X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FPairwiseAlignPanel.java;h=cf82ea090796f83405d08cd1792df55e594ee362;hb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;hp=e58dd76c133a376a6f3ab0b44947744519afc69c;hpb=621a628afc1f6ee7a2778b9d0ae2729b88fe5bfd;p=jalview.git

diff --git a/src/jalview/appletgui/PairwiseAlignPanel.java b/src/jalview/appletgui/PairwiseAlignPanel.java
index e58dd76..cf82ea0 100755
--- a/src/jalview/appletgui/PairwiseAlignPanel.java
+++ b/src/jalview/appletgui/PairwiseAlignPanel.java
@@ -1,143 +1,171 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 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;
-    float scores[][] = new float[ap.av.alignment.getHeight()][ap.av.alignment.
-        getHeight()];
-    double totscore = 0;
-    int count = ap.av.getSelectionGroup().getSize(false);
-
-    Sequence seq;
-    for (int i = 1; i < count; i++)
-    {
-      for (int j = 0; j < i; j++)
-      {
-        AlignSeq as = new AlignSeq(ap.av.getSelectionGroup().getSequenceAt(i),
-                                   ap.av.getSelectionGroup().getSequenceAt(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.addElement(seq);
-
-        seq = new Sequence(as.getS2().getName(),
-                           as.getAStr2(),
-                           as.getS2().getStart(), as.getS2().getEnd()
-            );
-
-        sequences.addElement(seq);
-      }
-    }
-
-    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);
-        }
-      }
-    }
-  }
-
-  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.alignFrame.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);
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+ * Copyright (C) 2009 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.*;
+import java.awt.event.*;
+
+import jalview.analysis.*;
+import jalview.datamodel.*;
+
+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();
+    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);
+  }
+
+}