/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* 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.
+ * 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/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io.vamsas;
-import java.util.Vector;
-
+import jalview.bin.Cache;
import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
import jalview.datamodel.Mapping;
import jalview.datamodel.SequenceI;
import jalview.gui.Desktop;
import jalview.io.VamsasAppDatastore;
-import uk.ac.vamsas.client.Vobject;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.MapList;
+
+import java.util.Vector;
+
import uk.ac.vamsas.objects.core.AlignmentSequence;
import uk.ac.vamsas.objects.core.DataSet;
-import uk.ac.vamsas.objects.core.Local;
-import uk.ac.vamsas.objects.core.RangeType;
-import uk.ac.vamsas.objects.core.Seg;
import uk.ac.vamsas.objects.core.Sequence;
import uk.ac.vamsas.objects.core.SequenceMapping;
import uk.ac.vamsas.objects.core.SequenceType;
+import uk.ac.vamsas.objects.utils.SymbolDictionary;
/**
* 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.
+ * with a 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 Sequencemapping(VamsasAppDatastore datastore,
SequenceMapping sequenceMapping)
{
- super(datastore, sequenceMapping, jalview.util.MapList.class);
+ super(datastore, sequenceMapping, MapList.class);
doJvUpdate();
}
* @param ds
*/
public Sequencemapping(VamsasAppDatastore datastore,
- jalview.datamodel.Mapping mjvmapping,
+ Mapping mjvmapping,
uk.ac.vamsas.objects.core.SequenceType from,
uk.ac.vamsas.objects.core.DataSet ds)
{
}
if (from != null && sequenceMapping.getLoc() != from)
{
- jalview.bin.Cache.log.warn("Probable IMPLEMENTATION ERROR: " + from
+ 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
+ Cache.log
.warn("Probable IMPLEMENTATION ERROR: "
+ ds
+ " doesn't match the parent of the bound sequence mapping object.");
public void updateFromDoc()
{
- update((SequenceMapping) vobj, (jalview.datamodel.Mapping) jvobj);
+ update((SequenceMapping) vobj, (Mapping) jvobj);
}
private void conflict(Mapping mjvmapping, SequenceMapping sequenceMapping)
SequenceType to = (SequenceType) getjv2vObj(jvto);
if (to == null)
{
- jalview.bin.Cache.log
+ Cache.log
.warn("FIXME NONFATAL - do a second update: Ignoring Forward Reference to seuqence not yet bound to vamsas seuqence object");
return;
}
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))
+ SymbolDictionary.STANDARD_NA))
{
if (((Sequence) sequenceMapping.getMap()).getDictionary().equals(
- uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_AA))
+ SymbolDictionary.STANDARD_AA))
{
dnaToProt = true;
sense = true;
else
{
if (((Sequence) sequenceMapping.getMap()).getDictionary().equals(
- uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA))
+ SymbolDictionary.STANDARD_NA))
{
dnaToProt = true;
sense = false;
if (!dnaToProt)
{
- jalview.bin.Cache.log
+ Cache.log
.warn("Ignoring Mapping - don't support protein to protein mapping in vamsas document yet.");
return;
}
// mapping
bindjvvobj(mjvmapping.getMap(), sequenceMapping);
- jalview.bin.Cache.log.debug("Successfully created mapping "
+ Cache.log.debug("Successfully created mapping "
+ sequenceMapping.getVorbaId());
}
- // private void update(jalview.util.MapList mjvmapping,
+ // private void update(MapList mjvmapping,
// SequenceMapping sequenceMapping)
{
- jalview.bin.Cache.log
+ Cache.log
.error("Not implemented: Jalview Update Alcodon Mapping:TODO!");
}
private void update(SequenceMapping sequenceMapping,
- jalview.datamodel.Mapping mjvmapping)
+ Mapping mjvmapping)
{
- jalview.bin.Cache.log
+ Cache.log
.error("Not implemented: Update DBRef Mapping from Jalview");
}
- private void update(jalview.datamodel.Mapping mjvmapping,
+ private void update(Mapping mjvmapping,
SequenceMapping sequenceMapping)
{
- jalview.bin.Cache.log
+ Cache.log
.error("Not implemented: Jalview Update Sequence DBRef Mapping");
}
}
if (sdloc == null || sdmap == null)
{
- jalview.bin.Cache.log.info("Ignoring non sequence-sequence mapping");
+ Cache.log.info("Ignoring non sequence-sequence mapping");
return;
}
- mobj = this.getvObj2jv((Vobject) sdloc);
+ mobj = this.getvObj2jv(sdloc);
if (mobj instanceof SequenceI)
{
from = (SequenceI) mobj;
}
- mobj = this.getvObj2jv((Vobject) sdmap);
+ mobj = this.getvObj2jv(sdmap);
if (mobj instanceof SequenceI)
{
to = (SequenceI) mobj;
if (from == null || to == null)
{
- jalview.bin.Cache.log
+ 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))
+SymbolDictionary.STANDARD_NA))
{
if (sdmap.getDictionary().equals(
- uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_AA))
+SymbolDictionary.STANDARD_AA))
{
dnaToProt = true;
sense = true;
else
{
if (sdmap.getDictionary().equals(
- uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA))
+SymbolDictionary.STANDARD_NA))
{
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());
- AlignedCodonFrame afc = new AlignedCodonFrame(0);
+ AlignmentI dsLoc = (AlignmentI) getvObj2jv(sdloc.getV_parent());
+ AlignmentI dsMap = (AlignmentI) getvObj2jv(sdmap.getV_parent());
+ AlignedCodonFrame acf = new AlignedCodonFrame();
if (dsLoc != null && dsLoc != dsMap)
{
- dsLoc.addCodonFrame(afc);
+ dsLoc.addCodonFrame(acf);
}
if (dsMap != null)
{
- dsMap.addCodonFrame(afc);
+ dsMap.addCodonFrame(acf);
}
// create and add the new mapping to (each) dataset's codonFrame
- jalview.util.MapList mapping = null;
+ MapList mapping = null;
if (dnaToProt)
{
if (!sense)
{
mapping = this.parsemapType(sequenceMapping, 1, 3); // invert sense
- mapping = new jalview.util.MapList(mapping.getToRanges(),
+ mapping = new MapList(mapping.getToRanges(),
mapping.getFromRanges(), mapping.getToRatio(),
mapping.getFromRatio());
- afc.addMap(to, from, mapping);
+ acf.addMap(to, from, mapping);
}
else
{
mapping = this.parsemapType(sequenceMapping, 3, 1); // correct sense
- afc.addMap(from, to, mapping);
+ acf.addMap(from, to, mapping);
}
}
else
{
mapping = this.parsemapType(sequenceMapping, 1, 1); // correct sense
- afc.addMap(from, to, mapping);
+ acf.addMap(from, to, mapping);
}
bindjvvobj(mapping, sequenceMapping);
- jalview.structure.StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance).addMappings(
- new AlignedCodonFrame[]
- { afc });
+ StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance).addMapping(acf);
// Try to link up any conjugate database references in the two sequences
// 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
+ * Complete any 'to' references in Mapping objects associated with conjugate
+ * DBRefEntry under given mapping
*
* @param from
* sequence corresponding to from reference for sequence mapping
* maplist parsed in same sense as from and to
*/
private void matchConjugateDBRefs(SequenceI from, SequenceI to,
- jalview.util.MapList smap)
+ MapList smap)
{
if (from.getDBRef() == null && to.getDBRef() == null)
{
- if (jalview.bin.Cache.log.isDebugEnabled())
+ if (Cache.log.isDebugEnabled())
{
- jalview.bin.Cache.log.debug("Not matching conjugate refs for "
+ Cache.log.debug("Not matching conjugate refs for "
+ from.getName() + " and " + to.getName());
}
return;
}
- if (jalview.bin.Cache.log.isDebugEnabled())
+ if (Cache.log.isDebugEnabled())
{
- jalview.bin.Cache.log.debug("Matching conjugate refs for "
+ 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
+ DBRefEntry[] fdb = from.getDBRef();
+ DBRefEntry[] tdb = new 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();
+ MapList smapI = smap.getInverse();
for (int f = 0; f < fdb.length; f++)
{
- jalview.datamodel.DBRefEntry fe = fdb[f];
- jalview.datamodel.Mapping fmp = fe.getMap();
+ DBRefEntry fe = fdb[f];
+ Mapping fmp = fe.getMap();
boolean fmpnnl = fmp != null;
// if (fmpnnl && fmp.getTo()!=null)
// {
- // jalview.bin.Cache.log.debug("Not overwriting existing To reference in
+ // Cache.log.debug("Not overwriting existing To reference in
// "+fe);
// continue;
// }
: false;
for (int t = 0; t < tdblen; t++)
{
- jalview.datamodel.DBRefEntry te = tdb[t];
+ DBRefEntry te = tdb[t];
if (te != null)
{
if (fe.getSource().equals(te.getSource())
&& fe.getAccessionId().equals(te.getAccessionId()))
{
- jalview.datamodel.Mapping tmp = te.getMap();
+ Mapping tmp = te.getMap();
boolean tmpnnl = tmp != null;
if (tmpnnl && tmp.getTo() != null)
{
git://source.jalview.org / jalview.git / blobdiff