/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * 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 jalview.bin.Cache;
import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.Mapping;
import jalview.datamodel.SequenceI;
+import jalview.io.VamsasAppDatastore;
+
import uk.ac.vamsas.objects.core.DataSet;
import uk.ac.vamsas.objects.core.DbRef;
import uk.ac.vamsas.objects.core.Map;
import uk.ac.vamsas.objects.core.Sequence;
-import uk.ac.vamsas.objects.core.SequenceType;
-import jalview.io.VamsasAppDatastore;
+import uk.ac.vamsas.objects.utils.SymbolDictionary;
public class Dbref extends Rangetype
{
- jalview.datamodel.SequenceI sq = null;
+ SequenceI sq = null;
uk.ac.vamsas.objects.core.Sequence sequence = null;
DataSet ds;
public Dbref(VamsasAppDatastore datastore, DBRefEntry dbentry,
- jalview.datamodel.SequenceI sq2,
- uk.ac.vamsas.objects.core.Sequence sequence2, DataSet dataset)
+ SequenceI sq2, uk.ac.vamsas.objects.core.Sequence sequence2,
+ DataSet dataset)
{
super(datastore, dbentry, DbRef.class);
// initialise object specific attributes
public Dbref(VamsasAppDatastore datastore, DbRef ref, Sequence vdseq,
SequenceI dsseq)
{
- super(datastore, ref, jalview.datamodel.DBRefEntry.class);
+ super(datastore, ref, DBRefEntry.class);
sequence = vdseq;
sq = dsseq;
ds = (DataSet) vdseq.getV_parent();
if (jvobj.getMap() != null)
{
// Record mapping to external database coordinate system.
- jalview.datamodel.Mapping mp = jvobj.getMap();
+ Mapping mp = jvobj.getMap();
if (mp.getMap() != null)
{
Map vMap = null;
}
else
{
- jalview.bin.Cache.log.debug("Ignoring mapless DbRef.Map "
+ Cache.log.debug("Ignoring mapless DbRef.Map "
+ jvobj.getSrcAccString());
}
*
* @param mp
*/
- private void updateMapTo(jalview.datamodel.Mapping mp)
+ private void updateMapTo(Mapping mp)
{
- log
- .info("Performing updateMapTo remove this message when we know what we're doing.");
+ log.info("Performing updateMapTo remove this message when we know what we're doing.");
// TODO determine how sequences associated with database mappings are stored
// in the document
if (mp != null && mp.getTo() != null)
mp.getTo(),
(mp.getMappedWidth() == mp.getWidth()) ? sequence
.getDictionary()
- : ((mp.getMappedWidth() == 3) ? uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA
- : uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_AA),
+ : ((mp.getMappedWidth() == 3) ? SymbolDictionary.STANDARD_NA
+ : SymbolDictionary.STANDARD_AA),
ds);
}
- //
+ //
// TODO: NOW add a mapping between new dataset sequence and sequence
// associated with the database reference
// TODO: Jalview ignores all the other maps
if (vobj.getMapCount() > 1)
{
- jalview.bin.Cache.log
+ Cache.log
.debug("Ignoring additional mappings on DbRef: "
+ jvobj.getSource() + ":" + jvobj.getAccessionId());
}
- jalview.datamodel.Mapping mp = new jalview.datamodel.Mapping(
- parsemapType(vobj.getMap(0)));
+ Mapping mp = new Mapping(parsemapType(vobj.getMap(0)));
if (jvobj.getMap() == null || !mp.equals(jvobj.getMap()))
{
jvobj.setMap(mp);
{
DbRef vobj = (DbRef) this.vobj;
DBRefEntry jvobj = (DBRefEntry) this.jvobj;
- jalview.bin.Cache.log.debug("Conflict in dbentry update for "
+ Cache.log.debug("Conflict in dbentry update for "
+ vobj.getAccessionId() + vobj.getSource() + " "
+ vobj.getVorbaId());
// TODO Auto-generated method stub
DbRef vobj = (DbRef) this.vobj;
DBRefEntry jvobj = (DBRefEntry) this.jvobj;
// add new dbref
- sq.addDBRef(jvobj = new jalview.datamodel.DBRefEntry(vobj.getSource()
+ sq.addDBRef(jvobj = new DBRefEntry(vobj.getSource()
.toString(), vobj.getVersion().toString(), vobj
.getAccessionId().toString()));
if (vobj.getMapCount() > 0)
// TODO: Jalview ignores all the other maps
if (vobj.getMapCount() > 1)
{
- jalview.bin.Cache.log
+ Cache.log
.debug("Ignoring additional mappings on DbRef: "
+ jvobj.getSource() + ":" + jvobj.getAccessionId());
}
- jalview.datamodel.Mapping mp = new jalview.datamodel.Mapping(
+ Mapping mp = new Mapping(
parsemapType(vobj.getMap(0)));
jvobj.setMap(mp);
}
sequence.addDbRef(dbref);
if (jvobj.getMap() != null)
{
- jalview.datamodel.Mapping mp = jvobj.getMap();
+ Mapping mp = jvobj.getMap();
if (mp.getMap() != null)
{
Map vMap = new Map();
}
else
{
- jalview.bin.Cache.log.debug("Ignoring mapless DbRef.Map "
+ Cache.log.debug("Ignoring mapless DbRef.Map "
+ jvobj.getSrcAccString());
}
}
git://source.jalview.org / jalview.git / blobdiff