X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FNJTree.java;h=98916e36a36b1c6996aadcdfc96b89c47e625415;hb=e33cdacd2ac2836504375c538574a0f1cafec7e3;hp=20d28f7e2fcbe49dd0deb690b65dc9d3de28260e;hpb=ddf4180014d2316824c4ecd4bcbbe20be4033d43;p=jalview.git

diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index 20d28f7..98916e3 100755
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -42,7 +42,7 @@ public class NJTree
 
     //SequenceData is a string representation of what the user
     //sees. The display may contain hidden columns.
-    String [] sequenceString;
+    CigarArray seqData=null;
 
     int[] done;
     int noseqs;
@@ -69,26 +69,51 @@ public class NJTree
 
     private boolean hasRootDistance = true;
 
+    /**
+     * Create a new NJTree object with leaves associated with sequences in seqs,
+     * and original alignment data represented by Cigar strings.
+     * @param seqs SequenceI[]
+     * @param odata Cigar[]
+     * @param treefile NewickFile
+     */
+    public NJTree(SequenceI[] seqs, CigarArray odata, NewickFile treefile) {
+      this(seqs, treefile);
+      if (odata!=null)
+        seqData = odata;
+      /*
+      sequenceString = new String[odata.length];
+      char gapChar = jalview.util.Comparison.GapChars.charAt(0);
+      for (int i = 0; i < odata.length; i++)
+      {
+        SequenceI oseq_aligned = odata[i].getSeq(gapChar);
+          sequenceString[i] = oseq_aligned.getSequence();
+      } */
+    }
 
     /**
-     * Creates a new NJTree object.
+     * Creates a new NJTree object from a tree from an external source
      *
-     * @param seqs DOCUMENT ME!
-     * @param treefile DOCUMENT ME!
+     * @param seqs SequenceI which should be associated with leafs of treefile
+     * @param treefile A parsed tree
      */
     public NJTree(SequenceI[] seqs,  NewickFile treefile)
     {
+        this.sequence = seqs;
         top = treefile.getTree();
 
+        /**
+         * There is no dependent alignment to be recovered from an
+         * imported tree.
+         *
         if (sequenceString == null)
         {
-          sequenceString = new String[sequence.length];
-          for (int i = 0; i < sequence.length; i++)
+          sequenceString = new String[seqs.length];
+          for (int i = 0; i < seqs.length; i++)
           {
-            sequenceString[i] = sequence[i].getSequence();
+            sequenceString[i] = seqs[i].getSequence();
           }
         }
-
+        */
 
         hasDistances = treefile.HasDistances();
         hasBootstrap = treefile.HasBootstrap();
@@ -142,7 +167,7 @@ public class NJTree
      * @param end DOCUMENT ME!
      */
     public NJTree(SequenceI[] sequence,
-                  String [] sequenceString,
+                  CigarArray seqData,
                   String type,
                   String pwtype,
                   int start, int end)
@@ -151,18 +176,17 @@ public class NJTree
         this.node = new Vector();
         this.type = type;
         this.pwtype = pwtype;
-
-        if (sequenceString == null)
-        {
-          this.sequenceString = new String[sequence.length];
+        if (seqData!=null) {
+          this.seqData = seqData;
+        } else {
+          SeqCigar[] seqs = new SeqCigar[sequence.length];
           for(int i=0; i<sequence.length; i++)
-          {
-            this.sequenceString[i] = sequence[i].getSequence(start, end);
-          }
+            {
+              seqs[i] = new SeqCigar(sequence[i], start, end);
+            }
+            this.seqData = new CigarArray(seqs);
+            this.seqData.addOperation(CigarArray.M, end-start+1);
         }
-        else
-          this.sequenceString = sequenceString;
-
 
         if (!(type.equals("NJ")))
         {
@@ -186,7 +210,7 @@ public class NJTree
 
         noseqs = i++;
 
-        distance = findDistances();
+        distance = findDistances(this.seqData.getSequenceStrings(Comparison.GapChars.charAt(0)));
 
         makeLeaves();
 
@@ -595,7 +619,7 @@ public class NJTree
      *
      * @return DOCUMENT ME!
      */
-    public float[][] findDistances()
+    public float[][] findDistances(String[] sequenceString)
     {
         float[][] distance = new float[noseqs][noseqs];
 
@@ -981,15 +1005,31 @@ public class NJTree
 
         return top;
     }
-
+    /**
+     *
+     * @return true if original sequence data can be recovered
+     */
+    public boolean hasOriginalSequenceData() {
+      return seqData!=null;
+    }
+    /**
+     * Returns original alignment data used for calculation - or null where
+     * not available.
+     *
+     * @return null or cut'n'pasteable alignment
+     */
     public String printOriginalSequenceData()
     {
+      if (seqData==null)
+        return null;
+//      return seqData.getSequenceString(Comparison.GapChars[0]);
       StringBuffer sb = new StringBuffer();
-      for(int i=0; i<sequenceString.length; i++)
+      String[] seqdatas = seqData.getSequenceStrings(Comparison.GapChars.charAt(0));
+      for(int i=0; i<seqdatas.length; i++)
       {
         sb.append(new jalview.util.Format("%-" + 15 + "s").form(
             sequence[i].getName()));
-        sb.append(" "+sequenceString[i]+"\n");
+        sb.append(" "+seqdatas[i]+"\n");
       }
       return sb.toString();
     }