- /**
- * Parses and saves fields of an Ensembl-style description e.g.
- * chromosome:GRCh38:17:45051610:45109016:1
- */
- protected void parseDescription()
- {
- if (description == null)
- {
- return;
- }
- String[] tokens = description.split(":");
- if (tokens.length == 6 && "chromosome".equals(tokens[0])) {
- String ref = tokens[1];
- String chrom = tokens[2];
- try {
- int chStart = Integer.parseInt(tokens[3]);
- int chEnd = Integer.parseInt(tokens[4]);
- boolean forwardStrand = "1".equals(tokens[5]);
- String species = ""; // dunno yet!
- int[] from = new int[] { start, end };
- int[] to = new int[] { forwardStrand ? chStart : chEnd,
- forwardStrand ? chEnd : chStart };
- MapList map = new MapList(from, to, 1, 1);
- GeneLoci gl = new GeneLoci(species, ref, chrom, map);
- setGeneLoci(gl);
- } catch (NumberFormatException e)
- {
- System.err.println("Bad integers in description " + description);
- }
- }
- }
-
- public void setGeneLoci(GeneLoci gl)
+ @Override
+ public void setGeneLoci(String speciesId, String assemblyId,
+ String chromosomeId, MapList map)