--- /dev/null
+package jalview.util;
+
+import jalview.analysis.AlignmentSorter;
+import jalview.api.AlignViewportI;
+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.AlignmentI;
+import jalview.datamodel.AlignmentOrder;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SearchResults.Match;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+
+import java.util.ArrayList;
+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.
+ *
+ * @author gmcarstairs
+ *
+ */
+public final class MappingUtils
+{
+
+ /**
+ * Helper method to map a CUT or PASTE command.
+ *
+ * @param edit
+ * the original command
+ * @param undo
+ * if true, the command is to be undone
+ * @param targetSeqs
+ * the mapped sequences to apply the mapped command to
+ * @param result
+ * the mapped EditCommand to add to
+ * @param mappings
+ */
+ protected static void mapCutOrPaste(Edit edit, boolean undo,
+ List<SequenceI> targetSeqs, EditCommand result,
+ Set<AlignedCodonFrame> mappings)
+ {
+ Action action = edit.getAction();
+ if (undo)
+ {
+ action = action.getUndoAction();
+ }
+ // TODO write this
+ System.err.println("MappingUtils.mapCutOrPaste not yet implemented");
+ }
+
+ /**
+ * Returns a new EditCommand representing the given command as mapped to the
+ * given sequences. If there is no mapping, returns null.
+ *
+ * @param command
+ * @param undo
+ * @param mapTo
+ * @param gapChar
+ * @param mappings
+ * @return
+ */
+ public static EditCommand mapEditCommand(EditCommand command,
+ boolean undo, final AlignmentI mapTo, char gapChar,
+ Set<AlignedCodonFrame> mappings)
+ {
+ /*
+ * For now, only support mapping from protein edits to cDna
+ */
+ if (!mapTo.isNucleotide())
+ {
+ return null;
+ }
+
+ /*
+ * 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>();
+ for (SequenceI seq : mapTo.getSequences())
+ {
+ SequenceI ds = seq.getDatasetSequence();
+ if (ds != null)
+ {
+ final SequenceI copy = new Sequence(seq);
+ copy.setDatasetSequence(ds);
+ targetCopies.put(ds, copy);
+ }
+ }
+
+ /*
+ * Compute 'source' sequences as they were before applying edits:
+ */
+ Map<SequenceI, SequenceI> originalSequences = command.priorState(undo);
+
+ EditCommand result = new EditCommand();
+ Iterator<Edit> edits = command.getEditIterator(!undo);
+ while (edits.hasNext())
+ {
+ Edit edit = edits.next();
+ if (edit.getAction() == Action.CUT
+ || edit.getAction() == Action.PASTE)
+ {
+ mapCutOrPaste(edit, undo, mapTo.getSequences(), result, mappings);
+ }
+ else if (edit.getAction() == Action.INSERT_GAP
+ || edit.getAction() == Action.DELETE_GAP)
+ {
+ mapInsertOrDelete(edit, undo, originalSequences,
+ mapTo.getSequences(), targetCopies, gapChar, result,
+ mappings);
+ }
+ }
+ return result.getSize() > 0 ? result : null;
+ }
+
+ /**
+ * Helper method to map an edit command to insert or delete gaps.
+ *
+ * @param edit
+ * the original command
+ * @param undo
+ * if true, the action is to undo the command
+ * @param originalSequences
+ * the sequences the command acted on
+ * @param targetSeqs
+ * @param targetCopies
+ * @param gapChar
+ * @param result
+ * the new EditCommand to add mapped commands to
+ * @param mappings
+ */
+ protected static void mapInsertOrDelete(Edit edit, boolean undo,
+ Map<SequenceI, SequenceI> originalSequences,
+ final List<SequenceI> targetSeqs,
+ Map<SequenceI, SequenceI> targetCopies, char gapChar,
+ EditCommand result, Set<AlignedCodonFrame> mappings)
+ {
+ Action action = edit.getAction();
+
+ /*
+ * Invert sense of action if an Undo.
+ */
+ if (undo)
+ {
+ action = action.getUndoAction();
+ }
+ final int count = edit.getNumber();
+ final int editPos = edit.getPosition();
+ for (SequenceI seq : edit.getSequences())
+ {
+ /*
+ * Get residue position at (or to right of) edit location. Note we use our
+ * 'copy' of the sequence before editing for this.
+ */
+ SequenceI ds = seq.getDatasetSequence();
+ if (ds == null)
+ {
+ continue;
+ }
+ final SequenceI actedOn = originalSequences.get(ds);
+ final int seqpos = actedOn.findPosition(editPos);
+
+ /*
+ * Determine all mappings from this position to mapped sequences.
+ */
+ SearchResults sr = buildSearchResults(seq, seqpos, mappings);
+
+ if (!sr.isEmpty())
+ {
+ for (SequenceI targetSeq : targetSeqs)
+ {
+ ds = targetSeq.getDatasetSequence();
+ if (ds == null)
+ {
+ continue;
+ }
+ SequenceI copyTarget = targetCopies.get(ds);
+ final int[] match = sr.getResults(copyTarget, 0,
+ copyTarget.getLength());
+ if (match != null)
+ {
+ final int ratio = 3; // TODO: compute this - how?
+ final int mappedCount = count * ratio;
+
+ /*
+ * Shift Delete start position left, as it acts on positions to its
+ * right.
+ */
+ 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);
+
+ /*
+ * and 'apply' the edit to our copy of its target sequence
+ */
+ if (action == Action.INSERT_GAP)
+ {
+ 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)));
+ }
+ }
+ }
+ }
+ /*
+ * and 'apply' the edit to our copy of its source sequence
+ */
+ if (action == Action.INSERT_GAP)
+ {
+ actedOn.setSequence(new String(StringUtils.insertCharAt(
+ actedOn.getSequence(), editPos, count, gapChar)));
+ }
+ else if (action == Action.DELETE_GAP)
+ {
+ actedOn.setSequence(new String(StringUtils.deleteChars(
+ actedOn.getSequence(), editPos, editPos + count)));
+ }
+ }
+ }
+
+ /**
+ * Returns a SearchResults object describing the mapped region corresponding
+ * to the specified sequence position.
+ *
+ * @param seq
+ * @param index
+ * @param seqmappings
+ * @return
+ */
+ public static SearchResults buildSearchResults(SequenceI seq, int index,
+ Set<AlignedCodonFrame> seqmappings)
+ {
+ SearchResults results;
+ results = new SearchResults();
+ if (index >= seq.getStart() && index <= seq.getEnd())
+ {
+ for (AlignedCodonFrame acf : seqmappings)
+ {
+ acf.markMappedRegion(seq, index, results);
+ }
+ }
+ return results;
+ }
+
+ /**
+ * Returns a (possibly empty) SequenceGroup containing any sequences in the
+ * mapped viewport corresponding to the given group in the source viewport.
+ *
+ * @param sg
+ * @param mapFrom
+ * @param mapTo
+ * @return
+ */
+ public static SequenceGroup mapSequenceGroup(SequenceGroup sg,
+ AlignViewportI mapFrom, AlignViewportI mapTo)
+ {
+ /*
+ * Note the SequenceGroup holds aligned sequences, the mappings hold dataset
+ * sequences.
+ */
+ boolean targetIsNucleotide = mapTo.isNucleotide();
+ AlignViewportI protein = targetIsNucleotide ? mapFrom : mapTo;
+ Set<AlignedCodonFrame> codonFrames = protein.getAlignment()
+ .getCodonFrames();
+
+ /*
+ * Copy group name, name colours, but not sequences or sequence colour
+ * scheme
+ */
+ SequenceGroup mappedGroup = new SequenceGroup(sg);
+ mappedGroup.cs = mapTo.getGlobalColourScheme();
+ mappedGroup.clear();
+ // TODO set width of mapped group
+
+ for (SequenceI selected : sg.getSequences())
+ {
+ for (AlignedCodonFrame acf : codonFrames)
+ {
+ SequenceI mappedSequence = targetIsNucleotide ? acf
+ .getDnaForAaSeq(selected) : acf.getAaForDnaSeq(selected);
+ if (mappedSequence != null)
+ {
+ for (SequenceI seq : mapTo.getAlignment().getSequences())
+ {
+ if (seq.getDatasetSequence() == mappedSequence)
+ {
+ mappedGroup.addSequence(seq, false);
+ break;
+ }
+ }
+ }
+ }
+ }
+ return mappedGroup;
+ }
+
+ /**
+ * Returns an OrderCommand equivalent to the given one, but acting on mapped
+ * sequences as described by the mappings, or null if no mapping can be made.
+ *
+ * @param command
+ * the original order command
+ * @param undo
+ * if true, the action is to undo the sort
+ * @param mapTo
+ * the alignment we are mapping to
+ * @param mappings
+ * the mappings available
+ * @return
+ */
+ public static CommandI mapOrderCommand(OrderCommand command,
+ boolean undo, AlignmentI mapTo, Set<AlignedCodonFrame> mappings)
+ {
+ SequenceI[] sortOrder = command.getSequenceOrder(undo);
+ List<SequenceI> mappedOrder = new ArrayList<SequenceI>();
+ int j = 0;
+ for (SequenceI seq : sortOrder)
+ {
+ for (AlignedCodonFrame acf : mappings)
+ {
+ /*
+ * Try protein-to-Dna, failing that try dna-to-protein
+ */
+ SequenceI mappedSeq = acf.getDnaForAaSeq(seq);
+ if (mappedSeq == null)
+ {
+ mappedSeq = acf.getAaForDnaSeq(seq);
+ }
+ if (mappedSeq != null)
+ {
+ for (SequenceI seq2 : mapTo.getSequences())
+ {
+ if (seq2.getDatasetSequence() == mappedSeq)
+ {
+ mappedOrder.add(seq2);
+ j++;
+ break;
+ }
+ }
+ }
+ }
+ }
+
+ /*
+ * Return null if no mappings made.
+ */
+ if (j == 0)
+ {
+ return null;
+ }
+
+ /*
+ * Add any unmapped sequences on the end of the sort in their original
+ * ordering.
+ */
+ if (j < mapTo.getHeight())
+ {
+ for (SequenceI seq : mapTo.getSequences())
+ {
+ if (!mappedOrder.contains(seq))
+ {
+ mappedOrder.add(seq);
+ }
+ }
+ }
+
+ /*
+ * Have to sort the sequences before constructing the OrderCommand - which
+ * then resorts them?!?
+ */
+ final SequenceI[] mappedOrderArray = mappedOrder
+ .toArray(new SequenceI[mappedOrder.size()]);
+ SequenceI[] oldOrder = mapTo.getSequencesArray();
+ AlignmentSorter.sortBy(mapTo, new AlignmentOrder(mappedOrderArray));
+ final OrderCommand result = new OrderCommand(command.getDescription(),
+ oldOrder, mapTo);
+ return result;
+ }
+
+ /**
+ * Returns a ColumnSelection in the 'mapTo' view which corresponds to the
+ * given selection in the 'mapFrom' view. We assume one is nucleotide, the
+ * other is protein (and holds the mappings from codons to protein residues).
+ *
+ * @param colsel
+ * @param mapFrom
+ * @param mapTo
+ * @return
+ */
+ public static ColumnSelection mapColumnSelection(ColumnSelection colsel,
+ AlignViewportI mapFrom, AlignViewportI mapTo)
+ {
+ boolean targetIsNucleotide = mapTo.isNucleotide();
+ AlignViewportI protein = targetIsNucleotide ? mapFrom : mapTo;
+ Set<AlignedCodonFrame> codonFrames = protein.getAlignment()
+ .getCodonFrames();
+ ColumnSelection mappedColumns = new ColumnSelection();
+ char fromGapChar = mapFrom.getAlignment().getGapCharacter();
+
+ // FIXME allow for hidden columns
+
+ /*
+ * For each mapped column, find the range of columns that residues in that
+ * column map to.
+ */
+ for (Object obj : colsel.getSelected())
+ {
+ int col = ((Integer) obj).intValue();
+ int mappedToMin = Integer.MAX_VALUE;
+ int mappedToMax = Integer.MIN_VALUE;
+
+ /*
+ * For each sequence in the 'from' alignment
+ */
+ for (SequenceI fromSeq : mapFrom.getAlignment().getSequences())
+ {
+ /*
+ * Ignore gaps (unmapped anyway)
+ */
+ if (fromSeq.getCharAt(col) == fromGapChar)
+ {
+ continue;
+ }
+
+ /*
+ * Get the residue position and find the mapped position.
+ */
+ int residuePos = fromSeq.findPosition(col);
+ SearchResults sr = buildSearchResults(fromSeq, residuePos,
+ codonFrames);
+ for (Match m : sr.getResults())
+ {
+ int mappedStartResidue = m.getStart();
+ int mappedEndResidue = m.getEnd();
+ SequenceI mappedSeq = m.getSequence();
+
+ /*
+ * Locate the aligned sequence whose dataset is mappedSeq. TODO a
+ * datamodel that can do this efficiently.
+ */
+ for (SequenceI toSeq : mapTo.getAlignment().getSequences())
+ {
+ if (toSeq.getDatasetSequence() == mappedSeq)
+ {
+ int mappedStartCol = toSeq.findIndex(mappedStartResidue);
+ int mappedEndCol = toSeq.findIndex(mappedEndResidue);
+ mappedToMin = Math.min(mappedToMin, mappedStartCol);
+ mappedToMax = Math.max(mappedToMax, mappedEndCol);
+ // System.out.println(fromSeq.getName() + " mapped to cols "
+ // + mappedStartCol + ":" + mappedEndCol);
+ break;
+ // note: remove break if we ever want to map one to many sequences
+ }
+ }
+ }
+ }
+ /*
+ * Add the range of mapped columns to the mapped selection (converting
+ * base 1 to base 0). Note that this may include intron-only regions which
+ * lie between the start and end ranges of the selection.
+ */
+ for (int i = mappedToMin; i <= mappedToMax; i++)
+ {
+ mappedColumns.addElement(i - 1);
+ }
+ }
+ return mappedColumns;
+ }
+
+ /**
+ * Returns the mapped codon for a given aligned sequence column position (base
+ * 0).
+ *
+ * @param seq
+ * an aligned peptide sequence
+ * @param col
+ * an aligned column position (base 0)
+ * @param mappings
+ * a set of codon mappings
+ * @return the bases of the mapped codon in the cDNA dataset sequence, or null
+ * if not found
+ */
+ public static char[] findCodonFor(SequenceI seq, int col,
+ Set<AlignedCodonFrame> mappings)
+ {
+ int dsPos = seq.findPosition(col);
+ for (AlignedCodonFrame mapping : mappings)
+ {
+ if (mapping.involvesSequence(seq))
+ {
+ return mapping.getMappedCodon(seq.getDatasetSequence(), dsPos);
+ }
+ }
+ return null;
+ }
+
+ /**
+ * Converts a series of [start, end] ranges into an array of individual
+ * positions.
+ *
+ * @param ranges
+ * @return
+ */
+ public static int[] flattenRanges(int[] ranges)
+ {
+ /*
+ * Count how many positions altogether
+ */
+ int count = 0;
+ for (int i = 0; i < ranges.length - 1; i += 2)
+ {
+ count += ranges[i + 1] - ranges[i] + 1;
+ }
+
+ int[] result = new int[count];
+ int k = 0;
+ for (int i = 0; i < ranges.length - 1; i += 2)
+ {
+ for (int j = ranges[i]; j <= ranges[i + 1]; j++)
+ {
+ result[k++] = j;
+ }
+ }
+ return result;
+ }
+}
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