2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
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.
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.
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.
21 package jalview.io.gff;
23 import jalview.datamodel.AlignmentI;
24 import jalview.datamodel.SequenceFeature;
25 import jalview.datamodel.SequenceI;
27 import java.io.IOException;
28 import java.util.List;
31 * An interface to described common functionality of different flavours of GFF
36 public interface GffHelperI
38 final String GFF_ENCODABLE = ",=;";
40 final String RENAME_TOKEN = "$RENAME_TO$";
43 * Process one GFF feature line
46 * the sequence with which this feature is associated
50 * the alignment we are adding GFF to
52 * any new sequences referenced by the GFF
53 * @param relaxedIdMatching
54 * if true, match word tokens in sequence names
55 * @return a SequenceFeature if one should be created, else null
58 SequenceFeature processGff(SequenceI seq, String[] gffColumns,
59 AlignmentI align, List<SequenceI> newseqs,
60 boolean relaxedIdMatching) throws IOException;
62 // java 8 will allow static methods in interfaces:
63 // static boolean recognises(String [] columns);