X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FPairwiseAlignPanel.java;h=d25cf7fcb2f6f5851acb5c46ec37a89513f14808;hb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;hp=939e2f44a82165a684ee603550ffbc83ea95e26b;hpb=ec955aa655d8320258b91eb079bc57f688cd0a07;p=jalview.git

diff --git a/src/jalview/appletgui/PairwiseAlignPanel.java b/src/jalview/appletgui/PairwiseAlignPanel.java
old mode 100755
new mode 100644
index 939e2f4..d25cf7f
--- a/src/jalview/appletgui/PairwiseAlignPanel.java
+++ b/src/jalview/appletgui/PairwiseAlignPanel.java
@@ -1,71 +1,177 @@
-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 (Version 2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview 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 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.appletgui;
+
+import jalview.analysis.AlignSeq;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
+
+import java.awt.BorderLayout;
+import java.awt.Button;
+import java.awt.Panel;
+import java.awt.ScrollPane;
+import java.awt.TextArea;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.Vector;
+
+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.getAlignment().getSequencesArray();
+    }
+    else
+    {
+      seqs = ap.av.getSelectionGroup().getSequencesInOrder(
+              ap.av.getAlignment());
+    }
+
+    float scores[][] = new float[seqs.length][seqs.length];
+    double totscore = 0;
+    int count = ap.av.getSelectionGroup().getSize();
+    String type = (ap.av.getAlignment().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());
+        sequences.add(as.getAlignedSeq1());
+        sequences.add(as.getAlignedSeq1());
+      }
+    }
+
+    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(MessageManager
+            .getString("label.view_alignment_editor"));
+    viewInEditorButton.addActionListener(this);
+    this.add(scrollPane, BorderLayout.CENTER);
+    scrollPane.add(textarea);
+    this.add(jPanel1, BorderLayout.SOUTH);
+    jPanel1.add(viewInEditorButton, null);
+  }
+
+}