1 package jalview.io.gff;
3 import jalview.datamodel.AlignmentI;
4 import jalview.datamodel.SequenceFeature;
5 import jalview.datamodel.SequenceI;
7 import java.io.IOException;
11 * An interface to described common functionality of different flavours of GFF
16 public interface GffHelperI
19 final String RENAME_TOKEN = "$RENAME_TO$";
22 * Process one GFF feature line
25 * the sequence with which this feature is associated
29 * the alignment we are adding GFF to
31 * any new sequences referenced by the GFF
32 * @param relaxedIdMatching
33 * if true, match word tokens in sequence names
34 * @return a SequenceFeature if one should be created, else null
37 SequenceFeature processGff(SequenceI seq, String[] gffColumns,
39 List<SequenceI> newseqs, boolean relaxedIdMatching)
42 // java 8 will allow static methods in interfaces:
43 // static boolean recognises(String [] columns);