+ 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++)
+ {
+ 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;
+ }
+ }