/*
* Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 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
*/
package jalview.gui;
-import jalview.analysis.*;
-
-import jalview.datamodel.*;
-
-import jalview.jbgui.*;
+import java.util.*;
import java.awt.event.*;
-import java.util.*;
-
+import jalview.analysis.*;
+import jalview.datamodel.*;
+import jalview.jbgui.*;
/**
* DOCUMENT ME!
* @author $author$
* @version $Revision$
*/
-public class PairwiseAlignPanel extends GPairwiseAlignPanel
+public class PairwiseAlignPanel
+ extends GPairwiseAlignPanel
{
- AlignViewport av;
- Vector sequences;
+ AlignViewport av;
+ Vector sequences;
+
+ /**
+ * Creates a new PairwiseAlignPanel object.
+ *
+ * @param av DOCUMENT ME!
+ */
+ public PairwiseAlignPanel(AlignViewport av)
+ {
+ super();
+ this.av = av;
- /**
- * Creates a new PairwiseAlignPanel object.
- *
- * @param av DOCUMENT ME!
- */
- public PairwiseAlignPanel(AlignViewport av)
+ sequences = new Vector();
+
+ SequenceI[] seqs;
+ String[] seqStrings = av.getViewAsString(true);
+
+ if (av.getSelectionGroup() == null)
+ {
+ seqs = av.alignment.getSequencesArray();
+ }
+ else
{
- super();
- this.av = av;
+ seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
+ }
- sequences = new Vector();
+ String type = (av.alignment.isNucleotide()) ? AlignSeq.DNA : AlignSeq.PEP;
- SequenceI [] seqs;
- String [] seqStrings = av.getViewAsString(true);
+ float[][] scores = new float[seqs.length][seqs.length];
+ double totscore = 0;
+ int count = seqs.length;
- if(av.getSelectionGroup()==null)
- {
- seqs = av.alignment.getSequencesArray();
- }
- else
- {
- seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
- }
+ Sequence seq;
- String type=(av.alignment.isNucleotide()) ? AlignSeq.DNA : AlignSeq.PEP;
-
- float[][] scores = new float[seqs.length][seqs.length];
- double totscore = 0;
- int count = seqs.length;
+ for (int i = 1; i < count; i++)
+ {
+ for (int j = 0; j < i; j++)
+ {
- Sequence seq;
+ AlignSeq as = new AlignSeq(seqs[i], seqStrings[i],
+ seqs[j], seqStrings[j], type);
- for (int i = 1; i < count; i++)
+ if (as.s1str.length() == 0 || as.s2str.length() == 0)
{
- 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);
- }
+ continue;
}
- 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");
- }
+ 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);
+ }
}
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- protected void viewInEditorButton_actionPerformed(ActionEvent e)
+ if (count > 2)
{
- Sequence[] seq = new Sequence[sequences.size()];
+ System.out.println(
+ "Pairwise alignment scaled similarity score matrix\n");
- for (int i = 0; i < sequences.size(); i++)
+ 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++)
{
- seq[i] = (Sequence) sequences.elementAt(i);
+ jalview.util.Format.print(System.out, "%7.3f",
+ scores[i][j] / totscore);
}
+ }
- 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);
+ 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);
+ }
}
git://source.jalview.org / jalview.git / blobdiff