List of writeSection() Examples

Examples of writeSection()

eu.isas.peptideshaker.export.sections.PsAnnotationSection.writeSection()
Writes the desired section. @param annotationPreferences the annotation preferences of the project @param waitingHandler the waiting handler @throws IOException exception thrown whenever an error occurred whilewriting the file.
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
eu.isas.peptideshaker.export.sections.PsInputFilterSection.writeSection()
Writes the desired section. @param idFilter the identification used for this project @param waitingHandler the waiting handler @throws IOException exception thrown whenever an error occurred whilewriting the file.
eu.isas.peptideshaker.export.sections.PsPeptideSection.writeSection()
Writes the desired section. @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 sequenceMatchingPreferences the sequence matching preferences @param keys the keys of the protein matches to output @param nSurroundingAA the number of surrounding amino acids to export @param linePrefix the line prefix to use. @param validatedOnly whether only validated matches should be exported @param decoys whether decoy matches should be exported as well @param waitingHandler the waiting handler @throws IOException exception thrown whenever an error occurred whilewriting the file. @throws IllegalArgumentException @throws SQLException @throws ClassNotFoundException @throws InterruptedException @throws MzMLUnmarshallerException
eu.isas.peptideshaker.export.sections.PsProjectSection.writeSection()
Writes the desired section. @param experiment the experiment name @param sample the sample name @param replicateNumber the replicate number @param projectDetails the details of this project @param waitingHandler the waiting handler @throws IOException exception thrown whenever an error occurred whilewriting the file.
eu.isas.peptideshaker.export.sections.PsProteinSection.writeSection()
Writes the desired section. @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 sequenceMatchingPreferences the sequence matching preferences @param keys the keys of the protein matches to output. if null allproteins will be exported. @param nSurroundingAas in case a peptide export is included withsurrounding amino-acids, the number of surrounding amino acids to use @param validatedOnly whether only validated matches should be exported @param decoys whether decoy matches should be exported as well @param waitingHandler the waiting handler @throws IOException exception thrown whenever an error occurred whilewriting the file. @throws IllegalArgumentException @throws SQLException @throws ClassNotFoundException @throws InterruptedException @throws MzMLUnmarshallerException @throws org.apache.commons.math.MathException
eu.isas.peptideshaker.export.sections.PsPsmSection.writeSection()
Writes the desired section. @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 sequenceMatchingPreferences the sequence matching preferences @param keys the keys of the PSM matches to output @param linePrefix the line prefix @param validatedOnly whether only validated matches should be exported @param decoys whether decoy matches should be exported as well @param waitingHandler the waiting handler @throws IOException exception thrown whenever an error occurred whilewriting the file. @throws IllegalArgumentException @throws SQLException @throws ClassNotFoundException @throws InterruptedException @throws MzMLUnmarshallerException
eu.isas.peptideshaker.export.sections.PsPtmScoringSection.writeSection()
Writes the desired section. @param ptmcoringPreferences the PTM scoring preferences of this project @param waitingHandler the waiting handler @throws IOException exception thrown whenever an error occurred whilewriting the file.
eu.isas.peptideshaker.export.sections.PsSearchParametersSection.writeSection()
Writes the desired section. @param searchParameters the search parameters of this project @param waitingHandler the waiting handler @throws IOException exception thrown whenever an error occurred whilewriting the file.
eu.isas.peptideshaker.export.sections.PsSpectrumCountingSection.writeSection()
Writes the desired section. @param spectrumCountingPreferences the spectrum counting preferences ofthis project @param waitingHandler the waiting handler @throws IOException exception thrown whenever an error occurred whilewriting the file.
eu.isas.peptideshaker.export.sections.PsValidationSection.writeSection()
Writes the desired section. @param psMaps the target/decoy maps of this project @param waitingHandler the waiting handler @throws IOException exception thrown whenever an error occurred whilewriting the file.

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

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

            } 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);

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

            } 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);

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

            } 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);

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

            } 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);

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

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

            if (sectionName.equals(PsAnnotationFeature.type)) {
                PsAnnotationSection section = new PsAnnotationSection(exportScheme.getExportFeatures(sectionName), exportScheme.isIndexes(), exportScheme.isHeader(), exportWriter);
                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);

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

            } 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);

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

            } 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);

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

            } 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);

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