Package com.compomics.util.preferences

Examples of com.compomics.util.preferences.ProcessingPreferences

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        spectrumCountingPreferences = new SpectrumCountingPreferences();
        ptmScoringPreferences = new PTMScoringPreferences();
        filterPreferences = new FilterPreferences();
        displayPreferences = new DisplayPreferences();
        searchParameters = new SearchParameters();
        processingPreferences = new ProcessingPreferences();
        genePreferences = new GenePreferences();
        sequenceMatchingPreferences = null;
        idFilter = new IdFilter();
    }
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        annotationPreferences.setAnnotationLevel(0.75);
        annotationPreferences.useAutomaticAnnotation(true);
        spectrumCountingPreferences = new SpectrumCountingPreferences();
        spectrumCountingPreferences.setSelectedMethod(SpectralCountingMethod.NSAF);
        spectrumCountingPreferences.setValidatedHits(true);
        processingPreferences = new ProcessingPreferences();
        ptmScoringPreferences = new PTMScoringPreferences();
        genePreferences = new GenePreferences();
        sequenceMatchingPreferences = SequenceMatchingPreferences.getDefaultSequenceMatching(searchParameters);
        idFilter = new IdFilter();
    }
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        idFilter.setMaxMzDeviation(cliInputBean.getMaxMzDeviation());
        idFilter.setIsPpm(cliInputBean.isMaxMassDeviationPpm());
        idFilter.setRemoveUnknownPTMs(cliInputBean.excludeUnknownPTMs());

        // set the processing settings
        processingPreferences = new ProcessingPreferences();
        processingPreferences.setPsmFDR(cliInputBean.getPsmFDR());
        processingPreferences.setPeptideFDR(cliInputBean.getPeptideFDR());
        processingPreferences.setProteinFDR(cliInputBean.getProteinFDR());
        processingPreferences.setProteinConfidenceMwPlots(cliInputBean.getProteinConfidenceMwPlots());
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     *
     * @return the initial processing preferences
     */
    public ProcessingPreferences getProcessingPreferences() {
        if (cpsBean.getProcessingPreferences() == null) {
            cpsBean.setProcessingPreferences(new ProcessingPreferences());
        }
        return cpsBean.getProcessingPreferences();
    }
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     * Sets the initial processing preferences.
     *
     * @param processingPreferences the initial processing preferences
     */
    public void setProcessingPreferences(ProcessingPreferences processingPreferences) {
        cpsBean.setProcessingPreferences(new ProcessingPreferences());
    }
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            // convert old settings files using utilities version 3.10.68 or older

            // convert the old ProcessingPreferences object
            PSSettings tempSettings = (PSSettings) experiment.getUrParam(experimentSettings);
            ProcessingPreferences tempProcessingPreferences = new ProcessingPreferences();
            tempProcessingPreferences.setProteinFDR(tempSettings.getProcessingPreferences().getProteinFDR());
            tempProcessingPreferences.setPeptideFDR(tempSettings.getProcessingPreferences().getPeptideFDR());
            tempProcessingPreferences.setPsmFDR(tempSettings.getProcessingPreferences().getPsmFDR());

            // convert the old PTMScoringPreferences object
            PTMScoringPreferences tempPTMScoringPreferences = new PTMScoringPreferences();
            tempPTMScoringPreferences.setaScoreCalculation(tempSettings.getPTMScoringPreferences().aScoreCalculation());
            tempPTMScoringPreferences.setaScoreNeutralLosses(tempSettings.getPTMScoringPreferences().isaScoreNeutralLosses());
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     *
     * @return the initial processing preferences
     */
    public ProcessingPreferences getProcessingPreferences() {
        if (processingPreferences == null) {
            processingPreferences = new ProcessingPreferences();
        }
        return processingPreferences;
    }
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Related Classes of com.compomics.util.preferences.ProcessingPreferences

  • eu.isas.peptideshaker.cmd.PeptideShakerCLI
  • eu.isas.peptideshaker.fileimport.CpsFileImporter
  • eu.isas.peptideshaker.gui.PeptideShakerGUI
  • eu.isas.peptideshaker.myparameters.PeptideShakerSettings
  • eu.isas.peptideshaker.utils.CpsParent
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