X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcommands%2FEditCommand.java;h=30595bce2afcec658ce343e5ee7067bcd3310c03;hb=9d2408483e451285fd555c3cd6e0273977acbaa7;hp=d319249c004aa95014be9f8c5b3a8f27ce38dc03;hpb=3d0101179759ef157b088ea135423cd909512d9f;p=jalview.git diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java index d319249..30595bc 100644 --- a/src/jalview/commands/EditCommand.java +++ b/src/jalview/commands/EditCommand.java @@ -20,12 +20,19 @@ */ package jalview.commands; +import java.util.Locale; + +import jalview.analysis.AlignSeq; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.Annotation; +import jalview.datamodel.ContiguousI; +import jalview.datamodel.Range; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; +import jalview.datamodel.features.SequenceFeaturesI; +import jalview.util.Comparison; import jalview.util.ReverseListIterator; import jalview.util.StringUtils; @@ -114,7 +121,7 @@ public class EditCommand implements CommandI public abstract Action getUndoAction(); }; - private List edits = new ArrayList(); + private List edits = new ArrayList<>(); String description; @@ -122,15 +129,15 @@ public class EditCommand implements CommandI { } - public EditCommand(String description) + public EditCommand(String desc) { - this.description = description; + this.description = desc; } - public EditCommand(String description, Action command, SequenceI[] seqs, + public EditCommand(String desc, Action command, SequenceI[] seqs, int position, int number, AlignmentI al) { - this.description = description; + this.description = desc; if (command == Action.CUT || command == Action.PASTE) { setEdit(new Edit(command, seqs, position, number, al)); @@ -139,10 +146,10 @@ public class EditCommand implements CommandI performEdit(0, null); } - public EditCommand(String description, Action command, String replace, + public EditCommand(String desc, Action command, String replace, SequenceI[] seqs, int position, int number, AlignmentI al) { - this.description = description; + this.description = desc; if (command == Action.REPLACE) { setEdit(new Edit(command, seqs, position, number, al, replace)); @@ -330,20 +337,8 @@ public class EditCommand implements CommandI int position, int number, AlignmentI al, boolean performEdit, AlignmentI[] views) { - Edit edit = new Edit(command, seqs, position, number, - al.getGapCharacter()); - if (al.getHeight() == seqs.length) - { - edit.al = al; - edit.fullAlignmentHeight = true; - } - - addEdit(edit); - - if (performEdit) - { - performEdit(edit, views); - } + Edit edit = new Edit(command, seqs, position, number, al); + appendEdit(edit, al, performEdit, views); } /** @@ -534,37 +529,62 @@ public class EditCommand implements CommandI command.string[i] = sequence.getSequence(command.position, command.position + command.number); SequenceI oldds = sequence.getDatasetSequence(); + ContiguousI cutPositions = sequence.findPositions( + command.position + 1, command.position + command.number); + boolean cutIsInternal = cutPositions != null + && sequence.getStart() != cutPositions + .getBegin() && sequence.getEnd() != cutPositions.getEnd(); + + /* + * perform the cut; if this results in a new dataset sequence, add + * that to the alignment dataset + */ + SequenceI ds = sequence.getDatasetSequence(); + sequence.deleteChars(command.position, command.position + + command.number); + if (command.oldds != null && command.oldds[i] != null) { - // we are redoing an undone cut. - sequence.setDatasetSequence(null); - } - sequence.deleteChars(command.position, - command.position + command.number); - if (command.oldds != null && command.oldds[i] != null) - { - // oldds entry contains the cut dataset sequence. + /* + * we are Redoing a Cut, or Undoing a Paste - so + * oldds entry contains the cut dataset sequence, + * with sequence features in expected place + */ sequence.setDatasetSequence(command.oldds[i]); command.oldds[i] = oldds; } else { - // modify the oldds if necessary + /* + * new cut operation: save the dataset sequence + * so it can be restored in an Undo + */ + if (command.oldds == null) + { + command.oldds = new SequenceI[command.seqs.length]; + } + command.oldds[i] = oldds;// todo not if !cutIsInternal? + + // do we need to edit sequence features for new sequence ? if (oldds != sequence.getDatasetSequence() - || sequence.getSequenceFeatures() != null) + || (cutIsInternal + && sequence.getFeatures().hasFeatures())) + // todo or just test cutIsInternal && cutPositions != null ? { - if (command.oldds == null) + if (cutPositions != null) { - command.oldds = new SequenceI[command.seqs.length]; + cutFeatures(command, sequence, cutPositions.getBegin(), + cutPositions.getEnd(), cutIsInternal); } - command.oldds[i] = oldds; - adjustFeatures(command, i, - sequence.findPosition(command.position), - sequence.findPosition( - command.position + command.number), - false); } } + SequenceI newDs = sequence.getDatasetSequence(); + if (newDs != ds && command.al != null + && command.al.getDataset() != null + && !command.al.getDataset().getSequences().contains(newDs)) + { + command.al.getDataset().addSequence(newDs); + } } if (sequence.getLength() < 1) @@ -586,90 +606,98 @@ public class EditCommand implements CommandI */ static void paste(Edit command, AlignmentI[] views) { - StringBuffer tmp; - boolean newDSNeeded; - boolean newDSWasNeeded; - int newstart, newend; boolean seqWasDeleted = false; - int start = 0, end = 0; for (int i = 0; i < command.seqs.length; i++) { - newDSNeeded = false; - newDSWasNeeded = command.oldds != null && command.oldds[i] != null; - if (command.seqs[i].getLength() < 1) + boolean newDSNeeded = false; + boolean newDSWasNeeded = command.oldds != null + && command.oldds[i] != null; + SequenceI sequence = command.seqs[i]; + if (sequence.getLength() < 1) { - // ie this sequence was deleted, we need to - // readd it to the alignment + /* + * sequence was deleted; re-add it to the alignment + */ if (command.alIndex[i] < command.al.getHeight()) { - List sequences; - synchronized (sequences = command.al.getSequences()) + List sequences = command.al.getSequences(); + synchronized (sequences) { if (!(command.alIndex[i] < 0)) { - sequences.add(command.alIndex[i], command.seqs[i]); + sequences.add(command.alIndex[i], sequence); } } } else { - command.al.addSequence(command.seqs[i]); + command.al.addSequence(sequence); } seqWasDeleted = true; } - newstart = command.seqs[i].getStart(); - newend = command.seqs[i].getEnd(); + int newStart = sequence.getStart(); + int newEnd = sequence.getEnd(); - tmp = new StringBuffer(); - tmp.append(command.seqs[i].getSequence()); + StringBuilder tmp = new StringBuilder(); + tmp.append(sequence.getSequence()); // Undo of a delete does not replace original dataset sequence on to // alignment sequence. + int start = 0; + int length = 0; + if (command.string != null && command.string[i] != null) { if (command.position >= tmp.length()) { // This occurs if padding is on, and residues // are removed from end of alignment - int length = command.position - tmp.length(); - while (length > 0) + int len = command.position - tmp.length(); + while (len > 0) { tmp.append(command.gapChar); - length--; + len--; } } tmp.insert(command.position, command.string[i]); for (int s = 0; s < command.string[i].length; s++) { - if (jalview.schemes.ResidueProperties.aaIndex[command.string[i][s]] != 23) + if (!Comparison.isGap(command.string[i][s])) { + length++; if (!newDSNeeded) { newDSNeeded = true; - start = command.seqs[i].findPosition(command.position); - end = command.seqs[i] - .findPosition(command.position + command.number); + start = sequence.findPosition(command.position); + // end = sequence + // .findPosition(command.position + command.number); } - if (command.seqs[i].getStart() == start) + if (sequence.getStart() == start) { - newstart--; + newStart--; } else { - newend++; + newEnd++; } } } command.string[i] = null; } - command.seqs[i].setSequence(tmp.toString()); - command.seqs[i].setStart(newstart); - command.seqs[i].setEnd(newend); + sequence.setSequence(tmp.toString()); + sequence.setStart(newStart); + sequence.setEnd(newEnd); + + /* + * command and Undo share the same dataset sequence if cut was + * at start or end of sequence + */ + boolean sameDatasetSequence = false; if (newDSNeeded) { - if (command.seqs[i].getDatasetSequence() != null) + if (sequence.getDatasetSequence() != null) { SequenceI ds; if (newDSWasNeeded) @@ -680,21 +708,29 @@ public class EditCommand implements CommandI { // make a new DS sequence // use new ds mechanism here - ds = new Sequence(command.seqs[i].getName(), - jalview.analysis.AlignSeq.extractGaps( - jalview.util.Comparison.GapChars, - command.seqs[i].getSequenceAsString()), - command.seqs[i].getStart(), command.seqs[i].getEnd()); - ds.setDescription(command.seqs[i].getDescription()); + String ungapped = AlignSeq.extractGaps(Comparison.GapChars, + sequence.getSequenceAsString()); + ds = new Sequence(sequence.getName(), ungapped, + sequence.getStart(), sequence.getEnd()); + ds.setDescription(sequence.getDescription()); } if (command.oldds == null) { command.oldds = new SequenceI[command.seqs.length]; } - command.oldds[i] = command.seqs[i].getDatasetSequence(); - command.seqs[i].setDatasetSequence(ds); + command.oldds[i] = sequence.getDatasetSequence(); + sameDatasetSequence = ds == sequence.getDatasetSequence(); + ds.setSequenceFeatures(sequence.getSequenceFeatures()); + if (!sameDatasetSequence && command.al.getDataset() != null) + { + // delete 'undone' sequence from alignment dataset + command.al.getDataset() + .deleteSequence(sequence.getDatasetSequence()); + } + sequence.setDatasetSequence(ds); } - adjustFeatures(command, i, start, end, true); + undoCutFeatures(command, command.seqs[i], start, length, + sameDatasetSequence); } } adjustAnnotations(command, true, seqWasDeleted, views); @@ -704,7 +740,7 @@ public class EditCommand implements CommandI static void replace(Edit command) { - StringBuffer tmp; + StringBuilder tmp; String oldstring; int start = command.position; int end = command.number; @@ -717,6 +753,7 @@ public class EditCommand implements CommandI { boolean newDSWasNeeded = command.oldds != null && command.oldds[i] != null; + boolean newStartEndWasNeeded = command.oldStartEnd!=null && command.oldStartEnd[i]!=null; /** * cut addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, @@ -729,49 +766,147 @@ public class EditCommand implements CommandI * EditCommand.PASTE, sequences, 0, alignment.getWidth(), alignment) ); * */ + ContiguousI beforeEditedPositions = command.seqs[i].findPositions(1, + start); + ContiguousI afterEditedPositions = command.seqs[i] + .findPositions(end + 1, command.seqs[i].getLength()); + oldstring = command.seqs[i].getSequenceAsString(); - tmp = new StringBuffer(oldstring.substring(0, start)); + tmp = new StringBuilder(oldstring.substring(0, start)); tmp.append(command.string[i]); - String nogaprep = jalview.analysis.AlignSeq.extractGaps( - jalview.util.Comparison.GapChars, + String nogaprep = AlignSeq.extractGaps(Comparison.GapChars, new String(command.string[i])); - int ipos = command.seqs[i].findPosition(start) - - command.seqs[i].getStart(); - tmp.append(oldstring.substring(end)); + if (end < oldstring.length()) + { + tmp.append(oldstring.substring(end)); + } + // stash end prior to updating the sequence object so we can save it if + // need be. + Range oldstartend = new Range(command.seqs[i].getStart(), + command.seqs[i].getEnd()); command.seqs[i].setSequence(tmp.toString()); - command.string[i] = oldstring.substring(start, end).toCharArray(); - String nogapold = jalview.analysis.AlignSeq.extractGaps( - jalview.util.Comparison.GapChars, + command.string[i] = oldstring + .substring(start, Math.min(end, oldstring.length())) + .toCharArray(); + String nogapold = AlignSeq.extractGaps(Comparison.GapChars, new String(command.string[i])); - if (!nogaprep.toLowerCase().equals(nogapold.toLowerCase())) + + if (!nogaprep.toLowerCase(Locale.ROOT).equals(nogapold.toLowerCase(Locale.ROOT))) { - if (newDSWasNeeded) + // we may already have dataset and limits stashed... + if (newDSWasNeeded || newStartEndWasNeeded) { + if (newDSWasNeeded) + { + // then just switch the dataset sequence SequenceI oldds = command.seqs[i].getDatasetSequence(); command.seqs[i].setDatasetSequence(command.oldds[i]); command.oldds[i] = oldds; + } + if (newStartEndWasNeeded) + { + Range newStart = command.oldStartEnd[i]; + command.oldStartEnd[i] = oldstartend; + command.seqs[i].setStart(newStart.getBegin()); + command.seqs[i].setEnd(newStart.getEnd()); + } } - else + else { - if (command.oldds == null) + // decide if we need a new dataset sequence or modify start/end + // first edit the original dataset sequence string + SequenceI oldds = command.seqs[i].getDatasetSequence(); + String osp = oldds.getSequenceAsString(); + int beforeStartOfEdit = -oldds.getStart() + 1 + + (beforeEditedPositions == null + ? ((afterEditedPositions != null) + ? afterEditedPositions.getBegin() - 1 + : oldstartend.getBegin() + + nogapold.length()) + : beforeEditedPositions.getEnd() + ); + int afterEndOfEdit = -oldds.getStart() + 1 + + ((afterEditedPositions == null) + ? oldstartend.getEnd() + : afterEditedPositions.getBegin() - 1); + String fullseq = osp.substring(0, + beforeStartOfEdit) + + nogaprep + + osp.substring(afterEndOfEdit); + + // and check if new sequence data is different.. + if (!fullseq.equalsIgnoreCase(osp)) { - command.oldds = new SequenceI[command.seqs.length]; - } - command.oldds[i] = command.seqs[i].getDatasetSequence(); - SequenceI newds = new Sequence( - command.seqs[i].getDatasetSequence()); - String fullseq, osp = newds.getSequenceAsString(); - fullseq = osp.substring(0, ipos) + nogaprep - + osp.substring(ipos + nogaprep.length()); - newds.setSequence(fullseq.toUpperCase()); - // TODO: JAL-1131 ensure newly created dataset sequence is added to - // the set of - // dataset sequences associated with the alignment. - // TODO: JAL-1131 fix up any annotation associated with new dataset - // sequence to ensure that original sequence/annotation relationships - // are preserved. - command.seqs[i].setDatasetSequence(newds); + // old ds and edited ds are different, so + // create the new dataset sequence + SequenceI newds = new Sequence(oldds); + newds.setSequence(fullseq.toUpperCase(Locale.ROOT)); + + if (command.oldds == null) + { + command.oldds = new SequenceI[command.seqs.length]; + } + command.oldds[i] = command.seqs[i].getDatasetSequence(); + + // And preserve start/end for good-measure + if (command.oldStartEnd == null) + { + command.oldStartEnd = new Range[command.seqs.length]; + } + command.oldStartEnd[i] = oldstartend; + // TODO: JAL-1131 ensure newly created dataset sequence is added to + // the set of + // dataset sequences associated with the alignment. + // TODO: JAL-1131 fix up any annotation associated with new dataset + // sequence to ensure that original sequence/annotation + // relationships + // are preserved. + command.seqs[i].setDatasetSequence(newds); + } + else + { + if (command.oldStartEnd == null) + { + command.oldStartEnd = new Range[command.seqs.length]; + } + command.oldStartEnd[i] = new Range(command.seqs[i].getStart(), + command.seqs[i].getEnd()); + if (beforeEditedPositions != null + && afterEditedPositions == null) + { + // modification at end + command.seqs[i].setEnd( + beforeEditedPositions.getEnd() + nogaprep.length() + - nogapold.length()); + } + else if (afterEditedPositions != null + && beforeEditedPositions == null) + { + // modification at start + command.seqs[i].setStart( + afterEditedPositions.getBegin() - nogaprep.length()); + } + else + { + // edit covered both start and end. Here we can only guess the + // new + // start/end + String nogapalseq = AlignSeq.extractGaps(Comparison.GapChars, + command.seqs[i].getSequenceAsString().toUpperCase(Locale.ROOT)); + int newStart = command.seqs[i].getDatasetSequence() + .getSequenceAsString().indexOf(nogapalseq); + if (newStart == -1) + { + throw new Error( + "Implementation Error: could not locate start/end " + + "in dataset sequence after an edit of the sequence string"); + } + int newEnd = newStart + nogapalseq.length() - 1; + command.seqs[i].setStart(newStart); + command.seqs[i].setEnd(newEnd); + } + } } } tmp = null; @@ -787,7 +922,7 @@ public class EditCommand implements CommandI if (modifyVisibility && !insert) { // only occurs if a sequence was added or deleted. - command.deletedAnnotationRows = new Hashtable(); + command.deletedAnnotationRows = new Hashtable<>(); } if (command.fullAlignmentHeight) { @@ -799,6 +934,8 @@ public class EditCommand implements CommandI AlignmentAnnotation[] tmp; for (int s = 0; s < command.seqs.length; s++) { + command.seqs[s].sequenceChanged(); + if (modifyVisibility) { // Rows are only removed or added to sequence object. @@ -888,8 +1025,7 @@ public class EditCommand implements CommandI } // and then duplicate added annotation on every other alignment // view - for (int vnum = 0; views != null - && vnum < views.length; vnum++) + for (int vnum = 0; views != null && vnum < views.length; vnum++) { if (views[vnum] != command.al) { @@ -944,7 +1080,7 @@ public class EditCommand implements CommandI if (!insert) { - command.deletedAnnotations = new Hashtable(); + command.deletedAnnotations = new Hashtable<>(); } int aSize; @@ -1105,81 +1241,97 @@ public class EditCommand implements CommandI } } - final static void adjustFeatures(Edit command, int index, int i, int j, - boolean insert) + /** + * Restores features to the state before a Cut. + *
    + *
  • re-add any features deleted by the cut
    • + *
  • remove any truncated features created by the cut
    • + *
  • shift right any features to the right of the cut
    • + *
+ * + * @param command + * the Cut command + * @param seq + * the sequence the Cut applied to + * @param start + * the start residue position of the cut + * @param length + * the number of residues cut + * @param sameDatasetSequence + * true if dataset sequence and frame of reference were left + * unchanged by the Cut + */ + final static void undoCutFeatures(Edit command, SequenceI seq, + final int start, final int length, boolean sameDatasetSequence) { - SequenceI seq = command.seqs[index]; SequenceI sequence = seq.getDatasetSequence(); if (sequence == null) { sequence = seq; } - if (insert) + /* + * shift right features that lie to the right of the restored cut (but not + * if dataset sequence unchanged - so coordinates were changed by Cut) + */ + if (!sameDatasetSequence) { - if (command.editedFeatures != null - && command.editedFeatures.containsKey(seq)) + /* + * shift right all features right of and not + * contiguous with the cut position + */ + seq.getFeatures().shiftFeatures(start + 1, length); + + /* + * shift right any features that start at the cut position, + * unless they were truncated + */ + List sfs = seq.getFeatures().findFeatures(start, + start); + for (SequenceFeature sf : sfs) { - sequence.setSequenceFeatures(command.editedFeatures.get(seq)); + if (sf.getBegin() == start) + { + if (!command.truncatedFeatures.containsKey(seq) + || !command.truncatedFeatures.get(seq).contains(sf)) + { + /* + * feature was shifted left to cut position (not truncated), + * so shift it back right + */ + SequenceFeature shifted = new SequenceFeature(sf, sf.getBegin() + + length, sf.getEnd() + length, sf.getFeatureGroup(), + sf.getScore()); + seq.addSequenceFeature(shifted); + seq.deleteFeature(sf); + } + } } - - return; } - SequenceFeature[] sf = sequence.getSequenceFeatures(); - - if (sf == null) - { - return; - } - - SequenceFeature[] oldsf = new SequenceFeature[sf.length]; - - int cSize = j - i; - - for (int s = 0; s < sf.length; s++) + /* + * restore any features that were deleted or truncated + */ + if (command.deletedFeatures != null + && command.deletedFeatures.containsKey(seq)) { - SequenceFeature copy = new SequenceFeature(sf[s]); - - oldsf[s] = copy; - - if (sf[s].getEnd() < i) - { - continue; - } - - if (sf[s].getBegin() > j) - { - sf[s].setBegin(copy.getBegin() - cSize); - sf[s].setEnd(copy.getEnd() - cSize); - continue; - } - - if (sf[s].getBegin() >= i) - { - sf[s].setBegin(i); - } - - if (sf[s].getEnd() < j) + for (SequenceFeature deleted : command.deletedFeatures.get(seq)) { - sf[s].setEnd(j - 1); - } - - sf[s].setEnd(sf[s].getEnd() - (cSize)); - - if (sf[s].getBegin() > sf[s].getEnd()) - { - sequence.deleteFeature(sf[s]); + sequence.addSequenceFeature(deleted); } } - if (command.editedFeatures == null) + /* + * delete any truncated features + */ + if (command.truncatedFeatures != null + && command.truncatedFeatures.containsKey(seq)) { - command.editedFeatures = new Hashtable(); + for (SequenceFeature amended : command.truncatedFeatures.get(seq)) + { + sequence.deleteFeature(amended); + } } - - command.editedFeatures.put(seq, oldsf); - } /** @@ -1212,7 +1364,7 @@ public class EditCommand implements CommandI */ public Map priorState(boolean forUndo) { - Map result = new HashMap(); + Map result = new HashMap<>(); if (getEdits() == null) { return result; @@ -1245,7 +1397,7 @@ public class EditCommand implements CommandI * Work backwards through the edit list, deriving the sequences before each * was applied. The final result is the sequence set before any edits. */ - Iterator editList = new ReverseListIterator(getEdits()); + Iterator editList = new ReverseListIterator<>(getEdits()); while (editList.hasNext()) { Edit oldEdit = editList.next(); @@ -1294,19 +1446,33 @@ public class EditCommand implements CommandI public class Edit { - public SequenceI[] oldds; + SequenceI[] oldds; + + /** + * start and end of sequence prior to edit + */ + Range[] oldStartEnd; boolean fullAlignmentHeight = false; - Hashtable deletedAnnotationRows; + Map deletedAnnotationRows; - Hashtable deletedAnnotations; + Map deletedAnnotations; - Hashtable editedFeatures; + /* + * features deleted by the cut (re-add on Undo) + * (including the original of any shortened features) + */ + Map> deletedFeatures; + + /* + * shortened features added by the cut (delete on Undo) + */ + Map> truncatedFeatures; AlignmentI al; - Action command; + final Action command; char[][] string; @@ -1314,55 +1480,64 @@ public class EditCommand implements CommandI int[] alIndex; - int position, number; + int position; + + int number; char gapChar; - public Edit(Action command, SequenceI[] seqs, int position, int number, - char gapChar) + /* + * flag that identifies edits inserted to balance + * user edits in a 'locked editing' region + */ + private boolean systemGenerated; + + public Edit(Action cmd, SequenceI[] sqs, int pos, int count, + char gap) { - this.command = command; - this.seqs = seqs; - this.position = position; - this.number = number; - this.gapChar = gapChar; + this.command = cmd; + this.seqs = sqs; + this.position = pos; + this.number = count; + this.gapChar = gap; } - Edit(Action command, SequenceI[] seqs, int position, int number, - AlignmentI al) + Edit(Action cmd, SequenceI[] sqs, int pos, int count, + AlignmentI align) { - this.gapChar = al.getGapCharacter(); - this.command = command; - this.seqs = seqs; - this.position = position; - this.number = number; - this.al = al; - - alIndex = new int[seqs.length]; - for (int i = 0; i < seqs.length; i++) + this(cmd, sqs, pos, count, align.getGapCharacter()); + + this.al = align; + + alIndex = new int[sqs.length]; + for (int i = 0; i < sqs.length; i++) { - alIndex[i] = al.findIndex(seqs[i]); + alIndex[i] = align.findIndex(sqs[i]); } - fullAlignmentHeight = (al.getHeight() == seqs.length); + fullAlignmentHeight = (align.getHeight() == sqs.length); } - Edit(Action command, SequenceI[] seqs, int position, int number, - AlignmentI al, String replace) + /** + * Constructor given a REPLACE command and the replacement string + * + * @param cmd + * @param sqs + * @param pos + * @param count + * @param align + * @param replace + */ + Edit(Action cmd, SequenceI[] sqs, int pos, int count, + AlignmentI align, String replace) { - this.command = command; - this.seqs = seqs; - this.position = position; - this.number = number; - this.al = al; - this.gapChar = al.getGapCharacter(); - string = new char[seqs.length][]; - for (int i = 0; i < seqs.length; i++) + this(cmd, sqs, pos, count, align); + + string = new char[sqs.length][]; + for (int i = 0; i < sqs.length; i++) { string[i] = replace.toCharArray(); } - - fullAlignmentHeight = (al.getHeight() == seqs.length); } public SequenceI[] getSequences() @@ -1389,6 +1564,16 @@ public class EditCommand implements CommandI { return gapChar; } + + public void setSystemGenerated(boolean b) + { + systemGenerated = b; + } + + public boolean isSystemGenerated() + { + return systemGenerated; + } } /** @@ -1406,7 +1591,163 @@ public class EditCommand implements CommandI } else { - return new ReverseListIterator(getEdits()); + return new ReverseListIterator<>(getEdits()); + } + } + + /** + * Adjusts features for Cut, and saves details of changes made to allow Undo + *
    + *
  • features left of the cut are unchanged
    • + *
  • features right of the cut are shifted left
    • + *
  • features internal to the cut region are deleted
    • + *
  • features that overlap or span the cut are shortened
    • + *
  • the originals of any deleted or shortened features are saved, to re-add + * on Undo
    • + *
  • any added (shortened) features are saved, to delete on Undo
    • + *
+ * + * @param command + * @param seq + * @param fromPosition + * @param toPosition + * @param cutIsInternal + */ + protected static void cutFeatures(Edit command, SequenceI seq, + int fromPosition, int toPosition, boolean cutIsInternal) + { + /* + * if the cut is at start or end of sequence + * then we don't modify the sequence feature store + */ + if (!cutIsInternal) + { + return; + } + List added = new ArrayList<>(); + List removed = new ArrayList<>(); + + SequenceFeaturesI featureStore = seq.getFeatures(); + if (toPosition < fromPosition || featureStore == null) + { + return; + } + + int cutStartPos = fromPosition; + int cutEndPos = toPosition; + int cutWidth = cutEndPos - cutStartPos + 1; + + synchronized (featureStore) + { + /* + * get features that overlap the cut region + */ + List toAmend = featureStore.findFeatures( + cutStartPos, cutEndPos); + + /* + * add any contact features that span the cut region + * (not returned by findFeatures) + */ + for (SequenceFeature contact : featureStore.getContactFeatures()) + { + if (contact.getBegin() < cutStartPos + && contact.getEnd() > cutEndPos) + { + toAmend.add(contact); + } + } + + /* + * adjust start-end of overlapping features; + * delete features enclosed by the cut; + * delete partially overlapping contact features + */ + for (SequenceFeature sf : toAmend) + { + int sfBegin = sf.getBegin(); + int sfEnd = sf.getEnd(); + int newBegin = sfBegin; + int newEnd = sfEnd; + boolean toDelete = false; + boolean follows = false; + + if (sfBegin >= cutStartPos && sfEnd <= cutEndPos) + { + /* + * feature lies within cut region - delete it + */ + toDelete = true; + } + else if (sfBegin < cutStartPos && sfEnd > cutEndPos) + { + /* + * feature spans cut region - left-shift the end + */ + newEnd -= cutWidth; + } + else if (sfEnd <= cutEndPos) + { + /* + * feature overlaps left of cut region - truncate right + */ + newEnd = cutStartPos - 1; + if (sf.isContactFeature()) + { + toDelete = true; + } + } + else if (sfBegin >= cutStartPos) + { + /* + * remaining case - feature overlaps right + * truncate left, adjust end of feature + */ + newBegin = cutIsInternal ? cutStartPos : cutEndPos + 1; + newEnd = newBegin + sfEnd - cutEndPos - 1; + if (sf.isContactFeature()) + { + toDelete = true; + } + } + + seq.deleteFeature(sf); + if (!follows) + { + removed.add(sf); + } + if (!toDelete) + { + SequenceFeature copy = new SequenceFeature(sf, newBegin, newEnd, + sf.getFeatureGroup(), sf.getScore()); + seq.addSequenceFeature(copy); + if (!follows) + { + added.add(copy); + } + } + } + + /* + * and left shift any features lying to the right of the cut region + */ + + featureStore.shiftFeatures(cutEndPos + 1, -cutWidth); + } + + /* + * save deleted and amended features, so that Undo can + * re-add or delete them respectively + */ + if (command.deletedFeatures == null) + { + command.deletedFeatures = new HashMap<>(); + } + if (command.truncatedFeatures == null) + { + command.truncatedFeatures = new HashMap<>(); } + command.deletedFeatures.put(seq, removed); + command.truncatedFeatures.put(seq, added); } }