Examples of eu.isas.peptideshaker.preferences.FilterPreferences

Package eu.isas.peptideshaker.preferences

Examples of eu.isas.peptideshaker.preferences.FilterPreferences

eu.isas.peptideshaker.preferences.FilterPreferences
This class groups the display filter preferences. @author Marc Vaudel

            genePreferences.setCurrentSpeciesType("Vertebrates");
        }


        // backwards compatability for the filter preferences
        if (filterPreferences == null) {
            filterPreferences = new FilterPreferences();
        }


        // backwards compatability for the display preferences
        if (displayPreferences != null) {
            displayPreferences.compatibilityCheck(searchParameters.getModificationProfile());

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     */
    public void clearPreferences() {
        annotationPreferences = new AnnotationPreferences();
        spectrumCountingPreferences = new SpectrumCountingPreferences();
        ptmScoringPreferences = new PTMScoringPreferences();
        filterPreferences = new FilterPreferences();
        displayPreferences = new DisplayPreferences();
        searchParameters = new SearchParameters();
        processingPreferences = new ProcessingPreferences();
        genePreferences = new GenePreferences();
        sequenceMatchingPreferences = null;

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     * @throws java.sql.SQLException
     * @throws java.lang.InterruptedException
     * @throws uk.ac.ebi.jmzml.xml.io.MzMLUnmarshallerException
     */
    public boolean isProteinHidden(String match) throws IOException, ClassNotFoundException, SQLException, InterruptedException, MzMLUnmarshallerException {
        FilterPreferences filterPreferences = peptideShakerGUI.getFilterPreferences();
        for (ProteinFilter matchFilter : filterPreferences.getProteinHideFilters().values()) {
            if (matchFilter.isActive() && matchFilter.isValidated(match, peptideShakerGUI.getIdentification(), peptideShakerGUI.getIdentificationFeaturesGenerator(), peptideShakerGUI.getSearchParameters(), peptideShakerGUI.getAnnotationPreferences())) {
                return true;
            }
        }
        return false;

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     * @throws java.lang.ClassNotFoundException
     * @throws java.sql.SQLException
     * @throws java.lang.InterruptedException
     */
    public boolean isPeptideHidden(String match) throws SQLException, IOException, ClassNotFoundException, InterruptedException {
        FilterPreferences filterPreferences = peptideShakerGUI.getFilterPreferences();


        for (PeptideFilter matchFilter : filterPreferences.getPeptideHideFilters().values()) {
            if (matchFilter.isActive() && matchFilter.isValidated(match, peptideShakerGUI.getIdentification(), peptideShakerGUI.getIdentificationFeaturesGenerator())) {
                return true;
            }
        }

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     * @throws java.sql.SQLException
     * @throws java.lang.InterruptedException
     * @throws uk.ac.ebi.jmzml.xml.io.MzMLUnmarshallerException
     */
    public boolean isPsmHidden(String match) throws SQLException, IOException, ClassNotFoundException, InterruptedException, MzMLUnmarshallerException {
        FilterPreferences filterPreferences = peptideShakerGUI.getFilterPreferences();


        for (PsmFilter matchFilter : filterPreferences.getPsmHideFilters().values()) {
            if (matchFilter.isActive() && matchFilter.isValidated(match, peptideShakerGUI.getIdentification(), peptideShakerGUI.getSearchParameters(), peptideShakerGUI.getAnnotationPreferences())) {
                return true;
            }
        }

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     * @throws java.sql.SQLException
     * @throws java.lang.InterruptedException
     * @throws uk.ac.ebi.jmzml.xml.io.MzMLUnmarshallerException
     */
    public boolean isProteinStarred(String match) throws IOException, ClassNotFoundException, SQLException, InterruptedException, MzMLUnmarshallerException {
        FilterPreferences filterPreferences = peptideShakerGUI.getFilterPreferences();


        for (ProteinFilter matchFilter : filterPreferences.getProteinStarFilters().values()) {
            if (matchFilter.isActive() && matchFilter.isValidated(match, peptideShakerGUI.getIdentification(), peptideShakerGUI.getIdentificationFeaturesGenerator(), peptideShakerGUI.getSearchParameters(), peptideShakerGUI.getAnnotationPreferences())) {
                return true;
            }
        }

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     * @throws java.io.IOException
     * @throws java.lang.ClassNotFoundException
     * @throws java.lang.InterruptedException
     */
    public boolean isPeptideStarred(String match) throws SQLException, IOException, ClassNotFoundException, InterruptedException {
        FilterPreferences filterPreferences = peptideShakerGUI.getFilterPreferences();


        for (PeptideFilter matchFilter : filterPreferences.getPeptideStarFilters().values()) {
            if (matchFilter.isActive() && matchFilter.isValidated(match, peptideShakerGUI.getIdentification(), peptideShakerGUI.getIdentificationFeaturesGenerator())) {
                return true;
            }
        }

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     * @throws java.lang.ClassNotFoundException
     * @throws uk.ac.ebi.jmzml.xml.io.MzMLUnmarshallerException
     * @throws java.lang.InterruptedException
     */
    public boolean isPsmStarred(String match) throws SQLException, IOException, ClassNotFoundException, InterruptedException, MzMLUnmarshallerException {
        FilterPreferences filterPreferences = peptideShakerGUI.getFilterPreferences();
        for (PsmFilter matchFilter : filterPreferences.getPsmStarFilters().values()) {
            if (matchFilter.isActive() && matchFilter.isValidated(match, peptideShakerGUI.getIdentification(), peptideShakerGUI.getSearchParameters(), peptideShakerGUI.getAnnotationPreferences())) {
                return true;
            }
        }
        return false;

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     * @throws java.lang.InterruptedException
     */
    public void starProtein(String match) throws IOException, ClassNotFoundException, SQLException, InterruptedException {
        try {
            Identification identification = peptideShakerGUI.getIdentification();
            FilterPreferences filterPreferences = peptideShakerGUI.getFilterPreferences();
            PSParameter psParameter = new PSParameter();
            psParameter = (PSParameter) identification.getProteinMatchParameter(match, psParameter);
            boolean validated = false;


            for (ProteinFilter matchFilter : filterPreferences.getProteinStarFilters().values()) {
                if (matchFilter.getExceptions().contains(match)) {
                    matchFilter.removeException(match);
                }
                if (matchFilter.isValidated(match, peptideShakerGUI.getIdentification(), peptideShakerGUI.getIdentificationFeaturesGenerator(), peptideShakerGUI.getSearchParameters(), peptideShakerGUI.getAnnotationPreferences())) {
                    validated = true;
                }
            }


            if (!validated) {
                ProteinFilter proteinFilter;
                if (!filterPreferences.getProteinStarFilters().containsKey(MatchFilter.MANUAL_SELECTION)) {
                    proteinFilter = new ProteinFilter(MatchFilter.MANUAL_SELECTION);
                    proteinFilter.setDescription("Manual selection via the graphical interface");
                    filterPreferences.getProteinStarFilters().put(proteinFilter.getName(), proteinFilter);
                } else {
                    proteinFilter = filterPreferences.getProteinStarFilters().get(MatchFilter.MANUAL_SELECTION);
                }
                proteinFilter.addManualValidation(match);
            }


            psParameter.setStarred(true);

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     */
    public void unStarProtein(String match) throws IOException, ClassNotFoundException, SQLException, InterruptedException {


        try {
            Identification identification = peptideShakerGUI.getIdentification();
            FilterPreferences filterPreferences = peptideShakerGUI.getFilterPreferences();
            PSParameter psParameter = new PSParameter();
            psParameter = (PSParameter) identification.getProteinMatchParameter(match, psParameter);


            for (ProteinFilter matchFilter : filterPreferences.getProteinStarFilters().values()) {
                if (matchFilter.getManualValidation().contains(match)) {
                    matchFilter.removeManualValidation(match);
                }
                if (matchFilter.isValidated(match, peptideShakerGUI.getIdentification(), peptideShakerGUI.getIdentificationFeaturesGenerator(), peptideShakerGUI.getSearchParameters(), peptideShakerGUI.getAnnotationPreferences())) {
                    matchFilter.addException(match);

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

eu.isas.peptideshaker.utils.CpsParent

eu.isas.peptideshaker.utils.StarHider

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