Examples of PeptideShaker

eu.isas.peptideshaker.PeptideShaker
This class will be responsible for the identification import and the associated calculations. @author Marc Vaudel @author Harald Barsnes

Examples of eu.isas.peptideshaker.PeptideShaker

            @Override
            public void run() {


                PSMaps pSMaps = new PSMaps();
                pSMaps = (PSMaps) peptideShakerGUI.getIdentification().getUrParam(pSMaps);
                PeptideShaker miniShaker = new PeptideShaker(peptideShakerGUI.getExperiment(), peptideShakerGUI.getSample(), peptideShakerGUI.getReplicateNumber(), pSMaps);


                try {
                    miniShaker.spectrumMapChanged(peptideShakerGUI.getIdentification(), progressDialog, peptideShakerGUI.getProcessingPreferences(), peptideShakerGUI.getSearchParameters(), peptideShakerGUI.getSequenceMatchingPreferences());
                } catch (Exception e) {
                    JOptionPane.showMessageDialog(peptideShakerGUI, JOptionEditorPane.getJOptionEditorPane(
                            "An identification conflict occured. If you can reproduce the error <br>"
                            + "Please <a href=\"http://code.google.com/p/peptide-shaker/issues/list\">contact the developers</a>."),
                            "Identification Conflict", JOptionPane.ERROR_MESSAGE);

View Full Code Here

Examples of eu.isas.peptideshaker.PeptideShaker

            @Override
            public void run() {


                PSMaps pSMaps = new PSMaps();
                pSMaps = (PSMaps) peptideShakerGUI.getIdentification().getUrParam(pSMaps);
                PeptideShaker miniShaker = new PeptideShaker(peptideShakerGUI.getExperiment(), peptideShakerGUI.getSample(), peptideShakerGUI.getReplicateNumber(), pSMaps);


                try {
                    miniShaker.peptideMapChanged(peptideShakerGUI.getIdentification(), progressDialog, peptideShakerGUI.getProcessingPreferences(), peptideShakerGUI.getSearchParameters(), peptideShakerGUI.getSequenceMatchingPreferences());
                } catch (Exception e) {
                    JOptionPane.showMessageDialog(peptideShakerGUI, JOptionEditorPane.getJOptionEditorPane(
                            "An identification conflict occured. If you can reproduce the error <br>"
                            + "Please <a href=\"http://code.google.com/p/peptide-shaker/issues/list\">contact the developers</a>."),
                            "Identification Conflict", JOptionPane.ERROR_MESSAGE);

View Full Code Here

Examples of eu.isas.peptideshaker.PeptideShaker

            public void run() {


                try {
                    PSMaps pSMaps = new PSMaps();
                    pSMaps = (PSMaps) peptideShakerGUI.getIdentification().getUrParam(pSMaps);
                    PeptideShaker miniShaker = new PeptideShaker(peptideShakerGUI.getExperiment(), peptideShakerGUI.getSample(), peptideShakerGUI.getReplicateNumber(), pSMaps);


                    miniShaker.proteinMapChanged(progressDialog, peptideShakerGUI.getProcessingPreferences());
                    modifiedMaps.put(0, false);
                } catch (Exception e) {
                    peptideShakerGUI.catchException(e);
                }

View Full Code Here

Examples of eu.isas.peptideshaker.PeptideShaker

        annotationPreferences.setPreferencesFromSearchParameters(searchParameters);
        IonFactory.getInstance().addDefaultNeutralLoss(NeutralLoss.NH3);
        IonFactory.getInstance().addDefaultNeutralLoss(NeutralLoss.H2O);


        // create a shaker which will perform the analysis
        PeptideShaker peptideShaker = new PeptideShaker(experiment, sample, replicateNumber);


        // import the files
        peptideShaker.importFiles(waitingHandler, idFilter, identificationFiles, spectrumFiles, searchParameters,
                annotationPreferences, projectDetails, processingPreferences, ptmScoringPreferences,
                spectrumCountingPreferences, sequenceMatchingPreferences, false);


        // show the warnings
        Iterator<String> iterator = peptideShaker.getWarnings().keySet().iterator();
        while (iterator.hasNext()) {
            FeedBack warning = peptideShaker.getWarnings().get(iterator.next());
            if (warning.getType() == FeedBack.FeedBackType.WARNING) {
                System.out.println(warning.getMessage()); // @TODO: better interaction between notes and feedback objetcs...
            }
        }


        if (!waitingHandler.isRunCanceled()) {


            // identification as created by PeptideShaker
            ProteomicAnalysis tempProteomicAnalysis = experiment.getAnalysisSet(sample).getProteomicAnalysis(replicateNumber);
            identification = tempProteomicAnalysis.getIdentification(IdentificationMethod.MS2_IDENTIFICATION);


            // metrics saved while processing the data
            metrics = peptideShaker.getMetrics();


            // the identification feature generator
            identificationFeaturesGenerator = peptideShaker.getIdentificationFeaturesGenerator();


            // the cache used for identification
            objectsCache = peptideShaker.getCache();


            if (waitingHandler instanceof WaitingDialog) {
                projectDetails.setReport(((WaitingDialog) waitingHandler).getReport(null));
                ((WaitingDialog) waitingHandler).setRunNotFinished();
                ((WaitingDialog) waitingHandler).setCloseDialogWhenImportCompletes(true, false);

View Full Code Here

Examples of eu.isas.peptideshaker.PeptideShaker

            sample = new Sample(sampleNameIdtxt.getText().trim());
            replicateNumber = getReplicateNumber();
            SampleAnalysisSet analysisSet = new SampleAnalysisSet(sample, new ProteomicAnalysis(replicateNumber));
            experiment.addAnalysisSet(sample, analysisSet);


            peptideShaker = new PeptideShaker(experiment, sample, replicateNumber);


            ArrayList<String> tips;
            try {
                tips = Tips.getTips();
            } catch (Exception e) {

View Full Code Here

TOP

All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.