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JAL-2110 random stuff
[jalview.git]
/
src
/
jalview
/
analysis
/
CrossRefs.java
diff --git
a/src/jalview/analysis/CrossRefs.java
b/src/jalview/analysis/CrossRefs.java
index
7d0c263
..
0f3f425
100644
(file)
--- a/
src/jalview/analysis/CrossRefs.java
+++ b/
src/jalview/analysis/CrossRefs.java
@@
-49,6
+49,8
@@
public class CrossRefs
List<SequenceI> foundSeqs = new ArrayList<SequenceI>();
AlignedCodonFrame mappings = new AlignedCodonFrame();
List<SequenceI> foundSeqs = new ArrayList<SequenceI>();
AlignedCodonFrame mappings = new AlignedCodonFrame();
+ List<DBRefEntry> sourceRefs = new ArrayList<DBRefEntry>();
+
for (SequenceI seq : seqs)
{
if (dna != Comparison.isNucleotide(seq))
for (SequenceI seq : seqs)
{
if (dna != Comparison.isNucleotide(seq))
@@
-62,28
+64,27
@@
public class CrossRefs
/*
* get this sequence's dbrefs to source database (if any)
*/
/*
* get this sequence's dbrefs to source database (if any)
*/
- List<DBRefEntry> sourceRefs = DBRefUtils.searchRefsForSource(
+ List<DBRefEntry> seqSourceRefs = DBRefUtils.searchRefsForSource(
seq.getDBRefs(), source);
/*
* first extract any mapped sequences from sourceRefs
*/
seq.getDBRefs(), source);
/*
* first extract any mapped sequences from sourceRefs
*/
- findMappedDbrefs(seq, sourceRefs, foundSeqs, mappings);
+ findMappedDbrefs(seq, seqSourceRefs, foundSeqs, mappings);
/*
* for remaining sourceRefs, try to match a
* complementary sequence in the dataset
*/
/*
* for remaining sourceRefs, try to match a
* complementary sequence in the dataset
*/
- findIndirectCrossReferences(seq, source, sourceRefs, dataset,
+ findIndirectCrossReferences(seq, source, seqSourceRefs, dataset,
foundSeqs, mappings);
foundSeqs, mappings);
-
- /*
- * fetch any remaining sourceRefs from the source database
- */
- fetchCrossReferences(seq, sourceRefs, foundSeqs, mappings, dna,
- dataset);
}
}
+ /*
+ * fetch any remaining sourceRefs from the source database
+ */
+ fetchCrossReferences(sourceRefs, foundSeqs, mappings, dna, dataset);
+
if (foundSeqs.isEmpty())
{
return null;
if (foundSeqs.isEmpty())
{
return null;