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 java.util.ArrayList;
+import java.util.List;
import java.util.Vector;
import uk.ac.vamsas.objects.core.AlignmentSequence;
}
bindjvvobj(mapping, sequenceMapping);
jalview.structure.StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance)
+ .getStructureSelectionManager(Desktop.getInstance())
.registerMapping(acf);
// Try to link up any conjugate database references in the two sequences
// matchConjugateDBRefs(from, to, mapping);
jalview.bin.Cache.log.debug("Matching conjugate refs for "
+ from.getName() + " and " + to.getName());
}
- jalview.datamodel.DBRefEntry[] fdb = from.getDBRefs();
- jalview.datamodel.DBRefEntry[] tdb = new jalview.datamodel.DBRefEntry[to
- .getDBRefs().length];
- int tdblen = to.getDBRefs().length;
- System.arraycopy(to.getDBRefs(), 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
: 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())