Package eu.isas.peptideshaker.export.sections

Examples of eu.isas.peptideshaker.export.sections.PsPeptideSection


                section.writeSection(annotationPreferences, waitingHandler);
            } else if (sectionName.equals(PsInputFilterFeature.type)) {
                PsInputFilterSection section = new PsInputFilterSection(exportScheme.getExportFeatures(sectionName), exportScheme.isIndexes(), exportScheme.isHeader(), exportWriter);
                section.writeSection(idFilter, waitingHandler);
            } else if (sectionName.equals(PsPeptideFeature.type)) {
                PsPeptideSection section = new PsPeptideSection(exportScheme.getExportFeatures(sectionName), exportScheme.isIndexes(), exportScheme.isHeader(), exportWriter);
                section.writeSection(identification, identificationFeaturesGenerator, searchParameters, annotationPreferences, sequenceMatchingPreferences, peptideKeys, nSurroundingAA, "", exportScheme.isValidatedOnly(), exportScheme.isIncludeDecoy(), waitingHandler);
            } else if (sectionName.equals(PsProjectFeature.type)) {
                PsProjectSection section = new PsProjectSection(exportScheme.getExportFeatures(sectionName), exportScheme.isIndexes(), exportScheme.isHeader(), exportWriter);
                section.writeSection(experiment, sample, replicateNumber, projectDetails, waitingHandler);
            } else if (sectionName.equals(PsProteinFeature.type)) {
                PsProteinSection section = new PsProteinSection(exportScheme.getExportFeatures(sectionName), exportScheme.isIndexes(), exportScheme.isHeader(), exportWriter);
                section.writeSection(identification, identificationFeaturesGenerator, searchParameters, annotationPreferences, sequenceMatchingPreferences, psmKeys, nSurroundingAA, exportScheme.isValidatedOnly(), exportScheme.isIncludeDecoy(), waitingHandler);
            } else if (sectionName.equals(PsPsmFeature.type)) {
                PsPsmSection section = new PsPsmSection(exportScheme.getExportFeatures(sectionName), exportScheme.isIndexes(), exportScheme.isHeader(), exportWriter);
                section.writeSection(identification, identificationFeaturesGenerator, searchParameters, annotationPreferences, sequenceMatchingPreferences, psmKeys, "", exportScheme.isValidatedOnly(), exportScheme.isIncludeDecoy(), waitingHandler);
            } else if (sectionName.equals(PsIdentificationAlgorithmMatchesFeature.type)) {
                PsIdentificationAlgorithmMatchesSection section = new PsIdentificationAlgorithmMatchesSection(exportScheme.getExportFeatures(sectionName), exportScheme.isIndexes(), exportScheme.isHeader(), exportWriter);
                section.writeSection(identification, identificationFeaturesGenerator, searchParameters, annotationPreferences, sequenceMatchingPreferences, psmKeys, "", waitingHandler);
            } else if (sectionName.equals(PsPtmScoringFeature.type)) {
                PsPtmScoringSection section = new PsPtmScoringSection(exportScheme.getExportFeatures(sectionName), exportScheme.isIndexes(), exportScheme.isHeader(), exportWriter);
                section.writeSection(ptmcoringPreferences, waitingHandler);
            } else if (sectionName.equals(PsSearchFeature.type)) {
                PsSearchParametersSection section = new PsSearchParametersSection(exportScheme.getExportFeatures(sectionName), exportScheme.isIndexes(), exportScheme.isHeader(), exportWriter);
                section.writeSection(searchParameters, waitingHandler);
            } else if (sectionName.equals(PsSpectrumCountingFeature.type)) {
                PsSpectrumCountingSection section = new PsSpectrumCountingSection(exportScheme.getExportFeatures(sectionName), exportScheme.isIndexes(), exportScheme.isHeader(), exportWriter);
                section.writeSection(spectrumCountingPreferences, waitingHandler);
            } else if (sectionName.equals(PsValidationFeature.type)) {
                PsValidationSection section = new PsValidationSection(exportScheme.getExportFeatures(sectionName), exportScheme.isIndexes(), exportScheme.isHeader(), exportWriter);
                PSMaps psMaps = new PSMaps();
                psMaps = (PSMaps) identification.getUrParam(psMaps);
                section.writeSection(psMaps, waitingHandler);
            } else {
                throw new UnsupportedOperationException("Sectrion " + sectionName + " not implemented.");
            }
        }
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