-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-\r
-// NewickFile.java\r
-// Tree I/O\r
-// http://evolution.genetics.washington.edu/phylip/newick_doc.html\r
-// TODO: Implement Basic NHX tag parsing and preservation\r
-// TODO: http://evolution.genetics.wustl.edu/eddy/forester/NHX.html\r
-// TODO: Extended SequenceNodeI to hold parsed NHX strings\r
-package jalview.io;\r
-\r
-import java.io.*;\r
-\r
-import jalview.datamodel.*;\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class NewickFile\r
- extends FileParse\r
-{\r
- SequenceNode root;\r
- private boolean HasBootstrap = false;\r
- private boolean HasDistances = false;\r
- private boolean RootHasDistance = false;\r
-\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
- {\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
- /**\r
- * Creates a new NewickFile object.\r
- *\r
- * @param inStr DOCUMENT ME!\r
- *\r
- * @throws IOException DOCUMENT ME!\r
- */\r
- public NewickFile(String inStr)\r
- throws IOException\r
- {\r
- super(inStr, "Paste");\r
- }\r
-\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)\r
- throws IOException\r
- {\r
- super(inFile, type);\r
- }\r
-\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
- /**\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
- /**\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
- {\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
- {\r
- return ( (Error == null) ? "" : Error) + Er + " at position " + p +\r
- " ( " +\r
- s.substring( ( (p - r) < 0) ? 0 : (p - r),\r
- ( (p + r) > s.length()) ? s.length() : (p + r)) + " )\n";\r
- }\r
-\r
- // @tree annotations\r
- // These are set automatically by the reader\r
- public boolean HasBootstrap()\r
- {\r
- return HasBootstrap;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public boolean HasDistances()\r
- {\r
- return HasDistances;\r
- }\r
-\r
- public boolean HasRootDistance()\r
- {\r
- return RootHasDistance;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @throws IOException DOCUMENT ME!\r
- */\r
- public void parse()\r
- 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
- {\r
- file.append(nf);\r
- }\r
-\r
- nf = file.toString();\r
- }\r
-\r
- root = new SequenceNode();\r
-\r
- SequenceNode realroot = null;\r
- SequenceNode c = root;\r
-\r
- int d = -1;\r
- int cp = 0;\r
- //int flen = nf.length();\r
-\r
- String Error = null;\r
- String nodename = null;\r
-\r
- float DefDistance = (float) 0.001; // @param Default distance for a node - very very small\r
- int DefBootstrap = 0; // @param Default bootstrap for a node\r
-\r
- float distance = DefDistance;\r
- int bootstrap = DefBootstrap;\r
-\r
- boolean ascending = false; // flag indicating that we are leaving the current node\r
-\r
- com.stevesoft.pat.Regex majorsyms = new com.stevesoft.pat.Regex(\r
- "[(\\['),;]");\r
-\r
- while (majorsyms.searchFrom(nf, cp) && (Error == null))\r
- {\r
- int fcp = majorsyms.matchedFrom();\r
-\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
- {\r
- // Skip the comment field\r
- cp = 1 + comment.matchedFrom();\r
- }\r
- else\r
- {\r
- Error = ErrorStringrange(Error, "Unterminated comment", 3,\r
- fcp, nf);\r
- }\r
-\r
- ;\r
-\r
- break;\r
-\r
- case '(':\r
-\r
- // ascending should not be set\r
- // New Internal node\r
- if (ascending)\r
- {\r
- Error = ErrorStringrange(Error, "Unexpected '('", 7, fcp, nf);\r
-\r
- continue;\r
- }\r
-\r
- ;\r
- d++;\r
-\r
- if (c.right() == null)\r
- {\r
- c.setRight(new SequenceNode(null, c, null, DefDistance,\r
- DefBootstrap, false));\r
- c = (SequenceNode) c.right();\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
- tmpn.SetChildren(c.left(), c.right());\r
- c.setRight(tmpn);\r
- }\r
-\r
- c.setLeft(new SequenceNode(null, c, null, DefDistance,\r
- DefBootstrap, false));\r
- c = (SequenceNode) c.left();\r
- }\r
-\r
- if (realroot == null)\r
- {\r
- realroot = c;\r
- }\r
-\r
- nodename = null;\r
- distance = DefDistance;\r
- bootstrap = DefBootstrap;\r
- cp = fcp + 1;\r
-\r
- break;\r
-\r
- // Deal with quoted fields\r
- case '\'':\r
-\r
- com.stevesoft.pat.Regex qnodename = new com.stevesoft.pat.Regex(\r
- "([^']|'')+'");\r
-\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
- }\r
- else\r
- {\r
- Error = ErrorStringrange(Error,\r
- "Unterminated quotes for nodename", 7, fcp,\r
- nf);\r
- }\r
-\r
- break;\r
-\r
- case ';':\r
-\r
- if (d != -1)\r
- {\r
- Error = ErrorStringrange(Error,\r
- "Wayward semicolon (depth=" + d + ")", 7,\r
- fcp, nf);\r
- }\r
-\r
- // cp advanced at the end of default\r
- default:\r
-\r
- // Parse simpler field strings\r
- String fstring = nf.substring(cp, fcp);\r
- com.stevesoft.pat.Regex uqnodename = new com.stevesoft.pat.Regex(\r
- "\\b([^' :;\\](),]+)");\r
- com.stevesoft.pat.Regex nbootstrap = new com.stevesoft.pat.Regex(\r
- "\\S+([0-9+]+)\\S*:");\r
- com.stevesoft.pat.Regex ndist = new com.stevesoft.pat.Regex(\r
- ":([-0-9Ee.+]+)");\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
- {\r
- if (ReplaceUnderscores)\r
- {\r
- nodename = uqnodename.stringMatched(1).replace('_',\r
- ' ');\r
- }\r
- else\r
- {\r
- nodename = uqnodename.stringMatched(1);\r
- }\r
- }\r
- else\r
- {\r
- Error = ErrorStringrange(Error,\r
- "File has broken algorithm - overwritten nodename",\r
- 10, fcp, nf);\r
- }\r
- }\r
-\r
- if (nbootstrap.search(fstring) &&\r
- (nbootstrap.matchedFrom(1) > (uqnodename.matchedFrom(1) +\r
- uqnodename.stringMatched().length())))\r
- {\r
- try\r
- {\r
- bootstrap = (new Integer(nbootstrap.stringMatched(1))).intValue();\r
- HasBootstrap = true;\r
- }\r
- catch (Exception e)\r
- {\r
- Error = ErrorStringrange(Error,\r
- "Can't parse bootstrap value", 4,\r
- cp + nbootstrap.matchedFrom(), nf);\r
- }\r
- }\r
-\r
- boolean nodehasdistance = false;\r
-\r
- if (ndist.search(fstring))\r
- {\r
- try\r
- {\r
- distance = (new Float(ndist.stringMatched(1))).floatValue();\r
- HasDistances = true;\r
- nodehasdistance = true;\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
- {\r
- // Write node info here\r
- c.setName(nodename);\r
- // Trees without distances still need a render distance\r
- c.dist = (HasDistances) ? distance : DefDistance;\r
- // be consistent for internal bootstrap defaults too\r
- c.setBootstrap( (HasBootstrap) ? bootstrap : DefBootstrap);\r
- if (c == realroot)\r
- {\r
- RootHasDistance = nodehasdistance; // JBPNote This is really UGLY!!! Ensure root node gets its given distance\r
- }\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
- {\r
- c.setRight(newnode);\r
- }\r
- else\r
- {\r
- if (c.left() == null)\r
- {\r
- c.setLeft(newnode);\r
- }\r
- else\r
- {\r
- // Insert a dummy node for polytomy\r
- // dummy nodes have distances\r
- SequenceNode newdummy = new SequenceNode(null, c,\r
- null, (HasDistances ? 0 : DefDistance), 0, true);\r
- newdummy.SetChildren(c.left(), newnode);\r
- c.setLeft(newdummy);\r
- }\r
- }\r
- }\r
-\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
- {\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
- {\r
- d--;\r
- ascending = true;\r
- }\r
- else\r
- {\r
- if (nf.charAt(fcp) == ',')\r
- {\r
- if (ascending)\r
- {\r
- ascending = false;\r
- }\r
- else\r
- {\r
- // Just advance focus, if we need to\r
- if ( (c.left() != null) && (!c.left().isLeaf()))\r
- {\r
- c = (SequenceNode) c.left();\r
- }\r
- }\r
- }\r
-\r
- // else : We do nothing if ';' is encountered.\r
- }\r
-\r
- // Reset new node properties to obvious fakes\r
- nodename = null;\r
- distance = DefDistance;\r
- bootstrap = DefBootstrap;\r
-\r
- cp = fcp + 1;\r
- }\r
- }\r
-\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
- {\r
- root.dist = (HasDistances) ? 0 : DefDistance;\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public SequenceNode getTree()\r
- {\r
- return root;\r
- }\r
-\r
- /**\r
- * Generate a newick format tree according to internal flags\r
- * for bootstraps, distances and root distances.\r
- *\r
- * @return new hampshire tree in a single line\r
- */\r
- public String print()\r
- {\r
- synchronized (this)\r
- {\r
- StringBuffer tf = new StringBuffer();\r
- print(tf, root);\r
-\r
- return (tf.append(";").toString());\r
- }\r
- }\r
-\r
- /**\r
- *\r
- *\r
- * Generate a newick format tree according to internal flags\r
- * for distances and root distances and user specificied writing of\r
- * bootstraps.\r
- * @param withbootstraps controls if bootstrap values are explicitly written.\r
- *\r
- * @return new hampshire tree in a single line\r
- */\r
- public String print(boolean withbootstraps)\r
- {\r
- synchronized (this)\r
- {\r
- boolean boots = this.HasBootstrap;\r
- this.HasBootstrap = withbootstraps;\r
-\r
- String rv = print();\r
- this.HasBootstrap = boots;\r
-\r
- return rv;\r
- }\r
- }\r
-\r
- /**\r
- *\r
- * Generate newick format tree according to internal flags\r
- * for writing root node distances.\r
- *\r
- * @param withbootstraps explicitly write bootstrap values\r
- * @param withdists explicitly write distances\r
- *\r
- * @return new hampshire tree in a single line\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
- String rv = print(withbootstraps);\r
- this.HasDistances = dists;\r
-\r
- return rv;\r
- }\r
- }\r
-\r
- /**\r
- * Generate newick format tree according to user specified flags\r
- *\r
- * @param withbootstraps explicitly write bootstrap values\r
- * @param withdists explicitly write distances\r
- * @param printRootInfo explicitly write root distance\r
- *\r
- * @return new hampshire tree in a single line\r
- */\r
- public String print(boolean withbootstraps, boolean withdists,\r
- boolean printRootInfo)\r
- {\r
- synchronized (this)\r
- {\r
- boolean rootinfo = printRootInfo;\r
- this.printRootInfo = printRootInfo;\r
-\r
- String rv = print(withbootstraps, withdists);\r
- this.printRootInfo = rootinfo;\r
-\r
- return rv;\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- char getQuoteChar()\r
- {\r
- return QuoteChar;\r
- }\r
-\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
- /**\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
- }\r
- else\r
- {\r
- return NodeSafeName[2].replaceAll(name);\r
- }\r
- }\r
-\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
- /**\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
- ? ( (root.getBootstrap() > -1) ? (" " + root.getBootstrap()) : "") :\r
- "") +\r
- ( (RootHasDistance) ? (":" + root.dist) : "")) : "";\r
- }\r
-\r
- // Non recursive call deals with root node properties\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
- }\r
- else\r
- {\r
- if (root.isDummy())\r
- {\r
- _print(tf, (SequenceNode) root.right());\r
- _print(tf, (SequenceNode) root.left());\r
- }\r
- else\r
- {\r
- tf.append("(");\r
- _print(tf, (SequenceNode) root.right());\r
-\r
- if (root.left() != null)\r
- {\r
- tf.append(",");\r
- }\r
-\r
- _print(tf, (SequenceNode) root.left());\r
- tf.append(")" + printRootField(root));\r
- }\r
- }\r
- }\r
- }\r
-\r
- // Recursive call for non-root nodes\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
- }\r
- else\r
- {\r
- if (c.isDummy())\r
- {\r
- _print(tf, (SequenceNode) c.left());\r
- if (c.left() != null)\r
- {\r
- tf.append(",");\r
- }\r
- _print(tf, (SequenceNode) c.right());\r
- }\r
- else\r
- {\r
- tf.append("(");\r
- _print(tf, (SequenceNode) c.right());\r
-\r
- if (c.left() != null)\r
- {\r
- tf.append(",");\r
- }\r
-\r
- _print(tf, (SequenceNode) c.left());\r
- tf.append(")" + printNodeField(c));\r
- }\r
- }\r
- }\r
- }\r
-\r
- // Test\r
- public static void main(String[] args)\r
- {\r
- try\r
- {\r
- if (args == null || args.length != 1)\r
- {\r
- System.err.println(\r
- "Takes one argument - file name of a newick tree file.");\r
- System.exit(0);\r
- }\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
- {\r
- newickfile.append(l);\r
- }\r
-\r
- treefile.close();\r
- System.out.println("Read file :\n");\r
-\r
- NewickFile trf = new NewickFile(args[0], "File");\r
- trf.parse();\r
- System.out.println("Original file :\n");\r
-\r
- com.stevesoft.pat.Regex nonl = new com.stevesoft.pat.Regex("\n+", "");\r
- System.out.println(nonl.replaceAll(newickfile.toString()) + "\n");\r
-\r
- System.out.println("Parsed file.\n");\r
- System.out.println("Default output type for original input.\n");\r
- System.out.println(trf.print());\r
- System.out.println("Without bootstraps.\n");\r
- System.out.println(trf.print(false));\r
- System.out.println("Without distances.\n");\r
- System.out.println(trf.print(true, false));\r
- System.out.println("Without bootstraps but with distanecs.\n");\r
- System.out.println(trf.print(false, true));\r
- System.out.println("Without bootstraps or distanecs.\n");\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
- }\r
- catch (java.io.IOException e)\r
- {\r
- System.err.println("Exception\n" + e);\r
- e.printStackTrace();\r
- }\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ */
+
+// NewickFile.java
+// Tree I/O
+// http://evolution.genetics.washington.edu/phylip/newick_doc.html
+// TODO: Implement Basic NHX tag parsing and preservation
+// TODO: http://evolution.genetics.wustl.edu/eddy/forester/NHX.html
+// TODO: Extended SequenceNodeI to hold parsed NHX strings
+package jalview.io;
+
+import java.io.*;
+
+import jalview.datamodel.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class NewickFile
+ extends FileParse
+{
+ SequenceNode root;
+ private boolean HasBootstrap = false;
+ private boolean HasDistances = false;
+ private boolean RootHasDistance = false;
+
+ // File IO Flags
+ boolean ReplaceUnderscores = false;
+ boolean printRootInfo = false;
+ private com.stevesoft.pat.Regex[] NodeSafeName = new com.stevesoft.pat.Regex[]
+ {
+ new com.stevesoft.pat.Regex().perlCode("m/[\\[,:'()]/"), // test for requiring quotes
+ new com.stevesoft.pat.Regex().perlCode("s/'/''/"), // escaping quote characters
+ new com.stevesoft.pat.Regex().perlCode("s/\\/w/_/") // unqoted whitespace transformation
+ };
+ char QuoteChar = '\'';
+
+ /**
+ * Creates a new NewickFile object.
+ *
+ * @param inStr DOCUMENT ME!
+ *
+ * @throws IOException DOCUMENT ME!
+ */
+ public NewickFile(String inStr)
+ throws IOException
+ {
+ super(inStr, "Paste");
+ }
+
+ /**
+ * Creates a new NewickFile object.
+ *
+ * @param inFile DOCUMENT ME!
+ * @param type DOCUMENT ME!
+ *
+ * @throws IOException DOCUMENT ME!
+ */
+ public NewickFile(String inFile, String type)
+ throws IOException
+ {
+ super(inFile, type);
+ }
+
+ /**
+ * Creates a new NewickFile object.
+ *
+ * @param newtree DOCUMENT ME!
+ */
+ public NewickFile(SequenceNode newtree)
+ {
+ root = newtree;
+ }
+
+ /**
+ * Creates a new NewickFile object.
+ *
+ * @param newtree DOCUMENT ME!
+ * @param bootstrap DOCUMENT ME!
+ */
+ public NewickFile(SequenceNode newtree, boolean bootstrap)
+ {
+ HasBootstrap = bootstrap;
+ root = newtree;
+ }
+
+ /**
+ * Creates a new NewickFile object.
+ *
+ * @param newtree DOCUMENT ME!
+ * @param bootstrap DOCUMENT ME!
+ * @param distances DOCUMENT ME!
+ */
+ public NewickFile(SequenceNode newtree, boolean bootstrap, boolean distances)
+ {
+ root = newtree;
+ HasBootstrap = bootstrap;
+ HasDistances = distances;
+ }
+
+ /**
+ * Creates a new NewickFile object.
+ *
+ * @param newtree DOCUMENT ME!
+ * @param bootstrap DOCUMENT ME!
+ * @param distances DOCUMENT ME!
+ * @param rootdistance DOCUMENT ME!
+ */
+ public NewickFile(SequenceNode newtree, boolean bootstrap,
+ boolean distances, boolean rootdistance)
+ {
+ root = newtree;
+ HasBootstrap = bootstrap;
+ HasDistances = distances;
+ RootHasDistance = rootdistance;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param Error DOCUMENT ME!
+ * @param Er DOCUMENT ME!
+ * @param r DOCUMENT ME!
+ * @param p DOCUMENT ME!
+ * @param s DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ private String ErrorStringrange(String Error, String Er, int r, int p,
+ String s)
+ {
+ return ( (Error == null) ? "" : Error) + Er + " at position " + p +
+ " ( " +
+ s.substring( ( (p - r) < 0) ? 0 : (p - r),
+ ( (p + r) > s.length()) ? s.length() : (p + r)) + " )\n";
+ }
+
+ // @tree annotations
+ // These are set automatically by the reader
+ public boolean HasBootstrap()
+ {
+ return HasBootstrap;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean HasDistances()
+ {
+ return HasDistances;
+ }
+
+ public boolean HasRootDistance()
+ {
+ return RootHasDistance;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws IOException DOCUMENT ME!
+ */
+ public void parse()
+ throws IOException
+ {
+ String nf;
+
+ { // fill nf with complete tree file
+
+ StringBuffer file = new StringBuffer();
+
+ while ( (nf = nextLine()) != null)
+ {
+ file.append(nf);
+ }
+
+ nf = file.toString();
+ }
+
+ root = new SequenceNode();
+
+ SequenceNode realroot = null;
+ SequenceNode c = root;
+
+ int d = -1;
+ int cp = 0;
+ //int flen = nf.length();
+
+ String Error = null;
+ String nodename = null;
+
+ float DefDistance = (float) 0.001; // @param Default distance for a node - very very small
+ int DefBootstrap = 0; // @param Default bootstrap for a node
+
+ float distance = DefDistance;
+ int bootstrap = DefBootstrap;
+
+ boolean ascending = false; // flag indicating that we are leaving the current node
+
+ com.stevesoft.pat.Regex majorsyms = new com.stevesoft.pat.Regex(
+ "[(\\['),;]");
+
+ while (majorsyms.searchFrom(nf, cp) && (Error == null))
+ {
+ int fcp = majorsyms.matchedFrom();
+
+ switch (nf.charAt(fcp))
+ {
+ case '[': // Comment or structured/extended NH format info
+
+ com.stevesoft.pat.Regex comment = new com.stevesoft.pat.Regex(
+ "]");
+
+ if (comment.searchFrom(nf, fcp))
+ {
+ // Skip the comment field
+ cp = 1 + comment.matchedFrom();
+ }
+ else
+ {
+ Error = ErrorStringrange(Error, "Unterminated comment", 3,
+ fcp, nf);
+ }
+
+ ;
+
+ break;
+
+ case '(':
+
+ // ascending should not be set
+ // New Internal node
+ if (ascending)
+ {
+ Error = ErrorStringrange(Error, "Unexpected '('", 7, fcp, nf);
+
+ continue;
+ }
+
+ ;
+ d++;
+
+ if (c.right() == null)
+ {
+ c.setRight(new SequenceNode(null, c, null, DefDistance,
+ DefBootstrap, false));
+ c = (SequenceNode) c.right();
+ }
+ else
+ {
+ if (c.left() != null)
+ {
+ // Dummy node for polytomy - keeps c.left free for new node
+ SequenceNode tmpn = new SequenceNode(null, c, null, 0,
+ 0, true);
+ tmpn.SetChildren(c.left(), c.right());
+ c.setRight(tmpn);
+ }
+
+ c.setLeft(new SequenceNode(null, c, null, DefDistance,
+ DefBootstrap, false));
+ c = (SequenceNode) c.left();
+ }
+
+ if (realroot == null)
+ {
+ realroot = c;
+ }
+
+ nodename = null;
+ distance = DefDistance;
+ bootstrap = DefBootstrap;
+ cp = fcp + 1;
+
+ break;
+
+ // Deal with quoted fields
+ case '\'':
+
+ com.stevesoft.pat.Regex qnodename = new com.stevesoft.pat.Regex(
+ "([^']|'')+'");
+
+ if (qnodename.searchFrom(nf, fcp))
+ {
+ int nl = qnodename.stringMatched().length();
+ nodename = new String(qnodename.stringMatched().substring(0,
+ nl - 1));
+ cp = fcp + nl + 1;
+ }
+ else
+ {
+ Error = ErrorStringrange(Error,
+ "Unterminated quotes for nodename", 7, fcp,
+ nf);
+ }
+
+ break;
+
+ case ';':
+
+ if (d != -1)
+ {
+ Error = ErrorStringrange(Error,
+ "Wayward semicolon (depth=" + d + ")", 7,
+ fcp, nf);
+ }
+
+ // cp advanced at the end of default
+ default:
+
+ // Parse simpler field strings
+ String fstring = nf.substring(cp, fcp);
+ com.stevesoft.pat.Regex uqnodename = new com.stevesoft.pat.Regex(
+ "\\b([^' :;\\](),]+)");
+ com.stevesoft.pat.Regex nbootstrap = new com.stevesoft.pat.Regex(
+ "\\S+([0-9+]+)\\S*:");
+ com.stevesoft.pat.Regex ndist = new com.stevesoft.pat.Regex(
+ ":([-0-9Ee.+]+)");
+
+ if (uqnodename.search(fstring) &&
+ ( (uqnodename.matchedFrom(1) == 0) ||
+ (fstring.charAt(uqnodename.matchedFrom(1) - 1) != ':'))) // JBPNote HACK!
+ {
+ if (nodename == null)
+ {
+ if (ReplaceUnderscores)
+ {
+ nodename = uqnodename.stringMatched(1).replace('_',
+ ' ');
+ }
+ else
+ {
+ nodename = uqnodename.stringMatched(1);
+ }
+ }
+ else
+ {
+ Error = ErrorStringrange(Error,
+ "File has broken algorithm - overwritten nodename",
+ 10, fcp, nf);
+ }
+ }
+
+ if (nbootstrap.search(fstring) &&
+ (nbootstrap.matchedFrom(1) > (uqnodename.matchedFrom(1) +
+ uqnodename.stringMatched().length())))
+ {
+ try
+ {
+ bootstrap = (new Integer(nbootstrap.stringMatched(1))).intValue();
+ HasBootstrap = true;
+ }
+ catch (Exception e)
+ {
+ Error = ErrorStringrange(Error,
+ "Can't parse bootstrap value", 4,
+ cp + nbootstrap.matchedFrom(), nf);
+ }
+ }
+
+ boolean nodehasdistance = false;
+
+ if (ndist.search(fstring))
+ {
+ try
+ {
+ distance = (new Float(ndist.stringMatched(1))).floatValue();
+ HasDistances = true;
+ nodehasdistance = true;
+ }
+ catch (Exception e)
+ {
+ Error = ErrorStringrange(Error,
+ "Can't parse node distance value", 7,
+ cp + ndist.matchedFrom(), nf);
+ }
+ }
+
+ if (ascending)
+ {
+ // Write node info here
+ c.setName(nodename);
+ // Trees without distances still need a render distance
+ c.dist = (HasDistances) ? distance : DefDistance;
+ // be consistent for internal bootstrap defaults too
+ c.setBootstrap( (HasBootstrap) ? bootstrap : DefBootstrap);
+ if (c == realroot)
+ {
+ RootHasDistance = nodehasdistance; // JBPNote This is really UGLY!!! Ensure root node gets its given distance
+ }
+ }
+ else
+ {
+ // Find a place to put the leaf
+ SequenceNode newnode = new SequenceNode(null, c, nodename,
+ (HasDistances) ? distance : DefDistance,
+ (HasBootstrap) ? bootstrap : DefBootstrap, false);
+
+ if (c.right() == null)
+ {
+ c.setRight(newnode);
+ }
+ else
+ {
+ if (c.left() == null)
+ {
+ c.setLeft(newnode);
+ }
+ else
+ {
+ // Insert a dummy node for polytomy
+ // dummy nodes have distances
+ SequenceNode newdummy = new SequenceNode(null, c,
+ null, (HasDistances ? 0 : DefDistance), 0, true);
+ newdummy.SetChildren(c.left(), newnode);
+ c.setLeft(newdummy);
+ }
+ }
+ }
+
+ if (ascending)
+ {
+ // move back up the tree from preceding closure
+ c = c.AscendTree();
+
+ if ( (d > -1) && (c == null))
+ {
+ Error = ErrorStringrange(Error,
+ "File broke algorithm: Lost place in tree (is there an extra ')' ?)",
+ 7, fcp, nf);
+ }
+ }
+
+ if (nf.charAt(fcp) == ')')
+ {
+ d--;
+ ascending = true;
+ }
+ else
+ {
+ if (nf.charAt(fcp) == ',')
+ {
+ if (ascending)
+ {
+ ascending = false;
+ }
+ else
+ {
+ // Just advance focus, if we need to
+ if ( (c.left() != null) && (!c.left().isLeaf()))
+ {
+ c = (SequenceNode) c.left();
+ }
+ }
+ }
+
+ // else : We do nothing if ';' is encountered.
+ }
+
+ // Reset new node properties to obvious fakes
+ nodename = null;
+ distance = DefDistance;
+ bootstrap = DefBootstrap;
+
+ cp = fcp + 1;
+ }
+ }
+
+ if (Error != null)
+ {
+ throw (new IOException("NewickFile: " + Error + "\n"));
+ }
+ if (root==null)
+ {
+ throw (new IOException("NewickFile: No Tree read in\n"));
+ }
+ // THe next line is failing for topali trees - not sure why yet. if (root.right()!=null && root.isDummy())
+ root = (SequenceNode) root.right().detach(); // remove the imaginary root.
+
+ if (!RootHasDistance)
+ {
+ root.dist = (HasDistances) ? 0 : DefDistance;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public SequenceNode getTree()
+ {
+ return root;
+ }
+
+ /**
+ * Generate a newick format tree according to internal flags
+ * for bootstraps, distances and root distances.
+ *
+ * @return new hampshire tree in a single line
+ */
+ public String print()
+ {
+ synchronized (this)
+ {
+ StringBuffer tf = new StringBuffer();
+ print(tf, root);
+
+ return (tf.append(";").toString());
+ }
+ }
+
+ /**
+ *
+ *
+ * Generate a newick format tree according to internal flags
+ * for distances and root distances and user specificied writing of
+ * bootstraps.
+ * @param withbootstraps controls if bootstrap values are explicitly written.
+ *
+ * @return new hampshire tree in a single line
+ */
+ public String print(boolean withbootstraps)
+ {
+ synchronized (this)
+ {
+ boolean boots = this.HasBootstrap;
+ this.HasBootstrap = withbootstraps;
+
+ String rv = print();
+ this.HasBootstrap = boots;
+
+ return rv;
+ }
+ }
+
+ /**
+ *
+ * Generate newick format tree according to internal flags
+ * for writing root node distances.
+ *
+ * @param withbootstraps explicitly write bootstrap values
+ * @param withdists explicitly write distances
+ *
+ * @return new hampshire tree in a single line
+ */
+ public String print(boolean withbootstraps, boolean withdists)
+ {
+ synchronized (this)
+ {
+ boolean dists = this.HasDistances;
+ this.HasDistances = withdists;
+
+ String rv = print(withbootstraps);
+ this.HasDistances = dists;
+
+ return rv;
+ }
+ }
+
+ /**
+ * Generate newick format tree according to user specified flags
+ *
+ * @param withbootstraps explicitly write bootstrap values
+ * @param withdists explicitly write distances
+ * @param printRootInfo explicitly write root distance
+ *
+ * @return new hampshire tree in a single line
+ */
+ public String print(boolean withbootstraps, boolean withdists,
+ boolean printRootInfo)
+ {
+ synchronized (this)
+ {
+ boolean rootinfo = printRootInfo;
+ this.printRootInfo = printRootInfo;
+
+ String rv = print(withbootstraps, withdists);
+ this.printRootInfo = rootinfo;
+
+ return rv;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ char getQuoteChar()
+ {
+ return QuoteChar;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param c DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ char setQuoteChar(char c)
+ {
+ char old = QuoteChar;
+ QuoteChar = c;
+
+ return old;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param name DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ private String nodeName(String name)
+ {
+ if (NodeSafeName[0].search(name))
+ {
+ return QuoteChar + NodeSafeName[1].replaceAll(name) + QuoteChar;
+ }
+ else
+ {
+ return NodeSafeName[2].replaceAll(name);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param c DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ private String printNodeField(SequenceNode c)
+ {
+ return ( (c.getName() == null) ? "" : nodeName(c.getName())) +
+ ( (HasBootstrap)
+ ? ( (c.getBootstrap() > -1) ? (" " + c.getBootstrap()) : "") : "") +
+ ( (HasDistances) ? (":" + c.dist) : "");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param root DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ private String printRootField(SequenceNode root)
+ {
+ return (printRootInfo)
+ ? ( ( (root.getName() == null) ? "" : nodeName(root.getName())) +
+ ( (HasBootstrap)
+ ? ( (root.getBootstrap() > -1) ? (" " + root.getBootstrap()) : "") :
+ "") +
+ ( (RootHasDistance) ? (":" + root.dist) : "")) : "";
+ }
+
+ // Non recursive call deals with root node properties
+ public void print(StringBuffer tf, SequenceNode root)
+ {
+ if (root != null)
+ {
+ if (root.isLeaf() && printRootInfo)
+ {
+ tf.append(printRootField(root));
+ }
+ else
+ {
+ if (root.isDummy())
+ {
+ _print(tf, (SequenceNode) root.right());
+ _print(tf, (SequenceNode) root.left());
+ }
+ else
+ {
+ tf.append("(");
+ _print(tf, (SequenceNode) root.right());
+
+ if (root.left() != null)
+ {
+ tf.append(",");
+ }
+
+ _print(tf, (SequenceNode) root.left());
+ tf.append(")" + printRootField(root));
+ }
+ }
+ }
+ }
+
+ // Recursive call for non-root nodes
+ public void _print(StringBuffer tf, SequenceNode c)
+ {
+ if (c != null)
+ {
+ if (c.isLeaf())
+ {
+ tf.append(printNodeField(c));
+ }
+ else
+ {
+ if (c.isDummy())
+ {
+ _print(tf, (SequenceNode) c.left());
+ if (c.left() != null)
+ {
+ tf.append(",");
+ }
+ _print(tf, (SequenceNode) c.right());
+ }
+ else
+ {
+ tf.append("(");
+ _print(tf, (SequenceNode) c.right());
+
+ if (c.left() != null)
+ {
+ tf.append(",");
+ }
+
+ _print(tf, (SequenceNode) c.left());
+ tf.append(")" + printNodeField(c));
+ }
+ }
+ }
+ }
+
+ // Test
+ public static void main(String[] args)
+ {
+ try
+ {
+ if (args == null || args.length != 1)
+ {
+ System.err.println(
+ "Takes one argument - file name of a newick tree file.");
+ System.exit(0);
+ }
+
+ File fn = new File(args[0]);
+
+ StringBuffer newickfile = new StringBuffer();
+ BufferedReader treefile = new BufferedReader(new FileReader(fn));
+ String l;
+
+ while ( (l = treefile.readLine()) != null)
+ {
+ newickfile.append(l);
+ }
+
+ treefile.close();
+ System.out.println("Read file :\n");
+
+ NewickFile trf = new NewickFile(args[0], "File");
+ trf.parse();
+ System.out.println("Original file :\n");
+
+ com.stevesoft.pat.Regex nonl = new com.stevesoft.pat.Regex("\n+", "");
+ System.out.println(nonl.replaceAll(newickfile.toString()) + "\n");
+
+ System.out.println("Parsed file.\n");
+ System.out.println("Default output type for original input.\n");
+ System.out.println(trf.print());
+ System.out.println("Without bootstraps.\n");
+ System.out.println(trf.print(false));
+ System.out.println("Without distances.\n");
+ System.out.println(trf.print(true, false));
+ System.out.println("Without bootstraps but with distanecs.\n");
+ System.out.println(trf.print(false, true));
+ System.out.println("Without bootstraps or distanecs.\n");
+ System.out.println(trf.print(false, false));
+ System.out.println("With bootstraps and with distances.\n");
+ System.out.println(trf.print(true, true));
+ }
+ catch (java.io.IOException e)
+ {
+ System.err.println("Exception\n" + e);
+ e.printStackTrace();
+ }
+ }
+}
git://source.jalview.org / jalview.git / commitdiff