Package au.org.intersect.samifier.domain

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

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

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

        PeptideSearchResultsParser peptideSearchResultsParser = new PeptideSearchResultsParserImpl(
                proteinToOLNMap);
        List<PeptideSearchResult> peptideSearchResults = peptideSearchResultsParser
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    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);

        PeptideSearchResultsParser peptideSearchResultsParser = new PeptideSearchResultsParserImpl(
                proteinToOLNMap);
        List<PeptideSearchResult> peptideSearchResults = peptideSearchResultsParser
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        File mascotFile = new File("test/resources/test_mascot_search_results.txt");

        File mapFile = new File("test/resources/test_accession.txt");
        try {
            ProteinToOLNParser proteinToOLNParser = new ProteinToOLNParserImpl();
            ProteinToOLNMap proteinToOLNMap = proteinToOLNParser.parseMappingFile(mapFile);
            PeptideSearchResultsParser peptideSearchResultsParser = new PeptideSearchResultsParserImpl(proteinToOLNMap);

            List<PeptideSearchResult> list = peptideSearchResultsParser.parseResults(mascotFile);
            // The parser should find sixteen results - same as mzid file
            System.out.println(list.toString());
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        File mascotFile = new File("test/resources/test_mascot_search_results.mzid");

        File mapFile = new File("test/resources/test_accession.txt");
        try {
            ProteinToOLNParser proteinToOLNParser = new ProteinToOLNParserImpl();
            ProteinToOLNMap proteinToOLNMap = proteinToOLNParser.parseMappingFile(mapFile);
            PeptideSearchResultsParser peptideSearchResultsParser = new PeptideSearchResultsParserImpl(proteinToOLNMap);

            List<PeptideSearchResult> list = peptideSearchResultsParser.parseResults(mascotFile);
            assertEquals("Parser should find sixteen ", 16, list.size());
            assertTrue(list.contains(new PeptideSearchResult(mascotFile.getName(), "PE_11_1_KPYK1_YEAST_0_469_474", "EFGILK", "KPYK1_YEAST", 469, 474 , new BigDecimal("25.95"))));
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    @Test
    public void testParsingProteinToOLNMappingFile()
    {
        File mapFile = new File("test/resources/test_accession.txt");
        ProteinToOLNMap proteinToOLNMap = null;
        try {
            ProteinToOLNParser proteinToOLNParser = new ProteinToOLNParserImpl();
            proteinToOLNMap = proteinToOLNParser.parseMappingFile(mapFile);
        }
        catch(Exception e)
        {
            fail("Unexpected exception: " + e.getMessage());
            e.printStackTrace();
        }

        assertTrue("Map has key KPYK1_YEAST", proteinToOLNMap.containsProtein("KPYK1_YEAST"));
        assertTrue("Map has key RL31A_YEAST", proteinToOLNMap.containsProtein("RL31A_YEAST"));
        assertTrue("Map has key RL36B_YEAST", proteinToOLNMap.containsProtein("RL36B_YEAST"));
        assertEquals("KPYK1_YEAST maps to YAL038W", "YAL038W", proteinToOLNMap.getOLN("KPYK1_YEAST"));
        assertEquals("RL31A_YEAST maps to YDL075W", "YDL075W", proteinToOLNMap.getOLN("RL31A_YEAST"));
        assertEquals("RL36B_YEAST maps to YPL249C-A", "YPL249C-A", proteinToOLNMap.getOLN("RL36B_YEAST"));
    }
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Related Classes of au.org.intersect.samifier.domain.ProteinToOLNMap

  • au.org.intersect.samifier.parser.PeptideSearchResultsParserImplUnitTest
  • au.org.intersect.samifier.parser.ProteinToOLNParserImplUnitTest
  • au.org.intersect.samifier.runner.ResultAnalyserRunner
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