Package au.org.intersect.samifier.parser

Examples of au.org.intersect.samifier.parser.FastaParserImpl

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        }
    }

    protected List<NucleotideSequence> extractSequenceParts(GeneInfo gene) throws IOException, FastaParserException {
        if (fastaParser == null) {
            fastaParser = new FastaParserImpl(chromosomeDirectory);
        }
        return fastaParser.extractSequenceParts(gene);
    }
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    @Override
    public List<ProteinLocation> generateLocations()
            throws LocationGeneratorException {
        try {
            this.fastaParser = new FastaParserImpl(chromosomeDir);
            List<ProteinLocation> locations = doGenerateLocations();
            locations = removeDuplicates(locations);
            locations = mergeProteins(locations);
            Collections.sort(locations);
            Iterator<ProteinLocation> setIterator = locations.iterator();
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        this.databaseName = databaseName;
        this.outputWriter = outputWriter;
        this.translationTableFile = translationTableFile;
        this.gffWriter = gffWriter;
        this.accessionWriter = accessionWriter;
        this.fastaParser = new FastaParserImpl(genomeFile);
    }
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    public static void main(String[] args) throws Exception {
        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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    @Test
    public void testCreateLocations()
    {
        try {
            File genomeFile = new File("test/resources/protein_generator/test_genome_short.faa");
            CodonsPerIntervalLocationGenerator locationGenerator = new CodonsPerIntervalLocationGenerator("20", new FastaParserImpl(genomeFile));

            List<ProteinLocation> locations = locationGenerator.generateLocations();
            for (ProteinLocation loc : locations)
            {
                System.out.println(loc);
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Related Classes of au.org.intersect.samifier.parser.FastaParserImpl

  • au.org.intersect.samifier.domain.NucleotideSequence
  • au.org.intersect.samifier.generator.CodonsPerIntervalLocationGeneratorUnitTest
  • au.org.intersect.samifier.generator.PeptideSequenceGeneratorImpl
  • au.org.intersect.samifier.generator.VirtualProteinMascotLocationGenerator
  • au.org.intersect.samifier.runner.ProteinGeneratorRunner
  • au.org.intersect.samifier.tool.CodonFinder
  • java.io.FileNotFoundException
  • java.io.FileReader
  • java.io.BufferedReader
  • java.util.regex.Matcher
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