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
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
- 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
- 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
- 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
+ /**\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
root = newtree;\r
HasBootstrap = bootstrap;\r
HasDistances = distances;\r
RootHasDistance = rootdistance;\r
}\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
private String ErrorStringrange(String Error, String Er, int r, int p,\r
return ((Error == null) ? "" : Error) + Er + " at position " + p +\r
" ( " +\r
s.substring(((p - r) < 0) ? 0 : (p - r),\r
return ((Error == null) ? "" : Error) + Er + " at position " + p +\r
" ( " +\r
s.substring(((p - r) < 0) ? 0 : (p - 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
case '[': // Comment or structured/extended NH format info\r
\r
com.stevesoft.pat.Regex comment = new com.stevesoft.pat.Regex(\r
"]");\r
\r
Error = ErrorStringrange(Error, "Unterminated comment", 3,\r
fcp, nf);\r
}\r
Error = ErrorStringrange(Error, "Unterminated comment", 3,\r
fcp, nf);\r
}\r
Error = ErrorStringrange(Error, "Unexpected '('", 7, fcp, nf);\r
\r
continue;\r
Error = ErrorStringrange(Error, "Unexpected '('", 7, fcp, nf);\r
\r
continue;\r
c.setRight(new SequenceNode(null, c, null, DefDistance,\r
DefBootstrap, false));\r
c = (SequenceNode) c.right();\r
c.setRight(new SequenceNode(null, c, null, DefDistance,\r
DefBootstrap, false));\r
c = (SequenceNode) c.right();\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
// Dummy node for polytomy - keeps c.left free for new node\r
SequenceNode tmpn = new SequenceNode(null, c, null, 0,\r
0, true);\r
int nl = qnodename.stringMatched().length();\r
nodename = new String(qnodename.stringMatched().substring(0,\r
nl - 1));\r
cp = fcp + nl + 1;\r
int nl = qnodename.stringMatched().length();\r
nodename = new String(qnodename.stringMatched().substring(0,\r
nl - 1));\r
cp = fcp + nl + 1;\r
Error = ErrorStringrange(Error,\r
"Unterminated quotes for nodename", 7, fcp, nf);\r
}\r
Error = ErrorStringrange(Error,\r
"Unterminated quotes for nodename", 7, fcp, nf);\r
}\r
Error = ErrorStringrange(Error,\r
"Wayward semicolon (depth=" + d + ")", 7, fcp, nf);\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
if (uqnodename.search(fstring) &&\r
((uqnodename.matchedFrom(1) == 0) ||\r
(fstring.charAt(uqnodename.matchedFrom(1) - 1) != ':'))) // JBPNote HACK!\r
Error = ErrorStringrange(Error,\r
"File has broken algorithm - overwritten nodename",\r
10, fcp, nf);\r
Error = ErrorStringrange(Error,\r
"File has broken algorithm - overwritten nodename",\r
10, fcp, nf);\r
Error = ErrorStringrange(Error,\r
"Can't parse bootstrap value", 4,\r
cp + nbootstrap.matchedFrom(), nf);\r
Error = ErrorStringrange(Error,\r
"Can't parse bootstrap value", 4,\r
cp + nbootstrap.matchedFrom(), nf);\r
Error = ErrorStringrange(Error,\r
"Can't parse node distance value", 7,\r
cp + ndist.matchedFrom(), nf);\r
}\r
}\r
\r
Error = ErrorStringrange(Error,\r
"Can't parse node distance value", 7,\r
cp + ndist.matchedFrom(), nf);\r
}\r
}\r
\r
// Write node info here\r
c.setName(nodename);\r
c.dist = (HasDistances) ? distance : 0;\r
c.setBootstrap((HasBootstrap) ? bootstrap : 0);\r
\r
// Write node info here\r
c.setName(nodename);\r
c.dist = (HasDistances) ? distance : 0;\r
c.setBootstrap((HasBootstrap) ? bootstrap : 0);\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
// 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
// Insert a dummy node for polytomy\r
SequenceNode newdummy = new SequenceNode(null, c,\r
null, 0, 0, true);\r
// Insert a dummy node for polytomy\r
SequenceNode newdummy = new SequenceNode(null, c,\r
null, 0, 0, true);\r
Error = ErrorStringrange(Error,\r
"File broke algorithm: Lost place in tree (is there an extra ')' ?)",\r
7, fcp, nf);\r
}\r
}\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
throw (new IOException("NewickFile: " + Error + "\n"));\r
}\r
\r
root = (SequenceNode) root.right().detach(); // remove the imaginary root.\r
\r
throw (new IOException("NewickFile: " + Error + "\n"));\r
}\r
\r
root = (SequenceNode) root.right().detach(); // remove the imaginary root.\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
- 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
- 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 ((c.getName() == null) ? "" : nodeName(c.getName())) +\r
((HasBootstrap)\r
? ((c.getBootstrap() > -1) ? (" " + c.getBootstrap()) : "") : "") +\r
((HasDistances) ? (":" + c.dist) : "");\r
}\r
\r
return ((c.getName() == null) ? "" : nodeName(c.getName())) +\r
((HasBootstrap)\r
? ((c.getBootstrap() > -1) ? (" " + c.getBootstrap()) : "") : "") +\r
((HasDistances) ? (":" + c.dist) : "");\r
}\r
\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
_print(tf, (SequenceNode) root.right());\r
_print(tf, (SequenceNode) root.left());\r
_print(tf, (SequenceNode) root.right());\r
_print(tf, (SequenceNode) root.left());\r
_print(tf, (SequenceNode) c.right());\r
_print(tf, (SequenceNode) c.left());\r
_print(tf, (SequenceNode) c.right());\r
_print(tf, (SequenceNode) c.left());\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
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
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
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