FTSRestClient.unMock((FTSRestClient) TDBeaconsFTSRestClient.getInstance());
+ FTSRestClient
+ .unMock((FTSRestClient) TDBeaconsFTSRestClient.getInstance());
PDBFTSRestClient.unMock((FTSRestClient) PDBFTSRestClient.getInstance());
SequenceI[] selectedSeqs = new SequenceI[] { seq };
StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
- // not mocked, wait for 2s
+ // not mocked, wait for 2s
ThreadwaitFor(2000, sc);
-
+
sc.fetchStructuresMetaData();
Collection<FTSData> ss = (Collection<FTSData>) PA.getValue(sc,
"discoveredStructuresSet");
SequenceI[] selectedSeqs = new SequenceI[] { upSeq };
StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
ThreadwaitFor(500, sc);
-
+
sc.fetchStructuresMetaData();
Collection<FTSData> ss = (Collection<FTSData>) PA.getValue(sc,
"discoveredStructuresSet");
private void ThreadwaitFor(int i, StructureChooser sc)
{
- long timeout = i+System.currentTimeMillis();
+ long timeout = i + System.currentTimeMillis();
while (!sc.isDialogVisible() && timeout > System.currentTimeMillis())
{
- try {
+ try
+ {
Thread.sleep(50);
} catch (InterruptedException x)
{
-
+
}
}
-
- }
+ }
@Test(groups = { "Functional" })
public void sanitizeSeqNameTest()
{
String name = "ab_cdEF|fwxyz012349";
- assertEquals(name, PDBStructureChooserQuerySource.sanitizeSeqName(name));
+ assertEquals(name,
+ PDBStructureChooserQuerySource.sanitizeSeqName(name));
// remove a [nn] substring
name = "abcde12[345]fg";
- assertEquals("abcde12fg", PDBStructureChooserQuerySource.sanitizeSeqName(name));
+ assertEquals("abcde12fg",
+ PDBStructureChooserQuerySource.sanitizeSeqName(name));
// remove characters other than a-zA-Z0-9 | or _
name = "ab[cd],.\t£$*!- \\\"@:e";
- assertEquals("abcde", PDBStructureChooserQuerySource.sanitizeSeqName(name));
+ assertEquals("abcde",
+ PDBStructureChooserQuerySource.sanitizeSeqName(name));
name = "abcde12[345a]fg";
- assertEquals("abcde12345afg", PDBStructureChooserQuerySource.sanitizeSeqName(name));
+ assertEquals("abcde12345afg",
+ PDBStructureChooserQuerySource.sanitizeSeqName(name));
}
}
*/
package jalview.gui.structurechooser;
-
import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertTrue;
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
- Sequence seq,upSeq,upSeq_insulin;
+ Sequence seq, upSeq, upSeq_insulin;
// same set up as for structurechooser test
-
-@BeforeMethod(alwaysRun = true)
+
+ @BeforeMethod(alwaysRun = true)
public void setUp() throws Exception
{
seq = new Sequence("PDB|4kqy|4KQY|A", "ABCDEFGHIJKLMNOPQRSTUVWXYZ", 1,
pdbIds.add(dbRef);
seq.setPDBId(pdbIds);
-
+
// Uniprot sequence for 3D-Beacons mocks
- upSeq = new Sequence("P38398",
+ upSeq = new Sequence("P38398",
"MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRS\n"
- + "LQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNRAKRLLQSEPEN\n"
- + "PSLQETSLSVQLSNLGTVRTLRTKQRIQPQKTSVYIELGSDSSEDTVNKATYCSVGDQELLQITPQGTRDEI\n"
- + "SLDSAKKAACEFSETDVTNTEHHQPSNNDLNTTEKRAAERHPEKYQGSSVSNLHVEPCGTNTHASSLQHENS\n"
- + "SLLLTKDRMNVEKAEFCNKSKQPGLARSQHNRWAGSKETCNDRRTPSTEKKVDLNADPLCERKEWNKQKLPC\n"
- + "SENPRDTEDVPWITLNSSIQKVNEWFSRSDELLGSDDSHDGESESNAKVADVLDVLNEVDEYSGSSEKIDLL\n"
- + "ASDPHEALICKSERVHSKSVESNIEDKIFGKTYRKKASLPNLSHVTENLIIGAFVTEPQIIQERPLTNKLKR\n"
- + "KRRPTSGLHPEDFIKKADLAVQKTPEMINQGTNQTEQNGQVMNITNSGHENKTKGDSIQNEKNPNPIESLEK\n"
- + "ESAFKTKAEPISSSISNMELELNIHNSKAPKKNRLRRKSSTRHIHALELVVSRNLSPPNCTELQIDSCSSSE\n"
- + "EIKKKKYNQMPVRHSRNLQLMEGKEPATGAKKSNKPNEQTSKRHDSDTFPELKLTNAPGSFTKCSNTSELKE\n"
- + "FVNPSLPREEKEEKLETVKVSNNAEDPKDLMLSGERVLQTERSVESSSISLVPGTDYGTQESISLLEVSTLG\n"
- + "KAKTEPNKCVSQCAAFENPKGLIHGCSKDNRNDTEGFKYPLGHEVNHSRETSIEMEESELDAQYLQNTFKVS\n"
- + "KRQSFAPFSNPGNAEEECATFSAHSGSLKKQSPKVTFECEQKEENQGKNESNIKPVQTVNITAGFPVVGQKD\n"
- + "KPVDNAKCSIKGGSRFCLSSQFRGNETGLITPNKHGLLQNPYRIPPLFPIKSFVKTKCKKNLLEENFEEHSM\n"
- + "SPEREMGNENIPSTVSTISRNNIRENVFKEASSSNINEVGSSTNEVGSSINEIGSSDENIQAELGRNRGPKL\n"
- + "NAMLRLGVLQPEVYKQSLPGSNCKHPEIKKQEYEEVVQTVNTDFSPYLISDNLEQPMGSSHASQVCSETPDD\n"
- + "LLDDGEIKEDTSFAENDIKESSAVFSKSVQKGELSRSPSPFTHTHLAQGYRRGAKKLESSEENLSSEDEELP\n"
- + "CFQHLLFGKVNNIPSQSTRHSTVATECLSKNTEENLLSLKNSLNDCSNQVILAKASQEHHLSEETKCSASLF\n"
- + "SSQCSELEDLTANTNTQDPFLIGSSKQMRHQSESQGVGLSDKELVSDDEERGTGLEENNQEEQSMDSNLGEA\n"
- + "ASGCESETSVSEDCSGLSSQSDILTTQQRDTMQHNLIKLQQEMAELEAVLEQHGSQPSNSYPSIISDSSALE\n"
- + "DLRNPEQSTSEKAVLTSQKSSEYPISQNPEGLSADKFEVSADSSTSKNKEPGVERSSPSKCPSLDDRWYMHS\n"
- + "CSGSLQNRNYPSQEELIKVVDVEEQQLEESGPHDLTETSYLPRQDLEGTPYLESGISLFSDDPESDPSEDRA\n"
- + "PESARVGNIPSSTSALKVPQLKVAESAQSPAAAHTTDTAGYNAMEESVSREKPELTASTERVNKRMSMVVSG\n"
- + "LTPEEFMLVYKFARKHHITLTNLITEETTHVVMKTDAEFVCERTLKYFLGIAGGKWVVSYFWVTQSIKERKM\n"
- + "LNEHDFEVRGDVVNGRNHQGPKRARESQDRKIFRGLEICCYGPFTNMPTDQLEWMVQLCGASVVKELSSFTL\n"
- + "GTGVHPIVVVQPDAWTEDNGFHAIGQMCEAPVVTREWVLDSVALYQCQELDTYLIPQIPHSHY\n"
- + "", 1,
-1863);
+ + "LQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNRAKRLLQSEPEN\n"
+ + "PSLQETSLSVQLSNLGTVRTLRTKQRIQPQKTSVYIELGSDSSEDTVNKATYCSVGDQELLQITPQGTRDEI\n"
+ + "SLDSAKKAACEFSETDVTNTEHHQPSNNDLNTTEKRAAERHPEKYQGSSVSNLHVEPCGTNTHASSLQHENS\n"
+ + "SLLLTKDRMNVEKAEFCNKSKQPGLARSQHNRWAGSKETCNDRRTPSTEKKVDLNADPLCERKEWNKQKLPC\n"
+ + "SENPRDTEDVPWITLNSSIQKVNEWFSRSDELLGSDDSHDGESESNAKVADVLDVLNEVDEYSGSSEKIDLL\n"
+ + "ASDPHEALICKSERVHSKSVESNIEDKIFGKTYRKKASLPNLSHVTENLIIGAFVTEPQIIQERPLTNKLKR\n"
+ + "KRRPTSGLHPEDFIKKADLAVQKTPEMINQGTNQTEQNGQVMNITNSGHENKTKGDSIQNEKNPNPIESLEK\n"
+ + "ESAFKTKAEPISSSISNMELELNIHNSKAPKKNRLRRKSSTRHIHALELVVSRNLSPPNCTELQIDSCSSSE\n"
+ + "EIKKKKYNQMPVRHSRNLQLMEGKEPATGAKKSNKPNEQTSKRHDSDTFPELKLTNAPGSFTKCSNTSELKE\n"
+ + "FVNPSLPREEKEEKLETVKVSNNAEDPKDLMLSGERVLQTERSVESSSISLVPGTDYGTQESISLLEVSTLG\n"
+ + "KAKTEPNKCVSQCAAFENPKGLIHGCSKDNRNDTEGFKYPLGHEVNHSRETSIEMEESELDAQYLQNTFKVS\n"
+ + "KRQSFAPFSNPGNAEEECATFSAHSGSLKKQSPKVTFECEQKEENQGKNESNIKPVQTVNITAGFPVVGQKD\n"
+ + "KPVDNAKCSIKGGSRFCLSSQFRGNETGLITPNKHGLLQNPYRIPPLFPIKSFVKTKCKKNLLEENFEEHSM\n"
+ + "SPEREMGNENIPSTVSTISRNNIRENVFKEASSSNINEVGSSTNEVGSSINEIGSSDENIQAELGRNRGPKL\n"
+ + "NAMLRLGVLQPEVYKQSLPGSNCKHPEIKKQEYEEVVQTVNTDFSPYLISDNLEQPMGSSHASQVCSETPDD\n"
+ + "LLDDGEIKEDTSFAENDIKESSAVFSKSVQKGELSRSPSPFTHTHLAQGYRRGAKKLESSEENLSSEDEELP\n"
+ + "CFQHLLFGKVNNIPSQSTRHSTVATECLSKNTEENLLSLKNSLNDCSNQVILAKASQEHHLSEETKCSASLF\n"
+ + "SSQCSELEDLTANTNTQDPFLIGSSKQMRHQSESQGVGLSDKELVSDDEERGTGLEENNQEEQSMDSNLGEA\n"
+ + "ASGCESETSVSEDCSGLSSQSDILTTQQRDTMQHNLIKLQQEMAELEAVLEQHGSQPSNSYPSIISDSSALE\n"
+ + "DLRNPEQSTSEKAVLTSQKSSEYPISQNPEGLSADKFEVSADSSTSKNKEPGVERSSPSKCPSLDDRWYMHS\n"
+ + "CSGSLQNRNYPSQEELIKVVDVEEQQLEESGPHDLTETSYLPRQDLEGTPYLESGISLFSDDPESDPSEDRA\n"
+ + "PESARVGNIPSSTSALKVPQLKVAESAQSPAAAHTTDTAGYNAMEESVSREKPELTASTERVNKRMSMVVSG\n"
+ + "LTPEEFMLVYKFARKHHITLTNLITEETTHVVMKTDAEFVCERTLKYFLGIAGGKWVVSYFWVTQSIKERKM\n"
+ + "LNEHDFEVRGDVVNGRNHQGPKRARESQDRKIFRGLEICCYGPFTNMPTDQLEWMVQLCGASVVKELSSFTL\n"
+ + "GTGVHPIVVVQPDAWTEDNGFHAIGQMCEAPVVTREWVLDSVALYQCQELDTYLIPQIPHSHY\n"
+ + "",
+ 1, 1863);
upSeq.createDatasetSequence();
upSeq.setDescription("Breast cancer type 1 susceptibility protein");
- upSeq.addDBRef(new DBRefEntry("UNIPROT","0","P38398",null,true));
-
- upSeq_insulin=new Sequence("INS_HUMAN",
+ upSeq.addDBRef(new DBRefEntry("UNIPROT", "0", "P38398", null, true));
+
+ upSeq_insulin = new Sequence("INS_HUMAN",
"MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGP"
- + "GAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN");
+ + "GAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN");
upSeq_insulin.createDatasetSequence();
upSeq_insulin.setDescription("Insulin");
- upSeq_insulin.addDBRef(new DBRefEntry("UNIPROT","0","P01308",null,true));
+ upSeq_insulin
+ .addDBRef(new DBRefEntry("UNIPROT", "0", "P01308", null, true));
}
-@AfterMethod(alwaysRun = true)
+ @AfterMethod(alwaysRun = true)
public void tearDown() throws Exception
{
seq = null;
- upSeq=null;
+ upSeq = null;
}
@SuppressWarnings("deprecation")
public void buildPDBQueryTest()
{
System.out.println("seq >>>> " + seq);
-
- StructureChooserQuerySource scquery = StructureChooserQuerySource.getQuerySourceFor(new SequenceI[] { seq});
- AssertJUnit.assertTrue(scquery instanceof PDBStructureChooserQuerySource);
+
+ StructureChooserQuerySource scquery = StructureChooserQuerySource
+ .getQuerySourceFor(new SequenceI[]
+ { seq });
+ AssertJUnit
+ .assertTrue(scquery instanceof PDBStructureChooserQuerySource);
String query = scquery.buildQuery(seq);
AssertJUnit.assertEquals("pdb_id:1tim", query);
seq.getAllPDBEntries().clear();
System.out.println("seq >>>> " + upSeq);
TDBeaconsFTSRestClientTest.setMock();
PDBFTSRestClientTest.setMock();
- StructureChooserQuerySource scquery = StructureChooserQuerySource.getQuerySourceFor(new SequenceI[] { upSeq});
- // gets the lightweight proxy rather than the ThreeDBStructureChooserQuerySource
- AssertJUnit.assertTrue(scquery instanceof ThreeDBStructureChooserQuerySource);
+ StructureChooserQuerySource scquery = StructureChooserQuerySource
+ .getQuerySourceFor(new SequenceI[]
+ { upSeq });
+ // gets the lightweight proxy rather than the
+ // ThreeDBStructureChooserQuerySource
+ AssertJUnit.assertTrue(
+ scquery instanceof ThreeDBStructureChooserQuerySource);
String query = scquery.buildQuery(upSeq);
AssertJUnit.assertEquals("P38398", query);
-
+
// query shouldn't change regardless of additional entries
// because 3DBeacons requires canonical entries.
upSeq.getAllPDBEntries().clear();
* ---> better to do a direct retrieval from uniprot to work out which is the canonical identifier..
* ----> need a test to check that accessions can be promoted to canonical!
*/
- //FIXME - need to be able to use ID to query here ?
+ // FIXME - need to be able to use ID to query here ?
AssertJUnit.assertEquals(null, query);
-
-
- // TODO:
+ // TODO:
/**
- * set of sequences:
- * - no protein -> TDB not applicable, query PDBe only (consider RNA or DNA - specific query adapter ?)
- * - protein but no uniprot -> first consider trying to get uniprot refs (need a mark to say none are available)
- * - protein and uniprot - no canonicals -> resolve to uniprot automatically to get canonicals
- * - query uniprot against 3DBeacons
- * --> decorate experimental structures with additional data from PDBe
- * - query remaining against PDBe
- * Ranking
- * - 3D Beacons
- * --> in memory ranking - no need to query twice
- * Rank by
- * - experimental > AlphaFold -> Model
- * - start > end
- * -> filters for
- * -> experimental only
- * -> experimental plus best models for other regions
- * -> "best cover"
- * -> need to be able to select correct reference (the longest one that covers all) for superposition
+ * set of sequences: - no protein -> TDB not applicable, query PDBe only
+ * (consider RNA or DNA - specific query adapter ?) - protein but no uniprot
+ * -> first consider trying to get uniprot refs (need a mark to say none are
+ * available) - protein and uniprot - no canonicals -> resolve to uniprot
+ * automatically to get canonicals - query uniprot against 3DBeacons -->
+ * decorate experimental structures with additional data from PDBe - query
+ * remaining against PDBe Ranking - 3D Beacons --> in memory ranking - no
+ * need to query twice Rank by - experimental > AlphaFold -> Model - start >
+ * end -> filters for -> experimental only -> experimental plus best models
+ * for other regions -> "best cover" -> need to be able to select correct
+ * reference (the longest one that covers all) for superposition
*/
-//
-// DBRefEntry uniprotDBRef = new DBRefEntry();
-// uniprotDBRef.setAccessionId("P12345");
-// uniprotDBRef.setSource(DBRefSource.UNIPROT);
-// upSeq.addDBRef(uniprotDBRef);
-//
-// DBRefEntry pdbDBRef = new DBRefEntry();
-// pdbDBRef.setAccessionId("1XYZ");
-// pdbDBRef.setSource(DBRefSource.PDB);
-// upSeq.addDBRef(pdbDBRef);
-//
-// for (int x = 1; x < 5; x++)
-// {
-// DBRefEntry dbRef = new DBRefEntry();
-// dbRef.setAccessionId("XYZ_" + x);
-// seq.addDBRef(dbRef);
-// }
-// System.out.println("");
-// System.out.println(seq.getDBRefs());
-// System.out.println(query);
-// query = scquery.buildQuery(seq);
-// assertEquals(
-// "uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz",
-// query);
+ //
+ // DBRefEntry uniprotDBRef = new DBRefEntry();
+ // uniprotDBRef.setAccessionId("P12345");
+ // uniprotDBRef.setSource(DBRefSource.UNIPROT);
+ // upSeq.addDBRef(uniprotDBRef);
+ //
+ // DBRefEntry pdbDBRef = new DBRefEntry();
+ // pdbDBRef.setAccessionId("1XYZ");
+ // pdbDBRef.setSource(DBRefSource.PDB);
+ // upSeq.addDBRef(pdbDBRef);
+ //
+ // for (int x = 1; x < 5; x++)
+ // {
+ // DBRefEntry dbRef = new DBRefEntry();
+ // dbRef.setAccessionId("XYZ_" + x);
+ // seq.addDBRef(dbRef);
+ // }
+ // System.out.println("");
+ // System.out.println(seq.getDBRefs());
+ // System.out.println(query);
+ // query = scquery.buildQuery(seq);
+ // assertEquals(
+ // "uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz",
+ // query);
}
- @Test(groups= {"Functional"},dataProvider = "testUpSeqs")
+
+ @Test(groups = { "Functional" }, dataProvider = "testUpSeqs")
public void cascadingThreeDBandPDBQuerys(SequenceI testUpSeq)
{
TDBeaconsFTSRestClientTest.setMock();
PDBFTSRestClientTest.setMock();
ThreeDBStructureChooserQuerySource tdbquery = new ThreeDBStructureChooserQuerySource();
- PDBStructureChooserQuerySource pdbquery = new PDBStructureChooserQuerySource();
-
+ PDBStructureChooserQuerySource pdbquery = new PDBStructureChooserQuerySource();
-
FTSRestResponse upResponse = null;
FTSRestResponse pdbResponse = null;
// TODO test available options
// Best Alphafold Model
// Best model (by confidence score)
// Will also need to develop a more sophisticated filtering system
- List<FilterOption> opts = tdbquery.getAvailableFilterOptions(StructureChooser.VIEWS_FILTER);
+ List<FilterOption> opts = tdbquery
+ .getAvailableFilterOptions(StructureChooser.VIEWS_FILTER);
FilterOption opt_singlebest = opts.get(0);
FilterOption opt_manybest = opts.get(1);
- assertEquals(opt_singlebest.getValue(), ThreeDBStructureChooserQuerySource.FILTER_FIRST_BEST_COVERAGE);
- assertEquals(opt_manybest.getValue(), ThreeDBStructureChooserQuerySource.FILTER_TDBEACONS_COVERAGE);
-
- try {
- upResponse = tdbquery.fetchStructuresMetaData(testUpSeq, tdbquery.getDocFieldPrefs().getStructureSummaryFields(), opt_singlebest, false);
- tdbquery.updateAvailableFilterOptions(StructureChooser.VIEWS_FILTER,opts,upResponse.getSearchSummary());
+ assertEquals(opt_singlebest.getValue(),
+ ThreeDBStructureChooserQuerySource.FILTER_FIRST_BEST_COVERAGE);
+ assertEquals(opt_manybest.getValue(),
+ ThreeDBStructureChooserQuerySource.FILTER_TDBEACONS_COVERAGE);
+
+ try
+ {
+ upResponse = tdbquery.fetchStructuresMetaData(testUpSeq,
+ tdbquery.getDocFieldPrefs().getStructureSummaryFields(),
+ opt_singlebest, false);
+ tdbquery.updateAvailableFilterOptions(StructureChooser.VIEWS_FILTER,
+ opts, upResponse.getSearchSummary());
// test ranking without additional PDBe data
- FTSRestResponse firstRanked = tdbquery.selectFirstRankedQuery(testUpSeq, upResponse.getSearchSummary(), tdbquery.getDocFieldPrefs().getStructureSummaryFields(), opt_singlebest.getValue(), false);
- assertEquals(firstRanked.getNumberOfItemsFound(),1);
+ FTSRestResponse firstRanked = tdbquery.selectFirstRankedQuery(
+ testUpSeq, upResponse.getSearchSummary(),
+ tdbquery.getDocFieldPrefs().getStructureSummaryFields(),
+ opt_singlebest.getValue(), false);
+ assertEquals(firstRanked.getNumberOfItemsFound(), 1);
// many best response
- upResponse = tdbquery.fetchStructuresMetaData(testUpSeq, tdbquery.getDocFieldPrefs().getStructureSummaryFields(), opt_manybest, false);
- assertTrue(firstRanked.getSearchSummary().size()<upResponse.getSearchSummary().size());
- // NB Could have race condition here
+ upResponse = tdbquery.fetchStructuresMetaData(testUpSeq,
+ tdbquery.getDocFieldPrefs().getStructureSummaryFields(),
+ opt_manybest, false);
+ assertTrue(firstRanked.getSearchSummary().size() < upResponse
+ .getSearchSummary().size());
+ // NB Could have race condition here
String pdb_Query = tdbquery.buildPDBFTSQueryFor(upResponse);
- assertTrue(pdb_Query.trim().length()>0);
- pdbResponse = tdbquery.fetchStructuresMetaDataFor(pdbquery, upResponse);
- assertTrue(pdbResponse.getNumberOfItemsFound()>0);
- FTSRestResponse joinedResp = tdbquery.joinResponses(upResponse, pdbResponse);
- assertEquals(upResponse.getNumberOfItemsFound(),joinedResp.getNumberOfItemsFound());
-
-
+ assertTrue(pdb_Query.trim().length() > 0);
+ pdbResponse = tdbquery.fetchStructuresMetaDataFor(pdbquery,
+ upResponse);
+ assertTrue(pdbResponse.getNumberOfItemsFound() > 0);
+ FTSRestResponse joinedResp = tdbquery.joinResponses(upResponse,
+ pdbResponse);
+ assertEquals(upResponse.getNumberOfItemsFound(),
+ joinedResp.getNumberOfItemsFound());
+
} catch (Exception x)
{
x.printStackTrace();
Assert.fail("Unexpected Exception");
}
- StructureChooserQuerySource scquery = StructureChooserQuerySource.getQuerySourceFor(new SequenceI[] { testUpSeq});
+ StructureChooserQuerySource scquery = StructureChooserQuerySource
+ .getQuerySourceFor(new SequenceI[]
+ { testUpSeq });
}
-
+
@DataProvider(name = "testUpSeqs")
public Object[][] testUpSeqs() throws Exception
{
setUp();
- return new Object[][] { {upSeq},{upSeq_insulin}};
+ return new Object[][] { { upSeq }, { upSeq_insulin } };
}
-
+
@Test(groups = { "Functional" })
public void sanitizeSeqNameTest()
{
String name = "ab_cdEF|fwxyz012349";
- AssertJUnit.assertEquals(name, PDBStructureChooserQuerySource.sanitizeSeqName(name));
+ AssertJUnit.assertEquals(name,
+ PDBStructureChooserQuerySource.sanitizeSeqName(name));
// remove a [nn] substring
name = "abcde12[345]fg";
- AssertJUnit.assertEquals("abcde12fg", PDBStructureChooserQuerySource.sanitizeSeqName(name));
+ AssertJUnit.assertEquals("abcde12fg",
+ PDBStructureChooserQuerySource.sanitizeSeqName(name));
// remove characters other than a-zA-Z0-9 | or _
name = "ab[cd],.\t£$*!- \\\"@:e";
- AssertJUnit.assertEquals("abcde", PDBStructureChooserQuerySource.sanitizeSeqName(name));
+ AssertJUnit.assertEquals("abcde",
+ PDBStructureChooserQuerySource.sanitizeSeqName(name));
name = "abcde12[345a]fg";
- AssertJUnit.assertEquals("abcde12345afg", PDBStructureChooserQuerySource.sanitizeSeqName(name));
+ AssertJUnit.assertEquals("abcde12345afg",
+ PDBStructureChooserQuerySource.sanitizeSeqName(name));
}
}
break;
}
}
- assertTrue(
- "Couldn't find sequence associated annotation "
- + aa.label
- + " on the sequence it is associated with.\nSequence associated editing will fail.",
+ assertTrue("Couldn't find sequence associated annotation "
+ + aa.label
+ + " on the sequence it is associated with.\nSequence associated editing will fail.",
found);
}
}
@BeforeClass(alwaysRun = true)
public static void setUpBeforeClass() throws Exception
{
- jalview.bin.Jalview.main(new String[] { "-props",
- "test/jalview/io/testProps.jvprops" });
+ jalview.bin.Jalview
+ .main(new String[]
+ { "-props", "test/jalview/io/testProps.jvprops" });
}
/**
String inFile = "examples/1gaq.txt";
String tfile = File.createTempFile("JalviewTest", ".jvp")
.getAbsolutePath();
- AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
- inFile, DataSourceType.FILE);
+ AlignFrame af = new jalview.io.FileLoader()
+ .LoadFileWaitTillLoaded(inFile, DataSourceType.FILE);
assertTrue("Didn't read input file " + inFile, af != null);
af.saveAlignment(tfile, FileFormat.Jalview);
assertTrue("Failed to store as a project.",
sq = sq.getDatasetSequence();
}
assertNotNull(sq.getAllPDBEntries());
- assertEquals("Expected only one PDB ID", 1, sq.getAllPDBEntries()
- .size());
+ assertEquals("Expected only one PDB ID", 1,
+ sq.getAllPDBEntries().size());
for (PDBEntry pdbentry : sq.getAllPDBEntries())
{
- System.err.println("PDB Entry " + pdbentry.getId() + " "
- + pdbentry.getFile());
+ System.err.println(
+ "PDB Entry " + pdbentry.getId() + " " + pdbentry.getFile());
boolean exists = false, found = false;
for (AlignmentAnnotation ana : sq.getAnnotation())
{
}
if (exists)
{
- assertTrue("Couldn't find any annotation for " + pdbentry.getId()
- + " (file handle " + pdbentry.getFile() + ")", found);
+ assertTrue(
+ "Couldn't find any annotation for " + pdbentry.getId()
+ + " (file handle " + pdbentry.getFile() + ")",
+ found);
}
}
}
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
- static String TestFiles[][] = {
- { "Test example annotation import/export", "examples/uniref50.fa",
- "examples/testdata/example_annot_file.jva" },
+ static String TestFiles[][] = { { "Test example annotation import/export",
+ "examples/uniref50.fa", "examples/testdata/example_annot_file.jva" },
{ "Test multiple combine annotation statements import/export",
"examples/uniref50.fa",
"examples/testdata/test_combine_annot.jva" },
- {
- "Test multiple combine annotation statements with sequence_ref import/export",
+ { "Test multiple combine annotation statements with sequence_ref import/export",
"examples/uniref50.fa", "examples/testdata/uniref50_iupred.jva" },
- {
- "Test group only annotation file parsing results in parser indicating annotation was parsed",
+ { "Test group only annotation file parsing results in parser indicating annotation was parsed",
"examples/uniref50.fa", "examples/testdata/test_grpannot.jva" },
{ "Test hiding/showing of insertions on sequence_ref",
- "examples/uniref50.fa", "examples/testdata/uniref50_seqref.jva" } };
+ "examples/uniref50.fa",
+ "examples/testdata/uniref50_seqref.jva" } };
@Test(groups = { "Functional" })
public void exampleAnnotationFileIO() throws Exception
{
for (String[] testPair : TestFiles)
{
- testAnnotationFileIO(testPair[0], new File(testPair[1]), new File(
- testPair[2]));
+ testAnnotationFileIO(testPair[0], new File(testPair[1]),
+ new File(testPair[2]));
}
}
{
e.printStackTrace();
}
- Assert.fail("Couln't read the alignment in file '" + f.toString() + "'");
+ Assert.fail(
+ "Couln't read the alignment in file '" + f.toString() + "'");
return null;
}
* - label for IO class used to write and read back in the data from
* f
*/
- void testAnnotationFileIO(String testname, File f,
- File annotFile)
+ void testAnnotationFileIO(String testname, File f, File annotFile)
{
System.out.println("Test: " + testname + "\nReading annotation file '"
+ annotFile + "' onto : " + f);
{
AlignmentI al = readAlignmentFile(f);
HiddenColumns cs = new HiddenColumns();
- assertTrue(
- "Test "
- + testname
- + "\nAlignment was not annotated - annotation file not imported.",
+ assertTrue("Test " + testname
+ + "\nAlignment was not annotated - annotation file not imported.",
new AnnotationFile().readAnnotationFile(al, cs, af,
DataSourceType.FILE));
String anfileout = new AnnotationFile().printAnnotations(
al.getAlignmentAnnotation(), al.getGroups(),
al.getProperties(), null, al, v);
- assertTrue(
- "Test "
- + testname
- + "\nAlignment annotation file was not regenerated. Null string",
+ assertTrue("Test " + testname
+ + "\nAlignment annotation file was not regenerated. Null string",
anfileout != null);
- assertTrue(
- "Test "
- + testname
- + "\nAlignment annotation file was not regenerated. Empty string",
+ assertTrue("Test " + testname
+ + "\nAlignment annotation file was not regenerated. Empty string",
anfileout.length() > "JALVIEW_ANNOTATION".length());
- System.out.println("Output annotation file:\n" + anfileout
- + "\n<<EOF\n");
+ System.out.println(
+ "Output annotation file:\n" + anfileout + "\n<<EOF\n");
AlignmentI al_new = readAlignmentFile(f);
- assertTrue(
- "Test "
- + testname
- + "\nregenerated annotation file did not annotate alignment.",
+ assertTrue("Test " + testname
+ + "\nregenerated annotation file did not annotate alignment.",
new AnnotationFile().readAnnotationFile(al_new, anfileout,
DataSourceType.PASTE));
{
e.printStackTrace();
}
- Assert.fail("Test "
- + testname
+ Assert.fail("Test " + testname
+ "\nCouldn't complete Annotation file roundtrip input/output/input test for '"
+ annotFile + "'.");
}
-
- @Test(groups="Functional")
+
+ @Test(groups = "Functional")
public void testAnnotateAlignmentView()
{
long t1 = System.currentTimeMillis();
+ "SEQUENCE_GROUP\tGroup2\t*\t*\t2\n"
+ "SEQUENCE_GROUP\tGroup1\t*\t*\t3\n"
+ "PROPERTIES\tGroup1\toutlineColour=blue\tidColour=red\n";
- new AnnotationFile().annotateAlignmentView(af.getViewport(), annotationFile, DataSourceType.PASTE);
-
+ new AnnotationFile().annotateAlignmentView(af.getViewport(),
+ annotationFile, DataSourceType.PASTE);
+
AlignmentI al = af.getViewport().getAlignment();
List<SequenceGroup> groups = al.getGroups();
assertEquals(3, groups.size());
sg = groups.get(1);
assertEquals("Group2", sg.getName());
assertTrue(sg.contains(al.getSequenceAt(1)));
-
+
/*
* the bug fix: a second group of the same name is also given properties
*/
{
e.printStackTrace();
}
- bjsTemplate = HTMLOutput.readFileAsString(BioJsHTMLOutput
- .getCurrentBJSTemplateFile());
+ bjsTemplate = HTMLOutput.readFileAsString(
+ BioJsHTMLOutput.getCurrentBJSTemplateFile());
// System.out.println(bjsTemplate);
} catch (IOException e)
{
}
@Test(
- groups = { "Functional" },
+ groups =
+ { "Functional" },
expectedExceptions = NullPointerException.class)
public void expectedNullPointerException()
{
TreeMap<String, File> versions = null;
try
{
- BioJsHTMLOutput
- .refreshVersionInfo(BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
+ BioJsHTMLOutput.refreshVersionInfo(
+ BioJsHTMLOutput.BJS_TEMPLATES_LOCAL_DIRECTORY);
versions = BioJsHTMLOutput.getBioJsMSAVersions();
} catch (URISyntaxException e)
{
public void testBioJsUpdate()
{
String url = BioJsHTMLOutput.BJS_TEMPLATE_GIT_REPO;
- AssertJUnit
- .assertTrue("URL not reacable : " + url, urlIsReachable(url));
+ AssertJUnit.assertTrue("URL not reacable : " + url,
+ urlIsReachable(url));
String response = BioJsHTMLOutput.getURLContentAsString(url);
AssertJUnit.assertNotNull("Null response read from url!", response);
BioJSRepositoryPojo repository = new BioJSRepositoryPojo(response);
System.out.println(">>> description : " + repository.getDescription());
- System.out.println(">>> latest version : "
- + repository.getLatestReleaseVersion());
- System.out.println(">>> repo count : "
- + repository.getReleases().size());
+ System.out.println(
+ ">>> latest version : " + repository.getLatestReleaseVersion());
+ System.out
+ .println(">>> repo count : " + repository.getReleases().size());
for (BioJSReleasePojo release : repository.getReleases())
{
System.out.println("repo type : " + release.getType());
public class ClustalFileTest
{
- @Test(groups="Functional")
+ @Test(groups = "Functional")
public void testParse_withNumbering() throws IOException
{
//@formatter:off
assertTrue(seqs[0].getSequenceAsString().endsWith("ASYKVKLI"));
}
- @Test(groups="Functional")
+ @Test(groups = "Functional")
public void testParse_noNumbering() throws IOException
{
//@formatter:off
{
assertEquals((ranges = map.getFromRanges()).size(), 1);
assertEquals(ranges.get(0)[0], 1579);
- assertEquals(ranges.get(0)[1], 2931); // excludes stop 2934
+ assertEquals(ranges.get(0)[1], 2931); // excludes stop 2934
assertEquals((ranges = map.getToRanges()).size(), 1);
assertEquals(ranges.get(0)[0], 1);
assertEquals(ranges.get(0)[1], 451);
{
assertEquals((ranges = map.getFromRanges()).size(), 1);
assertEquals(ranges.get(0)[0], 2928);
- assertEquals(ranges.get(0)[1], 3989); // excludes stop 3992
+ assertEquals(ranges.get(0)[1], 3989); // excludes stop 3992
assertEquals((ranges = map.getToRanges()).size(), 1);
assertEquals(ranges.get(0)[0], 1);
assertEquals(ranges.get(0)[1], 354);
}
assertEquals(uniprotCount, 8);
}
+
/**
* A fairly tough test, using J03321 (circular DNA), which has 8 CDS features,
* one of them reverse strand
FileParse fp = new FileParse(dataFile, DataSourceType.FILE);
EmblFlatFile parser = new EmblFlatFile(fp, "EmblTest");
List<SequenceI> seqs = parser.getSeqs();
- assertTrue(seqs.get(0).getSequenceAsString().indexOf("u")>-1);
+ assertTrue(seqs.get(0).getSequenceAsString().indexOf("u") > -1);
}
@Test(groups = "Functional")
* dna should have dbref to itself, and to inferred EMBLCDSPROTEIN:QHD43415.1
*/
assertEquals(dbrefs.size(), 2);
-
+
// dbref to self
DBRefEntry dbref = dbrefs.get(0);
assertEquals(dbref.getSource(), "EMBLTEST");
assertEquals(map.getToHighest(), 40);
assertEquals(map.getFromRatio(), 1);
assertEquals(map.getToRatio(), 1);
-
+
// dbref to inferred EMBLCDSPROTEIN:
dbref = dbrefs.get(1);
assertEquals(dbref.getSource(), "EMBLCDSPROTEIN");
assertSame(exons, EmblFlatFile.adjustForProteinLength(6, exons));
// patch from JAL-3725 in EmblXmlSource propagated to Flatfile
- // match if we assume exons include stop codon not in protein:
+ // match if we assume exons include stop codon not in protein:
int[] truncated = EmblFlatFile.adjustForProteinLength(5, exons);
assertEquals(Arrays.toString(truncated), "[11, 15, 21, 25, 31, 35]");
-
+
// truncate last exon by 6bp
truncated = EmblFlatFile.adjustForProteinLength(4, exons);
- assertEquals(Arrays.toString(truncated),"[11, 15, 21, 25, 31, 32]");
+ assertEquals(Arrays.toString(truncated), "[11, 15, 21, 25, 31, 32]");
// remove last exon and truncate preceding by 1bp (so 3bp in total)
truncated = EmblFlatFile.adjustForProteinLength(3, exons);
- assertEquals(Arrays.toString(truncated),"[11, 15, 21, 24]");
+ assertEquals(Arrays.toString(truncated), "[11, 15, 21, 24]");
// exact removal of exon case:
exons = new int[] { 11, 15, 21, 27, 33, 38 }; // 18 bp
public void testRemoveQuotes()
{
assertNull(EmblFlatFile.removeQuotes(null));
- assertEquals(EmblFlatFile.removeQuotes("No quotes here"), "No quotes here");
- assertEquals(EmblFlatFile.removeQuotes("\"Enclosing quotes\""), "Enclosing quotes");
- assertEquals(EmblFlatFile.removeQuotes("\"Escaped \"\"quotes\"\" example\""), "Escaped \"quotes\" example");
+ assertEquals(EmblFlatFile.removeQuotes("No quotes here"),
+ "No quotes here");
+ assertEquals(EmblFlatFile.removeQuotes("\"Enclosing quotes\""),
+ "Enclosing quotes");
+ assertEquals(
+ EmblFlatFile.removeQuotes("\"Escaped \"\"quotes\"\" example\""),
+ "Escaped \"quotes\" example");
}
}
.getFeatureColours();
FeaturesFile featuresFile = new FeaturesFile(
"examples/exampleFeatures.txt", DataSourceType.FILE);
- assertTrue("Test " + "Features file test"
- + "\nFailed to parse features file.",
+ assertTrue(
+ "Test " + "Features file test"
+ + "\nFailed to parse features file.",
featuresFile.parse(al.getDataset(), colours, true));
/*
Map<String, FeatureColourI> colours = af.getFeatureRenderer()
.getFeatureColours();
// GFF2 uses space as name/value separator in column 9
- String gffData = "METAL\tcc9900\n"
- + "GFF\n"
+ String gffData = "METAL\tcc9900\n" + "GFF\n"
+ "FER_CAPAA\tuniprot\tMETAL\t44\t45\t4.0\t.\t.\tNote Iron-sulfur; Note 2Fe-2S\n"
+ "FER1_SOLLC\tuniprot\tPfam\t55\t130\t2.0\t.\t.";
FeaturesFile featuresFile = new FeaturesFile(gffData,
Map<String, FeatureColourI> colours = af.getFeatureRenderer()
.getFeatureColours();
// GFF3 uses '=' separator for name/value pairs in column 9
- // comma (%2C) equals (%3D) or semi-colon (%3B) should be url-escaped in values
+ // comma (%2C) equals (%3D) or semi-colon (%3B) should be url-escaped in
+ // values
String gffData = "##gff-version 3\n"
+ "FER_CAPAA\tuniprot\tMETAL\t39\t39\t0.0\t.\t.\t"
+ "Note=Iron-sulfur (2Fe-2S);Note=another note,and another;evidence=ECO%3B0000255%2CPROSITE%3DProRule:PRU00465;"
assertEquals("21", sf.getValueAsString("CSQ", "AF"));
assertEquals("benign,possibly_damaging",
sf.getValueAsString("CSQ", "POLYPHEN"));
- assertEquals("Benign=good", sf.getValueAsString("CSQ", "clin_sig")); // url decoded
+ assertEquals("Benign=good", sf.getValueAsString("CSQ", "clin_sig")); // url
+ // decoded
// todo change STRAND and !Phase into fields of SequenceFeature instead
assertEquals(".", sf.otherDetails.get("STRAND"));
assertEquals(0, sf.getStrand());
SequenceI seq2 = dataset.findName("seq2");
assertNotNull(seq1);
assertNotNull(seq2);
- assertFalse(
- "Failed to replace dummy seq1 with real sequence",
+ assertFalse("Failed to replace dummy seq1 with real sequence",
seq1 instanceof SequenceDummy
&& ((SequenceDummy) seq1).isDummy());
- assertFalse(
- "Failed to replace dummy seq2 with real sequence",
+ assertFalse("Failed to replace dummy seq2 with real sequence",
seq2 instanceof SequenceDummy
&& ((SequenceDummy) seq2).isDummy());
String placeholderseq = new SequenceDummy("foo").getSequenceAsString();
assertFalse("dummy replacement buggy for seq2",
placeholderseq.equals(seq2.getSequenceAsString()));
assertNotNull("No features added to seq1", seq1.getSequenceFeatures());
- assertEquals("Wrong number of features", 3, seq1.getSequenceFeatures()
- .size());
+ assertEquals("Wrong number of features", 3,
+ seq1.getSequenceFeatures().size());
assertTrue(seq2.getSequenceFeatures().isEmpty());
- assertEquals(
- "Wrong number of features",
- 0,
- seq2.getSequenceFeatures() == null ? 0 : seq2
- .getSequenceFeatures().size());
- assertTrue(
- "Expected at least one CDNA/Protein mapping for seq1",
+ assertEquals("Wrong number of features", 0,
+ seq2.getSequenceFeatures() == null ? 0
+ : seq2.getSequenceFeatures().size());
+ assertTrue("Expected at least one CDNA/Protein mapping for seq1",
dataset.getCodonFrame(seq1) != null
&& dataset.getCodonFrame(seq1).size() > 0);
AlignmentI dataset = new Alignment(new SequenceI[] {});
FeaturesFile ffile = new FeaturesFile(simpleGffFile,
DataSourceType.FILE);
-
+
boolean parseResult = ffile.parse(dataset, null, false, false);
assertTrue("return result should be true", parseResult);
checkDatasetfromSimpleGff3(dataset);
@Test(groups = { "Functional" })
public void simpleGff3FileLoader() throws IOException
{
- AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
- simpleGffFile, DataSourceType.FILE);
+ AlignFrame af = new FileLoader(false)
+ .LoadFileWaitTillLoaded(simpleGffFile, DataSourceType.FILE);
assertTrue(
"Didn't read the alignment into an alignframe from Gff3 File",
af != null);
AlignmentI dataset = new Alignment(new SequenceI[] {});
FeaturesFile ffile = new FeaturesFile(simpleGffFile,
DataSourceType.FILE);
-
+
boolean parseResult = ffile.parse(dataset, null, false, true);
assertTrue("return result (relaxedID matching) should be true",
parseResult);
.getFeatureColours();
String features = "METAL\tcc9900\n"
+ "GAMMA-TURN\tred|0,255,255|20.0|95.0|below|66.0\n"
- + "Pfam\tred\n"
- + "STARTGROUP\tuniprot\n"
+ + "Pfam\tred\n" + "STARTGROUP\tuniprot\n"
+ "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\n" // non-positional feature
+ "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
+ "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\n"
* empty feature group to check handled correctly
*/
SequenceI seq = al.getSequenceAt(1); // FER_CAPAN
- seq.addSequenceFeature(new SequenceFeature("Pfam", "desc1", 0, 0, 1.3f,
- null));
- seq.addSequenceFeature(new SequenceFeature("Pfam", "desc2", 4, 9,
- Float.NaN, null));
+ seq.addSequenceFeature(
+ new SequenceFeature("Pfam", "desc1", 0, 0, 1.3f, null));
+ seq.addSequenceFeature(
+ new SequenceFeature("Pfam", "desc2", 4, 9, Float.NaN, null));
seq = al.getSequenceAt(2); // FER1_SOLLC
- seq.addSequenceFeature(new SequenceFeature("Pfam", "desc3", 0, 0,
- Float.NaN, ""));
- seq.addSequenceFeature(new SequenceFeature("Pfam", "desc4", 5, 8,
- -2.6f, ""));
+ seq.addSequenceFeature(
+ new SequenceFeature("Pfam", "desc3", 0, 0, Float.NaN, ""));
+ seq.addSequenceFeature(
+ new SequenceFeature("Pfam", "desc4", 5, 8, -2.6f, ""));
/*
* first with no features displayed, exclude non-positional features
/*
* features are output within group, ordered by sequence and type
*/
- expected = "METAL\tcc9900\n"
- + "Pfam\tff0000\n"
+ expected = "METAL\tcc9900\n" + "Pfam\tff0000\n"
+ "GAMMA-TURN\tscore|ff0000|00ffff|noValueMin|20.0|95.0|below|66.0\n"
+ "\nSTARTGROUP\tuniprot\n"
+ "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
fr, false, false);
String gffHeader = "##gff-version 2\n";
assertEquals(gffHeader, exported);
- exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
- true, false);
+ exported = featuresFile.printGffFormat(al.getSequencesArray(), fr, true,
+ false);
assertEquals(gffHeader, exported);
/*
new SequenceFeature("Domain", "Cath", 0, 0, 0f, "Uniprot"));
al.getSequenceAt(0).addSequenceFeature(
new SequenceFeature("METAL", "Cath", 39, 39, 1.2f, null));
- al.getSequenceAt(1)
- .addSequenceFeature(
- new SequenceFeature("GAMMA-TURN", "Turn", 36, 38, 2.1f,
- "s3dm"));
+ al.getSequenceAt(1).addSequenceFeature(new SequenceFeature("GAMMA-TURN",
+ "Turn", 36, 38, 2.1f, "s3dm"));
SequenceFeature sf = new SequenceFeature("Pfam", "", 20, 20, 0f,
"Uniprot");
sf.setStrand("+");
*/
fr.setGroupVisibility("Uniprot", true);
fr.setGroupVisibility("s3dm", false);
- exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
- true, false);
+ exported = featuresFile.printGffFormat(al.getSequencesArray(), fr, true,
+ false);
String expected = gffHeader
+ "FER_CAPAA\tUniprot\tDomain\t0\t0\t0.0\t.\t.\n";
assertEquals(expected, exported);
exported = featuresFile.printGffFormat(al.getSequencesArray(), fr,
false, false);
// Pfam feature columns include strand(+), phase(2), attributes
- expected = gffHeader
- + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
- // CSQ output as CSQ=att1=value1,att2=value2
- // note all commas are encoded here which is wrong - it should be
- // SIFT=benign,mostly benign,cloudy%2C with meatballs
+ expected = gffHeader + "FER_CAPAA\tCath\tMETAL\t39\t39\t1.2\t.\t.\n"
+ // CSQ output as CSQ=att1=value1,att2=value2
+ // note all commas are encoded here which is wrong - it should be
+ // SIFT=benign,mostly benign,cloudy%2C with meatballs
+ "FER_CAPAN\tUniprot\tPfam\t20\t20\t0.0\t+\t2\tx=y;black=white;"
+ "CSQ=SIFT=benign%2Cmostly benign%2Ccloudy%2C with meatballs,consequence=missense_variant\n"
+ "FER_CAPAN\ts3dm\tGAMMA-TURN\t36\t38\t2.1\t.\t.\n";
sf2.setValue("clin_sig", "Benign");
sf2.setValue("AF", "46");
al.getSequenceAt(0).addSequenceFeature(sf2);
-
+
FeaturesFile featuresFile = new FeaturesFile();
FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
final String gffHeader = "##gff-version 2\n";
sf2.setValue("clin_sig", "Benign");
sf2.setValue("AF", "46");
al.getSequenceAt(0).addSequenceFeature(sf2);
-
+
FeaturesFile featuresFile = new FeaturesFile();
FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
fr.findAllFeatures(true);
-
+
fr.setVisible("METAL");
fr.setColour("METAL", new FeatureColour(Color.PINK));
- String exported = featuresFile.printJalviewFormat(
- al.getSequencesArray(),
- fr, false, false);
+ String exported = featuresFile
+ .printJalviewFormat(al.getSequencesArray(), fr, false, false);
String expected = "METAL\tffafaf\n\nSTARTGROUP\tgrp1\n"
+ "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
+ "ENDGROUP\tgrp1\n\nSTARTGROUP\tgrp2\n"
+ "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n"
+ "ENDGROUP\tgrp2\n";
assertEquals(expected, exported);
-
+
/*
* now threshold to Score > 1.1 - should exclude sf2
* (and there should be no empty STARTGROUP/ENDGROUP output)
+ "Cath\tFER_CAPAA\t-1\t39\t39\tMETAL\t1.2\n"
+ "ENDGROUP\tgrp1\n";
assertEquals(expected, exported);
-
+
/*
* remove threshold and check sf2 is exported
*/
+ "Cath\tFER_CAPAA\t-1\t41\t41\tMETAL\t0.6\n"
+ "ENDGROUP\tgrp2\n";
assertEquals(expected, exported);
-
+
/*
* filter on (clin_sig contains Benign) - should include sf2 and exclude sf1
*/
for (FileFormatI ff : FileFormat.values())
{
assertSame(ff, formats.forName(ff.getName()));
- assertSame(ff, formats.forName(ff.getName().toUpperCase(Locale.ROOT)));
- assertSame(ff, formats.forName(ff.getName().toLowerCase(Locale.ROOT)));
+ assertSame(ff,
+ formats.forName(ff.getName().toUpperCase(Locale.ROOT)));
+ assertSame(ff,
+ formats.forName(ff.getName().toLowerCase(Locale.ROOT)));
}
assertNull(formats.forName(null));
assertNull(formats.forName("rubbish"));
public void testIsGzipInputStream() throws IOException
{
InputStream is = new FileInputStream(ALIGN_FILE);
-
+
/*
* first try fails - FileInputStream does not support mark/reset
*/
assertFalse(FileParse.isGzipStream(is));
-
+
/*
* wrap in a BufferedInputStream and try again
*/
is = new BufferedInputStream(is, 16);
assertTrue(FileParse.isGzipStream(is));
-
+
/*
* check recognition of non-gzipped input
*/
assertFalse(FileParse.isGzipStream(new BufferedInputStream(
- new ByteArrayInputStream("NOT A GZIP".getBytes()))));
+ new ByteArrayInputStream("NOT A GZIP".getBytes()))));
}
@Test(groups = { "Functional" })
* special case: MSF always uses '.' as gap character
*/
sequenceString = adjustForGapTreatment(sequenceString, gap, format);
- assertEquals(
- String.format("Sequence %d: %s", i, seqs[i].getName()),
+ assertEquals(String.format("Sequence %d: %s", i, seqs[i].getName()),
seqs[i].getSequenceAsString(), sequenceString);
i++;
}
} catch (IOException e)
{
- fail(String
- .format("Format %s failed with %s", format, e.getMessage()));
+ fail(String.format("Format %s failed with %s", format,
+ e.getMessage()));
}
}
grpSeqs.add(seqs[2]);
grpSeqs.add(seqs[3]);
grpSeqs.add(seqs[4]);
- SequenceGroup seqGrp = new SequenceGroup(grpSeqs,
- "JGroup:1883305585",
+ SequenceGroup seqGrp = new SequenceGroup(grpSeqs, "JGroup:1883305585",
null, true, true, false, 21, 29);
- ColourSchemeI scheme = ColourSchemeMapper.getJalviewColourScheme(
- "zappo", seqGrp);
+ ColourSchemeI scheme = ColourSchemeMapper
+ .getJalviewColourScheme("zappo", seqGrp);
seqGrp.cs.setColourScheme(scheme);
seqGrp.setShowNonconserved(false);
seqGrp.setDescription(null);
AlignFrame.DEFAULT_HEIGHT);
af.getViewport().setShowSequenceFeatures(jf.isShowSeqFeatures());
String colourSchemeName = jf.getGlobalColourScheme();
- ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
- colourSchemeName, alignment);
+ ColourSchemeI cs = ColourSchemeMapper
+ .getJalviewColourScheme(colourSchemeName, alignment);
af.changeColour(cs);
af.getViewport().setFeaturesDisplayed(jf.getDisplayedFeatures());
- formatAdapter = new AppletFormatAdapter(af.alignPanel, exportSettings);
+ formatAdapter = new AppletFormatAdapter(af.alignPanel,
+ exportSettings);
String jsonOutput = formatAdapter.formatSequences(FileFormat.Json,
af.alignPanel.getAlignment(), false);
SequenceGroup sg = new SequenceGroup();
sg.addSequence(_alignment.getSequenceAt(0), false);
sg.setColourScheme(null);
- ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
- ResidueColourScheme.NONE, _alignment);
+ ColourSchemeI cs = ColourSchemeMapper
+ .getJalviewColourScheme(ResidueColourScheme.NONE, _alignment);
alignFrame.changeColour(cs);
- alignFrame.getViewport().setFeaturesDisplayed(
- bioJsonFile.getDisplayedFeatures());
+ alignFrame.getViewport()
+ .setFeaturesDisplayed(bioJsonFile.getDisplayedFeatures());
formatAdapter = new AppletFormatAdapter(alignFrame.alignPanel,
exportSettings);
// export BioJSON string
for (AlignmentAnnotation annot : testAlignment.getAlignmentAnnotation())
{
AlignmentAnnotation expectedAnnot = expectedAnnots.get(annot.label);
- AssertJUnit.assertTrue("Failed AlignmentAnnotation Test for >>> "
- + annot.label, isAnnotationMatched(expectedAnnot, annot));
+ AssertJUnit.assertTrue(
+ "Failed AlignmentAnnotation Test for >>> " + annot.label,
+ isAnnotationMatched(expectedAnnot, annot));
passedCount++;
}
AssertJUnit.assertEquals("Some Sequences did not pass the test",
System.out.println("Testing >>> " + actualSeq.getName());
if (expectedSeq.getName().equals(actualSeq.getName())
- && expectedSeq.getSequenceAsString().equals(
- actualSeq.getSequenceAsString())
+ && expectedSeq.getSequenceAsString()
+ .equals(actualSeq.getSequenceAsString())
&& expectedSeq.getStart() == actualSeq.getStart()
&& expectedSeq.getEnd() == actualSeq.getEnd()
&& featuresMatched(expectedSeq, actualSeq))
+ actualGrp.getIgnoreGapsConsensus());
System.out.println(expectedGrp.getSequences().size() + " | "
+ actualGrp.getSequences().size());
- System.out.println(expectedGrp.getStartRes() + " | "
- + actualGrp.getStartRes());
- System.out.println(expectedGrp.getEndRes() + " | "
- + actualGrp.getEndRes());
+ System.out.println(
+ expectedGrp.getStartRes() + " | " + actualGrp.getStartRes());
+ System.out.println(
+ expectedGrp.getEndRes() + " | " + actualGrp.getEndRes());
System.out.println(expectedGrp.cs.getColourScheme() + " | "
+ actualGrp.cs.getColourScheme());
- boolean colourSchemeMatches = (expectedGrp.cs.getColourScheme() == null && actualGrp.cs
- .getColourScheme() == null)
+ boolean colourSchemeMatches = (expectedGrp.cs.getColourScheme() == null
+ && actualGrp.cs.getColourScheme() == null)
|| expectedGrp.cs.getColourScheme().getClass()
.equals(actualGrp.cs.getColourScheme().getClass());
if (expectedGrp.getName().equals(actualGrp.getName())
&& expectedGrp.getIgnoreGapsConsensus() == actualGrp
.getIgnoreGapsConsensus()
&& colourSchemeMatches
- && expectedGrp.getSequences().size() == actualGrp
- .getSequences().size()
+ && expectedGrp.getSequences().size() == actualGrp.getSequences()
+ .size()
&& expectedGrp.getStartRes() == actualGrp.getStartRes()
&& expectedGrp.getEndRes() == actualGrp.getEndRes())
{
*/
if (!in.equals(out))
{
- System.err.println("Mismatch of " + in.toString() + " "
- + out.toString());
+ System.err.println(
+ "Mismatch of " + in.toString() + " " + out.toString());
return false;
}
/*
{
if (m1 != null || m2 != null)
{
- System.err
- .println("only one SequenceFeature.otherDetails is not null");
+ System.err.println(
+ "only one SequenceFeature.otherDetails is not null");
return false;
}
else
System.err.println(key + " in only one otherDetails");
return false;
}
- if (m1.get(key) == null && m2.get(key) != null || m1.get(key) != null
- && m2.get(key) == null || !m1.get(key).equals(m2.get(key)))
+ if (m1.get(key) == null && m2.get(key) != null
+ || m1.get(key) != null && m2.get(key) == null
+ || !m1.get(key).equals(m2.get(key)))
{
System.err.println(key + " values in otherDetails don't match");
return false;
AlignmentI copy = new Alignment(testAlignment);
SequenceGroup sg = testAlignment.getGroups().get(0);
SequenceGroup copySg = new SequenceGroup(new ArrayList<SequenceI>(),
- sg.getName(),
- null, sg.getDisplayBoxes(), sg.getDisplayText(),
+ sg.getName(), null, sg.getDisplayBoxes(), sg.getDisplayText(),
sg.getColourText(), sg.getStartRes(), sg.getEndRes());
for (SequenceI seq : sg.getSequences())
{
AlignFrame af = new AlignFrame(copy, copy.getWidth(), copy.getHeight());
AppletFormatAdapter formatAdapter = new AppletFormatAdapter(
af.alignPanel);
- String jsonOutput = formatAdapter.formatSequences(FileFormat.Json,
- copy, false);
+ String jsonOutput = formatAdapter.formatSequences(FileFormat.Json, copy,
+ false);
formatAdapter = new AppletFormatAdapter();
AlignmentI newAlignment = formatAdapter.readFile(jsonOutput,
DataSourceType.PASTE, FileFormat.Json);
* set news feed last read to a future time to ensure no
* 'unread' news item is displayed
*/
- Date oneHourFromNow = new Date(System.currentTimeMillis() + 3600 * 1000);
+ Date oneHourFromNow = new Date(
+ System.currentTimeMillis() + 3600 * 1000);
Cache.setDateProperty("JALVIEW_NEWS_RSS_LASTMODIFIED", oneHourFromNow);
Jalview.main(new String[] {});
@BeforeClass(alwaysRun = true)
public static void setUpBeforeClass() throws Exception
{
- jalview.bin.Jalview.main(new String[] { "-props",
- "test/jalview/io/testProps.jvprops" });
+ jalview.bin.Jalview
+ .main(new String[]
+ { "-props", "test/jalview/io/testProps.jvprops" });
}
/**
sg.setStartRes(1);
sg.setEndRes(7);
af.getViewport().setSelectionGroup(sg);
- String fseqs = new FormatAdapter(af.alignPanel).formatSequences(
- FileFormat.Fasta, af.alignPanel, true);
+ String fseqs = new FormatAdapter(af.alignPanel)
+ .formatSequences(FileFormat.Fasta, af.alignPanel, true);
assertTrue("Couldn't find '.' in the exported region\n" + fseqs,
fseqs.indexOf(".") > -1);
}
public void testGetExtension()
{
assertEquals(JalviewFileView.getExtension(new File("text.txt")), "txt");
- assertEquals(JalviewFileView.getExtension(new File(
- "/a/longer/file/path/text.png.TXT")), "txt");
- assertNull(JalviewFileView.getExtension(new File(
- "/a/longer/file/path/text.")));
- assertNull(JalviewFileView.getExtension(new File(
- "/a/longer/file/path/text")));
+ assertEquals(JalviewFileView.getExtension(
+ new File("/a/longer/file/path/text.png.TXT")), "txt");
+ assertNull(JalviewFileView
+ .getExtension(new File("/a/longer/file/path/text.")));
+ assertNull(JalviewFileView
+ .getExtension(new File("/a/longer/file/path/text")));
}
@Test(groups = "Functional")
@Parameters
public static Collection data()
{
- return Arrays
- .asList(new Object[][] {
-
- new String[] {
- "Simple uniref50 newick",
- "(((FER_BRANA:128.0,FER3_RAPSA:128.0):50.75,FER_CAPAA:178.75):121.94443,(Q93Z60_ARATH:271.45456,((O80429_MAIZE:183.0,FER1_MAIZE:183.0):30.5,((Q7XA98_TRIPR:90.0,FER1_PEA:90.0):83.32143,(((FER2_ARATH:64.0,FER1_ARATH:64.0):94.375,(FER1_SPIOL:124.5,FER1_MESCR:124.5):33.875):6.4166718,((Q93XJ9_SOLTU:33.5,FER1_SOLLC:33.5):49.0,FER_CAPAN:82.5):82.29167):8.529755):40.178574):57.95456):29.239868);" },
- new String[] {
- "Tree with quotes",
- "('Syn_PROSU-1_IIh_3d(CA4)|CK_Syn_PROSU-1_1907':1.0638313,'Syn_MINOS11_5.3_3d(CA4)|CK_Syn_MINOS11_750':1.063831);" },
- new String[] {
- "Tree with double escaped comma in node",
- "('Syn_PROSU-1_IIh_3d(CA4)|CK_Syn_PROSU-1_1907':1.0638313,'Syn_MINOS11_5.3_3d(CA4)''|CK_Syn_MINOS11_750':1.063831);" } });
+ return Arrays.asList(new Object[][] {
+
+ new String[]
+ { "Simple uniref50 newick",
+ "(((FER_BRANA:128.0,FER3_RAPSA:128.0):50.75,FER_CAPAA:178.75):121.94443,(Q93Z60_ARATH:271.45456,((O80429_MAIZE:183.0,FER1_MAIZE:183.0):30.5,((Q7XA98_TRIPR:90.0,FER1_PEA:90.0):83.32143,(((FER2_ARATH:64.0,FER1_ARATH:64.0):94.375,(FER1_SPIOL:124.5,FER1_MESCR:124.5):33.875):6.4166718,((Q93XJ9_SOLTU:33.5,FER1_SOLLC:33.5):49.0,FER_CAPAN:82.5):82.29167):8.529755):40.178574):57.95456):29.239868);" },
+ new String[]
+ { "Tree with quotes",
+ "('Syn_PROSU-1_IIh_3d(CA4)|CK_Syn_PROSU-1_1907':1.0638313,'Syn_MINOS11_5.3_3d(CA4)|CK_Syn_MINOS11_750':1.063831);" },
+ new String[]
+ { "Tree with double escaped comma in node",
+ "('Syn_PROSU-1_IIh_3d(CA4)|CK_Syn_PROSU-1_1907':1.0638313,'Syn_MINOS11_5.3_3d(CA4)''|CK_Syn_MINOS11_750':1.063831);" } });
};
String name, testTree;
stage = "Compare original and generated tree" + treename;
Vector<SequenceNode> oseqs, nseqs;
- oseqs = new TreeModel(new SequenceI[0], null, nf).findLeaves(nf
- .getTree());
+ oseqs = new TreeModel(new SequenceI[0], null, nf)
+ .findLeaves(nf.getTree());
AssertJUnit.assertTrue(stage + "No nodes in original tree.",
oseqs.size() > 0);
SequenceI[] olsqs = new SequenceI[oseqs.size()];
olsqs[i] = (SequenceI) oseqs.get(i).element();
}
nseqs = new TreeModel(new SequenceI[0], null, nf_regen)
- .findLeaves(nf_regen
- .getTree());
+ .findLeaves(nf_regen.getTree());
AssertJUnit.assertTrue(stage + "No nodes in regerated tree.",
nseqs.size() > 0);
SequenceI[] nsqs = new SequenceI[nseqs.size()];
{
nsqs[i] = (SequenceI) nseqs.get(i).element();
}
- AssertJUnit.assertTrue(stage
- + " Different number of leaves (original " + olsqs.length
- + " and regen " + nsqs.length + ")",
+ AssertJUnit.assertTrue(
+ stage + " Different number of leaves (original "
+ + olsqs.length + " and regen " + nsqs.length + ")",
olsqs.length == nsqs.length);
- SequenceIdMatcher omatcher = new SequenceIdMatcher(olsqs), nmatcher = new SequenceIdMatcher(
- nsqs);
+ SequenceIdMatcher omatcher = new SequenceIdMatcher(olsqs),
+ nmatcher = new SequenceIdMatcher(nsqs);
SequenceI[] osmatches = omatcher.findIdMatch(nsqs);
SequenceI[] nsmatches = nmatcher.findIdMatch(olsqs);
@Test(groups = "Functional")
public void testPfamFormatNoLimits() throws IOException
{
- AlignmentI al = new AppletFormatAdapter().readFile("ASEQ"
- + '\t' + "...--FFAFAFF--", DataSourceType.PASTE,
+ AlignmentI al = new AppletFormatAdapter().readFile(
+ "ASEQ" + '\t' + "...--FFAFAFF--", DataSourceType.PASTE,
FileFormat.Pfam);
Assert.assertEquals(1, al.getHeight(), "Wrong number of sequences");
Assert.assertTrue(al.hasValidSequence(),
@Test(groups = "Functional")
public void testPfamFormatValidLimits() throws IOException
{
- AlignmentI al = new AppletFormatAdapter().readFile("ASEQ/15-25" + '\t'
- + "...--FFAFAFF--", DataSourceType.PASTE, FileFormat.Pfam);
+ AlignmentI al = new AppletFormatAdapter().readFile(
+ "ASEQ/15-25" + '\t' + "...--FFAFAFF--", DataSourceType.PASTE,
+ FileFormat.Pfam);
Assert.assertEquals(1, al.getHeight(), "Wrong number of sequences");
Assert.assertTrue(al.hasValidSequence(),
"Didn't extract limits from PFAM ID");
/**
* Test file for {@link PhylipFile}.
*
- * Tests use example data obtained from <a
- * href="http://www.molecularevolution.org/resources/fileformats"
+ * Tests use example data obtained from
+ * <a href="http://www.molecularevolution.org/resources/fileformats"
* >molecularrevolution.org<a>.
*
* @author David Corsar
private static Map<String, String> getTestData()
{
Map<String, String> data = new HashMap<String, String>();
- data.put(
- "Cow",
+ data.put("Cow",
"ATGGCATATCCCATACAACTAGGATTCCAAGATGCAACATCACCAATCATAGAAGAACTACTTCACTTTCATGACCACACGCTAATAATTGTCTTCTTAATTAGCTCATTAGTACTTTACATTATTTCACTAATACTAACGACAAAGCTGACCCATACAAGCACGATAGATGCACAAGAAGTAGAGACAATCTGAACCATTCTGCCCGCCATCATCTTAATTCTAATTGCTCTTCCTTCTTTACGAATTCTATACATAATAGATGAAATCAATAACCCATCTCTTACAGTAAAAACCATAGGACATCAGTGATACTGAAGCTATGAGTATACAGATTATGAGGACTTAAGCTTCGACTCCTACATAATTCCAACATCAGAATTAAAGCCAGGGGAGCTACGACTATTAGAAGTCGATAATCGAGTTGTACTACCAATAGAAATAACAATCCGAATGTTAGTCTCCTCTGAAGACGTATTACACTCATGAGCTGTGCCCTCTCTAGGACTAAAAACAGACGCAATCCCAGGCCGTCTAAACCAAACAACCCTTATATCGTCCCGTCCAGGCTTATATTACGGTCAATGCTCAGAAATTTGCGGGTCAAACCACAGTTTCATACCCATTGTCCTTGAGTTAGTCCCACTAAAGTACTTTGAAAAATGATCTGCGTCAATATTA---------------------TAA");
- data.put(
- "Carp",
+ data.put("Carp",
"ATGGCACACCCAACGCAACTAGGTTTCAAGGACGCGGCCATACCCGTTATAGAGGAACTTCTTCACTTCCACGACCACGCATTAATAATTGTGCTCCTAATTAGCACTTTAGTTTTATATATTATTACTGCAATGGTATCAACTAAACTTACTAATAAATATATTCTAGACTCCCAAGAAATCGAAATCGTATGAACCATTCTACCAGCCGTCATTTTAGTACTAATCGCCCTGCCCTCCCTACGCATCCTGTACCTTATAGACGAAATTAACGACCCTCACCTGACAATTAAAGCAATAGGACACCAATGATACTGAAGTTACGAGTATACAGACTATGAAAATCTAGGATTCGACTCCTATATAGTACCAACCCAAGACCTTGCCCCCGGACAATTCCGACTTCTGGAAACAGACCACCGAATAGTTGTTCCAATAGAATCCCCAGTCCGTGTCCTAGTATCTGCTGAAGACGTGCTACATTCTTGAGCTGTTCCATCCCTTGGCGTAAAAATGGACGCAGTCCCAGGACGACTAAATCAAGCCGCCTTTATTGCCTCACGCCCAGGGGTCTTTTACGGACAATGCTCTGAAATTTGTGGAGCTAATCACAGCTTTATACCAATTGTAGTTGAAGCAGTACCTCTCGAACACTTCGAAAACTGATCCTCATTAATACTAGAAGACGCCTCGCTAGGAAGCTAA");
- data.put(
- "Chicken",
+ data.put("Chicken",
"ATGGCCAACCACTCCCAACTAGGCTTTCAAGACGCCTCATCCCCCATCATAGAAGAGCTCGTTGAATTCCACGACCACGCCCTGATAGTCGCACTAGCAATTTGCAGCTTAGTACTCTACCTTCTAACTCTTATACTTATAGAAAAACTATCA---TCAAACACCGTAGATGCCCAAGAAGTTGAACTAATCTGAACCATCCTACCCGCTATTGTCCTAGTCCTGCTTGCCCTCCCCTCCCTCCAAATCCTCTACATAATAGACGAAATCGACGAACCTGATCTCACCCTAAAAGCCATCGGACACCAATGATACTGAACCTATGAATACACAGACTTCAAGGACCTCTCATTTGACTCCTACATAACCCCAACAACAGACCTCCCCCTAGGCCACTTCCGCCTACTAGAAGTCGACCATCGCATTGTAATCCCCATAGAATCCCCCATTCGAGTAATCATCACCGCTGATGACGTCCTCCACTCATGAGCCGTACCCGCCCTCGGGGTAAAAACAGACGCAATCCCTGGACGACTAAATCAAACCTCCTTCATCACCACTCGACCAGGAGTGTTTTACGGACAATGCTCAGAAATCTGCGGAGCTAACCACAGCTACATACCCATTGTAGTAGAGTCTACCCCCCTAAAACACTTTGAAGCCTGATCCTCACTA------------------CTGTCATCTTAA");
- data.put(
- "Human",
+ data.put("Human",
"ATGGCACATGCAGCGCAAGTAGGTCTACAAGACGCTACTTCCCCTATCATAGAAGAGCTTATCACCTTTCATGATCACGCCCTCATAATCATTTTCCTTATCTGCTTCCTAGTCCTGTATGCCCTTTTCCTAACACTCACAACAAAACTAACTAATACTAACATCTCAGACGCTCAGGAAATAGAAACCGTCTGAACTATCCTGCCCGCCATCATCCTAGTCCTCATCGCCCTCCCATCCCTACGCATCCTTTACATAACAGACGAGGTCAACGATCCCTCCCTTACCATCAAATCAATTGGCCACCAATGGTACTGAACCTACGAGTACACCGACTACGGCGGACTAATCTTCAACTCCTACATACTTCCCCCATTATTCCTAGAACCAGGCGACCTGCGACTCCTTGACGTTGACAATCGAGTAGTACTCCCGATTGAAGCCCCCATTCGTATAATAATTACATCACAAGACGTCTTGCACTCATGAGCTGTCCCCACATTAGGCTTAAAAACAGATGCAATTCCCGGACGTCTAAACCAAACCACTTTCACCGCTACACGACCGGGGGTATACTACGGTCAATGCTCTGAAATCTGTGGAGCAAACCACAGTTTCATGCCCATCGTCCTAGAATTAATTCCCCTAAAAATCTTTGAAATA---------------------GGGCCCGTATTTACCCTATAG");
- data.put(
- "Loach",
+ data.put("Loach",
"ATGGCACATCCCACACAATTAGGATTCCAAGACGCGGCCTCACCCGTAATAGAAGAACTTCTTCACTTCCATGACCATGCCCTAATAATTGTATTTTTGATTAGCGCCCTAGTACTTTATGTTATTATTACAACCGTCTCAACAAAACTCACTAACATATATATTTTGGACTCACAAGAAATTGAAATCGTATGAACTGTGCTCCCTGCCCTAATCCTCATTTTAATCGCCCTCCCCTCACTACGAATTCTATATCTTATAGACGAGATTAATGACCCCCACCTAACAATTAAGGCCATGGGGCACCAATGATACTGAAGCTACGAGTATACTGATTATGAAAACTTAAGTTTTGACTCCTACATAATCCCCACCCAGGACCTAACCCCTGGACAATTCCGGCTACTAGAGACAGACCACCGAATGGTTGTTCCCATAGAATCCCCTATTCGCATTCTTGTTTCCGCCGAAGATGTACTACACTCCTGGGCCCTTCCAGCCATGGGGGTAAAGATAGACGCGGTCCCAGGACGCCTTAACCAAACCGCCTTTATTGCCTCCCGCCCCGGGGTATTCTATGGGCAATGCTCAGAAATCTGTGGAGCAAACCACAGCTTTATACCCATCGTAGTAGAAGCGGTCCCACTATCTCACTTCGAAAACTGGTCCACCCTTATACTAAAAGACGCCTCACTAGGAAGCTAA");
- data.put(
- "Mouse",
+ data.put("Mouse",
"ATGGCCTACCCATTCCAACTTGGTCTACAAGACGCCACATCCCCTATTATAGAAGAGCTAATAAATTTCCATGATCACACACTAATAATTGTTTTCCTAATTAGCTCCTTAGTCCTCTATATCATCTCGCTAATATTAACAACAAAACTAACACATACAAGCACAATAGATGCACAAGAAGTTGAAACCATTTGAACTATTCTACCAGCTGTAATCCTTATCATAATTGCTCTCCCCTCTCTACGCATTCTATATATAATAGACGAAATCAACAACCCCGTATTAACCGTTAAAACCATAGGGCACCAATGATACTGAAGCTACGAATATACTGACTATGAAGACCTATGCTTTGATTCATATATAATCCCAACAAACGACCTAAAACCTGGTGAACTACGACTGCTAGAAGTTGATAACCGAGTCGTTCTGCCAATAGAACTTCCAATCCGTATATTAATTTCATCTGAAGACGTCCTCCACTCATGAGCAGTCCCCTCCCTAGGACTTAAAACTGATGCCATCCCAGGCCGACTAAATCAAGCAACAGTAACATCAAACCGACCAGGGTTATTCTATGGCCAATGCTCTGAAATTTGTGGATCTAACCATAGCTTTATGCCCATTGTCCTAGAAATGGTTCCACTAAAATATTTCGAAAACTGATCTGCTTCAATAATT---------------------TAA");
- data.put(
- "Rat",
+ data.put("Rat",
"ATGGCTTACCCATTTCAACTTGGCTTACAAGACGCTACATCACCTATCATAGAAGAACTTACAAACTTTCATGACCACACCCTAATAATTGTATTCCTCATCAGCTCCCTAGTACTTTATATTATTTCACTAATACTAACAACAAAACTAACACACACAAGCACAATAGACGCCCAAGAAGTAGAAACAATTTGAACAATTCTCCCAGCTGTCATTCTTATTCTAATTGCCCTTCCCTCCCTACGAATTCTATACATAATAGACGAGATTAATAACCCAGTTCTAACAGTAAAAACTATAGGACACCAATGATACTGAAGCTATGAATATACTGACTATGAAGACCTATGCTTTGACTCCTACATAATCCCAACCAATGACCTAAAACCAGGTGAACTTCGTCTATTAGAAGTTGATAATCGGGTAGTCTTACCAATAGAACTTCCAATTCGTATACTAATCTCATCCGAAGACGTCCTGCACTCATGAGCCATCCCTTCACTAGGGTTAAAAACCGACGCAATCCCCGGCCGCCTAAACCAAGCTACAGTCACATCAAACCGACCAGGTCTATTCTATGGCCAATGCTCTGAAATTTGCGGCTCAAATCACAGCTTCATACCCATTGTACTAGAAATAGTGCCTCTAAAATATTTCGAAAACTGATCAGCTTCTATAATT---------------------TAA");
- data.put(
- "Seal",
+ data.put("Seal",
"ATGGCATACCCCCTACAAATAGGCCTACAAGATGCAACCTCTCCCATTATAGAGGAGTTACTACACTTCCATGACCACACATTAATAATTGTGTTCCTAATTAGCTCATTAGTACTCTACATTATCTCACTTATACTAACCACGAAACTCACCCACACAAGTACAATAGACGCACAAGAAGTGGAAACGGTGTGAACGATCCTACCCGCTATCATTTTAATTCTCATTGCCCTACCATCATTACGAATCCTCTACATAATGGACGAGATCAATAACCCTTCCTTGACCGTAAAAACTATAGGACATCAGTGATACTGAAGCTATGAGTACACAGACTACGAAGACCTGAACTTTGACTCATATATGATCCCCACACAAGAACTAAAGCCCGGAGAACTACGACTGCTAGAAGTAGACAATCGAGTAGTCCTCCCAATAGAAATAACAATCCGCATACTAATCTCATCAGAAGATGTACTCCACTCATGAGCCGTACCGTCCCTAGGACTAAAAACTGATGCTATCCCAGGACGACTAAACCAAACAACCCTAATAACCATACGACCAGGACTGTACTACGGTCAATGCTCAGAAATCTGTGGTTCAAACCACAGCTTCATACCTATTGTCCTCGAATTGGTCCCACTATCCCACTTCGAGAAATGATCTACCTCAATGCTT---------------------TAA");
- data.put(
- "Whale",
+ data.put("Whale",
"ATGGCATATCCATTCCAACTAGGTTTCCAAGATGCAGCATCACCCATCATAGAAGAGCTCCTACACTTTCACGATCATACACTAATAATCGTTTTTCTAATTAGCTCTTTAGTTCTCTACATTATTACCCTAATGCTTACAACCAAATTAACACATACTAGTACAATAGACGCCCAAGAAGTAGAAACTGTCTGAACTATCCTCCCAGCCATTATCTTAATTTTAATTGCCTTGCCTTCATTACGGATCCTTTACATAATAGACGAAGTCAATAACCCCTCCCTCACTGTAAAAACAATAGGTCACCAATGATATTGAAGCTATGAGTATACCGACTACGAAGACCTAAGCTTCGACTCCTATATAATCCCAACATCAGACCTAAAGCCAGGAGAACTACGATTATTAGAAGTAGATAACCGAGTTGTCTTACCTATAGAAATAACAATCCGAATATTAGTCTCATCAGAAGACGTACTCCACTCATGGGCCGTACCCTCCTTGGGCCTAAAAACAGATGCAATCCCAGGACGCCTAAACCAAACAACCTTAATATCAACACGACCAGGCCTATTTTATGGACAATGCTCAGAGATCTGCGGCTCAAACCACAGTTTCATACCAATTGTCCTAGAACTAGTACCCCTAGAAGTCTTTGAAAAATGATCTGTATCAATACTA---------------------TAA");
- data.put(
- "Frog",
+ data.put("Frog",
"ATGGCACACCCATCACAATTAGGTTTTCAAGACGCAGCCTCTCCAATTATAGAAGAATTACTTCACTTCCACGACCATACCCTCATAGCCGTTTTTCTTATTAGTACGCTAGTTCTTTACATTATTACTATTATAATAACTACTAAACTAACTAATACAAACCTAATGGACGCACAAGAGATCGAAATAGTGTGAACTATTATACCAGCTATTAGCCTCATCATAATTGCCCTTCCATCCCTTCGTATCCTATATTTAATAGATGAAGTTAATGATCCACACTTAACAATTAAAGCAATCGGCCACCAATGATACTGAAGCTACGAATATACTAACTATGAGGATCTCTCATTTGACTCTTATATAATTCCAACTAATGACCTTACCCCTGGACAATTCCGGCTGCTAGAAGTTGATAATCGAATAGTAGTCCCAATAGAATCTCCAACCCGACTTTTAGTTACAGCCGAAGACGTCCTCCACTCGTGAGCTGTACCCTCCTTGGGTGTCAAAACAGATGCAATCCCAGGACGACTTCATCAAACATCATTTATTGCTACTCGTCCGGGAGTATTTTACGGACAATGTTCAGAAATTTGCGGAGCAAACCACAGCTTTATACCAATTGTAGTTGAAGCAGTACCGCTAACCGACTTTGAAAACTGATCTTCATCAATACTA---GAAGCATCACTA------AGA");
return data;
}
Map<String, String> data = PhylipFileTests.getTestData();
for (SequenceI s : al.getSequencesArray())
{
- assertTrue(s.getName() + " sequence did not match test data.", data
- .get(s.getName()).equals(s.getSequenceAsString()));
+ assertTrue(s.getName() + " sequence did not match test data.",
+ data.get(s.getName()).equals(s.getSequenceAsString()));
}
}
@Test(groups = { "Functional" })
public void testRnamlToStockholmIO()
{
- StockholmFileTest.testFileIOwithFormat(new File(
- "examples/testdata/rna-alignment.xml"), FileFormat.Stockholm,
- -1, -1, true, true, true);
+ StockholmFileTest.testFileIOwithFormat(
+ new File("examples/testdata/rna-alignment.xml"),
+ FileFormat.Stockholm, -1, -1, true, true, true);
}
public class ScoreMatrixFileTest
{
- @AfterMethod(alwaysRun=true)
+ @AfterMethod(alwaysRun = true)
public void tearDownAfterTest()
{
ScoreModels.getInstance().reset();
*/
@Test(groups = "Functional")
public void testParseMatrix_ncbiMixedDelimiters()
- throws MalformedURLException,
- IOException
+ throws MalformedURLException, IOException
{
/*
* some messy but valid input data, with comma, space
fail("expected exception");
} catch (IOException e)
{
- assertEquals(
- e.getMessage(),
+ assertEquals(e.getMessage(),
"Format error: expected 'ScoreMatrix <name>', found 'ScoreMatrix' at line 1");
}
}
* @throws MalformedURLException
*/
@Test(groups = "Functional")
- public void testParseMatrix_ncbiFormat() throws MalformedURLException,
- IOException
+ public void testParseMatrix_ncbiFormat()
+ throws MalformedURLException, IOException
{
// input including comment and blank lines
String data = "ScoreMatrix MyTest\n#comment\n\n" + "\tA\tB\tC\n"
FileParse fp = new FileParse(data, DataSourceType.PASTE);
ScoreMatrixFile parser = new ScoreMatrixFile(fp);
ScoreMatrix sm = parser.parseMatrix();
-
+
assertNotNull(sm);
assertEquals(sm.getName(), "MyTest");
assertEquals(parser.getMatrixName(), "MyTest");
*/
@Test(groups = "Functional")
public void testParseMatrix_aaIndexBlosum80()
- throws MalformedURLException,
- IOException
+ throws MalformedURLException, IOException
{
FileParse fp = new FileParse("resources/scoreModel/blosum80.scm",
DataSourceType.FILE);
ScoreMatrixFile parser = new ScoreMatrixFile(fp);
ScoreMatrix sm = parser.parseMatrix();
-
+
assertNotNull(sm);
assertEquals(sm.getName(), "HENS920103");
assertEquals(sm.getDescription(),
* @throws MalformedURLException
*/
@Test(groups = "Functional")
- public void testParseMatrix_aaindexFormat() throws MalformedURLException,
- IOException
+ public void testParseMatrix_aaindexFormat()
+ throws MalformedURLException, IOException
{
/*
* aaindex format has scores for diagonal and below only
String data = "H MyTest\n" + "D My description\n" + "R PMID:1438297\n"
+ "A Authors, names\n" + "T Journal title\n"
+ "J Journal reference\n" + "* matrix in 1/3 Bit Units\n"
- + "M rows = ABC, cols = ABC\n" + "A\t1.0\n"
- + "B\t4.0\t5.0\n"
+ + "M rows = ABC, cols = ABC\n" + "A\t1.0\n" + "B\t4.0\t5.0\n"
+ "C\t7.0\t8.0\t9.0\n";
FileParse fp = new FileParse(data, DataSourceType.PASTE);
ScoreMatrixFile parser = new ScoreMatrixFile(fp);
ScoreMatrix sm = parser.parseMatrix();
-
+
assertNotNull(sm);
assertEquals(sm.getSize(), 3);
assertEquals(sm.getName(), "MyTest");
@Test(groups = "Functional")
public void testParseMatrix_aaindex_mMissing()
- throws MalformedURLException,
- IOException
+ throws MalformedURLException, IOException
{
/*
* aaindex format but M cols=, rows= is missing
*/
- String data = "H MyTest\n" + "A\t1.0\n"
- + "B\t4.0\t5.0\n"
+ String data = "H MyTest\n" + "A\t1.0\n" + "B\t4.0\t5.0\n"
+ "C\t7.0\t8.0\t9.0\n";
FileParse fp = new FileParse(data, DataSourceType.PASTE);
ScoreMatrixFile parser = new ScoreMatrixFile(fp);
@Test(groups = "Functional")
public void testParseMatrix_aaindex_rowColMismatch()
- throws MalformedURLException,
- IOException
+ throws MalformedURLException, IOException
{
String data = "H MyTest\n" + "M rows=ABC, cols=ABD\n" + "A\t1.0\n"
- + "B\t4.0\t5.0\n"
- + "C\t7.0\t8.0\t9.0\n";
+ + "B\t4.0\t5.0\n" + "C\t7.0\t8.0\t9.0\n";
FileParse fp = new FileParse(data, DataSourceType.PASTE);
ScoreMatrixFile parser = new ScoreMatrixFile(fp);
try
fail("Expected exception");
} catch (FileFormatException e)
{
- assertEquals(
- e.getMessage(),
+ assertEquals(e.getMessage(),
"Unexpected aaIndex score matrix data at line 2: M rows=ABC, cols=ABD rows != cols");
}
}
@Test(groups = "Functional")
public void testParseMatrix_aaindex_tooManyRows()
- throws MalformedURLException,
- IOException
+ throws MalformedURLException, IOException
{
String data = "H MyTest\n" + "M rows=ABC, cols=ABC\n" + "A\t1.0\n"
+ "B\t4.0\t5.0\n" + "C\t7.0\t8.0\t9.0\n" + "C\t7.0\t8.0\t9.0\n";
@Test(groups = "Functional")
public void testParseMatrix_aaindex_extraDataLines()
- throws MalformedURLException,
- IOException
+ throws MalformedURLException, IOException
{
String data = "H MyTest\n" + "M rows=ABC, cols=ABC\n" + "A\t1.0\n"
+ "B\t4.0\t5.0\n" + "C\t7.0\t8.0\t9.0\n" + "something extra\n";
@Test(groups = "Functional")
public void testParseMatrix_aaindex_tooFewColumns()
- throws MalformedURLException,
- IOException
+ throws MalformedURLException, IOException
{
String data = "H MyTest\n" + "M rows=ABC, cols=ABC\n" + "A\t1.0\n"
+ "B\t4.0\t5.0\n" + "C\t7.0\t8.0\n";
fail("Expected exception");
} catch (FileFormatException e)
{
- assertEquals(
- e.getMessage(),
+ assertEquals(e.getMessage(),
"Expected 3 scores at line 5: 'C\t7.0\t8.0' but found 2");
}
}
* @throws MalformedURLException
*/
@Test(groups = "Functional")
- public void testParse_ncbiFormat() throws MalformedURLException,
- IOException
+ public void testParse_ncbiFormat()
+ throws MalformedURLException, IOException
{
assertNull(ScoreModels.getInstance().getScoreModel("MyNewTest", null));
ScoreMatrixFile parser = new ScoreMatrixFile(fp);
parser.parse();
-
- ScoreMatrix sm = (ScoreMatrix) ScoreModels.getInstance().getScoreModel(
- "MyNewTest", null);
+
+ ScoreMatrix sm = (ScoreMatrix) ScoreModels.getInstance()
+ .getScoreModel("MyNewTest", null);
assertNotNull(sm);
assertEquals(sm.getName(), "MyNewTest");
assertEquals(parser.getMatrixName(), "MyNewTest");
SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
StringBuilder sb = new StringBuilder();
sb.append("123456");
- SequenceFeature sf = new SequenceFeature("disulfide bond", "desc", 1,
- 3, 1.2f, "group");
+ SequenceFeature sf = new SequenceFeature("disulfide bond", "desc", 1, 3,
+ 1.2f, "group");
// residuePos == 2 does not match start or end of feature, nothing done:
sar.appendFeature(sb, 2, null, sf, null, 0);
sfl.add(sf);
sfl.add(sf);
sfl.add(sf);
- int n = sar.appendFeatures(sb, 1, sfl,
- new FeatureRenderer(null), 200); // text should terminate before 200 characters
+ int n = sar.appendFeatures(sb, 1, sfl, new FeatureRenderer(null), 200); // text
+ // should
+ // terminate
+ // before
+ // 200
+ // characters
String s = sb.toString();
assertTrue(s.length() < 200);
assertEquals(n, 7); // should be 7 features left over
/*
* positional features are ignored
*/
- seq.addSequenceFeature(new SequenceFeature("Domain", "Ferredoxin", 5,
- 10, 1f, null));
+ seq.addSequenceFeature(
+ new SequenceFeature("Domain", "Ferredoxin", 5, 10, 1f, null));
sar.createSequenceAnnotationReport(sb, seq, true, true, null);
assertEquals("<i>SeqDesc</i>", sb.toString());
/*
* non-positional feature
*/
- seq.addSequenceFeature(new SequenceFeature("Type1", "Nonpos", 0, 0, 1f,
- null));
+ seq.addSequenceFeature(
+ new SequenceFeature("Type1", "Nonpos", 0, 0, 1f, null));
sb.setLength(0);
sar.createSequenceAnnotationReport(sb, seq, true, true, null);
String expected = "<i>SeqDesc<br/>Type1 ; Nonpos Score=1.0</i>";
* score is only appended for positional features so ignored here!
* minMax are not recorded for non-positional features
*/
- seq.addSequenceFeature(new SequenceFeature("Metal", "Desc", 0, 0, 5f,
- null));
+ seq.addSequenceFeature(
+ new SequenceFeature("Metal", "Desc", 0, 0, 5f, null));
FeatureRendererModel fr = new FeatureRenderer(null);
Map<String, float[][]> minmax = fr.getMinMax();
sar.createSequenceAnnotationReport(sb, seq, true, true, fr);
expected = "<i>SeqDesc<br/>Metal ; Desc<br/>Type1 ; Nonpos</i>";
assertEquals(expected, sb.toString());
-
+
/*
* 'linkonly' features are ignored; this is obsolete, as linkonly
* is only set by DasSequenceFetcher, and DAS is history
* 'clinical_significance' attribute is only included in description
* when used for feature colouring
*/
- SequenceFeature sf2 = new SequenceFeature("Variant", "Havana", 0, 0,
- 5f, null);
+ SequenceFeature sf2 = new SequenceFeature("Variant", "Havana", 0, 0, 5f,
+ null);
sf2.setValue(GffConstants.CLINICAL_SIGNIFICANCE, "benign");
seq.addSequenceFeature(sf2);
sb.setLength(0);
{
SequenceAnnotationReport sar = new SequenceAnnotationReport(false);
StringBuilder sb = new StringBuilder();
-
+
SequenceI seq = new Sequence("s1", "ABC");
int maxSources = (int) PA.getValue(sar, "MAX_SOURCES");
{
seq.addDBRef(new DBRefEntry("PDB" + i, "0", "3iu1"));
}
-
+
int maxRefs = (int) PA.getValue(sar, "MAX_REFS_PER_SOURCE");
for (int i = 0; i <= maxRefs; i++)
{
seq.addDBRef(new DBRefEntry("Uniprot", "0", "P3041" + i));
}
-
+
sar.createSequenceAnnotationReport(sb, seq, true, true, null, true);
String report = sb.toString();
- assertTrue(report
- .startsWith(
- "<i><br/>UNIPROT P30410, P30411, P30412, P30413,...<br/>PDB0 3iu1"));
- assertTrue(report
- .endsWith(
- "<br/>PDB7 3iu1<br/>PDB8,...<br/>(Output Sequence Details to list all database references)</i>"));
+ assertTrue(report.startsWith(
+ "<i><br/>UNIPROT P30410, P30411, P30412, P30413,...<br/>PDB0 3iu1"));
+ assertTrue(report.endsWith(
+ "<br/>PDB7 3iu1<br/>PDB8,...<br/>(Output Sequence Details to list all database references)</i>"));
}
/**
* feature at 11-12 on peptide maps to 110-115 on CDS
* here we test for tooltip at 113 (t)
*/
- SequenceFeature sf2 = new SequenceFeature("metal", "Fe", 11, 12,
- 2.3f, "Uniprot");
+ SequenceFeature sf2 = new SequenceFeature("metal", "Fe", 11, 12, 2.3f,
+ "Uniprot");
features.clear();
features.add(sf2);
mapping = new Mapping(peptide, map);
assertTrue(
Pattern.compile(
"^#=GS\\s+FER2_SPIOL(/\\d+-\\d+)?\\s+AC\\s+P00224$",
- Pattern.MULTILINE).matcher(toStockholm)
- .find(),
+ Pattern.MULTILINE).matcher(toStockholm).find(),
"Couldn't locate UNIPROT Accession in generated Stockholm file.");
AlignmentI fromStockholm = af.readFile(toStockholm,
DataSourceType.PASTE, FileFormat.Stockholm);
SequenceI importedSeq = fromStockholm.getSequenceAt(0);
- assertTrue(importedSeq.getDBRefs()
- .size() == 1,
+ assertTrue(importedSeq.getDBRefs().size() == 1,
"Expected just one database reference to be added to sequence.");
assertTrue(
- importedSeq.getDBRefs().get(0).getAccessionId().indexOf(
- " ") == -1,
+ importedSeq.getDBRefs().get(0).getAccessionId()
+ .indexOf(" ") == -1,
"Spaces were found in accession ID.");
List<DBRefEntry> dbrefs = DBRefUtils.searchRefs(importedSeq.getDBRefs(),
"P00224");
* with no dataloss
*
* @param f
- * - source datafile (IdentifyFile.identify()
- * should work with it)
+ * - source datafile (IdentifyFile.identify() should work with it)
* @param ioformat
- * - label for IO class used to write and read
- * back in the data from f
+ * - label for IO class used to write and read back in the data from
+ * f
* @param ignoreFeatures
* @param ignoreRowVisibility
* @param allowNullAnnotations
al.getSequenceAt(i).createDatasetSequence();
}
String outputfile = rf.formatSequences(ioformat, al, true);
- System.out.println("Output file in '" + ioformat + "':\n"
- + outputfile + "\n<<EOF\n");
+ System.out.println("Output file in '" + ioformat + "':\n" + outputfile
+ + "\n<<EOF\n");
// test for consistency in io
AlignmentI al_input = new AppletFormatAdapter().readFile(outputfile,
DataSourceType.PASTE, ioformat);
assertTrue(
"Number of sequence associated annotations wasn't at least "
- + nminseqann, numsqswithali >= nminseqann);
+ + nminseqann,
+ numsqswithali >= nminseqann);
} catch (Exception e)
{
assertNotNull("Original alignment was null", al);
assertNotNull("Generated alignment was null", al_input);
- assertTrue("Alignment dimension mismatch: original: " + al.getHeight()
- + "x" + al.getWidth() + ", generated: " + al_input.getHeight()
- + "x" + al_input.getWidth(),
+ assertTrue(
+ "Alignment dimension mismatch: original: " + al.getHeight()
+ + "x" + al.getWidth() + ", generated: "
+ + al_input.getHeight() + "x" + al_input.getWidth(),
al.getHeight() == al_input.getHeight()
&& al.getWidth() == al_input.getWidth());
if (!ignoreRowVisibility)
{
assertEquals("Visibility not identical.",
- aa_original[i].visible,
- aa_new[i].visible);
+ aa_original[i].visible, aa_new[i].visible);
}
assertEquals("Threshold line not identical.",
aa_original[i].threshold, aa_new[i].threshold);
// check sequences, annotation and features
SequenceI[] seq_original = new SequenceI[al.getSequencesArray().length];
seq_original = al.getSequencesArray();
- SequenceI[] seq_new = new SequenceI[al_input.getSequencesArray().length];
+ SequenceI[] seq_new = new SequenceI[al_input
+ .getSequencesArray().length];
seq_new = al_input.getSequencesArray();
List<SequenceFeature> sequenceFeatures_original;
List<SequenceFeature> sequenceFeatures_new;
String name = seq_original[i].getName();
int start = seq_original[i].getStart();
int end = seq_original[i].getEnd();
- System.out.println("Check sequence: " + name + "/" + start + "-"
- + end);
+ System.out
+ .println("Check sequence: " + name + "/" + start + "-" + end);
// search equal sequence
for (int in = 0; in < al_input.getSequencesArray().length; in++)
"Sequence Features were not equivalent"
+ (ignoreFeatures ? " ignoring." : ""),
ignoreFeatures
- || (seq_original[i].getSequenceFeatures() == null && seq_new[in]
- .getSequenceFeatures() == null)
- || (seq_original[i].getSequenceFeatures() != null && seq_new[in]
- .getSequenceFeatures() != null));
+ || (seq_original[i].getSequenceFeatures() == null
+ && seq_new[in]
+ .getSequenceFeatures() == null)
+ || (seq_original[i].getSequenceFeatures() != null
+ && seq_new[in]
+ .getSequenceFeatures() != null));
// compare sequence features
if (seq_original[i].getSequenceFeatures() != null
&& seq_new[in].getSequenceFeatures() != null)
.getSequenceFeatures();
sequenceFeatures_new = seq_new[in].getSequenceFeatures();
- assertEquals("different number of features", seq_original[i]
- .getSequenceFeatures().size(), seq_new[in]
- .getSequenceFeatures().size());
+ assertEquals("different number of features",
+ seq_original[i].getSequenceFeatures().size(),
+ seq_new[in].getSequenceFeatures().size());
for (int feat = 0; feat < seq_original[i].getSequenceFeatures()
.size(); feat++)
if (al.getSequenceAt(i).getAnnotation() != null
&& al_input.getSequenceAt(in).getAnnotation() != null)
{
- for (int j = 0; j < al.getSequenceAt(i).getAnnotation().length; j++)
+ for (int j = 0; j < al.getSequenceAt(i)
+ .getAnnotation().length; j++)
{
- if (al.getSequenceAt(i).getAnnotation()[j] != null
- && al_input.getSequenceAt(in).getAnnotation()[j] != null)
+ if (al.getSequenceAt(i).getAnnotation()[j] != null && al_input
+ .getSequenceAt(in).getAnnotation()[j] != null)
{
annot_original = al.getSequenceAt(i).getAnnotation()[j];
annot_new = al_input.getSequenceAt(in).getAnnotation()[j];
+ annot_new.annotations.length);
}
boolean isRna = annot_or.isRNA();
- assertTrue("Expected " + (isRna ? " valid RNA " : " no RNA ")
- + " secondary structure in the row.",
+ assertTrue(
+ "Expected " + (isRna ? " valid RNA " : " no RNA ")
+ + " secondary structure in the row.",
isRna == annot_new.isRNA());
for (int i = 0; i < annot_or.annotations.length; i++)
{
- Annotation an_or = annot_or.annotations[i], an_new = annot_new.annotations[i];
+ Annotation an_or = annot_or.annotations[i],
+ an_new = annot_new.annotations[i];
if (an_or != null && an_new != null)
{
{
if (an_or.secondaryStructure != an_new.secondaryStructure
|| ((Float.isNaN(an_or.value) != Float
- .isNaN(an_new.value)) || an_or.value != an_new.value))
+ .isNaN(an_new.value))
+ || an_or.value != an_new.value))
{
fail("Different RNA secondary structure at column " + i
+ " expected: [" + annot_or.annotations[i].toString()
{
// not RNA secondary structure, so expect all elements to match...
if ((an_or.isWhitespace() != an_new.isWhitespace())
- || !an_or.displayCharacter.trim().equals(
- an_new.displayCharacter.trim())
- || !("" + an_or.secondaryStructure).trim().equals(
- ("" + an_new.secondaryStructure).trim())
- || (an_or.description != an_new.description && !((an_or.description == null && an_new.description
- .trim().length() == 0)
- || (an_new.description == null && an_or.description
- .trim().length() == 0) || an_or.description
- .trim().equals(an_new.description.trim())))
- || !((Float.isNaN(an_or.value) && Float
- .isNaN(an_new.value)) || an_or.value == an_new.value))
+ || !an_or.displayCharacter.trim()
+ .equals(an_new.displayCharacter.trim())
+ || !("" + an_or.secondaryStructure).trim()
+ .equals(("" + an_new.secondaryStructure).trim())
+ || (an_or.description != an_new.description
+ && !((an_or.description == null
+ && an_new.description.trim()
+ .length() == 0)
+ || (an_new.description == null
+ && an_or.description.trim()
+ .length() == 0)
+ || an_or.description.trim().equals(
+ an_new.description.trim())))
+ || !((Float.isNaN(an_or.value)
+ && Float.isNaN(an_new.value))
+ || an_or.value == an_new.value))
{
fail("Annotation Element Mismatch\nElement " + i
+ " in original: " + annot_or.annotations[i].toString()
}
if (!thrown)
{
- fail("Expected difference for [" + an_orig + "] and [" + an_new + "]");
+ fail("Expected difference for [" + an_orig + "] and [" + an_new
+ + "]");
}
}
+
private AlignmentAnnotation makeAnnot(Annotation ae)
{
- return new AlignmentAnnotation("label", "description", new Annotation[]
- { ae });
+ return new AlignmentAnnotation("label", "description",
+ new Annotation[]
+ { ae });
}
- @Test(groups={"Functional"})
+ @Test(groups = { "Functional" })
public void testAnnotationEquivalence()
{
AlignmentAnnotation one = makeAnnot(new Annotation("", "", ' ', 1));
- AlignmentAnnotation anotherOne = makeAnnot(new Annotation("", "", ' ',
- 1));
- AlignmentAnnotation sheet = makeAnnot(new Annotation("","",'E',0f));
- AlignmentAnnotation anotherSheet = makeAnnot(new Annotation("","",'E',0f));
- AlignmentAnnotation sheetWithLabel = makeAnnot(new Annotation("1", "",
- 'E', 0f));
- AlignmentAnnotation anotherSheetWithLabel = makeAnnot(new Annotation(
- "1", "", 'E', 0f));
- AlignmentAnnotation rnaNoDC = makeAnnot(new Annotation("","",'<',0f));
- AlignmentAnnotation anotherRnaNoDC = makeAnnot(new Annotation("","",'<',0f));
- AlignmentAnnotation rnaWithDC = makeAnnot(new Annotation("B", "", '<',
- 0f));
- AlignmentAnnotation anotherRnaWithDC = makeAnnot(new Annotation("B",
- "", '<', 0f));
-
+ AlignmentAnnotation anotherOne = makeAnnot(
+ new Annotation("", "", ' ', 1));
+ AlignmentAnnotation sheet = makeAnnot(new Annotation("", "", 'E', 0f));
+ AlignmentAnnotation anotherSheet = makeAnnot(
+ new Annotation("", "", 'E', 0f));
+ AlignmentAnnotation sheetWithLabel = makeAnnot(
+ new Annotation("1", "", 'E', 0f));
+ AlignmentAnnotation anotherSheetWithLabel = makeAnnot(
+ new Annotation("1", "", 'E', 0f));
+ AlignmentAnnotation rnaNoDC = makeAnnot(
+ new Annotation("", "", '<', 0f));
+ AlignmentAnnotation anotherRnaNoDC = makeAnnot(
+ new Annotation("", "", '<', 0f));
+ AlignmentAnnotation rnaWithDC = makeAnnot(
+ new Annotation("B", "", '<', 0f));
+ AlignmentAnnotation anotherRnaWithDC = makeAnnot(
+ new Annotation("B", "", '<', 0f));
+
// check self equivalence
for (boolean allowNull : new boolean[] { true, false })
{
if (p != q)
{
assertNotEqualSecondaryStructure("Should be different",
- aaSet.get(p), aaSet.get(q), false);
+ aaSet.get(p), aaSet.get(q), false);
}
else
{
}
String aliFile = ">Dm\nAAACCCUUUUACACACGGGAAAGGG";
+
String annFile = "JALVIEW_ANNOTATION\n# Created: Thu May 04 11:16:52 BST 2017\n\n"
+ "SEQUENCE_REF\tDm\nNO_GRAPH\tsecondary structure\tsecondary structure\t"
+ "(|(|(|(|, .|, .|, .|, .|)|)|)|)|\t0.0\nROWPROPERTIES\t"
+ "SEQUENCE_REF\tDm\nNO_GRAPH\tsecondary structure\tsecondary structure\t"
+ "(|(|(|(||{|{||{|{||)|)|)|)||}|}|}|}|\t0.0\nROWPROPERTIES\t"
+ "secondary structure\tscaletofit=true\tshowalllabs=true\tcentrelabs=false";
+
String annFileFullWuss = "JALVIEW_ANNOTATION\n# Created: Thu May 04 11:16:52 BST 2017\n\n"
+ "SEQUENCE_REF\tDm\nNO_GRAPH\tsecondary structure\tsecondary structure\t"
+ "(|(|(|(||{|{||[|[||)|)|)|)||}|}|]|]|\t0.0\nROWPROPERTIES\t"
"Shouldn't recognise '" + ch + "' as a WUSS bracket");
}
}
+
private static void roundTripSSForRNA(String aliFile, String annFile)
throws Exception
{
// this is the single sequence alignment and the SS annotations equivalent to
// the ones in file RnaSSTestFile
- String aliFileRnaSS = ">Test.sequence/1-14\n"
- + "GUACAAAAAAAAAA";
+ String aliFileRnaSS = ">Test.sequence/1-14\n" + "GUACAAAAAAAAAA";
+
String annFileRnaSSAlphaChars = "JALVIEW_ANNOTATION\n"
+ "# Created: Thu Aug 02 14:54:57 BST 2018\n" + "\n"
+ "NO_GRAPH\tSecondary Structure\tSecondary Structure\t<,<|(,(|E,E|H,H|B,B|h,h|e,e|b,b|(,(|E,E|),)|e,e|),)|>,>|\t2.0\n"
+ "\n"
+ "ROWPROPERTIES\tSecondary Structure\tscaletofit=true\tshowalllabs=true\tcentrelabs=false\n"
+ "\n" + "\n" + "ALIGNMENT\tID=RNA.SS.TEST\tTP=RNA;";
+
String wrongAnnFileRnaSSAlphaChars = "JALVIEW_ANNOTATION\n"
+ "# Created: Thu Aug 02 14:54:57 BST 2018\n" + "\n"
+ "NO_GRAPH\tSecondary Structure\tSecondary Structure\t<,<|(,(|H,H|E,E|B,B|h,h|e,e|b,b|(,(|E,E|),)|e,e|),)|>,>|\t2.0\n"
+ "\n"
+ "ROWPROPERTIES\tSecondary Structure\tscaletofit=true\tshowalllabs=true\tcentrelabs=false\n"
+ "\n" + "\n" + "ALIGNMENT\tID=RNA.SS.TEST\tTP=RNA;";
+
@Test(groups = { "Functional" })
public void stockholmFileRnaSSAlphaChars() throws Exception
{
}
char[] shouldBe = { '<', '(', 'E', 'H', 'B', 'h', 'e', 'b', '(', 'E',
')', 'e', ')', '>' };
- Assert.assertTrue(
- Arrays.equals(As, shouldBe),
- "Annotation is " + new String(As) + " but should be "
- + new String(shouldBe));
+ Assert.assertTrue(Arrays.equals(As, shouldBe), "Annotation is "
+ + new String(As) + " but should be " + new String(shouldBe));
// this should result in the same RNA SS Annotations
- AlignmentI newAl = new AppletFormatAdapter().readFile(
- aliFileRnaSS,
+ AlignmentI newAl = new AppletFormatAdapter().readFile(aliFileRnaSS,
DataSourceType.PASTE, jalview.io.FileFormat.Fasta);
AnnotationFile aaf = new AnnotationFile();
aaf.readAnnotationFile(newAl, annFileRnaSSAlphaChars,
+ "RNA SS A 2:" + newAl.getAlignmentAnnotation()[0]);
// this should NOT result in the same RNA SS Annotations
- newAl = new AppletFormatAdapter().readFile(
- aliFileRnaSS, DataSourceType.PASTE,
- jalview.io.FileFormat.Fasta);
+ newAl = new AppletFormatAdapter().readFile(aliFileRnaSS,
+ DataSourceType.PASTE, jalview.io.FileFormat.Fasta);
aaf = new AnnotationFile();
aaf.readAnnotationFile(newAl, wrongAnnFileRnaSSAlphaChars,
DataSourceType.PASTE);
- boolean mismatch = testRnaSSAnnotationsEquivalent(al.getAlignmentAnnotation()[0],
+ boolean mismatch = testRnaSSAnnotationsEquivalent(
+ al.getAlignmentAnnotation()[0],
newAl.getAlignmentAnnotation()[0]);
Assert.assertFalse(mismatch,
"RNA SS Annotations SHOULD NOT be pair-wise equivalent (but apparently are): \n"
}
private static boolean testRnaSSAnnotationsEquivalent(
- AlignmentAnnotation a1,
- AlignmentAnnotation a2)
+ AlignmentAnnotation a1, AlignmentAnnotation a2)
{
return a1.rnaSecondaryStructureEquivalent(a2);
}
+ "\n"
+ "ROWPROPERTIES\tSecondary Structure\tscaletofit=true\tshowalllabs=true\tcentrelabs=false\n"
+ "\n" + "\n" + "ALIGNMENT\tID=RNA.SS.TEST\tTP=RNA;";
+
String annFileRnaSSWithoutSpaceChars = "JALVIEW_ANNOTATION\n"
+ "# Created: Thu Aug 02 14:54:57 BST 2018\n" + "\n"
+ "NO_GRAPH\tSecondary Structure\tSecondary Structure\t<,<|.,.|H,H|.,.|B,B|h,h|.,.|b,b|(,(|E,E|.,.|e,e|),)|>,>|\t2.0\n"
jalview.io.FileFormat.Fasta);
AnnotationFile afWithoutSpaces = new AnnotationFile();
afWithoutSpaces.readAnnotationFile(alWithoutSpaces,
- annFileRnaSSWithoutSpaceChars,
- DataSourceType.PASTE);
+ annFileRnaSSWithoutSpaceChars, DataSourceType.PASTE);
Assert.assertTrue(
testRnaSSAnnotationsEquivalent(
jalview.io.FileFormat.Fasta);
AnnotationFile wrongAfWithoutSpaces = new AnnotationFile();
wrongAfWithoutSpaces.readAnnotationFile(wrongAlWithoutSpaces,
- wrongAnnFileRnaSSWithoutSpaceChars,
- DataSourceType.PASTE);
+ wrongAnnFileRnaSSWithoutSpaceChars, DataSourceType.PASTE);
Assert.assertFalse(
testRnaSSAnnotationsEquivalent(
Header header = scoreFile.header;
AssertJUnit.assertNotNull(header);
- AssertJUnit
- .assertEquals(
- "T-COFFEE, Version_9.02.r1228 (2012-02-16 18:15:12 - Revision 1228 - Build 336)",
- header.head);
+ AssertJUnit.assertEquals(
+ "T-COFFEE, Version_9.02.r1228 (2012-02-16 18:15:12 - Revision 1228 - Build 336)",
+ header.head);
AssertJUnit.assertEquals(90, header.score);
AssertJUnit.assertEquals(89, header.getScoreFor("1PHT"));
AssertJUnit.assertEquals(90, header.getScoreFor("1BB9"));
TCoffeeScoreFile parser = new TCoffeeScoreFile(SCORE_FILE.getPath(),
DataSourceType.FILE);
- AssertJUnit
- .assertEquals(
- "999999999999999999999999998762112222543211112134----------5666642367889999999999889",
- parser.getScoresFor("1PHT"));
- AssertJUnit
- .assertEquals(
- "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889",
- parser.getScoresFor("1BB9"));
- AssertJUnit
- .assertEquals(
- "99999999999999999999999999987-------5321----2246----------788774--66789999999999889",
- parser.getScoresFor("1UHC"));
- AssertJUnit
- .assertEquals(
- "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889",
- parser.getScoresFor("1YCS"));
- AssertJUnit
- .assertEquals(
- "999999999999999999999999999861-------3------1135----------78877--356789999999997-67",
- parser.getScoresFor("1OOT"));
- AssertJUnit
- .assertEquals(
- "99999999999999999999999999986-------422-------34----------687774--56779999999999889",
- parser.getScoresFor("1ABO"));
- AssertJUnit
- .assertEquals(
- "99999999999999999999999999985-------32--------35----------6888842356789999999999889",
- parser.getScoresFor("1FYN"));
- AssertJUnit
- .assertEquals(
- "99999999999999999999999999974-------2---------24----------6878742356789999999999889",
- parser.getScoresFor("1QCF"));
- AssertJUnit
- .assertEquals(
- "99999999999999999999999999985100011032110000113400100000006877641356789999999999889",
- parser.getScoresFor("cons"));
+ AssertJUnit.assertEquals(
+ "999999999999999999999999998762112222543211112134----------5666642367889999999999889",
+ parser.getScoresFor("1PHT"));
+ AssertJUnit.assertEquals(
+ "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889",
+ parser.getScoresFor("1BB9"));
+ AssertJUnit.assertEquals(
+ "99999999999999999999999999987-------5321----2246----------788774--66789999999999889",
+ parser.getScoresFor("1UHC"));
+ AssertJUnit.assertEquals(
+ "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889",
+ parser.getScoresFor("1YCS"));
+ AssertJUnit.assertEquals(
+ "999999999999999999999999999861-------3------1135----------78877--356789999999997-67",
+ parser.getScoresFor("1OOT"));
+ AssertJUnit.assertEquals(
+ "99999999999999999999999999986-------422-------34----------687774--56779999999999889",
+ parser.getScoresFor("1ABO"));
+ AssertJUnit.assertEquals(
+ "99999999999999999999999999985-------32--------35----------6888842356789999999999889",
+ parser.getScoresFor("1FYN"));
+ AssertJUnit.assertEquals(
+ "99999999999999999999999999974-------2---------24----------6878742356789999999999889",
+ parser.getScoresFor("1QCF"));
+ AssertJUnit.assertEquals(
+ "99999999999999999999999999985100011032110000113400100000006877641356789999999999889",
+ parser.getScoresFor("cons"));
}
@Test(groups = { "Functional" })
DataSourceType.FILE);
AssertJUnit.assertTrue(parser.getWarningMessage(), parser.isValid());
List<String> scores = parser.getScoresList();
- AssertJUnit
- .assertEquals(
- "999999999999999999999999998762112222543211112134----------5666642367889999999999889",
- scores.get(0));
- AssertJUnit
- .assertEquals(
- "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889",
- scores.get(1));
- AssertJUnit
- .assertEquals(
- "99999999999999999999999999987-------5321----2246----------788774--66789999999999889",
- scores.get(2));
- AssertJUnit
- .assertEquals(
- "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889",
- scores.get(3));
- AssertJUnit
- .assertEquals(
- "999999999999999999999999999861-------3------1135----------78877--356789999999997-67",
- scores.get(4));
- AssertJUnit
- .assertEquals(
- "99999999999999999999999999986-------422-------34----------687774--56779999999999889",
- scores.get(5));
- AssertJUnit
- .assertEquals(
- "99999999999999999999999999985-------32--------35----------6888842356789999999999889",
- scores.get(6));
- AssertJUnit
- .assertEquals(
- "99999999999999999999999999974-------2---------24----------6878742356789999999999889",
- scores.get(7));
- AssertJUnit
- .assertEquals(
- "99999999999999999999999999985100011032110000113400100000006877641356789999999999889",
- scores.get(8));
+ AssertJUnit.assertEquals(
+ "999999999999999999999999998762112222543211112134----------5666642367889999999999889",
+ scores.get(0));
+ AssertJUnit.assertEquals(
+ "99999999999999999999999999987-------4322----22341111111111676653-355679999999999889",
+ scores.get(1));
+ AssertJUnit.assertEquals(
+ "99999999999999999999999999987-------5321----2246----------788774--66789999999999889",
+ scores.get(2));
+ AssertJUnit.assertEquals(
+ "99999999999999999999999999986-------4321----1-35----------78777--356789999999999889",
+ scores.get(3));
+ AssertJUnit.assertEquals(
+ "999999999999999999999999999861-------3------1135----------78877--356789999999997-67",
+ scores.get(4));
+ AssertJUnit.assertEquals(
+ "99999999999999999999999999986-------422-------34----------687774--56779999999999889",
+ scores.get(5));
+ AssertJUnit.assertEquals(
+ "99999999999999999999999999985-------32--------35----------6888842356789999999999889",
+ scores.get(6));
+ AssertJUnit.assertEquals(
+ "99999999999999999999999999974-------2---------24----------6878742356789999999999889",
+ scores.get(7));
+ AssertJUnit.assertEquals(
+ "99999999999999999999999999985100011032110000113400100000006877641356789999999999889",
+ scores.get(8));
}
public void testHeightAndWidthWithResidueNumbers() throws Exception
{
String file = "test/jalview/io/tcoffee.score_ascii_with_residue_numbers";
- TCoffeeScoreFile result = new TCoffeeScoreFile(file, DataSourceType.FILE);
+ TCoffeeScoreFile result = new TCoffeeScoreFile(file,
+ DataSourceType.FILE);
AssertJUnit.assertTrue(result.isValid());
AssertJUnit.assertEquals(5, result.getHeight());
AssertJUnit.assertEquals(84, result.getWidth());
appCache.updateCacheLimit(TEST_CACHE_KEY, 99);
}
-
}
public void testGetMappingType()
{
// protein-to-dna:
- assertSame(MappingType.PeptideToNucleotide,
- ExonerateHelper
- .getMappingType("exonerate:protein2genome:local"));
+ assertSame(MappingType.PeptideToNucleotide, ExonerateHelper
+ .getMappingType("exonerate:protein2genome:local"));
assertSame(MappingType.PeptideToNucleotide,
ExonerateHelper.getMappingType("exonerate:protein2dna:local"));
assertSame(newseqs.get(0), mapping.getdnaSeqs()[0]);
assertEquals(1, mapping.getdnaToProt().length);
assertEquals(1, mapping.getdnaToProt()[0].getFromRanges().size());
- assertArrayEquals(new int[] { 400, 423 }, mapping.getdnaToProt()[0]
- .getFromRanges().get(0));
+ assertArrayEquals(new int[] { 400, 423 },
+ mapping.getdnaToProt()[0].getFromRanges().get(0));
assertEquals(1, mapping.getdnaToProt()[0].getToRanges().size());
- assertArrayEquals(new int[] { 3, 10 }, mapping.getdnaToProt()[0]
- .getToRanges().get(0));
+ assertArrayEquals(new int[] { 3, 10 },
+ mapping.getdnaToProt()[0].getToRanges().get(0));
}
/**
assertSame(newseqs.get(0), mapping.getdnaSeqs()[0]);
assertEquals(1, mapping.getdnaToProt().length);
assertEquals(1, mapping.getdnaToProt()[0].getFromRanges().size());
- assertArrayEquals(new int[] { 400, 377 }, mapping.getdnaToProt()[0]
- .getFromRanges().get(0));
+ assertArrayEquals(new int[] { 400, 377 },
+ mapping.getdnaToProt()[0].getFromRanges().get(0));
assertEquals(1, mapping.getdnaToProt()[0].getToRanges().size());
- assertArrayEquals(new int[] { 3, 10 }, mapping.getdnaToProt()[0]
- .getToRanges().get(0));
+ assertArrayEquals(new int[] { 3, 10 },
+ mapping.getdnaToProt()[0].getToRanges().get(0));
}
/**
assertEquals(1, mapping.getdnaSeqs().length);
assertEquals(1, mapping.getdnaToProt().length);
assertEquals(1, mapping.getdnaToProt()[0].getFromRanges().size());
- assertArrayEquals(new int[] { 400, 423 }, mapping.getdnaToProt()[0]
- .getFromRanges().get(0));
+ assertArrayEquals(new int[] { 400, 423 },
+ mapping.getdnaToProt()[0].getFromRanges().get(0));
assertEquals(1, mapping.getdnaToProt()[0].getToRanges().size());
- assertArrayEquals(new int[] { 3, 10 }, mapping.getdnaToProt()[0]
- .getToRanges().get(0));
+ assertArrayEquals(new int[] { 3, 10 },
+ mapping.getdnaToProt()[0].getToRanges().get(0));
}
/**
assertEquals(1, mapping.getdnaSeqs().length);
assertEquals(1, mapping.getdnaToProt().length);
assertEquals(1, mapping.getdnaToProt()[0].getFromRanges().size());
- assertArrayEquals(new int[] { 400, 377 }, mapping.getdnaToProt()[0]
- .getFromRanges().get(0));
+ assertArrayEquals(new int[] { 400, 377 },
+ mapping.getdnaToProt()[0].getFromRanges().get(0));
assertEquals(1, mapping.getdnaToProt()[0].getToRanges().size());
- assertArrayEquals(new int[] { 3, 10 }, mapping.getdnaToProt()[0]
- .getToRanges().get(0));
+ assertArrayEquals(new int[] { 3, 10 },
+ mapping.getdnaToProt()[0].getToRanges().get(0));
}
/**
{
FileLoader loader = new FileLoader(false);
AlignFrame af = loader.LoadFileWaitTillLoaded(
- "examples/testdata/exonerateseqs.fa",
- DataSourceType.FILE);
-
+ "examples/testdata/exonerateseqs.fa", DataSourceType.FILE);
+
af.loadJalviewDataFile("examples/testdata/exonerateoutput.gff",
DataSourceType.FILE, null, null);
-
+
/*
* verify one mapping to a dummy sequence, one to a real one
*/
- List<AlignedCodonFrame> mappings = af
- .getViewport().getAlignment().getDataset().getCodonFrames();
+ List<AlignedCodonFrame> mappings = af.getViewport().getAlignment()
+ .getDataset().getCodonFrames();
assertEquals(2, mappings.size());
Iterator<AlignedCodonFrame> iter = mappings.iterator();
-
+
// first mapping is to dummy sequence
AlignedCodonFrame mapping = iter.next();
Mapping[] mapList = mapping.getProtMappings();
// 143 in protein should map to codon [11270, 11269, 11268] in dna
int[] mappedRegion = mapList[0].getMap().locateInFrom(143, 143);
assertArrayEquals(new int[] { 11270, 11268 }, mappedRegion);
-
+
// second mapping is to a sequence in the alignment
mapping = iter.next();
mapList = mapping.getProtMappings();
.findName("DDB_G0280897");
assertSame(proteinSeq.getDatasetSequence(), mapList[0].getTo());
assertEquals(1, mapping.getdnaToProt().length);
-
+
// 143 in protein should map to codon [11270, 11269, 11268] in dna
mappedRegion = mapList[0].getMap().locateInFrom(143, 143);
assertArrayEquals(new int[] { 11270, 11268 }, mappedRegion);
-
+
// 182 in protein should map to codon [11153, 11152, 11151] in dna
mappedRegion = mapList[0].getMap().locateInFrom(182, 182);
assertArrayEquals(new int[] { 11153, 11151 }, mappedRegion);
-
+
// and the reverse mapping:
mappedRegion = mapList[0].getMap().locateInTo(11151, 11153);
assertArrayEquals(new int[] { 182, 182 }, mappedRegion);
-
+
// 11150 in dna should _not_ map to protein
mappedRegion = mapList[0].getMap().locateInTo(11150, 11150);
assertNull(mappedRegion);
-
+
// similarly 183 in protein should _not_ map to dna
mappedRegion = mapList[0].getMap().locateInFrom(183, 183);
assertNull(mappedRegion);
assertSame(newseqs.get(0), mapping.getAaSeqs()[0]);
assertEquals(1, mapping.getdnaToProt().length);
assertEquals(1, mapping.getdnaToProt()[0].getFromRanges().size());
- assertArrayEquals(new int[] { 12923, 13060 }, mapping.getdnaToProt()[0]
- .getFromRanges().get(0));
+ assertArrayEquals(new int[] { 12923, 13060 },
+ mapping.getdnaToProt()[0].getFromRanges().get(0));
assertEquals(1, mapping.getdnaToProt()[0].getToRanges().size());
- assertArrayEquals(new int[] { 1, 138 }, mapping.getdnaToProt()[0]
- .getToRanges().get(0));
+ assertArrayEquals(new int[] { 1, 138 },
+ mapping.getdnaToProt()[0].getToRanges().get(0));
}
/**
assertSame(newseqs.get(0), mapping.getAaSeqs()[0]);
assertEquals(1, mapping.getdnaToProt().length);
assertEquals(1, mapping.getdnaToProt()[0].getFromRanges().size());
- assertArrayEquals(new int[] { 12923, 13060 }, mapping.getdnaToProt()[0]
- .getFromRanges().get(0));
+ assertArrayEquals(new int[] { 12923, 13060 },
+ mapping.getdnaToProt()[0].getFromRanges().get(0));
assertEquals(1, mapping.getdnaToProt()[0].getToRanges().size());
- assertArrayEquals(new int[] { 138, 1 }, mapping.getdnaToProt()[0]
- .getToRanges().get(0));
+ assertArrayEquals(new int[] { 138, 1 },
+ mapping.getdnaToProt()[0].getToRanges().get(0));
}
/**
assertEquals(1, mapping.getdnaToProt().length);
assertEquals(2, mapping.getdnaToProt()[0].getFromRanges().size());
// the two spliced dna ranges are combined in one MapList
- assertArrayEquals(new int[] { 12923, 13060 }, mapping.getdnaToProt()[0]
- .getFromRanges().get(0));
- assertArrayEquals(new int[] { 13411, 13550 }, mapping.getdnaToProt()[0]
- .getFromRanges().get(1));
+ assertArrayEquals(new int[] { 12923, 13060 },
+ mapping.getdnaToProt()[0].getFromRanges().get(0));
+ assertArrayEquals(new int[] { 13411, 13550 },
+ mapping.getdnaToProt()[0].getFromRanges().get(1));
assertEquals(1, mapping.getdnaToProt()[0].getToRanges().size());
// the two cdna ranges are merged into one contiguous region
- assertArrayEquals(new int[] { 1, 278 }, mapping.getdnaToProt()[0]
- .getToRanges().get(0));
+ assertArrayEquals(new int[] { 1, 278 },
+ mapping.getdnaToProt()[0].getToRanges().get(0));
}
@Test(groups = "Functional")
// Ensembl variant feature - extract "alleles" value
// may be sequence_variant or a sub-type in the sequence ontology
- sf = new SequenceFeature("feature_variant", "desc", 10, 20, 3f, "group");
+ sf = new SequenceFeature("feature_variant", "desc", 10, 20, 3f,
+ "group");
List<String> atts = new ArrayList<String>();
atts.add("A");
atts.add("C");
{
assertTrue(GffHelperBase.parseNameValuePairs(null, ";", ' ', ",")
.isEmpty());
- assertTrue(GffHelperBase.parseNameValuePairs("", ";", ' ', ",")
- .isEmpty());
- assertTrue(GffHelperBase.parseNameValuePairs("hello=world", ";", ' ',
- ",").isEmpty());
+ assertTrue(
+ GffHelperBase.parseNameValuePairs("", ";", ' ', ",").isEmpty());
+ assertTrue(GffHelperBase
+ .parseNameValuePairs("hello=world", ";", ' ', ",").isEmpty());
- Map<String, List<String>> map = GffHelperBase.parseNameValuePairs(
- "hello world", ";", ' ', ", ");
+ Map<String, List<String>> map = GffHelperBase
+ .parseNameValuePairs("hello world", ";", ' ', ", ");
assertEquals(map.size(), 1);
assertEquals(map.get("hello").size(), 1);
assertEquals(map.get("hello").get(0), "world");
- map = GffHelperBase
- .parseNameValuePairs(
- "Method= manual curation ;nothing; Notes=F2 S ; Notes=Metal,Shiny%2Csmooth; Type=",
- ";", '=', ",");
+ map = GffHelperBase.parseNameValuePairs(
+ "Method= manual curation ;nothing; Notes=F2 S ; Notes=Metal,Shiny%2Csmooth; Type=",
+ ";", '=', ",");
// Type is ignored as no value was supplied
assertEquals(map.size(), 2);
*/
String gff = "submitted\taffine:local\tsimilarity\t20\t30\t99\t+\t.\t";
// no attributes (column 9 data):
- assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof Gff2Helper);
+ assertTrue(GffHelperFactory
+ .getHelper(gff.split(tabRegex)) instanceof Gff2Helper);
// attributes set but unhandled featureGroup - get generic handler
gff = "submitted\taffine:local\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
// handled featureGroup (exonerate model) values
gff = "submitted\texonerate:protein2dna:local\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
- assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
+ assertTrue(GffHelperFactory
+ .getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
gff = "submitted\tprotein2genome\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
- assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
+ assertTrue(GffHelperFactory
+ .getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
gff = "submitted\tcoding2coding\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
- assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
+ assertTrue(GffHelperFactory
+ .getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
gff = "submitted\tcoding2genome\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
- assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
+ assertTrue(GffHelperFactory
+ .getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
gff = "submitted\tcdna2genome\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
- assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
+ assertTrue(GffHelperFactory
+ .getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
gff = "submitted\tgenome2genome\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
- assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
+ assertTrue(GffHelperFactory
+ .getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
// not case-sensitive:
gff = "submitted\tgenome2genome\tSIMILARITY\t20\t30\t99\t+\t.\tID=$1";
- assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
+ assertTrue(GffHelperFactory
+ .getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
/*
* InterProScan has 'protein_match' in column 3
*/
gff = "Submitted\tPANTHER\tprotein_match\t1\t1174\t0.0\t+\t.\tName=PTHR32154";
- assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof InterProScanHelper);
+ assertTrue(GffHelperFactory
+ .getHelper(gff.split(tabRegex)) instanceof InterProScanHelper);
/*
* nothing specific - return the generic GFF3 class if Name=Value is present in col9
public void testResolveExonerateGff()
{
String proteinSeq = ">prot1/10-16\nYCWRSGA";
- AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
- proteinSeq, DataSourceType.PASTE);
+ AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(proteinSeq,
+ DataSourceType.PASTE);
/*
* exonerate GFF output mapping residues 11-15 (CWRSG)
assertSame(newseqs.get(0), mapping.getAaSeqs()[0]);
assertEquals(1, mapping.getdnaToProt().length);
assertEquals(1, mapping.getdnaToProt()[0].getFromRanges().size());
- assertArrayEquals(new int[] { 5, 30 }, mapping.getdnaToProt()[0]
- .getFromRanges().get(0));
+ assertArrayEquals(new int[] { 5, 30 },
+ mapping.getdnaToProt()[0].getFromRanges().get(0));
assertEquals(1, mapping.getdnaToProt()[0].getToRanges().size());
- assertArrayEquals(new int[] { 1, 26 }, mapping.getdnaToProt()[0]
- .getToRanges().get(0));
+ assertArrayEquals(new int[] { 1, 26 },
+ mapping.getdnaToProt()[0].getToRanges().get(0));
}
}
private static final float DELTA = 0.00001f;
// columns 9717- of gene P30419 from Ensembl (much modified)
- private static final String FASTA = ""
- +
- /*
- * forward strand 'gene' and 'transcript' with two exons
- */
+ private static final String FASTA = "" +
+ /*
+ * forward strand 'gene' and 'transcript' with two exons
+ */
">gene1/1-25 chromosome:GRCh38:17:45051610:45051634:1\n"
+ "CAAGCTGGCGGACGAGAGTGTGACA\n"
+ ">transcript1/1-18\n--AGCTGGCG----AGAGTGTGAC-\n"
* reverse strand gene and transcript (reverse complement alleles!)
*/
+ ">gene2/1-25 chromosome:GRCh38:17:45051610:45051634:-1\n"
- + "TGTCACACTCTCGTCCGCCAGCTTG\n"
- + ">transcript2/1-18\n" + "-GTCACACTCT----CGCCAGCT--\n"
+ + "TGTCACACTCTCGTCCGCCAGCTTG\n" + ">transcript2/1-18\n"
+ + "-GTCACACTCT----CGCCAGCT--\n"
/*
* 'gene' on chromosome 5 with two transcripts
+ ">transcript4/1-18\n-----TGG-GGACGAGAGTGTGA-A\n";
private static final String[] VCF = { "##fileformat=VCFv4.2",
- // fields other than AF are ignored when parsing as they have no INFO definition
+ // fields other than AF are ignored when parsing as they have no INFO
+ // definition
"##INFO=<ID=AF,Number=A,Type=Float,Description=\"Allele Frequency, for each ALT allele, in the same order as listed\">",
"##INFO=<ID=AC_Female,Number=A,Type=Integer,Description=\"Allele count in Female genotypes\"",
"##INFO=<ID=AF_AFR,Number=A,Type=Float,Description=\"Allele Frequency among African/African American genotypes\"",
SequenceI gene1 = alignment.findName("gene1");
int[] to = new int[] { 45051610, 45051634 };
int[] from = new int[] { gene1.getStart(), gene1.getEnd() };
- gene1.setGeneLoci("homo_sapiens", "GRCh38", "17", new MapList(from, to,
- 1, 1));
+ gene1.setGeneLoci("homo_sapiens", "GRCh38", "17",
+ new MapList(from, to, 1, 1));
/*
* map 'transcript1' to chromosome via 'gene1'
to = new int[] { 45051612, 45051619, 45051624, 45051633 };
SequenceI transcript1 = alignment.findName("transcript1");
from = new int[] { transcript1.getStart(), transcript1.getEnd() };
- transcript1.setGeneLoci("homo_sapiens", "GRCh38", "17", new MapList(
- from, to,
- 1, 1));
+ transcript1.setGeneLoci("homo_sapiens", "GRCh38", "17",
+ new MapList(from, to, 1, 1));
/*
* map gene2 to chromosome reverse strand
SequenceI gene2 = alignment.findName("gene2");
to = new int[] { 45051634, 45051610 };
from = new int[] { gene2.getStart(), gene2.getEnd() };
- gene2.setGeneLoci("homo_sapiens", "GRCh38", "17", new MapList(from, to,
- 1, 1));
+ gene2.setGeneLoci("homo_sapiens", "GRCh38", "17",
+ new MapList(from, to, 1, 1));
/*
* map 'transcript2' to chromosome via 'gene2'
to = new int[] { 45051633, 45051624, 45051619, 45051612 };
SequenceI transcript2 = alignment.findName("transcript2");
from = new int[] { transcript2.getStart(), transcript2.getEnd() };
- transcript2.setGeneLoci("homo_sapiens", "GRCh38", "17", new MapList(
- from, to,
- 1, 1));
+ transcript2.setGeneLoci("homo_sapiens", "GRCh38", "17",
+ new MapList(from, to, 1, 1));
/*
* add a protein product as a DBRef on transcript1
SequenceI gene3 = alignment.findName("gene3");
to = new int[] { 45051610, 45051634 };
from = new int[] { gene3.getStart(), gene3.getEnd() };
- gene3.setGeneLoci("homo_sapiens", "GRCh38", "5", new MapList(from, to,
- 1, 1));
+ gene3.setGeneLoci("homo_sapiens", "GRCh38", "5",
+ new MapList(from, to, 1, 1));
/*
* map 'transcript3' to chromosome
SequenceI transcript3 = alignment.findName("transcript3");
to = new int[] { 45051612, 45051619, 45051624, 45051633 };
from = new int[] { transcript3.getStart(), transcript3.getEnd() };
- transcript3.setGeneLoci("homo_sapiens", "GRCh38", "5", new MapList(
- from, to,
- 1, 1));
+ transcript3.setGeneLoci("homo_sapiens", "GRCh38", "5",
+ new MapList(from, to, 1, 1));
/*
* map 'transcript4' to chromosome
to = new int[] { 45051615, 45051617, 45051619, 45051632, 45051634,
45051634 };
from = new int[] { transcript4.getStart(), transcript4.getEnd() };
- transcript4.setGeneLoci("homo_sapiens", "GRCh38", "5", new MapList(
- from, to,
- 1, 1));
+ transcript4.setGeneLoci("homo_sapiens", "GRCh38", "5",
+ new MapList(from, to, 1, 1));
/*
* add a protein product as a DBRef on transcript3
@Test(groups = "Functional")
public void testLoadVCFContig() throws IOException
{
- VCFLoader loader = new VCFLoader(
- "test/jalview/io/vcf/testVcf2.vcf");
+ VCFLoader loader = new VCFLoader("test/jalview/io/vcf/testVcf2.vcf");
SequenceI seq = loader.loadVCFContig("contig123");
assertEquals(seq.getLength(), 15);
@Test(
groups = "Functional",
- expectedExceptions = { IllegalArgumentException.class })
+ expectedExceptions =
+ { IllegalArgumentException.class })
public void testPreMultiply_tooManyColumns()
{
Matrix m1 = new Matrix(new double[][] { { 2, 3, 4 }, { 3, 4, 5 } }); // 2x3
@Test(
groups = "Functional",
- expectedExceptions = { IllegalArgumentException.class })
+ expectedExceptions =
+ { IllegalArgumentException.class })
public void testPreMultiply_tooFewColumns()
{
Matrix m1 = new Matrix(new double[][] { { 2, 3, 4 }, { 3, 4, 5 } }); // 2x3
m1.preMultiply(m1);
fail("Expected exception");
}
-
-
- private boolean matrixEquals(Matrix m1, Matrix m2) {
+
+ private boolean matrixEquals(Matrix m1, Matrix m2)
+ {
if (m1.width() != m2.width() || m1.height() != m2.height())
{
return false;
* (5040 50400)
*/
MatrixI m1 = new Matrix(new double[][] { { 2, 3 }, { 4, 5 } });
- MatrixI m2 = new Matrix(new double[][] { { 10, 100 }, { 1000, 10000 } });
+ MatrixI m2 = new Matrix(
+ new double[][]
+ { { 10, 100 }, { 1000, 10000 } });
MatrixI m3 = m1.postMultiply(m2);
assertEquals(Arrays.toString(m3.getRow(0)), "[3020.0, 30200.0]");
assertEquals(Arrays.toString(m3.getRow(1)), "[5040.0, 50400.0]");
{
int n = Integer.parseInt(args[0]);
double[][] in = new double[n][n];
-
+
for (int i = 0; i < n; i++)
{
for (int j = 0; j < n; j++)
in[i][j] = Math.random();
}
}
-
+
Matrix origmat = new Matrix(in);
-
+
// System.out.println(" --- Original matrix ---- ");
// / origmat.print(System.out);
// System.out.println();
// System.out.println(" --- transpose matrix ---- ");
MatrixI trans = origmat.transpose();
-
+
// trans.print(System.out);
// System.out.println();
// System.out.println(" --- OrigT * Orig ---- ");
MatrixI symm = trans.postMultiply(origmat);
-
+
// symm.print(System.out);
// System.out.println();
// Copy the symmetric matrix for later
// Matrix origsymm = symm.copy();
-
+
// This produces the tridiagonal transformation matrix
// long tstart = System.currentTimeMillis();
symm.tred();
-
+
// long tend = System.currentTimeMillis();
-
+
// System.out.println("Time take for tred = " + (tend-tstart) + "ms");
// System.out.println(" ---Tridiag transform matrix ---");
// symm.print(System.out);
// tstart = System.currentTimeMillis();
symm.tqli();
// tend = System.currentTimeMillis();
-
+
// System.out.println("Time take for tqli = " + (tend-tstart) + " ms");
// System.out.println(" --- New diagonalization matrix ---");
// symm.print(System.out);
}
}
return d;
-
+
}
/**
int rows = 10;
int cols = rows;
double[][] d = getSparseValues(rows, cols, 3);
-
+
/*
* make a copy of the values so m1, m2 are not
* sharing arrays!
* normal case
*/
double[][] vals = new double[2][];
- vals[0] = new double[] {7d, 1d, -2.3d};
- vals[1] = new double[] {-12d, 94.3d, -102.34d};
+ vals[0] = new double[] { 7d, 1d, -2.3d };
+ vals[1] = new double[] { -12d, 94.3d, -102.34d };
m = new Matrix(vals);
double[] minMax = m.findMinMax();
assertEquals(minMax[0], -102.34d);
public void testReverseRange_maxToZero()
{
Matrix m1 = new Matrix(
- new double[][] { { 2, 3.5, 4 }, { -3.4, 4, 15 } });
+ new double[][]
+ { { 2, 3.5, 4 }, { -3.4, 4, 15 } });
/*
* subtract all from max: range -3.4 to 15 becomes 18.4 to 0
public void testReverseRange_swapMinMax()
{
Matrix m1 = new Matrix(
- new double[][] { { 2, 3.5, 4 }, { -3.4, 4, 15 } });
-
+ new double[][]
+ { { 2, 3.5, 4 }, { -3.4, 4, 15 } });
+
/*
* swap all values in min-max range
* = subtract from (min + max = 11.6)
assertEquals(m1.getValue(1, 0), 15d, DELTA);
assertEquals(m1.getValue(1, 1), 7.6d, DELTA);
assertEquals(m1.getValue(1, 2), -3.4d, DELTA);
-
+
/*
* repeat operation - original values restored
*/
@Test(groups = "Functional")
public void testMultiply()
{
- Matrix m = new Matrix(new double[][] { { 2, 3.5, 4 }, { -3.4, 4, 15 } });
+ Matrix m = new Matrix(
+ new double[][]
+ { { 2, 3.5, 4 }, { -3.4, 4, 15 } });
m.multiply(2d);
assertEquals(m.getValue(0, 0), 4d, DELTA);
assertEquals(m.getValue(0, 1), 7d, DELTA);
public void testConstructor()
{
MatrixI m1 = new SparseMatrix(
- new double[][] { { 2, 0, 4 }, { 0, 6, 0 } });
+ new double[][]
+ { { 2, 0, 4 }, { 0, 6, 0 } });
assertEquals(m1.getValue(0, 0), 2d);
assertEquals(m1.getValue(0, 1), 0d);
assertEquals(m1.getValue(0, 2), 4d);
public void testTranspose()
{
MatrixI m1 = new SparseMatrix(
- new double[][] { { 2, 0, 4 }, { 5, 6, 0 } });
+ new double[][]
+ { { 2, 0, 4 }, { 5, 6, 0 } });
MatrixI m2 = m1.transpose();
assertTrue(m2 instanceof SparseMatrix);
assertEquals(m2.height(), 3);
assertEquals(m2.getValue(2, 0), 4d);
assertEquals(m2.getValue(2, 1), 0d);
}
+
@Test(groups = "Functional")
public void testPreMultiply()
{
@Test(
groups = "Functional",
- expectedExceptions = { IllegalArgumentException.class })
+ expectedExceptions =
+ { IllegalArgumentException.class })
public void testPreMultiply_tooManyColumns()
{
Matrix m1 = new SparseMatrix(
- new double[][] { { 2, 3, 4 }, { 3, 4, 5 } }); // 2x3
+ new double[][]
+ { { 2, 3, 4 }, { 3, 4, 5 } }); // 2x3
/*
* 2x3 times 2x3 invalid operation -
@Test(
groups = "Functional",
- expectedExceptions = { IllegalArgumentException.class })
+ expectedExceptions =
+ { IllegalArgumentException.class })
public void testPreMultiply_tooFewColumns()
{
Matrix m1 = new SparseMatrix(
- new double[][] { { 2, 3, 4 }, { 3, 4, 5 } }); // 2x3
+ new double[][]
+ { { 2, 3, 4 }, { 3, 4, 5 } }); // 2x3
/*
* 3x2 times 3x2 invalid operation -
m1.preMultiply(m1);
fail("Expected exception");
}
-
+
@Test(groups = "Functional")
public void testPostMultiply()
{
* (5040 50400)
*/
MatrixI m1 = new SparseMatrix(new double[][] { { 2, 3 }, { 4, 5 } });
- MatrixI m2 = new SparseMatrix(new double[][] { { 10, 100 },
- { 1000, 10000 } });
+ MatrixI m2 = new SparseMatrix(
+ new double[][]
+ { { 10, 100 }, { 1000, 10000 } });
MatrixI m3 = m1.postMultiply(m2);
assertEquals(m3.getValue(0, 0), 3020d);
assertEquals(m3.getValue(0, 1), 30200d);
int rows = 6;
int cols = rows;
double[][] d = getSparseValues(rows, cols, 3);
-
+
/*
* make a copy of the values so m1, m2 are not
* sharing arrays!
@Test(groups = "Functional")
public void testPreMultiply_sparseProduct()
{
- MatrixI m1 = new SparseMatrix(new double[][] { { 1 }, { 0 }, { 0 },
- { 0 }, { 0 } }); // 5x1
+ MatrixI m1 = new SparseMatrix(
+ new double[][]
+ { { 1 }, { 0 }, { 0 }, { 0 }, { 0 } }); // 5x1
MatrixI m2 = new SparseMatrix(new double[][] { { 1, 1, 1, 1 } }); // 1x4
-
+
/*
* m1.m2 makes a row of 4 1's, and 4 rows of zeros
* 20% non-zero so not 'sparse'
@Test(groups = "Functional")
public void testFillRatio()
{
- SparseMatrix m1 = new SparseMatrix(new double[][] { { 2, 0, 4, 1, 0 },
- { 0, 6, 0, 0, 0 } });
+ SparseMatrix m1 = new SparseMatrix(
+ new double[][]
+ { { 2, 0, 4, 1, 0 }, { 0, 6, 0, 0, 0 } });
assertEquals(m1.getFillRatio(), 0.4f);
}
int rows = 10;
int cols = rows;
double[][] d = getSparseValues(rows, cols, 3);
-
+
/*
* make a copy of the values so m1, m2 are not
* sharing arrays!
assertNotNull(
ColourSchemeProperty.getColourScheme(viewport,
viewport.getAlignment(),
- viewport.getGlobalColourScheme()
- .getSchemeName()),
+ viewport.getGlobalColourScheme().getSchemeName()),
"Recognise T-Coffee score from string");
af.saveAlignment(tfile, FileFormat.Jalview);
Assert.assertEquals(Desktop.getAlignFrames().length,
Desktop.getAlignmentPanels(
af.getViewport().getSequenceSetId()).length);
- Assert.assertEquals(
- Desktop.getAlignmentPanels(
- af.getViewport().getSequenceSetId()).length,
+ Assert.assertEquals(Desktop
+ .getAlignmentPanels(af.getViewport().getSequenceSetId()).length,
oldviews);
}
"Mismatch PDBEntry 'Type'");
Assert.assertNotNull(recov.getFile(),
"Recovered PDBEntry should have a non-null file entry");
- Assert.assertEquals(recov.getFile().toLowerCase(Locale.ENGLISH).lastIndexOf("pdb"),recov.getFile().length()-3, "Recovered PDBEntry file should have PDB suffix");
+ Assert.assertEquals(
+ recov.getFile().toLowerCase(Locale.ENGLISH)
+ .lastIndexOf("pdb"),
+ recov.getFile().length() - 3,
+ "Recovered PDBEntry file should have PDB suffix");
}
}
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData,
DataSourceType.PASTE);
assertNotNull(af, "Didn't read in the example file correctly.");
-
+
AlignmentViewPanel ap = Desktop.getAlignmentPanels(null)[0];
SequenceI pep = ap.getAlignment().getSequenceAt(0);
SequenceI cds = ap.getAlignment().getSequenceAt(1);
Assert.fail("Didn't save the state", e);
}
Desktop.instance.closeAll_actionPerformed(null);
-
+
new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
DataSourceType.FILE);
AlignmentViewPanel rap = Desktop.getAlignmentPanels(null)[0];
import java.awt.Color;
import org.testng.annotations.Test;
+
public class OverviewRendererTest
{
Sequence seq2 = new Sequence("seq2", "FVE");
AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
AlignmentViewport av = new AlignViewport(al);
- OverviewDimensions od = new OverviewDimensionsShowHidden(new ViewportRanges(al), false);
+ OverviewDimensions od = new OverviewDimensionsShowHidden(
+ new ViewportRanges(al), false);
ResidueShaderI rs = new ResidueShader(new ZappoColourScheme());
FeatureRenderer fr = new FeatureRenderer(av);
OverviewRenderer or = new OverviewRenderer(fr, od, al, rs, cf);
// P is magenta (see ResidueProperties.zappo)
- assertEquals(or.getColumnColourFromSequence(null, seq1, 0), Color.magenta.getRGB());
+ assertEquals(or.getColumnColourFromSequence(null, seq1, 0),
+ Color.magenta.getRGB());
// Q is green
assertEquals(or.getColumnColourFromSequence(null, seq1, 1),
Color.green.getRGB());
// gaps are grey, residues white
assertEquals(Color.white, rcf.getResidueColour(true,
- av.getResidueShading(),
- null, seq, 0, null));
- assertEquals(Color.lightGray, rcf
- .getResidueColour(true, av.getResidueShading(), null, seq, 2,
- null));
+ av.getResidueShading(), null, seq, 0, null));
+ assertEquals(Color.lightGray, rcf.getResidueColour(true,
+ av.getResidueShading(), null, seq, 2, null));
// unaffected by showBoxes setting
assertEquals(Color.white, rcf.getResidueColour(false,
av.setGlobalColourScheme(new ZappoColourScheme());
// @see ResidueProperties.zappo
- assertEquals(Color.pink,
- rcf.getResidueColour(true, av.getResidueShading(),
- null, seq, 0, null)); // M
- assertEquals(Color.green,
- rcf.getResidueColour(true, av.getResidueShading(),
- null, seq, 2, null)); // T
- assertEquals(Color.magenta,
- rcf.getResidueColour(true, av.getResidueShading(),
- null, seq, 5, null)); // G
- assertEquals(Color.orange,
- rcf.getResidueColour(true, av.getResidueShading(),
- null, seq, 12, null)); // F
+ assertEquals(Color.pink, rcf.getResidueColour(true,
+ av.getResidueShading(), null, seq, 0, null)); // M
+ assertEquals(Color.green, rcf.getResidueColour(true,
+ av.getResidueShading(), null, seq, 2, null)); // T
+ assertEquals(Color.magenta, rcf.getResidueColour(true,
+ av.getResidueShading(), null, seq, 5, null)); // G
+ assertEquals(Color.orange, rcf.getResidueColour(true,
+ av.getResidueShading(), null, seq, 12, null)); // F
// gap colour not specified so gaps are lightGray
- assertEquals(Color.lightGray, rcf
- .getResidueColour(true, av.getResidueShading(), null, seq, 3,
- null));
+ assertEquals(Color.lightGray, rcf.getResidueColour(true,
+ av.getResidueShading(), null, seq, 3, null));
// unaffected by showBoxes setting
assertEquals(Color.pink, rcf.getResidueColour(false,
av.getResidueShading(), null, seq, 12, null)); // F
// gap colour not specified so gaps are lightGray
- assertEquals(Color.lightGray, rcf
- .getResidueColour(false, av.getResidueShading(), null, seq, 3,
- null));
+ assertEquals(Color.lightGray, rcf.getResidueColour(false,
+ av.getResidueShading(), null, seq, 3, null));
}
av.setGlobalColourScheme(new UserColourScheme(newColours));
// gap colour not specified so gaps are lightGray
- assertEquals(Color.lightGray, rcf
- .getResidueColour(true, av.getResidueShading(), null, seq, 3,
- null));
+ assertEquals(Color.lightGray, rcf.getResidueColour(true,
+ av.getResidueShading(), null, seq, 3, null));
newColours[23] = Color.pink;
av.setGlobalColourScheme(new UserColourScheme(newColours));
// gap colour specified as pink
assertEquals(Color.pink, rcf.getResidueColour(true,
- av.getResidueShading(),
- null, seq, 3, null));
+ av.getResidueShading(), null, seq, 3, null));
// unaffected by showBoxes setting
// gap colour not specified so gaps are lightGray
{
SequenceI seq = new Sequence("name", "MA--TVLGSPRAPAFF");
AlignmentI al = new Alignment(new SequenceI[] { seq });
-
+
ColourSchemeI cs = new ZappoColourScheme();
ArrayList<SequenceI> seqlist = new ArrayList<>();
seqlist.add(seq);
al.addGroup(sg);
SequenceGroup[] groups = new SequenceGroup[1];
groups[0] = sg;
-
+
final AlignViewport av = new AlignViewport(al);
ResidueColourFinder rcf = new OverviewResColourFinder();
-
+
// G in group specified as magenta in Zappo
assertEquals(Color.magenta, rcf.getResidueColour(false,
av.getResidueShading(), groups, seq, 7, null));
// use legacy colouring
rcf = new OverviewResColourFinder(true, Color.blue, Color.red);
-
+
// G in group specified as magenta in Zappo
assertEquals(Color.magenta, rcf.getResidueColour(false,
av.getResidueShading(), groups, seq, 7, null));
av.setGlobalColourScheme(new ZappoColourScheme());
// @see ResidueProperties.zappo
- assertEquals(Color.pink,
- rcf.getResidueColour(true, av.getResidueShading(), null, seq, 0,
- null)); // M
- assertEquals(Color.green,
- rcf.getResidueColour(true, av.getResidueShading(), null, seq, 2,
- null)); // T
- assertEquals(Color.magenta,
- rcf.getResidueColour(true, av.getResidueShading(), null, seq, 5,
- null)); // G
- assertEquals(Color.orange,
- rcf.getResidueColour(true, av.getResidueShading(), null, seq,
- 12,
- null)); // F
+ assertEquals(Color.pink, rcf.getResidueColour(true,
+ av.getResidueShading(), null, seq, 0, null)); // M
+ assertEquals(Color.green, rcf.getResidueColour(true,
+ av.getResidueShading(), null, seq, 2, null)); // T
+ assertEquals(Color.magenta, rcf.getResidueColour(true,
+ av.getResidueShading(), null, seq, 5, null)); // G
+ assertEquals(Color.orange, rcf.getResidueColour(true,
+ av.getResidueShading(), null, seq, 12, null)); // F
// everything is white if showBoxes is false
assertEquals(Color.white, rcf.getResidueColour(false,
final AlignViewport av = new AlignViewport(al);
ResidueColourFinder rcf = new ResidueColourFinder();
- assertEquals(Color.white,
- rcf.getResidueColour(true, av.getResidueShading(),
- null, seq, 0, null));
- assertEquals(Color.white,
- rcf.getResidueColour(true, av.getResidueShading(),
- null, seq, 2, null));
+ assertEquals(Color.white, rcf.getResidueColour(true,
+ av.getResidueShading(), null, seq, 0, null));
+ assertEquals(Color.white, rcf.getResidueColour(true,
+ av.getResidueShading(), null, seq, 2, null));
// no change if showBoxes is false
assertEquals(Color.white, rcf.getResidueColour(false,
// gap colour specified as pink
assertEquals(Color.pink, rcf.getResidueColour(true,
- av.getResidueShading(),
- null, seq, 3, null));
+ av.getResidueShading(), null, seq, 3, null));
// everything is white if showBoxes is false
newColours[23] = null;
assertEquals(Color.white, rcf.getResidueColour(false,
- av.getResidueShading(),
- null, seq, 3, null));
+ av.getResidueShading(), null, seq, 3, null));
newColours[23] = Color.pink;
av.setGlobalColourScheme(new UserColourScheme(newColours));
assertEquals(Color.WHITE, ccs.applyConservation(colour, 4));
assertEquals(Color.WHITE, ccs.applyConservation(colour, 5));
assertEquals(Color.WHITE, ccs.applyConservation(colour, 6));
- assertEquals(new Color(235, 225, 215), ccs.applyConservation(colour, 7));
- assertEquals(new Color(215, 195, 175), ccs.applyConservation(colour, 8));
- assertEquals(new Color(195, 165, 135), ccs.applyConservation(colour, 9));
+ assertEquals(new Color(235, 225, 215),
+ ccs.applyConservation(colour, 7));
+ assertEquals(new Color(215, 195, 175),
+ ccs.applyConservation(colour, 8));
+ assertEquals(new Color(195, 165, 135),
+ ccs.applyConservation(colour, 9));
assertEquals(colour, ccs.applyConservation(colour, 10));
assertEquals(colour, ccs.applyConservation(colour, 11));
assertEquals(Color.WHITE, ccs.applyConservation(colour, 12));
colours[23] = Color.red; // gap colour
ColourSchemeI cs = new UserColourScheme(colours);
rs = new ResidueShader(cs);
-
+
assertEquals(Color.red, rs.findColour(' ', 7, null));
assertEquals(Color.blue, rs.findColour('Q', 7, null));
-
+
/*
* stub Conservation to return a given consensus string
*/
}
};
rs.setConservation(cons);
-
+
/*
* with 0% threshold, there should be no fading
*/
rs.setConservationInc(0);
assertEquals(Color.red, rs.findColour(' ', 7, null));
assertEquals(Color.blue, rs.findColour('Q', 7, null));
-
+
/*
* with 40% threshold, 'fade factor' is
* (11-score)/10 * 40/20 = (11-score)/5
protected ProfilesI getStubConsensus(final String modalResidue,
final float pid)
{
- ProfilesI consensus = new ProfilesI() {
+ ProfilesI consensus = new ProfilesI()
+ {
@Override
public ProfileI get(int i)
{
- return new ProfileI() {
+ return new ProfileI()
+ {
@Override
public void setCounts(ResidueCount residueCounts)
{
public int getNonGapped()
{
return 0;
- }};
+ }
+ };
}
@Override
{
return 0;
}
-
+
};
return consensus;
}
{
// aligned column 8 is sequence position 6
String s = ">s1\nABCDE---FGHIJKLMNOPQRSTUVWXYZ\n";
- af = new FileLoader().LoadFileWaitTillLoaded(s,
- DataSourceType.PASTE);
+ af = new FileLoader().LoadFileWaitTillLoaded(s, DataSourceType.PASTE);
av = af.getViewport();
seq = av.getAlignment().getSequenceAt(0);
fr = af.getFeatureRenderer();
@Test(groups = "Functional")
public void testFindFeatureColour_gapPosition()
{
- seq.addSequenceFeature(new SequenceFeature("Metal", "Metal", 2, 12, 0f,
- null));
+ seq.addSequenceFeature(
+ new SequenceFeature("Metal", "Metal", 2, 12, 0f, null));
fr.setColour("Metal", new FeatureColour(Color.red));
fr.featuresAdded();
av.setShowSequenceFeatures(true);
/*
* currently contact feature == type "Disulphide Bond" or "Disulfide Bond" !!
*/
- seq.addSequenceFeature(new SequenceFeature("Disulphide Bond",
- "Contact", 2, 12, Float.NaN, "Disulphide"));
+ seq.addSequenceFeature(new SequenceFeature("Disulphide Bond", "Contact",
+ 2, 12, Float.NaN, "Disulphide"));
fr.setColour("Disulphide Bond", new FeatureColour(Color.red));
fr.featuresAdded();
av.setShowSequenceFeatures(true);
@Test(groups = "Functional")
public void testFindFeatureColour_graduatedFeatureColour()
{
- seq.addSequenceFeature(new SequenceFeature("kd", "hydrophobicity", 2,
- 2, 0f, "KdGroup"));
- seq.addSequenceFeature(new SequenceFeature("kd", "hydrophobicity", 4,
- 4, 5f, "KdGroup"));
- seq.addSequenceFeature(new SequenceFeature("kd", "hydrophobicity", 7,
- 7, 10f, "KdGroup"));
+ seq.addSequenceFeature(new SequenceFeature("kd", "hydrophobicity", 2, 2,
+ 0f, "KdGroup"));
+ seq.addSequenceFeature(new SequenceFeature("kd", "hydrophobicity", 4, 4,
+ 5f, "KdGroup"));
+ seq.addSequenceFeature(new SequenceFeature("kd", "hydrophobicity", 7, 7,
+ 10f, "KdGroup"));
/*
* graduated colour from 0 to 10
fr.setColour("Metal", red);
fr.featuresAdded();
av.setShowSequenceFeatures(true);
-
+
/*
* the FeatureSettings transparency slider has range 0-70 which
* corresponds to a transparency value of 1 - 0.3
fr.setColour("Domain", green);
fr.featuresAdded();
av.setShowSequenceFeatures(true);
-
+
/*
* Domain (green) rendered above Metal (red) above background (cyan)
* 1) 0.6 * red(255, 0, 0) + 0.4 * cyan(0, 255, 255) = (153, 102, 102)
fr.setTransparency(0.6f);
Color c = finder.findFeatureColour(Color.cyan, seq, 10);
assertEquals(c, new Color(61, 194, 41));
-
+
/*
* now promote Metal above Domain
* - currently no way other than mimicking reordering of
fr.setFeaturePriority(data);
c = finder.findFeatureColour(Color.cyan, seq, 10);
assertEquals(c, new Color(153, 102, 41));
-
+
/*
* ..and turn off display of Metal
* Domain (green) above background (pink)
{
String kdFeature = "kd";
String metalFeature = "Metal";
- seq.addSequenceFeature(new SequenceFeature(kdFeature, "hydrophobicity", 2,
- 2, 0f, "KdGroup"));
- seq.addSequenceFeature(new SequenceFeature(kdFeature, "hydrophobicity", 4,
- 4, 5f, "KdGroup"));
- seq.addSequenceFeature(new SequenceFeature(metalFeature, "Fe", 4, 4,
- 5f, "MetalGroup"));
- seq.addSequenceFeature(new SequenceFeature(kdFeature, "hydrophobicity", 7,
- 7, 10f, "KdGroup"));
-
+ seq.addSequenceFeature(new SequenceFeature(kdFeature, "hydrophobicity",
+ 2, 2, 0f, "KdGroup"));
+ seq.addSequenceFeature(new SequenceFeature(kdFeature, "hydrophobicity",
+ 4, 4, 5f, "KdGroup"));
+ seq.addSequenceFeature(new SequenceFeature(metalFeature, "Fe", 4, 4, 5f,
+ "MetalGroup"));
+ seq.addSequenceFeature(new SequenceFeature(kdFeature, "hydrophobicity",
+ 7, 7, 10f, "KdGroup"));
+
/*
* kd feature has graduated colour from 0 to 10
* above threshold value of 5
fr.setFeaturePriority(data);
av.setShowSequenceFeatures(true);
-
+
/*
* position 2, column 1, score 0 - below threshold - default colour
*/
*/
c = finder.findFeatureColour(Color.blue, seq, 3);
assertEquals(c, Color.green);
-
+
/*
* position 7, column 9, score 10 - maximum colour in range
*/
gc = new FeatureColour(Color.red, Color.yellow, Color.red, Color.green,
5f, 11f);
fr.getFeatureColours().put("Cath", gc);
- gc.setAutoScaled(false); // this does little other than save a checkbox setting!
+ gc.setAutoScaled(false); // this does little other than save a checkbox
+ // setting!
assertEquals(fr.getColour(sf2), new Color(255, 213, 0));
/*
SequenceFeature sf2 = new SequenceFeature("sequence_variant", "C, CA",
3, 3, "ensembl");
seq1.addSequenceFeature(sf2);
-
+
/*
* 'find' mapped features from the peptide position
* - first with CDS features _not_ shown on peptide alignment
}
seq = new Sequence("Seq", "");
- al = new Alignment(new SequenceI[]{ seq});
-
+ al = new Alignment(new SequenceI[] { seq });
+
/*
* AlignmentAnnotation constructor works out min-max range
*/
* expect white at or below threshold of 5
*/
Color expected = col <= 5 ? Color.white
- : new Color(50 + 10 * col,
- 200 - 10 * col,
- 150 + 10 * col);
+ : new Color(50 + 10 * col, 200 - 10 * col, 150 + 10 * col);
assertEquals(result, expected, "for column " + col);
}
-
+
/*
* now make 6-10 the span of the colour range
* (annotation value == column number in this test)
*/
int factor = col - THRESHOLD_FIVE;
Color expected = col <= 5 ? Color.white
- : new Color(50 + 20 * factor,
- 200 - 20 * factor,
- 150 + 20 * factor);
+ : new Color(50 + 20 * factor, 200 - 20 * factor,
+ 150 + 20 * factor);
Color result = testee.findColour('a', col, seq);
assertEquals(result, expected, "for column " + col);
}
AnnotationColourGradient testee = new AnnotationColourGradient(ann,
minColour, maxColour, AnnotationColourGradient.BELOW_THRESHOLD);
testee = (AnnotationColourGradient) testee.getInstance(null, al);
-
+
for (int col = 0; col < WIDTH; col++)
{
Color result = testee.findColour('a', col, seq);
Color expected = col >= 5 ? Color.white
- : new Color(50 + 10 * col,
- 200 - 10 * col, 150 + 10 * col);
+ : new Color(50 + 10 * col, 200 - 10 * col, 150 + 10 * col);
assertEquals(result, expected, "for column " + col);
}
-
+
/*
* now make 0-5 the span of the colour range
* (annotation value == column number in this test)
* range is 0-5 so steps of 100/5 = 20
*/
Color expected = col >= 5 ? Color.white
- : new Color(50 + 20 * col,
- 200 - 20 * col, 150 + 20 * col);
+ : new Color(50 + 20 * col, 200 - 20 * col, 150 + 20 * col);
Color result = testee.findColour('a', col, seq);
assertEquals(result, expected, "for column " + col);
}
{
int hue = col * 20;
Color c = col == 0 ? minColour : new Color(hue, hue, hue);
- assertEquals(testee.findColour('a', col, seq), c, "for column " + col);
+ assertEquals(testee.findColour('a', col, seq), c,
+ "for column " + col);
}
}
}
* <li>white if there is no consensus</li>
* <li>white if 'residue' is a gap</li>
* <li>dark blue if residue matches consensus (or joint consensus)</li>
- * <li>else, total the residue's Blosum score with the consensus residue(s)</li>
+ * <li>else, total the residue's Blosum score with the consensus
+ * residue(s)</li>
* <ul>
* <li>if positive, light blue, else white</li>
* </ul>
}
// @formatter:on
-
+
/**
* Test for colour calculation when the consensus percentage ignores gapped
* sequences
DataSourceType.PASTE);
AlignmentI al = af.getViewport().getAlignment();
ClustalxColourScheme cs = new ClustalxColourScheme(al, null);
-
+
/*
* column 1 is 66% C which is above Clustalx threshold of 60%
*/
*/
UserColourScheme ucs = (UserColourScheme) ColourSchemeProperty
.getColourScheme(null, al,
- "R,G=red;C=blue;c=green;Q=10,20,30;S,T=11ffdd");
+ "R,G=red;C=blue;c=green;Q=10,20,30;S,T=11ffdd");
assertEquals(ucs.findColour('H'), Color.white);
assertEquals(ucs.findColour('R'), Color.red);
assertEquals(ucs.findColour('r'), Color.red);
public ColourSchemeI getInstance(AlignViewportI view,
AnnotatedCollectionI sg)
{
- final ColourSchemeI cs1 = ColourSchemes.getInstance()
- .getColourScheme(JalviewColourScheme.Taylor.toString(),
- (AnnotatedCollectionI) null);
- final ColourSchemeI cs2 = ColourSchemes.getInstance()
- .getColourScheme(JalviewColourScheme.Zappo.toString(),
- (AnnotatedCollectionI) null);
+ final ColourSchemeI cs1 = ColourSchemes.getInstance().getColourScheme(
+ JalviewColourScheme.Taylor.toString(),
+ (AnnotatedCollectionI) null);
+ final ColourSchemeI cs2 = ColourSchemes.getInstance().getColourScheme(
+ JalviewColourScheme.Zappo.toString(),
+ (AnnotatedCollectionI) null);
return new Stripy(cs1, cs2);
}
return "stripy";
}
};
-
+
/*
* a colour scheme that is Clustal but using AWT colour equivalents
*/
* in the order in which they are declared in the JalviewColourScheme enum
* (this also determines their order in Colour menus)
*/
- Iterator<ColourSchemeI> schemes = ColourSchemes.getInstance().getColourSchemes().iterator();
+ Iterator<ColourSchemeI> schemes = ColourSchemes.getInstance()
+ .getColourSchemes().iterator();
JalviewColourScheme[] jalviewSchemes = JalviewColourScheme.values();
int i = 0;
while (schemes.hasNext() && i < jalviewSchemes.length)
}
af.closeMenuItem_actionPerformed(true);
}
-
+
@Test(groups = "Functional")
public void testRegisterColourScheme()
{
fc = new FeatureColour();
fc.setColourByLabel(true);
fc.setAttributeName("CLIN_SIG");
- assertEquals("domain\tattribute|CLIN_SIG", fc.toJalviewFormat("domain"));
-
+ assertEquals("domain\tattribute|CLIN_SIG",
+ fc.toJalviewFormat("domain"));
+
/*
* colour by label (autoscaled) (an odd state you can reach by selecting
* 'above threshold', then deselecting 'threshold is min/max' then 'colour
"domain\tscore|%s|%s|noValueMax|abso|12.0|25.0|none", greenHex,
redHex);
assertEquals(expected, fc.toJalviewFormat("domain"));
-
+
/*
* colour ranges over the actual score ranges (not min/max)
*/
fc.setThreshold(12.5f);
fc.setBelowThreshold(true);
expected = String.format(
- "domain\tscore|%s|%s|noValueMax|12.0|25.0|below|12.5",
- greenHex, redHex);
+ "domain\tscore|%s|%s|noValueMax|12.0|25.0|below|12.5", greenHex,
+ redHex);
assertEquals(expected, fc.toJalviewFormat("domain"));
/*
/*
* simple colour by hex code
*/
- fc = FeatureColour.parseJalviewFeatureColour(Format
- .getHexString(Color.RED));
+ fc = FeatureColour
+ .parseJalviewFeatureColour(Format.getHexString(Color.RED));
assertTrue(fc.isSimpleColour());
assertEquals(Color.RED, fc.getColour());
public void testIsOutwithThreshold()
{
FeatureColourI fc = new FeatureColour(Color.red);
- SequenceFeature sf = new SequenceFeature("METAL", "desc", 10, 12, 1.2f, "grp");
+ SequenceFeature sf = new SequenceFeature("METAL", "desc", 10, 12, 1.2f,
+ "grp");
assertFalse(fc.isOutwithThreshold(null));
assertFalse(fc.isOutwithThreshold(sf));
String.format("r=%d,g=%d,b=%d", Color.RED.getRed(),
Color.red.getGreen(), Color.red.getBlue()),
fc.getDescription());
-
+
/*
* colour by label (no threshold)
*/
fc = new FeatureColour();
fc.setColourByLabel(true);
assertEquals("By Label", fc.getDescription());
-
+
/*
* colour by attribute text (no threshold)
*/
fc.setColourByLabel(true);
fc.setAttributeName("CLIN_SIG");
assertEquals("By CLIN_SIG", fc.getDescription());
-
+
/*
* colour by label (above score threshold)
*/
fc.setAutoScaled(false);
fc.setThreshold(12.5f);
fc.setAboveThreshold(true);
- assertEquals("By Label (Score > 12.5)",
- fc.getDescription());
-
+ assertEquals("By Label (Score > 12.5)", fc.getDescription());
+
/*
* colour by label (below score threshold)
*/
fc.setBelowThreshold(true);
- assertEquals("By Label (Score < 12.5)",
- fc.getDescription());
-
+ assertEquals("By Label (Score < 12.5)", fc.getDescription());
+
/*
* colour by attributes text (below score threshold)
*/
fc.setBelowThreshold(true);
fc.setAttributeName("CSQ", "Consequence");
- assertEquals(
- "By CSQ:Consequence (Score < 12.5)",
- fc.getDescription());
-
+ assertEquals("By CSQ:Consequence (Score < 12.5)", fc.getDescription());
+
/*
* graduated colour by score, no threshold
*/
fc = new FeatureColour(null, Color.GREEN, Color.RED, null, 12f, 25f);
assertEquals("By Score", fc.getDescription());
-
+
/*
* graduated colour by score, below threshold
*/
fc.setThreshold(12.5f);
fc.setBelowThreshold(true);
- assertEquals("By Score (< 12.5)",
- fc.getDescription());
-
+ assertEquals("By Score (< 12.5)", fc.getDescription());
+
/*
* graduated colour by score, above threshold
*/
fc.setThreshold(12.5f);
fc.setAboveThreshold(true);
fc.setAutoScaled(false);
- assertEquals("By Score (> 12.5)",
- fc.getDescription());
+ assertEquals("By Score (> 12.5)", fc.getDescription());
/*
* graduated colour by attribute, no threshold
fc.setAboveThreshold(false);
fc.setAutoScaled(false);
assertEquals("By CSQ:AF", fc.getDescription());
-
+
/*
* graduated colour by attribute, above threshold
*/
fc.setAboveThreshold(true);
fc.setAutoScaled(false);
- assertEquals("By CSQ:AF (> 12.5)",
- fc.getDescription());
+ assertEquals("By CSQ:AF (> 12.5)", fc.getDescription());
}
}
float min = -3.9f;
float max = 4.5f;
float a = (1.8f - min) / (max - min);
- assertEquals(scheme.findColour('A', 0, null),
- new Color(a, 0, 1 - a));
+ assertEquals(scheme.findColour('A', 0, null), new Color(a, 0, 1 - a));
float d = (-3.5f - min) / (max - min);
- assertEquals(scheme.findColour('D', 0, null),
- new Color(d, 0, 1 - d));
+ assertEquals(scheme.findColour('D', 0, null), new Color(d, 0, 1 - d));
assertEquals(scheme.findColour('-', 0, null), Color.WHITE);
}
@Test(groups = "Functional")
public void testGetSchemeClass()
{
- assertTrue(JalviewColourScheme.Clustal.getSchemeClass() == ClustalxColourScheme.class);
- assertTrue(JalviewColourScheme.Blosum62.getSchemeClass() == Blosum62ColourScheme.class);
- assertTrue(JalviewColourScheme.PID.getSchemeClass() == PIDColourScheme.class);
- assertTrue(JalviewColourScheme.Hydrophobic.getSchemeClass() == HydrophobicColourScheme.class);
- assertTrue(JalviewColourScheme.Zappo.getSchemeClass() == ZappoColourScheme.class);
- assertTrue(JalviewColourScheme.Taylor.getSchemeClass() == TaylorColourScheme.class);
- assertTrue(JalviewColourScheme.Helix.getSchemeClass() == HelixColourScheme.class);
- assertTrue(JalviewColourScheme.Strand.getSchemeClass() == StrandColourScheme.class);
- assertTrue(JalviewColourScheme.Turn.getSchemeClass() == TurnColourScheme.class);
- assertTrue(JalviewColourScheme.Buried.getSchemeClass() == BuriedColourScheme.class);
- assertTrue(JalviewColourScheme.Nucleotide.getSchemeClass() == NucleotideColourScheme.class);
- assertTrue(JalviewColourScheme.PurinePyrimidine.getSchemeClass() == PurinePyrimidineColourScheme.class);
- assertTrue(JalviewColourScheme.TCoffee.getSchemeClass() == TCoffeeColourScheme.class);
- assertTrue(JalviewColourScheme.RNAHelices.getSchemeClass() == RNAHelicesColour.class);
+ assertTrue(JalviewColourScheme.Clustal
+ .getSchemeClass() == ClustalxColourScheme.class);
+ assertTrue(JalviewColourScheme.Blosum62
+ .getSchemeClass() == Blosum62ColourScheme.class);
+ assertTrue(JalviewColourScheme.PID
+ .getSchemeClass() == PIDColourScheme.class);
+ assertTrue(JalviewColourScheme.Hydrophobic
+ .getSchemeClass() == HydrophobicColourScheme.class);
+ assertTrue(JalviewColourScheme.Zappo
+ .getSchemeClass() == ZappoColourScheme.class);
+ assertTrue(JalviewColourScheme.Taylor
+ .getSchemeClass() == TaylorColourScheme.class);
+ assertTrue(JalviewColourScheme.Helix
+ .getSchemeClass() == HelixColourScheme.class);
+ assertTrue(JalviewColourScheme.Strand
+ .getSchemeClass() == StrandColourScheme.class);
+ assertTrue(JalviewColourScheme.Turn
+ .getSchemeClass() == TurnColourScheme.class);
+ assertTrue(JalviewColourScheme.Buried
+ .getSchemeClass() == BuriedColourScheme.class);
+ assertTrue(JalviewColourScheme.Nucleotide
+ .getSchemeClass() == NucleotideColourScheme.class);
+ assertTrue(JalviewColourScheme.PurinePyrimidine
+ .getSchemeClass() == PurinePyrimidineColourScheme.class);
+ assertTrue(JalviewColourScheme.TCoffee
+ .getSchemeClass() == TCoffeeColourScheme.class);
+ assertTrue(JalviewColourScheme.RNAHelices
+ .getSchemeClass() == RNAHelicesColour.class);
assertTrue(JalviewColourScheme.IdColour
.getSchemeClass() == IdColourScheme.class);
}
assertEquals(JalviewColourScheme.Taylor.toString(), "Taylor");
assertEquals(JalviewColourScheme.Hydrophobic.toString(), "Hydrophobic");
assertEquals(JalviewColourScheme.Helix.toString(), "Helix Propensity");
- assertEquals(JalviewColourScheme.Strand.toString(), "Strand Propensity");
+ assertEquals(JalviewColourScheme.Strand.toString(),
+ "Strand Propensity");
assertEquals(JalviewColourScheme.Turn.toString(), "Turn Propensity");
assertEquals(JalviewColourScheme.Buried.toString(), "Buried Index");
assertEquals(JalviewColourScheme.Nucleotide.toString(), "Nucleotide");
/*
* including gaps, A should be coloured for 50% consensus
*/
- Color c = viewport
- .getResidueShading().findColour('A', 0, seq);
+ Color c = viewport.getResidueShading().findColour('A', 0, seq);
assertEquals(c, over40);
/*
* now choose to ignore gaps; colour should be for 67%
*/
viewport.setIgnoreGapsConsensus(true, af.alignPanel);
- c = viewport
- .getResidueShading().findColour('A', 0, seq);
+ c = viewport.getResidueShading().findColour('A', 0, seq);
assertEquals(c, over60);
}
}
assertFalse(new NucleotideColourScheme().isApplicableTo(peptide));
assertTrue(new NucleotideColourScheme().isApplicableTo(nucleotide));
assertFalse(new PurinePyrimidineColourScheme().isApplicableTo(peptide));
- assertTrue(new PurinePyrimidineColourScheme()
- .isApplicableTo(nucleotide));
+ assertTrue(
+ new PurinePyrimidineColourScheme().isApplicableTo(nucleotide));
assertFalse(new RNAInteractionColourScheme().isApplicableTo(peptide));
assertTrue(new RNAInteractionColourScheme().isApplicableTo(nucleotide));
* TCoffee colour requires the presence of TCoffee score annotation
*/
assertFalse(new TCoffeeColourScheme(peptide).isApplicableTo(peptide));
- assertFalse(new TCoffeeColourScheme(nucleotide)
- .isApplicableTo(nucleotide));
+ assertFalse(
+ new TCoffeeColourScheme(nucleotide).isApplicableTo(nucleotide));
AlignmentAnnotation aa = new AlignmentAnnotation("T-COFFEE", "", null);
aa.setCalcId(TCoffeeScoreFile.TCOFFEE_SCORE);
peptide.addAnnotation(aa);
aa.setCalcId(TCoffeeScoreFile.TCOFFEE_SCORE);
nucleotide.addAnnotation(aa);
assertTrue(new TCoffeeColourScheme(peptide).isApplicableTo(peptide));
- assertTrue(new TCoffeeColourScheme(nucleotide)
- .isApplicableTo(nucleotide));
+ assertTrue(
+ new TCoffeeColourScheme(nucleotide).isApplicableTo(nucleotide));
/*
* RNAHelices requires the presence of rna secondary structure
*/
assertFalse(new RNAHelicesColour(peptide).isApplicableTo(peptide));
- assertFalse(new RNAHelicesColour(nucleotide).isApplicableTo(nucleotide));
+ assertFalse(
+ new RNAHelicesColour(nucleotide).isApplicableTo(nucleotide));
// add secondary structure (small but perfectly formed)
Annotation[] ss = new Annotation[2];
ss[0] = new Annotation("", "", '{', 0f);
SequenceI pep1 = new Sequence("pep1", "APQTWLS");
SequenceI pep2 = new Sequence("pep2", "AILFQYG");
AlignmentI peptide = new Alignment(new SequenceI[] { pep1, pep2 });
-
+
/*
* demonstrate that we can 'plug in' a colour scheme with specified
* criteria for applicability; here, that there are more than 2 sequences
assertEquals("Blosum62", new Blosum62ColourScheme().getSchemeName());
assertEquals("Buried Index", new BuriedColourScheme().getSchemeName());
- assertEquals("Helix Propensity", new HelixColourScheme().getSchemeName());
- assertEquals("Hydrophobic", new HydrophobicColourScheme().getSchemeName());
- assertEquals("Strand Propensity", new StrandColourScheme().getSchemeName());
+ assertEquals("Helix Propensity",
+ new HelixColourScheme().getSchemeName());
+ assertEquals("Hydrophobic",
+ new HydrophobicColourScheme().getSchemeName());
+ assertEquals("Strand Propensity",
+ new StrandColourScheme().getSchemeName());
assertEquals("Taylor", new TaylorColourScheme().getSchemeName());
assertEquals("Turn Propensity", new TurnColourScheme().getSchemeName());
assertEquals("Zappo", new ZappoColourScheme().getSchemeName());
- assertEquals("Nucleotide", new NucleotideColourScheme().getSchemeName());
+ assertEquals("Nucleotide",
+ new NucleotideColourScheme().getSchemeName());
assertEquals("Purine/Pyrimidine",
new PurinePyrimidineColourScheme().getSchemeName());
assertEquals("RNA Interaction type",
new RNAInteractionColourScheme().getSchemeName());
assertEquals("User Defined", new UserColourScheme().getSchemeName());
- assertEquals("Score", new ScoreColourScheme(new int[] {},
- new double[] {}, 0, 0d).getSchemeName());
+ assertEquals("Score",
+ new ScoreColourScheme(new int[] {}, new double[] {}, 0, 0d)
+ .getSchemeName());
assertEquals("% Identity", new PIDColourScheme().getSchemeName());
assertEquals("Follower", new FollowerColourScheme().getSchemeName());
assertEquals("T-Coffee Scores",
float min = 0.37f;
float max = 1.7f;
float a = (0.83f - min) / (max - min);
- assertEquals(scheme.findColour('A', 0, null),
- new Color(a, a, 1 - a));
+ assertEquals(scheme.findColour('A', 0, null), new Color(a, a, 1 - a));
float d = (0.54f - min) / (max - min);
- assertEquals(scheme.findColour('D', 0, null),
- new Color(d, d, 1 - d));
+ assertEquals(scheme.findColour('D', 0, null), new Color(d, d, 1 - d));
assertEquals(scheme.findColour('-', 0, null), Color.WHITE);
}
assertEquals(Color.WHITE, cs.findColour(' '));
cs = new UserColourScheme("white");
- cs.parseAppletParameter("D,E=red; K,R,H=0022FF; c=10 , 20,30;t=orange;lowercase=blue;s=pink");
+ cs.parseAppletParameter(
+ "D,E=red; K,R,H=0022FF; c=10 , 20,30;t=orange;lowercase=blue;s=pink");
assertEquals(Color.RED, cs.findColour('D'));
assertEquals(Color.blue, cs.findColour('d'));
assertEquals(Color.RED, cs.findColour('E'));
public class AtomSpecModelTest
{
- @Test(groups="Functional")
+ @Test(groups = "Functional")
public void testGetRanges()
{
AtomSpecModel model = new AtomSpecModel();
assertEquals(as.getPdbResNum(), 12);
assertEquals(as.getChain(), "B");
assertNull(as.getPdbFile());
-
+
// no model - default to zero
as = AtomSpec.fromChimeraXAtomspec("/C:13");
assertEquals(as.getModelNumber(), 0);
assertEquals(as.getPdbResNum(), 13);
assertEquals(as.getChain(), "C");
assertNull(as.getPdbFile());
-
+
// model.submodel
as = AtomSpec.fromChimeraXAtomspec("#3.2/:15");
assertEquals(as.getModelNumber(), 3);
assertEquals(as.getPdbResNum(), 15);
assertEquals(as.getChain(), "");
assertNull(as.getPdbFile());
-
+
String spec = "3:12.B";
try
{
{
// ok
}
-
+
spec = "#3:12-14.B";
try
{
{
// ok
}
-
+
spec = "";
try
{
{
// ok
}
-
+
spec = null;
try
{
// original numbers taken from
// http://www.ebi.ac.uk/pdbe-srv/view/entry/1qcf/secondary.html
// these are in numbering relative to the subsequence above
- int coils[] = { 266, 275, 278, 287, 289, 298, 302, 316 }, helices[] = new int[]
- { 303, 315 }, sheets[] = new int[] { 267, 268, 269, 270 };
+ int coils[] = { 266, 275, 278, 287, 289, 298, 302, 316 },
+ helices[] = new int[]
+ { 303, 315 }, sheets[] = new int[] { 267, 268, 269, 270 };
StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
StructureFile pmap = ssm.setMapping(true, new SequenceI[] { uprot },
- new String[] { "A" }, "test/jalview/ext/jmol/1QCF.pdb",
+ new String[]
+ { "A" }, "test/jalview/ext/jmol/1QCF.pdb",
DataSourceType.FILE);
assertTrue(pmap != null);
SequenceI protseq = pmap.getSeqsAsArray()[0];
char expected = 'H';
for (int p : helices)
{
- Annotation a = ss.annotations[op = (uprot.findIndex(offset + p) - 1)];
- assertTrue(
- "Expected a helix at position " + p + uprot.getCharAt(op)
- + " but got coil", a != null);
+ Annotation a = ss.annotations[op = (uprot.findIndex(offset + p)
+ - 1)];
+ assertTrue("Expected a helix at position " + p
+ + uprot.getCharAt(op) + " but got coil", a != null);
assertEquals("Expected a helix at position " + p,
a.secondaryStructure, expected);
}
for (int p : sheets)
{
Annotation a = ss.annotations[uprot.findIndex(offset + p) - 1];
- assertTrue(
- "Expected a strand at position " + p + " but got coil",
+ assertTrue("Expected a strand at position " + p + " but got coil",
a != null);
assertEquals("Expected a strand at position " + p,
a.secondaryStructure, expected);
public void testPDBentryMapping() throws Exception
{
Assert.fail("This test intentionally left to fail");
- Sequence sq = new Sequence(
- "1GAQ A subseq 126 to 219",
+ Sequence sq = new Sequence("1GAQ A subseq 126 to 219",
"EIVKGVCSNFLCDLQPGDNVQITGPVGKEMLMPKDPNATIIMLATGTGIAPFRSFLWKMFFEKHDDYKFNGLGWLFLGVPTSSSLLYKEEFGKM");
Sequence sq1 = new Sequence(sq);
String inFile;
// source
StructureFile pde = ssm.setMapping(true, new SequenceI[] { sq },
new String[]
- { "A" }, inFile = "examples/1gaq.txt", DataSourceType.FILE);
+ { "A" }, inFile = "examples/1gaq.txt", DataSourceType.FILE);
assertTrue("PDB File couldn't be found", pde != null);
StructureMapping[] mp = ssm.getMapping(inFile);
assertTrue("No mappings made.", mp != null && mp.length > 0);
if (origMap.getSequence() == sq)
{
assertEquals("Mapping was incomplete.", sq.getLength() - 1,
- (origMap.getPDBResNum(sq.getEnd()) - origMap
- .getPDBResNum(sq.getStart())));
+ (origMap.getPDBResNum(sq.getEnd())
+ - origMap.getPDBResNum(sq.getStart())));
// sanity check - if this fails, mapping from first position in sequence
// we want to transfer to is not where we expect
assertEquals(1, origMap.getSeqPos(126));
{
// walk along the pdb chain's jalview sequence
int rseqpos;
- int fpos = origMap.getSeqPos(rseqpos = firstChain
- .findPosition(p));
+ int fpos = origMap
+ .getSeqPos(rseqpos = firstChain.findPosition(p));
// only look at positions where there is a corresponding position in
// mapping
if (fpos < 1)
break;
}
- Annotation a = transfer.annotations[tanpos], b = alan.annotations[p];
- assertEquals("Non-equivalent annotation element at " + p + "("
- + rseqpos + ")" + " expected at " + fpos + " (alIndex "
- + tanpos + ")", a == null ? a : a.toString(),
+ Annotation a = transfer.annotations[tanpos],
+ b = alan.annotations[p];
+ assertEquals(
+ "Non-equivalent annotation element at " + p + "("
+ + rseqpos + ")" + " expected at " + fpos
+ + " (alIndex " + tanpos + ")",
+ a == null ? a : a.toString(),
b == null ? b : b.toString());
System.out.print("(" + a + "|" + b + ")");
}
@Test(groups = { "Functional" })
public void mapFer1From3W5V() throws Exception
{
- AlignFrame seqf = new FileLoader(false)
- .LoadFileWaitTillLoaded(
- ">FER1_MAIZE/1-150 Ferredoxin-1, chloroplast precursor\nMATVLGSPRAPAFFFSSSSLRAAPAPTAVALPAAKVGIMGRSASSRRRLRAQATYNVKLITPEGEVELQVPD\nDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDVVIETHKE\nEELTGA",
- DataSourceType.PASTE, FileFormat.Fasta);
+ AlignFrame seqf = new FileLoader(false).LoadFileWaitTillLoaded(
+ ">FER1_MAIZE/1-150 Ferredoxin-1, chloroplast precursor\nMATVLGSPRAPAFFFSSSSLRAAPAPTAVALPAAKVGIMGRSASSRRRLRAQATYNVKLITPEGEVELQVPD\nDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDVVIETHKE\nEELTGA",
+ DataSourceType.PASTE, FileFormat.Fasta);
SequenceI newseq = seqf.getViewport().getAlignment().getSequenceAt(0);
StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
StructureFile pmap = ssm.setMapping(true, new SequenceI[] { newseq },
- new String[] { null }, "examples/3W5V.pdb",
- DataSourceType.FILE);
+ new String[]
+ { null }, "examples/3W5V.pdb", DataSourceType.FILE);
if (pmap == null)
{
AssertJUnit.fail("Couldn't make a mapping for 3W5V to FER1_MAIZE");
StructureImportSettings.setProcessSecondaryStructure(true);
StructureImportSettings.setVisibleChainAnnotation(true);
StructureImportSettings.setShowSeqFeatures(true);
- AlignFrame ref = new FileLoader(false)
- .LoadFileWaitTillLoaded("test/jalview/ext/jmol/1QCF.pdb",
- DataSourceType.FILE);
+ AlignFrame ref = new FileLoader(false).LoadFileWaitTillLoaded(
+ "test/jalview/ext/jmol/1QCF.pdb", DataSourceType.FILE);
SequenceI refseq = ref.getViewport().getAlignment().getSequenceAt(0);
SequenceI newseq = new Sequence(refseq.getName() + "Copy",
refseq.getSequenceAsString());
ssm.setProcessSecondaryStructure(true);
ssm.setAddTempFacAnnot(true);
StructureFile pmap = ssm.setMapping(true, new SequenceI[] { newseq },
- new String[] { null }, "test/jalview/ext/jmol/1QCF.pdb",
+ new String[]
+ { null }, "test/jalview/ext/jmol/1QCF.pdb",
DataSourceType.FILE);
assertTrue(pmap != null);
assertEquals("Original and copied sequence of different lengths.",
{
for (int p = 0, pSize = refseq.getLength(); p < pSize; p++)
{
- Annotation orig = oannot.annotations[p], tran = tannot.annotations[p];
- assertTrue("Mismatch: coil and non coil site " + p, orig == tran
- || orig != null && tran != null);
+ Annotation orig = oannot.annotations[p],
+ tran = tannot.annotations[p];
+ assertTrue("Mismatch: coil and non coil site " + p,
+ orig == tran || orig != null && tran != null);
if (tran != null)
{
assertEquals("Mismatch in secondary structure at site " + p,
{
AlignedCodonFrame acf1 = new AlignedCodonFrame();
acf1.addMap(new Sequence("s1", "ttt"), new Sequence("p1", "p"),
- new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1));
+ new MapList(new int[]
+ { 1, 3 }, new int[] { 1, 1 }, 1, 1));
AlignedCodonFrame acf2 = new AlignedCodonFrame();
acf2.addMap(new Sequence("s2", "ttt"), new Sequence("p2", "p"),
- new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1));
+ new MapList(new int[]
+ { 1, 3 }, new int[] { 1, 1 }, 1, 1));
ssm.registerMapping(acf1);
assertEquals(1, ssm.getSequenceMappings().size());
{
AlignedCodonFrame acf1 = new AlignedCodonFrame();
acf1.addMap(new Sequence("s1", "ttt"), new Sequence("p1", "p"),
- new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1));
+ new MapList(new int[]
+ { 1, 3 }, new int[] { 1, 1 }, 1, 1));
AlignedCodonFrame acf2 = new AlignedCodonFrame();
acf2.addMap(new Sequence("s2", "ttt"), new Sequence("p2", "p"),
- new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1));
+ new MapList(new int[]
+ { 1, 3 }, new int[] { 1, 1 }, 1, 1));
AlignedCodonFrame acf3 = new AlignedCodonFrame();
acf3.addMap(new Sequence("s3", "ttt"), new Sequence("p3", "p"),
- new MapList(new int[] { 1, 3 }, new int[] { 1, 1 }, 1, 1));
+ new MapList(new int[]
+ { 1, 3 }, new int[] { 1, 1 }, 1, 1));
List<AlignedCodonFrame> set1 = new ArrayList<>();
set1.add(acf1);
@Test(groups = { "Functional" })
public void testSetMapping_seqFeatures()
{
- SequenceI seq = new Sequence(
- "1GAQ|B",
+ SequenceI seq = new Sequence("1GAQ|B",
"ATYNVKLITPEGEVELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDVVIETHKEEELTGA");
StructureSelectionManager sm = new StructureSelectionManager();
sm.setProcessSecondaryStructure(true);
sm.setAddTempFacAnnot(true);
StructureFile pmap = sm.setMapping(true, new SequenceI[] { seq },
- new String[] { null }, "examples/1gaq.txt", DataSourceType.FILE);
+ new String[]
+ { null }, "examples/1gaq.txt", DataSourceType.FILE);
assertTrue(pmap != null);
assertEquals(3, pmap.getSeqs().size());
// for some reason 'BeforeMethod' (which should be inherited from
// Jalview2XmlBase isn't always called)...
Desktop.instance.closeAll_actionPerformed(null);
- try {
+ try
+ {
Thread.sleep(200);
- } catch (Exception foo) {};
+ } catch (Exception foo)
+ {
+ }
+ ;
SequenceI seq = new Sequence("4IM2|A",
"LDFCIRNIEKTVMGEISDIHTKLLRLSSSQGTIE");
String P4IM2_MISSING = "examples/testdata/4IM2_missing.pdb";
sm.setAddTempFacAnnot(true);
StructureFile pmap = sm.setMapping(true, new SequenceI[] { seq },
new String[]
- { null }, P4IM2_MISSING,
- DataSourceType.FILE);
+ { null }, P4IM2_MISSING, DataSourceType.FILE);
assertTrue(pmap != null);
assertEquals(1, pmap.getSeqs().size());
// alignment
verifySeqFeats(pdb_viewseq, offset, fdesc);
-
JalviewStructureDisplayI viewr = openStructureViaChooser(alf,
pdb_viewseq, "4IM2");
PDBEntry pdbe = seq.getPDBEntry("4IM2");
StructureSelectionManager apssm = alf.alignPanel
.getStructureSelectionManager();
- StructureMapping[] smap = apssm
- .getMapping(pdbe.getFile());
+ StructureMapping[] smap = apssm.getMapping(pdbe.getFile());
assertNotNull(smap);
assertNotNull(smap[0]);
// find the last position in the alignment sequence - this is not
{ pdbe.getFile() },
new SequenceI[][]
{ new SequenceI[] { pdb_viewseq } },
- new SequenceRenderer(alf.alignPanel.getAlignViewport()),
- alf.alignPanel);
+ new SequenceRenderer(alf.alignPanel.getAlignViewport()),
+ alf.alignPanel);
// Expected - all residues are white
for (String c : smcr)
{
// currently this test fails if trimming is enabled
Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
Boolean.FALSE.toString());
- String TEMP_FACTOR_AA="Temperature Factor";
+ String TEMP_FACTOR_AA = "Temperature Factor";
String PDBID = "4IM2";
- String FullLengthSeq = ">TBK1_HUMAN Serine/threonine-protein kinase TBK1\n" +
- "MQSTSNHLWLLSDILGQGATANVFRGRHKKTGDLFAIKVFNNISFLRPVDVQMREFEVLKKLNHKNIVKLFA\n" +
- "IEEETTTRHKVLIMEFCPCGSLYTVLEEPSNAYGLPESEFLIVLRDVVGGMNHLRENGIVHRDIKPGNIMRV\n" +
- "IGEDGQSVYKLTDFGAARELEDDEQFVSLYGTEEYLHPDMYERAVLRKDHQKKYGATVDLWSIGVTFYHAAT\n" +
- "GSLPFRPFEGPRRNKEVMYKIITGKPSGAISGVQKAENGPIDWSGDMPVSCSLSRGLQVLLTPVLANILEAD\n" +
- "QEKCWGFDQFFAETSDILHRMVIHVFSLQQMTAHKIYIHSYNTATIFHELVYKQTKIISSNQELIYEGRRLV\n" +
- "LEPGRLAQHFPKTTEENPIFVVSREPLNTIGLIYEKISLPKVHPRYDLDGDASMAKAITGVVCYACRIASTL\n" +
- "LLYQELMRKGIRWLIELIKDDYNETVHKKTEVVITLDFCIRNIEKTVKVYEKLMKINLEAAELGEISDIHTK\n" +
- "LLRLSSSQGTIETSLQDIDSRLSPGGSLADAWAHQEGTHPKDRNVEKLQVLLNCMTEIYYQFKKDKAERRLA\n" +
- "YNEEQIHKFDKQKLYYHATKAMTHFTDECVKKYEAFLNKSEEWIRKMLHLRKQLLSLTNQCFDIEEEVSKYQ\n" +
- "EYTNELQETLPQKMFTASSGIKHTMTPIYPSSNTLVEMTLGMKKLKEEMEGVVKELAENNHILERFGSLTMD\n" +
- "GGLRNVDCL";
+ String FullLengthSeq = ">TBK1_HUMAN Serine/threonine-protein kinase TBK1\n"
+ + "MQSTSNHLWLLSDILGQGATANVFRGRHKKTGDLFAIKVFNNISFLRPVDVQMREFEVLKKLNHKNIVKLFA\n"
+ + "IEEETTTRHKVLIMEFCPCGSLYTVLEEPSNAYGLPESEFLIVLRDVVGGMNHLRENGIVHRDIKPGNIMRV\n"
+ + "IGEDGQSVYKLTDFGAARELEDDEQFVSLYGTEEYLHPDMYERAVLRKDHQKKYGATVDLWSIGVTFYHAAT\n"
+ + "GSLPFRPFEGPRRNKEVMYKIITGKPSGAISGVQKAENGPIDWSGDMPVSCSLSRGLQVLLTPVLANILEAD\n"
+ + "QEKCWGFDQFFAETSDILHRMVIHVFSLQQMTAHKIYIHSYNTATIFHELVYKQTKIISSNQELIYEGRRLV\n"
+ + "LEPGRLAQHFPKTTEENPIFVVSREPLNTIGLIYEKISLPKVHPRYDLDGDASMAKAITGVVCYACRIASTL\n"
+ + "LLYQELMRKGIRWLIELIKDDYNETVHKKTEVVITLDFCIRNIEKTVKVYEKLMKINLEAAELGEISDIHTK\n"
+ + "LLRLSSSQGTIETSLQDIDSRLSPGGSLADAWAHQEGTHPKDRNVEKLQVLLNCMTEIYYQFKKDKAERRLA\n"
+ + "YNEEQIHKFDKQKLYYHATKAMTHFTDECVKKYEAFLNKSEEWIRKMLHLRKQLLSLTNQCFDIEEEVSKYQ\n"
+ + "EYTNELQETLPQKMFTASSGIKHTMTPIYPSSNTLVEMTLGMKKLKEEMEGVVKELAENNHILERFGSLTMD\n"
+ + "GGLRNVDCL";
/*
* annotation exported after importing full length sequence to desktop, opening 4IM2 and selecting 'Add Reference Annotation'.
*
* Note - tabs must be replaced with \t - Eclipse expands them to spaces otherwise.
*/
- String FullLengthAnnot = "JALVIEW_ANNOTATION\n" +
- "# Created: Mon Feb 05 15:30:20 GMT 2018\n" +
- "# Updated: Fri Feb 09 17:05:17 GMT 2018\n" +
- "\n" +
- "\n" +
- "SEQUENCE_REF\tTBK1_HUMAN\n"
+ String FullLengthAnnot = "JALVIEW_ANNOTATION\n"
+ + "# Created: Mon Feb 05 15:30:20 GMT 2018\n"
+ + "# Updated: Fri Feb 09 17:05:17 GMT 2018\n" + "\n" + "\n"
+ + "SEQUENCE_REF\tTBK1_HUMAN\n"
+ "LINE_GRAPH\tTemperature Factor\tTemperature Factor for 4im2A\t125.22|128.51|120.35|113.12|122.6|114.44|91.49|102.53|98.22|111.41|111.32|116.64|103.55|100.53|95.07|105.55|114.76|128.29|133.55|142.14|121.12|110.36|95.79|95.39|87.14|99.56|93.55|94.21|100.33|110.68|97.85|82.37|75.87|76.53|77.85|82.49|80.92|96.88|122.58|133.31|160.15|180.51|||||242.88|258.97|247.01|227.12|223.24|211.62|184.65|183.51|168.96|160.04|150.88|131.68|130.43|139.87|148.59|136.57|125.7|96.51|74.49|74.08|85.87|70.93|86.47|101.59|97.51|97.39|117.19|114.27|129.5|112.98|147.52|170.26|154.98|168.18|157.51|131.95|105.85|97.78|97.35|76.51|76.31|72.55|71.43|78.82|79.94|75.04|79.54|77.95|83.56|88.5|71.51|71.73|75.96|82.36|81.75|66.51|67.23|69.35|67.92|54.75|71.19|61.85|65.34|67.97|64.51|67.41|62.28|72.85|72.76|70.64|65.23|71.07|67.73|87.72|64.93|75.92|94.02|99.35|93.71|103.59|106.29|115.46|118.69|147.18|130.62|171.64|158.95|164.11||107.42|88.53|83.52|88.06|94.06|80.82|59.01|59.73|78.89|69.21|70.34|81.95|74.53|60.92|64.65|55.79|75.71|68.86|70.95|75.08|87.76|85.43|105.84|||||||||||||||||137.46|151.33|145.17|122.79|111.56|126.72|124.06|161.75|176.84|180.51|198.49|196.75|187.41||195.23|202.27|203.16|226.55|221.75|193.83||||||172.33|177.97|151.47|132.65|99.22|93.7|91.15|88.24|72.35|70.05|70.0|74.92|66.51|68.37|65.76|70.12|74.97|76.89|80.83|70.21|69.48|79.54|82.65|96.54|114.31|140.46|168.51|176.99|205.08|209.27|155.83|139.41|151.3|129.33|111.31|119.62|121.37|102.26|115.39|129.97|128.65|110.38|110.66|116.1|82.53|84.02|82.17|87.63|86.42|77.23|91.23|95.53|102.21|120.73|133.26|109.67|108.49|93.25|92.85|86.39|95.66|94.92|85.82|80.13|76.17|86.61|78.9|77.97|105.6|70.66|69.35|78.94|66.68|63.03|69.91|79.05|75.43|70.73|70.02|80.57|81.74|77.99|84.1|91.66|92.42|94.03|116.47|132.01|154.55|163.99|161.37|155.23|132.78|109.3|90.38|101.83|99.61|91.68|82.77|86.12|82.73|90.13|85.14|79.54|74.27|74.06|72.88|86.34|72.0|69.32|60.9|68.15|52.99|63.53|61.3|66.01|68.28|77.41|71.52|67.18|66.17|71.51|65.47|52.63|65.08|66.37|73.76|77.79|67.58|79.53|84.75|87.42|78.9|79.19|85.57|73.67|80.56|86.19|72.17|66.27|72.8|86.28|78.89|74.5|90.6|80.42|92.5|92.84|96.18|92.08|88.5|87.25|64.6|68.95|65.56|67.55|71.62|78.24|84.95|71.35|86.41|84.73|94.41|95.09|84.74|87.64|88.85|75.1|86.42|79.28|73.14|78.54|80.81|60.66|67.93|71.64|59.85|64.7|61.22|63.84|65.9|62.18|74.95|72.92|93.37|90.47|96.0|93.8|88.46|79.78|83.4|66.55|68.7|73.2|78.76|85.67|84.8|89.59|96.52|79.53|103.51|134.72|126.7|145.31|156.17|149.35|128.48|117.29|118.98|131.59|109.36|90.39|87.68|91.81|78.77|80.11|91.39|75.57|78.98|71.53|76.85|70.9|64.71|73.55|73.45|60.0|69.92|57.89|69.07|66.45|62.85|57.83|57.89|66.4|61.61|60.85|66.47|63.53|63.84|65.96|73.06|70.82|64.51|63.66|73.37|73.59|68.09|78.93|76.99|75.05|71.32|88.4|78.88|93.08|110.61|94.32|99.24|128.99|129.49|132.74|124.21|120.32|142.06|166.41|149.87|153.29|172.19|165.89|181.6|223.11|237.73|176.41|171.09|189.65|188.61|154.84|142.72|154.25|170.99|175.65|||||||110.61||||||||||158.07|170.73|167.93|198.47|212.36|181.71|157.69|163.31|138.96|120.29|131.63|152.26|125.06|136.66|148.97|129.68|120.52|135.31|136.05|119.39|124.18|128.94|123.02|103.37|128.44|134.12|118.88|120.94|130.38|124.67|112.21|113.69|123.65|132.06|114.97|110.75|92.38|101.2|103.25|94.84|85.3|82.19|89.81|98.81|83.03|68.91|65.24|70.31|63.49|86.38|71.07|62.65|63.95|66.98|58.06|68.28|62.11|63.86|67.4|68.69|69.57|68.03|74.23|75.66|70.67|81.08|81.31|82.49|88.15|95.99|92.97|100.01|113.18|122.37|110.99|122.19|159.27|147.74|133.96|111.2|115.64|126.55|107.15|102.85|117.06|116.56|109.55|96.82|98.92|96.53|86.0|88.11|92.76|85.77|79.41|93.06|86.96|76.35|72.37|74.19|68.6|67.46|74.47|76.25|66.73|73.18|75.2|88.21|84.93|75.04|71.09|82.6|80.03|76.22|75.76|83.72|75.85|79.36|90.35|86.9|78.24|95.64|97.38|86.41|85.02|91.87|87.36|77.56|81.25|91.66|83.65|77.67|85.07|89.21|92.66|92.46|89.0|100.83|96.71|94.81|101.37|111.28|124.48|119.73|127.81|134.41|132.4|140.32|140.86|166.52|160.16|168.39|176.74|174.63|172.86|168.55|155.9|132.71|113.44|113.49|123.9|151.11|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n"
- +
- "\n" +
- "";
- AlignFrame alf_full=new
- FileLoader(false).LoadFileWaitTillLoaded(FullLengthSeq,DataSourceType.PASTE);
- alf_full.loadJalviewDataFile(FullLengthAnnot, DataSourceType.PASTE, null, null);
+ + "\n" + "";
+ AlignFrame alf_full = new FileLoader(false)
+ .LoadFileWaitTillLoaded(FullLengthSeq, DataSourceType.PASTE);
+ alf_full.loadJalviewDataFile(FullLengthAnnot, DataSourceType.PASTE,
+ null, null);
AlignmentI al_full = alf_full.getViewport().getAlignment();
- AlignmentAnnotation fullseq_tf = al_full.findAnnotations(al_full.getSequences().get(0), null, TEMP_FACTOR_AA).iterator()
- .next();
+ AlignmentAnnotation fullseq_tf = al_full
+ .findAnnotations(al_full.getSequences().get(0), null,
+ TEMP_FACTOR_AA)
+ .iterator().next();
assertNotNull(fullseq_tf);
-
+
// getMappingFor
// AlignmentI al_full=alf_full.getViewport().getAlignment();
//
JalviewStructureDisplayI sview = openStructureViaChooser(alf, seq,
PDBID);
- AlignmentAnnotation subseq_tf=null;
+ AlignmentAnnotation subseq_tf = null;
assertTrue(seq.getDBRefs() != null && seq.getDBRefs().size() > 0);
-
+
if (!al.findAnnotations(seq, null, TEMP_FACTOR_AA).iterator().hasNext())
{
// FIXME JAL-2321 - don't see reference annotation on alignment the first
// verify location of secondary structure annotation
// Specific positions: LYS477 (h),THR478 (no helix), ... GLY496(no helix),
// GLU497 (helix),
-
+
// check there is or is not a tempfactor for each mapped position, and that
// values are equal for those positions.
- for (int p=seq.getStart();p<=seq.getEnd();p++)
+ for (int p = seq.getStart(); p <= seq.getEnd(); p++)
{
- Annotation orig,subseq;
+ Annotation orig, subseq;
orig = fullseq_tf.getAnnotationForPosition(p);
subseq = subseq_tf.getAnnotationForPosition(p);
if (orig == null)
}
private JalviewStructureDisplayI openStructureViaChooser(AlignFrame alf,
- SequenceI seq,
- String pDBID)
+ SequenceI seq, String pDBID)
{
SequenceI[] selectedSeqs = new SequenceI[] { seq };
// TODO: JAL-2227 - import mmCIF PISA assembly & identify master/copy chains
- @Test(groups= {"Functional"})
+ @Test(groups = { "Functional" })
public void testImportPDBPreservesChainMappings() throws IOException
{
AlignmentI importedAl = new jalview.io.FormatAdapter().readFile(
// ideally, we would match on the actual data for the 'File' handle for
// pasted files,
// see JAL-623 - pasting is still not correctly handled...
- PDBEntry importedPDB = new PDBEntry("3A6S", "", Type.PDB,
- "Paste");
+ PDBEntry importedPDB = new PDBEntry("3A6S", "", Type.PDB, "Paste");
AAStructureBindingModel binder = new AAStructureBindingModel(
new StructureSelectionManager(), new PDBEntry[]
{ importedPDB },
new SequenceI[][]
{ importedAl.getSequencesArray() }, null)
{
-
+
@Override
public void updateColours(Object source)
{
}
-
+
@Override
public void releaseReferences(Object svl)
{
}
-
+
@Override
public String[] getStructureFiles()
{
return null;
}
-
+
@Override
public void highlightAtoms(List<AtomSpec> atoms)
{
}
-
+
@Override
- public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
+ public SequenceRenderer getSequenceRenderer(
+ AlignmentViewPanel alignment)
{
return null;
}
assertEquals(chains[0][0], "A");
assertEquals(chains[0][1], "B");
}
+
AAStructureBindingModel testee;
AlignmentI al = null;
* @param pdbFiles
* @param seqs
* @param ssm
- * @param alignPanel
+ * @param alignPanel
*/
protected AAStructureBindingModel newBindingModel(PDBEntry[] pdbFiles,
- SequenceI[][] seqs,
- StructureSelectionManager ssm, AlignmentViewPanel avp)
+ SequenceI[][] seqs, StructureSelectionManager ssm,
+ AlignmentViewPanel avp)
{
AAStructureBindingModel model = new AAStructureBindingModel(ssm,
pdbFiles, seqs, null)
}
@Override
- public SequenceRenderer getSequenceRenderer(
- AlignmentViewPanel avp)
+ public SequenceRenderer getSequenceRenderer(AlignmentViewPanel avp)
{
return avp == null ? null
- : new jalview.gui.SequenceRenderer(
- avp.getAlignViewport());
+ : new jalview.gui.SequenceRenderer(avp.getAlignViewport());
}
@Override
/*
* create a data bean to hold data per structure file
*/
- AAStructureBindingModel.SuperposeData[] structs = new AAStructureBindingModel.SuperposeData[testee.getStructureFiles().length];
+ AAStructureBindingModel.SuperposeData[] structs = new AAStructureBindingModel.SuperposeData[testee
+ .getStructureFiles().length];
for (int i = 0; i < structs.length; i++)
{
- structs[i] = new AAStructureBindingModel.SuperposeData(al.getWidth(), "0");
+ structs[i] = new AAStructureBindingModel.SuperposeData(al.getWidth(),
+ "0");
}
/*
* initialise BitSet of 'superposable columns' to true (would be false for
matched.set(i);
}
- int refStructure = testee
- .findSuperposableResidues(al, matched, structs);
+ int refStructure = testee.findSuperposableResidues(al, matched,
+ structs);
assertEquals(refStructure, 0);
@Test(groups = { "Functional" })
public void testFindSuperposableResidues_hiddenColumn()
{
- AAStructureBindingModel.SuperposeData[] structs = new AAStructureBindingModel.SuperposeData[al.getHeight()];
+ AAStructureBindingModel.SuperposeData[] structs = new AAStructureBindingModel.SuperposeData[al
+ .getHeight()];
for (int i = 0; i < structs.length; i++)
{
- structs[i] = new AAStructureBindingModel.SuperposeData(al.getWidth(), "0");
+ structs[i] = new AAStructureBindingModel.SuperposeData(al.getWidth(),
+ "0");
}
/*
* initialise BitSet of 'superposable columns' to true (would be false for
// treat column 5 of the alignment as hidden
matched.clear(4);
- int refStructure = testee
- .findSuperposableResidues(al, matched, structs);
+ int refStructure = testee.findSuperposableResidues(al, matched,
+ structs);
assertEquals(refStructure, 0);
pdbFiles[0] = new PDBEntry("PDB1", "A", Type.PDB, "seq1.pdb");
pdbFiles[1] = new PDBEntry("PDB2", "B", Type.PDB, "seq2.pdb");
StructureSelectionManager ssm = new StructureSelectionManager();
-
+
/*
* map residues 1-10 to residues 21-30 (atoms 105-150) in structures
*/
Map<Object, AtomSpecModel> colours = binding.buildColoursMap(ssm, seqs,
af.alignPanel);
ChimeraCommands helper = new ChimeraCommands();
-
+
/*
* M colour is #82827d (see strand.html help page)
* sequence residue 1 mapped to structure residue 21
Color mColor = new Color(0x82827d);
AtomSpecModel atomSpec = colours.get(mColor);
assertNotNull(atomSpec);
- assertEquals(helper.getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY), "#0:21.A|#1:21.B");
+ assertEquals(helper.getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY),
+ "#0:21.A|#1:21.B");
/*
* H colour is #60609f, seq1.2 mapped to structure 0 residue 22
Color hColor = new Color(0x60609f);
atomSpec = colours.get(hColor);
assertNotNull(atomSpec);
- assertEquals(helper.getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY), "#0:22.A");
+ assertEquals(helper.getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY),
+ "#0:22.A");
/*
* V colour is #ffff00, seq2.2 mapped to structure 1 residue 22
Color vColor = new Color(0xffff00);
atomSpec = colours.get(vColor);
assertNotNull(atomSpec);
- assertEquals(helper.getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY), "#1:22.B");
+ assertEquals(helper.getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY),
+ "#1:22.B");
/*
* hidden columns are Gray (128, 128, 128)
Color gray = new Color(128, 128, 128);
atomSpec = colours.get(gray);
assertNotNull(atomSpec);
- assertEquals(helper.getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY), "#0:23-25.A|#1:23-25.B");
+ assertEquals(helper.getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY),
+ "#0:23-25.A|#1:23-25.B");
/*
* S and G are both coloured #4949b6, structure residues 26-30
import org.testng.Assert;
import org.testng.annotations.Test;
-public class AppletUrlProviderFactoryTest {
+public class AppletUrlProviderFactoryTest
+{
@Test(groups = { "Functional" })
public void testCreateUrlProvider()
// default url correctly set
Assert.assertEquals(prov.getPrimaryUrlId(), "Test2");
Assert.assertEquals(prov.getPrimaryUrl("FER_CAPAN"),
- defaultUrl.replace("$SEQUENCE_ID$",
- "FER_CAPAN"));
+ defaultUrl.replace("$SEQUENCE_ID$", "FER_CAPAN"));
List<UrlLinkDisplay> allLinks = prov.getLinksForTable();
private static final HashMap<String, String> urlMap = new HashMap<String, String>()
{
{
- put("TEST","http://someurl.blah/$DB_ACCESSION$");
- put("ANOTHER","http://test/t$SEQUENCE_ID$");
+ put("TEST", "http://someurl.blah/$DB_ACCESSION$");
+ put("ANOTHER", "http://test/t$SEQUENCE_ID$");
put("TEST2", "http://address/$SEQUENCE_ID$");
put("SRS", "http://theSRSlink/$SEQUENCE_ID$");
}
};
-
+
private static final HashMap<String, String> unselUrlMap = new HashMap<String, String>()
{
{
private static final String[] dlinks = {
"TEST|http://someurl.blah/$DB_ACCESSION$",
"ANOTHER|http://test/t$SEQUENCE_ID$",
- "TEST2|http://address/$SEQUENCE_ID$",
- UrlConstants.DEFAULT_STRING };
+ "TEST2|http://address/$SEQUENCE_ID$", UrlConstants.DEFAULT_STRING };
private static final String[] unselDlinks = {
"NON1|http://x/y/$DB_ACCESSION$", "NON2|http://a/b/c/$DB_ACCESSION" };
private static final Vector<String> unselDisplayLinks = new Vector<String>(
Arrays.asList(unselDlinks));
- private static final String[] dlinks2 = { "a|http://x.y.z/$SEQUENCE_ID$" };
+ private static final String[] dlinks2 = {
+ "a|http://x.y.z/$SEQUENCE_ID$" };
private static final Vector<String> displayLinks2 = new Vector<String>(
Arrays.asList(dlinks2));
{
UrlProviderI customProv = new CustomUrlProvider(cachedList,
unselectedList);
-
+
// default url can be set
assertTrue(customProv.setPrimaryUrl("ANOTHER"));
assertFalse(customProv.setPrimaryUrl("No default"));
result = customProv.getPrimaryUrl("testid");
assertEquals(null, result);
-
+
// choosing the default picks the DEFAULT_STRING option
customProv.choosePrimaryUrl();
result = customProv.getPrimaryUrl("seqid");
- assertEquals(
- UrlConstants.DEFAULT_STRING.split("\\|")[1].split("\\$")[0]
- + "seqid",
- result);
+ assertEquals(UrlConstants.DEFAULT_STRING.split("\\|")[1].split("\\$")[0]
+ + "seqid", result);
}
/*
bw.close();
} catch (IOException e)
{
- System.out
- .println("Error initialising DesktopUrlProviderFactoryTest test: "
+ System.out.println(
+ "Error initialising DesktopUrlProviderFactoryTest test: "
+ e.getMessage());
}
// 5 links in menu (cachedUrlList)
Assert.assertEquals(menulinks.size(), 5);
- Assert.assertTrue(menulinks
- .contains("Test1|http://blah.blah/$SEQUENCE_ID$"));
- Assert.assertTrue(menulinks
- .contains("Test2|http://test2/$DB_ACCESSION$"));
- Assert.assertTrue(menulinks
- .contains("Test3|http://test3/$SEQUENCE_ID$"));
- Assert.assertTrue(menulinks
- .contains("UniProt Knowledgebase|http://identifiers.org/uniprot/$DB_ACCESSION$|uniprot"));
- Assert.assertTrue(menulinks
- .contains("InterPro|http://identifiers.org/interpro/$DB_ACCESSION$|interpro"));
+ Assert.assertTrue(
+ menulinks.contains("Test1|http://blah.blah/$SEQUENCE_ID$"));
+ Assert.assertTrue(
+ menulinks.contains("Test2|http://test2/$DB_ACCESSION$"));
+ Assert.assertTrue(
+ menulinks.contains("Test3|http://test3/$SEQUENCE_ID$"));
+ Assert.assertTrue(menulinks.contains(
+ "UniProt Knowledgebase|http://identifiers.org/uniprot/$DB_ACCESSION$|uniprot"));
+ Assert.assertTrue(menulinks.contains(
+ "InterPro|http://identifiers.org/interpro/$DB_ACCESSION$|interpro"));
}
}
+ "\"url\":\"http://identifiers.org/interpro\"},"
+ "{\"id\":\"MIR:00000372\",\"name\":\"ENA\",\"pattern\":\"^[A-Z]+[0-9]+(\\.\\d+)?$\",\"definition\":\"The European Nucleotide Archive (ENA),\""
+ "\"prefix\":\"ena.embl\",\"url\":\"http://identifiers.org/ena.embl\"}]}";
-
+
private static final String[] dlinks = {
"UniProt Knowledgebase|http://identifiers.org/uniprot/$DB_ACCESSION$|uniprot",
"InterPro|http://identifiers.org/interpro/$DB_ACCESSION$|interpro",
+ "MIR:00000011|http://identifiers.org/interpro/$DB_ACCESSION$"
+ "MIR:00000372|http://identifiers.org/ena.embl/$DB_ACCESSION$";
- private static final String[] unselDlinks = { "ChEBI|http://identifiers.org/chebi/$DB_ACCESSION$" };
+ private static final String[] unselDlinks = {
+ "ChEBI|http://identifiers.org/chebi/$DB_ACCESSION$" };
private static final Vector<String> displayLinks = new Vector<String>(
- Arrays.asList(dlinks));
-
+ Arrays.asList(dlinks));
+
private static final Vector<String> unselDisplayLinks = new Vector<String>(
Arrays.asList(unselDlinks));
private String testfile = "";
-
@BeforeClass(alwaysRun = true)
public void setup()
{
// creation from cached id list
String idList = "MIR:00000005|MIR:00000011|MIR:00000372";
UrlProviderI idProv = new IdentifiersUrlProvider(idList);
-
+
assertTrue(displayLinks.containsAll(idProv.getLinksForMenu()));
// because UrlProvider does not guarantee order of links, we can't just
// creation from cached id list
String idList = "MIR:00000005|MIR:00000011|MIR:00000372";
UrlProviderI idProv = new IdentifiersUrlProvider(idList);
-
+
// initially no default
assertEquals(null, idProv.getPrimaryUrl("seqid"));
-
+
// set and then retrieve default
assertTrue(idProv.setPrimaryUrl("MIR:00000005"));
assertEquals("http://identifiers.org/uniprot/seqid",
idProv.getPrimaryUrl("seqid"));
// ids less than length 4 return null
- assertEquals(null,
- idProv.getPrimaryUrl("123"));
+ assertEquals(null, idProv.getPrimaryUrl("123"));
// attempt to set bad default
assertFalse(idProv.setPrimaryUrl("MIR:00001234"));
import org.testng.Assert;
import org.testng.annotations.Test;
-public class UrlLinkDisplayTest {
+public class UrlLinkDisplayTest
+{
@Test(groups = { "Functional" })
public void testDisplayColumnNames()
// default only editable if link contains $SEQUENCE_ID$
UrlLink link = new UrlLink("Test Url",
- "http://identifiers.org/$DB_ACCESSION$",
- "TestName");
+ "http://identifiers.org/$DB_ACCESSION$", "TestName");
UrlLinkDisplay u = new UrlLinkDisplay("Test", link, false, false);
Assert.assertFalse(u.isEditable(UrlLinkDisplay.PRIMARY));
UrlLinkDisplay u = new UrlLinkDisplay("Test", link, false, false);
// Url initially as input in link
- Assert.assertEquals(u.getUrl(), "http://identifiers.org/$DB_ACCESSION$");
+ Assert.assertEquals(u.getUrl(),
+ "http://identifiers.org/$DB_ACCESSION$");
// Setting updates url
u.setUrl("http://something.new/$SEQUENCE_ID$");
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
-public class UrlLinkTableModelTest {
+public class UrlLinkTableModelTest
+{
private static final String inmenu = "TEST|http://someurl.blah/$DB_ACCESSION$|"
+ "ANOTHER|http://test/t$SEQUENCE_ID$|"
Assert.assertEquals(m.getValueAt(10, 4), false);
// check data source has new row insrte
- Assert.assertTrue(prov.getLinksForMenu().contains(
- "newname" + SEP + "newurl"));
+ Assert.assertTrue(
+ prov.getLinksForMenu().contains("newname" + SEP + "newurl"));
}
/*
// get original default
int olddefault;
boolean isDefault = false;
- for (olddefault = 0; olddefault < m.getRowCount() && !isDefault; olddefault++)
+ for (olddefault = 0; olddefault < m.getRowCount()
+ && !isDefault; olddefault++)
{
isDefault = (boolean) m.getValueAt(olddefault, 3);
}
}
// check table updated
- Assert.assertTrue(prov.writeUrlsAsString(true).contains(
- "descchanged" + SEP + m.getValueAt(6, 2)));
- Assert.assertTrue(prov.writeUrlsAsString(true).contains(
- m.getValueAt(7, 1) + SEP + "urlchanged"));
- Assert.assertTrue(prov.writeUrlsAsString(false).contains(
- (String) m.getValueAt(8, 1)));
+ Assert.assertTrue(prov.writeUrlsAsString(true)
+ .contains("descchanged" + SEP + m.getValueAt(6, 2)));
+ Assert.assertTrue(prov.writeUrlsAsString(true)
+ .contains(m.getValueAt(7, 1) + SEP + "urlchanged"));
+ Assert.assertTrue(prov.writeUrlsAsString(false)
+ .contains((String) m.getValueAt(8, 1)));
Assert.assertEquals(prov.getPrimaryUrl("seqid"), m.getValueAt(6, 2)
.toString().replace(DELIM + SEQUENCE_ID + DELIM, "seqid"));
}
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
+public class UrlProviderTest
+{
-public class UrlProviderTest {
-
// Test identifiers.org download file
private static final String testIdOrgString = "{\"Local\": [{\"id\":\"MIR:00000002\",\"name\":\"ChEBI\",\"pattern\":\"^CHEBI:\\d+$\","
- + "\"definition\":\"Chemical Entities of Biological Interest (ChEBI)\",\"prefix\":\"chebi\","
- + "\"url\":\"http://identifiers.org/chebi\"},{\"id\":\"MIR:00000005\",\"name\":\"UniProt Knowledgebase\","
- + "\"pattern\":\"^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\\.\\d+)?$\","
- + "\"definition\":\"The UniProt Knowledgebase (UniProtKB)\",\"prefix\":\"uniprot\",\"url\":\"http://identifiers.org/uniprot\"},"
- + "{\"id\":\"MIR:00000011\",\"name\":\"InterPro\",\"pattern\":\"^IPR\\d{6}$\",\"definition\":\"InterPro\",\"prefix\":\"interpro\","
- + "\"url\":\"http://identifiers.org/interpro\"},"
- + "{\"id\":\"MIR:00000372\",\"name\":\"ENA\",\"pattern\":\"^[A-Z]+[0-9]+(\\.\\d+)?$\",\"definition\":\"The European Nucleotide Archive (ENA),\""
+ + "\"definition\":\"Chemical Entities of Biological Interest (ChEBI)\",\"prefix\":\"chebi\","
+ + "\"url\":\"http://identifiers.org/chebi\"},{\"id\":\"MIR:00000005\",\"name\":\"UniProt Knowledgebase\","
+ + "\"pattern\":\"^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2})|([O,P,Q][0-9][A-Z, 0-9][A-Z, 0-9][A-Z, 0-9][0-9])(\\.\\d+)?$\","
+ + "\"definition\":\"The UniProt Knowledgebase (UniProtKB)\",\"prefix\":\"uniprot\",\"url\":\"http://identifiers.org/uniprot\"},"
+ + "{\"id\":\"MIR:00000011\",\"name\":\"InterPro\",\"pattern\":\"^IPR\\d{6}$\",\"definition\":\"InterPro\",\"prefix\":\"interpro\","
+ + "\"url\":\"http://identifiers.org/interpro\"},"
+ + "{\"id\":\"MIR:00000372\",\"name\":\"ENA\",\"pattern\":\"^[A-Z]+[0-9]+(\\.\\d+)?$\",\"definition\":\"The European Nucleotide Archive (ENA),\""
+ "\"prefix\":\"ena.embl\",\"url\":\"http://identifiers.org/ena.embl\"}]}";
private UrlProviderI prov;
@BeforeMethod(alwaysRun = true)
public void setup()
{
- // make a dummy identifiers.org download file
- File temp = null;
-
- try
- {
- temp = File.createTempFile("tempfile", ".tmp");
- temp.deleteOnExit();
- BufferedWriter bw = new BufferedWriter(new FileWriter(temp));
- bw.write(testIdOrgString);
- bw.close();
- } catch (IOException e)
- {
- System.out.println("Error initialising UrlProviderTest test: "
- + e.getMessage());
- }
-
- IdOrgSettings.setDownloadLocation(temp.getPath());
+ // make a dummy identifiers.org download file
+ File temp = null;
+
+ try
+ {
+ temp = File.createTempFile("tempfile", ".tmp");
+ temp.deleteOnExit();
+ BufferedWriter bw = new BufferedWriter(new FileWriter(temp));
+ bw.write(testIdOrgString);
+ bw.close();
+ } catch (IOException e)
+ {
+ System.out.println(
+ "Error initialising UrlProviderTest test: " + e.getMessage());
+ }
+
+ IdOrgSettings.setDownloadLocation(temp.getPath());
String defaultUrlString = "No default";
String cachedUrlList = "MIR:00000005|MIR:00000011|Test1|http://blah.blah/$SEQUENCE_ID$|"
DesktopUrlProviderFactory factory = new DesktopUrlProviderFactory(
defaultUrlString, cachedUrlList, userUrlList);
prov = factory.createUrlProvider();
- }
+ }
@Test(groups = { "Functional" })
public void testInitUrlProvider()
// 6 links in menu (cachedUrlList) + new default
Assert.assertEquals(menulinks.size(), 6);
- Assert.assertTrue(menulinks
- .contains("Test1|http://blah.blah/$SEQUENCE_ID$"));
- Assert.assertTrue(menulinks
- .contains("Test2|http://test2/$DB_ACCESSION$"));
- Assert.assertTrue(menulinks
- .contains("Test3|http://test3/$SEQUENCE_ID$"));
- Assert.assertTrue(menulinks
- .contains("UniProt Knowledgebase|http://identifiers.org/uniprot/$DB_ACCESSION$|uniprot"));
- Assert.assertTrue(menulinks
- .contains("InterPro|http://identifiers.org/interpro/$DB_ACCESSION$|interpro"));
- Assert.assertTrue(menulinks.contains(UrlConstants.DEFAULT_LABEL
- + UrlConstants.SEP + emblUrl));
+ Assert.assertTrue(
+ menulinks.contains("Test1|http://blah.blah/$SEQUENCE_ID$"));
+ Assert.assertTrue(
+ menulinks.contains("Test2|http://test2/$DB_ACCESSION$"));
+ Assert.assertTrue(
+ menulinks.contains("Test3|http://test3/$SEQUENCE_ID$"));
+ Assert.assertTrue(menulinks.contains(
+ "UniProt Knowledgebase|http://identifiers.org/uniprot/$DB_ACCESSION$|uniprot"));
+ Assert.assertTrue(menulinks.contains(
+ "InterPro|http://identifiers.org/interpro/$DB_ACCESSION$|interpro"));
+ Assert.assertTrue(menulinks.contains(
+ UrlConstants.DEFAULT_LABEL + UrlConstants.SEP + emblUrl));
}
@Test(groups = { "Functional" })
}
@Test(
- groups = { "Functional" },
- expectedExceptions = { IllegalArgumentException.class })
+ groups =
+ { "Functional" },
+ expectedExceptions =
+ { IllegalArgumentException.class })
public void testSetDefaultUrlWrongly()
{
// don't allow default to be a non-key
/*
* value two-thirds of the way between min and max
*/
- col = ColorUtils
- .getGraduatedColour(30f, 10f, minColour, 40f, maxColour);
+ col = ColorUtils.getGraduatedColour(30f, 10f, minColour, 40f,
+ maxColour);
assertEquals(153, col.getRed());
// Color constructor rounds float value to nearest int
assertEquals(167, col.getGreen());
/*
* value = min
*/
- col = ColorUtils
- .getGraduatedColour(10f, 10f, minColour, 30f, maxColour);
+ col = ColorUtils.getGraduatedColour(10f, 10f, minColour, 30f,
+ maxColour);
assertEquals(minColour, col);
/*
* value = max
*/
- col = ColorUtils
- .getGraduatedColour(30f, 10f, minColour, 30f, maxColour);
+ col = ColorUtils.getGraduatedColour(30f, 10f, minColour, 30f,
+ maxColour);
assertEquals(maxColour, col);
/*
/*
* value > max
*/
- col = ColorUtils
- .getGraduatedColour(40f, 10f, minColour, 30f, maxColour);
+ col = ColorUtils.getGraduatedColour(40f, 10f, minColour, 30f,
+ maxColour);
assertEquals(maxColour, col);
/*
* min = max
*/
- col = ColorUtils
- .getGraduatedColour(40f, 10f, minColour, 10f, maxColour);
+ col = ColorUtils.getGraduatedColour(40f, 10f, minColour, 10f,
+ maxColour);
assertEquals(minColour, col);
}
assertNull(ColorUtils.parseColourString(null));
assertNull(ColorUtils.parseColourString("rubbish"));
assertEquals(Color.WHITE, ColorUtils.parseColourString("-1"));
- assertNull(ColorUtils.parseColourString(String
- .valueOf(Integer.MAX_VALUE)));
+ assertNull(ColorUtils
+ .parseColourString(String.valueOf(Integer.MAX_VALUE)));
assertNull(ColorUtils.parseColourString("100,200,300")); // out of range
assertNull(ColorUtils.parseColourString("100,200")); // too few
assertNull(ColorUtils.parseColourString("100,200,100,200")); // too many
}
@Test(groups = "Functional")
- public void testGetAWTColorFromName() {
+ public void testGetAWTColorFromName()
+ {
assertEquals(Color.white, ColorUtils.getAWTColorFromName("white"));
assertEquals(Color.white, ColorUtils.getAWTColorFromName("White"));
assertEquals(Color.white, ColorUtils.getAWTColorFromName("WHITE"));
public void testCreateColourFromName()
{
assertEquals(Color.white, ColorUtils.createColourFromName(null));
- assertEquals(new Color(20, 20, 20), ColorUtils.createColourFromName(""));
+ assertEquals(new Color(20, 20, 20),
+ ColorUtils.createColourFromName(""));
assertEquals(new Color(98, 131, 171),
ColorUtils.createColourFromName("None")); // no special treatment!
assertEquals(new Color(123, 211, 122),
{
SequenceI seq = new Sequence("eightypercent", "agctuAGCPV");
assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
- assertFalse(Comparison.isNucleotide(new SequenceI[][] { new SequenceI[]
- { seq } }));
+ assertFalse(
+ Comparison.isNucleotide(new SequenceI[][]
+ { new SequenceI[] { seq } }));
seq = new Sequence("eightyfivepercent", "agctuAGCPVagctuAGCUV");
assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
/*
* 90% DNA but one protein sequence - expect false
*/
- assertFalse(Comparison.isNucleotide(new SequenceI[] { seq, seq, seq,
- seq, seq, seq, seq, seq, seq, seq2 }));
- assertFalse(Comparison.isNucleotide(new SequenceI[][] {
- new SequenceI[] { seq }, new SequenceI[] { seq, seq, seq },
- new SequenceI[] { seq, seq, seq, seq, seq, seq2 } }));
+ assertFalse(
+ Comparison.isNucleotide(new SequenceI[]
+ { seq, seq, seq, seq, seq, seq, seq, seq, seq, seq2 }));
+ assertFalse(
+ Comparison.isNucleotide(new SequenceI[][]
+ { new SequenceI[] { seq }, new SequenceI[] { seq, seq, seq },
+ new SequenceI[]
+ { seq, seq, seq, seq, seq, seq2 } }));
/*
* 80% DNA but one protein sequence - Expect false
*/
- assertFalse(Comparison.isNucleotide(new SequenceI[] { seq, seq, seq,
- seq, seq, seq, seq, seq, seq2, seq2 }));
- assertFalse(Comparison.isNucleotide(new SequenceI[][] { new SequenceI[]
- { seq }, new SequenceI[] { seq, seq, seq },
- new SequenceI[] { seq, seq, seq, seq, seq2, seq2, null } }));
+ assertFalse(
+ Comparison.isNucleotide(new SequenceI[]
+ { seq, seq, seq, seq, seq, seq, seq, seq, seq2, seq2 }));
+ assertFalse(
+ Comparison.isNucleotide(new SequenceI[][]
+ { new SequenceI[] { seq }, new SequenceI[] { seq, seq, seq },
+ new SequenceI[]
+ { seq, seq, seq, seq, seq2, seq2, null } }));
seq = new Sequence("ProteinThatLooksLikeDNA", "WYATGCCTGAgtcgt");
// 12/14 = 85.7%
DBRefEntry ref2 = new DBRefEntry("UNIPROT", "1.2", "A12346");
// Source is converted to upper-case by this constructor!
DBRefEntry ref3 = new DBRefEntry("Uniprot", "1.2", "A12347");
- List<DBRefEntry> dbrefs = Arrays.asList(new DBRefEntry[] { ref1, ref2, ref3 });
+ List<DBRefEntry> dbrefs = Arrays
+ .asList(new DBRefEntry[]
+ { ref1, ref2, ref3 });
String[] sources = new String[] { "EMBL", "UNIPROT" };
List<DBRefEntry> selected = DBRefUtils.selectRefs(dbrefs, sources);
assertEquals("PDB", DBRefUtils.getCanonicalName("Pdb"));
assertEquals("UNIPROT",
DBRefUtils.getCanonicalName("uniprotkb/swiss-prot"));
- assertEquals("UNIPROT", DBRefUtils.getCanonicalName("uniprotkb/trembl"));
+ assertEquals("UNIPROT",
+ DBRefUtils.getCanonicalName("uniprotkb/trembl"));
assertEquals("UNIPROT",
DBRefUtils.getCanonicalName("UNIPROTKB/SWISS-PROT"));
- assertEquals("UNIPROT", DBRefUtils.getCanonicalName("UNIPROTKB/TREMBL"));
+ assertEquals("UNIPROT",
+ DBRefUtils.getCanonicalName("UNIPROTKB/TREMBL"));
assertEquals("UNIPROTKB/SWISS-CHEESE",
DBRefUtils.getCanonicalName("UNIPROTKB/SWISS-CHEESE"));
assertEquals("ENSEMBL", DBRefUtils.getCanonicalName("Ensembl"));
assertEquals("pfam", DBRefUtils.getCanonicalName("pfam"));
}
+
/**
* Test 'parsing' a DBRef - non PDB case
*/
DBRefEntry ref4 = new DBRefEntry("EMBLCDS", "1", "A1234"); // no match
// ref5 matches although it has a mapping - ignored
DBRefEntry ref5 = new DBRefEntry("EMBL", "1", "A1234");
- ref5.setMap(new Mapping(new MapList(new int[] { 1, 1 }, new int[] { 1,
- 1 }, 1, 1)));
+ ref5.setMap(
+ new Mapping(new MapList(new int[]
+ { 1, 1 }, new int[] { 1, 1 }, 1, 1)));
- List<DBRefEntry> matches = DBRefUtils.searchRefs(
- Arrays.asList(new DBRefEntry[] {
- ref1, ref2, ref3, ref4, ref5 }), target, DBRefUtils.SEARCH_MODE_FULL);
+ List<DBRefEntry> matches = DBRefUtils
+ .searchRefs(Arrays.asList(new DBRefEntry[]
+ { ref1, ref2, ref3, ref4, ref5 }), target,
+ DBRefUtils.SEARCH_MODE_FULL);
assertEquals(3, matches.size());
assertSame(ref1, matches.get(0));
assertSame(ref2, matches.get(1));
public void testSearchRefs_withMapping()
{
DBRefEntry target = new DBRefEntry("EMBL", "2", "A1234");
- final Mapping map1 = new Mapping(new MapList(new int[] { 1, 1 },
- new int[] { 1, 1 }, 1, 1));
+ final Mapping map1 = new Mapping(
+ new MapList(new int[]
+ { 1, 1 }, new int[] { 1, 1 }, 1, 1));
target.setMap(map1);
// these all match target iff mappings match
DBRefEntry ref1 = new DBRefEntry("EMBL", "1", "A1234"); // no map: matches
DBRefEntry ref2 = new DBRefEntry("EMBL", "1", "A1234"); // =map: matches
- final Mapping map2 = new Mapping(new MapList(new int[] { 1, 1 },
- new int[] { 1, 1 }, 1, 1));
+ final Mapping map2 = new Mapping(
+ new MapList(new int[]
+ { 1, 1 }, new int[] { 1, 1 }, 1, 1));
ref2.setMap(map2);
// different map: no match
DBRefEntry ref3 = new DBRefEntry("EMBL", "1", "A1234");
- final Mapping map3 = new Mapping(new MapList(new int[] { 1, 1 },
- new int[] { 1, 1 }, 2, 2));
+ final Mapping map3 = new Mapping(
+ new MapList(new int[]
+ { 1, 1 }, new int[] { 1, 1 }, 2, 2));
ref3.setMap(map3);
- List<DBRefEntry> matches = DBRefUtils.searchRefs(
- Arrays.asList(new DBRefEntry[] {
- ref1, ref2, ref3 }), target, DBRefUtils.SEARCH_MODE_FULL);
+ List<DBRefEntry> matches = DBRefUtils
+ .searchRefs(Arrays.asList(new DBRefEntry[]
+ { ref1, ref2, ref3 }), target, DBRefUtils.SEARCH_MODE_FULL);
assertEquals(2, matches.size());
assertSame(ref1, matches.get(0));
assertSame(ref2, matches.get(1));
DBRefEntry ref4 = new DBRefEntry("EMBLCDS", "1", "A1235"); // no match
// ref5 matches although it has a mapping - ignored
DBRefEntry ref5 = new DBRefEntry("EMBL", "1", "A1234");
- ref5.setMap(new Mapping(new MapList(new int[] { 1, 1 }, new int[] { 1,
- 1 }, 1, 1)));
+ ref5.setMap(
+ new Mapping(new MapList(new int[]
+ { 1, 1 }, new int[] { 1, 1 }, 1, 1)));
- List<DBRefEntry> dbrefs = Arrays.asList(new DBRefEntry[] {
- ref1, ref2, ref3, ref4, ref5 });
+ List<DBRefEntry> dbrefs = Arrays
+ .asList(new DBRefEntry[]
+ { ref1, ref2, ref3, ref4, ref5 });
List<DBRefEntry> matches = DBRefUtils.searchRefs(dbrefs, "A1234");
assertEquals(3, matches.size());
assertSame(ref1, matches.get(0));
DBRefEntry ref4 = new DBRefEntry("EMBLCDS", "1", "A1234"); // no match
// ref5 matches although it has a mapping - ignored
DBRefEntry ref5 = new DBRefEntry("EMBL", "1", "A1237");
- ref5.setMap(new Mapping(new MapList(new int[] { 1, 1 }, new int[] { 1,
- 1 }, 1, 1)));
+ ref5.setMap(
+ new Mapping(new MapList(new int[]
+ { 1, 1 }, new int[] { 1, 1 }, 1, 1)));
- List<DBRefEntry> matches = DBRefUtils.searchRefs(
- Arrays.asList(new DBRefEntry[] {
- ref1, ref2, ref3, ref4, ref5 }), target, DBRefUtils.SEARCH_MODE_FULL);
+ List<DBRefEntry> matches = DBRefUtils
+ .searchRefs(Arrays.asList(new DBRefEntry[]
+ { ref1, ref2, ref3, ref4, ref5 }), target,
+ DBRefUtils.SEARCH_MODE_FULL);
assertEquals(4, matches.size());
assertSame(ref1, matches.get(0));
assertSame(ref2, matches.get(1));
/*
* join of two complements
*/
- ranges = DnaUtils
- .parseLocation("join(complement(4918..5163),complement(2691..4571))");
+ ranges = DnaUtils.parseLocation(
+ "join(complement(4918..5163),complement(2691..4571))");
assertEquals(2, ranges.size());
assertEquals(5163, ranges.get(0)[0]);
assertEquals(4918, ranges.get(0)[1]);
* complement may not enclose multiple ranges
* parsing fails for the same reason
*/
- checkForParseException("join(complement(36618..36700,4000..4200),86988..87064)");
+ checkForParseException(
+ "join(complement(36618..36700,4000..4200),86988..87064)");
}
/**
}
long stop = System.currentTimeMillis();
long elapsed1 = stop - start;
- System.out.println(iterations + " x Format.form took " + elapsed1
- + "ms");
+ System.out
+ .println(iterations + " x Format.form took " + elapsed1 + "ms");
start = System.currentTimeMillis();
for (int i = 0; i < iterations; i++)
}
stop = System.currentTimeMillis();
long elapsed2 = stop - start;
- System.out.println(iterations + " x String.format took " + elapsed2
- + "ms");
+ System.out.println(
+ iterations + " x String.format took " + elapsed2 + "ms");
assertTrue(elapsed2 > elapsed1);
}
}
{
Console.initLogger();
}
-
+
@BeforeClass(alwaysRun = true)
public void setUpJvOptionPane()
{
assertArrayEquals(new int[] { 5, 6 }, merged.get(1));
assertArrayEquals(new int[] { 12, 8 }, merged.get(2));
assertArrayEquals(new int[] { 8, 7 }, merged.get(3));
-
+
// 'subsumed' ranges are preserved
ranges.clear();
ranges.add(new int[] { 10, 30 });
- ranges.add(new int[] { 15, 25 });
+ ranges.add(new int[] { 15, 25 });
merged = MapList.coalesceRanges(ranges);
assertEquals(2, merged.size());
overlap = MappingUtils.findOverlap(ranges, 13, 15);
assertNull(overlap);
}
-
+
/**
* Test mapping a sequence group where sequences in and outside the group
* share a dataset sequence (e.g. alternative CDS for the same gene)
* <p>
- * This scenario doesn't arise after JAL-3763 changes, but test left as still valid
+ * This scenario doesn't arise after JAL-3763 changes, but test left as still
+ * valid
+ *
* @throws IOException
*/
@Test(groups = { "Functional" })
"Please click on this%LINK% to learn more about this%LINK%",
testee.getNonHtmlContent());
assertEquals(2, testee.getLinks().size());
- assertEquals("on this|http://www.nowhere.com", testee.getLinks().get(0));
- assertEquals("this|http://www.somewhere.com/here", testee.getLinks()
- .get(1));
+ assertEquals("on this|http://www.nowhere.com",
+ testee.getLinks().get(0));
+ assertEquals("this|http://www.somewhere.com/here",
+ testee.getLinks().get(1));
}
@Test(groups = { "Functional" })
{
assertNull(Platform.escapeBackslashes(null));
assertEquals(Platform.escapeBackslashes("hello world"), "hello world");
- assertEquals(Platform.escapeBackslashes("hello\\world"), "hello\\\\world");
+ assertEquals(Platform.escapeBackslashes("hello\\world"),
+ "hello\\\\world");
}
}
String[] values = new String[] { "JOHN", "henry", "lucy", "henry",
"ALISON" };
QuickSort.sort(values, things);
- assertTrue(Arrays.equals(new String[] { "lucy", "henry", "henry",
- "JOHN", "ALISON" }, values));
+ assertTrue(
+ Arrays.equals(new String[]
+ { "lucy", "henry", "henry", "JOHN", "ALISON" }, values));
assertTrue(Arrays.equals(new Object[] { c3, c2, c4, c1, c5 }, things));
}
QuickSort.sort(values, letters);
assertTrue(Arrays.equals(new int[] { 1, 2, 3, 4, 4 }, values));
// this fails - do we care?
- assertTrue(Arrays.equals(new Object[] { "Z", "Y", "A", "X", "B" },
- letters));
+ assertTrue(
+ Arrays.equals(new Object[]
+ { "Z", "Y", "A", "X", "B" }, letters));
}
/**
QuickSort.sort(counts, residues);
}
long elapsed = System.currentTimeMillis() - start;
- System.out
- .println(String
- .format("Time for %d optimised sorts of mostly zeros array length %d was %dms",
- iterations, counts.length, elapsed));
+ System.out.println(String.format(
+ "Time for %d optimised sorts of mostly zeros array length %d was %dms",
+ iterations, counts.length, elapsed));
/*
* time it using unoptimised external sort
QuickSort.charSortByFloat(counts, residues, true);
}
elapsed = System.currentTimeMillis() - start;
- System.out
- .println(String
- .format("Time for %d external sorts of mostly zeros array length %d was %dms",
- iterations, counts.length, elapsed));
+ System.out.println(String.format(
+ "Time for %d external sorts of mostly zeros array length %d was %dms",
+ iterations, counts.length, elapsed));
/*
* optimised external sort, well-filled array
QuickSort.sort(counts, residues);
}
elapsed = System.currentTimeMillis() - start;
- System.out
- .println(String
- .format("Time for %d optimised sorts of non-zeros array length %d was %dms",
- iterations, counts.length, elapsed));
+ System.out.println(String.format(
+ "Time for %d optimised sorts of non-zeros array length %d was %dms",
+ iterations, counts.length, elapsed));
/*
* time unoptimised external sort, filled array
QuickSort.charSortByFloat(counts, residues, true);
}
elapsed = System.currentTimeMillis() - start;
- System.out
- .println(String
- .format("Time for %d external sorts of non-zeros array length %d was %dms",
- iterations, counts.length, elapsed));
+ System.out.println(String.format(
+ "Time for %d external sorts of non-zeros array length %d was %dms",
+ iterations, counts.length, elapsed));
}
/**
* sort descending
*/
QuickSort.sortByString(values, things, false);
- assertTrue(Arrays.equals(new String[] { "lucy", "henry", "henry",
- "JOHN", "ALISON" }, values));
+ assertTrue(
+ Arrays.equals(new String[]
+ { "lucy", "henry", "henry", "JOHN", "ALISON" }, values));
assertTrue(Arrays.equals(new Object[] { c3, c2, c4, c1, c5 }, things));
/*
* resort ascending
*/
QuickSort.sortByString(values, things, true);
- assertTrue(Arrays.equals(new String[] { "ALISON", "JOHN", "henry",
- "henry", "lucy" }, values));
+ assertTrue(
+ Arrays.equals(new String[]
+ { "ALISON", "JOHN", "henry", "henry", "lucy" }, values));
// sort is stable: c2/c4 do not swap order
assertTrue(Arrays.equals(new Object[] { c5, c1, c2, c4, c3 }, things));
}
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
+
public class SparseCountTest
{
char[] c1 = "ABC".toCharArray();
// delete second position
- assertTrue(Arrays.equals(new char[] { 'A', 'C' },
- StringUtils.deleteChars(c1, 1, 2)));
+ assertTrue(
+ Arrays.equals(new char[]
+ { 'A', 'C' }, StringUtils.deleteChars(c1, 1, 2)));
// delete positions 1 and 2
- assertTrue(Arrays.equals(new char[] { 'C' },
- StringUtils.deleteChars(c1, 0, 2)));
+ assertTrue(
+ Arrays.equals(new char[]
+ { 'C' }, StringUtils.deleteChars(c1, 0, 2)));
// delete positions 1-3
assertTrue(Arrays.equals(new char[] {},
StringUtils.deleteChars(c1, 0, 3)));
// delete position 3
- assertTrue(Arrays.equals(new char[] { 'A', 'B' },
- StringUtils.deleteChars(c1, 2, 3)));
+ assertTrue(
+ Arrays.equals(new char[]
+ { 'A', 'B' }, StringUtils.deleteChars(c1, 2, 3)));
// out of range deletion is ignore
assertTrue(Arrays.equals(c1, StringUtils.deleteChars(c1, 3, 4)));
* String delimited by | containing a quoted | (should not be treated as
* delimiter)
*/
- assertEquals("[abc='|'d, ef, g]", Arrays.toString(StringUtils
- .separatorListToArray("abc='|'d|ef|g", "|")));
+ assertEquals("[abc='|'d, ef, g]", Arrays.toString(
+ StringUtils.separatorListToArray("abc='|'d|ef|g", "|")));
}
@Test(groups = { "Functional" })
assertEquals("*", StringUtils.arrayToSeparatorList(null, "*"));
assertEquals("*",
StringUtils.arrayToSeparatorList(new String[] {}, "*"));
- assertEquals(
- "a*bc*cde",
- StringUtils.arrayToSeparatorList(new String[] { "a", "bc",
- "cde" }, "*"));
- assertEquals(
- "a*cde",
- StringUtils.arrayToSeparatorList(new String[] { "a", null,
- "cde" }, "*"));
- assertEquals("a**cde", StringUtils.arrayToSeparatorList(new String[] {
- "a", "", "cde" }, "*"));
+ assertEquals("a*bc*cde",
+ StringUtils.arrayToSeparatorList(new String[]
+ { "a", "bc", "cde" }, "*"));
+ assertEquals("a*cde",
+ StringUtils.arrayToSeparatorList(new String[]
+ { "a", null, "cde" }, "*"));
+ assertEquals("a**cde",
+ StringUtils.arrayToSeparatorList(new String[]
+ { "a", "", "cde" }, "*"));
// delimiter within token is not (yet) escaped
- assertEquals("a*b*c*cde", StringUtils.arrayToSeparatorList(new String[]
- { "a", "b*c", "cde" }, "*"));
+ assertEquals("a*b*c*cde",
+ StringUtils.arrayToSeparatorList(new String[]
+ { "a", "b*c", "cde" }, "*"));
}
@Test(groups = { "Functional" })
assertEquals("now", StringUtils.listToDelimitedString(list, ";"));
list.add("is");
assertEquals("now;is", StringUtils.listToDelimitedString(list, ";"));
- assertEquals("now ; is", StringUtils.listToDelimitedString(list, " ; "));
+ assertEquals("now ; is",
+ StringUtils.listToDelimitedString(list, " ; "));
list.add("the");
list.add("winter");
list.add("of");
assertEquals(-1, StringUtils.compareVersions("2.8.3", "2.9.2"));
assertEquals(-1, StringUtils.compareVersions("2.8", "2.8.3"));
assertEquals(-1, StringUtils.compareVersions("2.8.3", "2.8.3b1", "b"));
- assertEquals(-1, StringUtils.compareVersions("2.8.3b1", "2.8.3b2", "b"));
+ assertEquals(-1,
+ StringUtils.compareVersions("2.8.3b1", "2.8.3b2", "b"));
assertEquals(-1, StringUtils.compareVersions("2.8", "2.8.0", "b"));
assertEquals(-1, StringUtils.compareVersions("2", "12"));
assertEquals(-1, StringUtils.compareVersions("3.2.4", "3.12.11"));
{
assertNull(StringUtils.stripHtmlTags(null));
assertEquals("", StringUtils.stripHtmlTags(""));
- assertEquals(
- "<a href=\"something\">label</href>",
- StringUtils
- .stripHtmlTags("<html><a href=\"something\">label</href></html>"));
+ assertEquals("<a href=\"something\">label</href>",
+ StringUtils.stripHtmlTags(
+ "<html><a href=\"something\">label</href></html>"));
// if no "<html>" tag, < and > get html-encoded (not sure why)
assertEquals("<a href=\"something\">label</href>",
- StringUtils.stripHtmlTags("<a href=\"something\">label</href>"));
+ StringUtils
+ .stripHtmlTags("<a href=\"something\">label</href>"));
// </body> gets removed but not <body> (is this intentional?)
- assertEquals("<body><p>hello",
- StringUtils.stripHtmlTags("<html><body><p>hello</body></html>"));
+ assertEquals("<body><p>hello", StringUtils
+ .stripHtmlTags("<html><body><p>hello</body></html>"));
assertEquals("kdHydro < 12.53",
StringUtils.stripHtmlTags("kdHydro < 12.53"));
final static String DELIM = "$";
final static String REGEX_NESTED = "=/^(?:Label:)?(?:(?:gi\\|(\\d+))|([^:]+))/=";
-
+
final static String REGEX_RUBBISH = "=/[0-9]++/=";
/**
assertEquals(REGEX_RUBBISH.substring(2, REGEX_RUBBISH.length() - 2),
ul.getRegexReplace());
assertFalse(ul.isValid());
- assertEquals(
- "Invalid Regular Expression : '"
- + REGEX_RUBBISH.substring(2, REGEX_RUBBISH.length() - 2)
- + "'\n",
- ul.getInvalidMessage());
+ assertEquals("Invalid Regular Expression : '"
+ + REGEX_RUBBISH.substring(2, REGEX_RUBBISH.length() - 2)
+ + "'\n", ul.getInvalidMessage());
}
/**
List<DBRefEntry> refs = new ArrayList<>();
// links as might be added into Preferences | Connections dialog
- links.add("EMBL-EBI Search | http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$"
- + SEQUENCE_ID + "$");
+ links.add(
+ "EMBL-EBI Search | http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$"
+ + SEQUENCE_ID + "$");
links.add("UNIPROT | http://www.uniprot.org/uniprot/$" + DB_ACCESSION
+ "$");
links.add("INTERPRO | http://www.ebi.ac.uk/interpro/entry/$"
assertEquals(DB, linkset.get(key).get(0));
assertEquals(DB, linkset.get(key).get(1));
assertEquals(seq0.getName(), linkset.get(key).get(2));
- assertEquals(URL_PREFIX + seq0.getName() + URL_SUFFIX, linkset.get(key)
- .get(3));
+ assertEquals(URL_PREFIX + seq0.getName() + URL_SUFFIX,
+ linkset.get(key).get(3));
// Test where link takes a db annotation id and only has one dbref
ul = new UrlLink(links.get(1));
assertEquals(linkset.size(), 1);
assertTrue(linkset.containsKey(key));
assertEquals(DBRefSource.UNIPROT, linkset.get(key).get(0));
- assertEquals(DBRefSource.UNIPROT + SEP + "P83527", linkset.get(key)
- .get(1));
+ assertEquals(DBRefSource.UNIPROT + SEP + "P83527",
+ linkset.get(key).get(1));
assertEquals("P83527", linkset.get(key).get(2));
- assertEquals("http://www.uniprot.org/uniprot/P83527", linkset.get(key)
- .get(3));
+ assertEquals("http://www.uniprot.org/uniprot/P83527",
+ linkset.get(key).get(3));
// Test where link takes a db annotation id and has multiple dbrefs
ul = new UrlLink(links.get(2));
assertEquals("INTERPRO", linkset.get(key).get(0));
assertEquals("INTERPRO" + SEP + "IPR001041", linkset.get(key).get(1));
assertEquals("IPR001041", linkset.get(key).get(2));
- assertEquals("http://www.ebi.ac.uk/interpro/entry/IPR001041", linkset
- .get(key).get(3));
+ assertEquals("http://www.ebi.ac.uk/interpro/entry/IPR001041",
+ linkset.get(key).get(3));
key = "IPR006058|http://www.ebi.ac.uk/interpro/entry/IPR006058";
assertTrue(linkset.containsKey(key));
assertEquals("INTERPRO", linkset.get(key).get(0));
assertEquals("INTERPRO" + SEP + "IPR006058", linkset.get(key).get(1));
assertEquals("IPR006058", linkset.get(key).get(2));
- assertEquals("http://www.ebi.ac.uk/interpro/entry/IPR006058", linkset
- .get(key).get(3));
+ assertEquals("http://www.ebi.ac.uk/interpro/entry/IPR006058",
+ linkset.get(key).get(3));
key = "IPR012675|http://www.ebi.ac.uk/interpro/entry/IPR012675";
assertTrue(linkset.containsKey(key));
assertEquals("INTERPRO", linkset.get(key).get(0));
assertEquals("INTERPRO" + SEP + "IPR012675", linkset.get(key).get(1));
assertEquals("IPR012675", linkset.get(key).get(2));
- assertEquals("http://www.ebi.ac.uk/interpro/entry/IPR012675", linkset
- .get(key).get(3));
+ assertEquals("http://www.ebi.ac.uk/interpro/entry/IPR012675",
+ linkset.get(key).get(3));
// Test where there are no matching dbrefs for the link
ul = new UrlLink(DB + SEP + URL_PREFIX + DELIM + DB_ACCESSION + DELIM
package jalview.util.dialogrunner;
public class DialogRunnerTest
-{}
+{
+}
assertTrue(m.matches("2.0"));
assertTrue(m.matches("2.000000f"));
assertFalse(m.matches("2.01"));
-
+
/*
* NOT EQUALS test
*/
assertFalse(m.matches("123"));
assertFalse(m.matches("123.0"));
assertTrue(m.matches("-123"));
-
+
/*
* >= test
*/
assertTrue(m.matches("113890813"));
assertTrue(m.matches("113890814"));
assertFalse(m.matches("-113890813"));
-
+
/*
* > test
*/
m = new Matcher(Condition.GT, 113890813);
assertFalse(m.matches("113890813"));
assertTrue(m.matches("113890814"));
-
+
/*
* <= test
*/
assertTrue(m.matches("113890813"));
assertFalse(m.matches("113890814"));
assertTrue(m.matches("113890812"));
-
+
/*
* < test
*/
// cached widths and heights
int boxWidth;
+
int boxHeight;
+
int viewHeight;
+
int viewWidth;
+
int alheight;
+
int alwidth;
ViewportRanges vpranges;
}
ColumnSelection colsel = new ColumnSelection();
hiddenCols.revealAllHiddenColumns(colsel);
-
+
vpranges = new ViewportRanges(al);
vpranges.setViewportStartAndHeight(0, 18);
vpranges.setViewportStartAndWidth(0, 63);
alheight = vpranges.getVisibleAlignmentHeight();
alwidth = vpranges.getVisibleAlignmentWidth();
- boxWidth = Math.round((float) (vpranges.getEndRes()
- - vpranges.getStartRes() + 1)
- * od.getWidth() / alwidth);
- boxHeight = Math.round((float) (vpranges.getEndSeq()
- - vpranges.getStartSeq() + 1)
- * od.getSequencesHeight() / alheight);
+ boxWidth = Math.round(
+ (float) (vpranges.getEndRes() - vpranges.getStartRes() + 1)
+ * od.getWidth() / alwidth);
+ boxHeight = Math.round(
+ (float) (vpranges.getEndSeq() - vpranges.getStartSeq() + 1)
+ * od.getSequencesHeight() / alheight);
}
@AfterClass(alwaysRun = true)
assertEquals(od.getBoxHeight(), boxHeight);
assertEquals(vpranges.getStartRes(),
Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
- assertEquals(
- vpranges.getStartSeq(),
- Math.round((float) od.getBoxY() * alheight
- / od.getSequencesHeight()));
+ assertEquals(vpranges.getStartSeq(), Math.round(
+ (float) od.getBoxY() * alheight / od.getSequencesHeight()));
// overly large boxY value reset to sequenceHeight - boxHeight
mouseClick(od, 10, 520);
// here (float) od.getBoxY() * alheight / od.getSequencesHeight() = 507.5
// and round rounds to 508; however we get 507 working with row values
// hence the subtraction of 1
- assertEquals(
- vpranges.getStartSeq(),
- Math.round((float) od.getBoxY() * alheight
- / od.getSequencesHeight()) - 1);
+ assertEquals(vpranges.getStartSeq(), Math.round(
+ (float) od.getBoxY() * alheight / od.getSequencesHeight()) - 1);
// click past end of alignment, as above
mouseClick(od, 3000, 5);
assertEquals(od.getBoxHeight(), boxHeight);
assertEquals(vpranges.getStartRes(),
Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
- assertEquals(
- vpranges.getStartSeq(),
- Math.round((float) od.getBoxY() * alheight
- / od.getSequencesHeight()));
+ assertEquals(vpranges.getStartSeq(), Math.round(
+ (float) od.getBoxY() * alheight / od.getSequencesHeight()));
// move viewport so startRes non-zero and then mouseclick
moveViewportH(20);
assertEquals(vpranges.getStartRes(),
Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
assertEquals(od.getBoxY(), oldboxy + 3);
- assertEquals(
- vpranges.getStartSeq(),
- Math.round((float) od.getBoxY() * alheight
- / od.getSequencesHeight()));
+ assertEquals(vpranges.getStartSeq(), Math.round(
+ (float) od.getBoxY() * alheight / od.getSequencesHeight()));
// click at top corner
mouseClick(od, 0, 0);
assertEquals(od.getBoxWidth(), boxWidth);
assertEquals(vpranges.getStartRes(), 0);
assertEquals(vpranges.getStartSeq(), 0);
-
+
// hide columns 63-73, no change to box position or dimensions
int firstHidden = 63;
int lastHidden = 73;
// move box so that it overlaps with hidden cols on one side
// box width, boxX and scrollCol as for unhidden case
int xpos = 54 - boxWidth / 2; // 54 is position in overview approx halfway
- // between cols 60 and 70
+ // between cols 60 and 70
mouseClick(od, xpos, boxHeight / 2);
testBoxIsAtClickPoint(xpos, boxHeight / 2);
assertEquals(vpranges.getStartRes(), 1 + // rounding
xpos = 33;
mouseClick(od, xpos, boxHeight / 2);
testBoxIsAtClickPoint(xpos, boxHeight / 2);
- assertEquals(vpranges.getStartRes(),
- Math.round((float) (xpos - boxWidth / 2) * alwidth
- / od.getWidth()));
+ assertEquals(vpranges.getStartRes(), Math.round(
+ (float) (xpos - boxWidth / 2) * alwidth / od.getWidth()));
assertEquals(vpranges.getStartSeq(), 0);
// move box so boxX is in hidden cols, box overhangs at right
assertEquals(od.getBoxHeight(), boxHeight);
assertEquals(vpranges.getStartSeq(), 0);
assertEquals(vpranges.getStartRes(), 75);
-
+
// move box so it goes beyond full width of alignment
// boxX, scrollCol adjusted back, box width normal
xpos = 3000;
xpos = Math.round((float) 144 * od.getWidth() / alwidth) - boxWidth;
mouseClick(od, xpos, boxHeight / 2);
testBoxIsAtClickPoint(xpos, boxHeight / 2);
- assertEquals(vpranges.getStartRes(),
- Math.round((float) (xpos - boxWidth / 2) * alwidth
- / od.getWidth()));
+ assertEquals(vpranges.getStartRes(), Math.round(
+ (float) (xpos - boxWidth / 2) * alwidth / od.getWidth()));
assertEquals(vpranges.getStartSeq(), 0);
// click off end of alignment
// move viewport to end of alignment - need to make startRes by removing
// hidden cols because of how viewport/overview are implemented
moveViewport(98 - lastHidden - 1, 0);
- assertEquals(od.getBoxX(),
- Math.round((float) (98 - lastHidden - 1) * od.getWidth()
- / alwidth));
+ assertEquals(od.getBoxX(), Math.round(
+ (float) (98 - lastHidden - 1) * od.getWidth() / alwidth));
assertEquals(od.getBoxY(), 0);
assertEquals(od.getBoxWidth(), boxWidth);
assertEquals(od.getBoxHeight(), boxHeight);
// viewport can't actually extend into hidden cols,
// so move to the far right edge of the viewport
moveViewport(firstHidden - viewWidth, 0);
- assertEquals(od.getBoxX(),
- Math.round((float) (firstHidden - viewWidth)
- * od.getWidth() / alwidth));
+ assertEquals(od.getBoxX(), Math.round(
+ (float) (firstHidden - viewWidth) * od.getWidth() / alwidth));
assertEquals(od.getBoxY(), 0);
assertEquals(od.getBoxWidth(), boxWidth);
assertEquals(od.getBoxHeight(), boxHeight);
alheight = vpranges.getVisibleAlignmentHeight();
alwidth = vpranges.getVisibleAlignmentWidth();
- boxWidth = Math.round((float) (vpranges.getEndRes()
- - vpranges.getStartRes() + 1)
- * od.getWidth() / alwidth);
- boxHeight = Math.round((float) (vpranges.getEndSeq()
- - vpranges.getStartSeq() + 1)
- * od.getSequencesHeight() / alheight);
+ boxWidth = Math.round(
+ (float) (vpranges.getEndRes() - vpranges.getStartRes() + 1)
+ * od.getWidth() / alwidth);
+ boxHeight = Math.round(
+ (float) (vpranges.getEndSeq() - vpranges.getStartSeq() + 1)
+ * od.getSequencesHeight() / alheight);
// move viewport to start of alignment:
// box moves to below hidden rows, height remains same
// move viewport to end of alignment
moveViewport(0, 525 - viewHeight - lastHidden - 1);
assertEquals(od.getBoxX(), 0);
- assertEquals(
- od.getBoxY(),
+ assertEquals(od.getBoxY(),
Math.round((float) (525 - viewHeight - lastHidden - 1)
- * od.getSequencesHeight()
- / alheight));
+ * od.getSequencesHeight() / alheight));
assertEquals(od.getBoxWidth(), boxWidth);
assertEquals(od.getBoxHeight(), boxHeight);
}
alheight = vpranges.getVisibleAlignmentHeight();
alwidth = vpranges.getVisibleAlignmentWidth();
- boxWidth = Math.round((float) (vpranges.getEndRes()
- - vpranges.getStartRes() + 1)
- * od.getWidth() / alwidth);
- boxHeight = Math.round((float) (vpranges.getEndSeq()
- - vpranges.getStartSeq() + 1)
- * od.getSequencesHeight() / alheight);
+ boxWidth = Math.round(
+ (float) (vpranges.getEndRes() - vpranges.getStartRes() + 1)
+ * od.getWidth() / alwidth);
+ boxHeight = Math.round(
+ (float) (vpranges.getEndSeq() - vpranges.getStartSeq() + 1)
+ * od.getSequencesHeight() / alheight);
// move viewport to start of alignment:
// box, height etc as in non-hidden case
// move viewport to straddle hidden rows
moveViewport(0, 198);
assertEquals(od.getBoxX(), 0);
- assertEquals(od.getBoxY(), Math.round ((float)198 * od.getSequencesHeight()
- / alheight));
+ assertEquals(od.getBoxY(),
+ Math.round((float) 198 * od.getSequencesHeight() / alheight));
assertEquals(od.getBoxWidth(), boxWidth);
assertEquals(od.getBoxHeight(), boxHeight);
}
alheight = vpranges.getVisibleAlignmentHeight();
alwidth = vpranges.getVisibleAlignmentWidth();
- boxWidth = Math.round((float) (vpranges.getEndRes()
- - vpranges.getStartRes() + 1)
- * od.getWidth() / alwidth);
- boxHeight = Math.round((float) (vpranges.getEndSeq()
- - vpranges.getStartSeq() + 1)
- * od.getSequencesHeight() / alheight);
+ boxWidth = Math.round(
+ (float) (vpranges.getEndRes() - vpranges.getStartRes() + 1)
+ * od.getWidth() / alwidth);
+ boxHeight = Math.round(
+ (float) (vpranges.getEndSeq() - vpranges.getStartSeq() + 1)
+ * od.getSequencesHeight() / alheight);
// move viewport to start of alignment:
// box, height etc as in non-hidden case
// viewport sits above hidden rows and does not include them
moveViewport(0, firstHidden - viewHeight - 1);
assertEquals(od.getBoxX(), 0);
- assertEquals(
- od.getBoxY(),
+ assertEquals(od.getBoxY(),
Math.round((float) (firstHidden - viewHeight - 1)
* od.getSequencesHeight() / alheight));
assertEquals(od.getBoxWidth(), boxWidth);
alheight = vpranges.getVisibleAlignmentHeight();
alwidth = vpranges.getVisibleAlignmentWidth();
- boxWidth = Math.round((float) (vpranges.getEndRes()
- - vpranges.getStartRes() + 1)
- * od.getWidth() / alwidth);
- boxHeight = Math.round((float) (vpranges.getEndSeq()
- - vpranges.getStartSeq() + 1)
- * od.getSequencesHeight() / alheight);
+ boxWidth = Math.round(
+ (float) (vpranges.getEndRes() - vpranges.getStartRes() + 1)
+ * od.getWidth() / alwidth);
+ boxHeight = Math.round(
+ (float) (vpranges.getEndSeq() - vpranges.getStartSeq() + 1)
+ * od.getSequencesHeight() / alheight);
od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
assertEquals(od.getBoxX(), 0);
alheight = vpranges.getVisibleAlignmentHeight();
alwidth = vpranges.getVisibleAlignmentWidth();
- boxWidth = Math.round((float) (vpranges.getEndRes()
- - vpranges.getStartRes() + 1)
- * od.getWidth() / alwidth);
- boxHeight = Math.round((float) (vpranges.getEndSeq()
- - vpranges.getStartSeq() + 1)
- * od.getSequencesHeight() / alheight);
+ boxWidth = Math.round(
+ (float) (vpranges.getEndRes() - vpranges.getStartRes() + 1)
+ * od.getWidth() / alwidth);
+ boxHeight = Math.round(
+ (float) (vpranges.getEndSeq() - vpranges.getStartSeq() + 1)
+ * od.getSequencesHeight() / alheight);
od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
alheight = vpranges.getVisibleAlignmentHeight();
alwidth = vpranges.getVisibleAlignmentWidth();
- boxWidth = Math.round((float) (vpranges.getEndRes()
- - vpranges.getStartRes() + 1)
- * od.getWidth() / alwidth);
- boxHeight = Math.round((float) (vpranges.getEndSeq()
- - vpranges.getStartSeq() + 1)
- * od.getSequencesHeight() / alheight);
+ boxWidth = Math.round(
+ (float) (vpranges.getEndRes() - vpranges.getStartRes() + 1)
+ * od.getWidth() / alwidth);
+ boxHeight = Math.round(
+ (float) (vpranges.getEndSeq() - vpranges.getStartSeq() + 1)
+ * od.getSequencesHeight() / alheight);
od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
assertEquals(od.getBoxX(), 0);
mouseClick(od, 0,
Math.round((float) ypos * od.getSequencesHeight() / alheight));
assertEquals(od.getBoxX(), 0);
- assertEquals(
- od.getBoxY(),
- Math.round((float) firstHidden * od.getSequencesHeight()
- / alheight)
- - boxHeight);
+ assertEquals(od.getBoxY(), Math
+ .round((float) firstHidden * od.getSequencesHeight() / alheight)
+ - boxHeight);
assertEquals(od.getBoxWidth(), boxWidth);
assertEquals(od.getBoxHeight(), boxHeight);
}
public void testDragging()
{
od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
- od.setDragPoint(4, 16, al.getHiddenSequences(),
- hiddenCols);
- od.adjustViewportFromMouse(20, 22,
- al.getHiddenSequences(), hiddenCols);
+ od.setDragPoint(4, 16, al.getHiddenSequences(), hiddenCols);
+ od.adjustViewportFromMouse(20, 22, al.getHiddenSequences(), hiddenCols);
// updates require an OverviewPanel to exist which it doesn't here
// so call setBoxPosition() as it would be called by the AlignmentPanel
// normally
od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
}
-
+
/*
* Test that the box is positioned with the top left corner at xpos, ypos
* and with the original width and height
{
SequenceI[] allseqs = al.getSequencesArray();
SequenceGroup theseSeqs = new SequenceGroup();
-
+
for (int i = start; i <= end; i++)
{
theseSeqs.addSequence(allseqs[i], false);
public class OverviewDimensionsShowHiddenTest
{
AlignmentI al;
+
OverviewDimensionsShowHidden od;
// cached widths and heights
int boxWidth;
+
int boxHeight;
+
int viewHeight;
+
int viewWidth;
+
int alheight;
+
int alwidth;
ViewportRanges vpranges;
}
ColumnSelection colsel = new ColumnSelection();
hiddenCols.revealAllHiddenColumns(colsel);
-
+
vpranges = new ViewportRanges(al);
vpranges.setViewportStartAndHeight(0, 18);
vpranges.setViewportStartAndWidth(0, 63);
alheight = vpranges.getAbsoluteAlignmentHeight();
alwidth = vpranges.getAbsoluteAlignmentWidth();
- boxWidth = Math.round((float) (vpranges.getEndRes()
- - vpranges.getStartRes() + 1)
- * od.getWidth() / alwidth);
- boxHeight = Math.round((float) (vpranges.getEndSeq()
- - vpranges.getStartSeq() + 1)
- * od.getSequencesHeight() / alheight);
+ boxWidth = Math.round(
+ (float) (vpranges.getEndRes() - vpranges.getStartRes() + 1)
+ * od.getWidth() / alwidth);
+ boxHeight = Math.round(
+ (float) (vpranges.getEndSeq() - vpranges.getStartSeq() + 1)
+ * od.getSequencesHeight() / alheight);
}
@AfterClass(alwaysRun = true)
assertEquals(od.getBoxHeight(), boxHeight);
assertEquals(vpranges.getStartRes(),
Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
- assertEquals(
- vpranges.getStartSeq(),
- Math.round((float) od.getBoxY() * alheight
- / od.getSequencesHeight()));
+ assertEquals(vpranges.getStartSeq(), Math.round(
+ (float) od.getBoxY() * alheight / od.getSequencesHeight()));
// overly large boxY value reset to sequenceHeight - boxHeight
mouseClick(od, 10, 520);
// here (float) od.getBoxY() * alheight / od.getSequencesHeight() = 507.5
// and round rounds to 508; however we get 507 working with row values
// hence the subtraction of 1
- assertEquals(
- vpranges.getStartSeq(),
- Math.round((float) od.getBoxY() * alheight
- / od.getSequencesHeight()) - 1);
+ assertEquals(vpranges.getStartSeq(), Math.round(
+ (float) od.getBoxY() * alheight / od.getSequencesHeight()) - 1);
// click past end of alignment, as above
mouseClick(od, 3000, 5);
assertEquals(od.getBoxHeight(), boxHeight);
assertEquals(vpranges.getStartRes(),
Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
- assertEquals(
- vpranges.getStartSeq(),
- Math.round((float) od.getBoxY() * alheight
- / od.getSequencesHeight()));
+ assertEquals(vpranges.getStartSeq(), Math.round(
+ (float) od.getBoxY() * alheight / od.getSequencesHeight()));
// move viewport so startRes non-zero and then mouseclick
moveViewportH(20);
assertEquals(vpranges.getStartRes(),
Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
assertEquals(od.getBoxY(), oldboxy + 3);
- assertEquals(
- vpranges.getStartSeq(),
- Math.round((float) od.getBoxY() * alheight
- / od.getSequencesHeight()));
+ assertEquals(vpranges.getStartSeq(), Math.round(
+ (float) od.getBoxY() * alheight / od.getSequencesHeight()));
// click at top corner
mouseClick(od, 0, 0);
hiddenCols.hideColumns(0, lastHiddenCol);
od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
- assertEquals(od.getBoxX(),
- Math.round((float) (lastHiddenCol + 1) * od.getWidth()
- / alwidth));
+ assertEquals(od.getBoxX(), Math
+ .round((float) (lastHiddenCol + 1) * od.getWidth() / alwidth));
assertEquals(od.getBoxWidth(), boxWidth);
assertEquals(od.getBoxHeight(), boxHeight);
// try to click in hidden cols, check box does not move
int xpos = 10;
mouseClick(od, xpos, 0);
- assertEquals(
- od.getBoxX(),
- Math.round((float) (lastHiddenCol + 1) * od.getWidth()
- / alwidth));
+ assertEquals(od.getBoxX(), Math
+ .round((float) (lastHiddenCol + 1) * od.getWidth() / alwidth));
assertEquals(od.getBoxY(), 0);
assertEquals(od.getBoxWidth(), boxWidth);
assertEquals(od.getBoxHeight(), boxHeight);
assertEquals(od.getBoxHeight(), boxHeight);
assertEquals(vpranges.getStartSeq(), 0);
assertEquals(vpranges.getStartRes(),
- Math.round(
- (float) 60 * alwidth / od.getWidth())
+ Math.round((float) 60 * alwidth / od.getWidth())
- (lastHiddenCol + 1));
// click to right of hidden columns such that box runs over right hand side
assertEquals(vpranges.getStartRes(),
Math.round((float) od.getBoxX() * alwidth / od.getWidth())
- (lastHiddenCol + 1));
- assertEquals(
- vpranges.getStartSeq(),
- Math.round((float) od.getBoxY() * alheight
- / od.getSequencesHeight()));
+ assertEquals(vpranges.getStartSeq(), Math.round(
+ (float) od.getBoxY() * alheight / od.getSequencesHeight()));
}
/**
assertEquals(od.getBoxWidth(), boxWidth);
assertEquals(vpranges.getStartRes(), 0);
assertEquals(vpranges.getStartSeq(), 0);
-
+
// hide columns 63-73, no change to box position or dimensions
int firstHidden = 63;
int lastHidden = 73;
// move box so that it overlaps with hidden cols on one side
// box width changes, boxX and scrollCol as for unhidden case
int xpos = 54 - boxWidth / 2; // 54 is position in overview approx halfway
- // between cols 60 and 70
+ // between cols 60 and 70
mouseClick(od, xpos, boxHeight / 2);
assertEquals(od.getBoxX(), xpos - boxWidth / 2);
assertEquals(od.getBoxY(), 0);
- assertEquals(
- od.getBoxWidth(),
+ assertEquals(od.getBoxWidth(),
Math.round(boxWidth + (float) (lastHidden - firstHidden + 1)
* od.getWidth() / alwidth));
assertEquals(od.getBoxHeight(), boxHeight);
mouseClick(od, xpos, 0);
assertEquals(od.getBoxX(), 24);
assertEquals(od.getBoxY(), 0);
- assertEquals(
- od.getBoxWidth(),
+ assertEquals(od.getBoxWidth(),
Math.round(boxWidth + (float) (lastHidden - firstHidden + 1)
* od.getWidth() / alwidth));
assertEquals(od.getBoxHeight(), boxHeight);
assertEquals(vpranges.getStartSeq(), 0);
assertEquals(vpranges.getStartRes(),
75 - (lastHidden - firstHidden + 1));
-
+
// move box so it goes beyond full width of alignment
// boxX, scrollCol adjusted back, box width normal
xpos = 3000;
assertEquals(od.getBoxY(), 0);
assertEquals(od.getBoxWidth(), boxWidth);
assertEquals(od.getBoxHeight(), boxHeight);
- assertEquals(
- vpranges.getStartRes(),
+ assertEquals(vpranges.getStartRes(),
Math.round(((float) od.getBoxX() * alwidth / od.getWidth())
- (lastHidden - firstHidden + 1)));
- assertEquals(
- vpranges.getStartSeq(),
- Math.round((float) od.getBoxY() * alheight
- / od.getSequencesHeight()));
+ assertEquals(vpranges.getStartSeq(), Math.round(
+ (float) od.getBoxY() * alheight / od.getSequencesHeight()));
}
int xpos = 30;
int ypos = 6;
testBoxIsAtClickPoint(xpos, ypos);
- assertEquals(vpranges.getStartSeq(), Math
- .round((float) (ypos - boxHeight / 2) * alheight
- / od.getHeight()));
+ assertEquals(vpranges.getStartSeq(), Math.round(
+ (float) (ypos - boxHeight / 2) * alheight / od.getHeight()));
assertEquals(vpranges.getStartRes(), Math.round(
(float) (xpos - boxWidth / 2) * alwidth / od.getWidth()));
xpos = Math.round((float) 145 * od.getWidth() / alwidth) - boxWidth;
mouseClick(od, xpos + boxWidth / 2, boxHeight / 2);
assertEquals(od.getBoxX(),
- Math.round((float) (firstHidden - 1)
- * od.getWidth() / alwidth)
+ Math.round((float) (firstHidden - 1) * od.getWidth() / alwidth)
- boxWidth + 1);
assertEquals(od.getBoxY(), 0);
assertEquals(od.getBoxWidth(), boxWidth);
assertEquals(od.getBoxHeight(), boxHeight);
assertEquals(vpranges.getStartRes(),
- Math.round((float) (od.getBoxX()) * alwidth
- / od.getWidth()));
+ Math.round((float) (od.getBoxX()) * alwidth / od.getWidth()));
assertEquals(vpranges.getStartSeq(), 0);
// click in hidden cols
assertEquals(od.getBoxX(),
Math.round((float) 10 * od.getWidth() / alwidth));
assertEquals(od.getBoxY(), 0);
- assertEquals(
- od.getBoxWidth(),
- boxWidth
- + Math.round((float) (lastHidden - firstHidden + 1)
- * od.getWidth() / alwidth));
+ assertEquals(od.getBoxWidth(),
+ boxWidth + Math.round((float) (lastHidden - firstHidden + 1)
+ * od.getWidth() / alwidth));
assertEquals(od.getBoxHeight(), boxHeight);
// move viewport to straddle hidden columns
assertEquals(od.getBoxX(),
Math.round((float) 63 * od.getWidth() / alwidth));
assertEquals(od.getBoxY(), 0);
- assertEquals(
- od.getBoxWidth(),
- boxWidth
- + Math.round((lastHidden - firstHidden + 1)
- * od.getWidth() / alwidth));
+ assertEquals(od.getBoxWidth(), boxWidth + Math.round(
+ (lastHidden - firstHidden + 1) * od.getWidth() / alwidth));
assertEquals(od.getBoxHeight(), boxHeight);
// move viewport to right of hidden columns, no overlap
// viewport can't actually extend into hidden cols,
// so move to the far right edge of the viewport
moveViewport(firstHidden - viewWidth, 0);
- assertEquals(od.getBoxX(),
- Math.round((float) (firstHidden - viewWidth)
- * od.getWidth() / alwidth));
+ assertEquals(od.getBoxX(), Math.round(
+ (float) (firstHidden - viewWidth) * od.getWidth() / alwidth));
assertEquals(od.getBoxY(), 0);
assertEquals(od.getBoxWidth(), boxWidth);
assertEquals(od.getBoxHeight(), boxHeight);
// box moves to below hidden rows, height remains same
moveViewport(0, 0);
assertEquals(od.getBoxX(), 0);
- assertEquals(od.getBoxY(),
- Math.round((float) (lastHidden + 1) * od.getSequencesHeight()
- / alheight));
+ assertEquals(od.getBoxY(), Math.round(
+ (float) (lastHidden + 1) * od.getSequencesHeight() / alheight));
assertEquals(od.getBoxWidth(), boxWidth);
assertEquals(od.getBoxHeight(), boxHeight);
// move viewport to end of alignment
moveViewport(0, 525 - viewHeight - lastHidden - 1);
assertEquals(od.getBoxX(), 0);
- assertEquals(
- od.getBoxY(),
- Math.round((float) (525 - viewHeight) * od.getSequencesHeight()
- / alheight));
+ assertEquals(od.getBoxY(), Math.round((float) (525 - viewHeight)
+ * od.getSequencesHeight() / alheight));
assertEquals(od.getBoxWidth(), boxWidth);
assertEquals(od.getBoxHeight(), boxHeight);
}
// move viewport to straddle hidden rows
moveViewport(0, 198);
assertEquals(od.getBoxX(), 0);
- assertEquals(od.getBoxY(), Math.round ((float)198 * od.getSequencesHeight()
- / alheight));
+ assertEquals(od.getBoxY(),
+ Math.round((float) 198 * od.getSequencesHeight() / alheight));
assertEquals(od.getBoxWidth(), boxWidth);
- assertEquals(
- od.getBoxHeight(),
+ assertEquals(od.getBoxHeight(),
Math.round((float) (viewHeight + lastHidden - firstHidden + 1)
* od.getSequencesHeight() / alheight));
}
// viewport sits above hidden rows and does not include them
moveViewport(0, firstHidden - viewHeight - 1);
assertEquals(od.getBoxX(), 0);
- assertEquals(
- od.getBoxY(),
+ assertEquals(od.getBoxY(),
Math.round((float) (firstHidden - viewHeight - 1)
* od.getSequencesHeight() / alheight));
assertEquals(od.getBoxWidth(), boxWidth);
od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
assertEquals(od.getBoxX(), 0);
- assertEquals(od.getBoxY(),
- Math.round((float) (lastHiddenRow + 1)
- * od.getSequencesHeight() / alheight));
+ assertEquals(od.getBoxY(), Math.round((float) (lastHiddenRow + 1)
+ * od.getSequencesHeight() / alheight));
assertEquals(od.getBoxWidth(), boxWidth);
assertEquals(od.getBoxHeight(), boxHeight);
// click in hidden rows - same result
mouseClick(od, 0, 0);
assertEquals(od.getBoxX(), 0);
- assertEquals(
- od.getBoxY(),
- Math.round((float) (lastHiddenRow + 1)
- * od.getSequencesHeight() / alheight));
+ assertEquals(od.getBoxY(), Math.round((float) (lastHiddenRow + 1)
+ * od.getSequencesHeight() / alheight));
assertEquals(od.getBoxWidth(), boxWidth);
assertEquals(od.getBoxHeight(), boxHeight);
// click below hidden rows
- mouseClick(od, 0, 150 + boxHeight/2);
+ mouseClick(od, 0, 150 + boxHeight / 2);
assertEquals(od.getBoxX(), 0);
assertEquals(od.getBoxY(), 150);
assertEquals(od.getBoxWidth(), boxWidth);
// click above hidden rows, so that box overlaps
int rowpos = 35; // row value in residues
int centrepos = 43; // centre row
- mouseClick(od, 0,
- Math.round((float) centrepos * od.getSequencesHeight()
- / alheight));
+ mouseClick(od, 0, Math
+ .round((float) centrepos * od.getSequencesHeight() / alheight));
assertEquals(od.getBoxX(), 0);
- assertEquals(od.getBoxY(),
- Math.round(
- (float) rowpos * od.getSequencesHeight() / alheight));
+ assertEquals(od.getBoxY(), Math
+ .round((float) rowpos * od.getSequencesHeight() / alheight));
assertEquals(od.getBoxWidth(), boxWidth);
- assertEquals(
- od.getBoxHeight(),
- boxHeight
- + Math.round((float) (lastHiddenRow - firstHiddenRow + 1)
+ assertEquals(od.getBoxHeight(),
+ boxHeight + Math
+ .round((float) (lastHiddenRow - firstHiddenRow + 1)
* od.getSequencesHeight() / alheight));
}
mouseClick(od, 0,
Math.round((float) ypos * od.getSequencesHeight() / alheight));
assertEquals(od.getBoxX(), 0);
- assertEquals(
- od.getBoxY(),
- Math.round((float) (firstHidden - viewHeight)
- * od.getSequencesHeight() / alheight));
+ assertEquals(od.getBoxY(), Math.round((float) (firstHidden - viewHeight)
+ * od.getSequencesHeight() / alheight));
assertEquals(od.getBoxWidth(), boxWidth);
assertEquals(od.getBoxHeight(), boxHeight);
mouseClick(od, 0,
Math.round((float) ypos * od.getSequencesHeight() / alheight));
assertEquals(od.getBoxX(), 0);
- assertEquals(
- od.getBoxY(),
- Math.round((firstHidden - viewHeight) * od.getSequencesHeight()
- / alheight));
+ assertEquals(od.getBoxY(), Math.round((firstHidden - viewHeight)
+ * od.getSequencesHeight() / alheight));
assertEquals(od.getBoxWidth(), boxWidth);
assertEquals(od.getBoxHeight(), boxHeight);
}
// normally
od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
}
-
+
/*
* Test that the box is positioned with the centre at xpos, ypos
* and with the original width and height
{
SequenceI[] allseqs = al.getSequencesArray();
SequenceGroup theseSeqs = new SequenceGroup();
-
+
for (int i = start; i <= end; i++)
{
theseSeqs.addSequence(allseqs[i], false);
assertEquals(od.getBoxWidth(), boxWidth);
assertEquals(vpranges.getStartRes(), 0);
assertEquals(vpranges.getStartSeq(), 0);
-
+
// hide rows at start and check updated box position is correct
// changes boxY but not boxheight
int lastHiddenRow = 30;
hideSequences(0, lastHiddenRow);
-
+
od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
assertEquals(od.getBoxX(), 0);
- assertEquals(od.getBoxY(),
- Math.round((float) (lastHiddenRow + 1)
- * od.getSequencesHeight() / alheight));
+ assertEquals(od.getBoxY(), Math.round((float) (lastHiddenRow + 1)
+ * od.getSequencesHeight() / alheight));
assertEquals(od.getBoxWidth(), boxWidth);
assertEquals(od.getBoxHeight(), boxHeight);
-
+
// click in hidden rows - same result
mouseClick(od, 0, 0);
assertEquals(od.getBoxX(), 0);
int boxY = od.getBoxY();
- assertEquals(
- boxY,
- Math.round((float) (lastHiddenRow + 1)
- * od.getSequencesHeight() / alheight));
+ assertEquals(boxY, Math.round((float) (lastHiddenRow + 1)
+ * od.getSequencesHeight() / alheight));
assertEquals(od.getBoxWidth(), boxWidth);
assertEquals(od.getBoxHeight(), boxHeight);
-
+
// click below hidden rows
// vertical move of overview box is suppressed in wrapped mode
mouseClick(od, 0, 150);
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
-public class ViewportRangesTest {
+public class ViewportRangesTest
+{
AlignmentGenerator gen = new AlignmentGenerator(false);
}
@Test(groups = { "Functional" })
- public void testViewportRanges()
+ public void testViewportRanges()
{
ViewportRanges vr = new ViewportRanges(al);
-
- assertEquals(vr.getStartRes(),0);
- assertEquals(vr.getEndRes(), al.getWidth()-1);
+
+ assertEquals(vr.getStartRes(), 0);
+ assertEquals(vr.getEndRes(), al.getWidth() - 1);
assertEquals(vr.getStartSeq(), 0);
assertEquals(vr.getEndSeq(), al.getHeight() - 1);
}
public void testScrollToVisible()
{
ViewportRanges vr = new ViewportRanges(al);
- vr.setViewportStartAndWidth(12,5);
- vr.setViewportStartAndHeight(10,6);
+ vr.setViewportStartAndWidth(12, 5);
+ vr.setViewportStartAndHeight(10, 6);
vr.scrollToVisible(13, 14);
-
+
// no change
assertEquals(vr.getStartRes(), 12);
assertEquals(vr.getStartSeq(), 10);
-
- vr.scrollToVisible(5,6);
+
+ vr.scrollToVisible(5, 6);
assertEquals(vr.getStartRes(), 5);
assertEquals(vr.getStartSeq(), 6);
-
+
// test for hidden columns too
al.getHiddenColumns().hideColumns(1, 3);
vr.scrollToVisible(13, 3);
vr.setStartEndRes(-1, -1);
assertEquals(vr.getStartRes(), 0);
assertEquals(vr.getEndRes(), 0);
-
+
vr.setStartEndRes(5, 19);
assertEquals(vr.getStartRes(), 5);
assertEquals(vr.getEndRes(), 19);
-
+
// bounds are not constrained to alignment width
// when in wrapped mode
vr.setStartEndRes(88, 888);
assertEquals(vr.getStartRes(), 88);
assertEquals(vr.getEndRes(), 888);
-
+
ViewportRanges vrsmall = new ViewportRanges(smallAl);
vrsmall.setWrappedMode(true);
vrsmall.setStartEndRes(88, 888);
assertEquals(vrsmall.getStartRes(), 88);
assertEquals(vrsmall.getEndRes(), 888);
-
+
// make visible alignment width = 0
smallAl.getHiddenColumns().hideColumns(0, 6);
vrsmall.setStartEndRes(0, 4);
vr.setViewportStartAndWidth(2, 6);
assertEquals(vr.getViewportWidth(), 6);
assertEquals(vr.getStartRes(), 2);
-
+
// reset -ve values of start to 0
vr.setViewportStartAndWidth(-1, 7);
assertEquals(vr.getViewportWidth(), 7);
assertEquals(vr.getStartRes(), 0);
-
+
// out of bounds values are not forced to within bounds
vr.setViewportStartAndWidth(35, 5);
assertEquals(vr.getViewportWidth(), 5);
assertEquals(vr.getStartRes(), 35);
-
+
// small alignment doesn't get bounds reset
ViewportRanges vrsmall = new ViewportRanges(smallAl);
vrsmall.setViewportStartAndWidth(0, 63);
vr.setStartEndRes(0, 39);
int width = vr.getViewportWidth(); // 40
int partWidth = alignmentWidth % width; // 20
-
+
/*
* there are 3 * 40 remainder 20 residues
* number of widths depends on offset (scroll right)
* @throws IllegalArgumentException
*/
@Test(groups = { "Functional" })
- public void testCopyConstructor() throws IllegalArgumentException,
- IllegalAccessException
+ public void testCopyConstructor()
+ throws IllegalArgumentException, IllegalAccessException
{
ViewStyle vs1 = new ViewStyle();
Field[] fields = ViewStyle.class.getDeclaredFields();
final Object value1 = field1.get(vs1);
final Object value2 = field1.get(vs2);
String msg = "Mismatch in " + field1.getName() + "(" + value1 + "/"
- + value2 + ") - not set in copy constructor?";
+ + value2 + ") - not set in copy constructor?";
assertEquals(msg, value1, value2);
}
}
}
/**
- * Add tests here for any fields that we expect to be ignored by
- * the copy constructor
+ * Add tests here for any fields that we expect to be ignored by the copy
+ * constructor
*
* @param field
* @return
return false;
}
-
+
/**
- * Change the value of one field in a ViewStyle object
- *
- * @param vs
- * @param field
- * @throws IllegalAccessException
- */
+ * Change the value of one field in a ViewStyle object
+ *
+ * @param vs
+ * @param field
+ * @throws IllegalAccessException
+ */
protected void changeValue(ViewStyle vs, Field field)
throws IllegalAccessException
{
}
else if (type.equals(Color.class))
{
- field.set(vs, Color.RED.equals(field.get(vs)) ? Color.BLACK
- : Color.RED);
+ field.set(vs,
+ Color.RED.equals(field.get(vs)) ? Color.BLACK : Color.RED);
}
else
{
* @throws IllegalArgumentException
*/
@Test(groups = { "Functional" })
- public void testEquals() throws IllegalArgumentException,
- IllegalAccessException
+ public void testEquals()
+ throws IllegalArgumentException, IllegalAccessException
{
ViewStyle vs1 = new ViewStyle();
ViewStyle vs2 = new ViewStyle(vs1);
Object oldValue = field.get(vs2);
changeValue(vs2, field);
assertFalse("equals method ignores " + field.getName(),
- vs1.equals(vs2));
+ vs1.equals(vs2));
if (vs1.hashCode() == vs2.hashCode())
{
public void testRemoveWorkerForAnnotation()
{
AlignCalcManagerI acm = alignFrame.getViewport().getCalcManager();
- final AlignmentAnnotation ann1 = new AlignmentAnnotation("Ann1",
- "desc", new Annotation[] {});
- final AlignmentAnnotation ann2 = new AlignmentAnnotation("Ann2",
- "desc", new Annotation[] {});
+ final AlignmentAnnotation ann1 = new AlignmentAnnotation("Ann1", "desc",
+ new Annotation[] {});
+ final AlignmentAnnotation ann2 = new AlignmentAnnotation("Ann2", "desc",
+ new Annotation[] {});
/*
* make two workers for ann1, one deletable, one not
* - should delete worker1 but not worker2
*/
acm.removeWorkerForAnnotation(ann1);
- assertEquals(1, acm.getRegisteredWorkersOfClass(worker1.getClass())
- .size());
+ assertEquals(1,
+ acm.getRegisteredWorkersOfClass(worker1.getClass()).size());
assertTrue(acm.getRegisteredWorkersOfClass(worker1.getClass())
.contains(worker2));
assertFalse(acm.isDisabled(worker1));
@BeforeMethod(alwaysRun = true)
public void setUp()
{
- AlignmentI al = new Alignment(new SequenceI[] { new Sequence("Seq1",
- "ABC") });
+ AlignmentI al = new Alignment(
+ new SequenceI[]
+ { new Sequence("Seq1", "ABC") });
al.setDataset(null);
alignFrame = new AlignFrame(al, 3, 1);
}
List<SequenceFeature> sf = sq.findFeatures(col, col, "RESNUM");
if (sf.size() != 1)
{
- errors.append(
- str.id + ": " +
- "Expected one feature at column (position): "
- + (col - 1)
- + " (" + sq.findPosition(col - 1) + ")"
- + ": saw "
- + sf.size());
+ errors.append(str.id + ": "
+ + "Expected one feature at column (position): "
+ + (col - 1) + " (" + sq.findPosition(col - 1) + ")"
+ + ": saw " + sf.size());
errors.append("\n");
if (prev != null)
{
System.out.println("Type: " + source);
SequenceI[] prod = crossRef.findXrefSequences(source, dna)
.getSequencesArray();
- System.out.println("Found "
- + ((prod == null) ? "no" : "" + prod.length)
- + " products");
+ System.out.println(
+ "Found " + ((prod == null) ? "no" : "" + prod.length)
+ + " products");
if (prod != null)
{
for (int p = 0; p < prod.length; p++)
{
- System.out.println("Prod " + p + ": "
- + prod[p].getDisplayId(true));
+ System.out.println(
+ "Prod " + p + ": " + prod[p].getDisplayId(true));
}
}
}
}
else
{
- noProds.addElement((dna ? new Object[] { al, al }
- : new Object[] { al }));
+ noProds.addElement(
+ (dna ? new Object[]
+ { al, al } : new Object[] { al }));
}
}
// present)
for (int p = 0; p < prod.length; p++)
{
- System.out.println("Prod " + p + ": "
- + prod[p].getDisplayId(true));
+ System.out.println(
+ "Prod " + p + ": " + prod[p].getDisplayId(true));
}
}
}
protected Object[][] getAccessions()
{
return new Object[][] { { DBRefSource.UNIPROT, "P30419" },
- { DBRefSource.PDB, "1QIP" }, { DBRefSource.EMBL, "X53828" },
+ { DBRefSource.PDB, "1QIP" },
+ { DBRefSource.EMBL, "X53828" },
{ DBRefSource.EMBLCDS, "CAA37824" },
{ DBRefSource.ENSEMBL, "ENSG00000157764" },
{ new EnsemblGenomes().getDbSource(), "DDB_G0283883" },
wantedFields.add(client.getDataColumnByNameOrCode("organism"));
wantedFields.add(client.getDataColumnByNameOrCode("reviewed")); // Status
wantedFields.add(client.getDataColumnByNameOrCode("length"));
-
+
FTSRestRequest request = new FTSRestRequest();
request.setAllowEmptySeq(false);
request.setResponseSize(100);
request.setFieldToSearchBy("Search All");
request.setSearchTerm("metanephrops"); // lobster!
request.setWantedFields(wantedFields);
-
+
FTSRestResponse response;
response = client.executeRequest(request);
assertTrue(response.getNumberOfItemsFound() > 20);
+ "<uniprot xmlns=\"http://uniprot.org/uniprot\">"
+ "<entry dataset=\"TrEMBL\" created=\"2008-01-15\" modified=\"2015-03-04\" version=\"38\">"
+ "<accession>A9CKP4</accession>"
- + "<accession>A9CKP5</accession>"
- + "<name>A9CKP4_AGRT5</name>"
+ + "<accession>A9CKP5</accession>" + "<name>A9CKP4_AGRT5</name>"
+ "<name>A9CKP4_AGRT6</name>"
+ "<protein><recommendedName><fullName>Mitogen-activated protein kinase 13</fullName></recommendedName></protein>"
+ "<dbReference type=\"PDB\" id=\"2FSQ\"><property type=\"method\" value=\"X-ray\"/><property type=\"resolution\" value=\"1.40\"/></dbReference>"
sf = features.get(6);
assertEquals("sequence variant", sf.getType());
- assertEquals("Foo",
- sf.getDescription());
+ assertEquals("Foo", sf.getDescription());
assertEquals(42,
sf.getLocation().getPosition().getPosition().intValue());
assertNull(sf.getLocation().getBegin());
assertNull(sf.getLocation().getEnd());
- Assert.assertEquals(Uniprot.getDescription(sf),
- "<html>p.Met42Leu" + "<br/> "
- + "p.Met42LeuMetVal Foo</html>");
+ Assert.assertEquals(Uniprot.getDescription(sf), "<html>p.Met42Leu"
+ + "<br/> " + "p.Met42LeuMetVal Foo</html>");
sf = features.get(7);
assertNull(sf.getLocation().getPosition());
assertEquals(42, sf.getLocation().getBegin().getPosition().intValue());
assertEquals(43, sf.getLocation().getEnd().getPosition().intValue());
- Assert.assertEquals(Uniprot.getDescription(sf),
- "<html>p.MetLeu42LeuLeu" + "<br/> "
- + "p.MetLeu42LeuMetVal Foo</html>");
+ Assert.assertEquals(Uniprot.getDescription(sf), "<html>p.MetLeu42LeuLeu"
+ + "<br/> " + "p.MetLeu42LeuMetVal Foo</html>");
sf = features.get(8);
assertNull(sf.getLocation().getPosition());
assertEquals(42, sf.getLocation().getBegin().getPosition().intValue());
assertEquals(45, sf.getLocation().getEnd().getPosition().intValue());
- Assert.assertEquals(Uniprot.getDescription(sf),
- "<html>p.MLML42LeuLeu" + "<br/> "
- + "p.MLML42LMVK Foo Too</html>");
+ Assert.assertEquals(Uniprot.getDescription(sf), "<html>p.MLML42LeuLeu"
+ + "<br/> " + "p.MLML42LMVK Foo Too</html>");
/*
* Check cross-references
public void testGetUniprotSequence() throws UnsupportedEncodingException
{
InputStream is = new ByteArrayInputStream(UNIPROT_XML.getBytes());
- Entry entry = new Uniprot().getUniprotEntries(
- is).get(0);
+ Entry entry = new Uniprot().getUniprotEntries(is).get(0);
SequenceI seq = new Uniprot().uniprotEntryToSequence(entry);
assertNotNull(seq);
assertEquals(6, seq.getDBRefs().size()); // 2*Uniprot, PDB, PDBsum, 2*EMBL
assertEquals(seq.getSequenceAsString(),
seq.createDatasetSequence().getSequenceAsString());
- assertEquals(2,seq.getPrimaryDBRefs().size());
- List<DBRefEntry> res = DBRefUtils.searchRefs(seq.getPrimaryDBRefs(), "A9CKP4");
- assertEquals(1,res.size());
+ assertEquals(2, seq.getPrimaryDBRefs().size());
+ List<DBRefEntry> res = DBRefUtils.searchRefs(seq.getPrimaryDBRefs(),
+ "A9CKP4");
+ assertEquals(1, res.size());
assertTrue(res.get(0).isCanonical());
- res = DBRefUtils.searchRefsForSource(seq.getDBRefs(), DBRefSource.UNIPROT);
- assertEquals(2,res.size());
+ res = DBRefUtils.searchRefsForSource(seq.getDBRefs(),
+ DBRefSource.UNIPROT);
+ assertEquals(2, res.size());
/*
* NB this test fragile - relies on ordering being preserved
*/
* name formatted with Uniprot Entry name
*/
String expectedName = "A9CKP4_AGRT5|A9CKP4_AGRT6";
- assertEquals(expectedName,
- Uniprot.getUniprotEntryId(entry));
+ assertEquals(expectedName, Uniprot.getUniprotEntryId(entry));
}
/**
AlignmentI fullpf = pff.getSequenceRecords(pff.getTestQuery());
Assert.assertNotNull(fullpf, "Full Alignment for " + pff.getTestQuery()
+ " didn't retrieve.");
- Assert.assertTrue(fullpf.getHeight() > 1,
- "Full Alignment for " + pff.getTestQuery()
- + " didn't have more than one sequence.");
+ Assert.assertTrue(fullpf.getHeight() > 1, "Full Alignment for "
+ + pff.getTestQuery() + " didn't have more than one sequence.");
AlignmentI seedpf = pfseed.getSequenceRecords(pff.getTestQuery());
Assert.assertNotNull(seedpf, "Seed Alignment for " + pff.getTestQuery()
+ " didn't retrieve.");
/*
* EMBL
*/
- assertEquals("https://www.ebi.ac.uk/ena/browser/api/embl/x53838?download=true&gzip=true",
+ assertEquals(
+ "https://www.ebi.ac.uk/ena/browser/api/embl/x53838?download=true&gzip=true",
EBIFetchClient.buildUrl("X53838", "EMBL", "display=xml"));
/*
* EMBLCDS
*/
- assertEquals("https://www.ebi.ac.uk/ena/browser/api/embl/caa37824?download=true&gzip=true",
+ assertEquals(
+ "https://www.ebi.ac.uk/ena/browser/api/embl/caa37824?download=true&gzip=true",
EBIFetchClient.buildUrl("CAA37824", "EMBL", "display=xml"));
/*
Iterator<String> presetEnum = presetTests.iterator();
for (Jws2Instance service : disc.getServices())
{
- if (serviceTests.size() == 0
- || serviceTests.contains(service.serviceType.toLowerCase(Locale.ROOT)))
+ if (serviceTests.size() == 0 || serviceTests
+ .contains(service.serviceType.toLowerCase(Locale.ROOT)))
{
List<Preset> prl = null;
Preset pr = null;
}
WsJobParameters pgui = new WsJobParameters(service,
new JabaPreset(service, pr));
- JFrame jf = new JFrame(MessageManager.formatMessage(
- "label.ws_parameters_for",
- new String[] { service.getActionText() }));
+ JFrame jf = new JFrame(MessageManager
+ .formatMessage("label.ws_parameters_for", new String[]
+ { service.getActionText() }));
jf.setSize(700, 800);
JPanel cont = new JPanel(new BorderLayout());
pgui.validate();
iupreds = new ArrayList<Jws2Instance>();
for (Jws2Instance svc : disc.getServices())
{
- if (svc.getServiceTypeURI().toLowerCase(Locale.ROOT).contains("iupredws"))
+ if (svc.getServiceTypeURI().toLowerCase(Locale.ROOT)
+ .contains("iupredws"))
{
iupreds.add(svc);
}
assertTrue("Couldn't discover any IUPred services to use to test.",
iupreds.size() > 0);
jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
- af = fl.LoadFileWaitTillLoaded(testseqs, jalview.io.DataSourceType.FILE);
+ af = fl.LoadFileWaitTillLoaded(testseqs,
+ jalview.io.DataSourceType.FILE);
assertNotNull("Couldn't load test data ('" + testseqs + "')", af);
}
{
try
{
- String aligfileout = FileFormat.Pfam.getWriter(al).print(
- al.getSequencesArray(), true);
+ String aligfileout = FileFormat.Pfam.getWriter(al)
+ .print(al.getSequencesArray(), true);
String anfileout = new AnnotationFile()
.printAnnotationsForAlignment(al);
- assertTrue(
- "Test "
- + testname
- + "\nAlignment annotation file was not regenerated. Null string",
+ assertTrue("Test " + testname
+ + "\nAlignment annotation file was not regenerated. Null string",
anfileout != null);
- assertTrue(
- "Test "
- + testname
- + "\nAlignment annotation file was not regenerated. Empty string",
+ assertTrue("Test " + testname
+ + "\nAlignment annotation file was not regenerated. Empty string",
anfileout.length() > "JALVIEW_ANNOTATION".length());
- System.out.println("Output annotation file:\n" + anfileout
- + "\n<<EOF\n");
+ System.out.println(
+ "Output annotation file:\n" + anfileout + "\n<<EOF\n");
AlignmentI al_new = new FormatAdapter().readFile(aligfileout,
DataSourceType.PASTE, FileFormat.Pfam);
- assertTrue(
- "Test "
- + testname
- + "\nregenerated annotation file did not annotate alignment.",
+ assertTrue("Test " + testname
+ + "\nregenerated annotation file did not annotate alignment.",
new AnnotationFile().readAnnotationFile(al_new, anfileout,
DataSourceType.PASTE));
{
e.printStackTrace();
}
- Assert.fail("Test "
- + testname
+ Assert.fail("Test " + testname
+ "\nCouldn't complete Annotation file roundtrip input/output/input test.");
}
} catch (Exception e)
{
e.printStackTrace();
- Assert.fail("Aborting. Problem discovering services. Tried "
- + svcurls);
+ Assert.fail(
+ "Aborting. Problem discovering services. Tried " + svcurls);
}
Assert.assertTrue(disc.getServices().size() > 0,
"Failed to discover any services at ");
public void msaTest() throws Exception
{
String url;
- RegistryWS registry = Jws2Client
- .connectToRegistry(url = "http://www.compbio.dundee.ac.uk/jabaws");
+ RegistryWS registry = Jws2Client.connectToRegistry(
+ url = "http://www.compbio.dundee.ac.uk/jabaws");
if (registry != null)
{
}
if (msaservice == null)
{
- Assert.fail("couldn't find a clustalO service on the public registry");
+ Assert.fail(
+ "couldn't find a clustalO service on the public registry");
}
FastaSequence fsq = new FastaSequence("seqA",
"SESESESESESESESSESESSESESESESESESESESESEEEEEESSESESESESSSSESESESESESESE");
for (Jws2Instance svc : disc.getServices())
{
- if (svc.getServiceTypeURI().toLowerCase(Locale.ROOT).contains("rnaalifoldws"))
+ if (svc.getServiceTypeURI().toLowerCase(Locale.ROOT)
+ .contains("rnaalifoldws"))
{
rnaalifoldws = svc;
}
jalview.io.FileLoader fl = new jalview.io.FileLoader(false);
- af = fl.LoadFileWaitTillLoaded(testseqs, jalview.io.DataSourceType.FILE);
+ af = fl.LoadFileWaitTillLoaded(testseqs,
+ jalview.io.DataSourceType.FILE);
assertNotNull("Couldn't load test data ('" + testseqs + "')", af);
try
{
// what format would be appropriate for RNAalifold annotations?
- String aligfileout = FileFormat.Pfam.getWriter(null).print(
- al.getSequencesArray(), true);
+ String aligfileout = FileFormat.Pfam.getWriter(null)
+ .print(al.getSequencesArray(), true);
String anfileout = new AnnotationFile()
.printAnnotationsForAlignment(al);
- assertNotNull(
- "Test "
- + testname
- + "\nAlignment annotation file was not regenerated. Null string",
+ assertNotNull("Test " + testname
+ + "\nAlignment annotation file was not regenerated. Null string",
anfileout);
- assertTrue(
- "Test "
- + testname
- + "\nAlignment annotation file was not regenerated. Empty string",
+ assertTrue("Test " + testname
+ + "\nAlignment annotation file was not regenerated. Empty string",
anfileout.length() > "JALVIEW_ANNOTATION".length());
- System.out.println("Output annotation file:\n" + anfileout
- + "\n<<EOF\n");
+ System.out.println(
+ "Output annotation file:\n" + anfileout + "\n<<EOF\n");
// again what format would be appropriate?
AlignmentI al_new = new FormatAdapter().readFile(aligfileout,
DataSourceType.PASTE, FileFormat.Pfam);
- assertTrue(
- "Test "
- + testname
- + "\nregenerated annotation file did not annotate alignment.",
+ assertTrue("Test " + testname
+ + "\nregenerated annotation file did not annotate alignment.",
new AnnotationFile().readAnnotationFile(al_new, anfileout,
DataSourceType.PASTE));
{
e.printStackTrace();
}
- Assert.fail("Test "
- + testname
+ Assert.fail("Test " + testname
+ "\nCouldn't complete Annotation file roundtrip input/output/input test.");
}
}
;
} while (af.getViewport().getCalcManager().isWorking());
- AutoCalcSetting oldacs = af.getViewport().getCalcIdSettingsFor(
- alifoldClient.getCalcId());
+ AutoCalcSetting oldacs = af.getViewport()
+ .getCalcIdSettingsFor(alifoldClient.getCalcId());
String oldsettings = oldacs.getWsParamFile();
// write out parameters
jalview.gui.AlignFrame nalf = null;
- assertTrue("Couldn't write out the Jar file",
- new Jalview2XML(false).saveAlignment(af, JAR_FILE_NAME,
- "trial parameter writeout"));
- assertTrue("Couldn't read back the Jar file", (nalf = new Jalview2XML(
- false).loadJalviewAlign(JAR_FILE_NAME)) != null);
+ assertTrue("Couldn't write out the Jar file", new Jalview2XML(false)
+ .saveAlignment(af, JAR_FILE_NAME, "trial parameter writeout"));
+ assertTrue("Couldn't read back the Jar file",
+ (nalf = new Jalview2XML(false)
+ .loadJalviewAlign(JAR_FILE_NAME)) != null);
if (nalf != null)
{
- AutoCalcSetting acs = af.getViewport().getCalcIdSettingsFor(
- alifoldClient.getCalcId());
+ AutoCalcSetting acs = af.getViewport()
+ .getCalcIdSettingsFor(alifoldClient.getCalcId());
assertTrue("Calc ID settings not recovered from viewport stash",
acs.equals(oldacs));
assertTrue(
}
;
}
- AutoCalcSetting acs2 = af.getViewport().getCalcIdSettingsFor(
- alifoldClient.getCalcId());
+ AutoCalcSetting acs2 = af.getViewport()
+ .getCalcIdSettingsFor(alifoldClient.getCalcId());
assertTrue(
"Calc ID settings after recalculation has not been recovered.",
acs2.getWsParamFile().equals(oldsettings));
String on = o.next();
String sn = s.next();
String st = t.next();
- final String errorMsg = "Original was " + on
- + " Phase 1 wrote " + sn + "\tPhase 2 wrote " + st;
+ final String errorMsg = "Original was " + on + " Phase 1 wrote "
+ + sn + "\tPhase 2 wrote " + st;
assertEquals(errorMsg, sn, st);
assertEquals(errorMsg, sn, on);
}
*/
public boolean isForTesting(Jws2Instance service)
{
- return serviceTests.size() == 0
- || serviceTests.contains(service.serviceType.toLowerCase(Locale.ROOT));
+ return serviceTests.size() == 0 || serviceTests
+ .contains(service.serviceType.toLowerCase(Locale.ROOT));
}
@Test(groups = { "Network" })
assertTrue(
"Couldn't load the test data's annotation file (should be 5 groups but found "
+ alf.getViewport().getAlignment().getGroups().size()
- + ").", alf.getViewport().getAlignment().getGroups()
- .size() == 5);
+ + ").",
+ alf.getViewport().getAlignment().getGroups().size() == 5);
RestClient rc = new RestClient(_rc.service, alf, true);
return testRsdExchange(desc, newService);
} catch (Throwable x)
{
- System.err.println("Failed for service (" + desc + "): "
- + servicestring);
+ System.err.println(
+ "Failed for service (" + desc + "): " + servicestring);
x.printStackTrace();
return false;
}
fromservicetostring);
if (!newService.isValid())
{
- throw new Error("Failed to create service from '"
- + fromservicetostring + "'.\n"
- + newService.getInvalidMessage());
+ throw new Error(
+ "Failed to create service from '" + fromservicetostring
+ + "'.\n" + newService.getInvalidMessage());
}
if (!service.equals(newService))
}
} catch (Throwable x)
{
- System.err.println("Failed for service (" + desc + "): "
- + service.toString());
+ System.err.println(
+ "Failed for service (" + desc + "): " + service.toString());
x.printStackTrace();
return false;
}
{
}
- @Test(groups= {"Network"})
+ @Test(groups = { "Network" })
public void checkUniprotCanonicalFlagSet()
{
- // TODO - mock this - for moment it is a live request.
+ // TODO - mock this - for moment it is a live request.
SequenceI uniprotSeq = new Sequence("FER1_SPIOL",
"MAATTTTMMGMATTFVPKPQAPPMMAALPSNTGRSLFGLKTGSRGGRMTMAAYKVTLVTPTGNVEFQCPDDV"
- + "YILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLDDDQIDEGWVLTCAAYPVSDVTIETHKEEE"
- + "LTA");
+ + "YILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLDDDQIDEGWVLTCAAYPVSDVTIETHKEEE"
+ + "LTA");
DBRefFetcher dbr = new DBRefFetcher(new SequenceI[] { uniprotSeq });
dbr.fetchDBRefs(true);
List<DBRefEntry> primRefs = uniprotSeq.getPrimaryDBRefs();
assertNotNull(primRefs);
- assertTrue(primRefs.size()>0);
- boolean canonicalUp=false;
- for (DBRefEntry ref:primRefs) {
+ assertTrue(primRefs.size() > 0);
+ boolean canonicalUp = false;
+ for (DBRefEntry ref : primRefs)
+ {
assertEquals(DBRefSource.UNIPROT, ref.getCanonicalSourceName());
canonicalUp |= ref.isCanonical();
}
assertTrue("No Canonical Uniprot reference detected", canonicalUp);
}
+
/**
* Tests that standard protein database sources include Uniprot (as the first)
* and also PDB. (Additional sources are dependent on availability of DAS
public void testEmblUniprotProductRecovery() throws Exception
{
String retrievalId = "V00488";
- DbSourceProxy embl = new SequenceFetcher().getSourceProxy(
- DBRefSource.EMBL).get(0);
+ DbSourceProxy embl = new SequenceFetcher()
+ .getSourceProxy(DBRefSource.EMBL).get(0);
assertNotNull("Couldn't find the EMBL retrieval client", embl);
verifyProteinNucleotideXref(retrievalId, embl);
}
public void testEmblCDSUniprotProductRecovery() throws Exception
{
String retrievalId = "AAH29712";
- DbSourceProxy embl = new SequenceFetcher().getSourceProxy(
- DBRefSource.EMBLCDS).get(0);
+ DbSourceProxy embl = new SequenceFetcher()
+ .getSourceProxy(DBRefSource.EMBLCDS).get(0);
assertNotNull("Couldn't find the EMBL retrieval client", embl);
verifyProteinNucleotideXref(retrievalId, embl);
}
assertEquals("Didn't retrieve right number of records", 1,
alsq.getHeight());
SequenceI seq = alsq.getSequenceAt(0);
- assertEquals("Wrong sequence name", embl.getDbSource() + "|"
- + retrievalId, seq.getName());
+ assertEquals("Wrong sequence name",
+ embl.getDbSource() + "|" + retrievalId, seq.getName());
List<SequenceFeature> sfs = seq.getSequenceFeatures();
assertFalse("Sequence features missing", sfs.isEmpty());
- assertTrue(
- "Feature not CDS",
- FeatureProperties.isCodingFeature(embl.getDbSource(),
- sfs.get(0).getType()));
+ assertTrue("Feature not CDS", FeatureProperties
+ .isCodingFeature(embl.getDbSource(), sfs.get(0).getType()));
assertEquals(embl.getDbSource(), sfs.get(0).getFeatureGroup());
List<DBRefEntry> dr = DBRefUtils.selectRefs(seq.getDBRefs(),
- new String[] { DBRefSource.UNIPROT });
+ new String[]
+ { DBRefSource.UNIPROT });
assertNotNull(dr);
assertEquals("Expected a single Uniprot cross reference", 1, dr.size());
- assertEquals("Expected cross reference map to be one amino acid", dr.get(0)
- .getMap().getMappedWidth(), 1);
- assertEquals("Expected local reference map to be 3 nucleotides", dr.get(0)
- .getMap().getWidth(), 3);
+ assertEquals("Expected cross reference map to be one amino acid",
+ dr.get(0).getMap().getMappedWidth(), 1);
+ assertEquals("Expected local reference map to be 3 nucleotides",
+ dr.get(0).getMap().getWidth(), 3);
AlignmentI sprods = new CrossRef(alsq.getSequencesArray(), alsq)
.findXrefSequences(dr.get(0).getSource(), true);
assertNotNull(
assertEquals("Didn't xref right number of records", 1,
sprods.getHeight());
SequenceI proteinSeq = sprods.getSequenceAt(0);
- assertEquals(proteinSeq.getSequenceAsString(), dr.get(0).getMap().getTo()
- .getSequenceAsString());
+ assertEquals(proteinSeq.getSequenceAsString(),
+ dr.get(0).getMap().getTo().getSequenceAsString());
assertEquals(dr.get(0).getSource() + "|" + dr.get(0).getAccessionId(),
proteinSeq.getName());
}
}
public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = System
- .getProperty("user.home")
- + File.separatorChar
+ .getProperty("user.home") + File.separatorChar
+ ".sifts_downloads" + File.separatorChar;
private String testPDBId = "1a70";
private SiftsClient siftsClient = null;
- SequenceI testSeq = new Sequence(
- "P00221",
+ SequenceI testSeq = new Sequence("P00221",
"MAAT..TTTMMG..MATTFVPKPQAPPMMAALPSNTGR..SLFGLKT.GSR..GGRMTMA"
+ "AYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDD"
- + "QSFLDDDQIDEGWVLTCAAYPVSDVTIETHKEEELTA.", 1, 147);
+ + "QSFLDDDQIDEGWVLTCAAYPVSDVTIETHKEEELTA.",
+ 1, 147);
int u = SiftsClient.UNASSIGNED;
// SIFTs entries are updated weekly - so use saved SIFTs file to enforce
// test reproducibility
new SiftsSettings();
- SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache.getDefault(
- "sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR));
+ SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache
+ .getDefault("sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR));
SiftsSettings.setMapWithSifts(true);
SiftsSettings.setCacheThresholdInDays("2");
SiftsSettings.setFailSafePIDThreshold("70");
PDBfile pdbFile;
- pdbFile = new PDBfile(false, false, false, "test/jalview/io/"
- + testPDBId + ".pdb", DataSourceType.FILE);
+ pdbFile = new PDBfile(false, false, false,
+ "test/jalview/io/" + testPDBId + ".pdb", DataSourceType.FILE);
siftsClient = new SiftsClient(pdbFile);
}
try
{
- HashMap<Integer, int[]> actualMapping = siftsClient.getGreedyMapping(
- "A", testSeq, null);
+ HashMap<Integer, int[]> actualMapping = siftsClient
+ .getGreedyMapping("A", testSeq, null);
Assert.assertEquals(testSeq.getStart(), 1);
Assert.assertEquals(testSeq.getEnd(), 147);
// Can't do Assert.assertEquals(actualMapping, expectedMapping);
}
@Test(
- groups = { "Network" },
+ groups =
+ { "Network" },
expectedExceptions = IllegalArgumentException.class)
private void getAtomIndexNullTest()
{
}
- @Test(
-groups = { "Network" },
- expectedExceptions = SiftsException.class)
+ @Test(groups = { "Network" }, expectedExceptions = SiftsException.class)
private void populateAtomPositionsNullTest1()
throws IllegalArgumentException, SiftsException
{
siftsClient.populateAtomPositions(null, null);
}
- @Test(
-groups = { "Network" },
- expectedExceptions = SiftsException.class)
+ @Test(groups = { "Network" }, expectedExceptions = SiftsException.class)
private void populateAtomPositionsNullTest2()
throws IllegalArgumentException, SiftsException
{
Assert.assertEquals(actualValidSrcDBRef, expectedDBRef);
}
- @Test(
-groups = { "Network" },
- expectedExceptions = SiftsException.class)
+ @Test(groups = { "Network" }, expectedExceptions = SiftsException.class)
public void getValidSourceDBRefExceptionTest() throws SiftsException
{
SequenceI invalidTestSeq = new Sequence("testSeq", "ABCDEFGH");
siftsClient.getValidSourceDBRef(invalidTestSeq);
}
- @Test(
-groups = { "Network" },
- expectedExceptions = SiftsException.class)
+ @Test(groups = { "Network" }, expectedExceptions = SiftsException.class)
public void getValidSourceDBRefExceptionXTest() throws SiftsException
{
SequenceI invalidTestSeq = new Sequence("testSeq", "ABCDEFGH");
public void getSiftsStructureMappingTest() throws SiftsException
{
Assert.assertTrue(SiftsSettings.isMapWithSifts());
- StructureMapping strucMapping = siftsClient.getSiftsStructureMapping(
- testSeq, testPDBId, "A");
+ StructureMapping strucMapping = siftsClient
+ .getSiftsStructureMapping(testSeq, testPDBId, "A");
String expectedMappingOutput = "\nSequence ⟷ Structure mapping details\n"
- + "Method: SIFTS\n\n"
- + "P00221 : 51 - 147 Maps to \n"
+ + "Method: SIFTS\n\n" + "P00221 : 51 - 147 Maps to \n"
+ "1A70|A : 1 - 97\n\n"
+ "P00221 AAYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLD\n"
+ " |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n"
while (it.hasNext())
{
Map.Entry<Integer, int[]> pair = it.next();
- Assert.assertTrue(strucMapping.getMapping()
- .containsKey(pair.getKey()));
+ Assert.assertTrue(
+ strucMapping.getMapping().containsKey(pair.getKey()));
Assert.assertEquals(strucMapping.getMapping().get(pair.getKey()),
pair.getValue());
}
}
@Test(groups = { "Network" })
- public void getEntityByMostOptimalMatchedIdTest1() throws IOException,
- SiftsException
+ public void getEntityByMostOptimalMatchedIdTest1()
+ throws IOException, SiftsException
{
SiftsClient siftsClientX = null;
PDBfile pdbFile;
- pdbFile = new PDBfile(false, false, false, "test/jalview/io/2nq2"
- + ".pdb", DataSourceType.FILE);
+ pdbFile = new PDBfile(false, false, false,
+ "test/jalview/io/2nq2" + ".pdb", DataSourceType.FILE);
siftsClientX = new SiftsClient(pdbFile);
Entity entityA = siftsClientX.getEntityByMostOptimalMatchedId("A");
Assert.assertEquals(entityA.getEntityId(), "A");
}
@Test(groups = { "Network" })
- public void getEntityByMostOptimalMatchedIdTest2() throws IOException,
- SiftsException
+ public void getEntityByMostOptimalMatchedIdTest2()
+ throws IOException, SiftsException
{
// This test is for a SIFTS file in which entity A should map to chain P for
// the given PDB Id. All the other chains shouldn't be mapped as there are
@Test(groups = { "Network" })
public void getLeadingIntegerFromString()
{
- Assert.assertEquals(
- SiftsClient.getLeadingIntegerValue("1234abcd", -1), 1234);
- Assert.assertEquals(
- SiftsClient.getLeadingIntegerValue("1234", -1),
+ Assert.assertEquals(SiftsClient.getLeadingIntegerValue("1234abcd", -1),
+ 1234);
+ Assert.assertEquals(SiftsClient.getLeadingIntegerValue("1234", -1),
1234);
- Assert.assertEquals(
- SiftsClient.getLeadingIntegerValue("abcd", -1), -1);
- Assert.assertEquals(
- SiftsClient.getLeadingIntegerValue("abcd1234", -1), -1);
- Assert.assertEquals(
- SiftsClient.getLeadingIntegerValue("None", -1), -1);
- Assert.assertEquals(
- SiftsClient.getLeadingIntegerValue("Null", -1), -1);
+ Assert.assertEquals(SiftsClient.getLeadingIntegerValue("abcd", -1), -1);
+ Assert.assertEquals(SiftsClient.getLeadingIntegerValue("abcd1234", -1),
+ -1);
+ Assert.assertEquals(SiftsClient.getLeadingIntegerValue("None", -1), -1);
+ Assert.assertEquals(SiftsClient.getLeadingIntegerValue("Null", -1), -1);
}
}
import org.testng.Assert;
import org.testng.annotations.Test;
-public class UrlDownloadClientTest {
+public class UrlDownloadClientTest
+{
/**
* Test that url is successfully loaded into download file
* Test that garbage in results in IOException
*/
@Test(
- groups = { "Network" },
+ groups =
+ { "Network" },
enabled = true,
- expectedExceptions = { IOException.class })
+ expectedExceptions =
+ { IOException.class })
public void DownloadGarbageUrlTest() throws IOException
{
UrlDownloadClient client = new UrlDownloadClient();
import java.util.Collection;
/**
- * This class is used to access a method or field of an object no matter what the access modifier of the method or field. The syntax
- * for accessing fields and methods is out of the ordinary because this class uses reflection to peel away protection.
+ * This class is used to access a method or field of an object no matter what
+ * the access modifier of the method or field. The syntax for accessing fields
+ * and methods is out of the ordinary because this class uses reflection to peel
+ * away protection.
* <p>
* a.k.a. The "ObjectMolester"
* <p>
* Given the following class <code>MyClass</code>: <br>
*
* <pre>
- * public class MyClass {
- * private String name; // private attribute
+ * public class MyClass
+ * {
+ * private String name; // private attribute
*
- * // private constructor
- * private MyClass() {
- * super();
- * }
+ * // private constructor
+ * private MyClass()
+ * {
+ * super();
+ * }
*
- * // private method
- * private void setName(String newName) {
- * this.name = newName;
- * }
+ * // private method
+ * private void setName(String newName)
+ * {
+ * this.name = newName;
+ * }
* }
* </pre>
*
* String name = PA.getValue(myObj, "name");
* </pre>
*
- * This class extends {@link PrivilegedAccessor} by re-throwing checked {@link Exception}s as {@link RuntimeException}s.
+ * This class extends {@link PrivilegedAccessor} by re-throwing checked
+ * {@link Exception}s as {@link RuntimeException}s.
*
*
* @see PrivilegedAccessor
* @author Sebastian Dietrich (sebastian.dietrich@e-movimento.com)
* @author Lubos Bistak (lubos@bistak.sk)
*/
-public class PA {
- private final Object instanceOrClass;
+public class PA
+{
+ private final Object instanceOrClass;
- /**
- * Private constructor to make it impossible to instantiate this class from outside of PA.
- *
- * @param instanceOrClass
- */
- private PA(Object instanceOrClass) {
- this.instanceOrClass = instanceOrClass;
- }
+ /**
+ * Private constructor to make it impossible to instantiate this class from
+ * outside of PA.
+ *
+ * @param instanceOrClass
+ */
+ private PA(Object instanceOrClass)
+ {
+ this.instanceOrClass = instanceOrClass;
+ }
- /**
- * Returns a string representation of the given object. The string has the following format: "<classname> {<attributes and values>}"
- * whereas <attributes and values> is a comma separated list with <attributeName>=<attributeValue> <atributes and values> includes
- * all attributes of the objects class followed by the attributes of its superclass (if any) and so on.
- *
- * @param instanceOrClass the object or class to get a string representation of
- * @return a string representation of the given object
- *
- * @see PrivilegedAccessor#toString(Object)
- */
- public static String toString(final Object instanceOrClass) {
- return PrivilegedAccessor.toString(instanceOrClass);
- }
+ /**
+ * Returns a string representation of the given object. The string has the
+ * following format: "<classname> {<attributes and values>}" whereas
+ * <attributes and values> is a comma separated list with
+ * <attributeName>=<attributeValue> <atributes and values> includes all
+ * attributes of the objects class followed by the attributes of its
+ * superclass (if any) and so on.
+ *
+ * @param instanceOrClass
+ * the object or class to get a string representation of
+ * @return a string representation of the given object
+ *
+ * @see PrivilegedAccessor#toString(Object)
+ */
+ public static String toString(final Object instanceOrClass)
+ {
+ return PrivilegedAccessor.toString(instanceOrClass);
+ }
- /**
- * Gets the name of all fields (public, private, protected, default) of the given instance or class. This includes as well all
- * fields (public, private, protected, default) of all its super classes.
- *
- * @param instanceOrClass the instance or class to get the fields of
- * @return the collection of field names of the given instance or class
- *
- * @see PrivilegedAccessor#getFieldNames(Object)
- */
- public static Collection<String> getFieldNames(final Object instanceOrClass) {
- return PrivilegedAccessor.getFieldNames(instanceOrClass);
- }
+ /**
+ * Gets the name of all fields (public, private, protected, default) of the
+ * given instance or class. This includes as well all fields (public, private,
+ * protected, default) of all its super classes.
+ *
+ * @param instanceOrClass
+ * the instance or class to get the fields of
+ * @return the collection of field names of the given instance or class
+ *
+ * @see PrivilegedAccessor#getFieldNames(Object)
+ */
+ public static Collection<String> getFieldNames(
+ final Object instanceOrClass)
+ {
+ return PrivilegedAccessor.getFieldNames(instanceOrClass);
+ }
- /**
- * Gets the signatures of all methods (public, private, protected, default) of the given instance or class. This includes as well
- * all methods (public, private, protected, default) of all its super classes. This does not include constructors.
- *
- * @param instanceOrClass the instance or class to get the method signatures of
- * @return the collection of method signatures of the given instance or class
- *
- * @see PrivilegedAccessor#getMethodSignatures(Object)
- */
- public static Collection<String> getMethodSignatures(final Object instanceOrClass) {
- return PrivilegedAccessor.getMethodSignatures(instanceOrClass);
- }
+ /**
+ * Gets the signatures of all methods (public, private, protected, default) of
+ * the given instance or class. This includes as well all methods (public,
+ * private, protected, default) of all its super classes. This does not
+ * include constructors.
+ *
+ * @param instanceOrClass
+ * the instance or class to get the method signatures of
+ * @return the collection of method signatures of the given instance or class
+ *
+ * @see PrivilegedAccessor#getMethodSignatures(Object)
+ */
+ public static Collection<String> getMethodSignatures(
+ final Object instanceOrClass)
+ {
+ return PrivilegedAccessor.getMethodSignatures(instanceOrClass);
+ }
- /**
- * Gets the value of the named field and returns it as an object. If instanceOrClass is a class then a static field is returned.
- *
- * @param instanceOrClass the instance or class to get the field from
- * @param fieldName the name of the field
- * @return an object representing the value of the field
- * @throws IllegalArgumentException if the field does not exist
- *
- * @see PrivilegedAccessor#getValue(Object,String)
- */
- public static Object getValue(final Object instanceOrClass, final String fieldName) {
- try {
- return PrivilegedAccessor.getValue(instanceOrClass, fieldName);
- } catch (Exception e) {
- throw new IllegalArgumentException("Can't get value of " + fieldName + " from " + instanceOrClass, e);
- }
- }
+ /**
+ * Gets the value of the named field and returns it as an object. If
+ * instanceOrClass is a class then a static field is returned.
+ *
+ * @param instanceOrClass
+ * the instance or class to get the field from
+ * @param fieldName
+ * the name of the field
+ * @return an object representing the value of the field
+ * @throws IllegalArgumentException
+ * if the field does not exist
+ *
+ * @see PrivilegedAccessor#getValue(Object,String)
+ */
+ public static Object getValue(final Object instanceOrClass,
+ final String fieldName)
+ {
+ try
+ {
+ return PrivilegedAccessor.getValue(instanceOrClass, fieldName);
+ } catch (Exception e)
+ {
+ throw new IllegalArgumentException("Can't get value of " + fieldName
+ + " from " + instanceOrClass, e);
+ }
+ }
- /**
- * Gets the value of the named field and returns it as an object.
- *
- * @param fieldName the name of the field
- * @return an object representing the value of the field
- * @throws IllegalArgumentException if the field does not exist
- *
- * @see PA#getValue(Object,String)
- */
- public Object getValue(final String fieldName) {
- return PA.getValue(instanceOrClass, fieldName);
- }
+ /**
+ * Gets the value of the named field and returns it as an object.
+ *
+ * @param fieldName
+ * the name of the field
+ * @return an object representing the value of the field
+ * @throws IllegalArgumentException
+ * if the field does not exist
+ *
+ * @see PA#getValue(Object,String)
+ */
+ public Object getValue(final String fieldName)
+ {
+ return PA.getValue(instanceOrClass, fieldName);
+ }
- /**
- * Instantiates an object of the given class with the given arguments and the given argument types. If you want to instantiate a
- * member class, you must provide the object it is a member of as first argument.
- *
- * @param fromClass the class to instantiate an object from
- * @param arguments the arguments to pass to the constructor
- * @param argumentTypes the fully qualified types of the arguments of the constructor
- * @return an object of the given type
- * @throws IllegalArgumentException if the class can't be instantiated. This could be the case if the number of actual and formal
- * parameters differ; if an unwrapping conversion for primitive arguments fails; if, after possible unwrapping, a
- * parameter value cannot be converted to the corresponding formal parameter type by a method invocation conversion; if
- * this Constructor object enforces Java language access control and the underlying constructor is inaccessible; if the
- * underlying constructor throws an exception; if the constructor could not be found; or if the class that declares the
- * underlying constructor represents an abstract class.
- *
- * @see PrivilegedAccessor#instantiate(Class,Class[],Object[])
- */
- public static <T> T instantiate(final Class<? extends T> fromClass, final Class<?>[] argumentTypes, final Object... arguments) {
- try {
- return PrivilegedAccessor.instantiate(fromClass, argumentTypes, correctVarargs(arguments));
- } catch (Exception e) {
- throw new IllegalArgumentException("Can't instantiate class " + fromClass + " with arguments " + arguments, e);
- }
- }
+ /**
+ * Instantiates an object of the given class with the given arguments and the
+ * given argument types. If you want to instantiate a member class, you must
+ * provide the object it is a member of as first argument.
+ *
+ * @param fromClass
+ * the class to instantiate an object from
+ * @param arguments
+ * the arguments to pass to the constructor
+ * @param argumentTypes
+ * the fully qualified types of the arguments of the constructor
+ * @return an object of the given type
+ * @throws IllegalArgumentException
+ * if the class can't be instantiated. This could be the case if the
+ * number of actual and formal parameters differ; if an unwrapping
+ * conversion for primitive arguments fails; if, after possible
+ * unwrapping, a parameter value cannot be converted to the
+ * corresponding formal parameter type by a method invocation
+ * conversion; if this Constructor object enforces Java language
+ * access control and the underlying constructor is inaccessible; if
+ * the underlying constructor throws an exception; if the
+ * constructor could not be found; or if the class that declares the
+ * underlying constructor represents an abstract class.
+ *
+ * @see PrivilegedAccessor#instantiate(Class,Class[],Object[])
+ */
+ public static <T> T instantiate(final Class<? extends T> fromClass,
+ final Class<?>[] argumentTypes, final Object... arguments)
+ {
+ try
+ {
+ return PrivilegedAccessor.instantiate(fromClass, argumentTypes,
+ correctVarargs(arguments));
+ } catch (Exception e)
+ {
+ throw new IllegalArgumentException("Can't instantiate class "
+ + fromClass + " with arguments " + arguments, e);
+ }
+ }
- /**
- * Instantiates an object of the given class with the given arguments. If you want to instantiate a member class, you must provide
- * the object it is a member of as first argument.
- *
- * @param fromClass the class to instantiate an object from
- * @param arguments the arguments to pass to the constructor
- * @return an object of the given type
- * @throws IllegalArgumentException if the class can't be instantiated. This could be the case if the number of actual and formal
- * parameters differ; if an unwrapping conversion for primitive arguments fails; or if, after possible unwrapping, a
- * parameter value cannot be converted to the corresponding formal parameter type by a method invocation conversion; if
- * this Constructor object enforces Java language access control and the underlying constructor is inaccessible; if the
- * underlying constructor throws an exception; if the constructor could not be found; or if the class that declares the
- * underlying constructor represents an abstract class.
- *
- * @see PrivilegedAccessor#instantiate(Class,Object[])
- */
- public static <T> T instantiate(final Class<? extends T> fromClass, final Object... arguments) {
- try {
- return PrivilegedAccessor.instantiate(fromClass, correctVarargs(arguments));
- } catch (Exception e) {
- throw new IllegalArgumentException("Can't instantiate class " + fromClass + " with arguments " + arguments, e);
- }
- }
+ /**
+ * Instantiates an object of the given class with the given arguments. If you
+ * want to instantiate a member class, you must provide the object it is a
+ * member of as first argument.
+ *
+ * @param fromClass
+ * the class to instantiate an object from
+ * @param arguments
+ * the arguments to pass to the constructor
+ * @return an object of the given type
+ * @throws IllegalArgumentException
+ * if the class can't be instantiated. This could be the case if the
+ * number of actual and formal parameters differ; if an unwrapping
+ * conversion for primitive arguments fails; or if, after possible
+ * unwrapping, a parameter value cannot be converted to the
+ * corresponding formal parameter type by a method invocation
+ * conversion; if this Constructor object enforces Java language
+ * access control and the underlying constructor is inaccessible; if
+ * the underlying constructor throws an exception; if the
+ * constructor could not be found; or if the class that declares the
+ * underlying constructor represents an abstract class.
+ *
+ * @see PrivilegedAccessor#instantiate(Class,Object[])
+ */
+ public static <T> T instantiate(final Class<? extends T> fromClass,
+ final Object... arguments)
+ {
+ try
+ {
+ return PrivilegedAccessor.instantiate(fromClass,
+ correctVarargs(arguments));
+ } catch (Exception e)
+ {
+ throw new IllegalArgumentException("Can't instantiate class "
+ + fromClass + " with arguments " + arguments, e);
+ }
+ }
- /**
- * Calls a method on the given object instance with the given arguments. Arguments can be object types or representations for
- * primitives.
- *
- * @param instanceOrClass the instance or class to invoke the method on
- * @param methodSignature the name of the method and the parameters <br>
- * (e.g. "myMethod(java.lang.String, com.company.project.MyObject)")
- * @param arguments an array of objects to pass as arguments
- * @return the return value of this method or null if void
- * @throws IllegalArgumentException if the method could not be invoked. This could be the case if the method is inaccessible; if the
- * underlying method throws an exception; if no method with the given <code>methodSignature</code> could be found; or if
- * an argument couldn't be converted to match the expected type
- *
- * @see PrivilegedAccessor#invokeMethod(Object,String,Object[])
- */
- public static Object invokeMethod(final Object instanceOrClass, final String methodSignature, final Object... arguments) {
- try {
- return PrivilegedAccessor.invokeMethod(instanceOrClass, methodSignature, correctVarargs(arguments));
- } catch (Exception e) {
- throw new IllegalArgumentException("Can't invoke method " + methodSignature + " on " + instanceOrClass + " with arguments "
- + arguments, e);
- }
- }
+ /**
+ * Calls a method on the given object instance with the given arguments.
+ * Arguments can be object types or representations for primitives.
+ *
+ * @param instanceOrClass
+ * the instance or class to invoke the method on
+ * @param methodSignature
+ * the name of the method and the parameters <br>
+ * (e.g. "myMethod(java.lang.String, com.company.project.MyObject)")
+ * @param arguments
+ * an array of objects to pass as arguments
+ * @return the return value of this method or null if void
+ * @throws IllegalArgumentException
+ * if the method could not be invoked. This could be the case if the
+ * method is inaccessible; if the underlying method throws an
+ * exception; if no method with the given
+ * <code>methodSignature</code> could be found; or if an argument
+ * couldn't be converted to match the expected type
+ *
+ * @see PrivilegedAccessor#invokeMethod(Object,String,Object[])
+ */
+ public static Object invokeMethod(final Object instanceOrClass,
+ final String methodSignature, final Object... arguments)
+ {
+ try
+ {
+ return PrivilegedAccessor.invokeMethod(instanceOrClass,
+ methodSignature, correctVarargs(arguments));
+ } catch (Exception e)
+ {
+ throw new IllegalArgumentException(
+ "Can't invoke method " + methodSignature + " on "
+ + instanceOrClass + " with arguments " + arguments,
+ e);
+ }
+ }
- /**
- * Calls a method with the given arguments. Arguments can be object types or representations for primitives.
- *
- * @param methodSignature the name of the method and the parameters <br>
- * (e.g. "myMethod(java.lang.String, com.company.project.MyObject)")
- * @param arguments an array of objects to pass as arguments
- * @return the return value of this method or null if void
- * @throws IllegalArgumentException if the method could not be invoked. This could be the case if the method is inaccessible; if the
- * underlying method throws an exception; if no method with the given <code>methodSignature</code> could be found; or if
- * an argument couldn't be converted to match the expected type
- * @see PA#invokeMethod(Object, String, Object...)
- */
- public Object invokeMethod(final String methodSignature, final Object... arguments) {
- return PA.invokeMethod(instanceOrClass, methodSignature, arguments);
- }
+ /**
+ * Calls a method with the given arguments. Arguments can be object types or
+ * representations for primitives.
+ *
+ * @param methodSignature
+ * the name of the method and the parameters <br>
+ * (e.g. "myMethod(java.lang.String, com.company.project.MyObject)")
+ * @param arguments
+ * an array of objects to pass as arguments
+ * @return the return value of this method or null if void
+ * @throws IllegalArgumentException
+ * if the method could not be invoked. This could be the case if the
+ * method is inaccessible; if the underlying method throws an
+ * exception; if no method with the given
+ * <code>methodSignature</code> could be found; or if an argument
+ * couldn't be converted to match the expected type
+ * @see PA#invokeMethod(Object, String, Object...)
+ */
+ public Object invokeMethod(final String methodSignature,
+ final Object... arguments)
+ {
+ return PA.invokeMethod(instanceOrClass, methodSignature, arguments);
+ }
- /**
- * Corrects varargs to their initial form. If you call a method with an object-array as last argument the Java varargs mechanism
- * converts this array in single arguments. This method returns an object array if the arguments are all of the same type.
- *
- * @param arguments the possibly converted arguments of a vararg method
- * @return arguments possibly converted
- */
- private static Object[] correctVarargs(final Object... arguments) {
- if ((arguments == null) || changedByVararg(arguments)) return new Object[] {arguments};
- return arguments;
- }
+ /**
+ * Corrects varargs to their initial form. If you call a method with an
+ * object-array as last argument the Java varargs mechanism converts this
+ * array in single arguments. This method returns an object array if the
+ * arguments are all of the same type.
+ *
+ * @param arguments
+ * the possibly converted arguments of a vararg method
+ * @return arguments possibly converted
+ */
+ private static Object[] correctVarargs(final Object... arguments)
+ {
+ if ((arguments == null) || changedByVararg(arguments))
+ return new Object[] { arguments };
+ return arguments;
+ }
- /**
- * Tests if the arguments were changed by vararg. Arguments are changed by vararg if they are of a non primitive array type. E.g.
- * arguments[] = Object[String[]] is converted to String[] while e.g. arguments[] = Object[int[]] is not converted and stays
- * Object[int[]]
- *
- * Unfortunately we can't detect the difference for arg = Object[primitive] since arguments[] = Object[Object[primitive]] which is
- * converted to Object[primitive] and arguments[] = Object[primitive] which stays Object[primitive]
- *
- * and we can't detect the difference for arg = Object[non primitive] since arguments[] = Object[Object[non primitive]] is converted
- * to Object[non primitive] and arguments[] = Object[non primitive] stays Object[non primitive]
- *
- * @param parameters the parameters
- * @return true if parameters were changes by varargs, false otherwise
- */
- private static boolean changedByVararg(final Object[] parameters) {
- if ((parameters.length == 0) || (parameters[0] == null)) return false;
+ /**
+ * Tests if the arguments were changed by vararg. Arguments are changed by
+ * vararg if they are of a non primitive array type. E.g. arguments[] =
+ * Object[String[]] is converted to String[] while e.g. arguments[] =
+ * Object[int[]] is not converted and stays Object[int[]]
+ *
+ * Unfortunately we can't detect the difference for arg = Object[primitive]
+ * since arguments[] = Object[Object[primitive]] which is converted to
+ * Object[primitive] and arguments[] = Object[primitive] which stays
+ * Object[primitive]
+ *
+ * and we can't detect the difference for arg = Object[non primitive] since
+ * arguments[] = Object[Object[non primitive]] is converted to Object[non
+ * primitive] and arguments[] = Object[non primitive] stays Object[non
+ * primitive]
+ *
+ * @param parameters
+ * the parameters
+ * @return true if parameters were changes by varargs, false otherwise
+ */
+ private static boolean changedByVararg(final Object[] parameters)
+ {
+ if ((parameters.length == 0) || (parameters[0] == null))
+ return false;
- if (parameters.getClass() == Object[].class) return false;
+ if (parameters.getClass() == Object[].class)
+ return false;
- return true;
- }
+ return true;
+ }
- /**
- * Sets the value of the named field. If fieldName denotes a static field, provide a class, otherwise provide an instance. If the
- * fieldName denotes a final field, this method could fail with an IllegalAccessException, since setting the value of final fields
- * at other times than instantiation can have unpredictable effects.<br/>
- * <br/>
- * Example:<br/>
- * <br/>
- * <code>
- * String myString = "Test"; <br/>
- * <br/>
- * //setting the private field value<br/>
- * PrivilegedAccessor.setValue(myString, "value", new char[] {'T', 'e', 's', 't'});<br/>
- * <br/>
- * //setting the static final field serialVersionUID - MIGHT FAIL<br/>
- * PrivilegedAccessor.setValue(myString.getClass(), "serialVersionUID", 1);<br/>
- * <br/>
- * </code>
- *
- * @param instanceOrClass the instance or class to set the field
- * @param fieldName the name of the field
- * @param value the new value of the field
- * @throws IllegalArgumentException if the value could not be set. This could be the case if no field with the given
- * <code>fieldName</code> can be found; or if the field was final
- *
- * @see PrivilegedAccessor.setValue(Object,String,Object)
- */
- public static PA setValue(final Object instanceOrClass, final String fieldName, final Object value) {
- try {
- PrivilegedAccessor.setValue(instanceOrClass, fieldName, value);
- } catch (Exception e) {
- throw new IllegalArgumentException("Can't set value " + value + " at " + fieldName + " in " + instanceOrClass, e);
- }
- return new PA(instanceOrClass);
- }
+ /**
+ * Sets the value of the named field. If fieldName denotes a static field,
+ * provide a class, otherwise provide an instance. If the fieldName denotes a
+ * final field, this method could fail with an IllegalAccessException, since
+ * setting the value of final fields at other times than instantiation can
+ * have unpredictable effects.<br/>
+ * <br/>
+ * Example:<br/>
+ * <br/>
+ * <code>
+ * String myString = "Test"; <br/>
+ * <br/>
+ * //setting the private field value<br/>
+ * PrivilegedAccessor.setValue(myString, "value", new char[] {'T', 'e', 's', 't'});<br/>
+ * <br/>
+ * //setting the static final field serialVersionUID - MIGHT FAIL<br/>
+ * PrivilegedAccessor.setValue(myString.getClass(), "serialVersionUID", 1);<br/>
+ * <br/>
+ * </code>
+ *
+ * @param instanceOrClass
+ * the instance or class to set the field
+ * @param fieldName
+ * the name of the field
+ * @param value
+ * the new value of the field
+ * @throws IllegalArgumentException
+ * if the value could not be set. This could be the case if no field
+ * with the given <code>fieldName</code> can be found; or if the
+ * field was final
+ *
+ * @see PrivilegedAccessor.setValue(Object,String,Object)
+ */
+ public static PA setValue(final Object instanceOrClass,
+ final String fieldName, final Object value)
+ {
+ try
+ {
+ PrivilegedAccessor.setValue(instanceOrClass, fieldName, value);
+ } catch (Exception e)
+ {
+ throw new IllegalArgumentException("Can't set value " + value + " at "
+ + fieldName + " in " + instanceOrClass, e);
+ }
+ return new PA(instanceOrClass);
+ }
- /**
- * Sets the value of the named field. If fieldName denotes a static field, provide a class, otherwise provide an instance. If the
- * fieldName denotes a final field, this method could fail with an IllegalAccessException, since setting the value of final fields
- * at other times than instantiation can have unpredictable effects.<br/>
- * <br/>
- * Example:<br/>
- * <br/>
- * <code>
- * String myString = "Test"; <br/>
- * <br/>
- * //setting the private field value<br/>
- * PrivilegedAccessor.setValue(myString, "value", new char[] {'T', 'e', 's', 't'});<br/>
- * <br/>
- * //setting the static final field serialVersionUID - MIGHT FAIL<br/>
- * PrivilegedAccessor.setValue(myString.getClass(), "serialVersionUID", 1);<br/>
- * <br/>
- * </code>
- *
- * @param fieldName the name of the field
- * @param value the new value of the field
- * @throws IllegalArgumentException if the value could not be set. This could be the case if no field with the given
- * <code>fieldName</code> can be found; or if the field was final
- *
- * @see PA.setValue(Object,String,Object)
- */
- public PA setValue(final String fieldName, final Object value) {
- PA.setValue(instanceOrClass, fieldName, value);
- return this;
- }
+ /**
+ * Sets the value of the named field. If fieldName denotes a static field,
+ * provide a class, otherwise provide an instance. If the fieldName denotes a
+ * final field, this method could fail with an IllegalAccessException, since
+ * setting the value of final fields at other times than instantiation can
+ * have unpredictable effects.<br/>
+ * <br/>
+ * Example:<br/>
+ * <br/>
+ * <code>
+ * String myString = "Test"; <br/>
+ * <br/>
+ * //setting the private field value<br/>
+ * PrivilegedAccessor.setValue(myString, "value", new char[] {'T', 'e', 's', 't'});<br/>
+ * <br/>
+ * //setting the static final field serialVersionUID - MIGHT FAIL<br/>
+ * PrivilegedAccessor.setValue(myString.getClass(), "serialVersionUID", 1);<br/>
+ * <br/>
+ * </code>
+ *
+ * @param fieldName
+ * the name of the field
+ * @param value
+ * the new value of the field
+ * @throws IllegalArgumentException
+ * if the value could not be set. This could be the case if no field
+ * with the given <code>fieldName</code> can be found; or if the
+ * field was final
+ *
+ * @see PA.setValue(Object,String,Object)
+ */
+ public PA setValue(final String fieldName, final Object value)
+ {
+ PA.setValue(instanceOrClass, fieldName, value);
+ return this;
+ }
}
import java.util.StringTokenizer;
/**
- * This class is used to access a method or field of an object no matter what the access modifier of the method or field. The syntax
- * for accessing fields and methods is out of the ordinary because this class uses reflection to peel away protection.
+ * This class is used to access a method or field of an object no matter what
+ * the access modifier of the method or field. The syntax for accessing fields
+ * and methods is out of the ordinary because this class uses reflection to peel
+ * away protection.
* <p>
* a.k.a. The "ObjectMolester"
* <p>
* Here is an example of using this to access a private member: <br>
- * <code>myObject</code> is an object of type <code>MyClass</code>. <code>setName(String)</code> is a private method of
- * <code>MyClass</code>.
+ * <code>myObject</code> is an object of type <code>MyClass</code>.
+ * <code>setName(String)</code> is a private method of <code>MyClass</code>.
*
* <pre>
- * PrivilegedAccessor.invokeMethod(myObject, "setName(java.lang.String)", "newName");
+ * PrivilegedAccessor.invokeMethod(myObject, "setName(java.lang.String)",
+ * "newName");
* </pre>
*
* @author Charlie Hubbard (chubbard@iss.net)
* @author Prashant Dhokte (pdhokte@iss.net)
* @author Sebastian Dietrich (sebastian.dietrich@e-movimento.com)
*
- * @deprecated use PA instead. PA improves the functionality of PrivilegedAccessor by introducing support for varargs and removal of
- * the necessity to catch exceptions.
+ * @deprecated use PA instead. PA improves the functionality of
+ * PrivilegedAccessor by introducing support for varargs and removal
+ * of the necessity to catch exceptions.
*/
@Deprecated
final class PrivilegedAccessor
{
- /**
- * Private constructor to make it impossible to instantiate this class.
- */
- private PrivilegedAccessor() {
- assert false : "You mustn't instantiate PrivilegedAccessor, use its methods statically";
- }
-
- /**
- * Returns a string representation of the given object. The string has the following format: "<classname> {<attributes and values>}"
- * whereas <attributes and values> is a comma separated list with <attributeName>=<attributeValue> <atributes and values> includes
- * all attributes of the objects class followed by the attributes of its superclass (if any) and so on.
- *
- * @param instanceOrClass the object or class to get a string representation of
- * @return a string representation of the given object
- */
- public static String toString(final Object instanceOrClass) {
- Collection<String> fields = getFieldNames(instanceOrClass);
-
- if (fields.isEmpty())
+ /**
+ * Private constructor to make it impossible to instantiate this class.
+ */
+ private PrivilegedAccessor()
+ {
+ assert false : "You mustn't instantiate PrivilegedAccessor, use its methods statically";
+ }
+
+ /**
+ * Returns a string representation of the given object. The string has the
+ * following format: "<classname> {<attributes and values>}" whereas
+ * <attributes and values> is a comma separated list with
+ * <attributeName>=<attributeValue> <atributes and values> includes all
+ * attributes of the objects class followed by the attributes of its
+ * superclass (if any) and so on.
+ *
+ * @param instanceOrClass
+ * the object or class to get a string representation of
+ * @return a string representation of the given object
+ */
+ public static String toString(final Object instanceOrClass)
+ {
+ Collection<String> fields = getFieldNames(instanceOrClass);
+
+ if (fields.isEmpty())
+ {
+ return getClass(instanceOrClass).getName();
+ }
+
+ StringBuffer stringBuffer = new StringBuffer();
+
+ stringBuffer.append(getClass(instanceOrClass).getName() + " {");
+
+ for (String fieldName : fields)
+ {
+ try
{
- return getClass(instanceOrClass).getName();
- }
-
- StringBuffer stringBuffer = new StringBuffer();
-
- stringBuffer.append(getClass(instanceOrClass).getName() + " {");
-
- for (String fieldName : fields) {
- try {
- stringBuffer.append(fieldName + "=" + getValue(instanceOrClass, fieldName) + ", ");
- } catch (NoSuchFieldException e) {
- assert false : "It should always be possible to get a field that was just here";
- }
- }
-
- stringBuffer.replace(stringBuffer.lastIndexOf(", "), stringBuffer.length(), "}");
- return stringBuffer.toString();
- }
-
- /**
- * Gets the name of all fields (public, private, protected, default) of the given instance or class. This includes as well all
- * fields (public, private, protected, default) of all its super classes.
- *
- * @param instanceOrClass the instance or class to get the fields of
- * @return the collection of field names of the given instance or class
- */
- public static Collection<String> getFieldNames(final Object instanceOrClass) {
- if (instanceOrClass == null)
- {
- return Collections.EMPTY_LIST;
- }
-
- Class<?> clazz = getClass(instanceOrClass);
- Field[] fields = clazz.getDeclaredFields();
- Collection<String> fieldNames = new ArrayList<String>(fields.length);
-
- for (Field field : fields) {
- fieldNames.add(field.getName());
- }
- fieldNames.addAll(getFieldNames(clazz.getSuperclass()));
-
- return fieldNames;
- }
-
- /**
- * Gets the signatures of all methods (public, private, protected, default) of the given instance or class. This includes as well
- * all methods (public, private, protected, default) of all its super classes. This does not include constructors.
- *
- * @param instanceOrClass the instance or class to get the method signatures of
- * @return the collection of method signatures of the given instance or class
- */
- public static Collection<String> getMethodSignatures(final Object instanceOrClass) {
- if (instanceOrClass == null)
- {
- return Collections.EMPTY_LIST;
- }
-
- Class<?> clazz = getClass(instanceOrClass);
- Method[] methods = clazz.getDeclaredMethods();
- Collection<String> methodSignatures = new ArrayList<String>(methods.length + Object.class.getDeclaredMethods().length);
-
- for (Method method : methods) {
- methodSignatures.add(method.getName() + "(" + getParameterTypesAsString(method.getParameterTypes()) + ")");
- }
- methodSignatures.addAll(getMethodSignatures(clazz.getSuperclass()));
-
- return methodSignatures;
- }
-
- /**
- * Gets the value of the named field and returns it as an object. If instanceOrClass is a class then a static field is returned.
- *
- * @param instanceOrClass the instance or class to get the field from
- * @param fieldName the name of the field
- * @return an object representing the value of the field
- * @throws NoSuchFieldException if the field does not exist
- */
- public static Object getValue(final Object instanceOrClass, final String fieldName) throws NoSuchFieldException {
- Field field = getField(instanceOrClass, fieldName);
- try {
- return field.get(instanceOrClass);
- } catch (IllegalAccessException e) {
- assert false : "getField() should have setAccessible(true), so an IllegalAccessException should not occur in this place";
- return null;
- }
- }
-
- /**
- * Instantiates an object of the given class with the given arguments. If you want to instantiate a member class, you must provide
- * the object it is a member of as first argument.
- *
- * @param fromClass the class to instantiate an object from
- * @param args the arguments to pass to the constructor
- * @return an object of the given type
- * @throws IllegalArgumentException if the number of actual and formal parameters differ; if an unwrapping conversion for primitive
- * arguments fails; or if, after possible unwrapping, a parameter value cannot be converted to the corresponding formal
- * parameter type by a method invocation conversion.
- * @throws IllegalAccessException if this Constructor object enforces Java language access control and the underlying constructor is
- * inaccessible.
- * @throws InvocationTargetException if the underlying constructor throws an exception.
- * @throws NoSuchMethodException if the constructor could not be found
- * @throws InstantiationException if the class that declares the underlying constructor represents an abstract class.
- *
- * @see PrivilegedAccessor#instantiate(Class,Class[],Object[])
- */
- public static <T> T instantiate(final Class<? extends T> fromClass, final Object[] args) throws IllegalArgumentException,
- InstantiationException, IllegalAccessException, InvocationTargetException, NoSuchMethodException {
- return instantiate(fromClass, getParameterTypes(args), args);
- }
-
- /**
- * Instantiates an object of the given class with the given arguments and the given argument types. If you want to instantiate a
- * member class, you must provide the object it is a member of as first argument.
- *
- *
- * @param fromClass the class to instantiate an object from
- * @param args the arguments to pass to the constructor
- * @param argumentTypes the fully qualified types of the arguments of the constructor
- * @return an object of the given type
- * @throws IllegalArgumentException if the number of actual and formal parameters differ; if an unwrapping conversion for primitive
- * arguments fails; or if, after possible unwrapping, a parameter value cannot be converted to the corresponding formal
- * parameter type by a method invocation conversion.
- * @throws IllegalAccessException if this Constructor object enforces Java language access control and the underlying constructor is
- * inaccessible.
- * @throws InvocationTargetException if the underlying constructor throws an exception.
- * @throws NoSuchMethodException if the constructor could not be found
- * @throws InstantiationException if the class that declares the underlying constructor represents an abstract class.
- *
- * @see PrivilegedAccessor#instantiate(Class,Object[])
- */
- public static <T> T instantiate(final Class<? extends T> fromClass, final Class<?>[] argumentTypes, final Object[] args)
- throws IllegalArgumentException, InstantiationException, IllegalAccessException, InvocationTargetException,
- NoSuchMethodException {
- return getConstructor(fromClass, argumentTypes).newInstance(args);
- }
-
- /**
- * Calls a method on the given object instance with the given arguments. Arguments can be object types or representations for
- * primitives.
- *
- * @param instanceOrClass the instance or class to invoke the method on
- * @param methodSignature the name of the method and the parameters <br>
- * (e.g. "myMethod(java.lang.String, com.company.project.MyObject)")
- * @param arguments an array of objects to pass as arguments
- * @return the return value of this method or null if void
- * @throws IllegalAccessException if the method is inaccessible
- * @throws InvocationTargetException if the underlying method throws an exception.
- * @throws NoSuchMethodException if no method with the given <code>methodSignature</code> could be found
- * @throws IllegalArgumentException if an argument couldn't be converted to match the expected type
- */
- public static Object invokeMethod(final Object instanceOrClass, final String methodSignature, final Object[] arguments)
- throws IllegalArgumentException, IllegalAccessException, InvocationTargetException, NoSuchMethodException {
- if ((methodSignature.indexOf('(') == -1) || (methodSignature.indexOf('(') >= methodSignature.indexOf(')')))
- {
- throw new NoSuchMethodException(methodSignature);
- }
- Class<?>[] parameterTypes = getParameterTypes(methodSignature);
- return getMethod(instanceOrClass, getMethodName(methodSignature), parameterTypes).invoke(instanceOrClass,
- getCorrectedArguments(parameterTypes, arguments));
- }
-
- /**
- * Gets the given arguments corrected to match the given methodSignature. Correction is necessary for array arguments not to be
- * mistaken by varargs.
- *
- * @param parameterTypes the method signatue the given arguments should match
- * @param arguments the arguments that should be corrected
- * @return the corrected arguments
- */
- private static Object[] getCorrectedArguments(Class<?>[] parameterTypes, Object[] arguments) {
- if (arguments == null)
- {
- return arguments;
- }
- if (parameterTypes.length > arguments.length)
- {
- return arguments;
- }
- if (parameterTypes.length < arguments.length)
- {
- return getCorrectedArguments(parameterTypes, new Object[] {arguments});
- }
-
- Object[] correctedArguments = new Object[arguments.length];
- int currentArgument = 0;
- for (Class<?> parameterType : parameterTypes) {
- correctedArguments[currentArgument] = getCorrectedArgument(parameterType, arguments[currentArgument]);
- currentArgument++;
- }
- return correctedArguments;
- }
-
- /**
- * Gets the given argument corrected to match the given parameterType. Correction is necessary for array arguments not to be
- * mistaken by varargs.
- *
- * @param parameterType the type to match the given argument upon
- * @param argument the argument to match the given parameterType
- * @return the corrected argument
- */
- private static Object getCorrectedArgument(Class<?> parameterType, Object argument) {
- if (!parameterType.isArray() || (argument == null)) {
- return argument; // normal argument for normal parameterType
- }
-
- if (!argument.getClass().isArray()) {
- return new Object[] {argument};
- }
-
- if (parameterType.equals(argument.getClass()))
- {
- return argument; // no need to cast
- }
-
- // (typed) array argument for (object) array parameterType, elements need to be casted
- Object correctedArrayArgument = Array.newInstance(parameterType.getComponentType(), Array.getLength(argument));
- for (int index = 0; index < Array.getLength(argument); index++) {
- if (parameterType.getComponentType().isPrimitive()) { // rely on autoboxing
- Array.set(correctedArrayArgument, index, Array.get(argument, index));
- } else { // cast to expected type
- try {
- Array.set(correctedArrayArgument, index, parameterType.getComponentType().cast(Array.get(argument, index)));
- } catch (ClassCastException e) {
- throw new IllegalArgumentException("Argument " + argument + " of type " + argument.getClass()
- + " does not match expected argument type " + parameterType + ".");
- }
- }
- }
- return correctedArrayArgument;
- }
-
- /**
- * Sets the value of the named field. If fieldName denotes a static field, provide a class, otherwise provide an instance. If the
- * fieldName denotes a final field, this method could fail with an IllegalAccessException, since setting the value of final fields
- * at other times than instantiation can have unpredictable effects.<br/>
- * <br/>
- * Example:<br/>
- * <br/>
- * <code>
- * String myString = "Test"; <br/>
- * <br/>
- * //setting the private field value<br/>
- * PrivilegedAccessor.setValue(myString, "value", new char[] {'T', 'e', 's', 't'});<br/>
- * <br/>
- * //setting the static final field serialVersionUID - MIGHT FAIL<br/>
- * PrivilegedAccessor.setValue(myString.getClass(), "serialVersionUID", 1);<br/>
- * <br/>
- * </code>
- *
- * @param instanceOrClass the instance or class to set the field
- * @param fieldName the name of the field
- * @param value the new value of the field
- * @throws NoSuchFieldException if no field with the given <code>fieldName</code> can be found
- * @throws IllegalAccessException possibly if the field was final
- */
- public static void setValue(final Object instanceOrClass, final String fieldName, final Object value) throws NoSuchFieldException,
- IllegalAccessException {
- Field field = getField(instanceOrClass, fieldName);
- if (Modifier.isFinal(field.getModifiers())) {
- PrivilegedAccessor.setValue(field, "modifiers", field.getModifiers() ^ Modifier.FINAL);
- }
- field.set(instanceOrClass, value);
- }
-
- /**
- * Gets the class with the given className.
- *
- * @param className the name of the class to get
- * @return the class for the given className
- * @throws ClassNotFoundException if the class could not be found
- */
- private static Class<?> getClassForName(final String className) throws ClassNotFoundException {
- if (className.indexOf('[') > -1) {
- Class<?> clazz = getClassForName(className.substring(0, className.indexOf('[')));
- return Array.newInstance(clazz, 0).getClass();
- }
-
- if (className.indexOf("...") > -1) {
- Class<?> clazz = getClassForName(className.substring(0, className.indexOf("...")));
- return Array.newInstance(clazz, 0).getClass();
- }
-
- try {
- return Class.forName(className, false, Thread.currentThread().getContextClassLoader());
- } catch (ClassNotFoundException e) {
- return getSpecialClassForName(className);
- }
- }
-
- /**
- * Maps string representation of primitives to their corresponding classes.
- */
- private static final Map<String, Class<?>> PRIMITIVE_MAPPER = new HashMap<String, Class<?>>(8);
-
- /**
- * Fills the map with all java primitives and their corresponding classes.
- */
- static {
- PRIMITIVE_MAPPER.put("int", Integer.TYPE);
- PRIMITIVE_MAPPER.put("float", Float.TYPE);
- PRIMITIVE_MAPPER.put("double", Double.TYPE);
- PRIMITIVE_MAPPER.put("short", Short.TYPE);
- PRIMITIVE_MAPPER.put("long", Long.TYPE);
- PRIMITIVE_MAPPER.put("byte", Byte.TYPE);
- PRIMITIVE_MAPPER.put("char", Character.TYPE);
- PRIMITIVE_MAPPER.put("boolean", Boolean.TYPE);
- }
-
- /**
- * Gets special classes for the given className. Special classes are primitives and "standard" Java types (like String)
- *
- * @param className the name of the class to get
- * @return the class for the given className
- * @throws ClassNotFoundException if the class could not be found
- */
- private static Class<?> getSpecialClassForName(final String className) throws ClassNotFoundException {
- if (PRIMITIVE_MAPPER.containsKey(className))
+ stringBuffer.append(fieldName + "="
+ + getValue(instanceOrClass, fieldName) + ", ");
+ } catch (NoSuchFieldException e)
{
- return PRIMITIVE_MAPPER.get(className);
- }
-
- if (missesPackageName(className))
- {
- return getStandardClassForName(className);
- }
-
- throw new ClassNotFoundException(className);
- }
-
- /**
- * Gets a 'standard' java class for the given className.
- *
- * @param className the className
- * @return the class for the given className (if any)
- * @throws ClassNotFoundException of no 'standard' java class was found for the given className
- */
- private static Class<?> getStandardClassForName(String className) throws ClassNotFoundException {
- try {
- return Class.forName("java.lang." + className, false, Thread.currentThread().getContextClassLoader());
- } catch (ClassNotFoundException e) {
- try {
- return Class.forName("java.util." + className, false, Thread.currentThread().getContextClassLoader());
- } catch (ClassNotFoundException e1) {
- throw new ClassNotFoundException(className);
- }
+ assert false : "It should always be possible to get a field that was just here";
+ }
+ }
+
+ stringBuffer.replace(stringBuffer.lastIndexOf(", "),
+ stringBuffer.length(), "}");
+ return stringBuffer.toString();
+ }
+
+ /**
+ * Gets the name of all fields (public, private, protected, default) of the
+ * given instance or class. This includes as well all fields (public, private,
+ * protected, default) of all its super classes.
+ *
+ * @param instanceOrClass
+ * the instance or class to get the fields of
+ * @return the collection of field names of the given instance or class
+ */
+ public static Collection<String> getFieldNames(
+ final Object instanceOrClass)
+ {
+ if (instanceOrClass == null)
+ {
+ return Collections.EMPTY_LIST;
+ }
+
+ Class<?> clazz = getClass(instanceOrClass);
+ Field[] fields = clazz.getDeclaredFields();
+ Collection<String> fieldNames = new ArrayList<String>(fields.length);
+
+ for (Field field : fields)
+ {
+ fieldNames.add(field.getName());
+ }
+ fieldNames.addAll(getFieldNames(clazz.getSuperclass()));
+
+ return fieldNames;
+ }
+
+ /**
+ * Gets the signatures of all methods (public, private, protected, default) of
+ * the given instance or class. This includes as well all methods (public,
+ * private, protected, default) of all its super classes. This does not
+ * include constructors.
+ *
+ * @param instanceOrClass
+ * the instance or class to get the method signatures of
+ * @return the collection of method signatures of the given instance or class
+ */
+ public static Collection<String> getMethodSignatures(
+ final Object instanceOrClass)
+ {
+ if (instanceOrClass == null)
+ {
+ return Collections.EMPTY_LIST;
+ }
+
+ Class<?> clazz = getClass(instanceOrClass);
+ Method[] methods = clazz.getDeclaredMethods();
+ Collection<String> methodSignatures = new ArrayList<String>(
+ methods.length + Object.class.getDeclaredMethods().length);
+
+ for (Method method : methods)
+ {
+ methodSignatures.add(method.getName() + "("
+ + getParameterTypesAsString(method.getParameterTypes())
+ + ")");
+ }
+ methodSignatures.addAll(getMethodSignatures(clazz.getSuperclass()));
+
+ return methodSignatures;
+ }
+
+ /**
+ * Gets the value of the named field and returns it as an object. If
+ * instanceOrClass is a class then a static field is returned.
+ *
+ * @param instanceOrClass
+ * the instance or class to get the field from
+ * @param fieldName
+ * the name of the field
+ * @return an object representing the value of the field
+ * @throws NoSuchFieldException
+ * if the field does not exist
+ */
+ public static Object getValue(final Object instanceOrClass,
+ final String fieldName) throws NoSuchFieldException
+ {
+ Field field = getField(instanceOrClass, fieldName);
+ try
+ {
+ return field.get(instanceOrClass);
+ } catch (IllegalAccessException e)
+ {
+ assert false : "getField() should have setAccessible(true), so an IllegalAccessException should not occur in this place";
+ return null;
+ }
+ }
+
+ /**
+ * Instantiates an object of the given class with the given arguments. If you
+ * want to instantiate a member class, you must provide the object it is a
+ * member of as first argument.
+ *
+ * @param fromClass
+ * the class to instantiate an object from
+ * @param args
+ * the arguments to pass to the constructor
+ * @return an object of the given type
+ * @throws IllegalArgumentException
+ * if the number of actual and formal parameters differ; if an
+ * unwrapping conversion for primitive arguments fails; or if, after
+ * possible unwrapping, a parameter value cannot be converted to the
+ * corresponding formal parameter type by a method invocation
+ * conversion.
+ * @throws IllegalAccessException
+ * if this Constructor object enforces Java language access control
+ * and the underlying constructor is inaccessible.
+ * @throws InvocationTargetException
+ * if the underlying constructor throws an exception.
+ * @throws NoSuchMethodException
+ * if the constructor could not be found
+ * @throws InstantiationException
+ * if the class that declares the underlying constructor represents
+ * an abstract class.
+ *
+ * @see PrivilegedAccessor#instantiate(Class,Class[],Object[])
+ */
+ public static <T> T instantiate(final Class<? extends T> fromClass,
+ final Object[] args) throws IllegalArgumentException,
+ InstantiationException, IllegalAccessException,
+ InvocationTargetException, NoSuchMethodException
+ {
+ return instantiate(fromClass, getParameterTypes(args), args);
+ }
+
+ /**
+ * Instantiates an object of the given class with the given arguments and the
+ * given argument types. If you want to instantiate a member class, you must
+ * provide the object it is a member of as first argument.
+ *
+ *
+ * @param fromClass
+ * the class to instantiate an object from
+ * @param args
+ * the arguments to pass to the constructor
+ * @param argumentTypes
+ * the fully qualified types of the arguments of the constructor
+ * @return an object of the given type
+ * @throws IllegalArgumentException
+ * if the number of actual and formal parameters differ; if an
+ * unwrapping conversion for primitive arguments fails; or if, after
+ * possible unwrapping, a parameter value cannot be converted to the
+ * corresponding formal parameter type by a method invocation
+ * conversion.
+ * @throws IllegalAccessException
+ * if this Constructor object enforces Java language access control
+ * and the underlying constructor is inaccessible.
+ * @throws InvocationTargetException
+ * if the underlying constructor throws an exception.
+ * @throws NoSuchMethodException
+ * if the constructor could not be found
+ * @throws InstantiationException
+ * if the class that declares the underlying constructor represents
+ * an abstract class.
+ *
+ * @see PrivilegedAccessor#instantiate(Class,Object[])
+ */
+ public static <T> T instantiate(final Class<? extends T> fromClass,
+ final Class<?>[] argumentTypes, final Object[] args)
+ throws IllegalArgumentException, InstantiationException,
+ IllegalAccessException, InvocationTargetException,
+ NoSuchMethodException
+ {
+ return getConstructor(fromClass, argumentTypes).newInstance(args);
+ }
+
+ /**
+ * Calls a method on the given object instance with the given arguments.
+ * Arguments can be object types or representations for primitives.
+ *
+ * @param instanceOrClass
+ * the instance or class to invoke the method on
+ * @param methodSignature
+ * the name of the method and the parameters <br>
+ * (e.g. "myMethod(java.lang.String, com.company.project.MyObject)")
+ * @param arguments
+ * an array of objects to pass as arguments
+ * @return the return value of this method or null if void
+ * @throws IllegalAccessException
+ * if the method is inaccessible
+ * @throws InvocationTargetException
+ * if the underlying method throws an exception.
+ * @throws NoSuchMethodException
+ * if no method with the given <code>methodSignature</code> could be
+ * found
+ * @throws IllegalArgumentException
+ * if an argument couldn't be converted to match the expected type
+ */
+ public static Object invokeMethod(final Object instanceOrClass,
+ final String methodSignature, final Object[] arguments)
+ throws IllegalArgumentException, IllegalAccessException,
+ InvocationTargetException, NoSuchMethodException
+ {
+ if ((methodSignature.indexOf('(') == -1) || (methodSignature
+ .indexOf('(') >= methodSignature.indexOf(')')))
+ {
+ throw new NoSuchMethodException(methodSignature);
+ }
+ Class<?>[] parameterTypes = getParameterTypes(methodSignature);
+ return getMethod(instanceOrClass, getMethodName(methodSignature),
+ parameterTypes).invoke(instanceOrClass,
+ getCorrectedArguments(parameterTypes, arguments));
+ }
+
+ /**
+ * Gets the given arguments corrected to match the given methodSignature.
+ * Correction is necessary for array arguments not to be mistaken by varargs.
+ *
+ * @param parameterTypes
+ * the method signatue the given arguments should match
+ * @param arguments
+ * the arguments that should be corrected
+ * @return the corrected arguments
+ */
+ private static Object[] getCorrectedArguments(Class<?>[] parameterTypes,
+ Object[] arguments)
+ {
+ if (arguments == null)
+ {
+ return arguments;
+ }
+ if (parameterTypes.length > arguments.length)
+ {
+ return arguments;
+ }
+ if (parameterTypes.length < arguments.length)
+ {
+ return getCorrectedArguments(parameterTypes,
+ new Object[]
+ { arguments });
+ }
+
+ Object[] correctedArguments = new Object[arguments.length];
+ int currentArgument = 0;
+ for (Class<?> parameterType : parameterTypes)
+ {
+ correctedArguments[currentArgument] = getCorrectedArgument(
+ parameterType, arguments[currentArgument]);
+ currentArgument++;
+ }
+ return correctedArguments;
+ }
+
+ /**
+ * Gets the given argument corrected to match the given parameterType.
+ * Correction is necessary for array arguments not to be mistaken by varargs.
+ *
+ * @param parameterType
+ * the type to match the given argument upon
+ * @param argument
+ * the argument to match the given parameterType
+ * @return the corrected argument
+ */
+ private static Object getCorrectedArgument(Class<?> parameterType,
+ Object argument)
+ {
+ if (!parameterType.isArray() || (argument == null))
+ {
+ return argument; // normal argument for normal parameterType
+ }
+
+ if (!argument.getClass().isArray())
+ {
+ return new Object[] { argument };
+ }
+
+ if (parameterType.equals(argument.getClass()))
+ {
+ return argument; // no need to cast
+ }
+
+ // (typed) array argument for (object) array parameterType, elements need to
+ // be casted
+ Object correctedArrayArgument = Array.newInstance(
+ parameterType.getComponentType(), Array.getLength(argument));
+ for (int index = 0; index < Array.getLength(argument); index++)
+ {
+ if (parameterType.getComponentType().isPrimitive())
+ { // rely on autoboxing
+ Array.set(correctedArrayArgument, index,
+ Array.get(argument, index));
+ }
+ else
+ { // cast to expected type
+ try
+ {
+ Array.set(correctedArrayArgument, index, parameterType
+ .getComponentType().cast(Array.get(argument, index)));
+ } catch (ClassCastException e)
+ {
+ throw new IllegalArgumentException(
+ "Argument " + argument + " of type " + argument.getClass()
+ + " does not match expected argument type "
+ + parameterType + ".");
+ }
}
- }
-
- /**
- * Tests if the given className possibly misses its package name.
- *
- * @param className the className
- * @return true if the className might miss its package name, otherwise false
- */
- private static boolean missesPackageName(String className) {
- if (className.contains("."))
+ }
+ return correctedArrayArgument;
+ }
+
+ /**
+ * Sets the value of the named field. If fieldName denotes a static field,
+ * provide a class, otherwise provide an instance. If the fieldName denotes a
+ * final field, this method could fail with an IllegalAccessException, since
+ * setting the value of final fields at other times than instantiation can
+ * have unpredictable effects.<br/>
+ * <br/>
+ * Example:<br/>
+ * <br/>
+ * <code>
+ * String myString = "Test"; <br/>
+ * <br/>
+ * //setting the private field value<br/>
+ * PrivilegedAccessor.setValue(myString, "value", new char[] {'T', 'e', 's', 't'});<br/>
+ * <br/>
+ * //setting the static final field serialVersionUID - MIGHT FAIL<br/>
+ * PrivilegedAccessor.setValue(myString.getClass(), "serialVersionUID", 1);<br/>
+ * <br/>
+ * </code>
+ *
+ * @param instanceOrClass
+ * the instance or class to set the field
+ * @param fieldName
+ * the name of the field
+ * @param value
+ * the new value of the field
+ * @throws NoSuchFieldException
+ * if no field with the given <code>fieldName</code> can be found
+ * @throws IllegalAccessException
+ * possibly if the field was final
+ */
+ public static void setValue(final Object instanceOrClass,
+ final String fieldName, final Object value)
+ throws NoSuchFieldException, IllegalAccessException
+ {
+ Field field = getField(instanceOrClass, fieldName);
+ if (Modifier.isFinal(field.getModifiers()))
+ {
+ PrivilegedAccessor.setValue(field, "modifiers",
+ field.getModifiers() ^ Modifier.FINAL);
+ }
+ field.set(instanceOrClass, value);
+ }
+
+ /**
+ * Gets the class with the given className.
+ *
+ * @param className
+ * the name of the class to get
+ * @return the class for the given className
+ * @throws ClassNotFoundException
+ * if the class could not be found
+ */
+ private static Class<?> getClassForName(final String className)
+ throws ClassNotFoundException
+ {
+ if (className.indexOf('[') > -1)
+ {
+ Class<?> clazz = getClassForName(
+ className.substring(0, className.indexOf('[')));
+ return Array.newInstance(clazz, 0).getClass();
+ }
+
+ if (className.indexOf("...") > -1)
+ {
+ Class<?> clazz = getClassForName(
+ className.substring(0, className.indexOf("...")));
+ return Array.newInstance(clazz, 0).getClass();
+ }
+
+ try
+ {
+ return Class.forName(className, false,
+ Thread.currentThread().getContextClassLoader());
+ } catch (ClassNotFoundException e)
+ {
+ return getSpecialClassForName(className);
+ }
+ }
+
+ /**
+ * Maps string representation of primitives to their corresponding classes.
+ */
+ private static final Map<String, Class<?>> PRIMITIVE_MAPPER = new HashMap<String, Class<?>>(
+ 8);
+
+ /**
+ * Fills the map with all java primitives and their corresponding classes.
+ */
+ static
+ {
+ PRIMITIVE_MAPPER.put("int", Integer.TYPE);
+ PRIMITIVE_MAPPER.put("float", Float.TYPE);
+ PRIMITIVE_MAPPER.put("double", Double.TYPE);
+ PRIMITIVE_MAPPER.put("short", Short.TYPE);
+ PRIMITIVE_MAPPER.put("long", Long.TYPE);
+ PRIMITIVE_MAPPER.put("byte", Byte.TYPE);
+ PRIMITIVE_MAPPER.put("char", Character.TYPE);
+ PRIMITIVE_MAPPER.put("boolean", Boolean.TYPE);
+ }
+
+ /**
+ * Gets special classes for the given className. Special classes are
+ * primitives and "standard" Java types (like String)
+ *
+ * @param className
+ * the name of the class to get
+ * @return the class for the given className
+ * @throws ClassNotFoundException
+ * if the class could not be found
+ */
+ private static Class<?> getSpecialClassForName(final String className)
+ throws ClassNotFoundException
+ {
+ if (PRIMITIVE_MAPPER.containsKey(className))
+ {
+ return PRIMITIVE_MAPPER.get(className);
+ }
+
+ if (missesPackageName(className))
+ {
+ return getStandardClassForName(className);
+ }
+
+ throw new ClassNotFoundException(className);
+ }
+
+ /**
+ * Gets a 'standard' java class for the given className.
+ *
+ * @param className
+ * the className
+ * @return the class for the given className (if any)
+ * @throws ClassNotFoundException
+ * of no 'standard' java class was found for the given className
+ */
+ private static Class<?> getStandardClassForName(String className)
+ throws ClassNotFoundException
+ {
+ try
+ {
+ return Class.forName("java.lang." + className, false,
+ Thread.currentThread().getContextClassLoader());
+ } catch (ClassNotFoundException e)
+ {
+ try
{
- return false;
- }
- if (className.startsWith(className.substring(0, 1).toUpperCase(Locale.ROOT)))
+ return Class.forName("java.util." + className, false,
+ Thread.currentThread().getContextClassLoader());
+ } catch (ClassNotFoundException e1)
{
- return true;
- }
+ throw new ClassNotFoundException(className);
+ }
+ }
+ }
+
+ /**
+ * Tests if the given className possibly misses its package name.
+ *
+ * @param className
+ * the className
+ * @return true if the className might miss its package name, otherwise false
+ */
+ private static boolean missesPackageName(String className)
+ {
+ if (className.contains("."))
+ {
return false;
- }
-
- /**
- * Gets the constructor for a given class with the given parameters.
- *
- * @param type the class to instantiate
- * @param parameterTypes the types of the parameters
- * @return the constructor
- * @throws NoSuchMethodException if the method could not be found
- */
- private static <T> Constructor<T> getConstructor(final Class<T> type, final Class<?>[] parameterTypes) throws NoSuchMethodException {
- Constructor<T> constructor = type.getDeclaredConstructor(parameterTypes);
- constructor.setAccessible(true);
- return constructor;
- }
-
- /**
- * Return the named field from the given instance or class. Returns a static field if instanceOrClass is a class.
- *
- * @param instanceOrClass the instance or class to get the field from
- * @param fieldName the name of the field to get
- * @return the field
- * @throws NoSuchFieldException if no such field can be found
- * @throws InvalidParameterException if instanceOrClass was null
- */
- private static Field getField(final Object instanceOrClass, final String fieldName) throws NoSuchFieldException,
- InvalidParameterException {
- if (instanceOrClass == null)
+ }
+ if (className
+ .startsWith(className.substring(0, 1).toUpperCase(Locale.ROOT)))
+ {
+ return true;
+ }
+ return false;
+ }
+
+ /**
+ * Gets the constructor for a given class with the given parameters.
+ *
+ * @param type
+ * the class to instantiate
+ * @param parameterTypes
+ * the types of the parameters
+ * @return the constructor
+ * @throws NoSuchMethodException
+ * if the method could not be found
+ */
+ private static <T> Constructor<T> getConstructor(final Class<T> type,
+ final Class<?>[] parameterTypes) throws NoSuchMethodException
+ {
+ Constructor<T> constructor = type
+ .getDeclaredConstructor(parameterTypes);
+ constructor.setAccessible(true);
+ return constructor;
+ }
+
+ /**
+ * Return the named field from the given instance or class. Returns a static
+ * field if instanceOrClass is a class.
+ *
+ * @param instanceOrClass
+ * the instance or class to get the field from
+ * @param fieldName
+ * the name of the field to get
+ * @return the field
+ * @throws NoSuchFieldException
+ * if no such field can be found
+ * @throws InvalidParameterException
+ * if instanceOrClass was null
+ */
+ private static Field getField(final Object instanceOrClass,
+ final String fieldName)
+ throws NoSuchFieldException, InvalidParameterException
+ {
+ if (instanceOrClass == null)
+ {
+ throw new InvalidParameterException(
+ "Can't get field on null object/class");
+ }
+
+ Class<?> type = getClass(instanceOrClass);
+
+ try
+ {
+ Field field = type.getDeclaredField(fieldName);
+ field.setAccessible(true);
+ return field;
+ } catch (NoSuchFieldException e)
+ {
+ if (type.getSuperclass() == null)
{
- throw new InvalidParameterException("Can't get field on null object/class");
- }
-
- Class<?> type = getClass(instanceOrClass);
-
- try {
- Field field = type.getDeclaredField(fieldName);
- field.setAccessible(true);
- return field;
- } catch (NoSuchFieldException e) {
- if (type.getSuperclass() == null)
- {
- throw e;
- }
- return getField(type.getSuperclass(), fieldName);
- }
- }
-
- /**
- * Gets the class of the given parameter. If the parameter is a class, it is returned, if it is an object, its class is returned
- *
- * @param instanceOrClass the instance or class to get the class of
- * @return the class of the given parameter
- */
- private static Class<?> getClass(final Object instanceOrClass) {
- if (instanceOrClass instanceof Class)
+ throw e;
+ }
+ return getField(type.getSuperclass(), fieldName);
+ }
+ }
+
+ /**
+ * Gets the class of the given parameter. If the parameter is a class, it is
+ * returned, if it is an object, its class is returned
+ *
+ * @param instanceOrClass
+ * the instance or class to get the class of
+ * @return the class of the given parameter
+ */
+ private static Class<?> getClass(final Object instanceOrClass)
+ {
+ if (instanceOrClass instanceof Class)
+ {
+ return (Class<?>) instanceOrClass;
+ }
+
+ return instanceOrClass.getClass();
+ }
+
+ /**
+ * Return the named method with a method signature matching classTypes from
+ * the given class.
+ *
+ * @param type
+ * the class to get the method from
+ * @param methodName
+ * the name of the method to get
+ * @param parameterTypes
+ * the parameter-types of the method to get
+ * @return the method
+ * @throws NoSuchMethodException
+ * if the method could not be found
+ */
+ private static Method getMethod(final Class<?> type,
+ final String methodName, final Class<?>[] parameterTypes)
+ throws NoSuchMethodException
+ {
+ try
+ {
+ return type.getDeclaredMethod(methodName, parameterTypes);
+ } catch (NoSuchMethodException e)
+ {
+ if (type.getSuperclass() == null)
{
- return (Class<?>) instanceOrClass;
- }
-
- return instanceOrClass.getClass();
- }
-
- /**
- * Return the named method with a method signature matching classTypes from the given class.
- *
- * @param type the class to get the method from
- * @param methodName the name of the method to get
- * @param parameterTypes the parameter-types of the method to get
- * @return the method
- * @throws NoSuchMethodException if the method could not be found
- */
- private static Method getMethod(final Class<?> type, final String methodName, final Class<?>[] parameterTypes)
- throws NoSuchMethodException {
- try {
- return type.getDeclaredMethod(methodName, parameterTypes);
- } catch (NoSuchMethodException e) {
- if (type.getSuperclass() == null)
- {
- throw e;
- }
- return getMethod(type.getSuperclass(), methodName, parameterTypes);
- }
- }
-
- /**
- * Gets the method with the given name and parameters from the given instance or class. If instanceOrClass is a class, then we get a
- * static method.
- *
- * @param instanceOrClass the instance or class to get the method of
- * @param methodName the name of the method
- * @param parameterTypes the parameter-types of the method to get
- * @return the method
- * @throws NoSuchMethodException if the method could not be found
- */
- private static Method getMethod(final Object instanceOrClass, final String methodName, final Class<?>[] parameterTypes)
- throws NoSuchMethodException {
- Class<?> type;
-
- type = getClass(instanceOrClass);
-
- Method accessMethod = getMethod(type, methodName, parameterTypes);
- accessMethod.setAccessible(true);
- return accessMethod;
- }
-
- /**
- * Gets the name of a method.
- *
- * @param methodSignature the signature of the method
- * @return the name of the method
- */
- private static String getMethodName(final String methodSignature) {
- try {
- return methodSignature.substring(0, methodSignature.indexOf('(')).trim();
- } catch (StringIndexOutOfBoundsException e) {
- assert false : "Signature must have been checked before this method was called";
- return null;
- }
- }
-
- /**
- * Gets the types of the parameters.
- *
- * @param parameters the parameters
- * @return the class-types of the arguments
- */
- private static Class<?>[] getParameterTypes(final Object[] parameters) {
- if (parameters == null)
+ throw e;
+ }
+ return getMethod(type.getSuperclass(), methodName, parameterTypes);
+ }
+ }
+
+ /**
+ * Gets the method with the given name and parameters from the given instance
+ * or class. If instanceOrClass is a class, then we get a static method.
+ *
+ * @param instanceOrClass
+ * the instance or class to get the method of
+ * @param methodName
+ * the name of the method
+ * @param parameterTypes
+ * the parameter-types of the method to get
+ * @return the method
+ * @throws NoSuchMethodException
+ * if the method could not be found
+ */
+ private static Method getMethod(final Object instanceOrClass,
+ final String methodName, final Class<?>[] parameterTypes)
+ throws NoSuchMethodException
+ {
+ Class<?> type;
+
+ type = getClass(instanceOrClass);
+
+ Method accessMethod = getMethod(type, methodName, parameterTypes);
+ accessMethod.setAccessible(true);
+ return accessMethod;
+ }
+
+ /**
+ * Gets the name of a method.
+ *
+ * @param methodSignature
+ * the signature of the method
+ * @return the name of the method
+ */
+ private static String getMethodName(final String methodSignature)
+ {
+ try
+ {
+ return methodSignature.substring(0, methodSignature.indexOf('('))
+ .trim();
+ } catch (StringIndexOutOfBoundsException e)
+ {
+ assert false : "Signature must have been checked before this method was called";
+ return null;
+ }
+ }
+
+ /**
+ * Gets the types of the parameters.
+ *
+ * @param parameters
+ * the parameters
+ * @return the class-types of the arguments
+ */
+ private static Class<?>[] getParameterTypes(final Object[] parameters)
+ {
+ if (parameters == null)
+ {
+ return new Class[0];
+ }
+
+ Class<?>[] typesOfParameters = new Class[parameters.length];
+
+ for (int i = 0; i < parameters.length; i++)
+ {
+ typesOfParameters[i] = parameters[i].getClass();
+ }
+ return typesOfParameters;
+ }
+
+ /**
+ * Gets the types of the given parameters. If the parameters don't match the
+ * given methodSignature an IllegalArgumentException is thrown.
+ *
+ * @param methodSignature
+ * the signature of the method
+ * @return the parameter types as class[]
+ * @throws NoSuchMethodException
+ * if the method could not be found
+ * @throws IllegalArgumentException
+ * if one of the given parameters doesn't math the given
+ * methodSignature
+ */
+ private static Class<?>[] getParameterTypes(final String methodSignature)
+ throws NoSuchMethodException, IllegalArgumentException
+ {
+ String signature = getSignatureWithoutBraces(methodSignature);
+
+ StringTokenizer tokenizer = new StringTokenizer(signature, ", *");
+ Class<?>[] typesInSignature = new Class[tokenizer.countTokens()];
+
+ for (int x = 0; tokenizer.hasMoreTokens(); x++)
+ {
+ String className = tokenizer.nextToken();
+ try
{
- return new Class[0];
- }
-
- Class<?>[] typesOfParameters = new Class[parameters.length];
-
- for (int i = 0; i < parameters.length; i++) {
- typesOfParameters[i] = parameters[i].getClass();
- }
- return typesOfParameters;
- }
-
- /**
- * Gets the types of the given parameters. If the parameters don't match the given methodSignature an IllegalArgumentException is
- * thrown.
- *
- * @param methodSignature the signature of the method
- * @return the parameter types as class[]
- * @throws NoSuchMethodException if the method could not be found
- * @throws IllegalArgumentException if one of the given parameters doesn't math the given methodSignature
- */
- private static Class<?>[] getParameterTypes(final String methodSignature) throws NoSuchMethodException, IllegalArgumentException {
- String signature = getSignatureWithoutBraces(methodSignature);
-
- StringTokenizer tokenizer = new StringTokenizer(signature, ", *");
- Class<?>[] typesInSignature = new Class[tokenizer.countTokens()];
-
- for (int x = 0; tokenizer.hasMoreTokens(); x++) {
- String className = tokenizer.nextToken();
- try {
- typesInSignature[x] = getClassForName(className);
- } catch (ClassNotFoundException e) {
- NoSuchMethodException noSuchMethodException = new NoSuchMethodException(methodSignature);
- noSuchMethodException.initCause(e);
- throw noSuchMethodException;
- }
- }
- return typesInSignature;
- }
-
- /**
- * Gets the parameter types as a string.
- *
- * @param classTypes the types to get as names.
- * @return the parameter types as a string
- *
- * @see java.lang.Class#argumentTypesToString(Class[])
- */
- private static String getParameterTypesAsString(final Class<?>[] classTypes) {
- assert classTypes != null : "getParameterTypes() should have been called before this method and should have provided not-null classTypes";
- if (classTypes.length == 0)
+ typesInSignature[x] = getClassForName(className);
+ } catch (ClassNotFoundException e)
{
- return "";
- }
-
- StringBuilder parameterTypes = new StringBuilder();
- for (Class<?> clazz : classTypes) {
- assert clazz != null : "getParameterTypes() should have been called before this method and should have provided not-null classTypes";
- parameterTypes.append(clazz.getName()).append(", ");
- }
-
- return parameterTypes.substring(0, parameterTypes.length() - 2);
- }
-
- /**
- * Removes the braces around the methods signature.
- *
- * @param methodSignature the signature with braces
- * @return the signature without braces
- */
- private static String getSignatureWithoutBraces(final String methodSignature) {
- try {
- return methodSignature.substring(methodSignature.indexOf('(') + 1, methodSignature.indexOf(')'));
- } catch (IndexOutOfBoundsException e) {
- assert false : "signature must have been checked before this method";
- return null;
- }
- }
+ NoSuchMethodException noSuchMethodException = new NoSuchMethodException(
+ methodSignature);
+ noSuchMethodException.initCause(e);
+ throw noSuchMethodException;
+ }
+ }
+ return typesInSignature;
+ }
+
+ /**
+ * Gets the parameter types as a string.
+ *
+ * @param classTypes
+ * the types to get as names.
+ * @return the parameter types as a string
+ *
+ * @see java.lang.Class#argumentTypesToString(Class[])
+ */
+ private static String getParameterTypesAsString(
+ final Class<?>[] classTypes)
+ {
+ assert classTypes != null : "getParameterTypes() should have been called before this method and should have provided not-null classTypes";
+ if (classTypes.length == 0)
+ {
+ return "";
+ }
+
+ StringBuilder parameterTypes = new StringBuilder();
+ for (Class<?> clazz : classTypes)
+ {
+ assert clazz != null : "getParameterTypes() should have been called before this method and should have provided not-null classTypes";
+ parameterTypes.append(clazz.getName()).append(", ");
+ }
+
+ return parameterTypes.substring(0, parameterTypes.length() - 2);
+ }
+
+ /**
+ * Removes the braces around the methods signature.
+ *
+ * @param methodSignature
+ * the signature with braces
+ * @return the signature without braces
+ */
+ private static String getSignatureWithoutBraces(
+ final String methodSignature)
+ {
+ try
+ {
+ return methodSignature.substring(methodSignature.indexOf('(') + 1,
+ methodSignature.indexOf(')'));
+ } catch (IndexOutOfBoundsException e)
+ {
+ assert false : "signature must have been checked before this method";
+ return null;
+ }
+ }
}
assertEquals(0, chainA.seqend); // not set
assertEquals(18, chainA.sequence.getStart());
assertEquals(314, chainA.sequence.getEnd());
- assertTrue(chainA.sequence.getSequenceAsString().startsWith("KCSKKQEE"));
+ assertTrue(
+ chainA.sequence.getSequenceAsString().startsWith("KCSKKQEE"));
assertTrue(chainA.sequence.getSequenceAsString().endsWith("WNVEVY"));
assertEquals("3W5V|A", chainA.sequence.getName());
assertNull(chainA.sequence.getAnnotation());
PDBChain chainC = pf.getChains().get(2);
assertEquals(18, chainC.sequence.getStart());
assertEquals(314, chainC.sequence.getEnd());
- assertTrue(chainC.sequence.getSequenceAsString().startsWith("KCSKKQEE"));
+ assertTrue(
+ chainC.sequence.getSequenceAsString().startsWith("KCSKKQEE"));
assertTrue(chainC.sequence.getSequenceAsString().endsWith("WNVEVY"));
assertEquals("3W5V|C", chainC.sequence.getName());
* @throws IOException
*/
@Test(groups = { "Functional" })
- public void testParse_withJmolAddAlignmentAnnotations()
- throws IOException
+ public void testParse_withJmolAddAlignmentAnnotations() throws IOException
{
PDBfile pf = new PDBfile(true, true, false, "examples/3W5V.pdb",
DataSourceType.FILE);
git://source.jalview.org / jalview.git / commitdiff