Package eu.isas.peptideshaker.preferences

Examples of eu.isas.peptideshaker.preferences.ProjectDetails

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        // Create the analysis set of this PeptideShaker process
        SampleAnalysisSet analysisSet = new SampleAnalysisSet(sample, new ProteomicAnalysis(replicateNumber));
        experiment.addAnalysisSet(sample, analysisSet);

        // Set the project details
        projectDetails = new ProjectDetails();
        projectDetails.setCreationDate(new Date());
        projectDetails.setPeptideShakerVersion(new Properties().getVersion());

        // Get the search parameters
        searchParameters = cliInputBean.getIdentificationParameters();
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     * Creates the project details for this new project.
     *
     * @return the project details
     */
    private ProjectDetails getProjectDetails() {
        ProjectDetails projectDetails = new ProjectDetails();
        projectDetails.setCreationDate(new Date());
        projectDetails.setPeptideShakerVersion(new eu.isas.peptideshaker.utils.Properties().getVersion());
        return projectDetails;
    }
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                        PTMFactory ptmFactory = PTMFactory.getInstance();
                        ModificationProfile ptmProfile = peptideShakerGUI.getSearchParameters().getModificationProfile();
                        PTMScoringPreferences ptmScoringPreferences = peptideShakerGUI.getPtmScoringPreferences();

                        ProjectDetails projectDetails = peptideShakerGUI.getProjectDetails();
                        ArrayList<Integer> algorithms = projectDetails.getIdentificationAlgorithms();

                        progressDialog.setPrimaryProgressCounterIndeterminate(false);
                        progressDialog.setMaxPrimaryProgressCounter(identification.getSpectrumIdentificationSize());

                        writer.write("Index" + SEPARATOR);
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     * @throws ClassNotFoundException thrown if ClassNotFoundException occurs
     * @throws InterruptedException thrown if InterruptedException occurs
     */
    public static void exportMzId(MzidCLIInputBean mzidCLIInputBean, CpsParent cpsParent, WaitingHandler waitingHandler) throws IOException, ClassNotFoundException, MzMLUnmarshallerException, InterruptedException, SQLException {

        ProjectDetails projectDetails = cpsParent.getProjectDetails();
        projectDetails.setContactFirstName(mzidCLIInputBean.getContactFirstName());
        projectDetails.setContactLastName(mzidCLIInputBean.getContactLastName());
        projectDetails.setContactEmail(mzidCLIInputBean.getContactEmail());
        projectDetails.setContactAddress(mzidCLIInputBean.getContactAddress());
        projectDetails.setContactUrl(mzidCLIInputBean.getContactUrl());
        projectDetails.setOrganizationName(mzidCLIInputBean.getOrganizationName());
        projectDetails.setOrganizationEmail(mzidCLIInputBean.getOrganizationMail());
        projectDetails.setOrganizationAddress(mzidCLIInputBean.getOrganizationAddress());
        projectDetails.setOrganizationUrl(mzidCLIInputBean.getOrganizationUrl());
        projectDetails.setPrideOutputFolder(mzidCLIInputBean.getOutputFile().getAbsolutePath());

        MzIdentMLExport mzIdentMLExport = new MzIdentMLExport(PeptideShaker.getVersion(), cpsParent.getIdentification(), cpsParent.getProjectDetails(),
                cpsParent.getProcessingPreferences(), cpsParent.getSearchParameters(), cpsParent.getPtmScoringPreferences(),
                cpsParent.getSpectrumCountingPreferences(), cpsParent.getIdentificationFeaturesGenerator(),
                cpsParent.getAnnotationPreferences(), cpsParent.getSequenceMatchingPreferences(), mzidCLIInputBean.getOutputFile(), waitingHandler);
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Related Classes of eu.isas.peptideshaker.preferences.ProjectDetails

  • com.compomics.util.experiment.identification.Advocate
  • com.compomics.util.experiment.io.identifications.IdfileReader
  • com.compomics.util.experiment.io.identifications.IdfileReaderFactory
  • eu.isas.peptideshaker.cmd.CLIMethods
  • eu.isas.peptideshaker.cmd.PeptideShakerCLI
  • eu.isas.peptideshaker.export.OutputGenerator
  • eu.isas.peptideshaker.gui.NewDialog
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