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Remove variables not used
[jalview.git]
/
src
/
jalview
/
gui
/
PairwiseAlignPanel.java
diff --git
a/src/jalview/gui/PairwiseAlignPanel.java
b/src/jalview/gui/PairwiseAlignPanel.java
index
f52a1d8
..
248a54c
100755
(executable)
--- a/
src/jalview/gui/PairwiseAlignPanel.java
+++ b/
src/jalview/gui/PairwiseAlignPanel.java
@@
-1,6
+1,6
@@
/*
\r
* Jalview - A Sequence Alignment Editor and Viewer
\r
/*
\r
* Jalview - A Sequence Alignment Editor and Viewer
\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
\r
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
\r
*
\r
* This program is free software; you can redistribute it and/or
\r
* modify it under the terms of the GNU General Public License
\r
*
\r
* This program is free software; you can redistribute it and/or
\r
* modify it under the terms of the GNU General Public License
\r
@@
-54,7
+54,7
@@
public class PairwiseAlignPanel extends GPairwiseAlignPanel
sequences = new Vector();
\r
\r
SequenceI [] seqs;
\r
sequences = new Vector();
\r
\r
SequenceI [] seqs;
\r
- String [] seqStrings = av.getSelectionAsString();
\r
+ String [] seqStrings = av.getViewAsString(true);
\r
\r
if(av.getSelectionGroup()==null)
\r
{
\r
\r
if(av.getSelectionGroup()==null)
\r
{
\r
@@
-70,20
+70,25
@@
public class PairwiseAlignPanel extends GPairwiseAlignPanel
double totscore = 0;
\r
int count = seqs.length;
\r
\r
double totscore = 0;
\r
int count = seqs.length;
\r
\r
- int acount = 0;
\r
Sequence seq;
\r
\r
for (int i = 1; i < count; i++)
\r
{
\r
for (int j = 0; j < i; j++)
\r
{
\r
Sequence seq;
\r
\r
for (int i = 1; i < count; i++)
\r
{
\r
for (int j = 0; j < i; j++)
\r
{
\r
- acount++;
\r
\r
AlignSeq as = new AlignSeq(seqs[i], seqStrings[i],
\r
seqs[j], seqStrings[j], "pep");
\r
\r
\r
AlignSeq as = new AlignSeq(seqs[i], seqStrings[i],
\r
seqs[j], seqStrings[j], "pep");
\r
\r
+ if(as.s1str.length()==0 || as.s2str.length()==0)
\r
+ {
\r
+ continue;
\r
+ }
\r
+
\r
as.calcScoreMatrix();
\r
as.traceAlignment();
\r
as.calcScoreMatrix();
\r
as.traceAlignment();
\r
+
\r
+
\r
as.printAlignment(System.out);
\r
scores[i][j] = (float) as.getMaxScore() / (float) as.getASeq1().length;
\r
totscore = totscore + scores[i][j];
\r
as.printAlignment(System.out);
\r
scores[i][j] = (float) as.getMaxScore() / (float) as.getASeq1().length;
\r
totscore = totscore + scores[i][j];
\r
@@
-91,7
+96,8
@@
public class PairwiseAlignPanel extends GPairwiseAlignPanel
textarea.append(as.getOutput());
\r
seq = new Sequence(as.getS1().getName(),
\r
as.getAStr1(),
\r
textarea.append(as.getOutput());
\r
seq = new Sequence(as.getS1().getName(),
\r
as.getAStr1(),
\r
- as.getS1().getStart(), as.getS1().getEnd()
\r
+ as.getS1().getStart(),
\r
+ as.getS1().getEnd()
\r
);
\r
sequences.add(seq);
\r
\r
);
\r
sequences.add(seq);
\r
\r
@@
-144,8
+150,11
@@
public class PairwiseAlignPanel extends GPairwiseAlignPanel
seq[i] = (Sequence) sequences.elementAt(i);
\r
}
\r
\r
seq[i] = (Sequence) sequences.elementAt(i);
\r
}
\r
\r
- AlignFrame af = new AlignFrame(new Alignment(seq));
\r
+ AlignFrame af = new AlignFrame(new Alignment(seq),
\r
+ AlignFrame.DEFAULT_WIDTH,
\r
+ AlignFrame.DEFAULT_HEIGHT);
\r
+
\r
Desktop.addInternalFrame(af, "Pairwise Aligned Sequences",
\r
Desktop.addInternalFrame(af, "Pairwise Aligned Sequences",
\r
- AlignFrame.NEW_WINDOW_WIDTH, AlignFrame.NEW_WINDOW_HEIGHT);
\r
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
\r
}
\r
}
\r
}
\r
}
\r