Examples of parseResults()

Examples of au.org.intersect.samifier.parser.PeptideSearchResultsParser.parseResults()

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

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

        FileWriter bedWriter = null;
        if (bedfilePath != null) {
            bedWriter = new FileWriter(bedfilePath);
        }
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Examples of au.org.intersect.samifier.parser.PeptideSearchResultsParser.parseResults()

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        proteinToOLNMap = new EqualProteinOLNMap();

        PeptideSearchResultsParser peptideSearchResultsParser = new PeptideSearchResultsParserImpl(
                proteinToOLNMap);
        List<PeptideSearchResult> peptideSearchResults = peptideSearchResultsParser
                .parseResults(searchResultsPaths);
        translationTable = CodonTranslationTable
                .parseTableFile(translationTableFile);

        for (PeptideSearchResult peptideSearchResult : peptideSearchResults) {
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Examples of au.org.intersect.samifier.parser.PeptideSearchResultsParser.parseResults()

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        ProteinToOLNMap proteinToOLNMap = proteinToOLNParser
                .parseMappingFile(proteinToOLNMapFile);

        PeptideSearchResultsParser peptideSearchResultsParser = new PeptideSearchResultsParserImpl(
                proteinToOLNMap);
        List<PeptideSearchResult> peptideSearchResults = peptideSearchResultsParser
                .parseResults(searchResultsPaths);
        peptideSearchResults = peptideSearchResultsParser
                .sortResultsByChromosome(peptideSearchResults, proteinToOLNMap,
                        genome);
        PeptideSequenceGenerator sequenceGenerator = new PeptideSequenceGeneratorImpl(
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Examples of au.org.intersect.samifier.parser.PeptideSearchResultsParser.parseResults()

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        ProteinToOLNMap proteinToOLNMap = proteinToOLNParser
                .parseMappingFile(proteinToOLNMapFile);

        PeptideSearchResultsParser peptideSearchResultsParser = new PeptideSearchResultsParserImpl(
                proteinToOLNMap);
        List<PeptideSearchResult> peptideSearchResults = peptideSearchResultsParser
                .parseResults(searchResultsPaths);
        PeptideSequenceGenerator sequenceGenerator = new PeptideSequenceGeneratorImpl(
                genome, proteinToOLNMap, chromosomeDir);
        peptideSearchResults = peptideSearchResultsParser
                .sortResultsByChromosome(peptideSearchResults, proteinToOLNMap,
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Examples of au.org.intersect.samifier.parser.PeptideSearchResultsParserImpl.parseResults()

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

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

        FileWriter bedWriter = null;
        if (bedfilePath != null) {
            bedWriter = new FileWriter(bedfilePath);
        }
View Full Code Here

Examples of au.org.intersect.samifier.parser.PeptideSearchResultsParserImpl.parseResults()

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        proteinToOLNMap = new EqualProteinOLNMap();

        PeptideSearchResultsParser peptideSearchResultsParser = new PeptideSearchResultsParserImpl(
                proteinToOLNMap);
        List<PeptideSearchResult> peptideSearchResults = peptideSearchResultsParser
                .parseResults(searchResultsPaths);
        translationTable = CodonTranslationTable
                .parseTableFile(translationTableFile);

        for (PeptideSearchResult peptideSearchResult : peptideSearchResults) {
View Full Code Here

Examples of au.org.intersect.samifier.parser.PeptideSearchResultsParserImpl.parseResults()

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        ProteinToOLNMap proteinToOLNMap = proteinToOLNParser
                .parseMappingFile(proteinToOLNMapFile);

        PeptideSearchResultsParser peptideSearchResultsParser = new PeptideSearchResultsParserImpl(
                proteinToOLNMap);
        List<PeptideSearchResult> peptideSearchResults = peptideSearchResultsParser
                .parseResults(searchResultsPaths);
        peptideSearchResults = peptideSearchResultsParser
                .sortResultsByChromosome(peptideSearchResults, proteinToOLNMap,
                        genome);
        PeptideSequenceGenerator sequenceGenerator = new PeptideSequenceGeneratorImpl(
View Full Code Here

Examples of au.org.intersect.samifier.parser.PeptideSearchResultsParserImpl.parseResults()

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        ProteinToOLNMap proteinToOLNMap = proteinToOLNParser
                .parseMappingFile(proteinToOLNMapFile);

        PeptideSearchResultsParser peptideSearchResultsParser = new PeptideSearchResultsParserImpl(
                proteinToOLNMap);
        List<PeptideSearchResult> peptideSearchResults = peptideSearchResultsParser
                .parseResults(searchResultsPaths);
        PeptideSequenceGenerator sequenceGenerator = new PeptideSequenceGeneratorImpl(
                genome, proteinToOLNMap, chromosomeDir);
        peptideSearchResults = peptideSearchResultsParser
                .sortResultsByChromosome(peptideSearchResults, proteinToOLNMap,
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Examples of parsers.GeneralParser.parseResults()

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    GeneralParser generalParser = new GeneralParser(jncssPath, pmdPath,
        clocPath, clocLanguage);
   
    try {
      generalParser.parseResults();
      generalParser.saveResults(idVersion);
    } catch (InterruptedException e) {
      e.printStackTrace();
    } catch (Exception e) {
      e.printStackTrace();
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