Class |
Line # |
Actions |
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RemoveGapColCommand | 26 | 27 | 13 |
1 | /* | |
2 | * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) | |
3 | * Copyright (C) $$Year-Rel$$ The Jalview Authors | |
4 | * | |
5 | * This file is part of Jalview. | |
6 | * | |
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. | |
11 | * | |
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. | |
16 | * | |
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. | |
20 | */ | |
21 | package jalview.commands; | |
22 | ||
23 | import jalview.datamodel.AlignmentI; | |
24 | import jalview.datamodel.SequenceI; | |
25 | ||
26 | public class RemoveGapColCommand extends EditCommand | |
27 | { | |
28 | int columnsDeleted; | |
29 | ||
30 | 3 | public RemoveGapColCommand(String description, SequenceI[] seqs, |
31 | int start, int end, AlignmentI al) | |
32 | { | |
33 | 3 | this.description = description; |
34 | ||
35 | 3 | int j, jSize = seqs.length; |
36 | ||
37 | 3 | int startCol = -1, endCol = -1; |
38 | 3 | columnsDeleted = 0; |
39 | ||
40 | 3 | clearEdits(); |
41 | ||
42 | 3 | boolean delete = true; |
43 | 58 | for (int i = start; i <= end; i++) |
44 | { | |
45 | 55 | delete = true; |
46 | ||
47 | 89 | for (j = 0; j < jSize; j++) |
48 | { | |
49 | 81 | if (seqs[j].getLength() > i) |
50 | { | |
51 | 72 | if (!jalview.util.Comparison.isGap(seqs[j].getCharAt(i))) |
52 | { | |
53 | 47 | if (delete) |
54 | { | |
55 | 47 | endCol = i; |
56 | } | |
57 | ||
58 | 47 | delete = false; |
59 | 47 | break; |
60 | } | |
61 | } | |
62 | } | |
63 | ||
64 | 55 | if (delete && startCol == -1) |
65 | { | |
66 | 7 | startCol = i; |
67 | } | |
68 | ||
69 | 55 | if (!delete && startCol > -1) |
70 | { | |
71 | 7 | this.appendEdit(Action.DELETE_GAP, seqs, startCol - columnsDeleted, |
72 | endCol - startCol, al, false, null); | |
73 | ||
74 | 7 | columnsDeleted += (endCol - startCol); |
75 | 7 | startCol = -1; |
76 | 7 | endCol = -1; |
77 | } | |
78 | } | |
79 | ||
80 | 3 | if (delete && startCol > -1) |
81 | { | |
82 | // This is for empty columns at the | |
83 | // end of the alignment | |
84 | ||
85 | 0 | this.appendEdit(Action.DELETE_GAP, seqs, startCol - columnsDeleted, |
86 | end - startCol + 1, al, false, null); | |
87 | ||
88 | 0 | columnsDeleted += (end - startCol + 1); |
89 | } | |
90 | ||
91 | 3 | performEdit(0, null); |
92 | } | |
93 | ||
94 | 0 | @Override |
95 | public int getSize() | |
96 | { | |
97 | // We're interested in the number of columns deleted, | |
98 | // Not the number of sequence edits. | |
99 | 0 | return columnsDeleted; |
100 | } | |
101 | ||
102 | } |