Package au.org.intersect.samifier.domain

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

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            } else {
                peptideAbsoluteStart = virtualGeneStop - startOffset;
                peptideAbsoluteStop = virtualGeneStop - stopOffset;
            }

            GenomeNucleotides genomeNucleotides = getGenomeNucleotides(geneInfo.getChromosome());
            int startPosition = searchStart(peptideSearchResult, peptideAbsoluteStart, genomeNucleotides, geneInfo);
            int stopPosition = searchStop(peptideSearchResult, peptideAbsoluteStop, genomeNucleotides, geneInfo, false);
            if (startPosition == NOT_FOUND || stopPosition == NOT_FOUND) {
                continue;
            }
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    }

    private GenomeNucleotides getGenomeNucleotides(String gene)
            throws FastaParserException, IOException {
        if (!genomeNucleotidesMap.containsKey(gene)) {
            genomeNucleotidesMap.put(gene, new GenomeNucleotides(fastaParser.readCode(gene)));
        }
        return genomeNucleotidesMap.get(gene);
    }
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        try {
            File fastaFile = new File(args[0]);
            File translationTableFile = new File(args[1]);
            int direction = "+".equals(args[2]) ? 1 : -1;
            FastaParser parser = new FastaParserImpl(fastaFile);
            nucleotides = new GenomeNucleotides(parser.readCode(FilenameUtils.getBaseName(fastaFile.getName())));
            translationTable = CodonTranslationTable
                    .parseTableFile(translationTableFile);

            if (args.length == 4) {
                int codonPosition = Integer.parseInt(args[3]);
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Related Classes of au.org.intersect.samifier.domain.GenomeNucleotides

  • au.org.intersect.samifier.generator.VirtualProteinMascotLocationGenerator
  • au.org.intersect.samifier.tool.CodonFinder
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