import jalview.analysis.AlignmentSorter;
import jalview.api.AlignViewportI;
+import jalview.bin.Cache;
import jalview.commands.CommandI;
import jalview.commands.EditCommand;
import jalview.commands.EditCommand.Action;
action = action.getUndoAction();
}
// TODO write this
- System.err.println("MappingUtils.mapCutOrPaste not yet implemented");
+ Cache.log.error("MappingUtils.mapCutOrPaste not yet implemented");
}
/**
{
for (AlignedCodonFrame acf : mappings)
{
- SequenceI mappedSeq = mappingToNucleotide ? acf.getDnaForAaSeq(seq)
- : acf.getAaForDnaSeq(seq);
- if (mappedSeq != null)
- {
for (SequenceI seq2 : mapTo.getSequences())
{
- if (seq2.getDatasetSequence() == mappedSeq)
+ /*
+ * the corresponding peptide / CDS is the one for which there is
+ * a complete ('covering') mapping to 'seq'
+ */
+ SequenceI peptide = mappingToNucleotide ? seq2 : seq;
+ SequenceI cds = mappingToNucleotide ? seq : seq2;
+ SequenceToSequenceMapping s2s = acf.getCoveringMapping(cds,
+ peptide);
+ if (s2s != null)
{
mappedOrder.add(seq2);
j++;
break;
}
}
- }
}
}