/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.appletgui;
-import java.util.*;
-
-import java.awt.event.*;
-
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import java.awt.*;
-
-public class PairwiseAlignPanel
- extends Panel implements ActionListener
+import jalview.analysis.AlignSeq;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
+
+import java.awt.BorderLayout;
+import java.awt.Button;
+import java.awt.Panel;
+import java.awt.ScrollPane;
+import java.awt.TextArea;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.Vector;
+
+public class PairwiseAlignPanel extends Panel implements ActionListener
{
Vector sequences = new Vector();
+
AlignmentPanel ap;
public PairwiseAlignPanel(AlignmentPanel ap)
try
{
jbInit();
- }
- catch (Exception e)
+ } catch (Exception e)
{
e.printStackTrace();
}
if (ap.av.getSelectionGroup() == null)
{
- seqs = ap.av.alignment.getSequencesArray();
+ seqs = ap.av.getAlignment().getSequencesArray();
}
else
{
- seqs = ap.av.getSelectionGroup().getSequencesInOrder(ap.av.alignment);
+ seqs = ap.av.getSelectionGroup()
+ .getSequencesInOrder(ap.av.getAlignment());
}
float scores[][] = new float[seqs.length][seqs.length];
double totscore = 0;
- int count = ap.av.getSelectionGroup().getSize(false);
- String type=(ap.av.alignment.isNucleotide()) ? AlignSeq.DNA : AlignSeq.PEP;
+ int count = ap.av.getSelectionGroup().getSize();
+ String type = (ap.av.getAlignment().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);
+ 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.addElement(seq);
-
- seq = new Sequence(as.getS2().getName(),
- as.getAStr2(),
- as.getS2().getStart(),
- as.getS2().getEnd());
- sequences.addElement(seq);
+ sequences.add(as.getAlignedSeq1());
+ sequences.add(as.getAlignedSeq1());
}
}
if (count > 2)
{
System.out.println(
- "Pairwise alignment scaled similarity score matrix\n");
+ "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());
+ ("" + 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);
+ scores[i][j] / totscore);
}
}
System.out.println("\n");
}
}
+
public void actionPerformed(ActionEvent evt)
{
- if(evt.getSource()==viewInEditorButton)
+ if (evt.getSource() == viewInEditorButton)
+ {
viewInEditorButton_actionPerformed();
+ }
}
protected void viewInEditorButton_actionPerformed()
seq[i] = (Sequence) sequences.elementAt(i);
}
- new AlignFrame(new Alignment(seq),
- ap.av.applet,
- "Pairwise Aligned Sequences",
- false);
+ 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);
+ 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(
+ MessageManager.getString("label.view_alignment_editor"));
+ viewInEditorButton.addActionListener(this);
+ this.add(scrollPane, BorderLayout.CENTER);
+ scrollPane.add(textarea);
+ this.add(jPanel1, BorderLayout.SOUTH);
+ jPanel1.add(viewInEditorButton, null);
}
}
git://source.jalview.org / jalview.git / blobdiff