X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FPairwiseAlignPanel.java;h=792c906ec411d6943b7e9ada626eb7c7180e55c5;hb=2eb95f4ffb0191ddcfc94551790ec02ed7f0dab5;hp=939e2f44a82165a684ee603550ffbc83ea95e26b;hpb=ec955aa655d8320258b91eb079bc57f688cd0a07;p=jalview.git

diff --git a/src/jalview/appletgui/PairwiseAlignPanel.java b/src/jalview/appletgui/PairwiseAlignPanel.java
index 939e2f4..792c906 100755
--- a/src/jalview/appletgui/PairwiseAlignPanel.java
+++ b/src/jalview/appletgui/PairwiseAlignPanel.java
@@ -1,71 +1,170 @@
-package jalview.appletgui;
-
-import jalview.datamodel.*;
-import jalview.jbappletgui.GPairwiseAlignPanel;
-import jalview.analysis.*;
-import java.awt.event.*;
-import java.util.*;
-
-
-public class PairwiseAlignPanel extends GPairwiseAlignPanel
-{
-    Vector sequences = new Vector();
-    AlignViewport av;
-
-    public PairwiseAlignPanel(AlignViewport av)
-    {
-      super();
-      this.av = av;
-      float scores[][] = new float[av.getAlignment().getHeight()][av.getAlignment().getHeight()];
-      double totscore = 0;
-      int count = av.getSelectionGroup().getSize();
-
-      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");
-
-            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.addElement( new Sequence( as.getS1().getName(), as.getAStr1()) );
-            sequences.addElement( new Sequence( as.getS2().getName(), as.getAStr2()) );
-
-
-          }
-        }
-
-        if (count > 2)
-        {
-          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);
-        }
-      }
-
-
-  protected void viewInEditorButton_actionPerformed(ActionEvent e)
-  {
-
-      Sequence [] seq = new Sequence[sequences.size()];
-
-      for (int i=0;i<sequences.size();i++)
-       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);
-
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+
+package jalview.appletgui;
+
+import java.util.*;
+
+import java.awt.event.*;
+
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import java.awt.*;
+
+public class PairwiseAlignPanel
+    extends Panel implements ActionListener
+{
+  Vector sequences = new Vector();
+  AlignmentPanel ap;
+
+  public PairwiseAlignPanel(AlignmentPanel ap)
+  {
+    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 = ap.av.getSelectionGroup().getSize(false);
+    String type=(ap.av.alignment.isNucleotide()) ? AlignSeq.DNA : AlignSeq.PEP;
+    Sequence seq;
+
+    for (int i = 1; i < count; i++)
+    {
+      for (int j = 0; j < i; j++)
+      {
+
+        AlignSeq as = new AlignSeq(seqs[i], seqStrings[i],
+                                   seqs[j], seqStrings[j], type);
+
+        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.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++)
+        {
+          jalview.util.Format.print(System.out, "%7.3f",
+                                    scores[i][j] / totscore);
+        }
+      }
+
+      System.out.println("\n");
+    }
+  }
+  public void actionPerformed(ActionEvent evt)
+  {
+    if(evt.getSource()==viewInEditorButton)
+      viewInEditorButton_actionPerformed();
+  }
+
+  protected void viewInEditorButton_actionPerformed()
+  {
+
+    Sequence[] seq = new Sequence[sequences.size()];
+
+    for (int i = 0; i < sequences.size(); i++)
+    {
+      seq[i] = (Sequence) sequences.elementAt(i);
+    }
+
+    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);
+  }
+
+}