jalviewX
File InterProScanHelper.java
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Classes
| Class | Line # | Actions | ||||
|---|---|---|---|---|---|---|
| InterProScanHelper | 35 | 18 | 11 | 9 |
Contributing tests
This file is covered by 9 tests.
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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.gff; | |
| 22 | ||
| 23 | import jalview.datamodel.AlignmentI; | |
| 24 | import jalview.datamodel.SequenceFeature; | |
| 25 | import jalview.datamodel.SequenceI; | |
| 26 | import jalview.util.StringUtils; | |
| 27 | ||
| 28 | import java.io.IOException; | |
| 29 | import java.util.List; | |
| 30 | import java.util.Map; | |
| 31 | ||
| 32 | /** | |
| 33 | * A handler to parse GFF in the format generated by InterProScan | |
| 34 | */ | |
| 35 | public class InterProScanHelper extends Gff3Helper | |
| 36 | { | |
| 37 | private static final String INTER_PRO_SCAN = "InterProScan"; | |
| 38 | ||
| 39 | private static final String SIGNATURE_DESC = "signature_desc"; | |
| 40 | ||
| 41 | /** | |
| 42 | * Process one GFF feature line (as modelled by SequenceFeature) | |
| 43 | * | |
| 44 | * @param seq | |
| 45 | * the sequence with which this feature is associated | |
| 46 | * @param gff | |
| 47 | * the gff column data | |
| 48 | * @param align | |
| 49 | * the alignment we are adding GFF to | |
| 50 | * @param newseqs | |
| 51 | * any new sequences referenced by the GFF | |
| 52 | * @param relaxedIdMatching | |
| 53 | * if true, match word tokens in sequence names | |
| 54 | * @return a sequence feature if one should be added to the sequence, else | |
| 55 | * null (i.e. it has been processed in another way e.g. to generate a | |
| 56 | * mapping) | |
| 57 | * @throws IOException | |
| 58 | */ | |
| 59 | 0 |  @Override |
| 60 | public SequenceFeature processGff(SequenceI seq, String[] gff, | |
| 61 | AlignmentI align, List<SequenceI> newseqs, | |
| 62 | boolean relaxedIdMatching) throws IOException | |
| 63 | { | |
| 64 | /* | |
| 65 | * ignore the 'polypeptide' match of the whole sequence | |
| 66 | */ | |
| 67 | 0 | if (".".equals(gff[SOURCE_COL])) |
| 68 | { | |
| 69 | 0 | return null; |
| 70 | } | |
| 71 | ||
| 72 | 0 | return super.processGff(seq, gff, align, newseqs, relaxedIdMatching); |
| 73 | } | |
| 74 | ||
| 75 | /** | |
| 76 | * An override that | |
| 77 | * <ul> | |
| 78 | * <li>uses Source (column 2) as feature type instead of the default column 3</li> | |
| 79 | * <li>sets "InterProScan" as the feature group</li> | |
| 80 | * <li>extracts "signature_desc" attribute as the feature description</li> | |
| 81 | * </ul> | |
| 82 | */ | |
| 83 | 1 | @Override |
| 84 | protected SequenceFeature buildSequenceFeature(String[] gff, | |
| 85 | Map<String, List<String>> attributes) | |
| 86 | { | |
| 87 | 1 | SequenceFeature sf = super.buildSequenceFeature(gff, SOURCE_COL, |
| 88 | INTER_PRO_SCAN, attributes); | |
| 89 | ||
| 90 | /* | |
| 91 | * signature_desc is a more informative source of description | |
| 92 | */ | |
| 93 | 1 | List<String> desc = attributes.get(SIGNATURE_DESC); |
| 94 | 1 | String description = StringUtils.listToDelimitedString(desc, ", "); |
| 95 | 1 | if (description.length() > 0) |
| 96 | { | |
| 97 | 1 | sf.setDescription(description); |
| 98 | } | |
| 99 | ||
| 100 | 1 | return sf; |
| 101 | } | |
| 102 | ||
| 103 | /** | |
| 104 | * Tests whether the GFF data looks like it was generated by InterProScan | |
| 105 | * | |
| 106 | * @param columns | |
| 107 | * @return | |
| 108 | */ | |
| 109 | 24 | public static boolean recognises(String[] columns) |
| 110 | { | |
| 111 | 24 | SequenceOntologyI so = SequenceOntologyFactory.getInstance(); |
| 112 | 24 | String type = columns[TYPE_COL]; |
| 113 | 24 | if (so.isA(type, SequenceOntologyI.PROTEIN_MATCH) |
| 114 | || (".".equals(columns[SOURCE_COL]) | |
| 115 | && so.isA(type, SequenceOntologyI.POLYPEPTIDE))) | |
| 116 | { | |
| 117 | 1 | return true; |
| 118 | } | |
| 119 | 23 | return false; |
| 120 | } | |
| 121 | ||
| 122 | /** | |
| 123 | * Overriden method, because InterProScan GFF has the target sequence id in | |
| 124 | * GFF field 'ID' rather than the usual 'Target' :-O | |
| 125 | */ | |
| 126 | 1 | @Override |
| 127 | protected String findTargetId(String target, | |
| 128 | Map<String, List<String>> set) | |
| 129 | { | |
| 130 | 1 | List<String> ids = set.get(ID); |
| 131 | 1 | if (ids == null || ids.size() != 1) |
| 132 | { | |
| 133 | 0 | return null; |
| 134 | } | |
| 135 | 1 | return ids.get(0); |
| 136 | } | |
| 137 | ||
| 138 | } |