package jalview.util;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
import jalview.analysis.AlignmentSorter;
import jalview.api.AlignViewportI;
import jalview.commands.CommandI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
/**
* Helper methods for manipulations involving sequence mappings.
*
*/
int mappedEditPos = action == Action.DELETE_GAP ? match[0]
- mappedCount : match[0];
- Edit e = result.new Edit(action, new SequenceI[]
- { targetSeq }, mappedEditPos, mappedCount, gapChar);
+ Edit e = result.new Edit(action, new SequenceI[] { targetSeq },
+ mappedEditPos, mappedCount, gapChar);
result.addEdit(e);
/*
*/
int startResiduePos = selected.findPosition(firstUngappedPos);
int endResiduePos = selected.findPosition(lastUngappedPos);
-
+
for (AlignedCodonFrame acf : codonFrames)
{
SequenceI mappedSequence = targetIsNucleotide ? acf
{
for (AlignedCodonFrame acf : mappings)
{
- SequenceI mappedSeq = mappingToNucleotide ? acf.getDnaForAaSeq(seq) : acf.getAaForDnaSeq(seq);
+ SequenceI mappedSeq = mappingToNucleotide ? acf.getDnaForAaSeq(seq)
+ : acf.getAaForDnaSeq(seq);
if (mappedSeq != null)
{
for (SequenceI seq2 : mapTo.getSequences())
Set<AlignedCodonFrame> codonFrames = protein.getAlignment()
.getCodonFrames();
ColumnSelection mappedColumns = new ColumnSelection();
+
+ if (colsel == null)
+ {
+ return mappedColumns;
+ }
+
char fromGapChar = mapFrom.getAlignment().getGapCharacter();
// FIXME allow for hidden columns
{
return result;
}
- for (AlignedCodonFrame mapping : mappings) {
- if (mapping.involvesSequence(sequence)) {
+ for (AlignedCodonFrame mapping : mappings)
+ {
+ if (mapping.involvesSequence(sequence))
+ {
result.add(mapping);
}
}