Package au.org.intersect.samifier.parser

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

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    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);
        List<PeptideSearchResult> peptideSearchResults = peptideSearchResultsParser.parseResults(searchResultsPaths);

        FileWriter bedWriter = null;
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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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    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();
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Related Classes of au.org.intersect.samifier.parser.ProteinToOLNParserImpl

  • au.org.intersect.samifier.domain.FileBasedProteinToOLNMap
  • au.org.intersect.samifier.parser.ProteinToOLNParserImplUnitTest
  • au.org.intersect.samifier.runner.ResultAnalyserRunner
  • au.org.intersect.samifier.runner.SamifierRunner
  • java.io.FileReader
  • java.io.BufferedReader
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