Package au.org.intersect.samifier.parser

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

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        this.bedfilePath = bedfilePath;
        this.confidenceScore = confidenceScore;
    }

    public void run() throws Exception {
        GenomeParserImpl genomeParser = new GenomeParserImpl();
        genome = genomeParser.parseGenomeFile(genomeFile);

        ProteinToOLNParser proteinToOLNParser = new ProteinToOLNParserImpl();
        proteinToOLNMap = proteinToOLNParser.parseMappingFile(mapFile);

        PeptideSearchResultsParser peptideSearchResultsParser = new PeptideSearchResultsParserImpl(proteinToOLNMap);
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    public List<ProteinLocation> doGenerateLocations()
            throws GenomeFileParsingException, MascotParsingException,
            IOException, TranslationTableParsingException, FastaParserException {
        List<ProteinLocation> proteinLocations = new ArrayList<ProteinLocation>();
        System.out.println("Generating locations");
        GenomeParserImpl genomeParser = new GenomeParserImpl();
        genome = genomeParser.parseGenomeFile(genomeFile);

        proteinToOLNMap = new EqualProteinOLNMap();

        PeptideSearchResultsParser peptideSearchResultsParser = new PeptideSearchResultsParserImpl(
                proteinToOLNMap);
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        hsqldb.connect();
        hsqldb.generateTables();
    }

    public void run() throws Exception {
        GenomeParserImpl genomeParser = new GenomeParserImpl();
        Genome genome = genomeParser.parseGenomeFile(genomeFile);

        ProteinToOLNParser proteinToOLNParser = new ProteinToOLNParserImpl();
        ProteinToOLNMap proteinToOLNMap = proteinToOLNParser
                .parseMappingFile(proteinToOLNMapFile);
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        output.close();

    }

    public void runWithQuery(String sqlQuery) throws Exception {
        GenomeParserImpl genomeParser = new GenomeParserImpl();
        Genome genome = genomeParser.parseGenomeFile(genomeFile);

        ProteinToOLNParser proteinToOLNParser = new ProteinToOLNParserImpl();
        ProteinToOLNMap proteinToOLNMap = proteinToOLNParser
                .parseMappingFile(proteinToOLNMapFile);
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    }

    @Test
    public void testParsing() throws Exception
    {
        GenomeParserImpl genomeParser = new GenomeParserImpl();
        Genome genome = genomeParser.parseGenomeFile(genomeFile);
        assertEquals("GenomeParserImpl has 3 genes", 4, genome.getGeneEntries().size());
        assertTrue("GenomeParserImpl has gene YAL038W", genome.hasGene("YAL038W"));
        assertTrue("GenomeParserImpl has gene YAL038W", genome.hasGene("YDL075W"));
        assertTrue("GenomeParserImpl has gene YPL249C-A", genome.hasGene("YPL249C-A"));
    }
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    @Test
    public void testGetGene() throws Exception
    {
        //GeneInfo gene = new GeneInfo()
        GenomeParserImpl genomeParser = new GenomeParserImpl();
        Genome genome = genomeParser.parseGenomeFile(genomeFile);
        assertThat("GenomeParserImpl returns GeneInfo object for known genes", genome.getGene("YAL038W"), instanceOf(GeneInfo.class));
        assertNull("GenomeParserImpl returns null for unknown genes", genome.getGene("UNKNOWN"));
    }
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Related Classes of au.org.intersect.samifier.parser.GenomeParserImpl

  • au.org.intersect.samifier.domain.GeneInfo
  • au.org.intersect.samifier.domain.GeneSequence
  • au.org.intersect.samifier.domain.Genome
  • au.org.intersect.samifier.domain.GenomeUnitTest
  • au.org.intersect.samifier.domain.VirtualProtein
  • au.org.intersect.samifier.generator.VirtualProteinMascotLocationGenerator
  • au.org.intersect.samifier.runner.ResultAnalyserRunner
  • au.org.intersect.samifier.runner.SamifierRunner
  • java.io.FileReader
  • java.io.BufferedReader
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