2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.commands;
23 import jalview.datamodel.SequenceI;
24 import jalview.util.Comparison;
26 public class SlideSequencesCommand extends EditCommand
28 boolean gapsInsertedBegin = false;
30 public SlideSequencesCommand(String description, SequenceI[] seqsLeft,
31 SequenceI[] seqsRight, int slideSize, char gapChar)
33 this.description = description;
35 int lSize = seqsLeft.length;
36 gapsInsertedBegin = false;
38 for (i = 0; i < lSize; i++)
40 for (j = 0; j < slideSize; j++)
42 if (!Comparison.isGap(seqsLeft[i].getCharAt(j)))
44 gapsInsertedBegin = true;
52 if (!gapsInsertedBegin)
54 e = new Edit(Action.DELETE_GAP, seqsLeft, 0, slideSize, gapChar);
59 e = new Edit(Action.INSERT_GAP, seqsRight, 0, slideSize, gapChar);
66 public boolean getGapsInsertedBegin()
68 return gapsInsertedBegin;
71 public boolean appendSlideCommand(SlideSequencesCommand command)
75 if (command.getEdit(0).seqs.length == getEdit(0).seqs.length)
78 for (int i = 0; i < command.getEdit(0).seqs.length; i++)
80 if (getEdit(0).seqs[i] != command.getEdit(0).seqs[i])
89 command.addEdit(getEdit(0));