/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * 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.Console;
import jalview.datamodel.DBRefEntry;
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 jalview.io.VamsasAppDatastore;
public class Dbref extends Rangetype
{
}
else
{
- jalview.bin.Cache.log.debug("Ignoring mapless DbRef.Map "
- + jvobj.getSrcAccString());
+ Console.debug(
+ "Ignoring mapless DbRef.Map " + jvobj.getSrcAccString());
}
}
*/
private void updateMapTo(jalview.datamodel.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)
// sync the dataset sequence, if it hasn't been done already.
// TODO: ensure real dataset sequence corresponding to getTo is
// recovered
- dssync = new Datasetsequence(
- datastore,
- mp.getTo(),
- (mp.getMappedWidth() == mp.getWidth()) ? sequence
- .getDictionary()
- : ((mp.getMappedWidth() == 3) ? uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA
+ dssync = new Datasetsequence(datastore, 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),
ds);
}
// TODO: Jalview ignores all the other maps
if (vobj.getMapCount() > 1)
{
- jalview.bin.Cache.log
- .debug("Ignoring additional mappings on DbRef: "
- + jvobj.getSource() + ":" + jvobj.getAccessionId());
+ Console.debug("Ignoring additional mappings on DbRef: "
+ + jvobj.getSource() + ":" + jvobj.getAccessionId());
}
jalview.datamodel.Mapping mp = new jalview.datamodel.Mapping(
parsemapType(vobj.getMap(0)));
{
DbRef vobj = (DbRef) this.vobj;
DBRefEntry jvobj = (DBRefEntry) this.jvobj;
- jalview.bin.Cache.log.debug("Conflict in dbentry update for "
- + vobj.getAccessionId() + vobj.getSource() + " "
- + vobj.getVorbaId());
+ Console.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()
- .toString(), vobj.getVersion().toString(), vobj
- .getAccessionId().toString()));
+ sq.addDBRef(jvobj = new jalview.datamodel.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
- .debug("Ignoring additional mappings on DbRef: "
- + jvobj.getSource() + ":" + jvobj.getAccessionId());
+ Console.debug("Ignoring additional mappings on DbRef: "
+ + jvobj.getSource() + ":" + jvobj.getAccessionId());
}
jalview.datamodel.Mapping mp = new jalview.datamodel.Mapping(
parsemapType(vobj.getMap(0)));
}
else
{
- jalview.bin.Cache.log.debug("Ignoring mapless DbRef.Map "
- + jvobj.getSrcAccString());
+ Console.debug(
+ "Ignoring mapless DbRef.Map " + jvobj.getSrcAccString());
}
}
}