/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * 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.
- *
+ * 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/>.
+ * You should have received a copy of the GNU General Public License
+ * 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.*;
-import java.awt.event.*;
-
-import jalview.analysis.*;
-import jalview.datamodel.*;
+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
{
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();
- String type = (ap.av.alignment.isNucleotide()) ? AlignSeq.DNA
+ String type = (ap.av.getAlignment().isNucleotide()) ? AlignSeq.DNA
: AlignSeq.PEP;
Sequence seq;
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");
+ 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);
}
}
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.setLabel(
+ MessageManager.getString("label.view_alignment_editor"));
viewInEditorButton.addActionListener(this);
this.add(scrollPane, BorderLayout.CENTER);
scrollPane.add(textarea);