/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
* @version $Revision$
*/
-public class PairwiseAlignPanel
- extends GPairwiseAlignPanel
+public class PairwiseAlignPanel extends GPairwiseAlignPanel
{
AlignViewport av;
+
Vector sequences;
/**
* Creates a new PairwiseAlignPanel object.
- *
- * @param av DOCUMENT ME!
+ *
+ * @param av
+ * DOCUMENT ME!
*/
public PairwiseAlignPanel(AlignViewport av)
{
seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
}
- String type = (av.alignment.isNucleotide()) ? AlignSeq.DNA : AlignSeq.PEP;
+ String type = (av.alignment.isNucleotide()) ? AlignSeq.DNA
+ : AlignSeq.PEP;
float[][] scores = new float[seqs.length][seqs.length];
double totscore = 0;
for (int j = 0; j < i; j++)
{
- AlignSeq as = new AlignSeq(seqs[i], seqStrings[i],
- seqs[j], seqStrings[j], type);
+ AlignSeq as = new AlignSeq(seqs[i], seqStrings[i], seqs[j],
+ seqStrings[j], type);
if (as.s1str.length() == 0 || as.s2str.length() == 0)
{
as.traceAlignment();
as.printAlignment(System.out);
- scores[i][j] = (float) as.getMaxScore() / (float) as.getASeq1().length;
+ 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()
- );
+ 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());
+ 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");
+ 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());
+ jalview.util.Format.print(System.out, "%s \n", ("" + i) + " "
+ + seqs[i].getName());
}
System.out.println("\n");
{
for (int j = 0; j < i; j++)
{
- jalview.util.Format.print(System.out, "%7.3f",
- scores[i][j] / totscore);
+ jalview.util.Format.print(System.out, "%7.3f", scores[i][j]
+ / totscore);
}
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void viewInEditorButton_actionPerformed(ActionEvent e)
{
}
AlignFrame af = new AlignFrame(new Alignment(seq),
- AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
Desktop.addInternalFrame(af, "Pairwise Aligned Sequences",
- AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
}
}