X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FPairwiseAlignPanel.java;h=f75407caef708312bc990a4f51e0ac68d529b478;hb=bd894ca9f2aae448653d7431ab8a170e1105e85c;hp=e2f96f122527e687ed862d99f203ac9845b2e0fb;hpb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;p=jalview.git
diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index e2f96f1..f75407c 100755
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.java
@@ -1,30 +1,35 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
- * Copyright (C) 2014 The Jalview Authors
+ * 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
-import java.util.*;
-import java.awt.event.*;
-
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.jbgui.*;
+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 jalview.viewmodel.AlignmentViewport;
+
+import java.awt.event.ActionEvent;
+import java.util.Vector;
/**
* DOCUMENT ME!
@@ -35,7 +40,7 @@ import jalview.util.MessageManager;
public class PairwiseAlignPanel extends GPairwiseAlignPanel
{
- AlignViewport av;
+ AlignmentViewport av;
Vector sequences;
@@ -45,7 +50,7 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
* @param av
* DOCUMENT ME!
*/
- public PairwiseAlignPanel(AlignViewport av)
+ public PairwiseAlignPanel(AlignmentViewport av)
{
super();
this.av = av;
@@ -95,25 +100,20 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
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");
@@ -122,8 +122,8 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
{
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);
}
}
@@ -149,7 +149,8 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
AlignFrame af = new AlignFrame(new Alignment(seq),
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
- Desktop.addInternalFrame(af, MessageManager.getString("label.pairwise_aligned_sequences"),
+ Desktop.addInternalFrame(af,
+ MessageManager.getString("label.pairwise_aligned_sequences"),
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
}
}