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fixes bug 0013013 but reveals lack of a 'features retrieved' flag that should be...
author
jprocter
<Jim Procter>
Mon, 13 Mar 2006 16:52:54 +0000
(16:52 +0000)
committer
jprocter
<Jim Procter>
Mon, 13 Mar 2006 16:52:54 +0000
(16:52 +0000)
src/jalview/io/SequenceFeatureFetcher.java
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diff --git
a/src/jalview/io/SequenceFeatureFetcher.java
b/src/jalview/io/SequenceFeatureFetcher.java
index
7f11149
..
00afc39
100755
(executable)
--- a/
src/jalview/io/SequenceFeatureFetcher.java
+++ b/
src/jalview/io/SequenceFeatureFetcher.java
@@
-113,8
+113,14
@@
public class SequenceFeatureFetcher implements Runnable
seqIndex++, i++)
\r
{
\r
Sequence sequence = (Sequence) sequences.get(seqIndex);
\r
seqIndex++, i++)
\r
{
\r
Sequence sequence = (Sequence) sequences.get(seqIndex);
\r
- if(sequence.getSequenceFeatures()==null)
\r
+ Vector uprefs = jalview.util.DBRefUtils.selectRefs(sequence.getDBRef(), new String[] { "Uniprot"});
\r
+ if (uprefs!=null)
\r
{
\r
{
\r
+ // we know the id for this entry, so don't note its ID in the unknownSequences list
\r
+ for (int j=0,k=uprefs.size(); j<k; j++)
\r
+ ids.add(((DBRefEntry) uprefs.get(j)).getAccessionId());
\r
+ unknownSequences.add(sequence);
\r
+ } else {
\r
if (!ids.contains(sequence.getName()))
\r
{
\r
ids.add(sequence.getName());
\r
if (!ids.contains(sequence.getName()))
\r
{
\r
ids.add(sequence.getName());
\r
@@
-301,10
+307,12
@@
public class SequenceFeatureFetcher implements Runnable
}
\r
\r
sequence.setPDBId(onlyPdbEntries);
\r
}
\r
\r
sequence.setPDBId(onlyPdbEntries);
\r
- e = entry.getFeature().elements();
\r
- while(e.hasMoreElements())
\r
- {
\r
- sequence.addSequenceFeature((SequenceFeature)e.nextElement());
\r
+ if (entry.getFeature()!=null) {
\r
+ e = entry.getFeature().elements();
\r
+ while (e.hasMoreElements())
\r
+ {
\r
+ sequence.addSequenceFeature( (SequenceFeature) e.nextElement());
\r
+ }
\r
}
\r
sequence.setStart(absStart);
\r
sequence.setEnd(absEnd);
\r
}
\r
sequence.setStart(absStart);
\r
sequence.setEnd(absEnd);
\r