X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FNewickFile.java;h=d6966055f5c4bddbf732b845cac00d56a131f774;hb=f24dacb1da56fccf05d684e2f4899facec2aecf7;hp=d0af8a7399e79ace8615a9283ec6202fbc8d58aa;hpb=f008025f6aa0c2df0e1fbf556a89393e7052db72;p=jalview.git

diff --git a/src/jalview/io/NewickFile.java b/src/jalview/io/NewickFile.java
index d0af8a7..d696605 100755
--- a/src/jalview/io/NewickFile.java
+++ b/src/jalview/io/NewickFile.java
@@ -1,505 +1,768 @@
-// NewickFile.java
-// Tree I/O
-// http://evolution.genetics.washington.edu/phylip/newick_doc.html
-package jalview.io;
-
-import java.io.*;
-import java.util.*;
-import jalview.datamodel.*;
-
-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";
-  }
-
-  // @tree annotations
-  // These are set automatically by the reader
-  public boolean HasBootstrap() {
-    return HasBootstrap;
-  }
-
-  public boolean HasDistances() {
-    return HasDistances;
-  }
-  public NewickFile(String inStr) throws IOException
-  {
-    super(inStr, "Paste");
-  }
-
-  public NewickFile(String inFile, String type)
-      throws IOException
-  {
-
-    super(inFile, type);
-  }
-  // File IO Flags
-  boolean ReplaceUnderscores = false;
-
-  public void parse() throws IOException
-  {
-    String nf;
-
-    { // fill nf with complete tree file
-      StringBuffer file = new StringBuffer();
-      while ( (nf = nextLine()) != null)
-      {
-        file.append(nf);
-      }
-      nf = file.toString();
-    }
-
-    root = new SequenceNode();
-    SequenceNode realroot = null;
-    SequenceNode c = root;
-    int d = -1;
-    int cp = 0;
-    int flen = nf.length();
-    String Error = null;
-    String nodename = null;
-    float distance=-99999;
-    int bootstrap=-99999;
-    boolean ascending = false; // flag indicating that we are leaving the current node
-    com.stevesoft.pat.Regex majorsyms = new com.stevesoft.pat.Regex("[(\\['),;]");
-    while (majorsyms.searchFrom(nf, cp) && Error==null) {
-      int fcp = majorsyms.matchedFrom();
-      switch (nf.charAt(fcp)) {
-
-        case '[': // Comment or structured/extended NH format info
-          com.stevesoft.pat.Regex comment = new com.stevesoft.pat.Regex("]");
-          if (comment.searchFrom(nf, fcp))
-          {
-            // Skip the comment field
-            cp = 1 + comment.matchedFrom();
-          }
-          else
-          {
-            Error = ErrorStringrange(Error, "Unterminated comment", 3, fcp, nf);
-          }
-          ;
-          break;
-
-        case '(':
-
-          // ascending should not be set
-          // New Internal node
-          if (ascending)
-          {
-            Error = ErrorStringrange(Error, "Unexpected '('", 7, fcp, nf);
-            continue;
-          }
-          ;
-          d++;
-          if (c.right() == null)
-          {
-            c.setRight(new SequenceNode(null, c, 0, null));
-            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, 0, null));
-            c = (SequenceNode) c.left();
-          }
-          if (realroot==null) {
-            realroot = c;
-          }
-          nodename = null;
-          distance = -99999;
-          bootstrap = -99999;
-          cp = fcp + 1;
-          break;
-
-          // Deal with quoted fields
-        case '\'':
-          com.stevesoft.pat.Regex qnodename = new com.stevesoft.pat.Regex(
-              "([^']|'')+'");
-          if (qnodename.searchFrom(nf, fcp))
-          {
-            int nl = qnodename.stringMatched().length();
-            nodename = new String(qnodename.stringMatched().substring(0, nl - 1));
-            cp = fcp + nl + 1;
-          }
-          else
-          {
-            Error = ErrorStringrange(Error, "Unterminated quotes for nodename",
-                                     7, fcp, nf);
-          }
-          break;
-
-        case ';':
-          if (d != -1)
-          {
-            Error = ErrorStringrange(Error,
-                                     "Wayward semicolon (depth=" + d + ")", 7,
-                                     fcp, nf);
-          }
-          // cp advanced at the end of default
-
-        default:
-
-          // Parse simpler field strings
-          String fstring = nf.substring(cp, fcp);
-          com.stevesoft.pat.Regex uqnodename = new com.stevesoft.pat.Regex(
-              "\\b([^' :;\\](),]+)");
-          com.stevesoft.pat.Regex nbootstrap = new com.stevesoft.pat.Regex(
-              "\\S+([0-9+]+)\\S*:");
-          com.stevesoft.pat.Regex ndist = new com.stevesoft.pat.Regex(
-              ":([-0-9.+]+)");
-          if (uqnodename.search(fstring)
-              && (uqnodename.matchedFrom(1) == 0
-                  || fstring.charAt(uqnodename.matchedFrom(1) - 1) != ':')) // JBPNote HACK!
-
-          {
-            if (nodename == null)
-            {
-              if (ReplaceUnderscores) {
-                nodename = uqnodename.stringMatched(1).replace('_', ' ');
-              } else {
-                nodename = uqnodename.stringMatched(1);
-              }
-            }
-            else
-            {
-              Error = ErrorStringrange(Error,
-                                       "File has broken algorithm - overwritten nodename",
-                                       10, fcp,
-                                       nf);
-            }
-          }
-          if (nbootstrap.search(fstring)
-              &&
-              nbootstrap.matchedFrom(1)
-              > uqnodename.matchedFrom(1) + uqnodename.stringMatched().length())
-          {
-            try
-            {
-              bootstrap = (new Integer(nbootstrap.stringMatched(1))).intValue();
-              HasBootstrap = true;
-            }
-            catch (Exception e)
-            {
-              Error = ErrorStringrange(Error, "Can't parse bootstrap value", 4,
-                                       cp + nbootstrap.matchedFrom(), nf);
-            }
-          }
-          boolean nodehasdistance=false;
-          if (ndist.search(fstring))
-          {
-            try
-            {
-              distance = (new Float(ndist.stringMatched(1))).floatValue();
-              HasDistances = true;
-              nodehasdistance = true;
-            }
-            catch (Exception e)
-            {
-              Error = ErrorStringrange(Error, "Can't parse node distance value",
-                                       7, cp + ndist.matchedFrom(), nf);
-            }
-          }
-
-          if (ascending)
-          {
-            // Write node info here
-            c.setName(nodename);
-            c.dist = (HasDistances) ? distance : 0;
-            c.setBootstrap((HasBootstrap) ? bootstrap : 0);
-            if (c==realroot) {
-              RootHasDistance = nodehasdistance; // JBPNote This is really UGLY!!!
-            }
-          }
-          else
-          {
-            // Find a place to put the leaf
-            SequenceNode newnode = new SequenceNode(null, c,
-                (HasDistances) ? distance : 0,
-                nodename);
-
-            newnode.setBootstrap(HasBootstrap ? bootstrap : 0);
-
-            if (c.right() == null)
-            {
-              c.setRight(newnode);
-            }
-            else
-            {
-              if (c.left() == null)
-              {
-                c.setLeft(newnode);
-              }
-              else
-              {
-                // Insert a dummy node for polytomy
-                SequenceNode newdummy = new SequenceNode(null, c, null, 0, 0, true);
-                newdummy.SetChildren(c.left(), newnode);
-                c.setLeft(newdummy);
-              }
-            }
-          }
-          if (ascending)
-          {
-            // move back up the tree from preceding closure
-            c = c.AscendTree();
-            if (d > -1 && c == null)
-            {
-              Error = ErrorStringrange(Error,
-                                       "File broke algorithm: Lost place in tree (is there an extra ')' ?)",
-                                       7, fcp, nf);
-            }
-          }
-
-          if (nf.charAt(fcp) == ')') {
-            d--;
-            ascending = true;
-          } else {
-            if (nf.charAt(fcp) == ',') {
-              if (ascending) {
-               ascending = false;
-             } else {
-               // Just advance focus, if we need to
-               if (c.left()!=null && (!c.left().isLeaf())) {
-                 c = (SequenceNode) c.left();
-               }
-             }
-            } // else : We do nothing if ';' is encountered.
-          }
-          // Reset new node properties to obvious fakes
-          nodename = null;
-          distance = -99999;
-          bootstrap = -99999;
-
-          cp=fcp+1;
-      }
-    }
-
-    if (Error!=null) {
-      throw(new IOException("NewickFile: "+Error+"\n"));
-    }
-
-    root = (SequenceNode) root.right().detach(); // remove the imaginary root.
-    if (!RootHasDistance) {
-      root.dist = 0;
-    }
-  }
-
-  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;
-    }
-
-  public SequenceNode getTree() {
-    return root;
-  }
-
-  public String print() {
-    synchronized (this) {
-      StringBuffer tf = new StringBuffer();
-      print(tf, root);
-      return (tf.append(";").toString());
-    }
-  }
-
-  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) {
-      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) {
-      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() {
-    return QuoteChar;
-  }
-
-  char setQuoteChar(char c) {
-    char old = QuoteChar;
-    QuoteChar = c;
-    return old;
-  }
-
-  private String nodeName(String name) {
-    if (NodeSafeName[0].search(name)) {
-      return QuoteChar + NodeSafeName[1].replaceAll(name) + QuoteChar;
-    } 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 : "");
-  }
-  private String printRootField(SequenceNode root) {
-
-      return (printRootInfo)
-          ? (( (root.getName() == null) ? ""
-               : nodeName(root.getName()))
-             + ( (HasBootstrap)
-                 ? ( (root.getBootstrap() > -1)
-                     ? " " + root.getBootstrap()
-                     : "")
-                 : "")
-             + ( (RootHasDistance)
-                 ? ":" + root.dist : ""))
-          : "";
-    }
-
-// Non recursive call deals with root node properties
-  public void print(StringBuffer tf, SequenceNode root) {
-    if (root!=null) {
-      if (root.isLeaf() && printRootInfo) {
-        tf.append(printRootField(root));
-      } else {
-        if (root.isDummy()) {
-          _print(tf, (SequenceNode) root.right());
-          _print(tf, (SequenceNode) root.left());
-        } else {
-          tf.append("(");
-          _print(tf, (SequenceNode) root.right());
-          if (root.left() != null) {
-            tf.append(",");
-          }
-          _print(tf, (SequenceNode) root.left());
-          tf.append(")" + printRootField(root));
-        }
-      }
-    }
-  }
-
-  // Recursive call for non-root nodes
-  public void _print(StringBuffer tf, SequenceNode c) {
-    if (c!=null) {
-      if (c.isLeaf()) {
-        tf.append(printNodeField(c));
-      } else {
-        if (c.isDummy()) {
-          _print(tf, (SequenceNode) c.right());
-          _print(tf, (SequenceNode) c.left());
-        } else {
-          tf.append("(");
-          _print(tf, (SequenceNode) c.right());
-          if (c.left() != null) {
-            tf.append(",");
-          }
-          _print(tf, (SequenceNode) c.left());
-          tf.append(")" + printNodeField(c));
-        }
-      }
-    }
-  }
-
-// Test
-  public static void main(String[] args)
-{
-  try
-  {
-    File fn = new File(args[0]);
-
-    StringBuffer newickfile =  new StringBuffer();
-    BufferedReader treefile =
-        new BufferedReader(new FileReader(fn));
-    String l;
-    while ((l = treefile.readLine())!=null) {
-      newickfile.append(l);
-    }
-    treefile.close();
-    System.out.println("Read file :\n");
-    NewickFile trf = new NewickFile(args[0], "File");
-    trf.parse();
-    System.out.println("Original file :\n");
-    com.stevesoft.pat.Regex nonl = new com.stevesoft.pat.Regex("\n+", "");
-    System.out.println(nonl.replaceAll(newickfile.toString())+"\n");
-
-    System.out.println("Parsed file.\n");
-    System.out.println("Default output type for original input.\n");
-    System.out.println(trf.print());
-    System.out.println("Without bootstraps.\n");
-    System.out.println(trf.print(false));
-    System.out.println("Without distances.\n");
-    System.out.println(trf.print(true,false));
-    System.out.println("Without bootstraps but with distanecs.\n");
-    System.out.println(trf.print(false, true));
-    System.out.println("Without bootstraps or distanecs.\n");
-    System.out.println(trf.print(false, false));
-    System.out.println("With bootstraps and with distances.\n");
-    System.out.println(trf.print(true, true));
-  }
-  catch (java.io.IOException e)
-  {
-    System.out.println("Exception\n" + e);
-    e.printStackTrace();
-  }
-}
-
-}
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+*/
+
+// NewickFile.java
+// Tree I/O
+// http://evolution.genetics.washington.edu/phylip/newick_doc.html
+package jalview.io;
+
+import jalview.datamodel.*;
+
+import java.io.*;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class NewickFile extends FileParse
+{
+    SequenceNode root;
+    private boolean HasBootstrap = false;
+    private boolean HasDistances = false;
+    private boolean RootHasDistance = false;
+
+    // File IO Flags
+    boolean ReplaceUnderscores = false;
+    boolean printRootInfo = false;
+    private com.stevesoft.pat.Regex[] NodeSafeName = new com.stevesoft.pat.Regex[]
+        {
+            new com.stevesoft.pat.Regex().perlCode("m/[\\[,:'()]/"), // test for requiring quotes
+            new com.stevesoft.pat.Regex().perlCode("s/'/''/"), // escaping quote characters
+            new com.stevesoft.pat.Regex().perlCode("s/\\/w/_/") // unqoted whitespace transformation
+        };
+    char QuoteChar = '\'';
+
+    /**
+     * Creates a new NewickFile object.
+     *
+     * @param inStr DOCUMENT ME!
+     *
+     * @throws IOException DOCUMENT ME!
+     */
+    public NewickFile(String inStr) throws IOException
+    {
+        super(inStr, "Paste");
+    }
+
+    /**
+     * Creates a new NewickFile object.
+     *
+     * @param inFile DOCUMENT ME!
+     * @param type DOCUMENT ME!
+     *
+     * @throws IOException DOCUMENT ME!
+     */
+    public NewickFile(String inFile, String type) throws IOException
+    {
+        super(inFile, type);
+    }
+
+    /**
+     * Creates a new NewickFile object.
+     *
+     * @param newtree DOCUMENT ME!
+     */
+    public NewickFile(SequenceNode newtree)
+    {
+        root = newtree;
+    }
+
+    /**
+     * Creates a new NewickFile object.
+     *
+     * @param newtree DOCUMENT ME!
+     * @param bootstrap DOCUMENT ME!
+     */
+    public NewickFile(SequenceNode newtree, boolean bootstrap)
+    {
+        HasBootstrap = bootstrap;
+        root = newtree;
+    }
+
+    /**
+     * Creates a new NewickFile object.
+     *
+     * @param newtree DOCUMENT ME!
+     * @param bootstrap DOCUMENT ME!
+     * @param distances DOCUMENT ME!
+     */
+    public NewickFile(SequenceNode newtree, boolean bootstrap, boolean distances)
+    {
+        root = newtree;
+        HasBootstrap = bootstrap;
+        HasDistances = distances;
+    }
+
+    /**
+     * Creates a new NewickFile object.
+     *
+     * @param newtree DOCUMENT ME!
+     * @param bootstrap DOCUMENT ME!
+     * @param distances DOCUMENT ME!
+     * @param rootdistance DOCUMENT ME!
+     */
+    public NewickFile(SequenceNode newtree, boolean bootstrap,
+        boolean distances, boolean rootdistance)
+    {
+        root = newtree;
+        HasBootstrap = bootstrap;
+        HasDistances = distances;
+        RootHasDistance = rootdistance;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param Error DOCUMENT ME!
+     * @param Er DOCUMENT ME!
+     * @param r DOCUMENT ME!
+     * @param p DOCUMENT ME!
+     * @param s DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    private String ErrorStringrange(String Error, String Er, int r, int p,
+        String s)
+    {
+        return ((Error == null) ? "" : Error) + Er + " at position " + p +
+        " ( " +
+        s.substring(((p - r) < 0) ? 0 : (p - r),
+            ((p + r) > s.length()) ? s.length() : (p + r)) + " )\n";
+    }
+
+    // @tree annotations
+    // These are set automatically by the reader
+    public boolean HasBootstrap()
+    {
+        return HasBootstrap;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public boolean HasDistances()
+    {
+        return HasDistances;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @throws IOException DOCUMENT ME!
+     */
+    public void parse() throws IOException
+    {
+        String nf;
+
+        { // fill nf with complete tree file
+
+            StringBuffer file = new StringBuffer();
+
+            while ((nf = nextLine()) != null)
+            {
+                file.append(nf);
+            }
+
+            nf = file.toString();
+        }
+
+        root = new SequenceNode();
+
+        SequenceNode realroot = null;
+        SequenceNode c = root;
+
+        int d = -1;
+        int cp = 0;
+        //int flen = nf.length();
+
+        String Error = null;
+        String nodename = null;
+
+        float DefDistance = (float) 0.00001; // @param Default distance for a node - very very small
+        int DefBootstrap = 0; // @param Default bootstrap for a node
+
+        float distance = DefDistance;
+        int bootstrap = DefBootstrap;
+
+        boolean ascending = false; // flag indicating that we are leaving the current node
+
+        com.stevesoft.pat.Regex majorsyms = new com.stevesoft.pat.Regex(
+                "[(\\['),;]");
+
+        while (majorsyms.searchFrom(nf, cp) && (Error == null))
+        {
+            int fcp = majorsyms.matchedFrom();
+
+            switch (nf.charAt(fcp))
+            {
+            case '[': // Comment or structured/extended NH format info
+
+                com.stevesoft.pat.Regex comment = new com.stevesoft.pat.Regex(
+                        "]");
+
+                if (comment.searchFrom(nf, fcp))
+                {
+                    // Skip the comment field
+                    cp = 1 + comment.matchedFrom();
+                }
+                else
+                {
+                    Error = ErrorStringrange(Error, "Unterminated comment", 3,
+                            fcp, nf);
+                }
+
+                ;
+
+                break;
+
+            case '(':
+
+                // ascending should not be set
+                // New Internal node
+                if (ascending)
+                {
+                    Error = ErrorStringrange(Error, "Unexpected '('", 7, fcp, nf);
+
+                    continue;
+                }
+
+                ;
+                d++;
+
+                if (c.right() == null)
+                {
+                    c.setRight(new SequenceNode(null, c, null, DefDistance,
+                            DefBootstrap, false));
+                    c = (SequenceNode) c.right();
+                }
+                else
+                {
+                    if (c.left() != null)
+                    {
+                        // Dummy node for polytomy - keeps c.left free for new node
+                        SequenceNode tmpn = new SequenceNode(null, c, null, 0,
+                                0, true);
+                        tmpn.SetChildren(c.left(), c.right());
+                        c.setRight(tmpn);
+                    }
+
+                    c.setLeft(new SequenceNode(null, c, null, DefDistance,
+                            DefBootstrap, false));
+                    c = (SequenceNode) c.left();
+                }
+
+                if (realroot == null)
+                {
+                    realroot = c;
+                }
+
+                nodename = null;
+                distance = DefDistance;
+                bootstrap = DefBootstrap;
+                cp = fcp + 1;
+
+                break;
+
+            // Deal with quoted fields
+            case '\'':
+
+                com.stevesoft.pat.Regex qnodename = new com.stevesoft.pat.Regex(
+                        "([^']|'')+'");
+
+                if (qnodename.searchFrom(nf, fcp))
+                {
+                    int nl = qnodename.stringMatched().length();
+                    nodename = new String(qnodename.stringMatched().substring(0,
+                                nl - 1));
+                    cp = fcp + nl + 1;
+                }
+                else
+                {
+                    Error = ErrorStringrange(Error,
+                            "Unterminated quotes for nodename", 7, fcp, nf);
+                }
+
+                break;
+
+            case ';':
+
+                if (d != -1)
+                {
+                    Error = ErrorStringrange(Error,
+                            "Wayward semicolon (depth=" + d + ")", 7, fcp, nf);
+                }
+
+            // cp advanced at the end of default
+            default:
+
+                // Parse simpler field strings
+                String fstring = nf.substring(cp, fcp);
+                com.stevesoft.pat.Regex uqnodename = new com.stevesoft.pat.Regex(
+                        "\\b([^' :;\\](),]+)");
+                com.stevesoft.pat.Regex nbootstrap = new com.stevesoft.pat.Regex(
+                        "\\S+([0-9+]+)\\S*:");
+                com.stevesoft.pat.Regex ndist = new com.stevesoft.pat.Regex(
+                        ":([-0-9.+]+)");
+
+                if (uqnodename.search(fstring) &&
+                        ((uqnodename.matchedFrom(1) == 0) ||
+                        (fstring.charAt(uqnodename.matchedFrom(1) - 1) != ':'))) // JBPNote HACK!
+                {
+                    if (nodename == null)
+                    {
+                        if (ReplaceUnderscores)
+                        {
+                            nodename = uqnodename.stringMatched(1).replace('_',
+                                    ' ');
+                        }
+                        else
+                        {
+                            nodename = uqnodename.stringMatched(1);
+                        }
+                    }
+                    else
+                    {
+                        Error = ErrorStringrange(Error,
+                                "File has broken algorithm - overwritten nodename",
+                                10, fcp, nf);
+                    }
+                }
+
+                if (nbootstrap.search(fstring) &&
+                        (nbootstrap.matchedFrom(1) > (uqnodename.matchedFrom(1) +
+                        uqnodename.stringMatched().length())))
+                {
+                    try
+                    {
+                        bootstrap = (new Integer(nbootstrap.stringMatched(1))).intValue();
+                        HasBootstrap = true;
+                    }
+                    catch (Exception e)
+                    {
+                        Error = ErrorStringrange(Error,
+                                "Can't parse bootstrap value", 4,
+                                cp + nbootstrap.matchedFrom(), nf);
+                    }
+                }
+
+                boolean nodehasdistance = false;
+
+                if (ndist.search(fstring))
+                {
+                    try
+                    {
+                        distance = (new Float(ndist.stringMatched(1))).floatValue();
+                        HasDistances = true;
+                        nodehasdistance = true;
+                    }
+                    catch (Exception e)
+                    {
+                        Error = ErrorStringrange(Error,
+                                "Can't parse node distance value", 7,
+                                cp + ndist.matchedFrom(), nf);
+                    }
+                }
+
+                if (ascending)
+                {
+                    // Write node info here
+                    c.setName(nodename);
+                    c.dist = (HasDistances) ? distance : 0;
+                    c.setBootstrap((HasBootstrap) ? bootstrap : 0);
+
+                    if (c == realroot)
+                    {
+                        RootHasDistance = nodehasdistance; // JBPNote This is really UGLY!!!
+                    }
+                }
+                else
+                {
+                    // Find a place to put the leaf
+                    SequenceNode newnode = new SequenceNode(null, c, nodename,
+                            (HasDistances) ? distance : DefDistance,
+                            (HasBootstrap) ? bootstrap : DefBootstrap, false);
+
+                    if (c.right() == null)
+                    {
+                        c.setRight(newnode);
+                    }
+                    else
+                    {
+                        if (c.left() == null)
+                        {
+                            c.setLeft(newnode);
+                        }
+                        else
+                        {
+                            // Insert a dummy node for polytomy
+                            SequenceNode newdummy = new SequenceNode(null, c,
+                                    null, 0, 0, true);
+                            newdummy.SetChildren(c.left(), newnode);
+                            c.setLeft(newdummy);
+                        }
+                    }
+                }
+
+                if (ascending)
+                {
+                    // move back up the tree from preceding closure
+                    c = c.AscendTree();
+
+                    if ((d > -1) && (c == null))
+                    {
+                        Error = ErrorStringrange(Error,
+                                "File broke algorithm: Lost place in tree (is there an extra ')' ?)",
+                                7, fcp, nf);
+                    }
+                }
+
+                if (nf.charAt(fcp) == ')')
+                {
+                    d--;
+                    ascending = true;
+                }
+                else
+                {
+                    if (nf.charAt(fcp) == ',')
+                    {
+                        if (ascending)
+                        {
+                            ascending = false;
+                        }
+                        else
+                        {
+                            // Just advance focus, if we need to
+                            if ((c.left() != null) && (!c.left().isLeaf()))
+                            {
+                                c = (SequenceNode) c.left();
+                            }
+                        }
+                    }
+
+                    // else : We do nothing if ';' is encountered.
+                }
+
+                // Reset new node properties to obvious fakes
+                nodename = null;
+                distance = DefDistance;
+                bootstrap = DefBootstrap;
+
+                cp = fcp + 1;
+            }
+        }
+
+        if (Error != null)
+        {
+            throw (new IOException("NewickFile: " + Error + "\n"));
+        }
+
+        root = (SequenceNode) root.right().detach(); // remove the imaginary root.
+
+        if (!RootHasDistance)
+        {
+            root.dist = 0;
+        }
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public SequenceNode getTree()
+    {
+        return root;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String print()
+    {
+        synchronized (this)
+        {
+            StringBuffer tf = new StringBuffer();
+            print(tf, root);
+
+            return (tf.append(";").toString());
+        }
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param withbootstraps DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String print(boolean withbootstraps)
+    {
+        synchronized (this)
+        {
+            boolean boots = this.HasBootstrap;
+            this.HasBootstrap = withbootstraps;
+
+            String rv = print();
+            this.HasBootstrap = boots;
+
+            return rv;
+        }
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param withbootstraps DOCUMENT ME!
+     * @param withdists DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String print(boolean withbootstraps, boolean withdists)
+    {
+        synchronized (this)
+        {
+            boolean dists = this.HasDistances;
+            this.HasDistances = withdists;
+
+            String rv = print(withbootstraps);
+            this.HasDistances = dists;
+
+            return rv;
+        }
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param withbootstraps DOCUMENT ME!
+     * @param withdists DOCUMENT ME!
+     * @param printRootInfo DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public String print(boolean withbootstraps, boolean withdists,
+        boolean printRootInfo)
+    {
+        synchronized (this)
+        {
+            boolean rootinfo = printRootInfo;
+            this.printRootInfo = printRootInfo;
+
+            String rv = print(withbootstraps, withdists);
+            this.printRootInfo = rootinfo;
+
+            return rv;
+        }
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    char getQuoteChar()
+    {
+        return QuoteChar;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param c DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    char setQuoteChar(char c)
+    {
+        char old = QuoteChar;
+        QuoteChar = c;
+
+        return old;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param name DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    private String nodeName(String name)
+    {
+        if (NodeSafeName[0].search(name))
+        {
+            return QuoteChar + NodeSafeName[1].replaceAll(name) + QuoteChar;
+        }
+        else
+        {
+            return NodeSafeName[2].replaceAll(name);
+        }
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param c DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    private String printNodeField(SequenceNode c)
+    {
+        return ((c.getName() == null) ? "" : nodeName(c.getName())) +
+        ((HasBootstrap)
+        ? ((c.getBootstrap() > -1) ? (" " + c.getBootstrap()) : "") : "") +
+        ((HasDistances) ? (":" + c.dist) : "");
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param root DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    private String printRootField(SequenceNode root)
+    {
+        return (printRootInfo)
+        ? (((root.getName() == null) ? "" : nodeName(root.getName())) +
+        ((HasBootstrap)
+        ? ((root.getBootstrap() > -1) ? (" " + root.getBootstrap()) : "") : "") +
+        ((RootHasDistance) ? (":" + root.dist) : "")) : "";
+    }
+
+    // Non recursive call deals with root node properties
+    public void print(StringBuffer tf, SequenceNode root)
+    {
+        if (root != null)
+        {
+            if (root.isLeaf() && printRootInfo)
+            {
+                tf.append(printRootField(root));
+            }
+            else
+            {
+                if (root.isDummy())
+                {
+                    _print(tf, (SequenceNode) root.right());
+                    _print(tf, (SequenceNode) root.left());
+                }
+                else
+                {
+                    tf.append("(");
+                    _print(tf, (SequenceNode) root.right());
+
+                    if (root.left() != null)
+                    {
+                        tf.append(",");
+                    }
+
+                    _print(tf, (SequenceNode) root.left());
+                    tf.append(")" + printRootField(root));
+                }
+            }
+        }
+    }
+
+    // Recursive call for non-root nodes
+    public void _print(StringBuffer tf, SequenceNode c)
+    {
+        if (c != null)
+        {
+            if (c.isLeaf())
+            {
+                tf.append(printNodeField(c));
+            }
+            else
+            {
+                if (c.isDummy())
+                {
+                    _print(tf, (SequenceNode) c.right());
+                    _print(tf, (SequenceNode) c.left());
+                }
+                else
+                {
+                    tf.append("(");
+                    _print(tf, (SequenceNode) c.right());
+
+                    if (c.left() != null)
+                    {
+                        tf.append(",");
+                    }
+
+                    _print(tf, (SequenceNode) c.left());
+                    tf.append(")" + printNodeField(c));
+                }
+            }
+        }
+    }
+
+    // Test
+    public static void main(String[] args)
+    {
+        try
+        {
+            File fn = new File(args[0]);
+
+            StringBuffer newickfile = new StringBuffer();
+            BufferedReader treefile = new BufferedReader(new FileReader(fn));
+            String l;
+
+            while ((l = treefile.readLine()) != null)
+            {
+                newickfile.append(l);
+            }
+
+            treefile.close();
+            System.out.println("Read file :\n");
+
+            NewickFile trf = new NewickFile(args[0], "File");
+            trf.parse();
+            System.out.println("Original file :\n");
+
+            com.stevesoft.pat.Regex nonl = new com.stevesoft.pat.Regex("\n+", "");
+            System.out.println(nonl.replaceAll(newickfile.toString()) + "\n");
+
+            System.out.println("Parsed file.\n");
+            System.out.println("Default output type for original input.\n");
+            System.out.println(trf.print());
+            System.out.println("Without bootstraps.\n");
+            System.out.println(trf.print(false));
+            System.out.println("Without distances.\n");
+            System.out.println(trf.print(true, false));
+            System.out.println("Without bootstraps but with distanecs.\n");
+            System.out.println(trf.print(false, true));
+            System.out.println("Without bootstraps or distanecs.\n");
+            System.out.println(trf.print(false, false));
+            System.out.println("With bootstraps and with distances.\n");
+            System.out.println(trf.print(true, true));
+        }
+        catch (java.io.IOException e)
+        {
+            System.err.println("Exception\n" + e);
+            e.printStackTrace();
+        }
+    }
+}