X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcommands%2FEditCommand.java;h=b39d1ddb69302035d183b18778a8c6939ee39b46;hb=9157d82cb9213d9071c15203dddf96ae9081dfbe;hp=03b94d3ca6dcfe7921526636ea6f90fad7b353c5;hpb=4e665c174de86f7fb68b257ccb2b0aa2d62cb429;p=jalview.git diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java index 03b94d3..b39d1dd 100644 --- a/src/jalview/commands/EditCommand.java +++ b/src/jalview/commands/EditCommand.java @@ -1,25 +1,34 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) + * Copyright (C) 2014 The Jalview Authors * * This file is part of Jalview. * * Jalview 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 3 of the License, or (at your option) any later version. - * + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * * Jalview 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 Jalview. If not, see . + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.commands; -import java.util.*; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.Annotation; +import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceFeature; +import jalview.datamodel.SequenceI; -import jalview.datamodel.*; +import java.util.Hashtable; +import java.util.List; /** * @@ -54,8 +63,8 @@ public class EditCommand implements CommandI public static final int PASTE = 3; public static final int REPLACE = 4; - - public static final int INSERT_NUC=5; + + public static final int INSERT_NUC = 5; Edit[] edits; @@ -96,11 +105,13 @@ public class EditCommand implements CommandI performEdit(0, null); } + @Override final public String getDescription() { return description; } + @Override public int getSize() { return edits == null ? 0 : edits.length; @@ -194,42 +205,42 @@ public class EditCommand implements CommandI case REPLACE: replace(edits[e]); break; - //TODO:add deleteNuc for UNDO - case INSERT_NUC: - insertNuc(edits[e]); - break; + // TODO:add deleteNuc for UNDO + // case INSERT_NUC: + // insertNuc(edits[e]); + // break; } } } + @Override final public void doCommand(AlignmentI[] views) { performEdit(0, views); } + @Override 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; - } + { + for(Edit e : edits){ + switch (e.command) + { + case INSERT_GAP: + deleteGap(e); + break; + case DELETE_GAP: + insertGap(e); + break; + case CUT: + paste(e, views); + break; + case PASTE: + cut(e, views); + break; + case REPLACE: + replace(e); + break; + } } } @@ -240,23 +251,24 @@ public class EditCommand implements CommandI { command.seqs[s].insertCharAt(command.position, command.number, command.gapChar); - System.out.println("pos: "+command.position+" number: "+command.number); + // System.out.println("pos: "+command.position+" number: "+command.number); } adjustAnnotations(command, true, false, null); } - - final void insertNuc(Edit command) - { - for (int s = 0; s < command.seqs.length; s++) - { - System.out.println("pos: "+command.position+" number: "+command.number); - command.seqs[s].insertCharAt(command.position, command.number,'A'); - } - - adjustAnnotations(command, true, false, null); - } + // + // final void insertNuc(Edit command) + // { + // + // for (int s = 0; s < command.seqs.length; s++) + // { + // System.out.println("pos: "+command.position+" number: "+command.number); + // command.seqs[s].insertCharAt(command.position, command.number,'A'); + // } + // + // adjustAnnotations(command, true, false, null); + // } final void deleteGap(Edit command) { @@ -344,8 +356,13 @@ public class EditCommand implements CommandI // read it to the alignment if (command.alIndex[i] < command.al.getHeight()) { - command.al.getSequences().insertElementAt(command.seqs[i], - command.alIndex[i]); + List sequences; + synchronized (sequences = command.al.getSequences()) + { + // int index = command.al.findIndex(command.seqs[i]); + // sequences.add(index, command.seqs[i]); + sequences.add(command.alIndex[i] < 0 ? 0 : command.alIndex[i], command.seqs[i]); + } } else { @@ -387,9 +404,13 @@ public class EditCommand implements CommandI + command.number); } if (command.seqs[i].getStart() == start) + { newstart--; + } else + { newend++; + } } } command.string[i] = null; @@ -446,6 +467,9 @@ public class EditCommand implements CommandI command.number = start + command.string[0].length; for (int i = 0; i < command.seqs.length; i++) { + boolean newDSWasNeeded = command.oldds != null + && command.oldds[i] != null; + /** * cut addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, * cut, sg.getStartRes(), sg.getEndRes()-sg.getStartRes()+1, @@ -460,9 +484,48 @@ public class EditCommand implements CommandI oldstring = command.seqs[i].getSequenceAsString(); tmp = new StringBuffer(oldstring.substring(0, start)); tmp.append(command.string[i]); + String nogaprep = jalview.analysis.AlignSeq.extractGaps( + jalview.util.Comparison.GapChars, new String( + command.string[i])); + int ipos = command.seqs[i].findPosition(start) + - command.seqs[i].getStart(); tmp.append(oldstring.substring(end)); command.seqs[i].setSequence(tmp.toString()); command.string[i] = oldstring.substring(start, end).toCharArray(); + String nogapold = jalview.analysis.AlignSeq.extractGaps( + jalview.util.Comparison.GapChars, new String( + command.string[i])); + if (!nogaprep.toLowerCase().equals(nogapold.toLowerCase())) + { + if (newDSWasNeeded) + { + SequenceI oldds = command.seqs[i].getDatasetSequence(); + command.seqs[i].setDatasetSequence(command.oldds[i]); + command.oldds[i] = oldds; + } + else + { + if (command.oldds == null) + { + command.oldds = new SequenceI[command.seqs.length]; + } + command.oldds[i] = command.seqs[i].getDatasetSequence(); + SequenceI newds = new Sequence( + command.seqs[i].getDatasetSequence()); + String fullseq, osp = newds.getSequenceAsString(); + fullseq = osp.substring(0, ipos) + nogaprep + + osp.substring(ipos + nogaprep.length()); + newds.setSequence(fullseq.toUpperCase()); + // TODO: JAL-1131 ensure newly created dataset sequence is added to + // the set of + // dataset sequences associated with the alignment. + // TODO: JAL-1131 fix up any annotation associated with new dataset + // sequence to ensure that original sequence/annotation relationships + // are preserved. + command.seqs[i].setDatasetSequence(newds); + + } + } tmp = null; oldstring = null; } @@ -651,10 +714,12 @@ public class EditCommand implements CommandI { 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 { @@ -733,8 +798,10 @@ public class EditCommand implements CommandI 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)