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xrefs retrieved from Uniprot
[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
8e7893f
..
65141f8
100644
(file)
--- a/
src/jalview/ws/dbsources/Uniprot.java
+++ b/
src/jalview/ws/dbsources/Uniprot.java
@@
-149,9
+149,12
@@
public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
name.append(en2.nextElement());
\r
}
\r
\r
name.append(en2.nextElement());
\r
}
\r
\r
- if (entry.getProtein() != null)
\r
+ if (entry.getProtein()!=null && entry.getProtein().getName()!=null)
\r
{
\r
{
\r
- name.append(" " + entry.getProtein().getName().elementAt(0));
\r
+ for (int nm=0,nmSize=entry.getProtein().getName().size(); nm<nmSize;nm++)
\r
+ {
\r
+ name.append(" " + entry.getProtein().getName().elementAt(nm));
\r
+ }
\r
}
\r
\r
result.append(name + "\n"
\r
}
\r
\r
result.append(name + "\n"
\r
@@
-193,11
+196,17
@@
public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
UniprotEntry entry = (UniprotEntry) entries.elementAt(i);
\r
Enumeration e = entry.getDbReference().elements();
\r
Vector onlyPdbEntries = new Vector();
\r
UniprotEntry entry = (UniprotEntry) entries.elementAt(i);
\r
Enumeration e = entry.getDbReference().elements();
\r
Vector onlyPdbEntries = new Vector();
\r
+ Vector dbxrefs = new Vector();
\r
while (e.hasMoreElements())
\r
{
\r
PDBEntry pdb = (PDBEntry) e.nextElement();
\r
if (!pdb.getType().equals("PDB"))
\r
{
\r
while (e.hasMoreElements())
\r
{
\r
PDBEntry pdb = (PDBEntry) e.nextElement();
\r
if (!pdb.getType().equals("PDB"))
\r
{
\r
+ DBRefEntry dbr = new DBRefEntry();
\r
+ dbr.setSource(pdb.getType());
\r
+ dbr.setAccessionId(pdb.getId());
\r
+ dbr.setVersion(DBRefSource.UNIPROT+":"+getDbVersion());
\r
+ dbxrefs.addElement(dbr);
\r
continue;
\r
}
\r
\r
continue;
\r
}
\r
\r
@@
-217,6
+226,13
@@
public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
new DBRefEntry(DBRefSource.UNIPROT, getDbVersion(), en2.nextElement()
\r
.toString()));
\r
}
\r
new DBRefEntry(DBRefSource.UNIPROT, getDbVersion(), en2.nextElement()
\r
.toString()));
\r
}
\r
+ en2 = dbxrefs.elements();
\r
+ while (en2.hasMoreElements())
\r
+ {
\r
+ // we always add as uniprot if we retrieved from uniprot or uniprot name
\r
+ sq.addDBRef((DBRefEntry) en2.nextElement());
\r
+
\r
+ }
\r
sq.setPDBId(onlyPdbEntries);
\r
if (entry.getFeature() != null)
\r
{
\r
sq.setPDBId(onlyPdbEntries);
\r
if (entry.getFeature() != null)
\r
{
\r
@@
-249,6
+265,6
@@
public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
}
\r
public String getDbName()
\r
{
\r
}
\r
public String getDbName()
\r
{
\r
- return getDbSource();
\r
+ return "Uniprot"; // getDbSource();
\r
}
\r
}
\r
}
\r
}
\r