X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FNewickFile.java;h=027390a1e8fc6facd4f7ae1e5852df515acacf38;hb=d1e20f6a5654ea6baf378afa3277b4e751c69a96;hp=d6966055f5c4bddbf732b845cac00d56a131f774;hpb=f24dacb1da56fccf05d684e2f4899facec2aecf7;p=jalview.git
diff --git a/src/jalview/io/NewickFile.java b/src/jalview/io/NewickFile.java
index d696605..027390a 100755
--- a/src/jalview/io/NewickFile.java
+++ b/src/jalview/io/NewickFile.java
@@ -1,768 +1,992 @@
/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 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
-package jalview.io;
-
-import jalview.datamodel.*;
-
-import java.io.*;
-
-
-/**
- * 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;
- }
-
- /**
- * 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) 0.00001; // @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(
- ":([-0-9.+]+)");
-
- 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);
- c.dist = (HasDistances) ? distance : 0;
- c.setBootstrap((HasBootstrap) ? bootstrap : 0);
-
- if (c == realroot)
- {
- RootHasDistance = nodehasdistance; // JBPNote This is really UGLY!!!
- }
- }
- 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
- SequenceNode newdummy = new SequenceNode(null, c,
- null, 0, 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"));
- }
-
- root = (SequenceNode) root.right().detach(); // remove the imaginary root.
-
- if (!RootHasDistance)
- {
- root.dist = 0;
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public SequenceNode getTree()
- {
- return root;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String print()
- {
- synchronized (this)
- {
- StringBuffer tf = new StringBuffer();
- print(tf, root);
-
- return (tf.append(";").toString());
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param withbootstraps DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String print(boolean withbootstraps)
- {
- synchronized (this)
- {
- boolean boots = this.HasBootstrap;
- this.HasBootstrap = withbootstraps;
-
- String rv = print();
- this.HasBootstrap = boots;
-
- return rv;
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param withbootstraps DOCUMENT ME!
- * @param withdists DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- 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;
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param withbootstraps DOCUMENT ME!
- * @param withdists DOCUMENT ME!
- * @param printRootInfo DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- 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.right());
- _print(tf, (SequenceNode) c.left());
- }
- 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
- {
- 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();
- }
- }
-}
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview 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 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview 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 Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+// 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.util.Locale;
+
+import jalview.datamodel.SequenceNode;
+import jalview.util.MessageManager;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.StringTokenizer;
+
+import com.stevesoft.pat.Regex;
+
+/**
+ * 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
+ * this: NHX codes are appended in comments beginning with &&NHX. The codes are
+ * given below (from http://www.phylosoft.org/forester/NHX.html): Element Type
+ * Description Corresponding phyloXML element (parent element in parentheses) no
+ * tag string name of this node/clade (MUST BE FIRST, IF ASSIGNED)
+ * () : decimal branch length to parent node (MUST BE SECOND, IF
+ * ASSIGNED) () :GN= string gene name ()
+ * :AC= string sequence accession () :ND= string node
+ * identifier - if this is being used, it has to be unique within each phylogeny
+ * () :B= decimal confidence value for parent branch
+ * () :D= 'T', 'F', or '?' 'T' if this node represents a
+ * duplication event - 'F' if this node represents a speciation event, '?' if
+ * this node represents an unknown event (D= tag should be replaced by Ev= tag)
+ * n/a :Ev=duplications>speciations>gene losses>event type>duplication type int
+ * int int string string event (replaces the =D tag), number of duplication,
+ * speciation, and gene loss events, type of event (transfer, fusion, root,
+ * unknown, other, speciation_duplication_loss, unassigned) ()
+ * :E= string EC number at this node () :Fu= string
+ * function at this node ()
+ * :DS=protein-length>from>to>support>name>from>... int int int double string
+ * int ... domain structure at this node () :S=
+ * string species name of the species/phylum at this node ()
+ * :T= integer taxonomy ID of the species/phylum at this node ()
+ * :W= integer width of parent branch () :C=rrr.ggg.bbb
+ * integer.integer.integer color of parent branch () :Co= 'Y' or
+ * 'N' collapse this node when drawing the tree (default is not to collapse) n/a
+ * :XB= string custom data associated with a branch () :XN=
+ * string custom data associated with a node () :O= integer
+ * orthologous to this external node n/a :SN= integer subtree neighbors n/a :SO=
+ * integer super orthologous (no duplications on paths) to this external node
+ * n/a
+ *
+ * @author Jim Procter
+ * @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 = true;
+
+ 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 = '\'';
+
+ /**
+ * Creates a new NewickFile object.
+ *
+ * @param inStr
+ * DOCUMENT ME!
+ *
+ * @throws IOException
+ * DOCUMENT ME!
+ */
+ public NewickFile(String inStr) throws IOException
+ {
+ super(inStr, DataSourceType.PASTE);
+ }
+
+ /**
+ * Creates a new NewickFile object.
+ *
+ * @param inFile
+ * DOCUMENT ME!
+ * @param protocol
+ * DOCUMENT ME!
+ *
+ * @throws IOException
+ * DOCUMENT ME!
+ */
+ public NewickFile(String inFile, DataSourceType protocol)
+ throws IOException
+ {
+ super(inFile, protocol);
+ }
+
+ public NewickFile(FileParse source) throws IOException
+ {
+ super(source);
+ }
+
+ /**
+ * 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;
+ }
+
+ /**
+ * parse the filesource as a newick file (new hampshire and/or extended)
+ *
+ * @throws IOException
+ * with a line number and character position for badly formatted NH
+ * strings
+ */
+ 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;
+ String commentString2 = null; // comments after simple node props
+
+ double DefDistance = (float) 0.001; // @param Default distance for a node -
+ // very very small
+ int DefBootstrap = -1; // @param Default bootstrap for a node
+
+ double distance = DefDistance;
+ int bootstrap = DefBootstrap;
+
+ boolean ascending = false; // flag indicating that we are leaving the
+ // current node
+
+ Regex majorsyms = new Regex("[(\\['),;]");
+
+ int nextcp = 0;
+ int ncp = cp;
+ boolean parsednodename = false;
+ while (majorsyms.searchFrom(nf, cp) && (Error == null))
+ {
+ int fcp = majorsyms.matchedFrom();
+ char schar;
+ switch (schar = nf.charAt(fcp))
+ {
+ 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 '\'':
+
+ Regex qnodename = new Regex("'([^']|'')+'");
+
+ if (qnodename.searchFrom(nf, fcp))
+ {
+ int nl = qnodename.stringMatched().length();
+ nodename = new String(
+ qnodename.stringMatched().substring(1, nl - 1));
+ // unpack any escaped colons
+ Regex xpandquotes = Regex.perlCode("s/''/'/");
+ String widernodename = xpandquotes.replaceAll(nodename);
+ nodename = widernodename;
+ // jump to after end of quoted nodename
+ nextcp = fcp + nl + 1;
+ parsednodename = true;
+ }
+ else
+ {
+ Error = ErrorStringrange(Error,
+ "Unterminated quotes for nodename", 7, fcp, nf);
+ }
+
+ break;
+
+ default:
+ if (schar == ';')
+ {
+ if (d != -1)
+ {
+ Error = ErrorStringrange(Error,
+ "Wayward semicolon (depth=" + d + ")", 7, fcp, nf);
+ }
+ // cp advanced at the end of default
+ }
+ if (schar == '[')
+ {
+ // node string contains Comment or structured/extended NH format info
+ /*
+ * if ((fcp-cp>1 && nf.substring(cp,fcp).trim().length()>1)) { // will
+ * process in remains System.err.println("skipped text:
+ * '"+nf.substring(cp,fcp)+"'"); }
+ */
+ // verify termination.
+ Regex comment = new Regex("]");
+ if (comment.searchFrom(nf, fcp))
+ {
+ // Skip the comment field
+ nextcp = comment.matchedFrom() + 1;
+ warningMessage = "Tree file contained comments which may confuse input algorithm.";
+ break;
+
+ // cp advanced at the end of default to nextcp, ncp is unchanged so
+ // any node info can be read.
+ }
+ else
+ {
+ Error = ErrorStringrange(Error, "Unterminated comment", 3, fcp,
+ nf);
+ }
+ }
+ // Parse simpler field strings
+ String fstring = nf.substring(ncp, fcp);
+ // remove any comments before we parse the node info
+ // TODO: test newick file with quoted square brackets in node name (is
+ // this allowed?)
+ while (fstring.indexOf(']') > -1)
+ {
+ int cstart = fstring.indexOf('[');
+ int cend = fstring.indexOf(']');
+ commentString2 = fstring.substring(cstart + 1, cend);
+ fstring = fstring.substring(0, cstart)
+ + fstring.substring(cend + 1);
+
+ }
+ 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
+ .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);
+ }
+ }
+ // get comment bootstraps
+
+ if (nbootstrap.search(fstring))
+ {
+ if (nbootstrap.stringMatched(1)
+ .equals(uqnodename.stringMatched(1)))
+ {
+ nodename = null; // no nodename here.
+ }
+ if (nodename == null || nodename.length() == 0
+ || nbootstrap.matchedFrom(1) > (uqnodename.matchedFrom(1)
+ + uqnodename.stringMatched().length()))
+ {
+ try
+ {
+ bootstrap = (Integer.valueOf(nbootstrap.stringMatched(1)))
+ .intValue();
+ HasBootstrap = true;
+ } catch (Exception e)
+ {
+ Error = ErrorStringrange(Error, "Can't parse bootstrap value",
+ 4, ncp + nbootstrap.matchedFrom(), nf);
+ }
+ }
+ }
+
+ boolean nodehasdistance = false;
+
+ if (ndist.search(fstring))
+ {
+ try
+ {
+ distance = (Double.valueOf(ndist.stringMatched(1))).floatValue();
+ HasDistances = true;
+ nodehasdistance = true;
+ } catch (Exception e)
+ {
+ Error = ErrorStringrange(Error,
+ "Can't parse node distance value", 7,
+ ncp + 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
+ }
+ parseNHXNodeProps(c, commentString2);
+ commentString2 = null;
+ }
+ else
+ {
+ // Find a place to put the leaf
+ SequenceNode newnode = new SequenceNode(null, c, nodename,
+ (HasDistances) ? distance : DefDistance,
+ (HasBootstrap) ? bootstrap : DefBootstrap, false);
+ parseNHXNodeProps(c, commentString2);
+ commentString2 = null;
+
+ 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();
+ }
+ }
+ }
+ }
+
+ // Reset new node properties to obvious fakes
+ nodename = null;
+ distance = DefDistance;
+ bootstrap = DefBootstrap;
+ commentString2 = null;
+ parsednodename = false;
+ }
+ if (nextcp == 0)
+ {
+ ncp = cp = fcp + 1;
+ }
+ else
+ {
+ cp = nextcp;
+ nextcp = 0;
+ }
+ }
+
+ if (Error != null)
+ {
+ throw (new IOException(
+ MessageManager.formatMessage("exception.newfile", new String[]
+ { Error.toString() })));
+ }
+ if (root == null)
+ {
+ throw (new IOException(
+ MessageManager.formatMessage("exception.newfile", new String[]
+ { MessageManager.getString("label.no_tree_read_in") })));
+ }
+ // 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;
+ }
+ }
+
+ /**
+ * parse NHX codes in comment strings and update NewickFile state flags for
+ * distances and bootstraps, and add any additional properties onto the node.
+ *
+ * @param c
+ * @param commentString
+ * @param commentString2
+ */
+ private void parseNHXNodeProps(SequenceNode c, String commentString)
+ {
+ // TODO: store raw comment on the sequenceNode so it can be recovered when
+ // tree is output
+ if (commentString != null && commentString.startsWith("&&NHX"))
+ {
+ StringTokenizer st = new StringTokenizer(commentString.substring(5),
+ ":");
+ while (st.hasMoreTokens())
+ {
+ String tok = st.nextToken();
+ int colpos = tok.indexOf("=");
+
+ if (colpos > -1)
+ {
+ String code = tok.substring(0, colpos);
+ String value = tok.substring(colpos + 1);
+ try
+ {
+ // parse out code/value pairs
+ if (code.toLowerCase(Locale.ROOT).equals("b"))
+ {
+ int v = -1;
+ Float iv = Float.valueOf(value);
+ v = iv.intValue(); // jalview only does integer bootstraps
+ // currently
+ c.setBootstrap(v);
+ HasBootstrap = true;
+ }
+ // more codes here.
+ } catch (Exception e)
+ {
+ System.err.println(
+ "Couldn't parse code '" + code + "' = '" + value + "'");
+ e.printStackTrace(System.err);
+ }
+ }
+ }
+ }
+
+ }
+
+ /**
+ * 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.getName() != null ? " " : "") + 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.getName() != null ? " " : "")
+ + +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));
+ }
+ }
+ }
+ }
+
+ /**
+ *
+ * @param args
+ * @j2sIgnore
+ */
+ 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], DataSourceType.FILE);
+ trf.parse();
+ System.out.println("Original file :\n");
+
+ Regex nonl = new 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();
+ }
+ }
+}