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();
541 * perform the cut; if this results in a new dataset sequence, add
542 * that to the alignment dataset
544 SequenceI ds = sequence.getDatasetSequence();
545 sequence.deleteChars(command.position, command.position
547 SequenceI newDs = sequence.getDatasetSequence();
548 if (newDs != ds && command.al != null
549 && command.al.getDataset() != null
550 && !command.al.getDataset().getSequences().contains(newDs))
552 command.al.getDataset().addSequence(newDs);
555 if (command.oldds != null && command.oldds[i] != null)
557 // Undoing previous Paste - so
558 // oldds entry contains the cut dataset sequence,
559 // with sequence features in expected place.
560 sequence.setDatasetSequence(command.oldds[i]);
561 command.oldds[i] = oldds;
566 // We always keep track of the dataset sequence so we can safely
567 // restore it during the Undo
568 if (command.oldds == null)
570 command.oldds = new SequenceI[command.seqs.length];
572 command.oldds[i] = oldds;// todo not if !cutIsInternal?
574 // do we need to edit sequence features for new sequence ?
575 if (oldds != sequence.getDatasetSequence()
577 && sequence.getFeatures().hasFeatures()))
578 // todo or just test cutIsInternal && cutPositions != null ?
580 if (cutPositions != null)
582 cutFeatures(command, sequence, cutPositions.getBegin(),
583 cutPositions.getEnd(), cutIsInternal);
589 if (sequence.getLength() < 1)
591 command.al.deleteSequence(sequence);
596 adjustAnnotations(command, false, seqDeleted, views);
600 * Perform the given Paste command. This may be to add cut or copied sequences
601 * to an alignment, or to undo a 'Cut' action on a region of the alignment.
606 static void paste(Edit command, AlignmentI[] views)
608 boolean seqWasDeleted = false;
610 for (int i = 0; i < command.seqs.length; i++)
612 boolean newDSNeeded = false;
613 boolean newDSWasNeeded = command.oldds != null
614 && command.oldds[i] != null;
615 SequenceI sequence = command.seqs[i];
616 if (sequence.getLength() < 1)
619 * sequence was deleted; re-add it to the alignment
621 if (command.alIndex[i] < command.al.getHeight())
623 List<SequenceI> sequences;
624 synchronized (sequences = command.al.getSequences())
626 if (!(command.alIndex[i] < 0))
628 sequences.add(command.alIndex[i], sequence);
634 command.al.addSequence(sequence);
636 seqWasDeleted = true;
638 int newStart = sequence.getStart();
639 int newEnd = sequence.getEnd();
641 StringBuilder tmp = new StringBuilder();
642 tmp.append(sequence.getSequence());
643 // Undo of a delete does not replace original dataset sequence on to
644 // alignment sequence.
649 if (command.string != null && command.string[i] != null)
651 if (command.position >= tmp.length())
653 // This occurs if padding is on, and residues
654 // are removed from end of alignment
655 int len = command.position - tmp.length();
658 tmp.append(command.gapChar);
662 tmp.insert(command.position, command.string[i]);
663 for (int s = 0; s < command.string[i].length; s++)
665 if (!Comparison.isGap(command.string[i][s]))
671 start = sequence.findPosition(command.position);
673 // .findPosition(command.position + command.number);
675 if (sequence.getStart() == start)
685 command.string[i] = null;
688 sequence.setSequence(tmp.toString());
689 sequence.setStart(newStart);
690 sequence.setEnd(newEnd);
693 * command and Undo share the same dataset sequence if cut was
694 * at start or end of sequence
696 boolean sameDatasetSequence = false;
699 if (sequence.getDatasetSequence() != null)
704 ds = command.oldds[i];
708 // make a new DS sequence
709 // use new ds mechanism here
710 String ungapped = AlignSeq.extractGaps(Comparison.GapChars,
711 sequence.getSequenceAsString());
712 ds = new Sequence(sequence.getName(), ungapped,
713 sequence.getStart(), sequence.getEnd());
714 ds.setDescription(sequence.getDescription());
716 if (command.oldds == null)
718 command.oldds = new SequenceI[command.seqs.length];
720 command.oldds[i] = sequence.getDatasetSequence();
721 sameDatasetSequence = ds == sequence.getDatasetSequence();
722 ds.setSequenceFeatures(sequence.getSequenceFeatures());
723 sequence.setDatasetSequence(ds);
725 undoCutFeatures(command, command.seqs[i], start, length,
726 sameDatasetSequence);
729 adjustAnnotations(command, true, seqWasDeleted, views);
731 command.string = null;
734 static void replace(Edit command)
738 int start = command.position;
739 int end = command.number;
740 // TODO TUTORIAL - Fix for replacement with different length of sequence (or
742 // TODO Jalview 2.4 bugfix change to an aggregate command - original
743 // sequence string is cut, new string is pasted in.
744 command.number = start + command.string[0].length;
745 for (int i = 0; i < command.seqs.length; i++)
747 boolean newDSWasNeeded = command.oldds != null
748 && command.oldds[i] != null;
749 boolean newStartEndWasNeeded = command.oldStartEnd!=null && command.oldStartEnd[i]!=null;
752 * cut addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT,
753 * cut, sg.getStartRes(), sg.getEndRes()-sg.getStartRes()+1,
754 * viewport.alignment));
758 * then addHistoryItem(new EditCommand( "Add sequences",
759 * EditCommand.PASTE, sequences, 0, alignment.getWidth(), alignment) );
763 Range beforeEditedPositions = command.seqs[i].findPositions(1, start);
764 Range afterEditedPositions = command.seqs[i]
765 .findPositions(start + end + 1, command.seqs[i].getLength());
767 oldstring = command.seqs[i].getSequenceAsString();
768 tmp = new StringBuffer(oldstring.substring(0, start));
769 tmp.append(command.string[i]);
770 String nogaprep = jalview.analysis.AlignSeq.extractGaps(
771 jalview.util.Comparison.GapChars,
772 new String(command.string[i]));
773 int ipos = command.seqs[i].findPosition(start)
774 - command.seqs[i].getStart();
775 if (end < oldstring.length())
777 tmp.append(oldstring.substring(end));
779 command.seqs[i].setSequence(tmp.toString());
780 command.string[i] = oldstring
781 .substring(start, Math.min(end, oldstring.length()))
783 String nogapold = AlignSeq.extractGaps(Comparison.GapChars,
784 new String(command.string[i]));
786 if (!nogaprep.toLowerCase().equals(nogapold.toLowerCase()))
788 // probably need a new dataset sequence
791 // then just switch the dataset sequence
792 SequenceI oldds = command.seqs[i].getDatasetSequence();
793 command.seqs[i].setDatasetSequence(command.oldds[i]);
794 command.oldds[i] = oldds;
797 if (newStartEndWasNeeded)
799 Range newStart = command.oldStartEnd[i];
800 command.oldStartEnd[i] = new Range(command.seqs[i].getStart(),
801 command.seqs[i].getEnd());
802 command.seqs[i].setStart(newStart.getBegin());
803 command.seqs[i].setEnd(newStart.getEnd());
807 // first edit the original dataset sequence string
808 SequenceI oldds = command.seqs[i].getDatasetSequence();
809 String fullseq, osp = oldds.getSequenceAsString();
811 fullseq = osp.substring(0, ipos) + nogaprep
812 + osp.substring(ipos + nogaprep.length());
814 // and check if new sequence data is different..
815 if (!fullseq.equalsIgnoreCase(osp))
817 // old ds and edited ds are different, so
818 // create the new dataset sequence
819 SequenceI newds = new Sequence(oldds);
820 newds.setSequence(fullseq.toUpperCase());
822 if (command.oldds == null)
824 command.oldds = new SequenceI[command.seqs.length];
826 command.oldds[i] = command.seqs[i].getDatasetSequence();
827 // TODO: JAL-1131 ensure newly created dataset sequence is added to
829 // dataset sequences associated with the alignment.
830 // TODO: JAL-1131 fix up any annotation associated with new dataset
831 // sequence to ensure that original sequence/annotation
834 command.seqs[i].setDatasetSequence(newds);
838 if (command.oldStartEnd == null)
840 command.oldStartEnd = new Range[command.seqs.length];
842 command.oldStartEnd[i] = new Range(command.seqs[i].getStart(),
843 command.seqs[i].getEnd());
844 if (beforeEditedPositions != null
845 && afterEditedPositions == null)
847 // modification at end
848 command.seqs[i].setEnd(
849 beforeEditedPositions.getEnd() + nogaprep.length());
851 else if (afterEditedPositions != null
852 && beforeEditedPositions == null)
854 // modification at start
855 command.seqs[i].setStart(
856 afterEditedPositions.getBegin() - nogaprep.length());
860 // edit covered both start and end. Here we can only guess the
863 String nogapalseq = jalview.analysis.AlignSeq.extractGaps(
864 jalview.util.Comparison.GapChars,
865 command.seqs[i].getSequenceAsString().toUpperCase());
866 int newStart = command.seqs[i].getDatasetSequence()
867 .getSequenceAsString().indexOf(nogapalseq);
871 "Implementation Error: could not locate start/end "
872 + "in dataset sequence after an edit of the sequence string");
874 int newEnd = newStart + nogapalseq.length() - 1;
875 command.seqs[i].setStart(newStart);
876 command.seqs[i].setEnd(newEnd);
886 final static void adjustAnnotations(Edit command, boolean insert,
887 boolean modifyVisibility, AlignmentI[] views)
889 AlignmentAnnotation[] annotations = null;
891 if (modifyVisibility && !insert)
893 // only occurs if a sequence was added or deleted.
894 command.deletedAnnotationRows = new Hashtable<SequenceI, AlignmentAnnotation[]>();
896 if (command.fullAlignmentHeight)
898 annotations = command.al.getAlignmentAnnotation();
903 AlignmentAnnotation[] tmp;
904 for (int s = 0; s < command.seqs.length; s++)
906 command.seqs[s].sequenceChanged();
908 if (modifyVisibility)
910 // Rows are only removed or added to sequence object.
914 tmp = command.seqs[s].getAnnotation();
917 int alen = tmp.length;
918 for (int aa = 0; aa < tmp.length; aa++)
920 if (!command.al.deleteAnnotation(tmp[aa]))
922 // strip out annotation not in the current al (will be put
923 // back on insert in all views)
928 command.seqs[s].setAlignmentAnnotation(null);
929 if (alen != tmp.length)
931 // save the non-null annotation references only
932 AlignmentAnnotation[] saved = new AlignmentAnnotation[alen];
933 for (int aa = 0, aapos = 0; aa < tmp.length; aa++)
937 saved[aapos++] = tmp[aa];
942 command.deletedAnnotationRows.put(command.seqs[s], saved);
943 // and then remove any annotation in the other views
944 for (int alview = 0; views != null
945 && alview < views.length; alview++)
947 if (views[alview] != command.al)
949 AlignmentAnnotation[] toremove = views[alview]
950 .getAlignmentAnnotation();
951 if (toremove == null || toremove.length == 0)
955 // remove any alignment annotation on this sequence that's
956 // on that alignment view.
957 for (int aa = 0; aa < toremove.length; aa++)
959 if (toremove[aa].sequenceRef == command.seqs[s])
961 views[alview].deleteAnnotation(toremove[aa]);
969 // save all the annotation
970 command.deletedAnnotationRows.put(command.seqs[s], tmp);
977 if (command.deletedAnnotationRows != null
978 && command.deletedAnnotationRows
979 .containsKey(command.seqs[s]))
981 AlignmentAnnotation[] revealed = command.deletedAnnotationRows
982 .get(command.seqs[s]);
983 command.seqs[s].setAlignmentAnnotation(revealed);
984 if (revealed != null)
986 for (int aa = 0; aa < revealed.length; aa++)
988 // iterate through al adding original annotation
989 command.al.addAnnotation(revealed[aa]);
991 for (int aa = 0; aa < revealed.length; aa++)
993 command.al.setAnnotationIndex(revealed[aa], aa);
995 // and then duplicate added annotation on every other alignment
997 for (int vnum = 0; views != null && vnum < views.length; vnum++)
999 if (views[vnum] != command.al)
1001 int avwidth = views[vnum].getWidth() + 1;
1002 // duplicate in this view
1003 for (int a = 0; a < revealed.length; a++)
1005 AlignmentAnnotation newann = new AlignmentAnnotation(
1007 command.seqs[s].addAlignmentAnnotation(newann);
1008 newann.padAnnotation(avwidth);
1009 views[vnum].addAnnotation(newann);
1010 views[vnum].setAnnotationIndex(newann, a);
1020 if (command.seqs[s].getAnnotation() == null)
1027 annotations = command.seqs[s].getAnnotation();
1031 tmp = new AlignmentAnnotation[aSize
1032 + command.seqs[s].getAnnotation().length];
1034 System.arraycopy(annotations, 0, tmp, 0, aSize);
1036 System.arraycopy(command.seqs[s].getAnnotation(), 0, tmp, aSize,
1037 command.seqs[s].getAnnotation().length);
1041 aSize = annotations.length;
1045 if (annotations == null)
1052 command.deletedAnnotations = new Hashtable<String, Annotation[]>();
1057 for (int a = 0; a < annotations.length; a++)
1059 if (annotations[a].autoCalculated
1060 || annotations[a].annotations == null)
1067 aSize = annotations[a].annotations.length;
1070 temp = new Annotation[aSize + command.number];
1071 if (annotations[a].padGaps)
1073 for (int aa = 0; aa < temp.length; aa++)
1075 temp[aa] = new Annotation(command.gapChar + "", null, ' ', 0);
1081 if (command.position < aSize)
1083 if (command.position + command.number >= aSize)
1089 tSize = aSize - command.number;
1101 temp = new Annotation[tSize];
1106 if (command.position < annotations[a].annotations.length)
1108 System.arraycopy(annotations[a].annotations, 0, temp, 0,
1111 if (command.deletedAnnotations != null
1112 && command.deletedAnnotations
1113 .containsKey(annotations[a].annotationId))
1115 Annotation[] restore = command.deletedAnnotations
1116 .get(annotations[a].annotationId);
1118 System.arraycopy(restore, 0, temp, command.position,
1123 System.arraycopy(annotations[a].annotations, command.position,
1124 temp, command.position + command.number,
1125 aSize - command.position);
1129 if (command.deletedAnnotations != null
1130 && command.deletedAnnotations
1131 .containsKey(annotations[a].annotationId))
1133 Annotation[] restore = command.deletedAnnotations
1134 .get(annotations[a].annotationId);
1136 temp = new Annotation[annotations[a].annotations.length
1138 System.arraycopy(annotations[a].annotations, 0, temp, 0,
1139 annotations[a].annotations.length);
1140 System.arraycopy(restore, 0, temp,
1141 annotations[a].annotations.length, restore.length);
1145 temp = annotations[a].annotations;
1151 if (tSize != aSize || command.position < 2)
1153 int copylen = Math.min(command.position,
1154 annotations[a].annotations.length);
1157 System.arraycopy(annotations[a].annotations, 0, temp, 0,
1158 copylen); // command.position);
1161 Annotation[] deleted = new Annotation[command.number];
1162 if (copylen >= command.position)
1164 copylen = Math.min(command.number,
1165 annotations[a].annotations.length - command.position);
1168 System.arraycopy(annotations[a].annotations, command.position,
1169 deleted, 0, copylen); // command.number);
1173 command.deletedAnnotations.put(annotations[a].annotationId,
1175 if (annotations[a].annotations.length > command.position
1178 System.arraycopy(annotations[a].annotations,
1179 command.position + command.number, temp,
1180 command.position, annotations[a].annotations.length
1181 - command.position - command.number); // aSize
1186 int dSize = aSize - command.position;
1190 Annotation[] deleted = new Annotation[command.number];
1191 System.arraycopy(annotations[a].annotations, command.position,
1194 command.deletedAnnotations.put(annotations[a].annotationId,
1197 tSize = Math.min(annotations[a].annotations.length,
1199 temp = new Annotation[tSize];
1200 System.arraycopy(annotations[a].annotations, 0, temp, 0, tSize);
1204 temp = annotations[a].annotations;
1209 annotations[a].annotations = temp;
1214 * Restores features to the state before a Cut.
1216 * <li>re-add any features deleted by the cut</li>
1217 * <li>remove any truncated features created by the cut</li>
1218 * <li>shift right any features to the right of the cut</li>
1224 * the sequence the Cut applied to
1226 * the start residue position of the cut
1228 * the number of residues cut
1229 * @param sameDatasetSequence
1230 * true if dataset sequence and frame of reference were left
1231 * unchanged by the Cut
1233 final static void undoCutFeatures(Edit command, SequenceI seq,
1234 final int start, final int length, boolean sameDatasetSequence)
1236 SequenceI sequence = seq.getDatasetSequence();
1237 if (sequence == null)
1243 * shift right features that lie to the right of the restored cut (but not
1244 * if dataset sequence unchanged - so coordinates were changed by Cut)
1246 if (!sameDatasetSequence)
1249 * shift right all features right of and not
1250 * contiguous with the cut position
1252 seq.getFeatures().shiftFeatures(start + 1, length);
1255 * shift right any features that start at the cut position,
1256 * unless they were truncated
1258 List<SequenceFeature> sfs = seq.getFeatures().findFeatures(start,
1260 for (SequenceFeature sf : sfs)
1262 if (sf.getBegin() == start)
1264 if (!command.truncatedFeatures.containsKey(seq)
1265 || !command.truncatedFeatures.get(seq).contains(sf))
1268 * feature was shifted left to cut position (not truncated),
1269 * so shift it back right
1271 SequenceFeature shifted = new SequenceFeature(sf, sf.getBegin()
1272 + length, sf.getEnd() + length, sf.getFeatureGroup(),
1274 seq.addSequenceFeature(shifted);
1275 seq.deleteFeature(sf);
1282 * restore any features that were deleted or truncated
1284 if (command.deletedFeatures != null
1285 && command.deletedFeatures.containsKey(seq))
1287 for (SequenceFeature deleted : command.deletedFeatures.get(seq))
1289 sequence.addSequenceFeature(deleted);
1294 * delete any truncated features
1296 if (command.truncatedFeatures != null
1297 && command.truncatedFeatures.containsKey(seq))
1299 for (SequenceFeature amended : command.truncatedFeatures.get(seq))
1301 sequence.deleteFeature(amended);
1307 * Returns the list of edit commands wrapped by this object.
1311 public List<Edit> getEdits()
1317 * Returns a map whose keys are the dataset sequences, and values their
1318 * aligned sequences before the command edit list was applied. The aligned
1319 * sequences are copies, which may be updated without affecting the originals.
1321 * The command holds references to the aligned sequences (after editing). If
1322 * the command is an 'undo',then the prior state is simply the aligned state.
1323 * Otherwise, we have to derive the prior state by working backwards through
1324 * the edit list to infer the aligned sequences before editing.
1326 * Note: an alternative solution would be to cache the 'before' state of each
1327 * edit, but this would be expensive in space in the common case that the
1328 * original is never needed (edits are not mirrored).
1331 * @throws IllegalStateException
1332 * on detecting an edit command of a type that can't be unwound
1334 public Map<SequenceI, SequenceI> priorState(boolean forUndo)
1336 Map<SequenceI, SequenceI> result = new HashMap<SequenceI, SequenceI>();
1337 if (getEdits() == null)
1343 for (Edit e : getEdits())
1345 for (SequenceI seq : e.getSequences())
1347 SequenceI ds = seq.getDatasetSequence();
1348 // SequenceI preEdit = result.get(ds);
1349 if (!result.containsKey(ds))
1352 * copy sequence including start/end (but don't use copy constructor
1353 * as we don't need annotations)
1355 SequenceI preEdit = new Sequence("", seq.getSequenceAsString(),
1356 seq.getStart(), seq.getEnd());
1357 preEdit.setDatasetSequence(ds);
1358 result.put(ds, preEdit);
1366 * Work backwards through the edit list, deriving the sequences before each
1367 * was applied. The final result is the sequence set before any edits.
1369 Iterator<Edit> editList = new ReverseListIterator<Edit>(getEdits());
1370 while (editList.hasNext())
1372 Edit oldEdit = editList.next();
1373 Action action = oldEdit.getAction();
1374 int position = oldEdit.getPosition();
1375 int number = oldEdit.getNumber();
1376 final char gap = oldEdit.getGapCharacter();
1377 for (SequenceI seq : oldEdit.getSequences())
1379 SequenceI ds = seq.getDatasetSequence();
1380 SequenceI preEdit = result.get(ds);
1381 if (preEdit == null)
1383 preEdit = new Sequence("", seq.getSequenceAsString(),
1384 seq.getStart(), seq.getEnd());
1385 preEdit.setDatasetSequence(ds);
1386 result.put(ds, preEdit);
1389 * 'Undo' this edit action on the sequence (updating the value in the
1394 if (action == Action.DELETE_GAP)
1396 preEdit.setSequence(new String(StringUtils.insertCharAt(
1397 preEdit.getSequence(), position, number, gap)));
1399 else if (action == Action.INSERT_GAP)
1401 preEdit.setSequence(new String(StringUtils.deleteChars(
1402 preEdit.getSequence(), position, position + number)));
1406 System.err.println("Can't undo edit action " + action);
1407 // throw new IllegalStateException("Can't undo edit action " +
1418 public SequenceI[] oldds;
1421 * start and end of sequence prior to edit
1423 public Range[] oldStartEnd;
1425 boolean fullAlignmentHeight = false;
1427 Map<SequenceI, AlignmentAnnotation[]> deletedAnnotationRows;
1429 Map<String, Annotation[]> deletedAnnotations;
1432 * features deleted by the cut (re-add on Undo)
1433 * (including the original of any shortened features)
1435 Map<SequenceI, List<SequenceFeature>> deletedFeatures;
1438 * shortened features added by the cut (delete on Undo)
1440 Map<SequenceI, List<SequenceFeature>> truncatedFeatures;
1452 int position, number;
1456 public Edit(Action cmd, SequenceI[] sqs, int pos, int count,
1461 this.position = pos;
1462 this.number = count;
1466 Edit(Action cmd, SequenceI[] sqs, int pos, int count,
1469 this(cmd, sqs, pos, count, align.getGapCharacter());
1473 alIndex = new int[sqs.length];
1474 for (int i = 0; i < sqs.length; i++)
1476 alIndex[i] = align.findIndex(sqs[i]);
1479 fullAlignmentHeight = (align.getHeight() == sqs.length);
1482 Edit(Action cmd, SequenceI[] sqs, int pos, int count,
1483 AlignmentI align, String replace)
1485 this(cmd, sqs, pos, count, align);
1487 string = new char[sqs.length][];
1488 for (int i = 0; i < sqs.length; i++)
1490 string[i] = replace.toCharArray();
1494 public SequenceI[] getSequences()
1499 public int getPosition()
1504 public Action getAction()
1509 public int getNumber()
1514 public char getGapCharacter()
1521 * Returns an iterator over the list of edit commands which traverses the list
1522 * either forwards or backwards.
1527 public Iterator<Edit> getEditIterator(boolean forwards)
1531 return getEdits().iterator();
1535 return new ReverseListIterator<Edit>(getEdits());
1540 * Adjusts features for Cut, and saves details of changes made to allow Undo
1542 * <li>features left of the cut are unchanged</li>
1543 * <li>features right of the cut are shifted left</li>
1544 * <li>features internal to the cut region are deleted</li>
1545 * <li>features that overlap or span the cut are shortened</li>
1546 * <li>the originals of any deleted or shortened features are saved, to re-add
1548 * <li>any added (shortened) features are saved, to delete on Undo</li>
1553 * @param fromPosition
1555 * @param cutIsInternal
1557 protected static void cutFeatures(Edit command, SequenceI seq,
1558 int fromPosition, int toPosition, boolean cutIsInternal)
1561 * if the cut is at start or end of sequence
1562 * then we don't modify the sequence feature store
1568 List<SequenceFeature> added = new ArrayList<>();
1569 List<SequenceFeature> removed = new ArrayList<>();
1571 SequenceFeaturesI featureStore = seq.getFeatures();
1572 if (toPosition < fromPosition || featureStore == null)
1577 int cutStartPos = fromPosition;
1578 int cutEndPos = toPosition;
1579 int cutWidth = cutEndPos - cutStartPos + 1;
1581 synchronized (featureStore)
1584 * get features that overlap the cut region
1586 List<SequenceFeature> toAmend = featureStore.findFeatures(
1587 cutStartPos, cutEndPos);
1590 * add any contact features that span the cut region
1591 * (not returned by findFeatures)
1593 for (SequenceFeature contact : featureStore.getContactFeatures())
1595 if (contact.getBegin() < cutStartPos
1596 && contact.getEnd() > cutEndPos)
1598 toAmend.add(contact);
1603 * adjust start-end of overlapping features;
1604 * delete features enclosed by the cut;
1605 * delete partially overlapping contact features
1607 for (SequenceFeature sf : toAmend)
1609 int sfBegin = sf.getBegin();
1610 int sfEnd = sf.getEnd();
1611 int newBegin = sfBegin;
1613 boolean toDelete = false;
1614 boolean follows = false;
1616 if (sfBegin >= cutStartPos && sfEnd <= cutEndPos)
1619 * feature lies within cut region - delete it
1623 else if (sfBegin < cutStartPos && sfEnd > cutEndPos)
1626 * feature spans cut region - left-shift the end
1630 else if (sfEnd <= cutEndPos)
1633 * feature overlaps left of cut region - truncate right
1635 newEnd = cutStartPos - 1;
1636 if (sf.isContactFeature())
1641 else if (sfBegin >= cutStartPos)
1644 * remaining case - feature overlaps right
1645 * truncate left, adjust end of feature
1647 newBegin = cutIsInternal ? cutStartPos : cutEndPos + 1;
1648 newEnd = newBegin + sfEnd - cutEndPos - 1;
1649 if (sf.isContactFeature())
1655 seq.deleteFeature(sf);
1662 SequenceFeature copy = new SequenceFeature(sf, newBegin, newEnd,
1663 sf.getFeatureGroup(), sf.getScore());
1664 seq.addSequenceFeature(copy);
1673 * and left shift any features lying to the right of the cut region
1676 featureStore.shiftFeatures(cutEndPos + 1, -cutWidth);
1680 * save deleted and amended features, so that Undo can
1681 * re-add or delete them respectively
1683 if (command.deletedFeatures == null)
1685 command.deletedFeatures = new HashMap<>();
1687 if (command.truncatedFeatures == null)
1689 command.truncatedFeatures = new HashMap<>();
1691 command.deletedFeatures.put(seq, removed);
1692 command.truncatedFeatures.put(seq, added);