X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FPairwiseAlignPanel.java;h=b8a15d50bbc8fc2590bc9d0da972e882412e00e9;hb=559b96a91b710f3f2e116790c9cf7e3aa6c76766;hp=55cf2ccb95004792c97b9677d850cbf326143d0c;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/appletgui/PairwiseAlignPanel.java b/src/jalview/appletgui/PairwiseAlignPanel.java
index 55cf2cc..b8a15d5 100755
--- a/src/jalview/appletgui/PairwiseAlignPanel.java
+++ b/src/jalview/appletgui/PairwiseAlignPanel.java
@@ -25,48 +25,95 @@ import java.awt.event.*;
 
 import jalview.analysis.*;
 import jalview.datamodel.*;
-import jalview.jbappletgui.*;
+import java.awt.*;
 
 public class PairwiseAlignPanel
-    extends GPairwiseAlignPanel
+    extends Panel implements ActionListener
 {
   Vector sequences = new Vector();
-  AlignViewport av;
+  AlignmentPanel ap;
 
-  public PairwiseAlignPanel(AlignViewport av)
+  public PairwiseAlignPanel(AlignmentPanel ap)
   {
-    super();
-    this.av = av;
-    float scores[][] = new float[av.getAlignment().getHeight()][av.getAlignment().
-        getHeight()];
+    try
+    {
+      jbInit();
+    }
+    catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+    this.ap = ap;
+    sequences = new Vector();
+
+    SequenceI[] seqs;
+    String[] seqStrings = ap.av.getViewAsString(true);
+
+    if (ap.av.getSelectionGroup() == null)
+    {
+      seqs = ap.av.alignment.getSequencesArray();
+    }
+    else
+    {
+      seqs = ap.av.getSelectionGroup().getSequencesInOrder(ap.av.alignment);
+    }
+
+    float scores[][] = new float[seqs.length][seqs.length];
     double totscore = 0;
-    int count = av.getSelectionGroup().getSize();
+    int count = ap.av.getSelectionGroup().getSize(false);
+
+    Sequence seq;
 
-    int acount = 0;
     for (int i = 1; i < count; i++)
     {
       for (int j = 0; j < i; j++)
       {
-        acount++;
-        AlignSeq as = new AlignSeq(av.getSelectionGroup().getSequenceAt(i),
-                                   av.getSelectionGroup().getSequenceAt(j),
-                                   "pep");
+
+        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();
+
+        as.printAlignment(System.out);
         scores[i][j] = (float) as.getMaxScore() / (float) as.getASeq1().length;
         totscore = totscore + scores[i][j];
 
         textarea.append(as.getOutput());
-        sequences.addElement(new Sequence(as.getS1().getName(), as.getAStr1()));
-        sequences.addElement(new Sequence(as.getS2().getName(), as.getAStr2()));
-
+        seq = new Sequence(as.getS1().getName(),
+                           as.getAStr1(),
+                           as.getS1().getStart(),
+                           as.getS1().getEnd()
+            );
+        sequences.addElement(seq);
+
+        seq = new Sequence(as.getS2().getName(),
+                           as.getAStr2(),
+                           as.getS2().getStart(),
+                           as.getS2().getEnd());
+        sequences.addElement(seq);
       }
     }
 
     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++)
@@ -75,10 +122,17 @@ public class PairwiseAlignPanel
                                     scores[i][j] / totscore);
         }
       }
+
+      System.out.println("\n");
     }
   }
+  public void actionPerformed(ActionEvent evt)
+  {
+    if(evt.getSource()==viewInEditorButton)
+      viewInEditorButton_actionPerformed();
+  }
 
-  protected void viewInEditorButton_actionPerformed(ActionEvent e)
+  protected void viewInEditorButton_actionPerformed()
   {
 
     Sequence[] seq = new Sequence[sequences.size()];
@@ -88,11 +142,29 @@ public class PairwiseAlignPanel
       seq[i] = (Sequence) sequences.elementAt(i);
     }
 
-    AlignFrame af = new AlignFrame(new Alignment(seq));
-    jalview.bin.JalviewLite.addFrame(af, "Pairwise Aligned Sequences",
-                                     AlignFrame.NEW_WINDOW_WIDTH,
-                                     AlignFrame.NEW_WINDOW_HEIGHT);
+    new AlignFrame(new Alignment(seq),
+                                   ap.av.applet,
+                                   "Pairwise Aligned Sequences",
+                                   false);
 
   }
+  protected ScrollPane scrollPane = new ScrollPane();
+  protected TextArea textarea = new TextArea();
+  protected Button viewInEditorButton = new Button();
+  Panel jPanel1 = new Panel();
+  BorderLayout borderLayout1 = new BorderLayout();
+
+  private void jbInit() throws Exception {
+      this.setLayout(borderLayout1);
+      textarea.setFont(new java.awt.Font("Monospaced", 0, 12));
+      textarea.setText("");
+      viewInEditorButton.setFont(new java.awt.Font("Verdana", 0, 12));
+      viewInEditorButton.setLabel("View in alignment editor");
+      viewInEditorButton.addActionListener(this);
+      this.add(scrollPane, BorderLayout.CENTER);
+      scrollPane.add(textarea);
+      this.add(jPanel1, BorderLayout.SOUTH);
+      jPanel1.add(viewInEditorButton, null);
+  }
 
 }