From 88eaada36951276cf8b2863bb95aa37148166ea2 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 18 Jul 2006 15:29:35 +0000
Subject: [PATCH] Works on strings, not seqs

---
 src/jalview/analysis/AlignSeq.java        |   30 +++++++--
 src/jalview/analysis/AlignmentSorter.java |    3 +-
 src/jalview/analysis/NJTree.java          |   95 +++++++++++++++++------------
 3 files changed, 83 insertions(+), 45 deletions(-)

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index d3dfc9b..464abb0 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -98,7 +98,6 @@ public class AlignSeq
     String type;
     Runtime rt;
 
-
     /**
      * Creates a new AlignSeq object.
      *
@@ -109,7 +108,24 @@ public class AlignSeq
     public AlignSeq(SequenceI s1, SequenceI s2, String type)
     {
         rt = Runtime.getRuntime();
-        SeqInit(s1, s2, type);
+        SeqInit(s1, s1.getSequence(), s2,  s2.getSequence(), type);
+    }
+
+    /**
+     * Creates a new AlignSeq object.
+     *
+     * @param s1 DOCUMENT ME!
+     * @param s2 DOCUMENT ME!
+     * @param type DOCUMENT ME!
+     */
+    public AlignSeq(SequenceI s1,
+                    String string1,
+                    SequenceI s2,
+                    String string2,
+                    String type)
+    {
+        rt = Runtime.getRuntime();
+        SeqInit(s1, string1, s2,  string2,  type);
     }
 
     /**
@@ -239,10 +255,14 @@ public class AlignSeq
      * @param s2 DOCUMENT ME!
      * @param type DOCUMENT ME!
      */
-    public void SeqInit(SequenceI s1, SequenceI s2, String type)
+    public void SeqInit(SequenceI s1,
+                        String string1,
+                        SequenceI s2,
+                        String string2,
+                        String type)
     {
-        s1str = extractGaps(jalview.util.Comparison.GapChars, s1.getSequence());
-        s2str = extractGaps(jalview.util.Comparison.GapChars, s2.getSequence());
+        s1str = extractGaps(jalview.util.Comparison.GapChars, string1);
+        s2str = extractGaps(jalview.util.Comparison.GapChars, string2);
 
         this.s1 = s1;
         this.s2 = s2;
diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index c2814b8..27d1e7b 100755
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -52,7 +52,8 @@ public class AlignmentSorter
 
         for (int i = 0; i < nSeq; i++)
         {
-            scores[i] = Comparison.PID(align.getSequenceAt(i), s);
+            scores[i] = Comparison.PID(align.getSequenceAt(i).getSequence(),
+                                       s.getSequence());
             seqs[i] = align.getSequenceAt(i);
         }
 
diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index 40dfc9b..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;
@@ -58,23 +63,12 @@ public class NJTree
     String pwtype;
     Object found = null;
     Object leaves = null;
-    int start;
-    int end;
+
     boolean hasDistances = true; // normal case for jalview trees
-	boolean hasBootstrap = false; // normal case for jalview trees
+    boolean hasBootstrap = false; // normal case for jalview trees
 
     private boolean hasRootDistance = true;
 
-    /**
-     * Creates a new NJTree object.
-     *
-     * @param node DOCUMENT ME!
-     */
-    public NJTree(SequenceNode node)
-    {
-        top = node;
-        maxheight = findHeight(top);
-    }
 
     /**
      * Creates a new NJTree object.
@@ -82,10 +76,20 @@ 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();
@@ -132,32 +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")))
         {
@@ -607,7 +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];
                     }
                 }
@@ -616,20 +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)
                         {
@@ -656,7 +662,7 @@ public class NJTree
                 }
             }
         }
-        else if (pwtype.equals("SW"))
+      /*  else if (pwtype.equals("SW"))
         {
             float max = -1;
 
@@ -685,7 +691,7 @@ public class NJTree
                     distance[j][i] = distance[i][j];
                 }
             }
-        }
+        }/*/
 
         return distance;
     }
@@ -976,12 +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)
         {
-- 
1.7.10.2