* Cache a copy of the target sequences so we can mimic successive edits on
* them. This lets us compute mappings for all edits in the set.
*/
- Map<SequenceI, SequenceI> targetCopies = new HashMap<SequenceI, SequenceI>();
+ Map<SequenceI, SequenceI> targetCopies = new HashMap<>();
for (SequenceI seq : mapTo.getSequences())
{
SequenceI ds = seq.getDatasetSequence();
* Shift Delete start position left, as it acts on positions to its
* right.
*/
- int mappedEditPos = action == Action.DELETE_GAP ? match[0]
- - mappedCount : match[0];
+ int mappedEditPos = action == Action.DELETE_GAP
+ ? match[0] - mappedCount
+ : match[0];
Edit e = result.new Edit(action, new SequenceI[] { targetSeq },
mappedEditPos, mappedCount, gapChar);
result.addEdit(e);
*/
if (action == Action.INSERT_GAP)
{
- copyTarget.setSequence(new String(StringUtils.insertCharAt(
- copyTarget.getSequence(), mappedEditPos, mappedCount,
- gapChar)));
+ copyTarget.setSequence(new String(
+ StringUtils.insertCharAt(copyTarget.getSequence(),
+ mappedEditPos, mappedCount, gapChar)));
}
else if (action == Action.DELETE_GAP)
{
- copyTarget.setSequence(new String(StringUtils.deleteChars(
- copyTarget.getSequence(), mappedEditPos,
- mappedEditPos + mappedCount)));
+ copyTarget.setSequence(new String(
+ StringUtils.deleteChars(copyTarget.getSequence(),
+ mappedEditPos, mappedEditPos + mappedCount)));
}
}
}
for (AlignedCodonFrame acf : codonFrames)
{
- SequenceI mappedSequence = targetIsNucleotide ? acf
- .getDnaForAaSeq(selected) : acf.getAaForDnaSeq(selected);
+ SequenceI mappedSequence = targetIsNucleotide
+ ? acf.getDnaForAaSeq(selected)
+ : acf.getAaForDnaSeq(selected);
if (mappedSequence != null)
{
for (SequenceI seq : mapTo.getAlignment().getSequences())
* Found a sequence mapping. Locate the start/end mapped residues.
*/
List<AlignedCodonFrame> mapping = Arrays
- .asList(new AlignedCodonFrame[] { acf });
+ .asList(new AlignedCodonFrame[]
+ { acf });
SearchResultsI sr = buildSearchResults(selected,
startResiduePos, mapping);
for (SearchResultMatchI m : sr.getResults())
* returns a base 1 position, SequenceGroup uses base 0
*/
int mappedStartCol = seq.findIndex(mappedStartResidue) - 1;
- minStartCol = minStartCol == -1 ? mappedStartCol : Math.min(
- minStartCol, mappedStartCol);
+ minStartCol = minStartCol == -1 ? mappedStartCol
+ : Math.min(minStartCol, mappedStartCol);
int mappedEndCol = seq.findIndex(mappedEndResidue) - 1;
- maxEndCol = maxEndCol == -1 ? mappedEndCol : Math.max(
- maxEndCol, mappedEndCol);
+ maxEndCol = maxEndCol == -1 ? mappedEndCol
+ : Math.max(maxEndCol, mappedEndCol);
mappedGroup.addSequence(seq, false);
break;
}
* the mappings available
* @return
*/
- public static CommandI mapOrderCommand(OrderCommand command,
- boolean undo, AlignmentI mapTo, List<AlignedCodonFrame> mappings)
+ public static CommandI mapOrderCommand(OrderCommand command, boolean undo,
+ AlignmentI mapTo, List<AlignedCodonFrame> mappings)
{
SequenceI[] sortOrder = command.getSequenceOrder(undo);
- List<SequenceI> mappedOrder = new ArrayList<SequenceI>();
+ List<SequenceI> mappedOrder = new ArrayList<>();
int j = 0;
/*
AlignViewportI protein = targetIsNucleotide ? mapFrom : mapTo;
List<AlignedCodonFrame> codonFrames = protein.getAlignment()
.getCodonFrames();
- // ColumnSelection mappedColumns = new ColumnSelection();
if (colsel == null)
{
toSequences, fromGapChar);
}
- for (int[] hidden : hiddencols.getHiddenRegions())
+ for (int[] hidden : hiddencols.getHiddenColumnsCopy())
{
mapHiddenColumns(hidden, codonFrames, newHidden, fromSequences,
toSequences, fromGapChar);
* @param toSequences
* @param fromGapChar
*/
- protected static void mapColumn(int col,
- List<AlignedCodonFrame> mappings, ColumnSelection mappedColumns,
- List<SequenceI> fromSequences, List<SequenceI> toSequences,
- char fromGapChar)
+ protected static void mapColumn(int col, List<AlignedCodonFrame> mappings,
+ ColumnSelection mappedColumns, List<SequenceI> fromSequences,
+ List<SequenceI> toSequences, char fromGapChar)
{
int[] mappedTo = findMappedColumns(col, mappings, fromSequences,
toSequences, fromGapChar);
public static List<char[]> findCodonsFor(SequenceI seq, int col,
List<AlignedCodonFrame> mappings)
{
- List<char[]> result = new ArrayList<char[]>();
+ List<char[]> result = new ArrayList<>();
int dsPos = seq.findPosition(col);
for (AlignedCodonFrame mapping : mappings)
{
if (mapping.involvesSequence(seq))
{
- List<char[]> codons = mapping.getMappedCodons(
- seq.getDatasetSequence(), dsPos);
+ List<char[]> codons = mapping
+ .getMappedCodons(seq.getDatasetSequence(), dsPos);
if (codons != null)
{
result.addAll(codons);
SequenceI sequence, List<AlignedCodonFrame> mappings,
List<SequenceI> filterList)
{
- List<AlignedCodonFrame> result = new ArrayList<AlignedCodonFrame>();
+ List<AlignedCodonFrame> result = new ArrayList<>();
if (sequence == null || mappings == null)
{
return result;
SequenceI otherDataset = otherseq.getDatasetSequence();
if (otherseq == sequence
|| otherseq == sequence.getDatasetSequence()
- || (otherDataset != null && (otherDataset == sequence || otherDataset == sequence
- .getDatasetSequence())))
+ || (otherDataset != null && (otherDataset == sequence
+ || otherDataset == sequence
+ .getDatasetSequence())))
{
// skip sequences in subset which directly relate to sequence
continue;
{
if (range.length % 2 != 0)
{
- System.err.println("Error unbalance start/end ranges: "
- + ranges.toString());
+ System.err.println(
+ "Error unbalance start/end ranges: " + ranges.toString());
return 0;
}
for (int i = 0; i < range.length - 1; i += 2)
}
return copy;
}
+
+ /**
+ * Removes the specified number of positions from the given ranges. Provided
+ * to allow a stop codon to be stripped from a CDS sequence so that it matches
+ * the peptide translation length.
+ *
+ * @param positions
+ * @param ranges
+ * a list of (single) [start, end] ranges
+ * @return
+ */
+ public static void removeEndPositions(int positions,
+ List<int[]> ranges)
+ {
+ int toRemove = positions;
+ Iterator<int[]> it = new ReverseListIterator<>(ranges);
+ while (toRemove > 0)
+ {
+ int[] endRange = it.next();
+ if (endRange.length != 2)
+ {
+ /*
+ * not coded for [start1, end1, start2, end2, ...]
+ */
+ System.err
+ .println("MappingUtils.removeEndPositions doesn't handle multiple ranges");
+ return;
+ }
+
+ int length = endRange[1] - endRange[0] + 1;
+ if (length <= 0)
+ {
+ /*
+ * not coded for a reverse strand range (end < start)
+ */
+ System.err
+ .println("MappingUtils.removeEndPositions doesn't handle reverse strand");
+ return;
+ }
+ if (length > toRemove)
+ {
+ endRange[1] -= toRemove;
+ toRemove = 0;
+ }
+ else
+ {
+ toRemove -= length;
+ it.remove();
+ }
+ }
+ }
+
+
+ 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
+ {
+ jalview.bin.Cache.log.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