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Output new alignment bug fixed
author
amwaterhouse
<Andrew Waterhouse>
Thu, 16 Dec 2004 15:45:38 +0000
(15:45 +0000)
committer
amwaterhouse
<Andrew Waterhouse>
Thu, 16 Dec 2004 15:45:38 +0000
(15:45 +0000)
src/jalview/gui/PairwiseAlignPanel.java
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diff --git
a/src/jalview/gui/PairwiseAlignPanel.java
b/src/jalview/gui/PairwiseAlignPanel.java
index
c771693
..
b85cb94
100755
(executable)
--- a/
src/jalview/gui/PairwiseAlignPanel.java
+++ b/
src/jalview/gui/PairwiseAlignPanel.java
@@
-28,7
+28,6
@@
public class PairwiseAlignPanel extends GPairwiseAlignPanel
{
\r
acount++;
\r
AlignSeq as = new AlignSeq(av.getSelection().sequenceAt(i),av.getSelection().sequenceAt(j),"pep");
\r
{
\r
acount++;
\r
AlignSeq as = new AlignSeq(av.getSelection().sequenceAt(i),av.getSelection().sequenceAt(j),"pep");
\r
- //tf.status.setText("Aligning " + as.getS1().getName() + " and " + as.getS2().getName() + " (" + acount + "/" + (count*(count-1)/2) + ")");
\r
\r
as.calcScoreMatrix();
\r
as.traceAlignment();
\r
\r
as.calcScoreMatrix();
\r
as.traceAlignment();
\r
@@
-37,8
+36,9
@@
public class PairwiseAlignPanel extends GPairwiseAlignPanel
totscore = totscore + scores[i][j];
\r
\r
textarea.append(as.getOutput());
\r
totscore = totscore + scores[i][j];
\r
\r
textarea.append(as.getOutput());
\r
- sequences.add( as.getS1() );
\r
- sequences.add( as.getS2() );
\r
+ sequences.add( new Sequence( as.getS1().getName(), as.getAStr1()) );
\r
+ sequences.add( new Sequence( as.getS2().getName(), as.getAStr2()) );
\r
+
\r
\r
}
\r
}
\r
\r
}
\r
}
\r