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Uses RemoveGapsCommand
author
amwaterhouse
<Andrew Waterhouse>
Tue, 24 Oct 2006 11:19:30 +0000
(11:19 +0000)
committer
amwaterhouse
<Andrew Waterhouse>
Tue, 24 Oct 2006 11:19:30 +0000
(11:19 +0000)
src/jalview/ws/JPredThread.java
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diff --git
a/src/jalview/ws/JPredThread.java
b/src/jalview/ws/JPredThread.java
index
6aebfdc
..
15b8bd8
100644
(file)
--- a/
src/jalview/ws/JPredThread.java
+++ b/
src/jalview/ws/JPredThread.java
@@
-53,7
+53,7
@@
implements WSClientI
return false;
\r
}
\r
/**
\r
return false;
\r
}
\r
/**
\r
- *
\r
+ *
\r
* @return null or Object[] { annotated alignment for this prediction, ColumnSelection for this prediction} or null if no results available.
\r
* @throws Exception
\r
*/
\r
* @return null or Object[] { annotated alignment for this prediction, ColumnSelection for this prediction} or null if no results available.
\r
* @throws Exception
\r
*/
\r
@@
-102,7
+102,7
@@
implements WSClientI
for (int i = 0, j = al.getHeight(); i < j; i++)
\r
{
\r
sqs[i] = al.getSequenceAt(i);
\r
for (int i = 0, j = al.getHeight(); i < j; i++)
\r
{
\r
sqs[i] = al.getSequenceAt(i);
\r
- }
\r
+ }
\r
if (!jalview.analysis.SeqsetUtils.deuniquify( (Hashtable)
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SequenceInfo, sqs))
\r
{
\r
if (!jalview.analysis.SeqsetUtils.deuniquify( (Hashtable)
\r
SequenceInfo, sqs))
\r
{
\r
@@
-133,7
+133,14
@@
implements WSClientI
SequenceI[] sqs = (SequenceI[]) ((java.lang.Object[]) input.getAlignmentAndColumnSelection(gc))[0];
\r
if (this.msaIndex>=sqs.length)
\r
throw new Error("Implementation Error! Invalid msaIndex for JPredJob on parent MSA input object!");
\r
SequenceI[] sqs = (SequenceI[]) ((java.lang.Object[]) input.getAlignmentAndColumnSelection(gc))[0];
\r
if (this.msaIndex>=sqs.length)
\r
throw new Error("Implementation Error! Invalid msaIndex for JPredJob on parent MSA input object!");
\r
- sqs[msaIndex].removeGaps();
\r
+
\r
+ /////
\r
+ //Uses RemoveGapsCommand
\r
+ /////
\r
+ new jalview.commands.RemoveGapsCommand("Remove Gaps",
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+ new SequenceI[] {sqs[msaIndex]},
\r
+ gc);
\r
+
\r
SequenceI profileseq=al.getSequenceAt(FirstSeq);
\r
profileseq.setSequence(sqs[msaIndex].getSequence());
\r
}
\r
SequenceI profileseq=al.getSequenceAt(FirstSeq);
\r
profileseq.setSequence(sqs[msaIndex].getSequence());
\r
}
\r
@@
-250,7
+257,7
@@
implements WSClientI
int diff=origseq.getLength()-sq.length();
\r
while (diff>0) {
\r
sq=sq+((diff>=sb.length()) ? sb.toString() : sb.substring(0, diff));
\r
int diff=origseq.getLength()-sq.length();
\r
while (diff>0) {
\r
sq=sq+((diff>=sb.length()) ? sb.toString() : sb.substring(0, diff));
\r
- diff=origseq.getLength()-sq.length();
\r
+ diff=origseq.getLength()-sq.length();
\r
}
\r
}
\r
}
\r
}
\r
}
\r
}
\r
@@
-508,14
+515,14
@@
implements WSClientI
if (((SequenceI[])alandcolsel[0])[0].getLength()!=res.getWidth()) {
\r
if (msa) {
\r
throw new Error("Implementation Error! ColumnSelection from input alignment will not map to result alignment!");
\r
if (((SequenceI[])alandcolsel[0])[0].getLength()!=res.getWidth()) {
\r
if (msa) {
\r
throw new Error("Implementation Error! ColumnSelection from input alignment will not map to result alignment!");
\r
- }
\r
+ }
\r
}
\r
if (!msa) {
\r
// update hidden regions to account for loss of gaps in profile. - if any
\r
// gapMap returns insert list, interpreted as delete list by pruneDeletions
\r
//((ColumnSelection) alandcolsel[1]).pruneDeletions(ShiftList.parseMap(((SequenceI[]) alandcolsel[0])[0].gapMap()));
\r
}*/
\r
}
\r
if (!msa) {
\r
// update hidden regions to account for loss of gaps in profile. - if any
\r
// gapMap returns insert list, interpreted as delete list by pruneDeletions
\r
//((ColumnSelection) alandcolsel[1]).pruneDeletions(ShiftList.parseMap(((SequenceI[]) alandcolsel[0])[0].gapMap()));
\r
}*/
\r
-
\r
+
\r
af = new AlignFrame((Alignment) res[0], (ColumnSelection) res[1],AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
\r
}
\r
Desktop.addInternalFrame(af, altitle,
\r
af = new AlignFrame((Alignment) res[0], (ColumnSelection) res[1],AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
\r
}
\r
Desktop.addInternalFrame(af, altitle,
\r