Examples of eu.isas.peptideshaker.export.sections.PsIdentificationAlgorithmMatchesSection.writeSection()

eu.isas.peptideshaker.export.sections.PsIdentificationAlgorithmMatchesSection.writeSection()
Writes the desired section. Exports all algorithm assumptions including the decoy and non-validated matches. @param identification the identification of the project @param identificationFeaturesGenerator the identification featuresgenerator of the project @param searchParameters the search parameters of the project @param annotationPreferences the annotation preferences @param keys the keys of the PSM matches to output @param linePrefix the line prefix @param waitingHandler the waiting handler @param sequenceMatchingPreferences the sequence matching preferences @throws IOException exception thrown whenever an error occurred whilewriting the file. @throws IllegalArgumentException @throws SQLException @throws ClassNotFoundException @throws InterruptedException @throws MzMLUnmarshallerException

            } 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);

View Full Code Here

            } 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);

View Full Code Here

            } 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);

View Full Code Here

            } 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);

View Full Code Here

                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.");
            }
        }

View Full Code Here

TOP

All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.