Coverage Report
File OrderCommand.java
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Classes
| Class | Line # | Actions | |||
|---|---|---|---|---|---|
| OrderCommand | 33 | 10 | 7 |
Contributing tests
Source view
| 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.analysis.AlignmentSorter; | |
| 24 | import jalview.datamodel.AlignmentI; | |
| 25 | import jalview.datamodel.SequenceI; | |
| 26 | ||
| 27 | /** | |
| 28 | * An undoable command to reorder the sequences in an alignment. | |
| 29 | * | |
| 30 | * @author gmcarstairs | |
| 31 | * | |
| 32 | */ | |
| 33 | public class OrderCommand implements CommandI | |
| 34 | { | |
| 35 | String description; | |
| 36 | ||
| 37 | /* | |
| 38 | * The sequence order before sorting (target order for an undo) | |
| 39 | */ | |
| 40 | SequenceI[] seqs; | |
| 41 | ||
| 42 | /* | |
| 43 | * The sequence order specified by this command | |
| 44 | */ | |
| 45 | SequenceI[] seqs2; | |
| 46 | ||
| 47 | /* | |
| 48 | * The alignment the command acts on | |
| 49 | */ | |
| 50 | AlignmentI al; | |
| 51 | ||
| 52 | /** | |
| 53 | * Constructor given the 'undo' sequence order, and the (already) sorted | |
| 54 | * alignment. | |
| 55 | * | |
| 56 | * @param description | |
| 57 | * a text label for the 'undo' menu option | |
| 58 | * @param seqs | |
| 59 | * the sequence order for undo | |
| 60 | * @param al | |
| 61 | * the alignment as ordered by this command | |
| 62 | */ | |
| 63 | 1 |  public OrderCommand(String description, SequenceI[] seqs, AlignmentI al) |
| 64 | { | |
| 65 | 1 | this.description = description; |
| 66 | 1 | this.seqs = seqs; |
| 67 | 1 | this.seqs2 = al.getSequencesArray(); |
| 68 | 1 | this.al = al; |
| 69 | 1 | doCommand(null); |
| 70 | } | |
| 71 | ||
| 72 | 2 | public String getDescription() |
| 73 | { | |
| 74 | 2 | return description; |
| 75 | } | |
| 76 | ||
| 77 | 1 | public int getSize() |
| 78 | { | |
| 79 | 1 | return 1; |
| 80 | } | |
| 81 | ||
| 82 | 1 | public void doCommand(AlignmentI[] views) |
| 83 | { | |
| 84 | 1 | AlignmentSorter.setOrder(al, seqs2); |
| 85 | } | |
| 86 | ||
| 87 | 0 | public void undoCommand(AlignmentI[] views) |
| 88 | { | |
| 89 | 0 | AlignmentSorter.setOrder(al, seqs); |
| 90 | } | |
| 91 | ||
| 92 | /** | |
| 93 | * Returns the sequence order used to sort, or before sorting if undo=true. | |
| 94 | * | |
| 95 | * @param undo | |
| 96 | * @return | |
| 97 | */ | |
| 98 | 0 | public SequenceI[] getSequenceOrder(boolean undo) |
| 99 | { | |
| 100 | 0 | return undo ? seqs : seqs2; |
| 101 | } | |
| 102 | } |