X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FNewickFile.java;h=800d51adf9d213bc4d6e929a18dd5313cadbfa19;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=85ab084e8ca062008c384be18c92fb43a15b1bd0;hpb=e5127e5f27f02c8f328539eaac68eabfbee1d135;p=jalview.git
diff --git a/src/jalview/io/NewickFile.java b/src/jalview/io/NewickFile.java
index 85ab084..800d51a 100755
--- a/src/jalview/io/NewickFile.java
+++ b/src/jalview/io/NewickFile.java
@@ -1,446 +1,901 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.io.*;
-import java.util.*;
-import jalview.datamodel.*;
-
+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;
+
+/**
+ * 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;
- 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";
+ // 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
+ };
+
+ 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);
+ }
+
+ 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() {
+ public boolean HasBootstrap()
+ {
return HasBootstrap;
}
- public boolean HasDistances() {
- return HasDistances;
- }
- public NewickFile(String inStr) throws IOException
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean HasDistances()
{
- super(inStr, "Paste");
+ return HasDistances;
}
- public NewickFile(String inFile, String type)
- throws IOException
+ public boolean HasRootDistance()
{
-
- super(inFile, type);
+ return RootHasDistance;
}
- // File IO Flags
- boolean ReplaceUnderscores = false;
+ /**
+ * 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)
+
+ 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();
+ // int flen = nf.length();
String Error = null;
String nodename = null;
+ String commentString2 = null; // comments after simple node props
- float DefDistance = (float) 0.00001; // @param Default distance for a node - very very small
- int DefBootstrap = 0; // @param Default bootstrap for a node
+ 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;
+ 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("[(\\['),;]");
+ com.stevesoft.pat.Regex majorsyms = new com.stevesoft.pat.Regex(
+ "[(\\['),;]");
- while (majorsyms.searchFrom(nf, cp) && Error==null) {
+ int nextcp = 0;
+ int ncp = cp;
+ boolean parsednodename = false;
+ while (majorsyms.searchFrom(nf, cp) && (Error == null))
+ {
int fcp = majorsyms.matchedFrom();
- switch (nf.charAt(fcp)) {
+ 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);
- case '[': // Comment or structured/extended NH format info
+ 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(1,
+ nl - 1));
+ // unpack any escaped colons
+ com.stevesoft.pat.Regex xpandquotes = com.stevesoft.pat.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.
com.stevesoft.pat.Regex comment = new com.stevesoft.pat.Regex("]");
if (comment.searchFrom(nf, fcp))
{
// Skip the comment field
- cp = 1 + comment.matchedFrom();
+ 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);
+ 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
+ }
+ // 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);
+
+ }
+ 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 (!parsednodename
+ && uqnodename.search(fstring)
+ && ((uqnodename.matchedFrom(1) == 0) || (fstring
+ .charAt(uqnodename.matchedFrom(1) - 1) != ':'))) // JBPNote
+ // HACK!
+ {
+ if (nodename == null)
{
- if (c.left() != null)
+ if (ReplaceUnderscores)
{
- // 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);
+ nodename = uqnodename.stringMatched(1).replace('_', ' ');
+ }
+ else
+ {
+ nodename = uqnodename.stringMatched(1);
}
- 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);
+ "File has broken algorithm - overwritten nodename", 10,
+ 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!
+ }
+ // 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)
- &&
- 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,
- cp + nbootstrap.matchedFrom(), nf);
+ Error = ErrorStringrange(Error,
+ "Can't parse bootstrap value", 4,
+ ncp + nbootstrap.matchedFrom(), nf);
}
}
- boolean nodehasdistance=false;
- if (ndist.search(fstring))
+ }
+
+ boolean nodehasdistance = false;
+
+ 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);
+ }
+ }
+
+ 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)
{
- distance = (new Float(ndist.stringMatched(1))).floatValue();
- HasDistances = true;
- nodehasdistance = true;
+ c.setLeft(newnode);
}
- catch (Exception e)
+ else
{
- Error = ErrorStringrange(Error, "Can't parse node distance value",
- 7, cp + ndist.matchedFrom(), nf);
+ // 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)
+ if (ascending)
+ {
+ // move back up the tree from preceding closure
+ c = c.AscendTree();
+
+ if ((d > -1) && (c == null))
{
- // 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!!!
- }
+ 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) == ',')
{
- // 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 (ascending)
{
- c.setRight(newnode);
+ ascending = false;
}
else
{
- if (c.left() == null)
- {
- c.setLeft(newnode);
- }
- else
+ // Just advance focus, if we need to
+ if ((c.left() != null) && (!c.left().isLeaf()))
{
- // Insert a dummy node for polytomy
- SequenceNode newdummy = new SequenceNode(null, c, null, 0, 0, true);
- newdummy.SetChildren(c.left(), newnode);
- c.setLeft(newdummy);
+ c = (SequenceNode) c.left();
}
}
}
- 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;
+ // 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("NewickFile: "+Error+"\n"));
+ if (Error != null)
+ {
+ throw (new IOException(MessageManager.formatMessage(
+ "exception.newfile", new String[] { Error.toString() })));
}
-
- root = (SequenceNode) root.right().detach(); // remove the imaginary root.
- if (!RootHasDistance) {
- root.dist = 0;
+ 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;
+ }
}
- public NewickFile(SequenceNode newtree) {
- root = newtree;
- }
+ /**
+ * 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);
+ }
+ }
+ }
+ }
- public NewickFile(SequenceNode newtree, boolean bootstrap) {
- HasBootstrap = bootstrap;
- root=newtree;
- }
- public NewickFile(SequenceNode newtree, boolean bootstrap, boolean distances) {
- root = newtree;
- HasBootstrap = bootstrap;
- HasDistances = distances;
}
- public NewickFile(SequenceNode newtree, boolean bootstrap, boolean distances, boolean rootdistance) {
- root = newtree;
- HasBootstrap = bootstrap;
- HasDistances = distances;
- RootHasDistance = rootdistance;
- }
-
- public SequenceNode getTree() {
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public SequenceNode getTree()
+ {
return root;
}
- public String print() {
- synchronized (this) {
+ /**
+ * 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());
}
}
- public String print(boolean withbootstraps) {
- synchronized(this) {
+ /**
+ *
+ *
+ * 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;
}
}
- public String print(boolean withbootstraps, boolean withdists) {
- synchronized(this) {
+ /**
+ *
+ * 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;
}
}
- boolean printRootInfo = false;
-
- public String print(boolean withbootstraps, boolean withdists, boolean printRootInfo) {
- synchronized(this) {
+ /**
+ * 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;
}
}
- 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='\'';
- char getQuoteChar() {
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ char getQuoteChar()
+ {
return QuoteChar;
}
- char setQuoteChar(char c) {
+ /**
+ * DOCUMENT ME!
+ *
+ * @param c
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ char setQuoteChar(char c)
+ {
char old = QuoteChar;
QuoteChar = c;
+
return old;
}
- private String nodeName(String name) {
- if (NodeSafeName[0].search(name)) {
+ /**
+ * 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 {
+ }
+ else
+ {
return NodeSafeName[2].replaceAll(name);
}
}
- private String printNodeField(SequenceNode c) {
-
- return ( (c.getName() == null) ? ""
- : nodeName(c.getName()))
- + ( (HasBootstrap)
- ? ( (c.getBootstrap() > -1)
- ? " " + c.getBootstrap()
- : "")
- : "")
- + ( (HasDistances)
- ? ":" + c.dist : "");
+
+ /**
+ * 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) : "");
}
- 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) {
+ /**
+ * 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()) {
+ }
+ else
+ {
+ if (root.isDummy())
+ {
_print(tf, (SequenceNode) root.right());
_print(tf, (SequenceNode) root.left());
- } else {
+ }
+ else
+ {
tf.append("(");
_print(tf, (SequenceNode) root.right());
- if (root.left() != null) {
+
+ if (root.left() != null)
+ {
tf.append(",");
}
+
_print(tf, (SequenceNode) root.left());
tf.append(")" + printRootField(root));
}
@@ -449,20 +904,35 @@ public class NewickFile extends FileParse
}
// Recursive call for non-root nodes
- public void _print(StringBuffer tf, SequenceNode c) {
- if (c!=null) {
- if (c.isLeaf()) {
+ 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());
+ }
+ else
+ {
+ if (c.isDummy())
+ {
_print(tf, (SequenceNode) c.left());
- } else {
+ if (c.left() != null)
+ {
+ tf.append(",");
+ }
+ _print(tf, (SequenceNode) c.right());
+ }
+ else
+ {
tf.append("(");
_print(tf, (SequenceNode) c.right());
- if (c.left() != null) {
+
+ if (c.left() != null)
+ {
tf.append(",");
}
+
_print(tf, (SequenceNode) c.left());
tf.append(")" + printNodeField(c));
}
@@ -470,47 +940,56 @@ public class NewickFile extends FileParse
}
}
-// Test
+ // 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);
+ 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();
}
- 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();
- }
-}
-
}