2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.commands;
23 import jalview.analysis.AlignSeq;
24 import jalview.datamodel.AlignmentAnnotation;
25 import jalview.datamodel.AlignmentI;
26 import jalview.datamodel.Annotation;
27 import jalview.datamodel.Range;
28 import jalview.datamodel.Sequence;
29 import jalview.datamodel.SequenceFeature;
30 import jalview.datamodel.SequenceI;
31 import jalview.datamodel.features.SequenceFeaturesI;
32 import jalview.util.Comparison;
33 import jalview.util.ReverseListIterator;
34 import jalview.util.StringUtils;
36 import java.util.ArrayList;
37 import java.util.HashMap;
38 import java.util.Hashtable;
39 import java.util.Iterator;
40 import java.util.List;
41 import java.util.ListIterator;
51 * Description: Essential information for performing undo and redo for cut/paste
52 * insert/delete gap which can be stored in the HistoryList
56 * Copyright: Copyright (c) 2006
60 * Company: Dundee University
63 * @author not attributable
66 public class EditCommand implements CommandI
73 public Action getUndoAction()
81 public Action getUndoAction()
89 public Action getUndoAction()
97 public Action getUndoAction()
105 public Action getUndoAction()
113 public Action getUndoAction()
118 public abstract Action getUndoAction();
121 private List<Edit> edits = new ArrayList<Edit>();
129 public EditCommand(String desc)
131 this.description = desc;
134 public EditCommand(String desc, Action command, SequenceI[] seqs,
135 int position, int number, AlignmentI al)
137 this.description = desc;
138 if (command == Action.CUT || command == Action.PASTE)
140 setEdit(new Edit(command, seqs, position, number, al));
143 performEdit(0, null);
146 public EditCommand(String desc, Action command, String replace,
147 SequenceI[] seqs, int position, int number, AlignmentI al)
149 this.description = desc;
150 if (command == Action.REPLACE)
152 setEdit(new Edit(command, seqs, position, number, al, replace));
155 performEdit(0, null);
159 * Set the list of edits to the specified item (only).
163 protected void setEdit(Edit e)
170 * Add the given edit command to the stored list of commands. If simply
171 * expanding the range of the last command added, then modify it instead of
172 * adding a new command.
176 public void addEdit(Edit e)
178 if (!expandEdit(edits, e))
185 * Returns true if the new edit is incorporated by updating (expanding the
186 * range of) the last edit on the list, else false. We can 'expand' the last
187 * edit if the new one is the same action, on the same sequences, and acts on
188 * a contiguous range. This is the case where a mouse drag generates a series
189 * of contiguous gap insertions or deletions.
195 protected static boolean expandEdit(List<Edit> edits, Edit e)
197 if (edits == null || edits.isEmpty())
201 Edit lastEdit = edits.get(edits.size() - 1);
202 Action action = e.command;
203 if (lastEdit.command != action)
209 * Both commands must act on the same sequences - compare the underlying
210 * dataset sequences, rather than the aligned sequences, which change as
213 if (lastEdit.seqs.length != e.seqs.length)
217 for (int i = 0; i < e.seqs.length; i++)
219 if (lastEdit.seqs[i].getDatasetSequence() != e.seqs[i]
220 .getDatasetSequence())
227 * Check a contiguous edit; either
229 * <li>a new Insert <n> positions to the right of the last <insert n>,
231 * <li>a new Delete <n> gaps which is <n> positions to the left of the last
235 boolean contiguous = (action == Action.INSERT_GAP
236 && e.position == lastEdit.position + lastEdit.number)
237 || (action == Action.DELETE_GAP
238 && e.position + e.number == lastEdit.position);
242 * We are just expanding the range of the last edit. For delete gap, also
243 * moving the start position left.
245 lastEdit.number += e.number;
246 lastEdit.seqs = e.seqs;
247 if (action == Action.DELETE_GAP)
257 * Clear the list of stored edit commands.
260 protected void clearEdits()
266 * Returns the i'th stored Edit command.
271 protected Edit getEdit(int i)
273 if (i >= 0 && i < edits.size())
281 final public String getDescription()
293 * Return the alignment for the first edit (or null if no edit).
297 final public AlignmentI getAlignment()
299 return (edits.isEmpty() ? null : edits.get(0).al);
303 * append a new editCommand Note. this shouldn't be called if the edit is an
304 * operation affects more alignment objects than the one referenced in al (for
305 * example, cut or pasting whole sequences). Use the form with an additional
306 * AlignmentI[] views parameter.
315 final public void appendEdit(Action command, SequenceI[] seqs,
316 int position, int number, AlignmentI al, boolean performEdit)
318 appendEdit(command, seqs, position, number, al, performEdit, null);
322 * append a new edit command with a set of alignment views that may be
333 final public void appendEdit(Action command, SequenceI[] seqs,
334 int position, int number, AlignmentI al, boolean performEdit,
337 Edit edit = new Edit(command, seqs, position, number, al);
338 appendEdit(edit, al, performEdit, views);
342 * Overloaded method that accepts an Edit object with additional parameters.
349 final public void appendEdit(Edit edit, AlignmentI al,
350 boolean performEdit, AlignmentI[] views)
352 if (al.getHeight() == edit.seqs.length)
355 edit.fullAlignmentHeight = true;
362 performEdit(edit, views);
367 * Execute all the edit commands, starting at the given commandIndex
369 * @param commandIndex
372 public final void performEdit(int commandIndex, AlignmentI[] views)
374 ListIterator<Edit> iterator = edits.listIterator(commandIndex);
375 while (iterator.hasNext())
377 Edit edit = iterator.next();
378 performEdit(edit, views);
383 * Execute one edit command in all the specified alignment views
388 protected static void performEdit(Edit edit, AlignmentI[] views)
390 switch (edit.command)
408 // TODO:add deleteNuc for UNDO
410 // insertNuc(edits[e]);
418 final public void doCommand(AlignmentI[] views)
420 performEdit(0, views);
424 * Undo the stored list of commands, in reverse order.
427 final public void undoCommand(AlignmentI[] views)
429 ListIterator<Edit> iterator = edits.listIterator(edits.size());
430 while (iterator.hasPrevious())
432 Edit e = iterator.previous();
460 * Insert gap(s) in sequences as specified by the command, and adjust
465 final private static void insertGap(Edit command)
468 for (int s = 0; s < command.seqs.length; s++)
470 command.seqs[s].insertCharAt(command.position, command.number,
472 // System.out.println("pos: "+command.position+" number:
473 // "+command.number);
476 adjustAnnotations(command, true, false, null);
480 // final void insertNuc(Edit command)
483 // for (int s = 0; s < command.seqs.length; s++)
485 // System.out.println("pos: "+command.position+" number: "+command.number);
486 // command.seqs[s].insertCharAt(command.position, command.number,'A');
489 // adjustAnnotations(command, true, false, null);
493 * Delete gap(s) in sequences as specified by the command, and adjust
498 final static private void deleteGap(Edit command)
500 for (int s = 0; s < command.seqs.length; s++)
502 command.seqs[s].deleteChars(command.position,
503 command.position + command.number);
506 adjustAnnotations(command, false, false, null);
510 * Carry out a Cut action. The cut characters are saved in case Undo is
516 static void cut(Edit command, AlignmentI[] views)
518 boolean seqDeleted = false;
519 command.string = new char[command.seqs.length][];
521 for (int i = 0; i < command.seqs.length; i++)
523 final SequenceI sequence = command.seqs[i];
524 if (sequence.getLength() > command.position)
526 command.string[i] = sequence.getSequence(command.position,
527 command.position + command.number);
528 SequenceI oldds = sequence.getDatasetSequence();
529 if (command.oldds != null && command.oldds[i] != null)
531 // we are redoing an undone cut.
532 sequence.setDatasetSequence(null);
534 Range cutPositions = sequence.findPositions(command.position + 1,
535 command.position + command.number);
536 boolean cutIsInternal = cutPositions != null
537 && sequence.getStart() != cutPositions
538 .getBegin() && sequence.getEnd() != cutPositions.getEnd();
539 sequence.deleteChars(command.position, command.position
542 if (command.oldds != null && command.oldds[i] != null)
544 // Undoing previous Paste - so
545 // oldds entry contains the cut dataset sequence,
546 // with sequence features in expected place.
547 sequence.setDatasetSequence(command.oldds[i]);
548 command.oldds[i] = oldds;
553 // We always keep track of the dataset sequence so we can safely
554 // restore it during the Undo
555 if (command.oldds == null)
557 command.oldds = new SequenceI[command.seqs.length];
559 command.oldds[i] = oldds;
561 // do we need to edit sequence features for new sequence ?
562 if (oldds != sequence.getDatasetSequence()
564 && sequence.getFeatures().hasFeatures()))
566 if (cutPositions != null)
568 cutFeatures(command, sequence, cutPositions.getBegin(),
569 cutPositions.getEnd(), cutIsInternal);
575 if (sequence.getLength() < 1)
577 command.al.deleteSequence(sequence);
582 adjustAnnotations(command, false, seqDeleted, views);
586 * Perform the given Paste command. This may be to add cut or copied sequences
587 * to an alignment, or to undo a 'Cut' action on a region of the alignment.
592 static void paste(Edit command, AlignmentI[] views)
594 boolean seqWasDeleted = false;
596 for (int i = 0; i < command.seqs.length; i++)
598 boolean newDSNeeded = false;
599 boolean newDSWasNeeded = command.oldds != null
600 && command.oldds[i] != null;
601 SequenceI sequence = command.seqs[i];
602 if (sequence.getLength() < 1)
605 * sequence was deleted; re-add it to the alignment
607 if (command.alIndex[i] < command.al.getHeight())
609 List<SequenceI> sequences;
610 synchronized (sequences = command.al.getSequences())
612 if (!(command.alIndex[i] < 0))
614 sequences.add(command.alIndex[i], sequence);
620 command.al.addSequence(sequence);
622 seqWasDeleted = true;
624 int newStart = sequence.getStart();
625 int newEnd = sequence.getEnd();
627 StringBuilder tmp = new StringBuilder();
628 tmp.append(sequence.getSequence());
629 // Undo of a delete does not replace original dataset sequence on to
630 // alignment sequence.
635 if (command.string != null && command.string[i] != null)
637 if (command.position >= tmp.length())
639 // This occurs if padding is on, and residues
640 // are removed from end of alignment
641 int len = command.position - tmp.length();
644 tmp.append(command.gapChar);
648 tmp.insert(command.position, command.string[i]);
649 for (int s = 0; s < command.string[i].length; s++)
651 if (!Comparison.isGap(command.string[i][s]))
657 start = sequence.findPosition(command.position);
659 // .findPosition(command.position + command.number);
661 if (sequence.getStart() == start)
671 command.string[i] = null;
674 sequence.setSequence(tmp.toString());
675 sequence.setStart(newStart);
676 sequence.setEnd(newEnd);
679 * command and Undo share the same dataset sequence if cut was
680 * at start or end of sequence
682 boolean sameDatasetSequence = false;
685 if (sequence.getDatasetSequence() != null)
690 ds = command.oldds[i];
694 // make a new DS sequence
695 // use new ds mechanism here
696 String ungapped = AlignSeq.extractGaps(Comparison.GapChars,
697 sequence.getSequenceAsString());
698 ds = new Sequence(sequence.getName(), ungapped,
699 sequence.getStart(), sequence.getEnd());
700 ds.setDescription(sequence.getDescription());
702 if (command.oldds == null)
704 command.oldds = new SequenceI[command.seqs.length];
706 command.oldds[i] = sequence.getDatasetSequence();
707 sameDatasetSequence = ds == sequence.getDatasetSequence();
708 ds.setSequenceFeatures(sequence.getSequenceFeatures());
709 sequence.setDatasetSequence(ds);
711 undoCutFeatures(command, command.seqs[i], start, length,
712 sameDatasetSequence);
715 adjustAnnotations(command, true, seqWasDeleted, views);
717 command.string = null;
720 static void replace(Edit command)
724 int start = command.position;
725 int end = command.number;
726 // TODO TUTORIAL - Fix for replacement with different length of sequence (or
728 // TODO Jalview 2.4 bugfix change to an aggregate command - original
729 // sequence string is cut, new string is pasted in.
730 command.number = start + command.string[0].length;
731 for (int i = 0; i < command.seqs.length; i++)
733 boolean newDSWasNeeded = command.oldds != null
734 && command.oldds[i] != null;
735 boolean newStartEndWasNeeded = command.oldStartEnd!=null && command.oldStartEnd[i]!=null;
738 * cut addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT,
739 * cut, sg.getStartRes(), sg.getEndRes()-sg.getStartRes()+1,
740 * viewport.alignment));
744 * then addHistoryItem(new EditCommand( "Add sequences",
745 * EditCommand.PASTE, sequences, 0, alignment.getWidth(), alignment) );
749 Range beforeEditedPositions = command.seqs[i].findPositions(1, start);
750 Range afterEditedPositions = command.seqs[i]
751 .findPositions(start + end + 1, command.seqs[i].getLength());
753 oldstring = command.seqs[i].getSequenceAsString();
754 tmp = new StringBuffer(oldstring.substring(0, start));
755 tmp.append(command.string[i]);
756 String nogaprep = jalview.analysis.AlignSeq.extractGaps(
757 jalview.util.Comparison.GapChars,
758 new String(command.string[i]));
759 int ipos = command.seqs[i].findPosition(start)
760 - command.seqs[i].getStart();
761 tmp.append(oldstring.substring(end));
762 command.seqs[i].setSequence(tmp.toString());
763 command.string[i] = oldstring.substring(start, end).toCharArray();
764 String nogapold = AlignSeq.extractGaps(Comparison.GapChars,
765 new String(command.string[i]));
767 if (!nogaprep.toLowerCase().equals(nogapold.toLowerCase()))
769 // probably need a new dataset sequence
772 // then just switch the dataset sequence
773 SequenceI oldds = command.seqs[i].getDatasetSequence();
774 command.seqs[i].setDatasetSequence(command.oldds[i]);
775 command.oldds[i] = oldds;
778 if (newStartEndWasNeeded)
780 Range newStart = command.oldStartEnd[i];
781 command.oldStartEnd[i] = new Range(command.seqs[i].getStart(),
782 command.seqs[i].getEnd());
783 command.seqs[i].setStart(newStart.getBegin());
784 command.seqs[i].setEnd(newStart.getEnd());
788 // first edit the original dataset sequence string
789 SequenceI oldds = command.seqs[i].getDatasetSequence();
790 String fullseq, osp = oldds.getSequenceAsString();
792 fullseq = osp.substring(0, ipos) + nogaprep
793 + osp.substring(ipos + nogaprep.length());
795 // and check if new sequence data is different..
796 if (!fullseq.equalsIgnoreCase(osp))
798 // old ds and edited ds are different, so
799 // create the new dataset sequence
800 SequenceI newds = new Sequence(oldds);
801 newds.setSequence(fullseq.toUpperCase());
803 if (command.oldds == null)
805 command.oldds = new SequenceI[command.seqs.length];
807 command.oldds[i] = command.seqs[i].getDatasetSequence();
808 // TODO: JAL-1131 ensure newly created dataset sequence is added to
810 // dataset sequences associated with the alignment.
811 // TODO: JAL-1131 fix up any annotation associated with new dataset
812 // sequence to ensure that original sequence/annotation
815 command.seqs[i].setDatasetSequence(newds);
819 if (command.oldStartEnd == null)
821 command.oldStartEnd = new Range[command.seqs.length];
823 command.oldStartEnd[i] = new Range(command.seqs[i].getStart(),
824 command.seqs[i].getEnd());
825 if (beforeEditedPositions != null
826 && afterEditedPositions == null)
828 // modification at end
829 command.seqs[i].setEnd(
830 beforeEditedPositions.getEnd() + nogaprep.length());
832 else if (afterEditedPositions != null
833 && beforeEditedPositions == null)
835 // modification at start
836 command.seqs[i].setStart(
837 afterEditedPositions.getBegin() - nogaprep.length());
841 // edit covered both start and end. Here we can only guess the
844 String nogapalseq = jalview.analysis.AlignSeq.extractGaps(
845 jalview.util.Comparison.GapChars,
846 command.seqs[i].getSequenceAsString().toUpperCase());
847 int newStart = command.seqs[i].getDatasetSequence()
848 .getSequenceAsString().indexOf(nogapalseq);
852 "Implementation Error: could not locate start/end "
853 + "in dataset sequence after an edit of the sequence string");
855 int newEnd = newStart + nogapalseq.length() - 1;
856 command.seqs[i].setStart(newStart);
857 command.seqs[i].setEnd(newEnd);
867 final static void adjustAnnotations(Edit command, boolean insert,
868 boolean modifyVisibility, AlignmentI[] views)
870 AlignmentAnnotation[] annotations = null;
872 if (modifyVisibility && !insert)
874 // only occurs if a sequence was added or deleted.
875 command.deletedAnnotationRows = new Hashtable<SequenceI, AlignmentAnnotation[]>();
877 if (command.fullAlignmentHeight)
879 annotations = command.al.getAlignmentAnnotation();
884 AlignmentAnnotation[] tmp;
885 for (int s = 0; s < command.seqs.length; s++)
887 command.seqs[s].sequenceChanged();
889 if (modifyVisibility)
891 // Rows are only removed or added to sequence object.
895 tmp = command.seqs[s].getAnnotation();
898 int alen = tmp.length;
899 for (int aa = 0; aa < tmp.length; aa++)
901 if (!command.al.deleteAnnotation(tmp[aa]))
903 // strip out annotation not in the current al (will be put
904 // back on insert in all views)
909 command.seqs[s].setAlignmentAnnotation(null);
910 if (alen != tmp.length)
912 // save the non-null annotation references only
913 AlignmentAnnotation[] saved = new AlignmentAnnotation[alen];
914 for (int aa = 0, aapos = 0; aa < tmp.length; aa++)
918 saved[aapos++] = tmp[aa];
923 command.deletedAnnotationRows.put(command.seqs[s], saved);
924 // and then remove any annotation in the other views
925 for (int alview = 0; views != null
926 && alview < views.length; alview++)
928 if (views[alview] != command.al)
930 AlignmentAnnotation[] toremove = views[alview]
931 .getAlignmentAnnotation();
932 if (toremove == null || toremove.length == 0)
936 // remove any alignment annotation on this sequence that's
937 // on that alignment view.
938 for (int aa = 0; aa < toremove.length; aa++)
940 if (toremove[aa].sequenceRef == command.seqs[s])
942 views[alview].deleteAnnotation(toremove[aa]);
950 // save all the annotation
951 command.deletedAnnotationRows.put(command.seqs[s], tmp);
958 if (command.deletedAnnotationRows != null
959 && command.deletedAnnotationRows
960 .containsKey(command.seqs[s]))
962 AlignmentAnnotation[] revealed = command.deletedAnnotationRows
963 .get(command.seqs[s]);
964 command.seqs[s].setAlignmentAnnotation(revealed);
965 if (revealed != null)
967 for (int aa = 0; aa < revealed.length; aa++)
969 // iterate through al adding original annotation
970 command.al.addAnnotation(revealed[aa]);
972 for (int aa = 0; aa < revealed.length; aa++)
974 command.al.setAnnotationIndex(revealed[aa], aa);
976 // and then duplicate added annotation on every other alignment
978 for (int vnum = 0; views != null && vnum < views.length; vnum++)
980 if (views[vnum] != command.al)
982 int avwidth = views[vnum].getWidth() + 1;
983 // duplicate in this view
984 for (int a = 0; a < revealed.length; a++)
986 AlignmentAnnotation newann = new AlignmentAnnotation(
988 command.seqs[s].addAlignmentAnnotation(newann);
989 newann.padAnnotation(avwidth);
990 views[vnum].addAnnotation(newann);
991 views[vnum].setAnnotationIndex(newann, a);
1001 if (command.seqs[s].getAnnotation() == null)
1008 annotations = command.seqs[s].getAnnotation();
1012 tmp = new AlignmentAnnotation[aSize
1013 + command.seqs[s].getAnnotation().length];
1015 System.arraycopy(annotations, 0, tmp, 0, aSize);
1017 System.arraycopy(command.seqs[s].getAnnotation(), 0, tmp, aSize,
1018 command.seqs[s].getAnnotation().length);
1022 aSize = annotations.length;
1026 if (annotations == null)
1033 command.deletedAnnotations = new Hashtable<String, Annotation[]>();
1038 for (int a = 0; a < annotations.length; a++)
1040 if (annotations[a].autoCalculated
1041 || annotations[a].annotations == null)
1048 aSize = annotations[a].annotations.length;
1051 temp = new Annotation[aSize + command.number];
1052 if (annotations[a].padGaps)
1054 for (int aa = 0; aa < temp.length; aa++)
1056 temp[aa] = new Annotation(command.gapChar + "", null, ' ', 0);
1062 if (command.position < aSize)
1064 if (command.position + command.number >= aSize)
1070 tSize = aSize - command.number;
1082 temp = new Annotation[tSize];
1087 if (command.position < annotations[a].annotations.length)
1089 System.arraycopy(annotations[a].annotations, 0, temp, 0,
1092 if (command.deletedAnnotations != null
1093 && command.deletedAnnotations
1094 .containsKey(annotations[a].annotationId))
1096 Annotation[] restore = command.deletedAnnotations
1097 .get(annotations[a].annotationId);
1099 System.arraycopy(restore, 0, temp, command.position,
1104 System.arraycopy(annotations[a].annotations, command.position,
1105 temp, command.position + command.number,
1106 aSize - command.position);
1110 if (command.deletedAnnotations != null
1111 && command.deletedAnnotations
1112 .containsKey(annotations[a].annotationId))
1114 Annotation[] restore = command.deletedAnnotations
1115 .get(annotations[a].annotationId);
1117 temp = new Annotation[annotations[a].annotations.length
1119 System.arraycopy(annotations[a].annotations, 0, temp, 0,
1120 annotations[a].annotations.length);
1121 System.arraycopy(restore, 0, temp,
1122 annotations[a].annotations.length, restore.length);
1126 temp = annotations[a].annotations;
1132 if (tSize != aSize || command.position < 2)
1134 int copylen = Math.min(command.position,
1135 annotations[a].annotations.length);
1138 System.arraycopy(annotations[a].annotations, 0, temp, 0,
1139 copylen); // command.position);
1142 Annotation[] deleted = new Annotation[command.number];
1143 if (copylen >= command.position)
1145 copylen = Math.min(command.number,
1146 annotations[a].annotations.length - command.position);
1149 System.arraycopy(annotations[a].annotations, command.position,
1150 deleted, 0, copylen); // command.number);
1154 command.deletedAnnotations.put(annotations[a].annotationId,
1156 if (annotations[a].annotations.length > command.position
1159 System.arraycopy(annotations[a].annotations,
1160 command.position + command.number, temp,
1161 command.position, annotations[a].annotations.length
1162 - command.position - command.number); // aSize
1167 int dSize = aSize - command.position;
1171 Annotation[] deleted = new Annotation[command.number];
1172 System.arraycopy(annotations[a].annotations, command.position,
1175 command.deletedAnnotations.put(annotations[a].annotationId,
1178 tSize = Math.min(annotations[a].annotations.length,
1180 temp = new Annotation[tSize];
1181 System.arraycopy(annotations[a].annotations, 0, temp, 0, tSize);
1185 temp = annotations[a].annotations;
1190 annotations[a].annotations = temp;
1195 * Restores features to the state before a Cut.
1197 * <li>re-add any features deleted by the cut</li>
1198 * <li>remove any truncated features created by the cut</li>
1199 * <li>shift right any features to the right of the cut</li>
1205 * the sequence the Cut applied to
1207 * the start residue position of the cut
1209 * the number of residues cut
1210 * @param sameDatasetSequence
1211 * true if dataset sequence and frame of reference were left
1212 * unchanged by the Cut
1214 final static void undoCutFeatures(Edit command, SequenceI seq,
1215 final int start, final int length, boolean sameDatasetSequence)
1217 SequenceI sequence = seq.getDatasetSequence();
1218 if (sequence == null)
1224 * shift right features that lie to the right of the restored cut (but not
1225 * if dataset sequence unchanged - so coordinates were changed by Cut)
1227 if (!sameDatasetSequence)
1230 * shift right all features right of and not
1231 * contiguous with the cut position
1233 seq.getFeatures().shiftFeatures(start + 1, length);
1236 * shift right any features that start at the cut position,
1237 * unless they were truncated
1239 List<SequenceFeature> sfs = seq.getFeatures().findFeatures(start,
1241 for (SequenceFeature sf : sfs)
1243 if (sf.getBegin() == start)
1245 if (!command.truncatedFeatures.containsKey(seq)
1246 || !command.truncatedFeatures.get(seq).contains(sf))
1249 * feature was shifted left to cut position (not truncated),
1250 * so shift it back right
1252 SequenceFeature shifted = new SequenceFeature(sf, sf.getBegin()
1253 + length, sf.getEnd() + length, sf.getFeatureGroup(),
1255 seq.addSequenceFeature(shifted);
1256 seq.deleteFeature(sf);
1263 * restore any features that were deleted or truncated
1265 if (command.deletedFeatures != null
1266 && command.deletedFeatures.containsKey(seq))
1268 for (SequenceFeature deleted : command.deletedFeatures.get(seq))
1270 sequence.addSequenceFeature(deleted);
1275 * delete any truncated features
1277 if (command.truncatedFeatures != null
1278 && command.truncatedFeatures.containsKey(seq))
1280 for (SequenceFeature amended : command.truncatedFeatures.get(seq))
1282 sequence.deleteFeature(amended);
1288 * Returns the list of edit commands wrapped by this object.
1292 public List<Edit> getEdits()
1298 * Returns a map whose keys are the dataset sequences, and values their
1299 * aligned sequences before the command edit list was applied. The aligned
1300 * sequences are copies, which may be updated without affecting the originals.
1302 * The command holds references to the aligned sequences (after editing). If
1303 * the command is an 'undo',then the prior state is simply the aligned state.
1304 * Otherwise, we have to derive the prior state by working backwards through
1305 * the edit list to infer the aligned sequences before editing.
1307 * Note: an alternative solution would be to cache the 'before' state of each
1308 * edit, but this would be expensive in space in the common case that the
1309 * original is never needed (edits are not mirrored).
1312 * @throws IllegalStateException
1313 * on detecting an edit command of a type that can't be unwound
1315 public Map<SequenceI, SequenceI> priorState(boolean forUndo)
1317 Map<SequenceI, SequenceI> result = new HashMap<SequenceI, SequenceI>();
1318 if (getEdits() == null)
1324 for (Edit e : getEdits())
1326 for (SequenceI seq : e.getSequences())
1328 SequenceI ds = seq.getDatasetSequence();
1329 // SequenceI preEdit = result.get(ds);
1330 if (!result.containsKey(ds))
1333 * copy sequence including start/end (but don't use copy constructor
1334 * as we don't need annotations)
1336 SequenceI preEdit = new Sequence("", seq.getSequenceAsString(),
1337 seq.getStart(), seq.getEnd());
1338 preEdit.setDatasetSequence(ds);
1339 result.put(ds, preEdit);
1347 * Work backwards through the edit list, deriving the sequences before each
1348 * was applied. The final result is the sequence set before any edits.
1350 Iterator<Edit> editList = new ReverseListIterator<Edit>(getEdits());
1351 while (editList.hasNext())
1353 Edit oldEdit = editList.next();
1354 Action action = oldEdit.getAction();
1355 int position = oldEdit.getPosition();
1356 int number = oldEdit.getNumber();
1357 final char gap = oldEdit.getGapCharacter();
1358 for (SequenceI seq : oldEdit.getSequences())
1360 SequenceI ds = seq.getDatasetSequence();
1361 SequenceI preEdit = result.get(ds);
1362 if (preEdit == null)
1364 preEdit = new Sequence("", seq.getSequenceAsString(),
1365 seq.getStart(), seq.getEnd());
1366 preEdit.setDatasetSequence(ds);
1367 result.put(ds, preEdit);
1370 * 'Undo' this edit action on the sequence (updating the value in the
1375 if (action == Action.DELETE_GAP)
1377 preEdit.setSequence(new String(StringUtils.insertCharAt(
1378 preEdit.getSequence(), position, number, gap)));
1380 else if (action == Action.INSERT_GAP)
1382 preEdit.setSequence(new String(StringUtils.deleteChars(
1383 preEdit.getSequence(), position, position + number)));
1387 System.err.println("Can't undo edit action " + action);
1388 // throw new IllegalStateException("Can't undo edit action " +
1399 public SequenceI[] oldds;
1402 * start and end of sequence prior to edit
1404 public Range[] oldStartEnd;
1406 boolean fullAlignmentHeight = false;
1408 Map<SequenceI, AlignmentAnnotation[]> deletedAnnotationRows;
1410 Map<String, Annotation[]> deletedAnnotations;
1413 * features deleted by the cut (re-add on Undo)
1414 * (including the original of any shortened features)
1416 Map<SequenceI, List<SequenceFeature>> deletedFeatures;
1419 * shortened features added by the cut (delete on Undo)
1421 Map<SequenceI, List<SequenceFeature>> truncatedFeatures;
1433 int position, number;
1437 public Edit(Action cmd, SequenceI[] sqs, int pos, int count,
1442 this.position = pos;
1443 this.number = count;
1447 Edit(Action cmd, SequenceI[] sqs, int pos, int count,
1450 this(cmd, sqs, pos, count, align.getGapCharacter());
1454 alIndex = new int[sqs.length];
1455 for (int i = 0; i < sqs.length; i++)
1457 alIndex[i] = align.findIndex(sqs[i]);
1460 fullAlignmentHeight = (align.getHeight() == sqs.length);
1463 Edit(Action cmd, SequenceI[] sqs, int pos, int count,
1464 AlignmentI align, String replace)
1466 this(cmd, sqs, pos, count, align);
1468 string = new char[sqs.length][];
1469 for (int i = 0; i < sqs.length; i++)
1471 string[i] = replace.toCharArray();
1475 public SequenceI[] getSequences()
1480 public int getPosition()
1485 public Action getAction()
1490 public int getNumber()
1495 public char getGapCharacter()
1502 * Returns an iterator over the list of edit commands which traverses the list
1503 * either forwards or backwards.
1508 public Iterator<Edit> getEditIterator(boolean forwards)
1512 return getEdits().iterator();
1516 return new ReverseListIterator<Edit>(getEdits());
1521 * Adjusts features for Cut, and saves details of changes made to allow Undo
1523 * <li>features left of the cut are unchanged</li>
1524 * <li>features right of the cut are shifted left</li>
1525 * <li>features internal to the cut region are deleted</li>
1526 * <li>features that overlap or span the cut are shortened</li>
1527 * <li>the originals of any deleted or shorted features are saved, to re-add
1529 * <li>any added (shortened) features are saved, to delete on Undo</li>
1534 * @param fromPosition
1536 * @param cutIsInternal
1538 protected static void cutFeatures(Edit command, SequenceI seq,
1539 int fromPosition, int toPosition, boolean cutIsInternal)
1541 /* if the cut is at start or end of sequence
1542 * then we don't modify the seuqence feature store
1548 List<SequenceFeature> added = new ArrayList<>();
1549 List<SequenceFeature> removed = new ArrayList<>();
1551 SequenceFeaturesI featureStore = seq.getFeatures();
1552 if (toPosition < fromPosition || featureStore == null)
1557 int cutStartPos = fromPosition;
1558 int cutEndPos = toPosition;
1559 int cutWidth = cutEndPos - cutStartPos + 1;
1561 synchronized (featureStore)
1564 * get features that overlap the cut region
1566 List<SequenceFeature> toAmend = featureStore.findFeatures(
1567 cutStartPos, cutEndPos);
1570 * add any contact features that span the cut region
1571 * (not returned by findFeatures)
1573 for (SequenceFeature contact : featureStore.getContactFeatures())
1575 if (contact.getBegin() < cutStartPos
1576 && contact.getEnd() > cutEndPos)
1578 toAmend.add(contact);
1583 * adjust start-end of overlapping features;
1584 * delete features enclosed by the cut;
1585 * delete partially overlapping contact features
1587 for (SequenceFeature sf : toAmend)
1589 int sfBegin = sf.getBegin();
1590 int sfEnd = sf.getEnd();
1591 int newBegin = sfBegin;
1593 boolean toDelete = false;
1594 boolean follows = false;
1596 if (sfBegin >= cutStartPos && sfEnd <= cutEndPos)
1599 * feature lies within cut region - delete it
1603 else if (sfBegin < cutStartPos && sfEnd > cutEndPos)
1606 * feature spans cut region - left-shift the end
1610 else if (sfEnd <= cutEndPos)
1613 * feature overlaps left of cut region - truncate right
1615 newEnd = cutStartPos - 1;
1616 if (sf.isContactFeature())
1621 else if (sfBegin >= cutStartPos)
1624 * remaining case - feature overlaps right
1625 * truncate left, adjust end of feature
1627 newBegin = cutIsInternal ? cutStartPos : cutEndPos + 1;
1628 newEnd = newBegin + sfEnd - cutEndPos - 1;
1629 if (sf.isContactFeature())
1635 seq.deleteFeature(sf);
1642 SequenceFeature copy = new SequenceFeature(sf, newBegin, newEnd,
1643 sf.getFeatureGroup(), sf.getScore());
1644 seq.addSequenceFeature(copy);
1653 * and left shift any features lying to the right of the cut region
1656 featureStore.shiftFeatures(cutEndPos + 1, -cutWidth);
1660 * save deleted and amended features, so that Undo can
1661 * re-add or delete them respectively
1663 if (command.deletedFeatures == null)
1665 command.deletedFeatures = new HashMap<>();
1667 if (command.truncatedFeatures == null)
1669 command.truncatedFeatures = new HashMap<>();
1671 command.deletedFeatures.put(seq, removed);
1672 command.truncatedFeatures.put(seq, added);