From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Wed, 22 Aug 2007 12:50:47 +0000 (+0000)
Subject: fixed regex and made 'improper' support for parsing NHX style trees TODO: FIX THIS
X-Git-Tag: Release_0.2~78
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=b13bd9e539bc62536bcd723b0682914a133b0c5a;p=vamsas.git

fixed regex and made 'improper' support for parsing NHX style trees TODO: FIX THIS

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@442 be28352e-c001-0410-b1a7-c7978e42abec
---

diff --git a/src/uk/ac/vamsas/objects/utils/trees/NewickFile.java b/src/uk/ac/vamsas/objects/utils/trees/NewickFile.java
index f8e49aa..3c41744 100644
--- a/src/uk/ac/vamsas/objects/utils/trees/NewickFile.java
+++ b/src/uk/ac/vamsas/objects/utils/trees/NewickFile.java
@@ -27,7 +27,6 @@
 // TODO: Extended SequenceNodeI to hold parsed NHX strings
 package uk.ac.vamsas.objects.utils.trees;
 
-
 import java.io.*;
 import java.util.Enumeration;
 import java.util.Hashtable;
@@ -55,7 +54,7 @@ public class NewickFile {
   private boolean RootHasDistance = false;
 
   // File IO Flags
-  boolean ReplaceUnderscores = false;
+  boolean ReplaceUnderscores = true;
 
   boolean printRootInfo = false;
 
@@ -82,11 +81,14 @@ public class NewickFile {
     newickFile = inStr;
     parse();
   }
+
   public NewickFile(File inFile) throws IOException {
-    errormessage = "Problem's reading file "+inFile;
-    dataIn = new java.io.BufferedReader(new InputStreamReader(new java.io.FileInputStream(inFile)));
+    errormessage = "Problem's reading file " + inFile;
+    dataIn = new java.io.BufferedReader(new InputStreamReader(
+        new java.io.FileInputStream(inFile)));
     parse();
   }
+
   /**
    * Creates a new NewickFile object.
    * 
@@ -196,24 +198,29 @@ public class NewickFile {
   public boolean HasRootDistance() {
     return RootHasDistance;
   }
+
   /*
    * hacked out of jalview code
    */
   boolean error;
+
   String errormessage;
-  java.io.BufferedReader dataIn=null;
+
+  java.io.BufferedReader dataIn = null;
+
   public String nextLine() throws IOException {
-    if (dataIn==null && newickFile==null)
-      throw new IOException("IMPLEMENTATION ERROR: NewickFile has not been initialised for reading a newick string.");
-    if (dataIn==null)
-    {
+    if (dataIn == null && newickFile == null)
+      throw new IOException(
+          "IMPLEMENTATION ERROR: NewickFile has not been initialised for reading a newick string.");
+    if (dataIn == null) {
       dataIn = new BufferedReader(new StringReader(newickFile));
-      error=false;
+      error = false;
     }
     if (!error)
       return dataIn.readLine();
     throw new IOException("Invalid Source Stream:" + errormessage);
   }
+
   /**
    * call this to convert the newick string into a binary node linked tree
    * 
@@ -222,8 +229,7 @@ public class NewickFile {
    */
   public void parse() throws IOException {
     String nf;
-    if (newickFile==null)
-    {
+    if (newickFile == null) {
       // fill nf with complete tree file
 
       StringBuffer file = new StringBuffer();
@@ -233,11 +239,9 @@ public class NewickFile {
       }
 
       nf = file.toString();
-    } else
-    {
+    } else {
       nf = newickFile;
     }
-    
 
     root = new SequenceNode();
 
@@ -252,37 +256,23 @@ public class NewickFile {
     String nodename = null;
 
     float DefDistance = (float) 0.001; // @param Default distance for a node -
-                                        // very very small
+    // 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
+    // current node
 
-    Pattern majorsyms = Pattern.compile(
-        "[(\\['),;]");
+    Pattern majorsyms = Pattern.compile("[(\\['),;]");
 
     Matcher mjsyms = majorsyms.matcher(nf);
+    char schar;
     while (mjsyms.find(cp) && (Error == null)) {
       int fcp = mjsyms.start();
 
-      switch (nf.charAt(fcp)) {
-      case '[': // Comment or structured/extended NH format info
-
-
-        if (nf.indexOf(']',fcp)>-1) {
-          // Skip the comment field
-          cp = nf.indexOf(']',fcp);
-        } else {
-          Error = ErrorStringrange(Error, "Unterminated comment", 3, fcp, nf);
-        }
-
-        ;
-
-        break;
-
+      switch (schar = nf.charAt(fcp)) {
       case '(':
 
         // ascending should not be set
@@ -338,19 +328,34 @@ public class NewickFile {
 
         break;
 
-      case ';':
+      default:
+        int nextcp = 0;
+        // Skip Comment or structured/extended NH format info
+        if (schar == '[') {
+          if ((nextcp=nf.indexOf(']', fcp)) > -1) {
+            // Skip the comment field
+            // should advance fcp too here
+            nextcp++;
+            //fcp = nextcp;
+            //schar = nf.charAt(fcp);
+          } else {
+            Error = ErrorStringrange(Error, "Unterminated comment", 3, fcp, nf);
+            nextcp = 0;
+            break;
+          }
+          ;
+        }
 
-        if (d != -1) {
+        // Reached termininating root node label.
+        if (schar == ';' && 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);
-        Matcher uqnodename = Pattern.compile("\\b([^' :;\\](),]+)").matcher(fstring);
+        Matcher uqnodename = Pattern.compile("^([^' :;\\](),]+).*").matcher(
+            fstring);
         if (uqnodename.matches()
             && ((uqnodename.start(1) == 0) || (fstring.charAt(uqnodename
                 .start(1) - 1) != ':'))) // JBPNote HACK!
@@ -366,12 +371,11 @@ public class NewickFile {
                 "File has broken algorithm - overwritten nodename", 10, fcp, nf);
           }
         }
-        
-        Matcher nbootstrap = Pattern.compile("\\S+([0-9+]+)\\S*:").matcher(fstring);
 
+        Matcher nbootstrap = Pattern.compile("\\S+([0-9+]+)\\S*:").matcher(
+            fstring);
 
-        if (nbootstrap.matches()
-            && (nbootstrap.start(1) > uqnodename.end(1))) {
+        if (nbootstrap.matches() && (nbootstrap.start(1) > uqnodename.end(1))) {
           try {
             bootstrap = (new Integer(nbootstrap.group(1))).intValue();
             HasBootstrap = true;
@@ -381,8 +385,7 @@ public class NewickFile {
           }
         }
 
-        Matcher ndist = Pattern.compile(
-        ":([-0-9Ee.+]+)").matcher(fstring);
+        Matcher ndist = Pattern.compile(":([-0-9Ee.+]+)").matcher(fstring);
         boolean nodehasdistance = false;
 
         if (ndist.matches()) {
@@ -405,8 +408,8 @@ public class NewickFile {
           c.setBootstrap((HasBootstrap) ? bootstrap : DefBootstrap);
           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
           }
         } else {
           // Find a place to put the leaf
@@ -464,8 +467,10 @@ public class NewickFile {
         nodename = null;
         distance = DefDistance;
         bootstrap = DefBootstrap;
-
-        cp = fcp + 1;
+        if (nextcp == 0)
+          cp = fcp + 1;
+        else
+          cp = nextcp;
       }
     }
 
@@ -488,12 +493,14 @@ public class NewickFile {
   public SequenceNode getTree() {
     return root;
   }
-  public uk.ac.vamsas.objects.core.Treenode[] matchTreeNodeNames(String[] names, Vobject[] boundObjects)
-  {
+
+  public uk.ac.vamsas.objects.core.Treenode[] matchTreeNodeNames(
+      String[] names, Vobject[] boundObjects) {
     // todo!
     // also - need to reconstruct a names object id mapping (or BInaryNode) mapping for the parsed tree file
     return null;
   }
+
   /**
    * Generate a newick format tree according to internal flags for bootstraps,
    * distances and root distances.
@@ -615,7 +622,8 @@ public class NewickFile {
    */
   private String nodeName(String name) {
     if (NodeSafeName[0].matcher(name).find()) {
-      return QuoteChar + NodeSafeName[1].matcher(name).replaceAll("''") + QuoteChar; // quite 
+      return QuoteChar + NodeSafeName[1].matcher(name).replaceAll("''")
+          + QuoteChar; // quite 
     } else {
       return NodeSafeName[2].matcher(name).replaceAll("_"); // whitespace
     }
@@ -632,7 +640,7 @@ public class NewickFile {
   private String printNodeField(SequenceNode c) {
     return //c.getNewickNodeName()
     ((c.getName() == null) ? "" : nodeName(c.getName()))
-      + ((HasBootstrap) ? ((c.getBootstrap() > -1) ? (" " + c.getBootstrap())
+        + ((HasBootstrap) ? ((c.getBootstrap() > -1) ? (" " + c.getBootstrap())
             : "") : "") + ((HasDistances) ? (":" + c.dist) : "");
   }
 
@@ -729,7 +737,9 @@ public class NewickFile {
       // trf.parse();
       System.out.println("Original file :\n");
 
-      System.out.println(Pattern.compile("\n+").matcher(newickfile.toString()).replaceAll("") + "\n");
+      System.out.println(Pattern.compile("\n+").matcher(newickfile.toString())
+          .replaceAll("")
+          + "\n");
 
       System.out.println("Parsed file.\n");
       System.out.println("Default output type for original input.\n");
@@ -747,20 +757,19 @@ public class NewickFile {
       System.out.println("leaves.\n");
       Vector lvs = new Vector();
       trf.findLeaves(trf.root, lvs);
-      Enumeration lv =lvs.elements();
-      while (lv.hasMoreElements())
-      {
+      Enumeration lv = lvs.elements();
+      while (lv.hasMoreElements()) {
         BinaryNode leave = (BinaryNode) lv.nextElement();
-        if (leave.getName()!=null)
-        {
-          System.out.println("Node:'"+leave.getName()+"'");
+        if (leave.getName() != null) {
+          System.out.println("Node:'" + leave.getName() + "'");
         }
-      }      
+      }
     } catch (java.io.IOException e) {
       System.err.println("Exception\n" + e);
       e.printStackTrace();
     }
   }
+
   /**
    * Search for leaf nodes.
    *
@@ -769,27 +778,23 @@ public class NewickFile {
    *
    * @return Vector of leaf nodes on binary tree
    */
-  public Vector findLeaves(SequenceNode node, Vector leaves)
-  { 
-    if (node == null)
-    {
+  public Vector findLeaves(SequenceNode node, Vector leaves) {
+    if (node == null) {
       return leaves;
     }
 
-    if ( (node.left() == null) && (node.right() == null)) // Interior node detection
+    if ((node.left() == null) && (node.right() == null)) // Interior node detection
     {
       leaves.addElement(node);
 
       return leaves;
-    }
-    else
-    {
-/*  TODO: Identify internal nodes...    if (node.isSequenceLabel())
-      {
-        leaves.addElement(node);
-      }*/
-      findLeaves( (SequenceNode) node.left(), leaves);
-      findLeaves( (SequenceNode) node.right(), leaves);
+    } else {
+      /*  TODO: Identify internal nodes...    if (node.isSequenceLabel())
+       {
+       leaves.addElement(node);
+       }*/
+      findLeaves((SequenceNode) node.left(), leaves);
+      findLeaves((SequenceNode) node.right(), leaves);
     }
 
     return leaves;
@@ -803,30 +808,26 @@ public class NewickFile {
   public Treenode[] makeTreeNodes() {
     return makeTreeNodes(true);
   }
+
   /**
    * make treenode vector for a parsed tree with/out leaf node associations 
    * @param ignoreplaceholders if true means only associated nodes are returned
    * @return treenode vector for associated or all leaves
    */
-  public Treenode[] makeTreeNodes(boolean ignoreplaceholders) { 
+  public Treenode[] makeTreeNodes(boolean ignoreplaceholders) {
     Vector leaves = new Vector();
     findLeaves(root, leaves);
     Vector tnv = new Vector();
     Enumeration l = leaves.elements();
     Hashtable nodespecs = new Hashtable();
-    while (l.hasMoreElements())
-    {
+    while (l.hasMoreElements()) {
       BinaryNode tnode = (BinaryNode) l.nextElement();
-      if (tnode instanceof SequenceNode)
-      {
-        if (!(ignoreplaceholders && ((SequenceNode) tnode).isPlaceholder()))
-        {
+      if (tnode instanceof SequenceNode) {
+        if (!(ignoreplaceholders && ((SequenceNode) tnode).isPlaceholder())) {
           Object assocseq = ((SequenceNode) tnode).element();
-          if (assocseq instanceof Vobject)
-          {
+          if (assocseq instanceof Vobject) {
             Vobject vobj = (Vobject) assocseq;
-            if (vobj!=null)
-            {
+            if (vobj != null) {
               Treenode node = new Treenode();
               node.setNodespec(makeNodeSpec(nodespecs, tnode));
               node.setName(tnode.getName());
@@ -834,35 +835,35 @@ public class NewickFile {
               vr.addRefs(vobj);
               node.addVref(vr);
               tnv.addElement(node);
-            }
-            else
-            {
-              System.err.println("WARNING: Unassociated treeNode "+tnode.element().toString()+" "
-                      +((tnode.getName()!=null) ? " label "+tnode.getName() : ""));
+            } else {
+              System.err.println("WARNING: Unassociated treeNode "
+                  + tnode.element().toString()
+                  + " "
+                  + ((tnode.getName() != null) ? " label " + tnode.getName()
+                      : ""));
             }
           }
         }
       }
     }
-    if (tnv.size()>0)
-    {
+    if (tnv.size() > 0) {
       Treenode[] tn = new Treenode[tnv.size()];
-      tnv.copyInto(tn);  
+      tnv.copyInto(tn);
       return tn;
     }
     return new Treenode[] {};
   }
-  private String makeNodeSpec(Hashtable nodespecs, BinaryNode tnode)
-  { 
+
+  private String makeNodeSpec(Hashtable nodespecs, BinaryNode tnode) {
     String nname = new String(tnode.getName());
     Integer nindx = (Integer) nodespecs.get(nname);
-    if (nindx==null)
-    {
+    if (nindx == null) {
       nindx = new Integer(1);
     }
-    nname = nindx.toString()+" "+nname;
+    nname = nindx.toString() + " " + nname;
     return nname;
   }
+
   /**
    * call to match up Treenode specs to NJTree parsed from document object.
    * 
@@ -871,34 +872,30 @@ public class NewickFile {
    *          as returned from NJTree.findLeaves( .., ..) ..
    * @return
    */
-  private BinaryNode findNodeSpec(String nodespec, Vector leaves)
-  {
-    int occurence=-1;
-    String nspec = nodespec.substring(nodespec.indexOf(' ')+1);
+  private BinaryNode findNodeSpec(String nodespec, Vector leaves) {
+    int occurence = -1;
+    String nspec = nodespec.substring(nodespec.indexOf(' ') + 1);
     String oval = nodespec.substring(0, nodespec.indexOf(' '));
     try {
       occurence = new Integer(oval).intValue();
-    }
-    catch (Exception e)
-    {
-      System.err.println("Invalid nodespec '"+nodespec+"'");
+    } catch (Exception e) {
+      System.err.println("Invalid nodespec '" + nodespec + "'");
       return null;
     }
     BinaryNode bn = null;
-    
+
     int nocc = 0;
     Enumeration en = leaves.elements();
-    while (en.hasMoreElements() && nocc<occurence)
-    {
+    while (en.hasMoreElements() && nocc < occurence) {
       bn = (BinaryNode) en.nextElement();
-      if (bn instanceof SequenceNode && bn.getName().equals(nspec))
-      {
-         --occurence;
-      } else 
-        bn=null;
+      if (bn instanceof SequenceNode && bn.getName().equals(nspec)) {
+        --occurence;
+      } else
+        bn = null;
     }
     return bn;
   }
+
   /**
    *
    * re-decorate the newick node representation with the VorbaId of an object mapped by its corresponding TreeNode. 
@@ -906,50 +903,44 @@ public class NewickFile {
    * @param tn
    * @return vector of mappings { treenode, SequenceNode, Vobject for VorbaId on sequence node }
    */
-  public Vector attachTreeMap(Treenode[] tn)
-  {
-  if (root!=null || tn==null)
-    return null;
-  Vector leaves = new Vector();
-  Vector nodemap=new Vector();
-  findLeaves(root, leaves);
-  int sz = tn.length;
-  int i = 0;
-  
-  while (i < sz)
-  {
-    Treenode node = tn[i++];
-    BinaryNode mappednode = findNodeSpec(node.getNodespec(),leaves);
-    if (mappednode!=null && mappednode instanceof SequenceNode) {
-      SequenceNode leaf = (SequenceNode) leaves.elementAt(i++);
-      // check if we can make the specified association
-      Vobject noderef = null;
-      int vrf=0,refv=0;
-      while (noderef==null && vrf<node.getVrefCount())
-      {
-        if (refv<node.getVref(vrf).getRefsCount())
-        {
-          Object ref = node.getVref(vrf).getRefs(refv++);
-          if (ref instanceof Vobject)
-          {
-            noderef = (Vobject) ref;
+  public Vector attachTreeMap(Treenode[] tn) {
+    if (root != null || tn == null)
+      return null;
+    Vector leaves = new Vector();
+    Vector nodemap = new Vector();
+    findLeaves(root, leaves);
+    int sz = tn.length;
+    int i = 0;
+
+    while (i < sz) {
+      Treenode node = tn[i++];
+      BinaryNode mappednode = findNodeSpec(node.getNodespec(), leaves);
+      if (mappednode != null && mappednode instanceof SequenceNode) {
+        SequenceNode leaf = (SequenceNode) leaves.elementAt(i++);
+        // check if we can make the specified association
+        Vobject noderef = null;
+        int vrf = 0, refv = 0;
+        while (noderef == null && vrf < node.getVrefCount()) {
+          if (refv < node.getVref(vrf).getRefsCount()) {
+            Object ref = node.getVref(vrf).getRefs(refv++);
+            if (ref instanceof Vobject) {
+              noderef = (Vobject) ref;
+            }
+          } else {
+            refv = 0;
+            vrf++;
           }
+        }
+        if (noderef != null) {
+          nodemap.addElement(new Object[] { node, leaf, noderef });
+          leaf.setElement(noderef);
+          leaf.setPlaceholder(false);
         } else {
-          refv=0;
-          vrf++;
+          leaf.setPlaceholder(true);
         }
       }
-      if (noderef!=null)
-      {
-        nodemap.addElement(new Object[] { node, leaf, noderef });
-        leaf.setElement(noderef);
-        leaf.setPlaceholder(false);
-      } else {
-        leaf.setPlaceholder(true);
-      }
     }
+    return nodemap;
   }
-  return nodemap;
-}
 
 }