<concat destfile="${site.path}/j2s/com/stevesoft/core.js">
<fileset dir="${site.path}/j2s/com/stevesoft/pat">
<include name="**/*.js" />
- <exclude name="Regex.js" />
</fileset>
</concat>
<antcall target="call-core">
public class Regex extends RegRes implements FilenameFilter
{
- static
- {
- /**
- * This is the entry class. Load the core file directly, if it exists. See
- * buildcore.xml.
- *
- *
- * @j2sNative
- *
- * swingjs.JSUtil.loadStaticResource$S("core/core_stevesoft.z.js");
- */
- }
-
/**
* BackRefOffset gives the identity number of the first pattern. Version 1.0
* used zero, version 1.1 uses 1 to be more compatible with perl.
import jalview.datamodel.SequenceI;
import jalview.datamodel.VisibleContigsIterator;
import jalview.util.Comparison;
+import jalview.util.Platform;
import java.util.List;
import java.util.Vector;
{
String searchString = matchCase ? theSearchString
: theSearchString.toUpperCase();
- Regex searchPattern = new Regex(searchString);
+ Regex searchPattern = Platform.newRegex(searchString, null);
searchPattern.setIgnoreCase(!matchCase);
searchResults = new SearchResults();
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
+import jalview.util.Platform;
import com.stevesoft.pat.Regex;
String[] ScoreDescriptions, String regex, boolean repeat)
{
int count = 0;
- Regex pattern = new Regex(regex);
+ Regex pattern = Platform.newRegex(regex, null);
if (pattern.numSubs() > ScoreNames.length)
{
// Check that we have enough labels and descriptions for any parsed
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.io.gff.SequenceOntologyI;
+import jalview.util.Platform;
import java.util.ArrayList;
import java.util.List;
* or ENSMUST or similar for other species
* or CCDSnnnnn.nn with at least 3 digits
*/
- private static final Regex ACCESSION_REGEX = new Regex(
- "(ENS([A-Z]{3}|)[TG][0-9]{11}$)" + "|" + "(CCDS[0-9.]{3,}$)");
-
+ private static Regex ACCESSION_REGEX;
/*
* fetch exon features on genomic sequence (to identify the cdna regions)
* and cds and variation features (to retain)
@Override
public Regex getAccessionValidator()
{
+ if (ACCESSION_REGEX == null)
+ {
+ /*
+ * accepts ENSG/T/E/P with 11 digits
+ * or ENSMUSP or similar for other species
+ * or CCDSnnnnn.nn with at least 3 digits
+ */
+ ACCESSION_REGEX = Platform.newRegex(
+ "(ENS([A-Z]{3}|)[TG][0-9]{11}$)" + "|" + "(CCDS[0-9.]{3,}$)", null);
+ }
return ACCESSION_REGEX;
}
* accepts anything as we will attempt lookup of gene or
* transcript id or gene name
*/
- private static final Regex ACCESSION_REGEX = new Regex(".*");
+ private static Regex ACCESSION_REGEX;
private static final EnsemblFeatureType[] FEATURES_TO_FETCH = {
EnsemblFeatureType.gene, EnsemblFeatureType.transcript,
@Override
public Regex getAccessionValidator()
{
+ if (ACCESSION_REGEX == null)
+ {
+ ACCESSION_REGEX = Platform.newRegex(".*", null);
+ }
return ACCESSION_REGEX;
}
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.util.Platform;
import java.util.ArrayList;
import java.util.List;
* or ENSMUSP or similar for other species
* or CCDSnnnnn.nn with at least 3 digits
*/
- private static final Regex ACCESSION_REGEX = new Regex(
- "(ENS([A-Z]{3}|)P[0-9]{11}$)" + "|" + "(CCDS[0-9.]{3,}$)");
+ private static Regex ACCESSION_REGEX;
/**
* Default constructor (to use rest.ensembl.org)
@Override
public Regex getAccessionValidator()
{
+ if (ACCESSION_REGEX == null)
+ {
+ ACCESSION_REGEX = Platform.newRegex(
+ "(ENS([A-Z]{3}|)P[0-9]{11}$)" + "|" + "(CCDS[0-9.]{3,}$)", null);
+ }
return ACCESSION_REGEX;
}
import jalview.analysis.AlignmentUtils;
import jalview.bin.Cache;
import jalview.datamodel.DBRefSource;
+import jalview.util.Platform;
import jalview.ws.seqfetcher.DbSourceProxyImpl;
import com.stevesoft.pat.Regex;
// ensemblgenomes REST service merged to ensembl 9th April 2019
protected static final String DEFAULT_ENSEMBL_GENOMES_BASEURL = DEFAULT_ENSEMBL_BASEURL;
- /*
- * accepts ENSG/T/E/P with 11 digits
- * or ENSMUSP or similar for other species
- * or CCDSnnnnn.nn with at least 3 digits
- */
- private static final Regex ACCESSION_REGEX = new Regex(
- "(ENS([A-Z]{3}|)[GTEP]{1}[0-9]{11}$)" + "|"
- + "(CCDS[0-9.]{3,}$)");
+ private static Regex ACCESSION_REGEX;
protected final String ensemblGenomesDomain;
@Override
public Regex getAccessionValidator()
{
+ if (ACCESSION_REGEX == null)
+ {
+ /*
+ * accepts ENSG/T/E/P with 11 digits
+ * or ENSMUSP or similar for other species
+ * or CCDSnnnnn.nn with at least 3 digits
+ */
+ ACCESSION_REGEX = Platform
+ .newRegex("(ENS([A-Z]{3}|)[GTEP]{1}[0-9]{11}$)" + "|"
+ + "(CCDS[0-9.]{3,}$)", null);
+ }
return ACCESSION_REGEX;
}
import jalview.structure.StructureMapping;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
+import jalview.util.Platform;
import jalview.ws.DBRefFetcher;
import jalview.ws.sifts.SiftsSettings;
static
{
- /**
- * This is the entry class. Load the core file directly, if it exists. See
- * buildcore.xml.
- *
- *
- * @j2sNative
- *
- * swingjs.JSUtil.loadStaticResource$S("core/core_jvjmol.z.js");
- */
+ Platform.loadStaticResource("core/core_jvjmol.z.js",
+ "org.jmol.viewer.Viewer");
}
private static final String UNKNOWN_VIEWER_TYPE = "Unknown structure viewer type ";
{
for (int i = 0; !isBinary && i < data.length(); i++)
{
- char c = data.charAt(i);
+ int c = data.charAt(i);
isBinary = (c < 32 && c != '\t' && c != '\n' && c != '\r'
&& c != 5 && c != 27); // nominal binary character filter
// excluding CR, LF, tab,DEL and ^E
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;
+ break;
}
}
if (!lineswereskipped && data.startsWith("PK"))
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.SequenceI;
+import jalview.util.Platform;
import java.util.List;
}
};
+ private static Regex VALIDATION_REGEX;
+
+ private static Regex getRegex()
+ {
+ return (VALIDATION_REGEX == null
+ ? VALIDATION_REGEX = Platform
+ .newRegex("\\s*((([-0-9]+).?)|FIRST|LAST|@)", null)
+ : VALIDATION_REGEX);
+ }
+
private resCode validResidueCode(String field)
{
Integer val = null;
- Regex r = new Regex(
- "\\s*((([-0-9]+).?)|FIRST|LAST|@)");
-
+ Regex r = getRegex();
if (!r.search(field))
{
return null; // invalid
import jalview.datamodel.SequenceNode;
import jalview.util.MessageManager;
+import jalview.util.Platform;
import java.io.BufferedReader;
import java.io.File;
import com.stevesoft.pat.Regex;
+// TODO This class does not conform to Java standards for field name capitalization.
+
/**
* Parse a new hanpshire style tree Caveats: NHX files are NOT supported and the
* tree distances and topology are unreliable when they are parsed. TODO: on
*/
public class NewickFile extends FileParse
{
- SequenceNode root;
+ private SequenceNode root;
private boolean HasBootstrap = false;
private boolean RootHasDistance = false;
// File IO Flags
- boolean ReplaceUnderscores = false;
+ private boolean ReplaceUnderscores = false;
+
+ private boolean printRootInfo = true;
+
+ private static final int REGEX_PERL_NODE_REQUIRE_QUOTE = 0;
+
+ private static final int REGEX_PERL_NODE_ESCAPE_QUOTE = 1;
+
+ private static final int REGEX_PERL_NODE_UNQUOTED_WHITESPACE = 2;
+
+ private static final int REGEX_MAJOR_SYMS = 3;
+
+ private static final int REGEX_QNODE_NAME = 4;
+
+ private static final int REGEX_COMMENT = 5;
+
+ private static final int REGEX_UQNODE_NAME = 6;
- boolean printRootInfo = true;
+ private static final int REGEX_NBOOTSTRAP = 7;
+
+ private static final int REGEX_NDIST = 8;
+
+ private static final int REGEX_NO_LINES = 9;
+
+ private static final int REGEX_PERL_EXPAND_QUOTES = 10;
+
+ private static final int REGEX_MAX = 11;
+
+ private static final Regex[] REGEX = new Regex[REGEX_MAX];
+
+ private static Regex getRegex(int id)
+ {
+ if (REGEX[id] == null)
+ {
+ String code = null;
+ String code2 = null;
+ String codePerl = null;
+ switch (id)
+ {
+ case REGEX_PERL_NODE_REQUIRE_QUOTE:
+ codePerl = "m/[\\[,:'()]/";
+ break;
+ case REGEX_PERL_NODE_ESCAPE_QUOTE:
+ codePerl = "s/'/''/";
+ break;
+ case REGEX_PERL_NODE_UNQUOTED_WHITESPACE:
+ codePerl = "s/\\/w/_/";
+ break;
+ case REGEX_PERL_EXPAND_QUOTES:
+ codePerl = "s/''/'/";
+ break;
+ case REGEX_MAJOR_SYMS:
+ code = "[(\\['),;]";
+ break;
+ case REGEX_QNODE_NAME:
+ code = "'([^']|'')+'";
+ break;
+ case REGEX_COMMENT:
+ code = "]";
+ break;
+ case REGEX_UQNODE_NAME:
+ code = "\\b([^' :;\\](),]+)";
+ break;
+ case REGEX_NBOOTSTRAP:
+ code = "\\s*([0-9+]+)\\s*:";
+ break;
+ case REGEX_NDIST:
+ code = ":([-0-9Ee.+]+)";
+ break;
+ case REGEX_NO_LINES:
+ code = "\n+";
+ code2 = "";
+ break;
+ default:
+ return null;
+ }
+ return codePerl == null ? Platform.newRegex(code, code2)
+ : Platform.newRegexPerl(code2);
+ }
+ return REGEX[id];
+ }
- private Regex[] NodeSafeName = new Regex[] {
- new Regex().perlCode("m/[\\[,:'()]/"), // test for
- // requiring
- // quotes
- new Regex().perlCode("s/'/''/"), // escaping quote
- // characters
- new Regex().perlCode("s/\\/w/_/") // unqoted whitespace
- // transformation
- };
- char QuoteChar = '\'';
+ private char quoteChar = '\'';
/**
* Creates a new NewickFile object.
*/
public void parse() throws IOException
{
+ Platform.ensureRegex();
String nf;
{ // fill nf with complete tree file
boolean ascending = false; // flag indicating that we are leaving the
// current node
- Regex majorsyms = new Regex(
- "[(\\['),;]");
+ Regex majorsyms = getRegex(REGEX_MAJOR_SYMS); // "[(\\['),;]"
int nextcp = 0;
int ncp = cp;
// Deal with quoted fields
case '\'':
- Regex qnodename = new Regex(
- "'([^']|'')+'");
+ Regex qnodename = getRegex(REGEX_QNODE_NAME);// "'([^']|'')+'");
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 = getRegex(REGEX_PERL_EXPAND_QUOTES);
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 = getRegex(REGEX_COMMENT); // "]"
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 = getRegex(REGEX_UQNODE_NAME);// "\\b([^' :;\\](),]+)"
+ Regex nbootstrap = getRegex(REGEX_NBOOTSTRAP);// "\\s*([0-9+]+)\\s*:");
+ Regex ndist = getRegex(REGEX_NDIST);// ":([-0-9Ee.+]+)");
if (!parsednodename && uqnodename.search(fstring)
&& ((uqnodename.matchedFrom(1) == 0) || (fstring
*/
char getQuoteChar()
{
- return QuoteChar;
+ return quoteChar;
}
/**
*/
char setQuoteChar(char c)
{
- char old = QuoteChar;
- QuoteChar = c;
+ char old = quoteChar;
+ quoteChar = c;
return old;
}
*/
private String nodeName(String name)
{
- if (NodeSafeName[0].search(name))
+ if (getRegex(REGEX_PERL_NODE_REQUIRE_QUOTE).search(name))
{
- return QuoteChar + NodeSafeName[1].replaceAll(name) + QuoteChar;
+ return quoteChar
+ + getRegex(REGEX_PERL_NODE_ESCAPE_QUOTE).replaceAll(name)
+ + quoteChar;
}
else
{
- return NodeSafeName[2].replaceAll(name);
+ return getRegex(REGEX_PERL_NODE_UNQUOTED_WHITESPACE).replaceAll(name);
}
}
trf.parse();
System.out.println("Original file :\n");
- Regex nonl = new Regex("\n+", "");
+ Regex nonl = getRegex(REGEX_NO_LINES);// "\n+", "");
System.out.println(nonl.replaceAll(newickfile.toString()) + "\n");
System.out.println("Parsed file.\n");
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.util.MessageManager;
+import jalview.util.Platform;
import java.io.BufferedReader;
import java.io.FileNotFoundException;
dataName = dataName.substring(0, b - 1);
}
b = 0;
- Regex m = new Regex("[\\/]?([-A-Za-z0-9]+)\\.?");
+ Regex m = getSafeRegex();
String mm = dataName;
while (m.searchFrom(dataName, b))
{
}
return mm;
}
+
+ private static Regex SAFE_REGEX;
+
+ private static Regex getSafeRegex()
+ {
+ return (SAFE_REGEX == null
+ ? SAFE_REGEX = Platform.newRegex("[\\/]?([-A-Za-z0-9]+)\\.?", null)
+ : SAFE_REGEX);
+ }
}
import jalview.util.Comparison;
import jalview.util.Format;
import jalview.util.MessageManager;
+import jalview.util.Platform;
import java.io.BufferedReader;
import java.io.FileReader;
{
private static final String ANNOTATION = "annotation";
-// private static final Regex OPEN_PAREN = new Regex("(<|\\[)", "(");
-//
-// private static final Regex CLOSE_PAREN = new Regex("(>|\\])", ")");
+ // WUSS extended symbols. Avoid ambiguity with protein SS annotations by using
+ // NOT_RNASS first.
- public static final Regex DETECT_BRACKETS = new Regex(
- "(<|>|\\[|\\]|\\(|\\)|\\{|\\})");
-
- // WUSS extended symbols. Avoid ambiguity with protein SS annotations by using NOT_RNASS first.
public static final String RNASS_BRACKETS = "<>[](){}AaBbCcDdEeFfGgHhIiJjKkLlMmNnOoPpQqRrSsTtUuVvWwXxYyZz";
+ public static final int REGEX_STOCKHOLM = 0;
+
+ public static final int REGEX_BRACKETS = 1;
+
// use the following regex to decide an annotations (whole) line is NOT an RNA
// SS (it contains only E,H,e,h and other non-brace/non-alpha chars)
- private static final Regex NOT_RNASS = new Regex(
- "^[^<>[\\](){}A-DF-Za-df-z]*$");
+ public static final int REGEX_NOT_RNASS = 2;
+
+ private static final int REGEX_ANNOTATION = 3;
+
+ private static final int REGEX_PFAM = 4;
+
+ private static final int REGEX_RFAM = 5;
+
+ private static final int REGEX_ALIGN_END = 6;
+
+ private static final int REGEX_SPLIT_ID = 7;
+
+ private static final int REGEX_SUBTYPE = 8;
+
+ private static final int REGEX_ANNOTATION_LINE = 9;
+
+ private static final int REGEX_REMOVE_ID = 10;
+
+ private static final int REGEX_OPEN_PAREN = 11;
+
+ private static final int REGEX_CLOSE_PAREN = 12;
+
+ public static final int REGEX_MAX = 13;
+
+ private static Regex REGEX[] = new Regex[REGEX_MAX];
+
+ /**
+ * Centralize all actual Regex instantialization in Platform.
+ *
+ * @param id
+ * @return
+ */
+ private static Regex getRegex(int id)
+ {
+ if (REGEX[id] == null)
+ {
+ String pat = null, pat2 = null;
+ switch (id)
+ {
+ case REGEX_STOCKHOLM:
+ pat = "# STOCKHOLM ([\\d\\.]+)";
+ break;
+ case REGEX_BRACKETS:
+ // for reference; not used
+ pat = "(<|>|\\[|\\]|\\(|\\)|\\{|\\})";
+ break;
+ case REGEX_NOT_RNASS:
+ pat = "^[^<>[\\](){}A-DF-Za-df-z]*$";
+ break;
+ case REGEX_ANNOTATION:
+ pat = "(\\w+)\\s*(.*)";
+ break;
+ case REGEX_PFAM:
+ pat = "PF[0-9]{5}(.*)";
+ break;
+ case REGEX_RFAM:
+ pat = "RF[0-9]{5}(.*)";
+ break;
+ case REGEX_ALIGN_END:
+ pat = "^\\s*\\/\\/";
+ break;
+ case REGEX_SPLIT_ID:
+ pat = "(\\S+)\\/(\\d+)\\-(\\d+)";
+ break;
+ case REGEX_SUBTYPE:
+ pat = "(\\S+)\\s+(\\S*)\\s+(.*)";
+ break;
+ case REGEX_ANNOTATION_LINE:
+ pat = "#=(G[FSRC]?)\\s+(.*)";
+ break;
+ case REGEX_REMOVE_ID:
+ pat = "(\\S+)\\s+(\\S+)";
+ break;
+ case REGEX_OPEN_PAREN:
+ pat = "(<|\\[)";
+ pat2 = "(";
+ break;
+ case REGEX_CLOSE_PAREN:
+ pat = "(>|\\])";
+ pat2 = ")";
+ break;
+ default:
+ return null;
+ }
+ REGEX[id] = Platform.newRegex(pat, pat2);
+ }
+ return REGEX[id];
+ }
StringBuffer out; // output buffer
// First, we have to check that this file has STOCKHOLM format, i.e. the
// first line must match
- r = new Regex("# STOCKHOLM ([\\d\\.]+)");
+ r = getRegex(REGEX_STOCKHOLM);
if (!r.search(nextLine()))
{
throw new IOException(MessageManager
}
// We define some Regexes here that will be used regularily later
- rend = new Regex("^\\s*\\/\\/"); // Find the end of an alignment
- p = new Regex("(\\S+)\\/(\\d+)\\-(\\d+)"); // split sequence id in
+ rend = getRegex(REGEX_ALIGN_END);//"^\\s*\\/\\/"); // Find the end of an alignment
+ p = getRegex(REGEX_SPLIT_ID);//"(\\S+)\\/(\\d+)\\-(\\d+)"); // split sequence id in
// id/from/to
- s = new Regex("(\\S+)\\s+(\\S*)\\s+(.*)"); // Parses annotation subtype
- r = new Regex("#=(G[FSRC]?)\\s+(.*)"); // Finds any annotation line
- x = new Regex("(\\S+)\\s+(\\S+)"); // split id from sequence
+ s = getRegex(REGEX_SUBTYPE);// "(\\S+)\\s+(\\S*)\\s+(.*)"); // Parses
+ // annotation subtype
+ r = getRegex(REGEX_ANNOTATION_LINE);// "#=(G[FSRC]?)\\s+(.*)"); // Finds any
+ // annotation line
+ x = getRegex(REGEX_REMOVE_ID);// "(\\S+)\\s+(\\S+)"); // split id from
+ // sequence
// Convert all bracket types to parentheses (necessary for passing to VARNA)
- Regex openparen = new Regex("(<|\\[)", "(");
- Regex closeparen = new Regex("(>|\\])", ")");
+ Regex openparen = getRegex(REGEX_OPEN_PAREN);//"(<|\\[)", "(");
+ Regex closeparen = getRegex(REGEX_CLOSE_PAREN);//"(>|\\])", ")");
// // Detect if file is RNA by looking for bracket types
-// Regex detectbrackets = new Regex("(<|>|\\[|\\]|\\(|\\))");
+ // Regex detectbrackets = getRegex("(<|>|\\[|\\]|\\(|\\))");
rend.optimize();
p.optimize();
this.noSeqs = seqs.size();
String dbsource = null;
- Regex pf = new Regex("PF[0-9]{5}(.*)"); // Finds AC for Pfam
- Regex rf = new Regex("RF[0-9]{5}(.*)"); // Finds AC for Rfam
+ Regex pf = getRegex(REGEX_PFAM); // Finds AC for Pfam
+ Regex rf = getRegex(REGEX_RFAM); // Finds AC for Rfam
if (getAlignmentProperty("AC") != null)
{
String dbType = getAlignmentProperty("AC").toString();
*/
// Let's save the annotations, maybe we'll be able to do something
// with them later...
- Regex an = new Regex("(\\w+)\\s*(.*)");
+ Regex an = getRegex(REGEX_ANNOTATION);
if (an.search(annContent))
{
if (an.stringMatched(1).equals("NH"))
if (type.equalsIgnoreCase("secondary structure"))
{
ss = true;
- isrnass = !NOT_RNASS.search(annots); // sorry about the double negative
+ isrnass = !getRegex(REGEX_NOT_RNASS).search(annots); // sorry about the double
+ // negative
// here (it's easier for dealing with
// other non-alpha-non-brace chars)
}
while (en.hasMoreElements())
{
Object idd = en.nextElement();
- String type = (String) dataRef.remove(idd);
+ String type = dataRef.remove(idd);
out.append(new Format("%-" + (maxid - 2) + "s")
.form("#=GS " + idd.toString() + " "));
if (type.contains("PFAM") || type.contains("RFAM"))
String fileName, JarOutputStream jout)
{
+ // BH: Question: What is this Dataset for, as it seems to
+ // duplicate the actual XML file data.
+
for (String dssids : dsses.keySet())
{
AlignFrame _af = dsses.get(dssids);
{
jarentry = jin.getNextJarEntry();
}
-
- if (jarentry != null && jarentry.getName().endsWith(".xml"))
+ String name = (jarentry == null ? null : jarentry.getName());
+ if (name != null && name.endsWith(".xml")
+ // The question here is what to do with the two
+ // .xml files in the jvp file. They are identical?
+ // && name.indexOf(" Dataset for ") < 0 // BH 2019.05.21
+ )
{
JAXBContext jc = JAXBContext
.newInstance("jalview.xml.binding.jalview");
viewport.setViewName(view.getViewName());
af.setInitialTabVisible();
}
- af.setBounds(safeInt(view.getXpos()), safeInt(view.getYpos()),
- safeInt(view.getWidth()), safeInt(view.getHeight()));
+ int x = safeInt(view.getXpos());
+ int y = safeInt(view.getYpos());
+ int w = safeInt(view.getWidth());
+ int h = safeInt(view.getHeight());
+ // // BH we cannot let the title bar go off the top
+ // if (Platform.isJS())
+ // {
+ // x = Math.max(50 - w, x);
+ // y = Math.max(0, y);
+ // }
+
+ af.setBounds(x, y, w, h);
// startSeq set in af.alignPanel.updateLayout below
af.alignPanel.updateLayout();
ColourSchemeI cs = null;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
-import java.util.Set;
import com.stevesoft.pat.Regex;
}
// BH TODO (what?)
- HashSet<String> srcs = new HashSet<String>();
+ HashSet<String> srcs = new HashSet<>();
for (String src : sources)
{
srcs.add(src.toUpperCase());
}
int nrefs = dbrefs.size();
- List<DBRefEntry> res = new ArrayList<DBRefEntry>();
+ List<DBRefEntry> res = new ArrayList<>();
for (int ib = 0; ib < nrefs; ib++)
{
DBRefEntry dbr = dbrefs.get(ib);
* @return
*/
public static List<DBRefEntry> searchRefs(List<DBRefEntry> refs, String accId) {
- List<DBRefEntry> rfs = new ArrayList<DBRefEntry>();
+ List<DBRefEntry> rfs = new ArrayList<>();
if (refs == null || accId == null) {
return rfs;
}
* @return
*/
static List<DBRefEntry> searchRefs(List<DBRefEntry> refs, DBRefEntry entry, DbRefComp comparator, int mode) {
- List<DBRefEntry> rfs = new ArrayList<DBRefEntry>();
+ List<DBRefEntry> rfs = new ArrayList<>();
if (refs == null || entry == null) {
return rfs;
}
return matches;
}
+ private static Regex PARSE_REGEX;
+
+ private static Regex getParseRegex()
+ {
+ return (PARSE_REGEX == null ? PARSE_REGEX = Platform.newRegex(
+ "([0-9][0-9A-Za-z]{3})\\s*(.?)\\s*;\\s*([0-9]+)-([0-9]+)", null)
+ : PARSE_REGEX);
+ }
/**
* Parses a DBRefEntry and adds it to the sequence, also a PDBEntry if the
* database is PDB.
/*
* Check for PFAM style stockhom PDB accession id citation e.g. "1WRI A; 7-80;"
*/
- Regex r = new com.stevesoft.pat.Regex("([0-9][0-9A-Za-z]{3})\\s*(.?)\\s*;\\s*([0-9]+)-([0-9]+)");
+ Regex r = getParseRegex();
if (r.search(acn.trim())) {
String pdbid = r.stringMatched(1);
String chaincode = r.stringMatched(2);
* @return
*/
public static List<DBRefEntry> searchRefsForSource(List<DBRefEntry> dbRefs, String source) {
- List<DBRefEntry> matches = new ArrayList<DBRefEntry>();
+ List<DBRefEntry> matches = new ArrayList<>();
if (dbRefs != null && source != null) {
for (DBRefEntry dbref : dbRefs) {
if (source.equalsIgnoreCase(dbref.getSource())) {
bsSelect.set(0, dbrefs.size());
if (!selectRefsBS(dbrefs, isProtein ? DBRefSource.PROTEIN_MASK : DBRefSource.DNA_CODING_MASK, bsSelect))
- return;
+ {
+ return;
+ }
// selfs.addAll(selfArray);
// }
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);
+ {
+ bsSelect.clear(i);
+ }
}
// while (selfs.contains(p))
// {
// TODO: promote transcript refs ??
}
if (keys == 0 || !selectRefsBS(dbrefs, keys, bsSelect))
- return;
+ {
+ return;
+ }
// if (candidates != null)
{
for (int ic = bsSelect.nextSetBit(0); ic >= 0; ic = bsSelect.nextSetBit(ic + 1))
import java.util.Hashtable;
+import com.stevesoft.pat.Regex;
+
/**
* This class is not implemented because Preferences never puts anything in
* groupURLLinks.
regexReplace[pass] = link.substring(ptok[pass] + mlength, p);
try
{
- com.stevesoft.pat.Regex rg = com.stevesoft.pat.Regex
- .perlCode("/" + regexReplace[pass] + "/");
+ Regex rg = Platform.newRegexPerl("/" + regexReplace[pass] + "/");
if (rg == null)
{
invalidMessage = "Invalid Regular Expression : '"
// iterate through input, collating segments to be inserted into url
StringBuffer matched[] = new StringBuffer[idseq.length];
// and precompile regexes
- com.stevesoft.pat.Regex[] rgxs = new com.stevesoft.pat.Regex[matched.length];
+ Regex[] rgxs = new Regex[matched.length];
for (pass = 0; pass < matched.length; pass++)
{
matched[pass] = new StringBuffer();
if (regexReplace[pass] != null)
{
- rgxs[pass] = com.stevesoft.pat.Regex
- .perlCode("/" + regexReplace[pass] + "/");
+ rgxs[pass] = Platform.newRegexPerl("/" + regexReplace[pass] + "/");
}
else
{
import org.json.simple.parser.JSONParser;
import org.json.simple.parser.ParseException;
+import com.stevesoft.pat.Regex;
+
/**
* System platform information used by Applet and Application
*
return null;
}
+ /**
+ * load a resource -- probably a core file -- if and only if a particular
+ * class has not been instantialized. We use a String here because if we used
+ * a .class object, that reference itself would simply load the class, and we
+ * want the core package to include that as well.
+ *
+ * @param resourcePath
+ * @param className
+ */
+ public static void loadStaticResource(Object resourcePath,
+ String className)
+ {
+ /**
+ *
+ * @j2sNative if (!swingjs.JSUtil.isClassLoaded$S(className))
+ * swingjs.JSUtil.loadStaticResource$S(resourcePath);
+ */
+ }
+
+ public static void ensureRegex()
+ {
+ loadStaticResource("core/core_stevesoft.z.js",
+ "com.stevesoft.pat.Regex");
+ }
+
+ public static Regex newRegex(String searchString, String replaceString)
+ {
+ ensureRegex();
+ return (replaceString == null ? new Regex(searchString)
+ : new Regex(searchString, replaceString));
+ }
+
+ public static Regex newRegexPerl(String code)
+ {
+ ensureRegex();
+ return Regex.perlCode(code);
+ }
+
}
import java.util.Map;
import java.util.Vector;
+import com.stevesoft.pat.Regex;
+
/**
* A helper class to parse URL Link strings taken from applet parameters or
* jalview properties file using the com.stevesoft.pat.Regex implementation.
{
if (regexReplace != null)
{
- com.stevesoft.pat.Regex rg = com.stevesoft.pat.Regex
- .perlCode("/" + regexReplace + "/");
+ Regex rg = Platform.newRegexPerl("/" + regexReplace + "/");
if (rg.search(idstring))
{
int ns = rg.numSubs();
{
// Extract Regex and suffix
urlSuffix = link.substring(p + endDelimiter.length());
- regexReplace = link.substring(sqidPos + startLength, p);
- try
- {
- com.stevesoft.pat.Regex rg = com.stevesoft.pat.Regex
- .perlCode("/" + regexReplace + "/");
- if (rg == null)
- {
- invalidMessage = "Invalid Regular Expression : '" + regexReplace
- + "'\n";
- }
- } catch (Exception e)
- {
- invalidMessage = "Invalid Regular Expression : '" + regexReplace
- + "'\n";
- }
+ testRegexPerl(
+ regexReplace = link.substring(sqidPos + startLength, p));
}
else
{
return p;
}
+ private void testRegexPerl(String r)
+ {
+ Regex rg = null;
+ try
+ {
+ rg = Platform.newRegexPerl("/" + r + "/");
+ } catch (Exception e)
+ {
+ }
+ if (rg == null)
+ {
+ invalidMessage = "Invalid Regular Expression : '" + r + "'\n";
+ }
+ }
+
/**
* Create a set of URL links for a sequence
*
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefSource;
+import jalview.util.Platform;
import com.stevesoft.pat.Regex;
public class EmblCdsSource extends EmblXmlSource
{
+ private Regex ACCESSION_REGEX = null;
+
public EmblCdsSource()
{
super();
@Override
public Regex getAccessionValidator()
{
- return new Regex("^[A-Z]+[0-9]+");
+ if (ACCESSION_REGEX == null)
+ {
+ ACCESSION_REGEX = Platform.newRegex("^[A-Z]+[0-9]+", null);
+ }
+ return ACCESSION_REGEX;
}
@Override
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefSource;
+import jalview.util.Platform;
import com.stevesoft.pat.Regex;
public class EmblSource extends EmblXmlSource
{
+ private static Regex ACCESSION_REGEX;
+
public EmblSource()
{
super();
@Override
public Regex getAccessionValidator()
{
- return new Regex("^[A-Z]+[0-9]+");
+ if (ACCESSION_REGEX == null)
+ {
+ ACCESSION_REGEX = Platform.newRegex("^[A-Z]+[0-9]+", null);
+ }
+ return ACCESSION_REGEX;
}
/*
import jalview.io.PDBFeatureSettings;
import jalview.structure.StructureImportSettings;
import jalview.util.MessageManager;
+import jalview.util.Platform;
import jalview.ws.ebi.EBIFetchClient;
import java.io.File;
private static final int PDB_ID_LENGTH = 4;
+ private static Regex ACCESSION_REGEX;
+
public Pdb()
{
super();
@Override
public Regex getAccessionValidator()
{
- return new Regex("([1-9][0-9A-Za-z]{3}):?([ _A-Za-z0-9]?)");
+ if (ACCESSION_REGEX == null)
+ {
+ ACCESSION_REGEX = Platform
+ .newRegex("([1-9][0-9A-Za-z]{3}):?([ _A-Za-z0-9]?)", null);
+ }
+ return ACCESSION_REGEX;
}
/*
fileFormat);
if (pdbAlignment != null)
{
- List<SequenceI> toremove = new ArrayList<SequenceI>();
+ List<SequenceI> toremove = new ArrayList<>();
for (SequenceI pdbcs : pdbAlignment.getSequences())
{
String chid = null;
import jalview.datamodel.SequenceI;
import jalview.gui.Preferences;
import jalview.schemes.ResidueProperties;
+import jalview.util.Platform;
import jalview.util.StringUtils;
import jalview.ws.seqfetcher.DbSourceProxyImpl;
import jalview.xml.binding.uniprot.DbReferenceType;
private static final String BAR_DELIMITER = "|";
+ private static Regex ACCESSION_REGEX;
+
/**
* Constructor
*/
@Override
public Regex getAccessionValidator()
{
- return new Regex("([A-Z]+[0-9]+[A-Z0-9]+|[A-Z0-9]+_[A-Z0-9]+)");
+ if (ACCESSION_REGEX == null)
+ {
+ ACCESSION_REGEX = Platform
+ .newRegex("([A-Z]+[0-9]+[A-Z0-9]+|[A-Z0-9]+_[A-Z0-9]+)", null);
+ }
+ return ACCESSION_REGEX;
}
/*
-20190518175634
+20190522032238
-20190518175634
+20190522032238
git://source.jalview.org / jalview.git / commitdiff