import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
+ " doesn't match the local mapping sequence.");
}
if (ds != null && sequenceMapping.is__stored_in_document()
&& sequenceMapping.getV_parent() != ds)
{
+ " doesn't match the local mapping sequence.");
}
if (ds != null && sequenceMapping.is__stored_in_document()
&& sequenceMapping.getV_parent() != ds)
{
"Successfully created mapping " + sequenceMapping.getVorbaId());
}
// private void update(jalview.util.MapList mjvmapping,
// SequenceMapping sequenceMapping)
{
"Successfully created mapping " + sequenceMapping.getVorbaId());
}
// private void update(jalview.util.MapList mjvmapping,
// SequenceMapping sequenceMapping)
{
}
private void update(SequenceMapping sequenceMapping,
jalview.datamodel.Mapping mjvmapping)
{
}
private void update(SequenceMapping sequenceMapping,
jalview.datamodel.Mapping mjvmapping)
{
}
private void update(jalview.datamodel.Mapping mjvmapping,
SequenceMapping sequenceMapping)
{
}
private void update(jalview.datamodel.Mapping mjvmapping,
SequenceMapping sequenceMapping)
{
- jalview.bin.Cache.log.debug("Not matching conjugate refs for "
- + from.getName() + " and " + to.getName());
+ Console.debug("Not matching conjugate refs for " + from.getName()
+ + " and " + to.getName());
}
List<DBRefEntry> fdb = from.getDBRefs();
List<DBRefEntry> tdb = new ArrayList<DBRefEntry>(to.getDBRefs());
int tdblen = to.getDBRefs().size();
}
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);
-//
-//
-//
-//
+ //
+ //
+ // YOWSER
+ //
+ // System.arraycopy(to.getDBRefs(), 0, tdb, 0, tdblen);
+ //
+ //
+ //
+ //
Vector matched = new Vector();
jalview.util.MapList smapI = smap.getInverse();
for (int f = 0, fn = fdb.size(); f < fn; f++)
Vector matched = new Vector();
jalview.util.MapList smapI = smap.getInverse();
for (int f = 0, fn = fdb.size(); f < fn; f++)