X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FNewickFile.java;h=aa9a129fa54246d567278eb56708d6a0e4fc41d5;hb=9518023410bdd4b7835df7606a30f7a55ad23222;hp=d0af8a7399e79ace8615a9283ec6202fbc8d58aa;hpb=f008025f6aa0c2df0e1fbf556a89393e7052db72;p=jalview.git

diff --git a/src/jalview/io/NewickFile.java b/src/jalview/io/NewickFile.java
index d0af8a7..aa9a129 100755
--- a/src/jalview/io/NewickFile.java
+++ b/src/jalview/io/NewickFile.java
@@ -1,95 +1,234 @@
+/*
+ * 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 distance=-99999;
-    int bootstrap=-99999;
+
+    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
-    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;
+    com.stevesoft.pat.Regex majorsyms = new com.stevesoft.pat.Regex(
+        "[(\\['),;]");
 
+    int nextcp=0;
+    int ncp = cp;
+    while (majorsyms.searchFrom(nf, cp) && (Error == null))
+    {
+      int fcp = majorsyms.matchedFrom();
+      char schar;
+      switch (schar=nf.charAt(fcp))
+      {
         case '(':
 
           // ascending should not be set
@@ -97,13 +236,17 @@ public class NewickFile extends FileParse
           if (ascending)
           {
             Error = ErrorStringrange(Error, "Unexpected '('", 7, fcp, nf);
+
             continue;
           }
+
           ;
           d++;
+
           if (c.right() == null)
           {
-            c.setRight(new SequenceNode(null, c, 0, null));
+            c.setRight(new SequenceNode(null, c, null, DefDistance,
+                                        DefBootstrap, false));
             c = (SequenceNode) c.right();
           }
           else
@@ -111,68 +254,122 @@ public class NewickFile extends FileParse
             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, 0, null));
+
+            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 = -99999;
-          bootstrap = -99999;
+          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);
               }
             }
@@ -180,14 +377,18 @@ public class NewickFile extends FileParse
             {
               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
             {
@@ -196,11 +397,15 @@ public class NewickFile extends FileParse
             }
             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
@@ -211,8 +416,9 @@ public class NewickFile extends FileParse
             }
             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);
             }
           }
 
@@ -220,20 +426,21 @@ public class NewickFile extends FileParse
           {
             // 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,
-                (HasDistances) ? distance : 0,
-                nodename);
-
-            newnode.setBootstrap(HasBootstrap ? bootstrap : 0);
+            SequenceNode newnode = new SequenceNode(null, c, nodename,
+                (HasDistances) ? distance : DefDistance,
+                (HasBootstrap) ? bootstrap : DefBootstrap, false);
 
             if (c.right() == null)
             {
@@ -248,17 +455,21 @@ public class NewickFile extends FileParse
               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 ')' ?)",
@@ -266,170 +477,264 @@ public class NewickFile extends FileParse
             }
           }
 
-          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 = -99999;
-          bootstrap = -99999;
-
-          cp=fcp+1;
+          distance = DefDistance;
+          bootstrap = DefBootstrap;
+      }
+      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"));
     }
-  }
-
-  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;
-  }
+    // 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, 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));
         }
@@ -438,20 +743,35 @@ 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));
         }
@@ -459,47 +779,57 @@ 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.out.println("Exception\n" + e);
-    e.printStackTrace();
   }
 }
-
-}