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friendlier sequence names for protein products
author
jprocter
<Jim Procter>
Sat, 29 Sep 2007 13:50:38 +0000
(13:50 +0000)
committer
jprocter
<Jim Procter>
Sat, 29 Sep 2007 13:50:38 +0000
(13:50 +0000)
src/jalview/datamodel/xdb/embl/EmblEntry.java
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diff --git
a/src/jalview/datamodel/xdb/embl/EmblEntry.java
b/src/jalview/datamodel/xdb/embl/EmblEntry.java
index
350c44e
..
9d12ccf
100644
(file)
--- a/
src/jalview/datamodel/xdb/embl/EmblEntry.java
+++ b/
src/jalview/datamodel/xdb/embl/EmblEntry.java
@@
-542,10
+542,10
@@
public class EmblEntry
if (prseq != null && prname != null && prid != null)
{
// extract proteins.
if (prseq != null && prname != null && prid != null)
{
// extract proteins.
- product = new Sequence(sourceDb + "|" + "EMBLCDS|" + prid
- +((prname.length()==0) ? "" : " " + prname), prseq, prstart, prstart
+ product = new Sequence(prid
+ , prseq, prstart, prstart
+ prseq.length() - 1);
+ prseq.length() - 1);
- product.setDescription("Protein Product from " + sourceDb);
+ product.setDescription(((prname.length()==0) ? "Protein Product from " + sourceDb : prname));
if (!noPeptide)
{
if (!noPeptide)
{
@@
-584,7
+584,7
@@
public class EmblEntry
{
// TODO: Add a DbRef back to the parent EMBL sequence with the exon
// map
{
// TODO: Add a DbRef back to the parent EMBL sequence with the exon
// map
-
+ // if given a dataset reference, search dataset for parent EMBL sequence if it exists and set its map
// make a new feature annotating the coding contig
}
else
// make a new feature annotating the coding contig
}
else
@@
-646,6
+646,10
@@
public class EmblEntry
if (map!=null && map.getTo()!=null)
{
map.getTo().addDBRef(new DBRefEntry(ref.getSource(), ref.getVersion(), ref.getAccessionId())); // don't copy map over.
if (map!=null && map.getTo()!=null)
{
map.getTo().addDBRef(new DBRefEntry(ref.getSource(), ref.getVersion(), ref.getAccessionId())); // don't copy map over.
+ if (map.getTo().getName().indexOf(prid)==0)
+ {
+ map.getTo().setName(jalview.datamodel.DBRefSource.UNIPROT+"|"+ref.getAccessionId());
+ }
}
}
if (product != null)
}
}
if (product != null)