X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fcommands%2FEditCommand.java;h=85e6ad59b93b9df4b6d8903e02d726e473beefaa;hb=057425f8881d0e8986e9e7a8004b709e42334f34;hp=1d4880a189a55c85854000b5dfe828449c44b6de;hpb=1e968e44cb033e74e9f81d7140b5393f8ad6e305;p=jalview.git diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java index 1d4880a..85e6ad5 100644 --- a/src/jalview/commands/EditCommand.java +++ b/src/jalview/commands/EditCommand.java @@ -1,603 +1,922 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 - * of the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA - */ -package jalview.commands; - -import jalview.datamodel.*; - -import java.util.Hashtable; - -/** - * - *
Title: EditCommmand
- * - *Description: Essential information for performing - * undo and redo for cut/paste insert/delete gap - * which can be stored in the HistoryList
- * - *Copyright: Copyright (c) 2006
- * - *Company: Dundee University
- * - * @author not attributable - * @version 1.0 - */ -public class EditCommand implements CommandI -{ - public static final int INSERT_GAP = 0; - public static final int DELETE_GAP = 1; - public static final int CUT = 2; - public static final int PASTE = 3; - - Edit[] edits; - - String description; - - public EditCommand() - {} - - public EditCommand(String description) - { - this.description = description; - } - - public EditCommand( String description, - int command, - SequenceI[] seqs, - int position, - int number, - AlignmentI al) - { - this.description = description; - if ( command==CUT || command==PASTE) - { - edits = new Edit[]{new Edit(command, seqs, position, number, al)}; - } - - performEdit(0); - } - - - final public String getDescription() - { - return description; - } - - public int getSize() - { - return edits==null?0:edits.length; - } - - final public AlignmentI getAlignment() - { - return edits[0].al; - } - - - final public void appendEdit(int command, - SequenceI[] seqs, - int position, - int number, - AlignmentI al, - boolean performEdit) - { - Edit edit = new Edit(command, seqs, position, number, al.getGapCharacter()); - if(al.getHeight()==seqs.length) - { - edit.al = al; - edit.fullAlignmentHeight = true; - } - - if (edits != null) - { - Edit[] temp = new Edit[edits.length + 1]; - System.arraycopy(edits, 0, temp, 0, edits.length); - edits = temp; - edits[edits.length - 1] = edit; - } - else - edits = new Edit[] { edit }; - - if (performEdit) - performEdit(edits.length - 1); - } - - final void performEdit(int commandIndex) - { - int eSize = edits.length; - for (int e = commandIndex; e < eSize; e++) - { - if (edits[e].command==INSERT_GAP) - { - insertGap(edits[e]); - } - else if (edits[e].command==DELETE_GAP) - { - deleteGap(edits[e]); - } - else if(edits[e].command==CUT) - { - cut(edits[e]); - } - else if(edits[e].command==PASTE) - { - paste(edits[e]); - } - } - } - - final public void doCommand() - { - performEdit(0); - } - - final public void undoCommand() - { - int e = 0, eSize = edits.length; - for (e = eSize-1; e > -1; e--) - { - if (edits[e].command==INSERT_GAP) - { - deleteGap(edits[e]); - } - else if (edits[e].command==DELETE_GAP) - { - insertGap(edits[e]); - } - else if (edits[e].command==CUT) - { - paste(edits[e]); - } - else if (edits[e].command==PASTE) - { - cut(edits[e]); - } - } - } - - final void insertGap(Edit command) - { - for(int s=0; s+ * Description: Essential information for performing undo and redo for cut/paste + * insert/delete gap which can be stored in the HistoryList + *
+ * + *+ * Copyright: Copyright (c) 2006 + *
+ * + *+ * Company: Dundee University + *
+ * + * @author not attributable + * @version 1.0 + */ +public class EditCommand implements CommandI +{ + public static final int INSERT_GAP = 0; + + public static final int DELETE_GAP = 1; + + public static final int CUT = 2; + + public static final int PASTE = 3; + + public static final int REPLACE = 4; + + Edit[] edits; + + String description; + + public EditCommand() + { + } + + public EditCommand(String description) + { + this.description = description; + } + + public EditCommand(String description, int command, SequenceI[] seqs, + int position, int number, AlignmentI al) + { + this.description = description; + if (command == CUT || command == PASTE) + { + edits = new Edit[] + { new Edit(command, seqs, position, number, al) }; + } + + performEdit(0, null); + } + + public EditCommand(String description, int command, String replace, + SequenceI[] seqs, int position, int number, AlignmentI al) + { + this.description = description; + if (command == REPLACE) + { + edits = new Edit[] + { new Edit(command, seqs, position, number, al, replace) }; + } + + performEdit(0, null); + } + + final public String getDescription() + { + return description; + } + + public int getSize() + { + return edits == null ? 0 : edits.length; + } + + final public AlignmentI getAlignment() + { + return edits[0].al; + } + + /** + * append a new editCommand Note. this shouldn't be called if the edit is an + * operation affects more alignment objects than the one referenced in al (for + * example, cut or pasting whole sequences). Use the form with an additional + * AlignmentI[] views parameter. + * + * @param command + * @param seqs + * @param position + * @param number + * @param al + * @param performEdit + */ + final public void appendEdit(int command, SequenceI[] seqs, int position, + int number, AlignmentI al, boolean performEdit) + { + appendEdit(command, seqs, position, number, al, performEdit, null); + } + + /** + * append a new edit command with a set of alignment views that may be + * operated on + * + * @param command + * @param seqs + * @param position + * @param number + * @param al + * @param performEdit + * @param views + */ + final public void appendEdit(int command, SequenceI[] seqs, int position, + int number, AlignmentI al, boolean performEdit, AlignmentI[] views) + { + Edit edit = new Edit(command, seqs, position, number, al + .getGapCharacter()); + if (al.getHeight() == seqs.length) + { + edit.al = al; + edit.fullAlignmentHeight = true; + } + + if (edits != null) + { + Edit[] temp = new Edit[edits.length + 1]; + System.arraycopy(edits, 0, temp, 0, edits.length); + edits = temp; + edits[edits.length - 1] = edit; + } + else + { + edits = new Edit[] + { edit }; + } + + if (performEdit) + { + performEdit(edits.length - 1, views); + } + } + + final void performEdit(int commandIndex, AlignmentI[] views) + { + int eSize = edits.length; + for (int e = commandIndex; e < eSize; e++) + { + switch (edits[e].command) + { + case INSERT_GAP: + insertGap(edits[e]); + break; + case DELETE_GAP: + deleteGap(edits[e]); + break; + case CUT: + cut(edits[e], views); + break; + case PASTE: + paste(edits[e], views); + break; + case REPLACE: + replace(edits[e]); + break; + } + } + } + + final public void doCommand(AlignmentI[] views) + { + performEdit(0, views); + } + + final public void undoCommand(AlignmentI[] views) + { + int e = 0, eSize = edits.length; + for (e = eSize - 1; e > -1; e--) + { + switch (edits[e].command) + { + case INSERT_GAP: + deleteGap(edits[e]); + break; + case DELETE_GAP: + insertGap(edits[e]); + break; + case CUT: + paste(edits[e], views); + break; + case PASTE: + cut(edits[e], views); + break; + case REPLACE: + replace(edits[e]); + break; + } + } + } + + final void insertGap(Edit command) + { + + for (int s = 0; s < command.seqs.length; s++) + { + command.seqs[s].insertCharAt(command.position, command.number, + command.gapChar); + } + + adjustAnnotations(command, true, false, null); + } + + final void deleteGap(Edit command) + { + for (int s = 0; s < command.seqs.length; s++) + { + command.seqs[s].deleteChars(command.position, command.position + + command.number); + } + + adjustAnnotations(command, false, false, null); + } + + void cut(Edit command, AlignmentI[] views) + { + boolean seqDeleted = false; + command.string = new char[command.seqs.length][]; + + for (int i = 0; i < command.seqs.length; i++) + { + if (command.seqs[i].getLength() > command.position) + { + command.string[i] = command.seqs[i].getSequence(command.position, + command.position + command.number); + SequenceI oldds = command.seqs[i].getDatasetSequence(); + if (command.oldds != null && command.oldds[i] != null) + { + // we are redoing an undone cut. + command.seqs[i].setDatasetSequence(null); + } + command.seqs[i].deleteChars(command.position, command.position + + command.number); + if (command.oldds != null && command.oldds[i] != null) + { + // oldds entry contains the cut dataset sequence. + command.seqs[i].setDatasetSequence(command.oldds[i]); + command.oldds[i] = oldds; + } + else + { + // modify the oldds if necessary + if (oldds != command.seqs[i].getDatasetSequence() + || command.seqs[i].getSequenceFeatures() != null) + { + if (command.oldds == null) + { + command.oldds = new SequenceI[command.seqs.length]; + } + command.oldds[i] = oldds; + adjustFeatures(command, i, command.seqs[i] + .findPosition(command.position), command.seqs[i] + .findPosition(command.position + command.number), false); + } + } + } + + if (command.seqs[i].getLength() < 1) + { + command.al.deleteSequence(command.seqs[i]); + seqDeleted = true; + } + } + + adjustAnnotations(command, false, seqDeleted, views); + } + + void paste(Edit command, AlignmentI[] views) + { + StringBuffer tmp; + boolean newDSNeeded; + boolean newDSWasNeeded; + int newstart, newend; + boolean seqWasDeleted = false; + int start = 0, end = 0; + + for (int i = 0; i < command.seqs.length; i++) + { + newDSNeeded = false; + newDSWasNeeded = command.oldds != null && command.oldds[i] != null; + if (command.seqs[i].getLength() < 1) + { + // ie this sequence was deleted, we need to + // read it to the alignment + if (command.alIndex[i] < command.al.getHeight()) + { + command.al.getSequences().insertElementAt(command.seqs[i], + command.alIndex[i]); + } + else + { + command.al.addSequence(command.seqs[i]); + } + seqWasDeleted = true; + } + newstart = command.seqs[i].getStart(); + newend = command.seqs[i].getEnd(); + + tmp = new StringBuffer(); + tmp.append(command.seqs[i].getSequence()); + // Undo of a delete does not replace original dataset sequence on to + // alignment sequence. + + if (command.string != null && command.string[i] != null) + { + if (command.position >= tmp.length()) + { + // This occurs if padding is on, and residues + // are removed from end of alignment + int length = command.position - tmp.length(); + while (length > 0) + { + tmp.append(command.gapChar); + length--; + } + } + tmp.insert(command.position, command.string[i]); + for (int s = 0; s < command.string[i].length; s++) + { + if (jalview.schemes.ResidueProperties.aaIndex[command.string[i][s]] != 23) + { + if (!newDSNeeded) + { + newDSNeeded = true; + start = command.seqs[i].findPosition(command.position); + end = command.seqs[i].findPosition(command.position + + command.number); + } + if (command.seqs[i].getStart() == start) + newstart--; + else + newend++; + } + } + command.string[i] = null; + } + + command.seqs[i].setSequence(tmp.toString()); + command.seqs[i].setStart(newstart); + command.seqs[i].setEnd(newend); + if (newDSNeeded) + { + if (command.seqs[i].getDatasetSequence() != null) + { + SequenceI ds; + if (newDSWasNeeded) + { + ds = command.oldds[i]; + } + else + { + // make a new DS sequence + // use new ds mechanism here + ds = new Sequence(command.seqs[i].getName(), + jalview.analysis.AlignSeq.extractGaps( + jalview.util.Comparison.GapChars, + command.seqs[i].getSequenceAsString()), + command.seqs[i].getStart(), command.seqs[i].getEnd()); + ds.setDescription(command.seqs[i].getDescription()); + } + if (command.oldds == null) + { + command.oldds = new SequenceI[command.seqs.length]; + } + command.oldds[i] = command.seqs[i].getDatasetSequence(); + command.seqs[i].setDatasetSequence(ds); + } + adjustFeatures(command, i, start, end, true); + } + } + adjustAnnotations(command, true, seqWasDeleted, views); + + command.string = null; + } + + void replace(Edit command) + { + StringBuffer tmp; + String oldstring; + int start = command.position; + int end = command.number; + // TODO TUTORIAL - Fix for replacement with different length of sequence (or + // whole sequence) + // TODO Jalview 2.4 bugfix change to an aggregate command - original + // sequence string is cut, new string is pasted in. + command.number = start + command.string[0].length; + for (int i = 0; i < command.seqs.length; i++) + { + /** + * cut addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, + * cut, sg.getStartRes(), sg.getEndRes()-sg.getStartRes()+1, + * viewport.alignment)); + * + */ + /** + * then addHistoryItem(new EditCommand( "Add sequences", + * EditCommand.PASTE, sequences, 0, alignment.getWidth(), alignment) ); + * + */ + oldstring = command.seqs[i].getSequenceAsString(); + tmp = new StringBuffer(oldstring.substring(0, start)); + tmp.append(command.string[i]); + tmp.append(oldstring.substring(end)); + command.seqs[i].setSequence(tmp.toString()); + command.string[i] = oldstring.substring(start, end).toCharArray(); + tmp = null; + oldstring = null; + } + } + + final void adjustAnnotations(Edit command, boolean insert, + boolean modifyVisibility, AlignmentI[] views) + { + AlignmentAnnotation[] annotations = null; + + if (modifyVisibility && !insert) + { + // only occurs if a sequence was added or deleted. + command.deletedAnnotationRows = new Hashtable(); + } + if (command.fullAlignmentHeight) + { + annotations = command.al.getAlignmentAnnotation(); + } + else + { + int aSize = 0; + AlignmentAnnotation[] tmp; + for (int s = 0; s < command.seqs.length; s++) + { + if (modifyVisibility) + { + // Rows are only removed or added to sequence object. + if (!insert) + { + // remove rows + tmp = command.seqs[s].getAnnotation(); + if (tmp != null) + { + int alen = tmp.length; + for (int aa = 0; aa < tmp.length; aa++) + { + if (!command.al.deleteAnnotation(tmp[aa])) + { + // strip out annotation not in the current al (will be put + // back on insert in all views) + tmp[aa] = null; + alen--; + } + } + command.seqs[s].setAlignmentAnnotation(null); + if (alen != tmp.length) + { + // save the non-null annotation references only + AlignmentAnnotation[] saved = new AlignmentAnnotation[alen]; + for (int aa = 0, aapos = 0; aa < tmp.length; aa++) + { + if (tmp[aa] != null) + { + saved[aapos++] = tmp[aa]; + tmp[aa] = null; + } + } + tmp = saved; + command.deletedAnnotationRows.put(command.seqs[s], saved); + // and then remove any annotation in the other views + for (int alview = 0; views != null && alview < views.length; alview++) + { + if (views[alview] != command.al) + { + AlignmentAnnotation[] toremove = views[alview] + .getAlignmentAnnotation(); + if (toremove == null || toremove.length == 0) + { + continue; + } + // remove any alignment annotation on this sequence that's + // on that alignment view. + for (int aa = 0; aa < toremove.length; aa++) + { + if (toremove[aa].sequenceRef == command.seqs[s]) + { + views[alview].deleteAnnotation(toremove[aa]); + } + } + } + } + } + else + { + // save all the annotation + command.deletedAnnotationRows.put(command.seqs[s], tmp); + } + } + } + else + { + // recover rows + if (command.deletedAnnotationRows != null + && command.deletedAnnotationRows + .containsKey(command.seqs[s])) + { + AlignmentAnnotation[] revealed = (AlignmentAnnotation[]) command.deletedAnnotationRows + .get(command.seqs[s]); + command.seqs[s].setAlignmentAnnotation(revealed); + if (revealed != null) + { + for (int aa = 0; aa < revealed.length; aa++) + { + // iterate through al adding original annotation + command.al.addAnnotation(revealed[aa]); + } + for (int aa = 0; aa < revealed.length; aa++) + { + command.al.setAnnotationIndex(revealed[aa], aa); + } + // and then duplicate added annotation on every other alignment + // view + for (int vnum = 0; views != null && vnum < views.length; vnum++) + { + if (views[vnum] != command.al) + { + int avwidth = views[vnum].getWidth() + 1; + // duplicate in this view + for (int a = 0; a < revealed.length; a++) + { + AlignmentAnnotation newann = new AlignmentAnnotation( + revealed[a]); + command.seqs[s].addAlignmentAnnotation(newann); + newann.padAnnotation(avwidth); + views[vnum].addAnnotation(newann); + views[vnum].setAnnotationIndex(newann, a); + } + } + } + } + } + } + continue; + } + + if (command.seqs[s].getAnnotation() == null) + { + continue; + } + + if (aSize == 0) + { + annotations = command.seqs[s].getAnnotation(); + } + else + { + tmp = new AlignmentAnnotation[aSize + + command.seqs[s].getAnnotation().length]; + + System.arraycopy(annotations, 0, tmp, 0, aSize); + + System.arraycopy(command.seqs[s].getAnnotation(), 0, tmp, aSize, + command.seqs[s].getAnnotation().length); + + annotations = tmp; + } + aSize = annotations.length; + } + } + + if (annotations == null) + { + return; + } + + if (!insert) + { + command.deletedAnnotations = new Hashtable(); + } + + int aSize; + Annotation[] temp; + for (int a = 0; a < annotations.length; a++) + { + if (annotations[a].autoCalculated + || annotations[a].annotations == null) + { + continue; + } + + int tSize = 0; + + aSize = annotations[a].annotations.length; + if (insert) + { + temp = new Annotation[aSize + command.number]; + if (annotations[a].padGaps) + for (int aa = 0; aa < temp.length; aa++) + { + temp[aa] = new Annotation(command.gapChar + "", null, ' ', 0); + } + } + else + { + if (command.position < aSize) + { + if (command.position + command.number >= aSize) + { + tSize = aSize; + } + else + { + tSize = aSize - command.number; + } + } + else + { + tSize = aSize; + } + + if (tSize < 0) + { + tSize = aSize; + } + temp = new Annotation[tSize]; + } + + if (insert) + { + if (command.position < annotations[a].annotations.length) + { + System.arraycopy(annotations[a].annotations, 0, temp, 0, + command.position); + + if (command.deletedAnnotations != null + && command.deletedAnnotations + .containsKey(annotations[a].annotationId)) + { + Annotation[] restore = (Annotation[]) command.deletedAnnotations + .get(annotations[a].annotationId); + + System.arraycopy(restore, 0, temp, command.position, + command.number); + + } + + System.arraycopy(annotations[a].annotations, command.position, + temp, command.position + command.number, aSize + - command.position); + } + else + { + if (command.deletedAnnotations != null + && command.deletedAnnotations + .containsKey(annotations[a].annotationId)) + { + Annotation[] restore = (Annotation[]) command.deletedAnnotations + .get(annotations[a].annotationId); + + temp = new Annotation[annotations[a].annotations.length + + restore.length]; + System.arraycopy(annotations[a].annotations, 0, temp, 0, + annotations[a].annotations.length); + System.arraycopy(restore, 0, temp, + annotations[a].annotations.length, restore.length); + } + else + { + temp = annotations[a].annotations; + } + } + } + else + { + if (tSize != aSize || command.position < 2) + { + int copylen = Math.min(command.position, + annotations[a].annotations.length); + if (copylen > 0) + System.arraycopy(annotations[a].annotations, 0, temp, 0, + copylen); // command.position); + + Annotation[] deleted = new Annotation[command.number]; + if (copylen >= command.position) + { + copylen = Math.min(command.number, + annotations[a].annotations.length - command.position); + if (copylen > 0) + { + System.arraycopy(annotations[a].annotations, + command.position, deleted, 0, copylen); // command.number); + } + } + + command.deletedAnnotations.put(annotations[a].annotationId, + deleted); + if (annotations[a].annotations.length > command.position + + command.number) + { + System.arraycopy(annotations[a].annotations, command.position + + command.number, temp, command.position, + annotations[a].annotations.length - command.position + - command.number); // aSize + } + } + else + { + int dSize = aSize - command.position; + + if (dSize > 0) + { + Annotation[] deleted = new Annotation[command.number]; + System.arraycopy(annotations[a].annotations, command.position, + deleted, 0, dSize); + + command.deletedAnnotations.put(annotations[a].annotationId, + deleted); + + tSize = Math.min(annotations[a].annotations.length, + command.position); + temp = new Annotation[tSize]; + System.arraycopy(annotations[a].annotations, 0, temp, 0, tSize); + } + else + { + temp = annotations[a].annotations; + } + } + } + + annotations[a].annotations = temp; + } + } + + final void adjustFeatures(Edit command, int index, int i, int j, + boolean insert) + { + SequenceI seq = command.seqs[index]; + SequenceI sequence = seq.getDatasetSequence(); + if (sequence == null) + { + sequence = seq; + } + + if (insert) + { + if (command.editedFeatures != null + && command.editedFeatures.containsKey(seq)) + { + sequence + .setSequenceFeatures((SequenceFeature[]) command.editedFeatures + .get(seq)); + } + + return; + } + + SequenceFeature[] sf = sequence.getSequenceFeatures(); + + if (sf == null) + { + return; + } + + SequenceFeature[] oldsf = new SequenceFeature[sf.length]; + + int cSize = j - i; + + for (int s = 0; s < sf.length; s++) + { + SequenceFeature copy = new SequenceFeature(sf[s]); + + oldsf[s] = copy; + + if (sf[s].getEnd() < i) + { + continue; + } + + if (sf[s].getBegin() > j) + { + sf[s].setBegin(copy.getBegin() - cSize); + sf[s].setEnd(copy.getEnd() - cSize); + continue; + } + + if (sf[s].getBegin() >= i) + { + sf[s].setBegin(i); + } + + if (sf[s].getEnd() < j) + { + sf[s].setEnd(j - 1); + } + + sf[s].setEnd(sf[s].getEnd() - (cSize)); + + if (sf[s].getBegin() > sf[s].getEnd()) + { + sequence.deleteFeature(sf[s]); + } + } + + if (command.editedFeatures == null) + { + command.editedFeatures = new Hashtable(); + } + + command.editedFeatures.put(seq, oldsf); + + } + + class Edit + { + public SequenceI[] oldds; + + boolean fullAlignmentHeight = false; + + Hashtable deletedAnnotationRows; + + Hashtable deletedAnnotations; + + Hashtable editedFeatures; + + AlignmentI al; + + int command; + + char[][] string; + + SequenceI[] seqs; + + int[] alIndex; + + int position, number; + + char gapChar; + + Edit(int command, SequenceI[] seqs, int position, int number, + char gapChar) + { + this.command = command; + this.seqs = seqs; + this.position = position; + this.number = number; + this.gapChar = gapChar; + } + + Edit(int command, SequenceI[] seqs, int position, int number, + AlignmentI al) + { + this.gapChar = al.getGapCharacter(); + this.command = command; + this.seqs = seqs; + this.position = position; + this.number = number; + this.al = al; + + alIndex = new int[seqs.length]; + for (int i = 0; i < seqs.length; i++) + { + alIndex[i] = al.findIndex(seqs[i]); + } + + fullAlignmentHeight = (al.getHeight() == seqs.length); + } + + Edit(int command, SequenceI[] seqs, int position, int number, + AlignmentI al, String replace) + { + this.command = command; + this.seqs = seqs; + this.position = position; + this.number = number; + this.al = al; + this.gapChar = al.getGapCharacter(); + string = new char[seqs.length][]; + for (int i = 0; i < seqs.length; i++) + { + string[i] = replace.toCharArray(); + } + + fullAlignmentHeight = (al.getHeight() == seqs.length); + } + } +}