X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2Fvamsas%2FDbref.java;h=bdef00f9ff65e862a41525af12ebe564285d86de;hb=933ca77e913c56fc4c71cc0fe534df208bfd742d;hp=e247d9cba78a5be7dffdf0eb83eaccf3186a6913;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git
diff --git a/src/jalview/io/vamsas/Dbref.java b/src/jalview/io/vamsas/Dbref.java
index e247d9c..bdef00f 100644
--- a/src/jalview/io/vamsas/Dbref.java
+++ b/src/jalview/io/vamsas/Dbref.java
@@ -1,30 +1,33 @@
/*
- * 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io.vamsas;
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 uk.ac.vamsas.objects.core.SequenceType;
-import jalview.io.VamsasAppDatastore;
public class Dbref extends Rangetype
{
@@ -89,8 +92,8 @@ public class Dbref extends Rangetype
}
else
{
- jalview.bin.Cache.log.debug("Ignoring mapless DbRef.Map "
- + jvobj.getSrcAccString());
+ jalview.bin.Cache.log.debug(
+ "Ignoring mapless DbRef.Map " + jvobj.getSrcAccString());
}
}
@@ -103,8 +106,8 @@ public class Dbref extends Rangetype
*/
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)
@@ -118,16 +121,15 @@ public class Dbref extends Rangetype
// 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: NOW add a mapping between new dataset sequence and sequence
// associated with the database reference
@@ -173,9 +175,9 @@ public class Dbref extends Rangetype
{
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());
+ jalview.bin.Cache.log
+ .debug("Conflict in dbentry update for " + vobj.getAccessionId()
+ + vobj.getSource() + " " + vobj.getVorbaId());
// TODO Auto-generated method stub
}
@@ -185,9 +187,9 @@ public class Dbref extends Rangetype
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
@@ -228,8 +230,8 @@ public class Dbref extends Rangetype
}
else
{
- jalview.bin.Cache.log.debug("Ignoring mapless DbRef.Map "
- + jvobj.getSrcAccString());
+ jalview.bin.Cache.log.debug(
+ "Ignoring mapless DbRef.Map " + jvobj.getSrcAccString());
}
}
}