/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * 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
- * as published by the Free Software Foundation; either version 2
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 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.
- *
- * 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.
- *
+ *
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
-import java.util.*;
+import jalview.analysis.AlignSeq;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.jbgui.GPairwiseAlignPanel;
+import jalview.util.MessageManager;
-import java.awt.event.*;
-
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.jbgui.*;
+import java.awt.event.ActionEvent;
+import java.util.Vector;
/**
* 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)
{
if (av.getSelectionGroup() == null)
{
- seqs = av.alignment.getSequencesArray();
+ seqs = av.getAlignment().getSequencesArray();
}
else
{
- seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
+ seqs = av.getSelectionGroup().getSequencesInOrder(av.getAlignment());
}
- String type = (av.alignment.isNucleotide()) ? AlignSeq.DNA : AlignSeq.PEP;
+ String type = (av.getAlignment().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()
- );
- sequences.add(seq);
-
- seq = new Sequence(as.getS2().getName(),
- as.getAStr2(),
- as.getS2().getStart(),
- as.getS2().getEnd());
- sequences.add(seq);
+ sequences.add(as.getAlignedSeq1());
+ sequences.add(as.getAlignedSeq2());
}
}
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);
+ Desktop.addInternalFrame(af,
+ MessageManager.getString("label.pairwise_aligned_sequences"),
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
}
}
git://source.jalview.org / jalview.git / blobdiff