X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FNJTree.java;h=be3b96d01355532ffc897155761d70c24aeaa6d9;hb=88eaada36951276cf8b2863bb95aa37148166ea2;hp=6c239be1de8a3c2311e99ca0c59a2c0dc95a8ee2;hpb=83193bc5c3e150dc7331b5b27a67cb5f9efb477c;p=jalview.git

diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index 6c239be..be3b96d 100755
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -39,6 +39,11 @@ public class NJTree
 {
     Vector cluster;
     SequenceI[] sequence;
+
+    //SequenceData is a string representation of what the user
+    //sees. The display may contain hidden columns.
+    String [] sequenceString;
+
     int[] done;
     int noseqs;
     int noClus;
@@ -58,19 +63,12 @@ public class NJTree
     String pwtype;
     Object found = null;
     Object leaves = null;
-    int start;
-    int end;
 
-    /**
-     * Creates a new NJTree object.
-     *
-     * @param node DOCUMENT ME!
-     */
-    public NJTree(SequenceNode node)
-    {
-        top = node;
-        maxheight = findHeight(top);
-    }
+    boolean hasDistances = true; // normal case for jalview trees
+    boolean hasBootstrap = false; // normal case for jalview trees
+
+    private boolean hasRootDistance = true;
+
 
     /**
      * Creates a new NJTree object.
@@ -78,9 +76,24 @@ public class NJTree
      * @param seqs DOCUMENT ME!
      * @param treefile DOCUMENT ME!
      */
-    public NJTree(SequenceI[] seqs, NewickFile treefile)
+    public NJTree(SequenceI[] seqs,  NewickFile treefile)
     {
         top = treefile.getTree();
+
+        if (sequenceString == null)
+        {
+          sequenceString = new String[sequence.length];
+          for (int i = 0; i < sequence.length; i++)
+          {
+            sequenceString[i] = sequence[i].getSequence();
+          }
+        }
+
+
+        hasDistances = treefile.HasDistances();
+        hasBootstrap = treefile.HasBootstrap();
+        hasRootDistance = treefile.HasRootDistance();
+
         maxheight = findHeight(top);
 
         SequenceIdMatcher algnIds = new SequenceIdMatcher(seqs);
@@ -123,32 +136,33 @@ public class NJTree
      * Creates a new NJTree object.
      *
      * @param sequence DOCUMENT ME!
-     * @param start DOCUMENT ME!
-     * @param end DOCUMENT ME!
-     */
-    public NJTree(SequenceI[] sequence, int start, int end)
-    {
-        this(sequence, "NJ", "BL", start, end);
-    }
-
-    /**
-     * Creates a new NJTree object.
-     *
-     * @param sequence DOCUMENT ME!
      * @param type DOCUMENT ME!
      * @param pwtype DOCUMENT ME!
      * @param start DOCUMENT ME!
      * @param end DOCUMENT ME!
      */
-    public NJTree(SequenceI[] sequence, String type, String pwtype, int start,
-        int end)
+    public NJTree(SequenceI[] sequence,
+                  String [] sequenceString,
+                  String type,
+                  String pwtype,
+                  int start, int end)
     {
         this.sequence = sequence;
         this.node = new Vector();
         this.type = type;
         this.pwtype = pwtype;
-        this.start = start;
-        this.end = end;
+
+        if (sequenceString == null)
+        {
+          this.sequenceString = new String[sequence.length];
+          for(int i=0; i<sequence.length; i++)
+          {
+            this.sequenceString[i] = sequence[i].getSequence(start, end);
+          }
+        }
+        else
+          this.sequenceString = sequenceString;
+
 
         if (!(type.equals("NJ")))
         {
@@ -253,11 +267,11 @@ public class NJTree
         {
             if (type.equals("NJ"))
             {
-                float mind = findMinNJDistance();
+                findMinNJDistance();
             }
             else
             {
-                float mind = findMinDistance();
+                findMinDistance();
             }
 
             Cluster c = joinClusters(mini, minj);
@@ -291,7 +305,7 @@ public class NJTree
             }
         }
 
-        Cluster c = joinClusters(one, two);
+        joinClusters(one, two);
         top = (SequenceNode) (node.elementAt(one));
 
         reCount(top);
@@ -375,11 +389,6 @@ public class NJTree
     public void findNewNJDistances(SequenceNode tmpi, SequenceNode tmpj,
         float dist)
     {
-        float ih = 0;
-        float jh = 0;
-
-        SequenceNode sni = tmpi;
-        SequenceNode snj = tmpj;
 
         tmpi.dist = ((dist + ri) - rj) / 2;
         tmpj.dist = (dist - tmpi.dist);
@@ -469,8 +478,6 @@ public class NJTree
      */
     public void findClusterNJDistance(int i, int j)
     {
-        int noi = ((Cluster) cluster.elementAt(i)).value.length;
-        int noj = ((Cluster) cluster.elementAt(j)).value.length;
 
         // New distances from cluster to others
         float[] newdist = new float[noseqs];
@@ -605,7 +612,8 @@ public class NJTree
                     else
                     {
                         distance[i][j] = 100 -
-                            Comparison.PID(sequence[i], sequence[j], start, end);
+                             Comparison.PID(sequenceString[i], sequenceString[j]);
+
                         distance[j][i] = distance[i][j];
                     }
                 }
@@ -614,20 +622,20 @@ public class NJTree
         else if (pwtype.equals("BL"))
         {
             int maxscore = 0;
-
+            int end = sequenceString[0].length();
             for (int i = 0; i < (noseqs - 1); i++)
             {
                 for (int j = i; j < noseqs; j++)
                 {
                     int score = 0;
 
-                    for (int k = start; k < end; k++)
+                    for (int k = 0; k < end; k++)
                     {
                         try
                         {
-                            score += ResidueProperties.getBLOSUM62(sequence[i].getSequence(
-                                    k, k + 1), sequence[j].getSequence(k, k +
-                                    1));
+                            score += ResidueProperties.getBLOSUM62(
+                              sequenceString[i].substring(k, k + 1),
+                              sequenceString[j].substring(k, k + 1));
                         }
                         catch (Exception ex)
                         {
@@ -654,7 +662,7 @@ public class NJTree
                 }
             }
         }
-        else if (pwtype.equals("SW"))
+      /*  else if (pwtype.equals("SW"))
         {
             float max = -1;
 
@@ -665,7 +673,7 @@ public class NJTree
                     AlignSeq as = new AlignSeq(sequence[i], sequence[j], "pep");
                     as.calcScoreMatrix();
                     as.traceAlignment();
-                    as.printAlignment();
+                    as.printAlignment(System.out);
                     distance[i][j] = (float) as.maxscore;
 
                     if (max < distance[i][j])
@@ -683,7 +691,7 @@ public class NJTree
                     distance[j][i] = distance[i][j];
                 }
             }
-        }
+        }/*/
 
         return distance;
     }
@@ -974,12 +982,23 @@ public class NJTree
         return top;
     }
 
+    public String printOriginalSequenceData()
+    {
+      StringBuffer sb = new StringBuffer();
+      for(int i=0; i<sequenceString.length; i++)
+      {
+        sb.append(sequence[i].getName()+"\t");
+        sb.append(sequenceString[i]+"\n");
+      }
+      return sb.toString();
+    }
+
     /**
      * DOCUMENT ME!
      *
      * @param node DOCUMENT ME!
      */
-    public static void printN(SequenceNode node)
+    public void printN(SequenceNode node)
     {
         if (node == null)
         {
@@ -1121,15 +1140,6 @@ public class NJTree
         }
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param node DOCUMENT ME!
-     */
-    public void setMaxDist(SequenceNode node)
-    {
-        this.maxdist = maxdist;
-    }
 
     /**
      * DOCUMENT ME!
@@ -1150,6 +1160,27 @@ public class NJTree
     {
         return top;
     }
+    /**
+     *
+     * @return true if tree has real distances
+     */
+    public boolean isHasDistances() {
+      return hasDistances;
+    }
+
+    /**
+     *
+     * @return true if tree has real bootstrap values
+     */
+    public boolean isHasBootstrap() {
+      return hasBootstrap;
+    }
+
+  public boolean isHasRootDistance()
+  {
+    return hasRootDistance;
+  }
+
 }