-package jalview.io.vamsas;\r
-\r
-import jalview.datamodel.DBRefEntry;\r
-import jalview.datamodel.SequenceI;\r
-import uk.ac.vamsas.objects.core.DbRef;\r
-import uk.ac.vamsas.objects.core.Map;\r
-import uk.ac.vamsas.objects.core.Sequence;\r
-import jalview.io.VamsasAppDatastore;\r
-\r
-public class Dbref extends Rangetype\r
-{\r
- jalview.datamodel.SequenceI sq = null;\r
- uk.ac.vamsas.objects.core.Sequence sequence = null;\r
- DbRef dbref = null;\r
- DBRefEntry dbentry=null;\r
- public Dbref(VamsasAppDatastore datastore, DBRefEntry dbentry, jalview.datamodel.SequenceI sq2, uk.ac.vamsas.objects.core.Sequence sequence2)\r
- {\r
- super(datastore);\r
- dbref = (DbRef) getjv2vObj(dbentry);\r
- sq = sq2;\r
- sequence = sequence2;\r
- this.dbentry = dbentry;\r
- if (dbref==null)\r
- {\r
- add();\r
- } else {\r
- if (dbref.isUpdated())\r
- {\r
- conflict();\r
- } else {\r
- update();\r
- }\r
- \r
- }\r
- \r
- }\r
-\r
- public Dbref(VamsasAppDatastore datastore, DbRef ref, Sequence vdseq, SequenceI dsseq)\r
- {\r
- super(datastore);\r
- dbref = ref;\r
- sequence = vdseq;\r
- sq = dsseq;\r
- dbentry = (jalview.datamodel.DBRefEntry) getvObj2jv(dbref);\r
- if (dbentry == null)\r
- {\r
- addFromDocument();\r
- } else {\r
- if (dbref.isUpdated())\r
- {\r
- update();\r
- }\r
- }\r
- }\r
-\r
- private void update()\r
- {\r
- // TODO: verify and update dbrefs in vamsas document\r
- // there will be trouble when a dataset sequence is modified to\r
- // contain more residues than were originally referenced - we must\r
- // then make a number of dataset sequence entries - this info is already stored \r
- jalview.bin.Cache.log.debug("TODO verify update of dataset sequence database references.");\r
- }\r
-\r
- private void conflict()\r
- {\r
- jalview.bin.Cache.log.debug("Conflict in dbentry update for "+dbref.getAccessionId()+dbref.getSource()+" "+dbref.getVorbaId());\r
- // TODO Auto-generated method stub\r
- \r
- }\r
- private void addFromDocument()\r
- {\r
- // add new dbref\r
- sq.addDBRef(dbentry = new jalview.datamodel.DBRefEntry\r
- (\r
- dbref.getSource().toString(),\r
- dbref.getVersion().toString(),\r
- dbref.getAccessionId().toString()));\r
- if (dbref.getMapCount()>0)\r
- {\r
- // TODO: Jalview ignores all the other maps\r
- if (dbref.getMapCount()>1)\r
- {\r
- jalview.bin.Cache.log.debug("Ignoring additional mappings on DbRef: "+dbentry.getSource()+":"+dbentry.getAccessionId());\r
- }\r
- jalview.datamodel.Mapping mp = new jalview.datamodel.Mapping(parsemapType(dbref.getMap(0)));\r
- dbentry.setMap(mp);\r
- }\r
- // TODO: jalview ignores links and properties because it doesn't know what to do with them.\r
- \r
- bindjvvobj(dbentry, dbref);\r
- }\r
- private void add()\r
- {\r
- DbRef dbref = new DbRef();\r
- bindjvvobj(dbentry, dbref);\r
- dbref.setAccessionId(dbentry.getAccessionId());\r
- dbref.setSource(dbentry.getSource());\r
- dbref.setVersion(dbentry.getVersion());\r
- if (dbentry.getMap()!=null)\r
- {\r
- jalview.datamodel.Mapping mp = dbentry.getMap();\r
- if (mp.getMap()!=null)\r
- {\r
- Map vMap = new Map();\r
- initMapType(vMap, mp.getMap(), true);\r
- dbref.addMap(vMap);\r
- } else {\r
- jalview.bin.Cache.log.debug("Ignoring mapless DbRef.Map "+dbentry.getSrcAccString());\r
- }\r
- }\r
- sequence.addDbRef(dbref);\r
- }\r
-\r
-}\r
+package jalview.io.vamsas;
+
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.SequenceI;
+import uk.ac.vamsas.objects.core.DbRef;
+import uk.ac.vamsas.objects.core.Map;
+import uk.ac.vamsas.objects.core.Sequence;
+import jalview.io.VamsasAppDatastore;
+
+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)
+ {
+ super(datastore);
+ dbref = (DbRef) getjv2vObj(dbentry);
+ sq = sq2;
+ sequence = sequence2;
+ this.dbentry = dbentry;
+ if (dbref==null)
+ {
+ add();
+ } else {
+ if (dbref.isUpdated())
+ {
+ conflict();
+ } else {
+ update();
+ }
+
+ }
+
+ }
+
+ public Dbref(VamsasAppDatastore datastore, DbRef ref, Sequence vdseq, SequenceI dsseq)
+ {
+ super(datastore);
+ dbref = ref;
+ sequence = vdseq;
+ sq = dsseq;
+ dbentry = (jalview.datamodel.DBRefEntry) getvObj2jv(dbref);
+ if (dbentry == null)
+ {
+ addFromDocument();
+ } else {
+ if (dbref.isUpdated())
+ {
+ update();
+ }
+ }
+ }
+
+ private void 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.");
+ }
+
+ private void conflict()
+ {
+ 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)
+ {
+ // TODO: Jalview ignores all the other maps
+ if (dbref.getMapCount()>1)
+ {
+ 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)));
+ dbentry.setMap(mp);
+ }
+ // 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();
+ bindjvvobj(dbentry, dbref);
+ dbref.setAccessionId(dbentry.getAccessionId());
+ dbref.setSource(dbentry.getSource());
+ dbref.setVersion(dbentry.getVersion());
+ if (dbentry.getMap()!=null)
+ {
+ jalview.datamodel.Mapping mp = dbentry.getMap();
+ 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());
+ }
+ }
+ sequence.addDbRef(dbref);
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff