Coverage Report
File GffHelperI.java
Classes
| Class | Line # | Actions | |||
|---|---|---|---|---|---|
| GffHelperI | 36 | 0 | 0 |
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.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 | ||
| 30 | /** | |
| 31 | * An interface to described common functionality of different flavours of GFF | |
| 32 | * | |
| 33 | * @author gmcarstairs | |
| 34 | * | |
| 35 | */ | |
| 36 | public interface GffHelperI | |
| 37 | { | |
| 38 | /* | |
| 39 | * GFF3 spec requires comma, equals, semi-colon, tab, percent characters to be | |
| 40 | * encoded as %2C, %3D, %3B, %09, %25 respectively within data values | |
| 41 | * see https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md | |
| 42 | */ | |
| 43 | final String GFF_ENCODABLE = ",=;\t%"; | |
| 44 | ||
| 45 | final String RENAME_TOKEN = "$RENAME_TO$"; | |
| 46 | ||
| 47 | /** | |
| 48 | * Process one GFF feature line | |
| 49 | * | |
| 50 | * @param seq | |
| 51 | * the sequence with which this feature is associated | |
| 52 | * @param gffColumns | |
| 53 | * the GFF column data | |
| 54 | * @param align | |
| 55 | * the alignment we are adding GFF to | |
| 56 | * @param newseqs | |
| 57 | * any new sequences referenced by the GFF | |
| 58 | * @param relaxedIdMatching | |
| 59 | * if true, match word tokens in sequence names | |
| 60 | * @return a SequenceFeature if one should be created, else null | |
| 61 | * @throws IOException | |
| 62 | */ | |
| 63 | SequenceFeature processGff(SequenceI seq, String[] gffColumns, | |
| 64 | AlignmentI align, List<SequenceI> newseqs, | |
| 65 | boolean relaxedIdMatching) throws IOException; | |
| 66 | ||
| 67 | // java 8 will allow static methods in interfaces: | |
| 68 | // static boolean recognises(String [] columns); | |
| 69 | } |