X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPairwiseAlignPanel.java;h=ba3c9ac04001fc31a55d8b7947b1228436f56f6e;hb=acc9fa6c42fcdde3d55b483f1dea91e0058be06e;hp=69789b9c46e499bec5838ecdce516ff1792e115b;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index 69789b9..ba3c9ac 100755
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.java
@@ -18,101 +18,140 @@
  */
 package jalview.gui;
 
-import java.util.*;
-
-import java.awt.event.*;
-
 import jalview.analysis.*;
+
 import jalview.datamodel.*;
+
 import jalview.jbgui.*;
 
-public class PairwiseAlignPanel
-    extends GPairwiseAlignPanel
-{
-  Vector sequences = new Vector();
-  AlignViewport av;
+import java.awt.event.*;
 
-  public PairwiseAlignPanel(AlignViewport av)
-  {
-    super();
-    this.av = av;
+import java.util.*;
 
-    Vector selsubset = new Vector();
 
-    for (int i = 0, j = av.getSelectionGroup().getSize(); i < j; i++)
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class PairwiseAlignPanel extends GPairwiseAlignPanel
+{
+
+    AlignViewport av;
+    Vector sequences;
+
+    /**
+     * Creates a new PairwiseAlignPanel object.
+     *
+     * @param av DOCUMENT ME!
+     */
+    public PairwiseAlignPanel(AlignViewport av)
     {
-      if (av.getAlignment().getSequences().contains(av.getSelectionGroup()
-          .getSequenceAt(i)))
-      {
-        selsubset.add(av.getSelectionGroup().getSequenceAt(i));
-      }
-    }
+        super();
+        this.av = av;
 
-    float[][] scores = new float[selsubset.size()][selsubset.size()];
-    double totscore = 0;
-    int count = selsubset.size();
+        sequences = new Vector();
 
-    int acount = 0;
+        SequenceI [] seqs;
+        String []  seqStrings = av.getViewAsString(true);
 
-    for (int i = 1; i < count; i++)
-    {
-      for (int j = 0; j < i; j++)
-      {
-        acount++;
-
-        AlignSeq as = new AlignSeq( (SequenceI) selsubset.elementAt(i),
-                                   (SequenceI) selsubset.elementAt(j), "pep");
-        as.calcScoreMatrix();
-        as.traceAlignment();
-        as.printAlignment();
-        scores[i][j] = (float) as.getMaxScore() / (float) as.getASeq1().length;
-        totscore = totscore + scores[i][j];
-
-        textarea.append(as.getOutput());
-        sequences.add(new Sequence(as.getS1().getName(), as.getAStr1()));
-        sequences.add(new Sequence(as.getS2().getName(), as.getAStr2()));
-      }
-    }
+        if(av.getSelectionGroup()==null)
+        {
+          seqs = av.alignment.getSequencesArray();
+        }
+        else
+        {
+          seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
+        }
 
-    if (count > 2)
-    {
-      System.out.println(
-          "Pairwise alignment scaled similarity score matrix\n");
 
-      for (int i = 0; i < count; i++)
-      {
-        jalview.util.Format.print(System.out, "%s \n",
-                                  ("" + i) + " " +
-                                  ( (SequenceI) selsubset.elementAt(i)).getName());
-      }
+        float[][] scores = new float[seqs.length][seqs.length];
+        double totscore = 0;
+        int count = seqs.length;
 
-      System.out.println("\n");
+        Sequence seq;
 
-      for (int i = 0; i < count; i++)
-      {
-        for (int j = 0; j < i; j++)
+        for (int i = 1; i < count; i++)
         {
-          jalview.util.Format.print(System.out, "%7.3f",
-                                    scores[i][j] / totscore);
+            for (int j = 0; j < i; j++)
+            {
+
+                AlignSeq as = new AlignSeq(seqs[i], seqStrings[i],
+                        seqs[j], seqStrings[j], "pep");
+
+                if(as.s1str.length()==0 || as.s2str.length()==0)
+                {
+                  continue;
+                }
+
+                as.calcScoreMatrix();
+                as.traceAlignment();
+
+
+                as.printAlignment(System.out);
+                scores[i][j] = (float) as.getMaxScore() / (float) as.getASeq1().length;
+                totscore = totscore + scores[i][j];
+
+                textarea.append(as.getOutput());
+                seq = new Sequence(as.getS1().getName(),
+                                   as.getAStr1(),
+                                   as.getS1().getStart(),
+                                   as.getS1().getEnd()
+                );
+                sequences.add(seq);
+
+                seq = new Sequence(as.getS2().getName(),
+                                   as.getAStr2(),
+                                   as.getS2().getStart(),
+                                   as.getS2().getEnd() );
+                sequences.add(seq);
+            }
         }
-      }
 
-      System.out.println("\n");
+        if (count > 2)
+        {
+            System.out.println(
+                "Pairwise alignment scaled similarity score matrix\n");
+
+            for (int i = 0; i < count; i++)
+            {
+                jalview.util.Format.print(System.out, "%s \n",
+                    ("" + i) + " " +
+                    seqs[i].getName());
+            }
+
+            System.out.println("\n");
+
+            for (int i = 0; i < count; i++)
+            {
+                for (int j = 0; j < i; j++)
+                {
+                    jalview.util.Format.print(System.out, "%7.3f",
+                        scores[i][j] / totscore);
+                }
+            }
+
+            System.out.println("\n");
+        }
     }
-  }
-
-  protected void viewInEditorButton_actionPerformed(ActionEvent e)
-  {
-    Sequence[] seq = new Sequence[sequences.size()];
 
-    for (int i = 0; i < sequences.size(); i++)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    protected void viewInEditorButton_actionPerformed(ActionEvent e)
     {
-      seq[i] = (Sequence) sequences.elementAt(i);
-    }
+        Sequence[] seq = new Sequence[sequences.size()];
 
-    AlignFrame af = new AlignFrame(new Alignment(seq));
-    Desktop.addInternalFrame(af, "Pairwise Aligned Sequences",
-                             AlignFrame.NEW_WINDOW_WIDTH,
-                             AlignFrame.NEW_WINDOW_HEIGHT);
-  }
+        for (int i = 0; i < sequences.size(); i++)
+        {
+            seq[i] = (Sequence) sequences.elementAt(i);
+        }
+
+        AlignFrame af = new AlignFrame(new Alignment(seq));
+        Desktop.addInternalFrame(af, "Pairwise Aligned Sequences",
+            AlignFrame.NEW_WINDOW_WIDTH, AlignFrame.NEW_WINDOW_HEIGHT);
+    }
 }