jalviewX
File AMSAFile.java
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51% of files have more coverage
Classes
| Class | Line # | Actions | ||||
|---|---|---|---|---|---|---|
| AMSAFile | 29 | 31 | 14 | 43 |
Contributing tests
This file is covered by 1 test.
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| 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.io; | |
| 22 | ||
| 23 | import jalview.datamodel.AlignmentAnnotation; | |
| 24 | import jalview.datamodel.AlignmentI; | |
| 25 | import jalview.datamodel.SequenceI; | |
| 26 | ||
| 27 | import java.io.IOException; | |
| 28 | ||
| 29 | public class AMSAFile extends jalview.io.FastaFile | |
| 30 | { | |
| 31 | ||
| 32 | AlignmentI al; | |
| 33 | ||
| 34 | /** | |
| 35 | * Creates a new AMSAFile object for output. | |
| 36 | */ | |
| 37 | 1 |  public AMSAFile(AlignmentI al) |
| 38 | { | |
| 39 | 1 | this.al = al; |
| 40 | } | |
| 41 | ||
| 42 | 0 | public AMSAFile(String inFile, DataSourceType sourceType) |
| 43 | throws IOException | |
| 44 | { | |
| 45 | 0 | super(inFile, sourceType); |
| 46 | } | |
| 47 | ||
| 48 | 1 | public AMSAFile(FileParse source) throws IOException |
| 49 | { | |
| 50 | 1 | super(source); |
| 51 | } | |
| 52 | ||
| 53 | /** | |
| 54 | * DOCUMENT ME! | |
| 55 | * | |
| 56 | * @return DOCUMENT ME! | |
| 57 | */ | |
| 58 | 1 | @Override |
| 59 | public String print(SequenceI[] sqs, boolean jvsuffix) | |
| 60 | { | |
| 61 | 1 | super.print(sqs, jvsuffix); |
| 62 | ||
| 63 | 1 | AlignmentAnnotation aa; |
| 64 | 1 | if (al.getAlignmentAnnotation() != null) |
| 65 | { | |
| 66 | ||
| 67 | 0 | for (int i = 0; i < al.getAlignmentAnnotation().length; i++) |
| 68 | { | |
| 69 | 0 | aa = al.getAlignmentAnnotation()[i]; |
| 70 | ||
| 71 | 0 | if (aa.autoCalculated || !aa.visible) |
| 72 | { | |
| 73 | 0 | continue; |
| 74 | } | |
| 75 | ||
| 76 | 0 | out.append(">#_" + aa.label); |
| 77 | 0 | if (aa.description != null) |
| 78 | { | |
| 79 | 0 | out.append(" " + aa.description); |
| 80 | } | |
| 81 | ||
| 82 | 0 | out.append(newline); |
| 83 | ||
| 84 | 0 | int nochunks = Math.min(aa.annotations.length, al.getWidth()) / len |
| 85 | + 1; | |
| 86 | ||
| 87 | 0 | for (int j = 0; j < nochunks; j++) |
| 88 | { | |
| 89 | 0 | int start = j * len; |
| 90 | 0 | int end = start + len; |
| 91 | 0 | if (end > aa.annotations.length) |
| 92 | { | |
| 93 | 0 | end = aa.annotations.length; |
| 94 | } | |
| 95 | ||
| 96 | 0 | String ch; |
| 97 | 0 | for (int k = start; k < end; k++) |
| 98 | { | |
| 99 | 0 | if (aa.annotations[k] == null) |
| 100 | { | |
| 101 | 0 | ch = " "; |
| 102 | } | |
| 103 | else | |
| 104 | { | |
| 105 | 0 | ch = aa.annotations[k].displayCharacter; |
| 106 | } | |
| 107 | 0 | if (ch.length() > 1) |
| 108 | { | |
| 109 | 0 | this.warningMessage = "Truncated column annotation to first letter."; |
| 110 | 0 | ch = ch.substring(0, 1); |
| 111 | } | |
| 112 | 0 | out.append(ch); |
| 113 | ||
| 114 | } | |
| 115 | 0 | out.append(newline); |
| 116 | } | |
| 117 | } | |
| 118 | } | |
| 119 | 1 | return out.toString(); |
| 120 | } | |
| 121 | } |