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;
737 * cut addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT,
738 * cut, sg.getStartRes(), sg.getEndRes()-sg.getStartRes()+1,
739 * viewport.alignment));
743 * then addHistoryItem(new EditCommand( "Add sequences",
744 * EditCommand.PASTE, sequences, 0, alignment.getWidth(), alignment) );
747 oldstring = command.seqs[i].getSequenceAsString();
748 tmp = new StringBuffer(oldstring.substring(0, start));
749 tmp.append(command.string[i]);
750 String nogaprep = jalview.analysis.AlignSeq.extractGaps(
751 jalview.util.Comparison.GapChars,
752 new String(command.string[i]));
753 int ipos = command.seqs[i].findPosition(start)
754 - command.seqs[i].getStart();
755 tmp.append(oldstring.substring(end));
756 command.seqs[i].setSequence(tmp.toString());
757 command.string[i] = oldstring.substring(start, end).toCharArray();
758 String nogapold = AlignSeq.extractGaps(Comparison.GapChars,
759 new String(command.string[i]));
760 if (!nogaprep.toLowerCase().equals(nogapold.toLowerCase()))
764 SequenceI oldds = command.seqs[i].getDatasetSequence();
765 command.seqs[i].setDatasetSequence(command.oldds[i]);
766 command.oldds[i] = oldds;
770 if (command.oldds == null)
772 command.oldds = new SequenceI[command.seqs.length];
774 command.oldds[i] = command.seqs[i].getDatasetSequence();
775 SequenceI newds = new Sequence(
776 command.seqs[i].getDatasetSequence());
777 String fullseq, osp = newds.getSequenceAsString();
778 fullseq = osp.substring(0, ipos) + nogaprep
779 + osp.substring(ipos + nogaprep.length());
780 newds.setSequence(fullseq.toUpperCase());
781 // TODO: JAL-1131 ensure newly created dataset sequence is added to
783 // dataset sequences associated with the alignment.
784 // TODO: JAL-1131 fix up any annotation associated with new dataset
785 // sequence to ensure that original sequence/annotation relationships
787 command.seqs[i].setDatasetSequence(newds);
796 final static void adjustAnnotations(Edit command, boolean insert,
797 boolean modifyVisibility, AlignmentI[] views)
799 AlignmentAnnotation[] annotations = null;
801 if (modifyVisibility && !insert)
803 // only occurs if a sequence was added or deleted.
804 command.deletedAnnotationRows = new Hashtable<SequenceI, AlignmentAnnotation[]>();
806 if (command.fullAlignmentHeight)
808 annotations = command.al.getAlignmentAnnotation();
813 AlignmentAnnotation[] tmp;
814 for (int s = 0; s < command.seqs.length; s++)
816 command.seqs[s].sequenceChanged();
818 if (modifyVisibility)
820 // Rows are only removed or added to sequence object.
824 tmp = command.seqs[s].getAnnotation();
827 int alen = tmp.length;
828 for (int aa = 0; aa < tmp.length; aa++)
830 if (!command.al.deleteAnnotation(tmp[aa]))
832 // strip out annotation not in the current al (will be put
833 // back on insert in all views)
838 command.seqs[s].setAlignmentAnnotation(null);
839 if (alen != tmp.length)
841 // save the non-null annotation references only
842 AlignmentAnnotation[] saved = new AlignmentAnnotation[alen];
843 for (int aa = 0, aapos = 0; aa < tmp.length; aa++)
847 saved[aapos++] = tmp[aa];
852 command.deletedAnnotationRows.put(command.seqs[s], saved);
853 // and then remove any annotation in the other views
854 for (int alview = 0; views != null
855 && alview < views.length; alview++)
857 if (views[alview] != command.al)
859 AlignmentAnnotation[] toremove = views[alview]
860 .getAlignmentAnnotation();
861 if (toremove == null || toremove.length == 0)
865 // remove any alignment annotation on this sequence that's
866 // on that alignment view.
867 for (int aa = 0; aa < toremove.length; aa++)
869 if (toremove[aa].sequenceRef == command.seqs[s])
871 views[alview].deleteAnnotation(toremove[aa]);
879 // save all the annotation
880 command.deletedAnnotationRows.put(command.seqs[s], tmp);
887 if (command.deletedAnnotationRows != null
888 && command.deletedAnnotationRows
889 .containsKey(command.seqs[s]))
891 AlignmentAnnotation[] revealed = command.deletedAnnotationRows
892 .get(command.seqs[s]);
893 command.seqs[s].setAlignmentAnnotation(revealed);
894 if (revealed != null)
896 for (int aa = 0; aa < revealed.length; aa++)
898 // iterate through al adding original annotation
899 command.al.addAnnotation(revealed[aa]);
901 for (int aa = 0; aa < revealed.length; aa++)
903 command.al.setAnnotationIndex(revealed[aa], aa);
905 // and then duplicate added annotation on every other alignment
907 for (int vnum = 0; views != null && vnum < views.length; vnum++)
909 if (views[vnum] != command.al)
911 int avwidth = views[vnum].getWidth() + 1;
912 // duplicate in this view
913 for (int a = 0; a < revealed.length; a++)
915 AlignmentAnnotation newann = new AlignmentAnnotation(
917 command.seqs[s].addAlignmentAnnotation(newann);
918 newann.padAnnotation(avwidth);
919 views[vnum].addAnnotation(newann);
920 views[vnum].setAnnotationIndex(newann, a);
930 if (command.seqs[s].getAnnotation() == null)
937 annotations = command.seqs[s].getAnnotation();
941 tmp = new AlignmentAnnotation[aSize
942 + command.seqs[s].getAnnotation().length];
944 System.arraycopy(annotations, 0, tmp, 0, aSize);
946 System.arraycopy(command.seqs[s].getAnnotation(), 0, tmp, aSize,
947 command.seqs[s].getAnnotation().length);
951 aSize = annotations.length;
955 if (annotations == null)
962 command.deletedAnnotations = new Hashtable<String, Annotation[]>();
967 for (int a = 0; a < annotations.length; a++)
969 if (annotations[a].autoCalculated
970 || annotations[a].annotations == null)
977 aSize = annotations[a].annotations.length;
980 temp = new Annotation[aSize + command.number];
981 if (annotations[a].padGaps)
983 for (int aa = 0; aa < temp.length; aa++)
985 temp[aa] = new Annotation(command.gapChar + "", null, ' ', 0);
991 if (command.position < aSize)
993 if (command.position + command.number >= aSize)
999 tSize = aSize - command.number;
1011 temp = new Annotation[tSize];
1016 if (command.position < annotations[a].annotations.length)
1018 System.arraycopy(annotations[a].annotations, 0, temp, 0,
1021 if (command.deletedAnnotations != null
1022 && command.deletedAnnotations
1023 .containsKey(annotations[a].annotationId))
1025 Annotation[] restore = command.deletedAnnotations
1026 .get(annotations[a].annotationId);
1028 System.arraycopy(restore, 0, temp, command.position,
1033 System.arraycopy(annotations[a].annotations, command.position,
1034 temp, command.position + command.number,
1035 aSize - command.position);
1039 if (command.deletedAnnotations != null
1040 && command.deletedAnnotations
1041 .containsKey(annotations[a].annotationId))
1043 Annotation[] restore = command.deletedAnnotations
1044 .get(annotations[a].annotationId);
1046 temp = new Annotation[annotations[a].annotations.length
1048 System.arraycopy(annotations[a].annotations, 0, temp, 0,
1049 annotations[a].annotations.length);
1050 System.arraycopy(restore, 0, temp,
1051 annotations[a].annotations.length, restore.length);
1055 temp = annotations[a].annotations;
1061 if (tSize != aSize || command.position < 2)
1063 int copylen = Math.min(command.position,
1064 annotations[a].annotations.length);
1067 System.arraycopy(annotations[a].annotations, 0, temp, 0,
1068 copylen); // command.position);
1071 Annotation[] deleted = new Annotation[command.number];
1072 if (copylen >= command.position)
1074 copylen = Math.min(command.number,
1075 annotations[a].annotations.length - command.position);
1078 System.arraycopy(annotations[a].annotations, command.position,
1079 deleted, 0, copylen); // command.number);
1083 command.deletedAnnotations.put(annotations[a].annotationId,
1085 if (annotations[a].annotations.length > command.position
1088 System.arraycopy(annotations[a].annotations,
1089 command.position + command.number, temp,
1090 command.position, annotations[a].annotations.length
1091 - command.position - command.number); // aSize
1096 int dSize = aSize - command.position;
1100 Annotation[] deleted = new Annotation[command.number];
1101 System.arraycopy(annotations[a].annotations, command.position,
1104 command.deletedAnnotations.put(annotations[a].annotationId,
1107 tSize = Math.min(annotations[a].annotations.length,
1109 temp = new Annotation[tSize];
1110 System.arraycopy(annotations[a].annotations, 0, temp, 0, tSize);
1114 temp = annotations[a].annotations;
1119 annotations[a].annotations = temp;
1124 * Restores features to the state before a Cut.
1126 * <li>re-add any features deleted by the cut</li>
1127 * <li>remove any truncated features created by the cut</li>
1128 * <li>shift right any features to the right of the cut</li>
1134 * the sequence the Cut applied to
1136 * the start residue position of the cut
1138 * the number of residues cut
1139 * @param sameDatasetSequence
1140 * true if dataset sequence and frame of reference were left
1141 * unchanged by the Cut
1143 final static void undoCutFeatures(Edit command, SequenceI seq,
1144 final int start, final int length, boolean sameDatasetSequence)
1146 SequenceI sequence = seq.getDatasetSequence();
1147 if (sequence == null)
1153 * shift right features that lie to the right of the restored cut (but not
1154 * if dataset sequence unchanged - so coordinates were changed by Cut)
1156 if (!sameDatasetSequence)
1159 * shift right all features right of and not
1160 * contiguous with the cut position
1162 seq.getFeatures().shiftFeatures(start + 1, length);
1165 * shift right any features that start at the cut position,
1166 * unless they were truncated
1168 List<SequenceFeature> sfs = seq.getFeatures().findFeatures(start,
1170 for (SequenceFeature sf : sfs)
1172 if (sf.getBegin() == start)
1174 if (!command.truncatedFeatures.containsKey(seq)
1175 || !command.truncatedFeatures.get(seq).contains(sf))
1178 * feature was shifted left to cut position (not truncated),
1179 * so shift it back right
1181 SequenceFeature shifted = new SequenceFeature(sf, sf.getBegin()
1182 + length, sf.getEnd() + length, sf.getFeatureGroup(),
1184 seq.addSequenceFeature(shifted);
1185 seq.deleteFeature(sf);
1192 * restore any features that were deleted or truncated
1194 if (command.deletedFeatures != null
1195 && command.deletedFeatures.containsKey(seq))
1197 for (SequenceFeature deleted : command.deletedFeatures.get(seq))
1199 sequence.addSequenceFeature(deleted);
1204 * delete any truncated features
1206 if (command.truncatedFeatures != null
1207 && command.truncatedFeatures.containsKey(seq))
1209 for (SequenceFeature amended : command.truncatedFeatures.get(seq))
1211 sequence.deleteFeature(amended);
1217 * Returns the list of edit commands wrapped by this object.
1221 public List<Edit> getEdits()
1227 * Returns a map whose keys are the dataset sequences, and values their
1228 * aligned sequences before the command edit list was applied. The aligned
1229 * sequences are copies, which may be updated without affecting the originals.
1231 * The command holds references to the aligned sequences (after editing). If
1232 * the command is an 'undo',then the prior state is simply the aligned state.
1233 * Otherwise, we have to derive the prior state by working backwards through
1234 * the edit list to infer the aligned sequences before editing.
1236 * Note: an alternative solution would be to cache the 'before' state of each
1237 * edit, but this would be expensive in space in the common case that the
1238 * original is never needed (edits are not mirrored).
1241 * @throws IllegalStateException
1242 * on detecting an edit command of a type that can't be unwound
1244 public Map<SequenceI, SequenceI> priorState(boolean forUndo)
1246 Map<SequenceI, SequenceI> result = new HashMap<SequenceI, SequenceI>();
1247 if (getEdits() == null)
1253 for (Edit e : getEdits())
1255 for (SequenceI seq : e.getSequences())
1257 SequenceI ds = seq.getDatasetSequence();
1258 // SequenceI preEdit = result.get(ds);
1259 if (!result.containsKey(ds))
1262 * copy sequence including start/end (but don't use copy constructor
1263 * as we don't need annotations)
1265 SequenceI preEdit = new Sequence("", seq.getSequenceAsString(),
1266 seq.getStart(), seq.getEnd());
1267 preEdit.setDatasetSequence(ds);
1268 result.put(ds, preEdit);
1276 * Work backwards through the edit list, deriving the sequences before each
1277 * was applied. The final result is the sequence set before any edits.
1279 Iterator<Edit> editList = new ReverseListIterator<Edit>(getEdits());
1280 while (editList.hasNext())
1282 Edit oldEdit = editList.next();
1283 Action action = oldEdit.getAction();
1284 int position = oldEdit.getPosition();
1285 int number = oldEdit.getNumber();
1286 final char gap = oldEdit.getGapCharacter();
1287 for (SequenceI seq : oldEdit.getSequences())
1289 SequenceI ds = seq.getDatasetSequence();
1290 SequenceI preEdit = result.get(ds);
1291 if (preEdit == null)
1293 preEdit = new Sequence("", seq.getSequenceAsString(),
1294 seq.getStart(), seq.getEnd());
1295 preEdit.setDatasetSequence(ds);
1296 result.put(ds, preEdit);
1299 * 'Undo' this edit action on the sequence (updating the value in the
1304 if (action == Action.DELETE_GAP)
1306 preEdit.setSequence(new String(StringUtils.insertCharAt(
1307 preEdit.getSequence(), position, number, gap)));
1309 else if (action == Action.INSERT_GAP)
1311 preEdit.setSequence(new String(StringUtils.deleteChars(
1312 preEdit.getSequence(), position, position + number)));
1316 System.err.println("Can't undo edit action " + action);
1317 // throw new IllegalStateException("Can't undo edit action " +
1328 public SequenceI[] oldds;
1330 boolean fullAlignmentHeight = false;
1332 Map<SequenceI, AlignmentAnnotation[]> deletedAnnotationRows;
1334 Map<String, Annotation[]> deletedAnnotations;
1337 * features deleted by the cut (re-add on Undo)
1338 * (including the original of any shortened features)
1340 Map<SequenceI, List<SequenceFeature>> deletedFeatures;
1343 * shortened features added by the cut (delete on Undo)
1345 Map<SequenceI, List<SequenceFeature>> truncatedFeatures;
1357 int position, number;
1361 public Edit(Action cmd, SequenceI[] sqs, int pos, int count,
1366 this.position = pos;
1367 this.number = count;
1371 Edit(Action cmd, SequenceI[] sqs, int pos, int count,
1374 this(cmd, sqs, pos, count, align.getGapCharacter());
1378 alIndex = new int[sqs.length];
1379 for (int i = 0; i < sqs.length; i++)
1381 alIndex[i] = align.findIndex(sqs[i]);
1384 fullAlignmentHeight = (align.getHeight() == sqs.length);
1387 Edit(Action cmd, SequenceI[] sqs, int pos, int count,
1388 AlignmentI align, String replace)
1390 this(cmd, sqs, pos, count, align);
1392 string = new char[sqs.length][];
1393 for (int i = 0; i < sqs.length; i++)
1395 string[i] = replace.toCharArray();
1399 public SequenceI[] getSequences()
1404 public int getPosition()
1409 public Action getAction()
1414 public int getNumber()
1419 public char getGapCharacter()
1426 * Returns an iterator over the list of edit commands which traverses the list
1427 * either forwards or backwards.
1432 public Iterator<Edit> getEditIterator(boolean forwards)
1436 return getEdits().iterator();
1440 return new ReverseListIterator<Edit>(getEdits());
1445 * Adjusts features for Cut, and saves details of changes made to allow Undo
1447 * <li>features left of the cut are unchanged</li>
1448 * <li>features right of the cut are shifted left</li>
1449 * <li>features internal to the cut region are deleted</li>
1450 * <li>features that overlap or span the cut are shortened</li>
1451 * <li>the originals of any deleted or shorted features are saved, to re-add
1453 * <li>any added (shortened) features are saved, to delete on Undo</li>
1458 * @param fromPosition
1460 * @param cutIsInternal
1462 protected static void cutFeatures(Edit command, SequenceI seq,
1463 int fromPosition, int toPosition, boolean cutIsInternal)
1465 /* if the cut is at start or end of sequence
1466 * then we don't modify the seuqence feature store
1472 List<SequenceFeature> added = new ArrayList<>();
1473 List<SequenceFeature> removed = new ArrayList<>();
1475 SequenceFeaturesI featureStore = seq.getFeatures();
1476 if (toPosition < fromPosition || featureStore == null)
1481 int cutStartPos = fromPosition;
1482 int cutEndPos = toPosition;
1483 int cutWidth = cutEndPos - cutStartPos + 1;
1485 synchronized (featureStore)
1488 * get features that overlap the cut region
1490 List<SequenceFeature> toAmend = featureStore.findFeatures(
1491 cutStartPos, cutEndPos);
1494 * add any contact features that span the cut region
1495 * (not returned by findFeatures)
1497 for (SequenceFeature contact : featureStore.getContactFeatures())
1499 if (contact.getBegin() < cutStartPos
1500 && contact.getEnd() > cutEndPos)
1502 toAmend.add(contact);
1507 * adjust start-end of overlapping features;
1508 * delete features enclosed by the cut;
1509 * delete partially overlapping contact features
1511 for (SequenceFeature sf : toAmend)
1513 int sfBegin = sf.getBegin();
1514 int sfEnd = sf.getEnd();
1515 int newBegin = sfBegin;
1517 boolean toDelete = false;
1518 boolean follows = false;
1520 if (sfBegin >= cutStartPos && sfEnd <= cutEndPos)
1523 * feature lies within cut region - delete it
1527 else if (sfBegin < cutStartPos && sfEnd > cutEndPos)
1530 * feature spans cut region - left-shift the end
1534 else if (sfEnd <= cutEndPos)
1537 * feature overlaps left of cut region - truncate right
1539 newEnd = cutStartPos - 1;
1540 if (sf.isContactFeature())
1545 else if (sfBegin >= cutStartPos)
1548 * remaining case - feature overlaps right
1549 * truncate left, adjust end of feature
1551 newBegin = cutIsInternal ? cutStartPos : cutEndPos + 1;
1552 newEnd = newBegin + sfEnd - cutEndPos - 1;
1553 if (sf.isContactFeature())
1559 seq.deleteFeature(sf);
1566 SequenceFeature copy = new SequenceFeature(sf, newBegin, newEnd,
1567 sf.getFeatureGroup(), sf.getScore());
1568 seq.addSequenceFeature(copy);
1577 * and left shift any features lying to the right of the cut region
1580 featureStore.shiftFeatures(cutEndPos + 1, -cutWidth);
1584 * save deleted and amended features, so that Undo can
1585 * re-add or delete them respectively
1587 if (command.deletedFeatures == null)
1589 command.deletedFeatures = new HashMap<>();
1591 if (command.truncatedFeatures == null)
1593 command.truncatedFeatures = new HashMap<>();
1595 command.deletedFeatures.put(seq, removed);
1596 command.truncatedFeatures.put(seq, added);