X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPairwiseAlignPanel.java;h=5ca572c9e56f62cd2f3bd0d690faca5076c82828;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=28254671cd7299834066912e7b1026ced2780b06;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git

diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index 2825467..5ca572c 100755
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.java
@@ -1,98 +1,154 @@
-/*
-* 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.gui;
-
-import jalview.datamodel.*;
-import jalview.jbgui.GPairwiseAlignPanel;
-import jalview.analysis.*;
-import java.awt.event.*;
-import javax.swing.*;
-import java.util.*;
-
-
-public class PairwiseAlignPanel extends GPairwiseAlignPanel
-{
-    Vector sequences = new Vector();
-    AlignViewport av;
-
-    public PairwiseAlignPanel(AlignViewport av)
-    {
-      super();
-      this.av = av;
-      Vector selsubset = new Vector();
-      for (int i=0, j=av.getSelectionGroup().getSize(); i<j; i++)
-        if (av.getAlignment().getSequences().contains(av.getSelectionGroup().getSequenceAt(i)))
-          selsubset.add(av.getSelectionGroup().getSequenceAt(i));
-      float scores[][] = new float[selsubset.size()][selsubset.size()];
-      double totscore = 0;
-      int count = selsubset.size();
-
-      int acount = 0;
-      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 (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());
-        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++)
-       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);
-
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 
+ * 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/>.
+ */
+package jalview.gui;
+
+import java.util.*;
+
+import java.awt.event.*;
+
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.jbgui.*;
+
+/**
+ * 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)
+  {
+    super();
+    this.av = av;
+
+    sequences = new Vector();
+
+    SequenceI[] seqs;
+    String[] seqStrings = av.getViewAsString(true);
+
+    if (av.getSelectionGroup() == null)
+    {
+      seqs = av.alignment.getSequencesArray();
+    }
+    else
+    {
+      seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
+    }
+
+    String type = (av.alignment.isNucleotide()) ? AlignSeq.DNA
+            : AlignSeq.PEP;
+
+    float[][] scores = new float[seqs.length][seqs.length];
+    double totscore = 0;
+    int count = seqs.length;
+
+    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.add(seq);
+
+        seq = new Sequence(as.getS2().getName(), as.getAStr2(), as.getS2()
+                .getStart(), as.getS2().getEnd());
+        sequences.add(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");
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *          DOCUMENT ME!
+   */
+  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),
+            AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+
+    Desktop.addInternalFrame(af, "Pairwise Aligned Sequences",
+            AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+  }
+}