From 49967bcd77331a51ed428544d06fa3deb8961b17 Mon Sep 17 00:00:00 2001 From: Charles Ofoegbu Date: Wed, 19 Nov 2014 12:05:44 +0000 Subject: [PATCH] JAL-207 pairwise alignment context patch --- src/jalview/gui/PairwiseAlignPanel.java | 22 ++++++++++++---------- 1 file changed, 12 insertions(+), 10 deletions(-) diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java index dcddf88..82f0120 100755 --- a/src/jalview/gui/PairwiseAlignPanel.java +++ b/src/jalview/gui/PairwiseAlignPanel.java @@ -20,14 +20,16 @@ */ 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 java.awt.event.ActionEvent; +import java.util.Vector; + /** * DOCUMENT ME! * @@ -97,12 +99,12 @@ 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()); + seq = new Sequence(as.getAlignedSeq1().getName(), as.getAStr1(), as + .getAlignedSeq1().getStart(), as.getAlignedSeq1().getEnd()); sequences.add(seq); - seq = new Sequence(as.getS2().getName(), as.getAStr2(), as.getS2() - .getStart(), as.getS2().getEnd()); + seq = new Sequence(as.getAlignedSeq2().getName(), as.getAStr2(), as + .getAlignedSeq2().getStart(), as.getAlignedSeq2().getEnd()); sequences.add(seq); } } -- 1.7.10.2