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;
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
- System.err.println("MappingUtils.mapCutOrPaste not yet implemented");
+ Cache.log.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())
+ for (SequenceToSequenceMapping map: acf.getMappings())
+ {
+ if (map.covers(selected) && map.covers(seq))
{
- int mappedStartResidue = 0;
- int mappedEndResidue = 0;
- if (seq.getDatasetSequence() == mappedSequence)
+ /*
+ * Found a sequence mapping. Locate the start/end mapped residues.
+ */
+ List<AlignedCodonFrame> mapping = Arrays
+ .asList(new AlignedCodonFrame[]
+ { acf });
+ SearchResultsI sr = buildSearchResults(selected,
+ startResiduePos, mapping);
+ for (SearchResultMatchI m : sr.getResults())
{
- /*
- * Found a sequence mapping. Locate the start/end mapped residues.
- */
- List<AlignedCodonFrame> mapping = Arrays
- .asList(new AlignedCodonFrame[]
- { acf });
- SearchResultsI sr = buildSearchResults(selected,
- startResiduePos, mapping);
- for (SearchResultMatchI m : sr.getResults())
- {
- 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());
- }
-
- /*
- * 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;
+ 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());
}
+
+ /*
+ * 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;
}
- }
+ }}
}
}
mappedGroup.setStartRes(minStartCol < 0 ? 0 : minStartCol);
{
if (range.length % 2 != 0)
{
- System.err.println(
+ Cache.log.error(
"Error unbalance start/end ranges: " + ranges.toString());
return 0;
}
/*
* not coded for [start1, end1, start2, end2, ...]
*/
- System.err.println(
+ Cache.log.error(
"MappingUtils.removeEndPositions doesn't handle multiple ranges");
return;
}
/*
* not coded for a reverse strand range (end < start)
*/
- System.err.println(
+ Cache.log.error(
"MappingUtils.removeEndPositions doesn't handle reverse strand");
return;
}
}
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.
+ *
+ * <pre>
+ * Examples:
+ * if ranges is {[4, 8], [10, 12], [16, 19]}
+ * then
+ * findOverlap(ranges, 1, 20) == [4, 19]
+ * findOverlap(ranges, 6, 11) == [6, 11]
+ * findOverlap(ranges, 9, 15) == [10, 12]
+ * findOverlap(ranges, 13, 15) == null
+ * </pre>
+ *
+ * @param ranges
+ * @param begin
+ * @param end
+ * @return
+ */
+ protected static int[] findOverlap(List<int[]> ranges, final int begin,
+ final int end)
+ {
+ boolean foundStart = false;
+ int from = 0;
+ int to = 0;
+
+ /*
+ * traverse the ranges to find the first position (if any) >= begin,
+ * and the last position (if any) <= end
+ */
+ for (int[] range : ranges)
+ {
+ if (!foundStart)
+ {
+ if (range[0] >= begin)
+ {
+ /*
+ * first range that starts with, or follows, begin
+ */
+ foundStart = true;
+ from = Math.max(range[0], begin);
+ }
+ else if (range[1] >= begin)
+ {
+ /*
+ * first range that contains begin
+ */
+ foundStart = true;
+ from = begin;
+ }
+ }
+
+ if (range[0] <= end)
+ {
+ to = Math.min(end, range[1]);
+ }
+ }
+
+ return foundStart && to >= from ? new int[] { from, to } : null;
+ }
}
git://source.jalview.org / jalview.git / blobdiff