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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 | ||
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 | } |