Examples with FileImporter eu.isas.peptideshaker.fileimport.FileImporter used on opensource projects

Example 1 with FileImporter

use of eu.isas.peptideshaker.fileimport.FileImporter in project peptide-shaker by compomics.

the class PeptideShaker method importFiles.

/**
 * Imports identification results from result files.
 *
 * @param waitingHandler the handler displaying feedback to the user
 * @param idFiles the files to import
 * @param spectrumProvider the spectrum provider
 * @param identificationParameters identification parameters
 * @param projectDetails the project details
 * @param processingPreferences the initial processing preferences
 * @param exceptionHandler the exception handler
 *
 * @return 0 if the import went fine, 1 otherwise
 */
public int importFiles(WaitingHandler waitingHandler, ArrayList<File> idFiles, SpectrumProvider spectrumProvider, IdentificationParameters identificationParameters, ProjectDetails projectDetails, ProcessingParameters processingPreferences, ExceptionHandler exceptionHandler) {
    projectCreationDuration = new Duration();
    projectCreationDuration.start();
    waitingHandler.appendReport("Import process for " + projectParameters.getProjectUniqueName(), true, true);
    waitingHandler.appendReportEndLine();
    SimpleDateFormat df = new SimpleDateFormat("yyyyMMdd-HHmmss");
    String dbName = projectParameters.getProjectUniqueName() + df.format(projectParameters.getCreationTime()) + ".psdb";
    objectsDB = new ObjectsDB(PeptideShaker.getMatchesFolder().getAbsolutePath(), dbName);
    identification = new Identification(objectsDB);
    identification.addObject(ProjectParameters.key, projectParameters);
    fileImporter = new FileImporter(identification, identificationParameters, processingPreferences, metrics, projectDetails, spectrumProvider, waitingHandler, exceptionHandler);
    int outcome = fileImporter.importFiles(idFiles);
    if (outcome == 0) {
        geneMaps = fileImporter.getGeneMaps();
        sequenceProvider = fileImporter.getSequenceProvider();
        proteinDetailsProvider = fileImporter.getProteinDetailsProvider();
        inputMap = fileImporter.getInputMap();
        proteinCount = fileImporter.getProteinCount();
        return 0;
    } else {
        return 1;
    }
}