public class Dbref extends Rangetype
{
jalview.datamodel.SequenceI sq = null;
+
uk.ac.vamsas.objects.core.Sequence sequence = null;
+
DbRef dbref = null;
- DBRefEntry dbentry=null;
- public Dbref(VamsasAppDatastore datastore, DBRefEntry dbentry, jalview.datamodel.SequenceI sq2, uk.ac.vamsas.objects.core.Sequence sequence2)
+
+ DBRefEntry dbentry = null;
+
+ public Dbref(VamsasAppDatastore datastore, DBRefEntry dbentry,
+ jalview.datamodel.SequenceI sq2,
+ uk.ac.vamsas.objects.core.Sequence sequence2)
{
super(datastore);
dbref = (DbRef) getjv2vObj(dbentry);
sq = sq2;
sequence = sequence2;
this.dbentry = dbentry;
- if (dbref==null)
+ if (dbref == null)
{
add();
- } else {
+ }
+ else
+ {
if (dbref.isUpdated())
{
conflict();
- } else {
+ }
+ else
+ {
update();
}
-
+
}
-
+
}
- public Dbref(VamsasAppDatastore datastore, DbRef ref, Sequence vdseq, SequenceI dsseq)
+ public Dbref(VamsasAppDatastore datastore, DbRef ref, Sequence vdseq,
+ SequenceI dsseq)
{
super(datastore);
dbref = ref;
if (dbentry == null)
{
addFromDocument();
- } else {
+ }
+ else
+ {
if (dbref.isUpdated())
{
update();
// TODO: verify and update dbrefs in vamsas document
// there will be trouble when a dataset sequence is modified to
// contain more residues than were originally referenced - we must
- // then make a number of dataset sequence entries - this info is already stored
- jalview.bin.Cache.log.debug("TODO verify update of dataset sequence database references.");
+ // then make a number of dataset sequence entries - this info is already
+ // stored
+ jalview.bin.Cache.log
+ .debug("TODO verify update of dataset sequence database references.");
}
private void conflict()
{
- jalview.bin.Cache.log.debug("Conflict in dbentry update for "+dbref.getAccessionId()+dbref.getSource()+" "+dbref.getVorbaId());
+ jalview.bin.Cache.log.debug("Conflict in dbentry update for "
+ + dbref.getAccessionId() + dbref.getSource() + " "
+ + dbref.getVorbaId());
// TODO Auto-generated method stub
-
+
}
+
private void addFromDocument()
{
// add new dbref
- sq.addDBRef(dbentry = new jalview.datamodel.DBRefEntry
- (
- dbref.getSource().toString(),
- dbref.getVersion().toString(),
- dbref.getAccessionId().toString()));
- if (dbref.getMapCount()>0)
+ sq.addDBRef(dbentry = new jalview.datamodel.DBRefEntry(dbref
+ .getSource().toString(), dbref.getVersion().toString(), dbref
+ .getAccessionId().toString()));
+ if (dbref.getMapCount() > 0)
{
// TODO: Jalview ignores all the other maps
- if (dbref.getMapCount()>1)
+ if (dbref.getMapCount() > 1)
{
- jalview.bin.Cache.log.debug("Ignoring additional mappings on DbRef: "+dbentry.getSource()+":"+dbentry.getAccessionId());
+ jalview.bin.Cache.log
+ .debug("Ignoring additional mappings on DbRef: "
+ + dbentry.getSource() + ":"
+ + dbentry.getAccessionId());
}
- jalview.datamodel.Mapping mp = new jalview.datamodel.Mapping(parsemapType(dbref.getMap(0)));
+ jalview.datamodel.Mapping mp = new jalview.datamodel.Mapping(
+ parsemapType(dbref.getMap(0)));
dbentry.setMap(mp);
}
- // TODO: jalview ignores links and properties because it doesn't know what to do with them.
-
+ // TODO: jalview ignores links and properties because it doesn't know what
+ // to do with them.
+
bindjvvobj(dbentry, dbref);
}
+
private void add()
{
DbRef dbref = new DbRef();
dbref.setAccessionId(dbentry.getAccessionId());
dbref.setSource(dbentry.getSource());
dbref.setVersion(dbentry.getVersion());
- if (dbentry.getMap()!=null)
+ if (dbentry.getMap() != null)
{
jalview.datamodel.Mapping mp = dbentry.getMap();
- if (mp.getMap()!=null)
+ if (mp.getMap() != null)
{
Map vMap = new Map();
initMapType(vMap, mp.getMap(), true);
dbref.addMap(vMap);
- } else {
- jalview.bin.Cache.log.debug("Ignoring mapless DbRef.Map "+dbentry.getSrcAccString());
+ }
+ else
+ {
+ jalview.bin.Cache.log.debug("Ignoring mapless DbRef.Map "
+ + dbentry.getSrcAccString());
}
}
sequence.addDbRef(dbref);