import jalview.util.DBRefUtils;
import jalview.util.MapList;
import jalview.ws.SequenceFetcher;
+import jalview.ws.seqfetcher.ASequenceFetcher;
import java.util.ArrayList;
import java.util.Iterator;
private void retrieveCrossRef(List<DBRefEntry> sourceRefs, SequenceI seq,
List<DBRefEntry> xrfs, boolean fromDna, AlignedCodonFrame cf)
{
+ ASequenceFetcher sftch = SequenceFetcher.getInstance();// Factory.getSequenceFetcher();
SequenceI[] retrieved = null;
SequenceI dss = seq.getDatasetSequence() == null ? seq
: seq.getDatasetSequence();
}
try
{
- retrieved = SequenceFetcher.getInstance()
- .getSequences(sourceRefs, !fromDna);
+ retrieved = sftch.getSequences(sourceRefs, !fromDna);
} catch (Exception e)
{
System.err.println(
@Override
public boolean equals(Object o)
{
- return equals((SequenceFeature) o, true);
+ return super.equals(o, true);
}
};
matched.addSequenceFeature(newFeature);
if (fromDna)
{
- AlignmentUtils.computeProteinFeatures(mapFrom, mapTo, mapping);
+ // AlignmentUtils.computeProteinFeatures(mapFrom, mapTo, mapping);
mappings.addMap(mapFrom, mapTo, mapping);
}
else