Examples of sortResultsByChromosome()

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

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        if (bedfilePath != null) {
            bedWriter = new FileWriter(bedfilePath);
        }
        FileWriter sam = new FileWriter(outfile);
        // sort search result by proteins
        peptideSearchResults = peptideSearchResultsParser.sortResultsByChromosome(peptideSearchResults, proteinToOLNMap, genome);
        createSAM(peptideSearchResults, sam, bedWriter);
    }

    public void createSAM(List<PeptideSearchResult> peptideSearchResults,
            Writer output, Writer bedWriter)
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Examples of au.org.intersect.samifier.parser.PeptideSearchResultsParser.sortResultsByChromosome()

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

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                proteinToOLNMap);
        List<PeptideSearchResult> peptideSearchResults = peptideSearchResultsParser
                .parseResults(searchResultsPaths);
        PeptideSequenceGenerator sequenceGenerator = new PeptideSequenceGeneratorImpl(
                genome, proteinToOLNMap, chromosomeDir);
        peptideSearchResults = peptideSearchResultsParser
                .sortResultsByChromosome(peptideSearchResults, proteinToOLNMap,
                        genome);
        FileWriter output = new FileWriter(outputFile);

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

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        if (bedfilePath != null) {
            bedWriter = new FileWriter(bedfilePath);
        }
        FileWriter sam = new FileWriter(outfile);
        // sort search result by proteins
        peptideSearchResults = peptideSearchResultsParser.sortResultsByChromosome(peptideSearchResults, proteinToOLNMap, genome);
        createSAM(peptideSearchResults, sam, bedWriter);
    }

    public void createSAM(List<PeptideSearchResult> peptideSearchResults,
            Writer output, Writer bedWriter)
View Full Code Here

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

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

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

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                proteinToOLNMap);
        List<PeptideSearchResult> peptideSearchResults = peptideSearchResultsParser
                .parseResults(searchResultsPaths);
        PeptideSequenceGenerator sequenceGenerator = new PeptideSequenceGeneratorImpl(
                genome, proteinToOLNMap, chromosomeDir);
        peptideSearchResults = peptideSearchResultsParser
                .sortResultsByChromosome(peptideSearchResults, proteinToOLNMap,
                        genome);
        FileWriter output = new FileWriter(outputFile);

        for (PeptideSearchResult peptideSearchResult : peptideSearchResults) {
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