Examples with PsAnnotationSection eu.isas.peptideshaker.export.sections.PsAnnotationSection used on opensource projects

Example 1 with PsAnnotationSection

use of eu.isas.peptideshaker.export.sections.PsAnnotationSection in project peptide-shaker by compomics.

the class PSExportFactory method writeExport.

/**
 * Writes the desired export in text format. If an argument is not needed,
 * provide null (at your own risks).
 *
 * @param exportScheme the scheme of the export
 * @param destinationFile the destination file
 * @param exportFormat the format of export to use
 * @param gzip if true export text as gzipped file
 * @param experiment the experiment corresponding to this project (mandatory
 * for the Project section)
 * @param projectDetails the project details (mandatory for the Project
 * section)
 * @param identification the identification (mandatory for the Protein,
 * Peptide and PSM sections)
 * @param identificationFeaturesGenerator the identification features
 * generator (mandatory for the Protein, Peptide and PSM sections)
 * @param geneMaps the gene maps
 * @param proteinKeys the protein keys to export (mandatory for the Protein
 * section)
 * @param peptideKeys the peptide keys to export (mandatory for the Peptide
 * section)
 * @param psmKeys the keys of the PSMs to export (mandatory for the PSM
 * section)
 * @param nSurroundingAA the number of surrounding amino acids to export
 * (mandatory for the Peptide section)
 * @param identificationParameters the identification parameters
 * @param sequenceProvider a provider for the protein sequences
 * @param proteinDetailsProvider the protein details provider
 * @param spectrumProvider the spectrum provider
 * @param spectrumCountingPreferences the spectrum counting preferences
 * (mandatory for the spectrum counting section)
 * @param waitingHandler the waiting handler
 *
 * @throws IOException exception thrown whenever an IO exception occurred
 * while reading or writing to a file
 */
public static void writeExport(ExportScheme exportScheme, File destinationFile, ExportFormat exportFormat, boolean gzip, String experiment, ProjectDetails projectDetails, Identification identification, IdentificationFeaturesGenerator identificationFeaturesGenerator, GeneMaps geneMaps, long[] proteinKeys, long[] peptideKeys, long[] psmKeys, int nSurroundingAA, IdentificationParameters identificationParameters, SequenceProvider sequenceProvider, ProteinDetailsProvider proteinDetailsProvider, SpectrumProvider spectrumProvider, SpectrumCountingParameters spectrumCountingPreferences, WaitingHandler waitingHandler) throws IOException {
    ExportWriter exportWriter = ExportWriter.getExportWriter(exportFormat, destinationFile, exportScheme.getSeparator(), exportScheme.getSeparationLines(), gzip);
    if (exportWriter instanceof ExcelWriter) {
        ExcelWriter excelWriter = (ExcelWriter) exportWriter;
        PsExportStyle exportStyle = PsExportStyle.getReportStyle(excelWriter);
        excelWriter.setWorkbookStyle(exportStyle);
    }
    exportWriter.writeMainTitle(exportScheme.getMainTitle());
    for (String sectionName : exportScheme.getSections()) {
        if (exportScheme.isIncludeSectionTitles()) {
            exportWriter.startNewSection(sectionName);
        } else {
            exportWriter.startNewSection();
        }
        switch(sectionName) {
            case PsAnnotationFeature.type:
                PsAnnotationSection psAnnotationSection = new PsAnnotationSection(exportScheme.getExportFeatures(sectionName), exportScheme.isIndexes(), exportScheme.isHeader(), exportWriter);
                psAnnotationSection.writeSection(identificationParameters.getAnnotationParameters(), waitingHandler);
                break;
            case PsInputFilterFeature.type:
                PsInputFilterSection psInputFilterSection = new PsInputFilterSection(exportScheme.getExportFeatures(sectionName), exportScheme.isIndexes(), exportScheme.isHeader(), exportWriter);
                psInputFilterSection.writeSection(identificationParameters.getPeptideAssumptionFilter(), waitingHandler);
                break;
            case PsPeptideFeature.type:
                PsPeptideSection psPeptideSection = new PsPeptideSection(exportScheme.getExportFeatures(sectionName), exportScheme.isIndexes(), exportScheme.isHeader(), exportWriter);
                psPeptideSection.writeSection(identification, identificationFeaturesGenerator, sequenceProvider, proteinDetailsProvider, spectrumProvider, identificationParameters, peptideKeys, nSurroundingAA, "", exportScheme.isValidatedOnly(), exportScheme.isIncludeDecoy(), waitingHandler);
                break;
            case PsProjectFeature.type:
                PsProjectSection psProjectSection = new PsProjectSection(exportScheme.getExportFeatures(sectionName), exportScheme.isIndexes(), exportScheme.isHeader(), exportWriter);
                psProjectSection.writeSection(experiment, projectDetails, waitingHandler);
                break;
            case PsProteinFeature.type:
                PsProteinSection psProteinSection = new PsProteinSection(exportScheme.getExportFeatures(sectionName), exportScheme.isIndexes(), exportScheme.isHeader(), exportWriter);
                psProteinSection.writeSection(identification, identificationFeaturesGenerator, sequenceProvider, proteinDetailsProvider, spectrumProvider, geneMaps, identificationParameters, proteinKeys, nSurroundingAA, exportScheme.isValidatedOnly(), exportScheme.isIncludeDecoy(), waitingHandler);
                break;
            case PsPsmFeature.type:
                PsPsmSection psPsmSection = new PsPsmSection(exportScheme.getExportFeatures(sectionName), exportScheme.isIndexes(), exportScheme.isHeader(), exportWriter);
                psPsmSection.writeSection(identification, identificationFeaturesGenerator, sequenceProvider, proteinDetailsProvider, spectrumProvider, identificationParameters, psmKeys, "", nSurroundingAA, exportScheme.isValidatedOnly(), exportScheme.isIncludeDecoy(), waitingHandler);
                break;
            case PsIdentificationAlgorithmMatchesFeature.type:
                PsIdentificationAlgorithmMatchesSection psIdentificationAlgorithmMatchesSection = new PsIdentificationAlgorithmMatchesSection(exportScheme.getExportFeatures(sectionName), exportScheme.isIndexes(), exportScheme.isHeader(), exportWriter);
                psIdentificationAlgorithmMatchesSection.writeSection(identification, identificationFeaturesGenerator, sequenceProvider, proteinDetailsProvider, spectrumProvider, identificationParameters, psmKeys, "", nSurroundingAA, waitingHandler);
                break;
            case PsPtmScoringFeature.type:
                PsPtmScoringSection psPtmScoringSection = new PsPtmScoringSection(exportScheme.getExportFeatures(sectionName), exportScheme.isIndexes(), exportScheme.isHeader(), exportWriter);
                psPtmScoringSection.writeSection(identificationParameters.getModificationLocalizationParameters(), waitingHandler);
                break;
            case PsSearchFeature.type:
                PsSearchParametersSection psSearchParametersSection = new PsSearchParametersSection(exportScheme.getExportFeatures(sectionName), exportScheme.isIndexes(), exportScheme.isHeader(), exportWriter);
                psSearchParametersSection.writeSection(identificationParameters.getSearchParameters(), projectDetails, waitingHandler);
                break;
            case PsSpectrumCountingFeature.type:
                PsSpectrumCountingSection psSpectrumCountingSection = new PsSpectrumCountingSection(exportScheme.getExportFeatures(sectionName), exportScheme.isIndexes(), exportScheme.isHeader(), exportWriter);
                psSpectrumCountingSection.writeSection(spectrumCountingPreferences, waitingHandler);
                break;
            case PsValidationFeature.type:
                PsValidationSection psValidationSection = new PsValidationSection(exportScheme.getExportFeatures(sectionName), exportScheme.isIndexes(), exportScheme.isHeader(), exportWriter);
                PSMaps psMaps = new PSMaps();
                psMaps = (PSMaps) identification.getUrParam(psMaps);
                psValidationSection.writeSection(psMaps, identificationParameters, waitingHandler);
                break;
            default:
                throw new UnsupportedOperationException("Section " + sectionName + " not implemented.");
        }
    }
    exportWriter.close();
}