/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, 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.Console;
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 java.util.ArrayList;
+import java.util.List;
+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;
}
if (from != null && sequenceMapping.getLoc() != from)
{
- jalview.bin.Cache.log.warn("Probable IMPLEMENTATION ERROR: " + from
+ Console.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.");
+ Console.warn("Probable IMPLEMENTATION ERROR: " + ds
+ + " doesn't match the parent of the bound sequence mapping object.");
}
}
SequenceType to = (SequenceType) getjv2vObj(jvto);
if (to == null)
{
- jalview.bin.Cache.log
- .warn("FIXME NONFATAL - do a second update: Ignoring Forward Reference to seuqence not yet bound to vamsas seuqence object");
+ Console.warn(
+ "FIXME NONFATAL - do a second update: Ignoring Forward Reference to seuqence not yet bound to vamsas seuqence object");
return;
}
SequenceMapping sequenceMapping = new SequenceMapping();
if (!dnaToProt)
{
- jalview.bin.Cache.log
- .warn("Ignoring Mapping - don't support protein to protein mapping in vamsas document yet.");
+ Console.warn(
+ "Ignoring Mapping - don't support protein to protein mapping in vamsas document yet.");
return;
}
if (ds == null)
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
// mapping
bindjvvobj(mjvmapping.getMap(), sequenceMapping);
- jalview.bin.Cache.log.debug("Successfully created mapping "
- + sequenceMapping.getVorbaId());
+ Console.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!");
+ Console.error("Not implemented: Jalview Update Alcodon Mapping:TODO!");
}
private void update(SequenceMapping sequenceMapping,
jalview.datamodel.Mapping mjvmapping)
{
- jalview.bin.Cache.log
- .error("Not implemented: Update DBRef Mapping from Jalview");
+ Console.error("Not implemented: Update DBRef Mapping from Jalview");
}
private void update(jalview.datamodel.Mapping mjvmapping,
SequenceMapping sequenceMapping)
{
- jalview.bin.Cache.log
- .error("Not implemented: Jalview Update Sequence DBRef Mapping");
+ Console.error(
+ "Not implemented: Jalview Update Sequence DBRef Mapping");
}
/**
}
if (sdloc == null || sdmap == null)
{
- jalview.bin.Cache.log.info("Ignoring non sequence-sequence mapping");
+ Console.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
- .error("Probable Vamsas implementation error : unbound dataset sequences involved in a mapping are being parsed!");
+ Console.error(
+ "Probable Vamsas implementation error : unbound dataset sequences involved in a mapping are being parsed!");
return;
}
}
// 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
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);
+ mapping = new jalview.util.MapList(mapping.getToRanges(),
+ mapping.getFromRanges(), mapping.getToRatio(),
+ mapping.getFromRatio());
+ 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().addMappings(
- new AlignedCodonFrame[]
- { afc });
+ .getStructureSelectionManager(Desktop.instance)
+ .registerMapping(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.
private void matchConjugateDBRefs(SequenceI from, SequenceI to,
jalview.util.MapList smap)
{
- if (from.getDBRef() == null && to.getDBRef() == null)
+ if (from.getDBRefs() == null && to.getDBRefs() == null)
{
- if (jalview.bin.Cache.log.isDebugEnabled())
+ if (Console.isDebugEnabled())
{
- jalview.bin.Cache.log.debug("Not matching conjugate refs for "
+ Console.debug("Not matching conjugate refs for "
+ from.getName() + " and " + to.getName());
}
return;
}
- if (jalview.bin.Cache.log.isDebugEnabled())
+ if (Console.isDebugEnabled())
{
- jalview.bin.Cache.log.debug("Matching conjugate refs for "
+ Console.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];
- int tdblen = to.getDBRef().length;
- System.arraycopy(to.getDBRef(), 0, tdb, 0, tdblen);
+ List<DBRefEntry> fdb = from.getDBRefs();
+ List<DBRefEntry> tdb = new ArrayList<DBRefEntry>(to.getDBRefs());
+ int tdblen = to.getDBRefs().size();
+//
+//
+// YOWSER
+//
+// System.arraycopy(to.getDBRefs(), 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, fn = fdb.size(); f < fn; f++)
{
- jalview.datamodel.DBRefEntry fe = fdb[f];
+ jalview.datamodel.DBRefEntry fe = fdb.get(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
+ // Cache.debug("Not overwriting existing To reference in
// "+fe);
// continue;
// }
: false;
for (int t = 0; t < tdblen; t++)
{
- jalview.datamodel.DBRefEntry te = tdb[t];
+ jalview.datamodel.DBRefEntry te = tdb.get(t);
if (te != null)
{
if (fe.getSource().equals(te.getSource())
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
git://source.jalview.org / jalview.git / blobdiff