X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FNewickFile.java;h=b3c0011b52ea2d1ad4284cb7faf4fbc1566d6189;hb=42e022a59de649375c8878c1d26361cb6bc89cb8;hp=9a7f6fb9ff0dae4dccaa96bec65f06b94f141b74;hpb=ab9e5bf849afd2f41102db0bf9893de1df0512f6;p=jalview.git

diff --git a/src/jalview/io/NewickFile.java b/src/jalview/io/NewickFile.java
index 9a7f6fb..b3c0011 100755
--- a/src/jalview/io/NewickFile.java
+++ b/src/jalview/io/NewickFile.java
@@ -1,22 +1,23 @@
 /*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
  * of the License, or (at your option) any later version.
- *
- * 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.
- *
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
  * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
-
 // NewickFile.java
 // Tree I/O
 // http://evolution.genetics.washington.edu/phylip/newick_doc.html
@@ -25,10 +26,19 @@
 // TODO: Extended SequenceNodeI to hold parsed NHX strings
 package jalview.io;
 
-import java.io.*;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.Locale;
 import java.util.StringTokenizer;
 
-import jalview.datamodel.*;
+import com.stevesoft.pat.Regex;
+
+import jalview.bin.Jalview;
+import jalview.datamodel.BinaryNode;
+import jalview.datamodel.SequenceNode;
+import jalview.util.MessageManager;
 
 /**
  * Parse a new hanpshire style tree Caveats: NHX files are NOT supported and the
@@ -36,10 +46,10 @@ import jalview.datamodel.*;
  * this: NHX codes are appended in comments beginning with &&NHX. The codes are
  * given below (from http://www.phylosoft.org/forester/NHX.html): Element Type
  * Description Corresponding phyloXML element (parent element in parentheses) no
- * tag string name of this node/clade (MUST BE FIRST, IF ASSIGNED) <name>(<clade>) :
- * decimal branch length to parent node (MUST BE SECOND, IF ASSIGNED)
- * <branch_length>(<clade>) :GN= string gene name <name>(<sequence>) :AC=
- * string sequence accession <accession>(<sequence>) :ND= string node
+ * tag string name of this node/clade (MUST BE FIRST, IF ASSIGNED)
+ * <name>(<clade>) : decimal branch length to parent node (MUST BE SECOND, IF
+ * ASSIGNED) <branch_length>(<clade>) :GN= string gene name <name>(<sequence>)
+ * :AC= string sequence accession <accession>(<sequence>) :ND= string node
  * identifier - if this is being used, it has to be unique within each phylogeny
  * <node_id>(<clade>) :B= decimal confidence value for parent branch
  * <confidence>(<clade>) :D= 'T', 'F', or '?' 'T' if this node represents a
@@ -69,7 +79,7 @@ import jalview.datamodel.*;
  */
 public class NewickFile extends FileParse
 {
-  SequenceNode root;
+  BinaryNode root;
 
   private boolean HasBootstrap = false;
 
@@ -82,14 +92,14 @@ public class NewickFile extends FileParse
 
   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
+  private Regex[] NodeSafeName = new Regex[] {
+      new Regex().perlCode("m/[\\[,:'()]/"), // test for
+      // requiring
+      // quotes
+      new Regex().perlCode("s/'/''/"), // escaping quote
+      // characters
+      new Regex().perlCode("s/\\/w/_/") // unqoted whitespace
+      // transformation
   };
 
   char QuoteChar = '\'';
@@ -98,30 +108,31 @@ public class NewickFile extends FileParse
    * Creates a new NewickFile object.
    * 
    * @param inStr
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @throws IOException
-   *                 DOCUMENT ME!
+   *           DOCUMENT ME!
    */
   public NewickFile(String inStr) throws IOException
   {
-    super(inStr, "Paste");
+    super(inStr, DataSourceType.PASTE);
   }
 
   /**
    * Creates a new NewickFile object.
    * 
    * @param inFile
-   *                DOCUMENT ME!
-   * @param type
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
+   * @param protocol
+   *          DOCUMENT ME!
    * 
    * @throws IOException
-   *                 DOCUMENT ME!
+   *           DOCUMENT ME!
    */
-  public NewickFile(String inFile, String type) throws IOException
+  public NewickFile(String inFile, DataSourceType protocol)
+          throws IOException
   {
-    super(inFile, type);
+    super(inFile, protocol);
   }
 
   public NewickFile(FileParse source) throws IOException
@@ -133,9 +144,9 @@ public class NewickFile extends FileParse
    * Creates a new NewickFile object.
    * 
    * @param newtree
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
-  public NewickFile(SequenceNode newtree)
+  public NewickFile(BinaryNode newtree)
   {
     root = newtree;
   }
@@ -144,9 +155,9 @@ public class NewickFile extends FileParse
    * Creates a new NewickFile object.
    * 
    * @param newtree
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param bootstrap
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public NewickFile(SequenceNode newtree, boolean bootstrap)
   {
@@ -158,13 +169,13 @@ public class NewickFile extends FileParse
    * Creates a new NewickFile object.
    * 
    * @param newtree
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param bootstrap
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param distances
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
-  public NewickFile(SequenceNode newtree, boolean bootstrap,
+  public NewickFile(BinaryNode newtree, boolean bootstrap,
           boolean distances)
   {
     root = newtree;
@@ -176,15 +187,15 @@ public class NewickFile extends FileParse
    * Creates a new NewickFile object.
    * 
    * @param newtree
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param bootstrap
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param distances
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param rootdistance
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
-  public NewickFile(SequenceNode newtree, boolean bootstrap,
+  public NewickFile(BinaryNode newtree, boolean bootstrap,
           boolean distances, boolean rootdistance)
   {
     root = newtree;
@@ -197,28 +208,25 @@ public class NewickFile extends FileParse
    * DOCUMENT ME!
    * 
    * @param Error
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param Er
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param r
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param p
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param s
-   *                DOCUMENT ME!
+   *          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";
+    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
@@ -247,8 +255,8 @@ public class NewickFile extends FileParse
    * 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
+   *           with a line number and character position for badly formatted NH
+   *           strings
    */
   public void parse() throws IOException
   {
@@ -268,8 +276,8 @@ public class NewickFile extends FileParse
 
     root = new SequenceNode();
 
-    SequenceNode realroot = null;
-    SequenceNode c = root;
+    BinaryNode realroot = null;
+    BinaryNode c = root;
 
     int d = -1;
     int cp = 0;
@@ -279,21 +287,21 @@ public class NewickFile extends FileParse
     String nodename = null;
     String commentString2 = null; // comments after simple node props
 
-    float DefDistance = (float) 0.001; // @param Default distance for a node -
-                                        // very very small
+    double 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;
+    double distance = DefDistance;
     int bootstrap = DefBootstrap;
 
     boolean ascending = false; // flag indicating that we are leaving the
-                                // current node
+    // current node
 
-    com.stevesoft.pat.Regex majorsyms = new com.stevesoft.pat.Regex(
-            "[(\\['),;]");
+    Regex majorsyms = new Regex("[(\\['),;]");
 
     int nextcp = 0;
     int ncp = cp;
+    boolean parsednodename = false;
     while (majorsyms.searchFrom(nf, cp) && (Error == null))
     {
       int fcp = majorsyms.matchedFrom();
@@ -310,29 +318,27 @@ public class NewickFile extends FileParse
 
           continue;
         }
-
-        ;
         d++;
 
         if (c.right() == null)
         {
           c.setRight(new SequenceNode(null, c, null, DefDistance,
                   DefBootstrap, false));
-          c = (SequenceNode) c.right();
+          c = (BinaryNode) 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);
+            BinaryNode tmpn = new SequenceNode(null, c, null, 0, 0, true);
             tmpn.SetChildren(c.left(), c.right());
             c.setRight(tmpn);
           }
 
           c.setLeft(new SequenceNode(null, c, null, DefDistance,
                   DefBootstrap, false));
-          c = (SequenceNode) c.left();
+          c = (BinaryNode) c.left();
         }
 
         if (realroot == null)
@@ -350,15 +356,20 @@ public class NewickFile extends FileParse
       // Deal with quoted fields
       case '\'':
 
-        com.stevesoft.pat.Regex qnodename = new com.stevesoft.pat.Regex(
-                "([^']|'')+'");
+        Regex qnodename = new Regex("'([^']|'')+'");
 
         if (qnodename.searchFrom(nf, fcp))
         {
           int nl = qnodename.stringMatched().length();
-          nodename = new String(qnodename.stringMatched().substring(0,
-                  nl - 1));
-          cp = fcp + nl + 1;
+          nodename = new String(
+                  qnodename.stringMatched().substring(1, nl - 1));
+          // unpack any escaped colons
+          Regex xpandquotes = Regex.perlCode("s/''/'/");
+          String widernodename = xpandquotes.replaceAll(nodename);
+          nodename = widernodename;
+          // jump to after end of quoted nodename
+          nextcp = fcp + nl + 1;
+          parsednodename = true;
         }
         else
         {
@@ -373,8 +384,8 @@ public class NewickFile extends FileParse
         {
           if (d != -1)
           {
-            Error = ErrorStringrange(Error, "Wayward semicolon (depth=" + d
-                    + ")", 7, fcp, nf);
+            Error = ErrorStringrange(Error,
+                    "Wayward semicolon (depth=" + d + ")", 7, fcp, nf);
           }
           // cp advanced at the end of default
         }
@@ -387,7 +398,7 @@ public class NewickFile extends FileParse
            * '"+nf.substring(cp,fcp)+"'"); }
            */
           // verify termination.
-          com.stevesoft.pat.Regex comment = new com.stevesoft.pat.Regex("]");
+          Regex comment = new Regex("]");
           if (comment.searchFrom(nf, fcp))
           {
             // Skip the comment field
@@ -403,8 +414,6 @@ public class NewickFile extends FileParse
             Error = ErrorStringrange(Error, "Unterminated comment", 3, fcp,
                     nf);
           }
-
-          ;
         }
         // Parse simpler field strings
         String fstring = nf.substring(ncp, fcp);
@@ -420,17 +429,14 @@ public class NewickFile extends FileParse
                   + fstring.substring(cend + 1);
 
         }
-        com.stevesoft.pat.Regex uqnodename = new com.stevesoft.pat.Regex(
-                "\\b([^' :;\\](),]+)");
-        com.stevesoft.pat.Regex nbootstrap = new com.stevesoft.pat.Regex(
-                "\\s*([0-9+]+)\\s*:");
-        com.stevesoft.pat.Regex ndist = new com.stevesoft.pat.Regex(
-                ":([-0-9Ee.+]+)");
-
-        if (uqnodename.search(fstring)
+        Regex uqnodename = new Regex("\\b([^' :;\\](),]+)");
+        Regex nbootstrap = new Regex("\\s*([0-9+]+)\\s*:");
+        Regex ndist = new Regex(":([-0-9Ee.+]+)");
+
+        if (!parsednodename && uqnodename.search(fstring)
                 && ((uqnodename.matchedFrom(1) == 0) || (fstring
                         .charAt(uqnodename.matchedFrom(1) - 1) != ':'))) // JBPNote
-                                                                          // HACK!
+        // HACK!
         {
           if (nodename == null)
           {
@@ -454,26 +460,24 @@ public class NewickFile extends FileParse
 
         if (nbootstrap.search(fstring))
         {
-          if (nbootstrap.stringMatched(1).equals(
-                  uqnodename.stringMatched(1)))
+          if (nbootstrap.stringMatched(1)
+                  .equals(uqnodename.stringMatched(1)))
           {
             nodename = null; // no nodename here.
           }
-          if (nodename == null
-                  || nodename.length() == 0
-                  || nbootstrap.matchedFrom(1) > (uqnodename.matchedFrom(1) + uqnodename
-                          .stringMatched().length()))
+          if (nodename == null || nodename.length() == 0
+                  || nbootstrap.matchedFrom(1) > (uqnodename.matchedFrom(1)
+                          + uqnodename.stringMatched().length()))
           {
             try
             {
-              bootstrap = (new Integer(nbootstrap.stringMatched(1)))
+              bootstrap = (Integer.valueOf(nbootstrap.stringMatched(1)))
                       .intValue();
               HasBootstrap = true;
             } catch (Exception e)
             {
-              Error = ErrorStringrange(Error,
-                      "Can't parse bootstrap value", 4, ncp
-                              + nbootstrap.matchedFrom(), nf);
+              Error = ErrorStringrange(Error, "Can't parse bootstrap value",
+                      4, ncp + nbootstrap.matchedFrom(), nf);
             }
           }
         }
@@ -484,14 +488,15 @@ public class NewickFile extends FileParse
         {
           try
           {
-            distance = (new Float(ndist.stringMatched(1))).floatValue();
+            distance = (Double.valueOf(ndist.stringMatched(1)))
+                    .floatValue();
             HasDistances = true;
             nodehasdistance = true;
           } catch (Exception e)
           {
             Error = ErrorStringrange(Error,
-                    "Can't parse node distance value", 7, ncp
-                            + ndist.matchedFrom(), nf);
+                    "Can't parse node distance value", 7,
+                    ncp + ndist.matchedFrom(), nf);
           }
         }
 
@@ -506,8 +511,8 @@ public class NewickFile extends FileParse
           if (c == realroot)
           {
             RootHasDistance = nodehasdistance; // JBPNote This is really
-                                                // UGLY!!! Ensure root node gets
-                                                // its given distance
+            // UGLY!!! Ensure root node gets
+            // its given distance
           }
           parseNHXNodeProps(c, commentString2);
           commentString2 = null;
@@ -515,7 +520,7 @@ public class NewickFile extends FileParse
         else
         {
           // Find a place to put the leaf
-          SequenceNode newnode = new SequenceNode(null, c, nodename,
+          BinaryNode newnode = new SequenceNode(null, c, nodename,
                   (HasDistances) ? distance : DefDistance,
                   (HasBootstrap) ? bootstrap : DefBootstrap, false);
           parseNHXNodeProps(c, commentString2);
@@ -535,7 +540,7 @@ public class NewickFile extends FileParse
             {
               // Insert a dummy node for polytomy
               // dummy nodes have distances
-              SequenceNode newdummy = new SequenceNode(null, c, null,
+              BinaryNode newdummy = new SequenceNode(null, c, null,
                       (HasDistances ? 0 : DefDistance), 0, true);
               newdummy.SetChildren(c.left(), newnode);
               c.setLeft(newdummy);
@@ -550,8 +555,7 @@ public class NewickFile extends FileParse
 
           if ((d > -1) && (c == null))
           {
-            Error = ErrorStringrange(
-                    Error,
+            Error = ErrorStringrange(Error,
                     "File broke algorithm: Lost place in tree (is there an extra ')' ?)",
                     7, fcp, nf);
           }
@@ -575,7 +579,7 @@ public class NewickFile extends FileParse
               // Just advance focus, if we need to
               if ((c.left() != null) && (!c.left().isLeaf()))
               {
-                c = (SequenceNode) c.left();
+                c = (BinaryNode) c.left();
               }
             }
           }
@@ -585,7 +589,8 @@ public class NewickFile extends FileParse
         nodename = null;
         distance = DefDistance;
         bootstrap = DefBootstrap;
-        commentString2=null;
+        commentString2 = null;
+        parsednodename = false;
       }
       if (nextcp == 0)
       {
@@ -600,11 +605,15 @@ public class NewickFile extends FileParse
 
     if (Error != null)
     {
-      throw (new IOException("NewickFile: " + Error + "\n"));
+      throw (new IOException(
+              MessageManager.formatMessage("exception.newfile", new String[]
+              { Error.toString() })));
     }
     if (root == null)
     {
-      throw (new IOException("NewickFile: No Tree read in\n"));
+      throw (new IOException(
+              MessageManager.formatMessage("exception.newfile", new String[]
+              { MessageManager.getString("label.no_tree_read_in") })));
     }
     // THe next line is failing for topali trees - not sure why yet. if
     // (root.right()!=null && root.isDummy())
@@ -624,45 +633,46 @@ public class NewickFile extends FileParse
    * @param commentString
    * @param commentString2
    */
-  private void parseNHXNodeProps(SequenceNode c, String commentString)
+  private void parseNHXNodeProps(BinaryNode c, String commentString)
   {
     // TODO: store raw comment on the sequenceNode so it can be recovered when
     // tree is output
     if (commentString != null && commentString.startsWith("&&NHX"))
     {
-      StringTokenizer st = new StringTokenizer(commentString.substring(5),":");
+      StringTokenizer st = new StringTokenizer(commentString.substring(5),
+              ":");
       while (st.hasMoreTokens())
       {
         String tok = st.nextToken();
-        int colpos=tok.indexOf("=");
+        int colpos = tok.indexOf("=");
 
-        if (colpos>-1)
+        if (colpos > -1)
         {
           String code = tok.substring(0, colpos);
-          String value = tok.substring(colpos+1);
-          try {
+          String value = tok.substring(colpos + 1);
+          try
+          {
             // parse out code/value pairs
-            if (code.toLowerCase().equals("b"))
+            if (code.toLowerCase(Locale.ROOT).equals("b"))
             {
-              int v=-1;
-              Float iv = new Float(value);
+              int v = -1;
+              Float iv = Float.valueOf(value);
               v = iv.intValue(); // jalview only does integer bootstraps
-                                  // currently
+              // currently
               c.setBootstrap(v);
               HasBootstrap = true;
             }
             // more codes here.
-          }
-          catch (Exception e)
+          } catch (Exception e)
           {
-            System.err.println("Couldn't parse code '"+code+"' = '"+value+"'");
+            System.err.println(
+                    "Couldn't parse code '" + code + "' = '" + value + "'");
             e.printStackTrace(System.err);
           }
         }
       }
     }
-        
-      
+
   }
 
   /**
@@ -670,7 +680,7 @@ public class NewickFile extends FileParse
    * 
    * @return DOCUMENT ME!
    */
-  public SequenceNode getTree()
+  public BinaryNode getTree()
   {
     return root;
   }
@@ -699,7 +709,7 @@ public class NewickFile extends FileParse
    * root distances and user specificied writing of bootstraps.
    * 
    * @param withbootstraps
-   *                controls if bootstrap values are explicitly written.
+   *          controls if bootstrap values are explicitly written.
    * 
    * @return new hampshire tree in a single line
    */
@@ -723,9 +733,9 @@ public class NewickFile extends FileParse
    * node distances.
    * 
    * @param withbootstraps
-   *                explicitly write bootstrap values
+   *          explicitly write bootstrap values
    * @param withdists
-   *                explicitly write distances
+   *          explicitly write distances
    * 
    * @return new hampshire tree in a single line
    */
@@ -747,11 +757,11 @@ public class NewickFile extends FileParse
    * Generate newick format tree according to user specified flags
    * 
    * @param withbootstraps
-   *                explicitly write bootstrap values
+   *          explicitly write bootstrap values
    * @param withdists
-   *                explicitly write distances
+   *          explicitly write distances
    * @param printRootInfo
-   *                explicitly write root distance
+   *          explicitly write root distance
    * 
    * @return new hampshire tree in a single line
    */
@@ -784,7 +794,7 @@ public class NewickFile extends FileParse
    * DOCUMENT ME!
    * 
    * @param c
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
@@ -800,7 +810,7 @@ public class NewickFile extends FileParse
    * DOCUMENT ME!
    * 
    * @param name
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
@@ -820,39 +830,43 @@ public class NewickFile extends FileParse
    * DOCUMENT ME!
    * 
    * @param c
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
-  private String printNodeField(SequenceNode c)
+  private String printNodeField(BinaryNode c)
   {
     return ((c.getName() == null) ? "" : nodeName(c.getName()))
-            + ((HasBootstrap) ? ((c.getBootstrap() > -1) ? ((c.getName() != null ? " "
-                    : "") + c.getBootstrap())
-                    : "")
-                    : "") + ((HasDistances) ? (":" + c.dist) : "");
+            + ((HasBootstrap) ? ((c.getBootstrap() > -1)
+                    ? ((c.getName() != null ? " " : "") + c.getBootstrap())
+                    : "") : "")
+            + ((HasDistances) ? (":" + c.dist) : "");
   }
 
   /**
    * DOCUMENT ME!
    * 
    * @param root
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
-  private String printRootField(SequenceNode root)
+  private String printRootField(BinaryNode root)
   {
-    return (printRootInfo) ? (((root.getName() == null) ? ""
-            : nodeName(root.getName()))
-            + ((HasBootstrap) ? ((root.getBootstrap() > -1) ? ((root
-                    .getName() != null ? " " : "") + +root.getBootstrap())
-                    : "") : "") + ((RootHasDistance) ? (":" + root.dist)
-            : "")) : "";
+    return (printRootInfo)
+            ? (((root.getName() == null) ? "" : nodeName(root.getName()))
+                    + ((HasBootstrap)
+                            ? ((root.getBootstrap() > -1)
+                                    ? ((root.getName() != null ? " " : "")
+                                            + +root.getBootstrap())
+                                    : "")
+                            : "")
+                    + ((RootHasDistance) ? (":" + root.dist) : ""))
+            : "";
   }
 
   // Non recursive call deals with root node properties
-  public void print(StringBuffer tf, SequenceNode root)
+  public void print(StringBuffer tf, BinaryNode root)
   {
     if (root != null)
     {
@@ -864,20 +878,20 @@ public class NewickFile extends FileParse
       {
         if (root.isDummy())
         {
-          _print(tf, (SequenceNode) root.right());
-          _print(tf, (SequenceNode) root.left());
+          _print(tf, root.right());
+          _print(tf, root.left());
         }
         else
         {
           tf.append("(");
-          _print(tf, (SequenceNode) root.right());
+          _print(tf, root.right());
 
           if (root.left() != null)
           {
             tf.append(",");
           }
 
-          _print(tf, (SequenceNode) root.left());
+          _print(tf, root.left());
           tf.append(")" + printRootField(root));
         }
       }
@@ -885,7 +899,7 @@ public class NewickFile extends FileParse
   }
 
   // Recursive call for non-root nodes
-  public void _print(StringBuffer tf, SequenceNode c)
+  public void _print(StringBuffer tf, BinaryNode c)
   {
     if (c != null)
     {
@@ -897,40 +911,43 @@ public class NewickFile extends FileParse
       {
         if (c.isDummy())
         {
-          _print(tf, (SequenceNode) c.left());
+          _print(tf, c.left());
           if (c.left() != null)
           {
             tf.append(",");
           }
-          _print(tf, (SequenceNode) c.right());
+          _print(tf, c.right());
         }
         else
         {
           tf.append("(");
-          _print(tf, (SequenceNode) c.right());
+          _print(tf, c.right());
 
           if (c.left() != null)
           {
             tf.append(",");
           }
 
-          _print(tf, (SequenceNode) c.left());
+          _print(tf, c.left());
           tf.append(")" + printNodeField(c));
         }
       }
     }
   }
 
-  // Test
+  /**
+   * 
+   * @param args
+   * @j2sIgnore
+   */
   public static void main(String[] args)
   {
     try
     {
       if (args == null || args.length != 1)
       {
-        System.err
-                .println("Takes one argument - file name of a newick tree file.");
-        System.exit(0);
+        Jalview.exit(
+                "Takes one argument - file name of a newick tree file.", 0);
       }
 
       File fn = new File(args[0]);
@@ -947,11 +964,11 @@ public class NewickFile extends FileParse
       treefile.close();
       System.out.println("Read file :\n");
 
-      NewickFile trf = new NewickFile(args[0], "File");
+      NewickFile trf = new NewickFile(args[0], DataSourceType.FILE);
       trf.parse();
       System.out.println("Original file :\n");
 
-      com.stevesoft.pat.Regex nonl = new com.stevesoft.pat.Regex("\n+", "");
+      Regex nonl = new Regex("\n+", "");
       System.out.println(nonl.replaceAll(newickfile.toString()) + "\n");
 
       System.out.println("Parsed file.\n");