import java.util.*;\r
\r
\r
-public class NewickFile extends FileParse {\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class NewickFile extends FileParse\r
+{\r
SequenceNode root;\r
private boolean HasBootstrap = false;\r
private boolean HasDistances = false;\r
// File IO Flags\r
boolean ReplaceUnderscores = false;\r
boolean printRootInfo = false;\r
- private com.stevesoft.pat.Regex[] NodeSafeName = new com.stevesoft.pat.Regex[] {\r
+ private com.stevesoft.pat.Regex[] NodeSafeName = new com.stevesoft.pat.Regex[]\r
+ {\r
new com.stevesoft.pat.Regex().perlCode("m/[\\[,:'()]/"), // test for requiring quotes\r
new com.stevesoft.pat.Regex().perlCode("s/'/''/"), // escaping quote characters\r
new com.stevesoft.pat.Regex().perlCode("s/\\/w/_/") // unqoted whitespace transformation\r
};\r
char QuoteChar = '\'';\r
\r
- public NewickFile(String inStr) throws IOException {\r
+ /**\r
+ * Creates a new NewickFile object.\r
+ *\r
+ * @param inStr DOCUMENT ME!\r
+ *\r
+ * @throws IOException DOCUMENT ME!\r
+ */\r
+ public NewickFile(String inStr) throws IOException\r
+ {\r
super(inStr, "Paste");\r
}\r
\r
- public NewickFile(String inFile, String type) throws IOException {\r
+ /**\r
+ * Creates a new NewickFile object.\r
+ *\r
+ * @param inFile DOCUMENT ME!\r
+ * @param type DOCUMENT ME!\r
+ *\r
+ * @throws IOException DOCUMENT ME!\r
+ */\r
+ public NewickFile(String inFile, String type) throws IOException\r
+ {\r
super(inFile, type);\r
}\r
\r
- public NewickFile(SequenceNode newtree) {\r
+ /**\r
+ * Creates a new NewickFile object.\r
+ *\r
+ * @param newtree DOCUMENT ME!\r
+ */\r
+ public NewickFile(SequenceNode newtree)\r
+ {\r
root = newtree;\r
}\r
\r
- public NewickFile(SequenceNode newtree, boolean bootstrap) {\r
+ /**\r
+ * Creates a new NewickFile object.\r
+ *\r
+ * @param newtree DOCUMENT ME!\r
+ * @param bootstrap DOCUMENT ME!\r
+ */\r
+ public NewickFile(SequenceNode newtree, boolean bootstrap)\r
+ {\r
HasBootstrap = bootstrap;\r
root = newtree;\r
}\r
\r
- public NewickFile(SequenceNode newtree, boolean bootstrap, boolean distances) {\r
+ /**\r
+ * Creates a new NewickFile object.\r
+ *\r
+ * @param newtree DOCUMENT ME!\r
+ * @param bootstrap DOCUMENT ME!\r
+ * @param distances DOCUMENT ME!\r
+ */\r
+ public NewickFile(SequenceNode newtree, boolean bootstrap, boolean distances)\r
+ {\r
root = newtree;\r
HasBootstrap = bootstrap;\r
HasDistances = distances;\r
}\r
\r
+ /**\r
+ * Creates a new NewickFile object.\r
+ *\r
+ * @param newtree DOCUMENT ME!\r
+ * @param bootstrap DOCUMENT ME!\r
+ * @param distances DOCUMENT ME!\r
+ * @param rootdistance DOCUMENT ME!\r
+ */\r
public NewickFile(SequenceNode newtree, boolean bootstrap,\r
- boolean distances, boolean rootdistance) {\r
+ boolean distances, boolean rootdistance)\r
+ {\r
root = newtree;\r
HasBootstrap = bootstrap;\r
HasDistances = distances;\r
RootHasDistance = rootdistance;\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param Error DOCUMENT ME!\r
+ * @param Er DOCUMENT ME!\r
+ * @param r DOCUMENT ME!\r
+ * @param p DOCUMENT ME!\r
+ * @param s DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
private String ErrorStringrange(String Error, String Er, int r, int p,\r
- String s) {\r
+ String s)\r
+ {\r
return ((Error == null) ? "" : Error) + Er + " at position " + p +\r
" ( " +\r
s.substring(((p - r) < 0) ? 0 : (p - r),\r
\r
// @tree annotations\r
// These are set automatically by the reader\r
- public boolean HasBootstrap() {\r
+ public boolean HasBootstrap()\r
+ {\r
return HasBootstrap;\r
}\r
\r
- public boolean HasDistances() {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public boolean HasDistances()\r
+ {\r
return HasDistances;\r
}\r
\r
- public void parse() throws IOException {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @throws IOException DOCUMENT ME!\r
+ */\r
+ public void parse() throws IOException\r
+ {\r
String nf;\r
\r
{ // fill nf with complete tree file\r
\r
StringBuffer file = new StringBuffer();\r
\r
- while ((nf = nextLine()) != null) {\r
+ while ((nf = nextLine()) != null)\r
+ {\r
file.append(nf);\r
}\r
\r
com.stevesoft.pat.Regex majorsyms = new com.stevesoft.pat.Regex(\r
"[(\\['),;]");\r
\r
- while (majorsyms.searchFrom(nf, cp) && (Error == null)) {\r
+ while (majorsyms.searchFrom(nf, cp) && (Error == null))\r
+ {\r
int fcp = majorsyms.matchedFrom();\r
\r
- switch (nf.charAt(fcp)) {\r
+ switch (nf.charAt(fcp))\r
+ {\r
case '[': // Comment or structured/extended NH format info\r
\r
com.stevesoft.pat.Regex comment = new com.stevesoft.pat.Regex(\r
"]");\r
\r
- if (comment.searchFrom(nf, fcp)) {\r
+ if (comment.searchFrom(nf, fcp))\r
+ {\r
// Skip the comment field\r
cp = 1 + comment.matchedFrom();\r
- } else {\r
+ }\r
+ else\r
+ {\r
Error = ErrorStringrange(Error, "Unterminated comment", 3,\r
fcp, nf);\r
}\r
\r
// ascending should not be set\r
// New Internal node\r
- if (ascending) {\r
+ if (ascending)\r
+ {\r
Error = ErrorStringrange(Error, "Unexpected '('", 7, fcp, nf);\r
\r
continue;\r
;\r
d++;\r
\r
- if (c.right() == null) {\r
+ if (c.right() == null)\r
+ {\r
c.setRight(new SequenceNode(null, c, null, DefDistance,\r
DefBootstrap, false));\r
c = (SequenceNode) c.right();\r
- } else {\r
- if (c.left() != null) {\r
+ }\r
+ else\r
+ {\r
+ if (c.left() != null)\r
+ {\r
// Dummy node for polytomy - keeps c.left free for new node\r
SequenceNode tmpn = new SequenceNode(null, c, null, 0,\r
0, true);\r
c = (SequenceNode) c.left();\r
}\r
\r
- if (realroot == null) {\r
+ if (realroot == null)\r
+ {\r
realroot = c;\r
}\r
\r
com.stevesoft.pat.Regex qnodename = new com.stevesoft.pat.Regex(\r
"([^']|'')+'");\r
\r
- if (qnodename.searchFrom(nf, fcp)) {\r
+ if (qnodename.searchFrom(nf, fcp))\r
+ {\r
int nl = qnodename.stringMatched().length();\r
nodename = new String(qnodename.stringMatched().substring(0,\r
nl - 1));\r
cp = fcp + nl + 1;\r
- } else {\r
+ }\r
+ else\r
+ {\r
Error = ErrorStringrange(Error,\r
"Unterminated quotes for nodename", 7, fcp, nf);\r
}\r
\r
case ';':\r
\r
- if (d != -1) {\r
+ if (d != -1)\r
+ {\r
Error = ErrorStringrange(Error,\r
"Wayward semicolon (depth=" + d + ")", 7, fcp, nf);\r
}\r
if (uqnodename.search(fstring) &&\r
((uqnodename.matchedFrom(1) == 0) ||\r
(fstring.charAt(uqnodename.matchedFrom(1) - 1) != ':'))) // JBPNote HACK!\r
- {\r
- if (nodename == null) {\r
- if (ReplaceUnderscores) {\r
+ {\r
+ if (nodename == null)\r
+ {\r
+ if (ReplaceUnderscores)\r
+ {\r
nodename = uqnodename.stringMatched(1).replace('_',\r
' ');\r
- } else {\r
+ }\r
+ else\r
+ {\r
nodename = uqnodename.stringMatched(1);\r
}\r
- } else {\r
+ }\r
+ else\r
+ {\r
Error = ErrorStringrange(Error,\r
"File has broken algorithm - overwritten nodename",\r
10, fcp, nf);\r
\r
if (nbootstrap.search(fstring) &&\r
(nbootstrap.matchedFrom(1) > (uqnodename.matchedFrom(1) +\r
- uqnodename.stringMatched().length()))) {\r
- try {\r
+ uqnodename.stringMatched().length())))\r
+ {\r
+ try\r
+ {\r
bootstrap = (new Integer(nbootstrap.stringMatched(1))).intValue();\r
HasBootstrap = true;\r
- } catch (Exception e) {\r
+ }\r
+ catch (Exception e)\r
+ {\r
Error = ErrorStringrange(Error,\r
"Can't parse bootstrap value", 4,\r
cp + nbootstrap.matchedFrom(), nf);\r
\r
boolean nodehasdistance = false;\r
\r
- if (ndist.search(fstring)) {\r
- try {\r
+ if (ndist.search(fstring))\r
+ {\r
+ try\r
+ {\r
distance = (new Float(ndist.stringMatched(1))).floatValue();\r
HasDistances = true;\r
nodehasdistance = true;\r
- } catch (Exception e) {\r
+ }\r
+ catch (Exception e)\r
+ {\r
Error = ErrorStringrange(Error,\r
"Can't parse node distance value", 7,\r
cp + ndist.matchedFrom(), nf);\r
}\r
}\r
\r
- if (ascending) {\r
+ if (ascending)\r
+ {\r
// Write node info here\r
c.setName(nodename);\r
c.dist = (HasDistances) ? distance : 0;\r
c.setBootstrap((HasBootstrap) ? bootstrap : 0);\r
\r
- if (c == realroot) {\r
+ if (c == realroot)\r
+ {\r
RootHasDistance = nodehasdistance; // JBPNote This is really UGLY!!!\r
}\r
- } else {\r
+ }\r
+ else\r
+ {\r
// Find a place to put the leaf\r
SequenceNode newnode = new SequenceNode(null, c, nodename,\r
(HasDistances) ? distance : DefDistance,\r
(HasBootstrap) ? bootstrap : DefBootstrap, false);\r
\r
- if (c.right() == null) {\r
+ if (c.right() == null)\r
+ {\r
c.setRight(newnode);\r
- } else {\r
- if (c.left() == null) {\r
+ }\r
+ else\r
+ {\r
+ if (c.left() == null)\r
+ {\r
c.setLeft(newnode);\r
- } else {\r
+ }\r
+ else\r
+ {\r
// Insert a dummy node for polytomy\r
SequenceNode newdummy = new SequenceNode(null, c,\r
null, 0, 0, true);\r
}\r
}\r
\r
- if (ascending) {\r
+ if (ascending)\r
+ {\r
// move back up the tree from preceding closure\r
c = c.AscendTree();\r
\r
- if ((d > -1) && (c == null)) {\r
+ if ((d > -1) && (c == null))\r
+ {\r
Error = ErrorStringrange(Error,\r
"File broke algorithm: Lost place in tree (is there an extra ')' ?)",\r
7, fcp, nf);\r
}\r
}\r
\r
- if (nf.charAt(fcp) == ')') {\r
+ if (nf.charAt(fcp) == ')')\r
+ {\r
d--;\r
ascending = true;\r
- } else {\r
- if (nf.charAt(fcp) == ',') {\r
- if (ascending) {\r
+ }\r
+ else\r
+ {\r
+ if (nf.charAt(fcp) == ',')\r
+ {\r
+ if (ascending)\r
+ {\r
ascending = false;\r
- } else {\r
+ }\r
+ else\r
+ {\r
// Just advance focus, if we need to\r
- if ((c.left() != null) && (!c.left().isLeaf())) {\r
+ if ((c.left() != null) && (!c.left().isLeaf()))\r
+ {\r
c = (SequenceNode) c.left();\r
}\r
}\r
}\r
- // else : We do nothing if ';' is encountered.\r
+\r
+ // else : We do nothing if ';' is encountered.\r
}\r
\r
// Reset new node properties to obvious fakes\r
}\r
}\r
\r
- if (Error != null) {\r
+ if (Error != null)\r
+ {\r
throw (new IOException("NewickFile: " + Error + "\n"));\r
}\r
\r
root = (SequenceNode) root.right().detach(); // remove the imaginary root.\r
\r
- if (!RootHasDistance) {\r
+ if (!RootHasDistance)\r
+ {\r
root.dist = 0;\r
}\r
}\r
\r
- public SequenceNode getTree() {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public SequenceNode getTree()\r
+ {\r
return root;\r
}\r
\r
- public String print() {\r
- synchronized (this) {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String print()\r
+ {\r
+ synchronized (this)\r
+ {\r
StringBuffer tf = new StringBuffer();\r
print(tf, root);\r
\r
}\r
}\r
\r
- public String print(boolean withbootstraps) {\r
- synchronized (this) {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param withbootstraps DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String print(boolean withbootstraps)\r
+ {\r
+ synchronized (this)\r
+ {\r
boolean boots = this.HasBootstrap;\r
this.HasBootstrap = withbootstraps;\r
\r
}\r
}\r
\r
- public String print(boolean withbootstraps, boolean withdists) {\r
- synchronized (this) {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param withbootstraps DOCUMENT ME!\r
+ * @param withdists DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String print(boolean withbootstraps, boolean withdists)\r
+ {\r
+ synchronized (this)\r
+ {\r
boolean dists = this.HasDistances;\r
this.HasDistances = withdists;\r
\r
}\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param withbootstraps DOCUMENT ME!\r
+ * @param withdists DOCUMENT ME!\r
+ * @param printRootInfo DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
public String print(boolean withbootstraps, boolean withdists,\r
- boolean printRootInfo) {\r
- synchronized (this) {\r
+ boolean printRootInfo)\r
+ {\r
+ synchronized (this)\r
+ {\r
boolean rootinfo = printRootInfo;\r
this.printRootInfo = printRootInfo;\r
\r
}\r
}\r
\r
- char getQuoteChar() {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ char getQuoteChar()\r
+ {\r
return QuoteChar;\r
}\r
\r
- char setQuoteChar(char c) {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param c DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ char setQuoteChar(char c)\r
+ {\r
char old = QuoteChar;\r
QuoteChar = c;\r
\r
return old;\r
}\r
\r
- private String nodeName(String name) {\r
- if (NodeSafeName[0].search(name)) {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param name DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ private String nodeName(String name)\r
+ {\r
+ if (NodeSafeName[0].search(name))\r
+ {\r
return QuoteChar + NodeSafeName[1].replaceAll(name) + QuoteChar;\r
- } else {\r
+ }\r
+ else\r
+ {\r
return NodeSafeName[2].replaceAll(name);\r
}\r
}\r
\r
- private String printNodeField(SequenceNode c) {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param c DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ private String printNodeField(SequenceNode c)\r
+ {\r
return ((c.getName() == null) ? "" : nodeName(c.getName())) +\r
((HasBootstrap)\r
? ((c.getBootstrap() > -1) ? (" " + c.getBootstrap()) : "") : "") +\r
((HasDistances) ? (":" + c.dist) : "");\r
}\r
\r
- private String printRootField(SequenceNode root) {\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param root DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ private String printRootField(SequenceNode root)\r
+ {\r
return (printRootInfo)\r
? (((root.getName() == null) ? "" : nodeName(root.getName())) +\r
((HasBootstrap)\r
}\r
\r
// Non recursive call deals with root node properties\r
- public void print(StringBuffer tf, SequenceNode root) {\r
- if (root != null) {\r
- if (root.isLeaf() && printRootInfo) {\r
+ public void print(StringBuffer tf, SequenceNode root)\r
+ {\r
+ if (root != null)\r
+ {\r
+ if (root.isLeaf() && printRootInfo)\r
+ {\r
tf.append(printRootField(root));\r
- } else {\r
- if (root.isDummy()) {\r
+ }\r
+ else\r
+ {\r
+ if (root.isDummy())\r
+ {\r
_print(tf, (SequenceNode) root.right());\r
_print(tf, (SequenceNode) root.left());\r
- } else {\r
+ }\r
+ else\r
+ {\r
tf.append("(");\r
_print(tf, (SequenceNode) root.right());\r
\r
- if (root.left() != null) {\r
+ if (root.left() != null)\r
+ {\r
tf.append(",");\r
}\r
\r
}\r
\r
// Recursive call for non-root nodes\r
- public void _print(StringBuffer tf, SequenceNode c) {\r
- if (c != null) {\r
- if (c.isLeaf()) {\r
+ public void _print(StringBuffer tf, SequenceNode c)\r
+ {\r
+ if (c != null)\r
+ {\r
+ if (c.isLeaf())\r
+ {\r
tf.append(printNodeField(c));\r
- } else {\r
- if (c.isDummy()) {\r
+ }\r
+ else\r
+ {\r
+ if (c.isDummy())\r
+ {\r
_print(tf, (SequenceNode) c.right());\r
_print(tf, (SequenceNode) c.left());\r
- } else {\r
+ }\r
+ else\r
+ {\r
tf.append("(");\r
_print(tf, (SequenceNode) c.right());\r
\r
- if (c.left() != null) {\r
+ if (c.left() != null)\r
+ {\r
tf.append(",");\r
}\r
\r
}\r
\r
// Test\r
- public static void main(String[] args) {\r
- try {\r
+ public static void main(String[] args)\r
+ {\r
+ try\r
+ {\r
File fn = new File(args[0]);\r
\r
StringBuffer newickfile = new StringBuffer();\r
BufferedReader treefile = new BufferedReader(new FileReader(fn));\r
String l;\r
\r
- while ((l = treefile.readLine()) != null) {\r
+ while ((l = treefile.readLine()) != null)\r
+ {\r
newickfile.append(l);\r
}\r
\r
System.out.println(trf.print(false, false));\r
System.out.println("With bootstraps and with distances.\n");\r
System.out.println(trf.print(true, true));\r
- } catch (java.io.IOException e) {\r
+ }\r
+ catch (java.io.IOException e)\r
+ {\r
System.err.println("Exception\n" + e);\r
e.printStackTrace();\r
}\r
git://source.jalview.org / jalview.git / blobdiff