+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ */
package jalview.io.vamsas;
import java.util.Vector;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Mapping;
import jalview.datamodel.SequenceI;
+import jalview.gui.Desktop;
import jalview.io.VamsasAppDatastore;
import uk.ac.vamsas.client.Vobject;
import uk.ac.vamsas.objects.core.AlignmentSequence;
import uk.ac.vamsas.objects.core.SequenceMapping;
import uk.ac.vamsas.objects.core.SequenceType;
+/**
+ * binds a vamsas sequence mapping object from the vamsas document to a maplist
+ * object associated with a mapping in the Jalview model. We use the maplist
+ * object because these are referred to both in the Mapping object associated
+ * with a jalview.datamodel.DBRefEntry and in the array of
+ * jalview.datamodel.AlCodonFrame objects that Jalview uses to propagate
+ * sequence mapping position highlighting across the views.
+ *
+ * @author JimP
+ *
+ */
public class Sequencemapping extends Rangetype
{
- public Sequencemapping(VamsasAppDatastore datastore, SequenceMapping sequenceMapping)
+ public Sequencemapping(VamsasAppDatastore datastore,
+ SequenceMapping sequenceMapping)
{
- super(datastore);
- Object mjvmapping = getvObj2jv(sequenceMapping);
- if (mjvmapping==null)
- {
- add(sequenceMapping);
- } else {
- if (sequenceMapping.isUpdated())
- {
- update((jalview.util.MapList) mjvmapping, sequenceMapping);
- }
- }
+ super(datastore, sequenceMapping, jalview.util.MapList.class);
+ doJvUpdate();
}
+
+ private SequenceType from;
+
+ private DataSet ds;
+
+ private Mapping mjvmapping;
+
/**
* create or update a vamsas sequence mapping corresponding to a jalview
* Mapping between two dataset sequences
* @param from
* @param ds
*/
- public Sequencemapping(VamsasAppDatastore datastore, jalview.datamodel.Mapping mjvmapping, uk.ac.vamsas.objects.core.SequenceType from, uk.ac.vamsas.objects.core.DataSet ds)
+ public Sequencemapping(VamsasAppDatastore datastore,
+ jalview.datamodel.Mapping mjvmapping,
+ uk.ac.vamsas.objects.core.SequenceType from,
+ uk.ac.vamsas.objects.core.DataSet ds)
+ {
+ super(datastore, mjvmapping.getMap(), SequenceMapping.class);
+ this.from = from;
+ this.ds = ds;
+ this.mjvmapping = mjvmapping;
+ validate();
+ doSync();
+ }
+
+ /**
+ * local check that extant mapping context is valid
+ */
+ public void validate()
{
- super(datastore);
- SequenceMapping sequenceMapping = (SequenceMapping) getjv2vObj(mjvmapping);
- if (sequenceMapping==null)
+
+ SequenceMapping sequenceMapping = (SequenceMapping) vobj;
+ if (sequenceMapping == null)
{
- add(mjvmapping, from, ds);
- } else {
- if (from!=null && sequenceMapping.getLoc()!=from)
- {
- jalview.bin.Cache.log.warn("Probable IMPLEMENTATION ERROR: "+from+" doesn't match the local mapping sequence.");
- }
- if (ds!=null && sequenceMapping.is__stored_in_document() && sequenceMapping.getV_parent()!=ds)
- {
- jalview.bin.Cache.log.warn("Probable IMPLEMENTATION ERROR: "+ds+" doesn't match the parent of the bound sequence mapping object.");
- }
- if (sequenceMapping.isUpdated())
- {
- conflict(mjvmapping, sequenceMapping);
- } else {
- update(mjvmapping, sequenceMapping);
- }
+ return;
+ }
+ if (from != null && sequenceMapping.getLoc() != from)
+ {
+ jalview.bin.Cache.log.warn("Probable IMPLEMENTATION ERROR: " + from
+ + " doesn't match the local mapping sequence.");
+ }
+ if (ds != null && sequenceMapping.is__stored_in_document()
+ && sequenceMapping.getV_parent() != ds)
+ {
+ jalview.bin.Cache.log
+ .warn("Probable IMPLEMENTATION ERROR: "
+ + ds
+ + " doesn't match the parent of the bound sequence mapping object.");
}
}
- private void conflict(Mapping mjvmapping, SequenceMapping sequenceMapping)
+
+ public void addToDocument()
{
- // TODO Auto-generated method stub
+ add(mjvmapping, from, ds);
+ }
+ public void addFromDocument()
+ {
+ add((SequenceMapping) vobj);
}
- private void add(Mapping mjvmapping, uk.ac.vamsas.objects.core.SequenceType from, DataSet ds)
+
+ public void conflict()
+ {
+ conflict(mjvmapping, (SequenceMapping) vobj);
+
+ }
+
+ public void updateToDoc()
+ {
+ update(mjvmapping, (SequenceMapping) vobj);
+ }
+
+ public void updateFromDoc()
+ {
+ update((SequenceMapping) vobj, (jalview.datamodel.Mapping) jvobj);
+ }
+
+ private void conflict(Mapping mjvmapping, SequenceMapping sequenceMapping)
+ {
+ System.err.println("Conflict in update of sequenceMapping "
+ + sequenceMapping.getVorbaId());
+ }
+
+ private void add(Mapping mjvmapping,
+ uk.ac.vamsas.objects.core.SequenceType from, DataSet ds)
{
SequenceI jvto = mjvmapping.getTo();
- while (jvto.getDatasetSequence()!=null)
+ while (jvto.getDatasetSequence() != null)
{
jvto = jvto.getDatasetSequence();
}
SequenceType to = (SequenceType) getjv2vObj(jvto);
- if (to==null)
+ if (to == null)
{
- jalview.bin.Cache.log.warn("NONFATAL - do a second update: Ignoring Forward Reference to seuqence not yet bound to vamsas seuqence object");
+ jalview.bin.Cache.log
+ .warn("FIXME NONFATAL - do a second update: Ignoring Forward Reference to seuqence not yet bound to vamsas seuqence object");
return;
- }
+ }
SequenceMapping sequenceMapping = new SequenceMapping();
sequenceMapping.setLoc(from);
sequenceMapping.setMap(to);
- boolean dnaToProt=false,sense=false;
+ boolean dnaToProt = false, sense = false;
// ensure that we create a mapping with the correct sense
- if (((Sequence) sequenceMapping.getLoc())
- .getDictionary()
- .equals(uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA))
+ if (((Sequence) sequenceMapping.getLoc()).getDictionary().equals(
+ uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA))
{
- if (((Sequence) sequenceMapping.getMap())
- .getDictionary()
- .equals(uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_AA))
+ if (((Sequence) sequenceMapping.getMap()).getDictionary().equals(
+ uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_AA))
{
- dnaToProt=true;
- sense=true;
- }
- } else {
- if (((Sequence) sequenceMapping.getMap())
- .getDictionary()
- .equals(uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA))
+ dnaToProt = true;
+ sense = true;
+ }
+ }
+ else
+ {
+ if (((Sequence) sequenceMapping.getMap()).getDictionary().equals(
+ uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA))
{
- dnaToProt=true;
- sense=false;
- }
+ dnaToProt = true;
+ sense = false;
+ }
}
if (!dnaToProt)
{
- jalview.bin.Cache.log.warn("Ignoring Mapping - don't support protein to protein mapping in vamsas document yet.");
+ jalview.bin.Cache.log
+ .warn("Ignoring Mapping - don't support protein to protein mapping in vamsas document yet.");
return;
}
- if (ds==null)
+ if (ds == null)
{
// locate dataset for storage of SequenceMapping
if (sense)
{
- ds = (DataSet) ((uk.ac.vamsas.client.Vobject) sequenceMapping.getLoc()).getV_parent();
- } else {
- ds = (DataSet) ((uk.ac.vamsas.client.Vobject) sequenceMapping.getMap()).getV_parent();
- }
+ ds = (DataSet) ((uk.ac.vamsas.client.Vobject) sequenceMapping
+ .getLoc()).getV_parent();
+ }
+ else
+ {
+ ds = (DataSet) ((uk.ac.vamsas.client.Vobject) sequenceMapping
+ .getMap()).getV_parent();
+ }
}
if (sense)
{
this.initMapType(sequenceMapping, mjvmapping.getMap(), true);
- } else {
- this.initMapType(sequenceMapping, mjvmapping.getMap().getInverse(), true);
+ }
+ else
+ {
+ this.initMapType(sequenceMapping, mjvmapping.getMap().getInverse(),
+ true);
}
ds.addSequenceMapping(sequenceMapping);
- sequenceMapping.setProvenance(this.dummyProvenance("user defined coding region translation")); // TODO:
+ sequenceMapping.setProvenance(this
+ .dummyProvenance("user defined coding region translation")); // TODO:
// correctly
// construct
// provenance
// source
// of
// mapping
- bindjvvobj(mjvmapping, sequenceMapping);
+ bindjvvobj(mjvmapping.getMap(), sequenceMapping);
+
+ jalview.bin.Cache.log.debug("Successfully created mapping "
+ + sequenceMapping.getVorbaId());
+ }
- jalview.bin.Cache.log.debug("Successfully created mapping "+sequenceMapping.getVorbaId());
+ // private void update(jalview.util.MapList mjvmapping,
+ // SequenceMapping sequenceMapping)
+ {
+ jalview.bin.Cache.log
+ .error("Not implemented: Jalview Update Alcodon Mapping:TODO!");
}
- private void update(jalview.util.MapList mjvmapping, SequenceMapping sequenceMapping)
+
+ private void update(SequenceMapping sequenceMapping,
+ jalview.datamodel.Mapping mjvmapping)
{
- jalview.bin.Cache.log.error("Not implemented: Jalview Update Alcodon Mapping:TODO!");
+ jalview.bin.Cache.log
+ .error("Not implemented: Update DBRef Mapping from Jalview");
}
- private void update(jalview.datamodel.Mapping mjvmapping, SequenceMapping sequenceMapping)
+
+ private void update(jalview.datamodel.Mapping mjvmapping,
+ SequenceMapping sequenceMapping)
{
- jalview.bin.Cache.log.error("Not implemented: Jalview Update Sequence DBRef Mapping");
+ jalview.bin.Cache.log
+ .error("Not implemented: Jalview Update Sequence DBRef Mapping");
}
+
/**
- * limitations: Currently, jalview only deals with mappings between dataset
- * sequences, and even then, only between those that map from DNA to Protein.
+ * bind a SequenceMapping to a live AlCodonFrame element limitations:
+ * Currently, jalview only deals with mappings between dataset sequences, and
+ * even then, only between those that map from DNA to Protein.
*
* @param sequenceMapping
*/
private void add(SequenceMapping sequenceMapping)
{
Object mobj;
- SequenceI from=null,to=null;
- boolean dnaToProt=false,sense=false;
- Sequence sdloc=null, sdmap=null;
+ SequenceI from = null, to = null;
+ boolean dnaToProt = false, sense = false;
+ Sequence sdloc = null, sdmap = null;
if (sequenceMapping.getLoc() instanceof AlignmentSequence)
{
- sdloc = (Sequence) ((AlignmentSequence) sequenceMapping.getLoc()).getRefid();
- } else {
+ sdloc = (Sequence) ((AlignmentSequence) sequenceMapping.getLoc())
+ .getRefid();
+ }
+ else
+ {
sdloc = ((Sequence) sequenceMapping.getLoc());
}
if (sequenceMapping.getMap() instanceof AlignmentSequence)
{
- sdmap = (Sequence) ((AlignmentSequence) sequenceMapping.getMap()).getRefid();
- } else {
+ sdmap = (Sequence) ((AlignmentSequence) sequenceMapping.getMap())
+ .getRefid();
+ }
+ else
+ {
sdmap = ((Sequence) sequenceMapping.getMap());
}
- if (sdloc==null || sdmap == null)
+ if (sdloc == null || sdmap == null)
{
jalview.bin.Cache.log.info("Ignoring non sequence-sequence mapping");
return;
if (from == null || to == null)
{
- jalview.bin.Cache.log.error("Probable Vamsas implementation error : unbound dataset sequences involved in a mapping are being parsed!");
+ jalview.bin.Cache.log
+ .error("Probable Vamsas implementation error : unbound dataset sequences involved in a mapping are being parsed!");
return;
- }
+ }
- if (sdloc.getDictionary()
- .equals(uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA))
+ if (sdloc.getDictionary().equals(
+ uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA))
{
- if (sdmap.getDictionary()
- .equals(uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_AA))
+ if (sdmap.getDictionary().equals(
+ uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_AA))
{
- dnaToProt=true;
- sense=true;
- }
+ dnaToProt = true;
+ sense = true;
+ }
// else {
// }
- } else {
- if (sdmap.getDictionary()
- .equals(uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA))
+ }
+ else
+ {
+ if (sdmap.getDictionary().equals(
+ uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA))
{
- dnaToProt=true;
- sense=false;
- }
+ dnaToProt = true;
+ sense = false;
+ }
}
// create mapping storage object and make each dataset alignment reference
// it.
- jalview.datamodel.AlignmentI dsLoc = (jalview.datamodel.AlignmentI) getvObj2jv(sdloc.getV_parent());
- jalview.datamodel.AlignmentI dsMap = (jalview.datamodel.AlignmentI) getvObj2jv(sdmap.getV_parent());
+ jalview.datamodel.AlignmentI dsLoc = (jalview.datamodel.AlignmentI) getvObj2jv(sdloc
+ .getV_parent());
+ jalview.datamodel.AlignmentI dsMap = (jalview.datamodel.AlignmentI) getvObj2jv(sdmap
+ .getV_parent());
AlignedCodonFrame afc = new AlignedCodonFrame(0);
- if (dsLoc!=null && dsLoc!=dsMap)
+ if (dsLoc != null && dsLoc != dsMap)
{
dsLoc.addCodonFrame(afc);
}
- if (dsMap!=null)
+ if (dsMap != null)
{
dsMap.addCodonFrame(afc);
}
// create and add the new mapping to (each) dataset's codonFrame
- jalview.util.MapList mapping = null;
- if (!sense)
+ jalview.util.MapList mapping = null;
+ if (dnaToProt)
{
- mapping = this.parsemapType(sequenceMapping, 1, 3); // invert sense
- mapping = new jalview.util.MapList(mapping.getToRanges(), mapping.getFromRanges(), mapping.getToRatio(), mapping.getFromRatio());
- afc.addMap(to, from, mapping);
- } else {
- mapping = this.parsemapType(sequenceMapping, 3, 1); // correct sense
+ if (!sense)
+ {
+ mapping = this.parsemapType(sequenceMapping, 1, 3); // invert sense
+ mapping = new jalview.util.MapList(mapping.getToRanges(),
+ mapping.getFromRanges(), mapping.getToRatio(),
+ mapping.getFromRatio());
+ afc.addMap(to, from, mapping);
+ }
+ else
+ {
+ mapping = this.parsemapType(sequenceMapping, 3, 1); // correct sense
+ afc.addMap(from, to, mapping);
+ }
+ }
+ else
+ {
+ mapping = this.parsemapType(sequenceMapping, 1, 1); // correct sense
afc.addMap(from, to, mapping);
}
bindjvvobj(mapping, sequenceMapping);
- jalview.structure.StructureSelectionManager.getStructureSelectionManager().addMappings(new AlignedCodonFrame[] { afc });
+ jalview.structure.StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance).addMappings(
+ new AlignedCodonFrame[]
+ { afc });
// Try to link up any conjugate database references in the two sequences
- // matchConjugateDBRefs(from, to, mapping);
+ // matchConjugateDBRefs(from, to, mapping);
// Try to propagate any dbrefs across this mapping.
}
+
/**
- * Complete any 'to' references in jalview.datamodel.Mapping objects associated with conjugate DBRefEntry under given mapping
- * @param from sequence corresponding to from reference for sequence mapping
- * @param to sequence correspondeing to to reference for sequence mapping
- * @param smap maplist parsed in same sense as from and to
+ * Complete any 'to' references in jalview.datamodel.Mapping objects
+ * associated with conjugate DBRefEntry under given mapping
+ *
+ * @param from
+ * sequence corresponding to from reference for sequence mapping
+ * @param to
+ * sequence correspondeing to to reference for sequence mapping
+ * @param smap
+ * maplist parsed in same sense as from and to
*/
private void matchConjugateDBRefs(SequenceI from, SequenceI to,
jalview.util.MapList smap)
{
- if (from.getDBRef()==null && to.getDBRef()==null)
+ if (from.getDBRef() == null && to.getDBRef() == null)
{
if (jalview.bin.Cache.log.isDebugEnabled())
{
- jalview.bin.Cache.log.debug("Not matching conjugate refs for "+from.getName()+" and "+to.getName());
+ jalview.bin.Cache.log.debug("Not matching conjugate refs for "
+ + from.getName() + " and " + to.getName());
}
- return;
+ return;
}
if (jalview.bin.Cache.log.isDebugEnabled())
{
- jalview.bin.Cache.log.debug("Matching conjugate refs for "+from.getName()+" and "+to.getName());
+ jalview.bin.Cache.log.debug("Matching conjugate refs for "
+ + from.getName() + " and " + to.getName());
}
jalview.datamodel.DBRefEntry[] fdb = from.getDBRef();
- jalview.datamodel.DBRefEntry[] tdb = new jalview.datamodel.DBRefEntry[to.getDBRef().length];
+ jalview.datamodel.DBRefEntry[] tdb = new jalview.datamodel.DBRefEntry[to
+ .getDBRef().length];
int tdblen = to.getDBRef().length;
System.arraycopy(to.getDBRef(), 0, tdb, 0, tdblen);
Vector matched = new Vector();
jalview.util.MapList smapI = smap.getInverse();
- for (int f=0;f<fdb.length; f++)
+ for (int f = 0; f < fdb.length; f++)
{
jalview.datamodel.DBRefEntry fe = fdb[f];
jalview.datamodel.Mapping fmp = fe.getMap();
- boolean fmpnnl = fmp!=null;
+ boolean fmpnnl = fmp != null;
// if (fmpnnl && fmp.getTo()!=null)
- //{
- // jalview.bin.Cache.log.debug("Not overwriting existing To reference in "+fe);
- // continue;
- //}
+ // {
+ // jalview.bin.Cache.log.debug("Not overwriting existing To reference in
+ // "+fe);
+ // continue;
+ // }
// smap from maps from fe.local to fe.map
- boolean smapfromlocal2fe = (fmpnnl) ? smap.equals(fmp.getMap()) : false;
+ boolean smapfromlocal2fe = (fmpnnl) ? smap.equals(fmp.getMap())
+ : false;
// smap from maps from fe.map to fe.local.
- boolean smapfromfemap2local = (fmpnnl) ? smapI.equals(fmp.getMap()) : false;
- for (int t=0; t<tdblen; t++)
+ boolean smapfromfemap2local = (fmpnnl) ? smapI.equals(fmp.getMap())
+ : false;
+ for (int t = 0; t < tdblen; t++)
{
jalview.datamodel.DBRefEntry te = tdb[t];
- if (te!=null)
+ if (te != null)
{
if (fe.getSource().equals(te.getSource())
- && fe.getAccessionId().equals(te.getAccessionId()))
+ && fe.getAccessionId().equals(te.getAccessionId()))
{
jalview.datamodel.Mapping tmp = te.getMap();
- boolean tmpnnl = tmp!=null;
- if (tmpnnl && tmp.getTo()!=null)
+ boolean tmpnnl = tmp != null;
+ if (tmpnnl && tmp.getTo() != null)
{
-
+
}
// smap to maps from te.local to te.map
- boolean smaptolocal2tm = (tmpnnl) ? smap.equals(tmp.getMap()) : false;
+ boolean smaptolocal2tm = (tmpnnl) ? smap.equals(tmp.getMap())
+ : false;
// smap to maps from te.map to te.local
- boolean smaptotemap2local = (tmpnnl) ? smapI.equals(fmp.getMap()) : false;
+ boolean smaptotemap2local = (tmpnnl) ? smapI.equals(fmp
+ .getMap()) : false;
if (smapfromlocal2fe && smaptotemap2local)
{
// smap implies mapping from to to from
fmp.setTo(to);
tmp.setTo(from);
- } else
- if (smapfromfemap2local && smaptolocal2tm) {
- fmp.setTo(to);
- }
}
-
+ else if (smapfromfemap2local && smaptolocal2tm)
+ {
+ fmp.setTo(to);
+ }
+ }
+
}
}
}
- }
-}
\ No newline at end of file
+ }
+}
git://source.jalview.org / jalview.git / blobdiff