Package au.org.intersect.samifier.generator

Examples of au.org.intersect.samifier.generator.LocationGenerator

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        this.accessionWriter = accessionWriter;
        this.fastaParser = new FastaParserImpl(genomeFile);
    }

    public void run() throws Exception {
        LocationGenerator locationGenerator = createLocationGenerator();
        List<ProteinLocation> locations = locationGenerator.generateLocations();
        generateProteinsFile(locations,
                CodonTranslationTable.parseTableFile(translationTableFile));
        generateGffFile(locations);
        generateAccessionFile(locations);
    }
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        generateGffFile(locations);
        generateAccessionFile(locations);
    }

    private LocationGenerator createLocationGenerator() {
        LocationGenerator locationGenerator;
        if (glimmerFilePath != null) {
            locationGenerator = new GlimmerFileLocationGenerator(
                    glimmerFilePath);
        } else {
            locationGenerator = new CodonsPerIntervalLocationGenerator(
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Related Classes of au.org.intersect.samifier.generator.LocationGenerator

  • au.org.intersect.samifier.runner.ProteinGeneratorRunner
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