1. Project Clover database Fri Dec 6 2024 13:47:14 GMT
  2. Package jalview.io.gff

File GffHelperI.java

 

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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    }