X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FNJTree.java;h=d56464c0c35d6dde60f843b8a9b1b5bc945c98e5;hb=abe6225acb5316fd1f8c20e56a58c26aeced0b0c;hp=4aeee3d5807ed4f875fec2cf40eff0711e218955;hpb=1ecf6419aba86993b3c223bf5ec0fa79427baf85;p=jalview.git

diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index 4aeee3d..d56464c 100755
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -5,6 +5,8 @@ import jalview.util.*;
 import jalview.schemes.ResidueProperties;
 import java.util.*;
 
+import jalview.io.NewickFile;
+
 public class NJTree {
 
   Vector cluster;
@@ -46,6 +48,79 @@ public class NJTree {
     maxheight = findHeight(top);
   }
 
+  public String toString()
+  {
+    jalview.io.NewickFile fout = new jalview.io.NewickFile(getTopNode());
+    return fout.print(false,true); // distances only
+  }
+
+  public NJTree(SequenceI[] seqs, NewickFile treefile) {
+    top = treefile.getTree();
+    maxheight = findHeight(top);
+    SequenceIdMatcher algnIds = new SequenceIdMatcher(seqs);
+
+    Vector leaves = new Vector();
+    findLeaves(top, leaves);
+
+    int i = 0;
+    int namesleft = seqs.length;
+
+    SequenceNode j;
+    SequenceI nam;
+    String realnam;
+    while (i < leaves.size())
+    {
+      j = (SequenceNode) leaves.elementAt(i++);
+      realnam = j.getName();
+      nam = null;
+      if (namesleft>-1)
+        nam = algnIds.findIdMatch(realnam);
+      if (nam != null) {
+        j.setElement(nam);
+        namesleft--;
+      } else {
+        j.setElement(new Sequence(realnam, "THISISAPLACEHLDER"));
+        j.setPlaceholder(true);
+
+      }
+    }
+  }
+
+  /**
+   *
+   * used when the alignment associated to a tree has changed.
+   *
+   * @param alignment Vector
+   */
+  public void UpdatePlaceHolders(Vector alignment) {
+    Vector leaves = new Vector();
+    findLeaves(top, leaves);
+    int sz = leaves.size();
+    SequenceIdMatcher seqmatcher=null;
+    int i=0;
+    while (i<sz) {
+      SequenceNode leaf = (SequenceNode) leaves.elementAt(i++);
+      if (alignment.contains(leaf.element()))
+        leaf.setPlaceholder(false);
+      else {
+        if (seqmatcher==null) {
+          // Only create this the first time we need it
+          SequenceI[] seqs = new SequenceI[alignment.size()];
+          for (int j=0; j<seqs.length; j++)
+            seqs[j] = (SequenceI) alignment.elementAt(j);
+          seqmatcher = new SequenceIdMatcher(seqs);
+        }
+        SequenceI nam = seqmatcher.findIdMatch(leaf.getName());
+        if (nam!=null) {
+          leaf.setPlaceholder(false);
+          leaf.setElement(nam);
+        } else {
+          leaf.setPlaceholder(true);
+        }
+      }
+    }
+  }
+
   public NJTree(SequenceI[] sequence,int start, int end) {
     this(sequence,"NJ","BL",start,end);
   }
@@ -331,14 +406,13 @@ public class NJTree {
   public float[][] findDistances() {
 
     float[][] distance = new float[noseqs][noseqs];
-
     if (pwtype.equals("PID")) {
       for (int i = 0; i < noseqs-1; i++) {
         for (int j = i; j < noseqs; j++) {
           if (j==i) {
             distance[i][i] = 0;
           } else {
-            distance[i][j] = 100-Comparison.compare(sequence[i],sequence[j],start,end);
+            distance[i][j] = 100-Comparison.PID(sequence[i], sequence[j]);
             distance[j][i] = distance[i][j];
           }
         }
@@ -356,7 +430,7 @@ public class NJTree {
                   k + 1),
                                                 sequence[j].getSequence(k,
                   k + 1));
-            }catch(Exception ex){System.out.println("err creating BLOSUM62 tree");}
+            }catch(Exception ex){System.err.println("err creating BLOSUM62 tree");ex.printStackTrace();}
           }
           distance[i][j] = (float)score;
           if (score > maxscore) {
@@ -448,6 +522,11 @@ public class NJTree {
     return found;
   }
 
+  /**
+   * printNode is mainly for debugging purposes.
+   *
+   * @param node SequenceNode
+   */
   public void printNode(SequenceNode node) {
     if (node == null) {
       return;
@@ -470,8 +549,8 @@ public class NJTree {
 
       float dist = ((SequenceNode)node).dist;
       if (dist > maxDistValue) {
-	  maxdist      = (SequenceNode)node;
-	  maxDistValue = dist;
+          maxdist      = (SequenceNode)node;
+          maxDistValue = dist;
       }
     } else {
       findMaxDist((SequenceNode)node.left());
@@ -479,10 +558,10 @@ public class NJTree {
     }
   }
     public Vector getGroups() {
-	return groups;
+        return groups;
     }
     public float getMaxHeight() {
-	return maxheight;
+        return maxheight;
     }
   public void  groupNodes(SequenceNode node, float threshold) {
     if (node == null) {
@@ -571,8 +650,8 @@ public class NJTree {
   }
 
     public void reCount(SequenceNode node) {
-	ycount = 0;
-	_reCount(node);
+        ycount = 0;
+        _reCount(node);
     }
   public void _reCount(SequenceNode node) {
     if (node == null) {
@@ -596,13 +675,13 @@ public class NJTree {
 
   }
     public void swapNodes(SequenceNode node) {
-	if (node == null) {
-	    return;
-	}
-	SequenceNode tmp = (SequenceNode)node.left();
+        if (node == null) {
+            return;
+        }
+        SequenceNode tmp = (SequenceNode)node.left();
 
-	node.setLeft(node.right());
-	node.setRight(tmp);
+        node.setLeft(node.right());
+        node.setRight(tmp);
     }
   public void changeDirection(SequenceNode node, SequenceNode dir) {
     if (node == null) {
@@ -642,13 +721,13 @@ public class NJTree {
     }
   }
     public void setMaxDist(SequenceNode node) {
-	this.maxdist = maxdist;
+        this.maxdist = maxdist;
     }
     public SequenceNode getMaxDist() {
-	return maxdist;
+        return maxdist;
     }
     public SequenceNode getTopNode() {
-	return top;
+        return top;
     }
 
 }