X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FNewickFile.java;h=5fdcc01e8d5e2cb9b8f36159f4214473ca802426;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=74612a6f7f43ebcefe31153f821eb62ef2d1b529;hpb=3a993bbe274824870c78bd7695c42fa93908cb30;p=jalview.git
diff --git a/src/jalview/io/NewickFile.java b/src/jalview/io/NewickFile.java
index 74612a6..5fdcc01 100755
--- a/src/jalview/io/NewickFile.java
+++ b/src/jalview/io/NewickFile.java
@@ -1,22 +1,20 @@
/*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * 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 .
*/
-
// NewickFile.java
// Tree I/O
// http://evolution.genetics.washington.edu/phylip/newick_doc.html
@@ -26,68 +24,114 @@
package jalview.io;
import java.io.*;
+import java.util.StringTokenizer;
import jalview.datamodel.*;
/**
- * Parse a new hanpshire style tree
- * Caveats: NHX files are NOT supported and the tree distances and topology are unreliable when they are parsed.
+ * 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
+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 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
+ { 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!
+ *
+ * @param inStr
+ * DOCUMENT ME!
+ *
+ * @throws IOException
+ * DOCUMENT ME!
*/
- public NewickFile(String inStr)
- throws IOException
+ 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!
+ *
+ * @param inFile
+ * DOCUMENT ME!
+ * @param type
+ * DOCUMENT ME!
+ *
+ * @throws IOException
+ * DOCUMENT ME!
*/
- public NewickFile(String inFile, String type)
- throws IOException
+ public NewickFile(String inFile, String type) throws IOException
{
super(inFile, type);
}
+
public NewickFile(FileParse source) throws IOException
{
super(source);
}
+
/**
* Creates a new NewickFile object.
- *
- * @param newtree DOCUMENT ME!
+ *
+ * @param newtree
+ * DOCUMENT ME!
*/
public NewickFile(SequenceNode newtree)
{
@@ -96,9 +140,11 @@ public class NewickFile
/**
* Creates a new NewickFile object.
- *
- * @param newtree DOCUMENT ME!
- * @param bootstrap DOCUMENT ME!
+ *
+ * @param newtree
+ * DOCUMENT ME!
+ * @param bootstrap
+ * DOCUMENT ME!
*/
public NewickFile(SequenceNode newtree, boolean bootstrap)
{
@@ -108,12 +154,16 @@ public class NewickFile
/**
* Creates a new NewickFile object.
- *
- * @param newtree DOCUMENT ME!
- * @param bootstrap DOCUMENT ME!
- * @param distances DOCUMENT ME!
+ *
+ * @param newtree
+ * DOCUMENT ME!
+ * @param bootstrap
+ * DOCUMENT ME!
+ * @param distances
+ * DOCUMENT ME!
*/
- public NewickFile(SequenceNode newtree, boolean bootstrap, boolean distances)
+ public NewickFile(SequenceNode newtree, boolean bootstrap,
+ boolean distances)
{
root = newtree;
HasBootstrap = bootstrap;
@@ -122,14 +172,18 @@ public class NewickFile
/**
* Creates a new NewickFile object.
- *
- * @param newtree DOCUMENT ME!
- * @param bootstrap DOCUMENT ME!
- * @param distances DOCUMENT ME!
- * @param rootdistance DOCUMENT ME!
+ *
+ * @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)
+ boolean distances, boolean rootdistance)
{
root = newtree;
HasBootstrap = bootstrap;
@@ -139,22 +193,30 @@ public class NewickFile
/**
* DOCUMENT ME!
- *
- * @param Error DOCUMENT ME!
- * @param Er DOCUMENT ME!
- * @param r DOCUMENT ME!
- * @param p DOCUMENT ME!
- * @param s 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)
+ 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";
+ 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
@@ -166,7 +228,7 @@ public class NewickFile
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public boolean HasDistances()
@@ -181,11 +243,12 @@ public class NewickFile
/**
* 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
+ *
+ * @throws IOException
+ * with a line number and character position for badly formatted NH
+ * strings
*/
- public void parse()
- throws IOException
+ public void parse() throws IOException
{
String nf;
@@ -193,7 +256,7 @@ public class NewickFile
StringBuffer file = new StringBuffer();
- while ( (nf = nextLine()) != null)
+ while ((nf = nextLine()) != null)
{
file.append(nf);
}
@@ -208,314 +271,328 @@ public class NewickFile
int d = -1;
int cp = 0;
- //int flen = nf.length();
+ // int flen = nf.length();
String Error = null;
String nodename = null;
+ String commentString2 = null; // comments after simple node props
- float DefDistance = (float) 0.001; // @param Default distance for a node - very very small
+ float DefDistance = (float) 0.001; // @param Default distance for a node -
+ // very very small
int DefBootstrap = -1; // @param Default bootstrap for a node
float distance = DefDistance;
int bootstrap = DefBootstrap;
- boolean ascending = false; // flag indicating that we are leaving the current node
+ boolean ascending = false; // flag indicating that we are leaving the
+ // current node
com.stevesoft.pat.Regex majorsyms = new com.stevesoft.pat.Regex(
- "[(\\['),;]");
+ "[(\\['),;]");
- int nextcp=0;
+ int nextcp = 0;
int ncp = cp;
while (majorsyms.searchFrom(nf, cp) && (Error == null))
{
int fcp = majorsyms.matchedFrom();
char schar;
- switch (schar=nf.charAt(fcp))
+ switch (schar = nf.charAt(fcp))
{
- case '(':
+ case '(':
- // ascending should not be set
- // New Internal node
- if (ascending)
- {
- Error = ErrorStringrange(Error, "Unexpected '('", 7, fcp, nf);
+ // ascending should not be set
+ // New Internal node
+ if (ascending)
+ {
+ Error = ErrorStringrange(Error, "Unexpected '('", 7, fcp, nf);
- continue;
- }
+ continue;
+ }
- ;
- d++;
+ ;
+ d++;
- if (c.right() == null)
+ if (c.right() == null)
+ {
+ c.setRight(new SequenceNode(null, c, null, DefDistance,
+ DefBootstrap, false));
+ c = (SequenceNode) c.right();
+ }
+ else
+ {
+ if (c.left() != null)
{
- c.setRight(new SequenceNode(null, c, null, DefDistance,
- DefBootstrap, false));
- c = (SequenceNode) c.right();
+ // 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);
}
- 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();
- }
+ c.setLeft(new SequenceNode(null, c, null, DefDistance,
+ DefBootstrap, false));
+ c = (SequenceNode) c.left();
+ }
- if (realroot == null)
- {
- realroot = c;
- }
+ if (realroot == null)
+ {
+ realroot = c;
+ }
+
+ nodename = null;
+ distance = DefDistance;
+ bootstrap = DefBootstrap;
+ cp = fcp + 1;
- nodename = null;
- distance = DefDistance;
- bootstrap = DefBootstrap;
- cp = fcp + 1;
+ break;
- break;
+ // Deal with quoted fields
+ case '\'':
- // 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);
+ }
- com.stevesoft.pat.Regex qnodename = new com.stevesoft.pat.Regex(
- "([^']|'')+'");
+ break;
- if (qnodename.searchFrom(nf, fcp))
+ 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.
+ com.stevesoft.pat.Regex comment = new com.stevesoft.pat.Regex("]");
+ if (comment.searchFrom(nf, fcp))
{
- int nl = qnodename.stringMatched().length();
- nodename = new String(qnodename.stringMatched().substring(0,
- nl - 1));
- cp = fcp + nl + 1;
+ // 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 quotes for nodename", 7, fcp,
- nf);
+ Error = ErrorStringrange(Error, "Unterminated comment", 3, fcp,
+ nf);
}
- break;
+ ;
+ }
+ // 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);
- default:
- if (schar==';')
+ }
+ 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 (d != -1)
+ if (ReplaceUnderscores)
{
- 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.
- com.stevesoft.pat.Regex comment = new com.stevesoft.pat.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.
+ nodename = uqnodename.stringMatched(1).replace('_', ' ');
}
else
{
- Error = ErrorStringrange(Error, "Unterminated comment", 3,
- fcp, nf);
+ nodename = uqnodename.stringMatched(1);
}
-
- ;
}
- // 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)
+ else
{
- int cstart=fstring.indexOf('[');
- int cend=fstring.indexOf(']');
- String comment = fstring.substring(cstart+1,cend);
- fstring = fstring.substring(0, cstart)+fstring.substring(cend+1);
-
+ Error = ErrorStringrange(Error,
+ "File has broken algorithm - overwritten nodename", 10,
+ fcp, nf);
}
- 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!
+ }
+ // get comment bootstraps
+
+ if (nbootstrap.search(fstring))
+ {
+ if (nbootstrap.stringMatched(1).equals(
+ uqnodename.stringMatched(1)))
{
- 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);
- }
+ nodename = null; // no nodename here.
}
-
- 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()))
+ if (nodename == null
+ || nodename.length() == 0
+ || nbootstrap.matchedFrom(1) > (uqnodename.matchedFrom(1) + uqnodename
+ .stringMatched().length()))
{
try
{
- bootstrap = (new Integer(nbootstrap.stringMatched(1))).intValue();
+ bootstrap = (new Integer(nbootstrap.stringMatched(1)))
+ .intValue();
HasBootstrap = true;
- }
- catch (Exception e)
+ } catch (Exception e)
{
Error = ErrorStringrange(Error,
- "Can't parse bootstrap value", 4,
- ncp + nbootstrap.matchedFrom(), nf);
+ "Can't parse bootstrap value", 4,
+ ncp + nbootstrap.matchedFrom(), nf);
}
}
- }
+ }
- boolean nodehasdistance = false;
+ boolean nodehasdistance = false;
- if (ndist.search(fstring))
+ if (ndist.search(fstring))
+ {
+ try
{
- 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,
- ncp + ndist.matchedFrom(), nf);
- }
+ distance = (new Float(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)
+ 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)
{
- // 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
- }
+ 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
{
- // 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)
+ if (c.left() == null)
{
- c.setRight(newnode);
+ c.setLeft(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);
- }
+ // 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 (ascending)
+ {
+ // move back up the tree from preceding closure
+ c = c.AscendTree();
- if (nf.charAt(fcp) == ')')
+ if ((d > -1) && (c == null))
{
- d--;
- ascending = true;
+ Error = ErrorStringrange(
+ Error,
+ "File broke algorithm: Lost place in tree (is there an extra ')' ?)",
+ 7, fcp, nf);
}
- else
+ }
+
+ if (nf.charAt(fcp) == ')')
+ {
+ d--;
+ ascending = true;
+ }
+ else
+ {
+ if (nf.charAt(fcp) == ',')
{
- if (nf.charAt(fcp) == ',')
+ if (ascending)
{
- if (ascending)
- {
- ascending = false;
- }
- else
+ ascending = false;
+ }
+ else
+ {
+ // Just advance focus, if we need to
+ if ((c.left() != null) && (!c.left().isLeaf()))
{
- // Just advance focus, if we need to
- if ( (c.left() != null) && (!c.left().isLeaf()))
- {
- c = (SequenceNode) c.left();
- }
+ c = (SequenceNode) c.left();
}
}
}
+ }
- // Reset new node properties to obvious fakes
- nodename = null;
- distance = DefDistance;
- bootstrap = DefBootstrap;
+ // Reset new node properties to obvious fakes
+ nodename = null;
+ distance = DefDistance;
+ bootstrap = DefBootstrap;
+ commentString2 = null;
}
- if (nextcp==0)
+ if (nextcp == 0)
{
ncp = cp = fcp + 1;
}
- else {
- cp=nextcp;
- nextcp=0;
+ else
+ {
+ cp = nextcp;
+ nextcp = 0;
}
}
@@ -523,11 +600,12 @@ public class NewickFile
{
throw (new IOException("NewickFile: " + Error + "\n"));
}
- if (root==null)
+ 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())
+ // 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)
@@ -537,8 +615,58 @@ public class NewickFile
}
/**
+ * 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().equals("b"))
+ {
+ int v = -1;
+ Float iv = new Float(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()
@@ -547,9 +675,9 @@ public class NewickFile
}
/**
- * Generate a newick format tree according to internal flags
- * for bootstraps, distances and root distances.
- *
+ * 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()
@@ -564,13 +692,14 @@ public class NewickFile
}
/**
- *
- *
- * 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.
- *
+ *
+ *
+ * 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)
@@ -588,13 +717,15 @@ public class NewickFile
}
/**
- *
- * Generate newick format tree according to internal flags
- * for writing root node distances.
- *
- * @param withbootstraps explicitly write bootstrap values
- * @param withdists explicitly write distances
- *
+ *
+ * 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)
@@ -613,15 +744,18 @@ public class NewickFile
/**
* 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
- *
+ *
+ * @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)
+ boolean printRootInfo)
{
synchronized (this)
{
@@ -637,7 +771,7 @@ public class NewickFile
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
char getQuoteChar()
@@ -647,9 +781,10 @@ public class NewickFile
/**
* DOCUMENT ME!
- *
- * @param c DOCUMENT ME!
- *
+ *
+ * @param c
+ * DOCUMENT ME!
+ *
* @return DOCUMENT ME!
*/
char setQuoteChar(char c)
@@ -662,9 +797,10 @@ public class NewickFile
/**
* DOCUMENT ME!
- *
- * @param name DOCUMENT ME!
- *
+ *
+ * @param name
+ * DOCUMENT ME!
+ *
* @return DOCUMENT ME!
*/
private String nodeName(String name)
@@ -681,35 +817,37 @@ public class NewickFile
/**
* DOCUMENT ME!
- *
- * @param c 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) : "");
+ 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!
- *
+ *
+ * @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) : "")) : "";
+ 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
@@ -789,8 +927,8 @@ public class NewickFile
{
if (args == null || args.length != 1)
{
- System.err.println(
- "Takes one argument - file name of a newick tree file.");
+ System.err
+ .println("Takes one argument - file name of a newick tree file.");
System.exit(0);
}
@@ -800,7 +938,7 @@ public class NewickFile
BufferedReader treefile = new BufferedReader(new FileReader(fn));
String l;
- while ( (l = treefile.readLine()) != null)
+ while ((l = treefile.readLine()) != null)
{
newickfile.append(l);
}
@@ -828,8 +966,7 @@ public class NewickFile
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)
+ } catch (java.io.IOException e)
{
System.err.println("Exception\n" + e);
e.printStackTrace();