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ensured that seqeunce feature shift takes into account start position difference...
author
jprocter
<Jim Procter>
Tue, 22 Jan 2008 16:14:54 +0000
(16:14 +0000)
committer
jprocter
<Jim Procter>
Tue, 22 Jan 2008 16:14:54 +0000
(16:14 +0000)
src/jalview/ws/DBRefFetcher.java
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diff --git
a/src/jalview/ws/DBRefFetcher.java
b/src/jalview/ws/DBRefFetcher.java
index
c2d7ad5
..
ba6d57f
100644
(file)
--- a/
src/jalview/ws/DBRefFetcher.java
+++ b/
src/jalview/ws/DBRefFetcher.java
@@
-438,13
+438,14
@@
public class DBRefFetcher implements Runnable
SequenceFeature[] sf = sequence.getSequenceFeatures();
\r
int start = sequence.getStart();
\r
int end = sequence.getEnd();
\r
SequenceFeature[] sf = sequence.getSequenceFeatures();
\r
int start = sequence.getStart();
\r
int end = sequence.getEnd();
\r
+ int startShift = 1-absStart-start; // how much the features are to be shifted by
\r
for (int sfi = 0; sfi < sf.length; sfi++)
\r
{
\r
if (sf[sfi].getBegin() >= start && sf[sfi].getEnd() <= end)
\r
{
\r
// shift feature along by absstart
\r
for (int sfi = 0; sfi < sf.length; sfi++)
\r
{
\r
if (sf[sfi].getBegin() >= start && sf[sfi].getEnd() <= end)
\r
{
\r
// shift feature along by absstart
\r
- sf[sfi].setBegin(sf[sfi].getBegin() + absStart);
\r
- sf[sfi].setEnd(sf[sfi].getEnd() + absStart);
\r
+ sf[sfi].setBegin(sf[sfi].getBegin() + startShift);
\r
+ sf[sfi].setEnd(sf[sfi].getEnd() + startShift);
\r
}
\r
}
\r
}
\r
}
\r
}
\r
}
\r