Package au.org.intersect.samifier.domain

Examples of au.org.intersect.samifier.domain.GeneSequence

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                }
                if (GENE_RE.matcher(type).matches()) {
                    GeneInfo gene = parseGene(parts);
                    processGene(genome, gene);
                } else if (SEQUENCE_RE.matcher(type).find()) {
                    GeneSequence sequence = parseSequence(parts);
                    processSequence(genome, parts[CHROMOSOME_PART], sequence);
                }
            }
        } finally {
            if (reader != null) {
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        int stop = Integer.parseInt(parts[STOP_PART]);
        String direction = parts[STRAND_PART];
        if (start > stop) {
            throwParsingException("Start-stop invalid");
        }
        return new GeneSequence(extractParent(parts[ATTRIBUTES_PART]), parseSequenceType(type), start, stop, parseStrand(direction), parseVirtualProteins(extractParent(parts[ATTRIBUTES_PART]), parts[ATTRIBUTES_PART]));
    }
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Related Classes of au.org.intersect.samifier.domain.GeneSequence

  • au.org.intersect.samifier.parser.GenomeParserImpl
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