Examples with UnsupportedFormatException net.sf.mzmine.util.spectraldb.parser.UnsupportedFormatException used on opensource projects

Example 1 with UnsupportedFormatException

use of net.sf.mzmine.util.spectraldb.parser.UnsupportedFormatException in project mzmine2 by mzmine.

the class SelectedRowsLocalSpectralDBSearchTask method parseFile.

/**
 * Load all library entries from data base file
 *
 * @param dataBaseFile
 * @return
 */
private List<RowsSpectralMatchTask> parseFile(File dataBaseFile) throws UnsupportedFormatException, IOException {
    // 
    List<RowsSpectralMatchTask> tasks = new ArrayList<>();
    AutoLibraryParser parser = new AutoLibraryParser(100, new LibraryEntryProcessor() {

        @Override
        public void processNextEntries(List<SpectralDBEntry> list, int alreadyProcessed) {
            // start last task
            RowsSpectralMatchTask task = new RowsSpectralMatchTask(peakListRows.length + " rows", peakListRows, parameters, alreadyProcessed + 1, list, (match) -> {
                // one selected row -> show in dialog
                if (resultWindow != null) {
                    resultWindow.addMatches(match);
                    resultWindow.revalidate();
                    resultWindow.repaint();
                }
            });
            MZmineCore.getTaskController().addTask(task);
            tasks.add(task);
        }
    });
    // return tasks
    parser.parse(this, dataBaseFile);
    return tasks;
}

Example 2 with UnsupportedFormatException

use of net.sf.mzmine.util.spectraldb.parser.UnsupportedFormatException in project mzmine2 by mzmine.

the class SpectraIdentificationSpectralDatabaseTask method parseFile.

/**
 * Load all library entries from data base file
 *
 * @param dataBaseFile
 * @return
 */
private List<SpectralMatchTask> parseFile(File dataBaseFile) {
    // one task for every 1000 entries
    List<SpectralMatchTask> tasks = new ArrayList<>();
    AutoLibraryParser parser = new AutoLibraryParser(1000, new LibraryEntryProcessor() {

        @Override
        public void processNextEntries(List<SpectralDBEntry> list, int alreadyProcessed) {
            // start last task
            SpectralMatchTask task = new SpectralMatchTask(parameters, alreadyProcessed + 1, list, spectraPlot, currentScan, resultWindow);
            MZmineCore.getTaskController().addTask(task);
            tasks.add(task);
        }
    });
    // return tasks
    try {
        // parse and create spectral matching tasks for batches of entries
        parser.parse(this, dataBaseFile);
        return tasks;
    } catch (UnsupportedFormatException | IOException e) {
        logger.log(Level.WARNING, "Library parsing error for file " + dataBaseFile.getAbsolutePath(), e);
        return new ArrayList<>();
    }
}