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JAL-2759 BoundedStartRegionIterator test
[jalview.git]
/
src
/
jalview
/
ws
/
dbsources
/
Uniprot.java
diff --git
a/src/jalview/ws/dbsources/Uniprot.java
b/src/jalview/ws/dbsources/Uniprot.java
index
686cd83
..
c9beb8e
100644
(file)
--- a/
src/jalview/ws/dbsources/Uniprot.java
+++ b/
src/jalview/ws/dbsources/Uniprot.java
@@
-28,8
+28,9
@@
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
-import jalview.datamodel.UniprotEntry;
-import jalview.datamodel.UniprotFile;
+import jalview.datamodel.xdb.uniprot.UniprotEntry;
+import jalview.datamodel.xdb.uniprot.UniprotFeature;
+import jalview.datamodel.xdb.uniprot.UniprotFile;
import jalview.ws.seqfetcher.DbSourceProxyImpl;
import java.io.InputStream;
import jalview.ws.seqfetcher.DbSourceProxyImpl;
import java.io.InputStream;
@@
-208,7
+209,7
@@
public class Uniprot extends DbSourceProxyImpl
sequence.setDescription(getUniprotEntryDescription(entry));
final String dbVersion = getDbVersion();
sequence.setDescription(getUniprotEntryDescription(entry));
final String dbVersion = getDbVersion();
- ArrayList<DBRefEntry> dbRefs = new ArrayList<DBRefEntry>();
+ ArrayList<DBRefEntry> dbRefs = new ArrayList<>();
for (String accessionId : entry.getAccession())
{
DBRefEntry dbRef = new DBRefEntry(DBRefSource.UNIPROT, dbVersion,
for (String accessionId : entry.getAccession())
{
DBRefEntry dbRef = new DBRefEntry(DBRefSource.UNIPROT, dbVersion,
@@
-218,7
+219,7
@@
public class Uniprot extends DbSourceProxyImpl
dbRefs.add(dbRef);
}
dbRefs.add(dbRef);
}
- Vector<PDBEntry> onlyPdbEntries = new Vector<PDBEntry>();
+ Vector<PDBEntry> onlyPdbEntries = new Vector<>();
for (PDBEntry pdb : entry.getDbReference())
{
DBRefEntry dbr = new DBRefEntry();
for (PDBEntry pdb : entry.getDbReference())
{
DBRefEntry dbr = new DBRefEntry();
@@
-261,16
+262,17
@@
public class Uniprot extends DbSourceProxyImpl
}
}
}
}
-
}
sequence.setPDBId(onlyPdbEntries);
if (entry.getFeature() != null)
{
}
sequence.setPDBId(onlyPdbEntries);
if (entry.getFeature() != null)
{
- for (SequenceFeature sf : entry.getFeature())
+ for (UniprotFeature uf : entry.getFeature())
{
{
- sf.setFeatureGroup("Uniprot");
- sequence.addSequenceFeature(sf);
+ SequenceFeature copy = new SequenceFeature(uf.getType(),
+ uf.getDescription(), uf.getBegin(), uf.getEnd(), "Uniprot");
+ copy.setStatus(uf.getStatus());
+ sequence.addSequenceFeature(copy);
}
}
for (DBRefEntry dbr : dbRefs)
}
}
for (DBRefEntry dbr : dbRefs)