import jalview.analysis.AlignmentSorter;
import jalview.api.AlignViewportI;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.commands.CommandI;
import jalview.commands.EditCommand;
import jalview.commands.EditCommand.Action;
import jalview.commands.EditCommand.Edit;
import jalview.commands.OrderCommand;
import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentOrder;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.Mapping;
import jalview.datamodel.SearchResultMatchI;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SearchResultsI;
action = action.getUndoAction();
}
// TODO write this
- Cache.log.error("MappingUtils.mapCutOrPaste not yet implemented");
+ Console.error("MappingUtils.mapCutOrPaste not yet implemented");
}
/**
*/
int startResiduePos = selected.findPosition(firstUngappedPos);
int endResiduePos = selected.findPosition(lastUngappedPos);
-
- for (AlignedCodonFrame acf : codonFrames)
+ for (SequenceI seq : mapTo.getAlignment().getSequences())
{
- SequenceI mappedSequence = targetIsNucleotide
- ? acf.getDnaForAaSeq(selected)
- : acf.getAaForDnaSeq(selected);
- if (mappedSequence != null)
+ int mappedStartResidue = 0;
+ int mappedEndResidue = 0;
+ for (AlignedCodonFrame acf : codonFrames)
{
- for (SequenceI seq : mapTo.getAlignment().getSequences())
+ // rather than use acf.getCoveringMapping() we iterate through all
+ // mappings to make sure all CDS are selected for a protein
+ for (SequenceToSequenceMapping map : acf.getMappings())
{
- int mappedStartResidue = 0;
- int mappedEndResidue = 0;
- if (seq.getDatasetSequence() == mappedSequence)
+ if (map.covers(selected) && map.covers(seq))
{
/*
* Found a sequence mapping. Locate the start/end mapped residues.
List<AlignedCodonFrame> mapping = Arrays
.asList(new AlignedCodonFrame[]
{ acf });
+ // locate start
SearchResultsI sr = buildSearchResults(selected,
startResiduePos, mapping);
for (SearchResultMatchI m : sr.getResults())
mappedStartResidue = m.getStart();
mappedEndResidue = m.getEnd();
}
+ // locate end - allowing for adjustment of start range
sr = buildSearchResults(selected, endResiduePos, mapping);
for (SearchResultMatchI m : sr.getResults())
{
{
for (AlignedCodonFrame acf : mappings)
{
- SequenceI mappedSeq = mappingToNucleotide ? acf.getDnaForAaSeq(seq)
- : acf.getAaForDnaSeq(seq);
- if (mappedSeq != null)
+ for (SequenceI seq2 : mapTo.getSequences())
{
- for (SequenceI seq2 : mapTo.getSequences())
+ /*
+ * 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)
{
- if (seq2.getDatasetSequence() == mappedSeq)
- {
- mappedOrder.add(seq2);
- j++;
- break;
- }
+ mappedOrder.add(seq2);
+ j++;
+ break;
}
}
}
if (colsel == null)
{
- return; // mappedColumns;
+ return;
}
char fromGapChar = mapFrom.getAlignment().getGapCharacter();
mapHiddenColumns(regions.next(), codonFrames, newHidden,
fromSequences, toSequences, fromGapChar);
}
- return; // mappedColumns;
+ return;
}
/**
*/
for (SequenceI toSeq : toSequences)
{
- if (toSeq.getDatasetSequence() == mappedSeq)
+ if (toSeq.getDatasetSequence() == mappedSeq
+ && mappedStartResidue >= toSeq.getStart()
+ && mappedEndResidue <= toSeq.getEnd())
{
int mappedStartCol = toSeq.findIndex(mappedStartResidue);
int mappedEndCol = toSeq.findIndex(mappedEndResidue);
{
if (range.length % 2 != 0)
{
- Cache.log.error(
+ Console.error(
"Error unbalance start/end ranges: " + ranges.toString());
return 0;
}
/*
* not coded for [start1, end1, start2, end2, ...]
*/
- Cache.log.error(
+ Console.error(
"MappingUtils.removeEndPositions doesn't handle multiple ranges");
return;
}
/*
* not coded for a reverse strand range (end < start)
*/
- Cache.log.error(
+ Console.error(
"MappingUtils.removeEndPositions doesn't handle reverse strand");
return;
}