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Merge branch 'develop' into features/JAL-2110_crossRefDuplications
[jalview.git]
/
src
/
jalview
/
datamodel
/
xdb
/
embl
/
EmblEntry.java
diff --git
a/src/jalview/datamodel/xdb/embl/EmblEntry.java
b/src/jalview/datamodel/xdb/embl/EmblEntry.java
index
9a07c36
..
b750973
100644
(file)
--- a/
src/jalview/datamodel/xdb/embl/EmblEntry.java
+++ b/
src/jalview/datamodel/xdb/embl/EmblEntry.java
@@
-202,6
+202,7
@@
public class EmblEntry
{
for (DBRefEntry dbref : dbRefs)
{
{
for (DBRefEntry dbref : dbRefs)
{
+ dbref.setSource(DBRefUtils.getCanonicalName(dbref.getSource()));
dna.addDBRef(dbref);
}
}
dna.addDBRef(dbref);
}
}
@@
-214,6
+215,10
@@
public class EmblEntry
{
for (DBRefEntry dbref : feature.dbRefs)
{
{
for (DBRefEntry dbref : feature.dbRefs)
{
+ /*
+ * convert UniProtKB/Swiss-Prot to UNIPROT
+ */
+ dbref.setSource(DBRefUtils.getCanonicalName(dbref.getSource()));
dna.addDBRef(dbref);
}
}
dna.addDBRef(dbref);
}
}
@@
-421,14
+426,13
@@
public class EmblEntry
}
/*
}
/*
- * add dbRefs to sequence, and mappings for Uniprot xrefs
+ * add mappings for Uniprot xrefs
*/
if (feature.dbRefs != null)
{
boolean mappingUsed = false;
for (DBRefEntry ref : feature.dbRefs)
{
*/
if (feature.dbRefs != null)
{
boolean mappingUsed = false;
for (DBRefEntry ref : feature.dbRefs)
{
- ref.setSource(DBRefUtils.getCanonicalName(ref.getSource()));
if (ref.getSource().equals(DBRefSource.UNIPROT))
{
String proteinSeqName = DBRefSource.UNIPROT + "|"
if (ref.getSource().equals(DBRefSource.UNIPROT))
{
String proteinSeqName = DBRefSource.UNIPROT + "|"
@@
-484,7
+488,6
@@
public class EmblEntry
}
}
}
}
}
}
- dna.addDBRef(ref);
}
if (noProteinDbref && product != null)
{
}
if (noProteinDbref && product != null)
{