/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * 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.
*
*/
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!
public class PairwiseAlignPanel extends GPairwiseAlignPanel
{
- AlignViewport av;
+ AlignmentViewport av;
Vector sequences;
* @param av
* DOCUMENT ME!
*/
- public PairwiseAlignPanel(AlignViewport av)
+ public PairwiseAlignPanel(AlignmentViewport av)
{
super();
this.av = av;
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());
}
}