/*
-* 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
-*/
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ */
// NewickFile.java
// Tree I/O
// http://evolution.genetics.washington.edu/phylip/newick_doc.html
-
+// TODO: Implement Basic NHX tag parsing and preservation
+// TODO: http://evolution.genetics.wustl.edu/eddy/forester/NHX.html
+// TODO: Extended SequenceNodeI to hold parsed NHX strings
package jalview.io;
import java.io.*;
-import java.util.*;
+
import jalview.datamodel.*;
-public class NewickFile extends FileParse
+/**
+ * Parse a new hanpshire style tree
+ * Caveats: NHX files are NOT supported and the tree distances and topology are unreliable when they are parsed.
+ * @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);
+ }
+
+ /**
+ * 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;
- public void parse() throws IOException
+ /**
+ * 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();
+ //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 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
- 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;
+ 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;
-
+ char schar;
+ switch (schar=nf.charAt(fcp))
+ {
case '(':
// ascending should not be set
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.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);
+ 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.setLeft(new SequenceNode(null, c, null, DefDistance,
+ DefBootstrap, false));
c = (SequenceNode) c.left();
}
- if (realroot==null) {
+
+ 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));
+ nodename = new String(qnodename.stringMatched().substring(0,
+ nl - 1));
cp = fcp + nl + 1;
}
else
{
- Error = ErrorStringrange(Error, "Unterminated quotes for nodename",
- 7, fcp, nf);
+ Error = ErrorStringrange(Error,
+ "Unterminated quotes for nodename", 7, fcp,
+ nf);
}
+
break;
- case ';':
- if (d != -1)
+ default:
+ if (schar==';')
{
- Error = ErrorStringrange(Error,
+ if (d != -1)
+ {
+ Error = ErrorStringrange(Error,
"Wayward semicolon (depth=" + d + ")", 7,
fcp, nf);
+ }
+ // cp advanced at the end of default
}
- // cp advanced at the end of default
-
- 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.
+ }
+ else
+ {
+ Error = ErrorStringrange(Error, "Unterminated comment", 3,
+ fcp, nf);
+ }
+ ;
+ }
// Parse simpler field strings
- String fstring = nf.substring(cp, fcp);
+ 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(']');
+ String comment = 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*:");
+ "\\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!
+ ":([-0-9Ee.+]+)");
+ if (uqnodename.search(fstring) &&
+ ( (uqnodename.matchedFrom(1) == 0) ||
+ (fstring.charAt(uqnodename.matchedFrom(1) - 1) != ':'))) // JBPNote HACK!
{
if (nodename == null)
{
- if (ReplaceUnderscores) {
- nodename = uqnodename.stringMatched(1).replace('_', ' ');
- } else {
+ if (ReplaceUnderscores)
+ {
+ nodename = uqnodename.stringMatched(1).replace('_',
+ ' ');
+ }
+ else
+ {
nodename = uqnodename.stringMatched(1);
}
}
{
Error = ErrorStringrange(Error,
"File has broken algorithm - overwritten nodename",
- 10, fcp,
- nf);
+ 10, fcp, nf);
}
}
- if (nbootstrap.search(fstring)
- &&
- nbootstrap.matchedFrom(1)
- > uqnodename.matchedFrom(1) + uqnodename.stringMatched().length())
+
+ 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
{
}
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;
+ }
+
+ boolean nodehasdistance = false;
+
if (ndist.search(fstring))
{
try
}
catch (Exception e)
{
- Error = ErrorStringrange(Error, "Can't parse node distance value",
- 7, cp + ndist.matchedFrom(), nf);
+ Error = ErrorStringrange(Error,
+ "Can't parse node distance value", 7,
+ ncp + ndist.matchedFrom(), nf);
}
}
{
// 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!!!
+ // Trees without distances still need a render distance
+ c.dist = (HasDistances) ? distance : DefDistance;
+ // be consistent for internal bootstrap defaults too
+ c.setBootstrap( (HasBootstrap) ? bootstrap : DefBootstrap);
+ if (c == realroot)
+ {
+ RootHasDistance = nodehasdistance; // JBPNote This is really UGLY!!! Ensure root node gets its given distance
}
}
else
{
// Find a place to put the leaf
- SequenceNode newnode =
- new SequenceNode(null, c,
- nodename,
- (HasDistances) ? distance : DefDistance,
- (HasBootstrap) ? bootstrap : DefBootstrap,
- false);
+ SequenceNode newnode = new SequenceNode(null, c, nodename,
+ (HasDistances) ? distance : DefDistance,
+ (HasBootstrap) ? bootstrap : DefBootstrap, false);
if (c.right() == null)
{
else
{
// Insert a dummy node for polytomy
- SequenceNode newdummy = new SequenceNode(null, c, null, 0, 0, true);
+ // 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)
+
+ if ( (d > -1) && (c == null))
{
Error = ErrorStringrange(Error,
"File broke algorithm: Lost place in tree (is there an extra ')' ?)",
}
}
- if (nf.charAt(fcp) == ')') {
+ 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.
}
+ 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;
-
- cp=fcp+1;
+ }
+ 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("NewickFile: " + Error + "\n"));
}
-
- root = (SequenceNode) root.right().detach(); // remove the imaginary root.
- if (!RootHasDistance) {
- root.dist = 0;
+ if (root==null)
+ {
+ throw (new IOException("NewickFile: No Tree read in\n"));
}
+ // THe next line is failing for topali trees - not sure why yet. if (root.right()!=null && root.isDummy())
+ root = (SequenceNode) root.right().detach(); // remove the imaginary root.
- }
-
- public NewickFile(SequenceNode newtree) {
- root = newtree;
- }
-
- 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;
+ if (!RootHasDistance)
+ {
+ root.dist = (HasDistances) ? 0 : DefDistance;
}
+ }
- 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) : "");
+ }
+
+ /**
+ * 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) : "")) : "";
}
- 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) {
+ // 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));
}
}
// 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));
}
}
}
-// 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();
}
}
-
-}