jalviewX
File Gff2Helper.java
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Classes
| Class | Line # | Actions | ||||
|---|---|---|---|---|---|---|
| Gff2Helper | 31 | 6 | 4 | 2 |
Contributing tests
This file is covered by 11 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 | ||
| 27 | import java.io.IOException; | |
| 28 | import java.util.List; | |
| 29 | import java.util.Map; | |
| 30 | ||
| 31 | public class Gff2Helper extends GffHelperBase | |
| 32 | { | |
| 33 | /** | |
| 34 | * GFF2 uses space character to delimit name/value pairs on column 9 | |
| 35 | * | |
| 36 | * @param text | |
| 37 | * @return | |
| 38 | */ | |
| 39 | 22 |  public static Map<String, List<String>> parseNameValuePairs(String text) |
| 40 | { | |
| 41 | // TODO: can a value include a comma? if so it will be broken by this | |
| 42 | 22 | return parseNameValuePairs(text, ";", ' ', ","); |
| 43 | } | |
| 44 | ||
| 45 | /** | |
| 46 | * Return ' ' as the name-value separator used in column 9 attributes. | |
| 47 | */ | |
| 48 | 0 | @Override |
| 49 | protected char getNameValueSeparator() | |
| 50 | { | |
| 51 | 0 | return ' '; |
| 52 | } | |
| 53 | ||
| 54 | /** | |
| 55 | * Default processing if not overridden is just to construct a sequence | |
| 56 | * feature | |
| 57 | */ | |
| 58 | 17 | @Override |
| 59 | public SequenceFeature processGff(SequenceI seq, String[] gff, | |
| 60 | AlignmentI align, List<SequenceI> newseqs, | |
| 61 | boolean relaxedIdMatching) throws IOException | |
| 62 | { | |
| 63 | 17 | Map<String, List<String>> attributes = null; |
| 64 | 17 | if (gff.length > ATTRIBUTES_COL) |
| 65 | { | |
| 66 | 11 | attributes = parseNameValuePairs(gff[ATTRIBUTES_COL]); |
| 67 | } | |
| 68 | 17 | return buildSequenceFeature(gff, attributes); |
| 69 | } | |
| 70 | ||
| 71 | } |