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.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");
}
/**
firstUngappedPos++;
}
- boolean allGapped = (firstUngappedPos > selectionEndRes);
+ /*
+ * If this sequence is only gaps in the selected range, skip it
+ */
+ if (firstUngappedPos > selectionEndRes)
+ {
+ continue;
+ }
int lastUngappedPos = selectionEndRes;
- if (!allGapped)
+ while (lastUngappedPos >= selectionStartRes
+ && Comparison.isGap(selected.getCharAt(lastUngappedPos)))
{
- while (lastUngappedPos >= selectionStartRes
- && Comparison.isGap(selected.getCharAt(lastUngappedPos)))
- {
- lastUngappedPos--;
- }
+ lastUngappedPos--;
}
/*
* Find the selected start/end residue positions in sequence
*/
- int startResiduePos = allGapped ? 0 : selected.findPosition(firstUngappedPos);
- int endResiduePos = allGapped ? 0 : selected.findPosition(lastUngappedPos);
-
- for (AlignedCodonFrame acf : codonFrames)
+ int startResiduePos = selected.findPosition(firstUngappedPos);
+ int endResiduePos = selected.findPosition(lastUngappedPos);
+ for (SequenceI seq : mapTo.getAlignment().getSequences())
{
- for (SequenceI seq : mapTo.getAlignment().getSequences())
+ int mappedStartResidue = 0;
+ int mappedEndResidue = 0;
+ for (AlignedCodonFrame acf : codonFrames)
{
- SequenceI peptide = targetIsNucleotide ? selected : seq;
- SequenceI cds = targetIsNucleotide ? seq : selected;
- SequenceToSequenceMapping s2s = acf.getCoveringMapping(cds,
- peptide);
- if (s2s == null)
- {
- continue;
- }
- mappedGroup.addSequence(seq, false);
- if (allGapped)
- {
- /*
- * sequence is mapped but includes no mapped residues
- */
- continue;
- }
- int mappedStartResidue = 0;
- int mappedEndResidue = 0;
- List<AlignedCodonFrame> mapping = Arrays.asList(acf);
- SearchResultsI sr = buildSearchResults(selected, startResiduePos,
- mapping);
- for (SearchResultMatchI m : sr.getResults())
+ // 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())
{
- mappedStartResidue = m.getStart();
- mappedEndResidue = m.getEnd();
- }
- sr = buildSearchResults(selected, endResiduePos, mapping);
- for (SearchResultMatchI m : sr.getResults())
- {
- mappedStartResidue = Math.min(mappedStartResidue, m.getStart());
- mappedEndResidue = Math.max(mappedEndResidue, m.getEnd());
- }
+ 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())
+ {
+ mappedStartResidue = Math.min(mappedStartResidue,
+ m.getStart());
+ mappedEndResidue = Math.max(mappedEndResidue, m.getEnd());
+ }
- /*
- * Find the mapped aligned columns, save the range. Note findIndex
- * returns a base 1 position, SequenceGroup uses base 0
- */
- int mappedStartCol = seq.findIndex(mappedStartResidue) - 1;
- minStartCol = minStartCol == -1 ? mappedStartCol
- : Math.min(minStartCol, mappedStartCol);
- int mappedEndCol = seq.findIndex(mappedEndResidue) - 1;
- maxEndCol = maxEndCol == -1 ? mappedEndCol
- : Math.max(maxEndCol, mappedEndCol);
+ /*
+ * Find the mapped aligned columns, save the range. Note findIndex
+ * returns a base 1 position, SequenceGroup uses base 0
+ */
+ int mappedStartCol = seq.findIndex(mappedStartResidue) - 1;
+ minStartCol = minStartCol == -1 ? mappedStartCol
+ : Math.min(minStartCol, mappedStartCol);
+ int mappedEndCol = seq.findIndex(mappedEndResidue) - 1;
+ maxEndCol = maxEndCol == -1 ? mappedEndCol
+ : Math.max(maxEndCol, mappedEndCol);
+ mappedGroup.addSequence(seq, false);
+ break;
+ }
+ }
}
}
}
{
for (AlignedCodonFrame acf : mappings)
{
- 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)
{
- /*
- * 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;
- }
+ mappedOrder.add(seq2);
+ j++;
+ break;
}
+ }
}
}
if (colsel == null)
{
- return;
+ return;
}
char fromGapChar = mapFrom.getAlignment().getGapCharacter();
mapHiddenColumns(regions.next(), codonFrames, newHidden,
fromSequences, toSequences, fromGapChar);
}
- return;
+ return;
}
/**
{
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;
}
}
/**
- * Converts a list of [start, end] ranges to a single array of [start, end,
- * start, end ...]
+ * Converts a list of {@code start-end} ranges to a single array of
+ * {@code start1, end1, start2, ... } ranges
*
* @param ranges
* @return
*/
- public static int[] listToArray(List<int[]> ranges)
+ public static int[] rangeListToArray(List<int[]> ranges)
{
- int[] result = new int[ranges.size() * 2];
- int i = 0;
- for (int[] range : ranges)
+ int rangeCount = ranges.size();
+ int[] result = new int[rangeCount * 2];
+ int j = 0;
+ for (int i = 0; i < rangeCount; i++)
{
- result[i++] = range[0];
- result[i++] = range[1];
+ int[] range = ranges.get(i);
+ result[j++] = range[0];
+ result[j++] = range[1];
}
return result;
}
- /**
+ /*
* Returns the maximal start-end positions in the given (ordered) list of
* ranges which is overlapped by the given begin-end range, or null if there
* is no overlap.
return foundStart && to >= from ? new int[] { from, to } : null;
}
+
+ public static <K, V> Map<K, V> putWithDuplicationCheck(Map<K, V> map, K key,
+ V value)
+ {
+ if (!map.containsKey(key))
+ {
+ map.put(key, value);
+ }
+ else
+ {
+ Console.warn(
+ "Attempt to add duplicate entry detected for map with key: "
+ + key.toString() + " and value: " + value.toString());
+ }
+
+ return map;
+ }
}
git://source.jalview.org / jalview.git / blobdiff