Examples of eu.isas.peptideshaker.preferences.SpectrumCountingPreferences

Package eu.isas.peptideshaker.preferences

Examples of eu.isas.peptideshaker.preferences.SpectrumCountingPreferences

eu.isas.peptideshaker.preferences.SpectrumCountingPreferences
This class contains the spectrum counting preferences. @author Marc Vaudel @author Harald Barsnes

    /**
     * Resets the preferences.
     */
    public void clearPreferences() {
        annotationPreferences = new AnnotationPreferences();
        spectrumCountingPreferences = new SpectrumCountingPreferences();
        ptmScoringPreferences = new PTMScoringPreferences();
        filterPreferences = new FilterPreferences();
        displayPreferences = new DisplayPreferences();
        searchParameters = new SearchParameters();
        processingPreferences = new ProcessingPreferences();

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    public void setDefaultPreferences() {
        searchParameters = new SearchParameters();
        annotationPreferences = new AnnotationPreferences();
        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();

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                e.printStackTrace();
            }
        }


        // set the spectrum counting prefrences
        spectrumCountingPreferences = new SpectrumCountingPreferences();


        // set the annotation preferences
        annotationPreferences = new AnnotationPreferences();
        annotationPreferences.setPreferencesFromSearchParameters(searchParameters);
        IonFactory.getInstance().addDefaultNeutralLoss(NeutralLoss.NH3);

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                result = estimateSpectrumCounting(proteinMatchKey);
                identificationFeaturesCache.addObject(IdentificationFeaturesCache.ObjectType.spectrum_counting, proteinMatchKey, result);
            }
            return result;
        } else {
            SpectrumCountingPreferences tempPreferences = new SpectrumCountingPreferences();
            tempPreferences.setSelectedMethod(method);
            return estimateSpectrumCounting(identification, sequenceFactory, proteinMatchKey, tempPreferences,
                    searchParameters.getEnzyme(), idFilter.getMaxPepLength(), sequenceMatchingPreferences);
        }
    }

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Related Classes of eu.isas.peptideshaker.preferences.SpectrumCountingPreferences

eu.isas.peptideshaker.cmd.PeptideShakerCLI

eu.isas.peptideshaker.utils.CpsParent

eu.isas.peptideshaker.utils.IdentificationFeaturesGenerator

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