X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FNewickFile.java;h=b3c0011b52ea2d1ad4284cb7faf4fbc1566d6189;hb=9fd03d86789221ae4f6cf720cadf3d99cc68ac33;hp=2221f0090a29830112daf03331f4650e49dcac5c;hpb=3027bfb4b1b13af8686abcd419888e03141bd672;p=jalview.git

diff --git a/src/jalview/io/NewickFile.java b/src/jalview/io/NewickFile.java
index 2221f00..b3c0011 100755
--- a/src/jalview/io/NewickFile.java
+++ b/src/jalview/io/NewickFile.java
@@ -26,15 +26,20 @@
 // TODO: Extended SequenceNodeI to hold parsed NHX strings
 package jalview.io;
 
-import jalview.datamodel.SequenceNode;
-import jalview.util.MessageManager;
-
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileReader;
 import java.io.IOException;
+import java.util.Locale;
 import java.util.StringTokenizer;
 
+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
  * tree distances and topology are unreliable when they are parsed. TODO: on
@@ -74,7 +79,7 @@ import java.util.StringTokenizer;
  */
 public class NewickFile extends FileParse
 {
-  SequenceNode root;
+  BinaryNode root;
 
   private boolean HasBootstrap = false;
 
@@ -87,13 +92,13 @@ 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
+  private Regex[] NodeSafeName = new Regex[] {
+      new Regex().perlCode("m/[\\[,:'()]/"), // test for
       // requiring
       // quotes
-      new com.stevesoft.pat.Regex().perlCode("s/'/''/"), // escaping quote
+      new Regex().perlCode("s/'/''/"), // escaping quote
       // characters
-      new com.stevesoft.pat.Regex().perlCode("s/\\/w/_/") // unqoted whitespace
+      new Regex().perlCode("s/\\/w/_/") // unqoted whitespace
       // transformation
   };
 
@@ -141,7 +146,7 @@ public class NewickFile extends FileParse
    * @param newtree
    *          DOCUMENT ME!
    */
-  public NewickFile(SequenceNode newtree)
+  public NewickFile(BinaryNode newtree)
   {
     root = newtree;
   }
@@ -170,7 +175,7 @@ public class NewickFile extends FileParse
    * @param distances
    *          DOCUMENT ME!
    */
-  public NewickFile(SequenceNode newtree, boolean bootstrap,
+  public NewickFile(BinaryNode newtree, boolean bootstrap,
           boolean distances)
   {
     root = newtree;
@@ -190,7 +195,7 @@ public class NewickFile extends FileParse
    * @param rootdistance
    *          DOCUMENT ME!
    */
-  public NewickFile(SequenceNode newtree, boolean bootstrap,
+  public NewickFile(BinaryNode newtree, boolean bootstrap,
           boolean distances, boolean rootdistance)
   {
     root = newtree;
@@ -271,8 +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;
@@ -282,18 +287,17 @@ 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 -
+    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
 
-    com.stevesoft.pat.Regex majorsyms = new com.stevesoft.pat.Regex(
-            "[(\\['),;]");
+    Regex majorsyms = new Regex("[(\\['),;]");
 
     int nextcp = 0;
     int ncp = cp;
@@ -314,29 +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)
@@ -354,8 +356,7 @@ 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))
         {
@@ -363,8 +364,7 @@ public class NewickFile extends FileParse
           nodename = new String(
                   qnodename.stringMatched().substring(1, nl - 1));
           // unpack any escaped colons
-          com.stevesoft.pat.Regex xpandquotes = com.stevesoft.pat.Regex
-                  .perlCode("s/''/'/");
+          Regex xpandquotes = Regex.perlCode("s/''/'/");
           String widernodename = xpandquotes.replaceAll(nodename);
           nodename = widernodename;
           // jump to after end of quoted nodename
@@ -398,8 +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
@@ -415,8 +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);
@@ -432,12 +429,9 @@ 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.+]+)");
+        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
@@ -494,7 +488,8 @@ public class NewickFile extends FileParse
         {
           try
           {
-            distance = (Float.valueOf(ndist.stringMatched(1))).floatValue();
+            distance = (Double.valueOf(ndist.stringMatched(1)))
+                    .floatValue();
             HasDistances = true;
             nodehasdistance = true;
           } catch (Exception e)
@@ -525,7 +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);
@@ -545,7 +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);
@@ -584,7 +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();
               }
             }
           }
@@ -638,7 +633,7 @@ 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
@@ -658,7 +653,7 @@ public class NewickFile extends FileParse
           try
           {
             // parse out code/value pairs
-            if (code.toLowerCase().equals("b"))
+            if (code.toLowerCase(Locale.ROOT).equals("b"))
             {
               int v = -1;
               Float iv = Float.valueOf(value);
@@ -685,7 +680,7 @@ public class NewickFile extends FileParse
    * 
    * @return DOCUMENT ME!
    */
-  public SequenceNode getTree()
+  public BinaryNode getTree()
   {
     return root;
   }
@@ -839,7 +834,7 @@ public class NewickFile extends FileParse
    * 
    * @return DOCUMENT ME!
    */
-  private String printNodeField(SequenceNode c)
+  private String printNodeField(BinaryNode c)
   {
     return ((c.getName() == null) ? "" : nodeName(c.getName()))
             + ((HasBootstrap) ? ((c.getBootstrap() > -1)
@@ -856,7 +851,7 @@ public class NewickFile extends FileParse
    * 
    * @return DOCUMENT ME!
    */
-  private String printRootField(SequenceNode root)
+  private String printRootField(BinaryNode root)
   {
     return (printRootInfo)
             ? (((root.getName() == null) ? "" : nodeName(root.getName()))
@@ -871,7 +866,7 @@ public class NewickFile extends FileParse
   }
 
   // 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)
     {
@@ -883,20 +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));
         }
       }
@@ -904,7 +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)
     {
@@ -916,40 +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]);
@@ -970,7 +968,7 @@ public class NewickFile extends FileParse
       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");