/*
- * 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 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
* 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
+ * 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.
- *
- * 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
+ *
+ * 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 <http://www.gnu.org/licenses/>.
*/
package jalview.commands;
import jalview.datamodel.*;
/**
- *
+ *
* <p>
* Title: EditCommmand
* </p>
- *
+ *
* <p>
* Description: Essential information for performing undo and redo for cut/paste
* insert/delete gap which can be stored in the HistoryList
* </p>
- *
+ *
* <p>
* Copyright: Copyright (c) 2006
* </p>
- *
+ *
* <p>
* Company: Dundee University
* </p>
- *
+ *
* @author not attributable
* @version 1.0
*/
public static final int REPLACE = 4;
+ public static final int INSERT_NUC=5;
+
Edit[] edits;
String description;
performEdit(0, null);
}
+ @Override
final public String getDescription()
{
return description;
}
+ @Override
public int getSize()
{
return edits == null ? 0 : edits.length;
* 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
/**
* append a new edit command with a set of alignment views that may be
* operated on
- *
+ *
* @param command
* @param seqs
* @param position
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());
+ Edit edit = new Edit(command, seqs, position, number,
+ al.getGapCharacter());
if (al.getHeight() == seqs.length)
{
edit.al = al;
case REPLACE:
replace(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;
case REPLACE:
replace(edits[e]);
break;
- }
+ }
}
}
{
command.seqs[s].insertCharAt(command.position, command.number,
command.gapChar);
+// 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 deleteGap(Edit command)
{
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);
+ adjustFeatures(
+ command,
+ i,
+ command.seqs[i].findPosition(command.position),
+ command.seqs[i].findPosition(command.position
+ + command.number), false);
}
}
}
// read it to the alignment
if (command.alIndex[i] < command.al.getHeight())
{
- command.al.getSequences().insertElementAt(command.seqs[i],
- command.alIndex[i]);
+ List<SequenceI> sequences;
+ synchronized (sequences=command.al.getSequences()) {
+ sequences.add(command.alIndex[i], command.seqs[i]);
+ }
}
else
{
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,
* 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]);
+ 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;
}
if (command.editedFeatures != null
&& command.editedFeatures.containsKey(seq))
{
- sequence
- .setSequenceFeatures((SequenceFeature[]) command.editedFeatures
- .get(seq));
+ sequence.setSequenceFeatures((SequenceFeature[]) command.editedFeatures
+ .get(seq));
}
return;
git://source.jalview.org / jalview.git / blobdiff