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;
+ public static final int INSERT_NUC = 5;
Edit[] edits;
* 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
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;
}
}
}
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);
+ // 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)
{
if (command.alIndex[i] < command.al.getHeight())
{
List<SequenceI> sequences;
- synchronized (sequences=command.al.getSequences()) {
+ synchronized (sequences = command.al.getSequences())
+ {
sequences.add(command.alIndex[i], command.seqs[i]);
}
}
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;
+ 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));
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
+ // 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