- 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[] { seq.getStart(), seq.getEnd() };
- int[] to = new int[] { forwardStrand ? chStart : chEnd,
- forwardStrand ? chEnd : chStart };
- MapList map = new MapList(from, to, 1, 1);
- seq.setGeneLoci(species, ref, chrom, map);
- } catch (NumberFormatException e)
- {
- System.err.println("Bad integers in description " + description);
- }