Package com.compomics.util.preferences

Examples of com.compomics.util.preferences.GenePreferences

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     */
    public void displayResults() {

        if (peptideShakerGUI.getIdentification() != null) {

            GenePreferences genePreferences = peptideShakerGUI.getGenePreferences();
            String selectedSpecies = genePreferences.getCurrentSpecies();

            if (selectedSpecies == null) {
                new SpeciesDialog(peptideShakerGUI, genePreferences, true, peptideShakerGUI.getWaitingIcon(), peptideShakerGUI.getNormalIcon());
                selectedSpecies = genePreferences.getCurrentSpecies();
            }

            if (selectedSpecies != null) {

                String speciesDatabase = genePreferences.getAllSpeciesMap().get(genePreferences.getCurrentSpeciesType()).get(selectedSpecies);

                if (speciesDatabase != null) {

                    final File goMappingsFile = new File(genePreferences.getGeneMappingFolder(), speciesDatabase + GenePreferences.GO_MAPPING_FILE_SUFFIX);
                    final File geneMappingsFile = new File(genePreferences.getGeneMappingFolder(), speciesDatabase + GenePreferences.GENE_MAPPING_FILE_SUFFIX);

                    if (goMappingsFile.exists()) {

                        progressDialog = new ProgressDialogX(peptideShakerGUI,
                                Toolkit.getDefaultToolkit().getImage(getClass().getResource("/icons/peptide-shaker.gif")),
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        }

        // set the gene preferences
        if (cliInputBean.getSpecies() != null) {
            try {
                genePreferences = new GenePreferences();
                genePreferences.loadSpeciesAndGoDomains();
                genePreferences.setCurrentSpecies(cliInputBean.getSpecies());
                genePreferences.setCurrentSpeciesType(cliInputBean.getSpeciesType());

                // try to download gene and go information
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     * Open the species selection dialog.
     *
     * @param evt
     */
    private void speciesJMenuItemActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_speciesJMenuItemActionPerformed
        GenePreferences genePreferences = getGenePreferences();
        String oldSpecies = genePreferences.getCurrentSpecies();
        new SpeciesDialog(this, genePreferences, true, getWaitingIcon(), getNormalIcon());
        String newSpecies = genePreferences.getCurrentSpecies();

        if (oldSpecies == null || !oldSpecies.equals(newSpecies)) {
            clearGeneMappings(); // clear the old mappings
            if (newSpecies != null) {
                loadGeneMappings(); // load the new mappings
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        if (getSelectedTab() == PeptideShakerGUI.GO_ANALYSIS_TAB_INDEX) {
            goPanel.displayResults();
        } else {
            setUpdated(PeptideShakerGUI.GO_ANALYSIS_TAB_INDEX, false);

            GenePreferences genePreferences = getGenePreferences();
            String selectedSpecies = genePreferences.getCurrentSpecies();
            String currentSpeciesType = genePreferences.getCurrentSpeciesType();

            if (currentSpeciesType != null) {

                String speciesDatabase = genePreferences.getEnsemblDatabaseName(currentSpeciesType, selectedSpecies);

                if (speciesDatabase != null) {

                    final File goMappingsFile = new File(genePreferences.getGeneMappingFolder(), speciesDatabase + GenePreferences.GO_MAPPING_FILE_SUFFIX);

                    if (goMappingsFile.exists()) {

                        progressDialog = new ProgressDialogX(this,
                                Toolkit.getDefaultToolkit().getImage(getClass().getResource("/icons/peptide-shaker.gif")),
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            experimentSettings = new PeptideShakerSettings(tempSettings.getSearchParameters(), tempSettings.getAnnotationPreferences(),
                    tempSettings.getSpectrumCountingPreferences(), tempSettings.getProjectDetails(), tempSettings.getFilterPreferences(),
                    tempSettings.getDisplayPreferences(),
                    tempSettings.getMetrics(), tempProcessingPreferences, tempSettings.getIdentificationFeaturesCache(),
                    tempPTMScoringPreferences, new GenePreferences(), new IdFilter(), SequenceMatchingPreferences.getDefaultSequenceMatching(tempSettings.getSearchParameters()));

        } else {
            experimentSettings = (PeptideShakerSettings) experiment.getUrParam(experimentSettings);
        }
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        displayPreferences = experimentSettings.getDisplayPreferences();
        sequenceMatchingPreferences = experimentSettings.getSequenceMatchingPreferences();

        // backwards compatability for the gene preferences
        if (genePreferences.getCurrentSpecies() == null) {
            genePreferences = new GenePreferences();
        }
        if (genePreferences.getCurrentSpecies() != null && genePreferences.getCurrentSpeciesType() == null) {
            genePreferences.setCurrentSpeciesType("Vertebrates");
        }
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        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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        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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     *
     * @return the gene preferences
     */
    public GenePreferences getGenePreferences() {
        if (genePreferences == null) {
            genePreferences = new GenePreferences();
        }
        return genePreferences;
    }
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Related Classes of com.compomics.util.preferences.GenePreferences

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