Examples with LibrarySubmitTask net.sf.mzmine.modules.peaklistmethods.io.spectraldbsubmit.LibrarySubmitTask used on opensource projects

Example 1 with LibrarySubmitTask

use of net.sf.mzmine.modules.peaklistmethods.io.spectraldbsubmit.LibrarySubmitTask in project mzmine2 by mzmine.

the class MSMSLibrarySubmissionWindow method submitSpectra.

/**
 * Submit. Checks parameters and adduct for each selected ion
 */
private void submitSpectra() {
    if (checkParameters()) {
        // check number of ions
        int ions = countSelectedIons();
        // for ms level >1 (fragmentation scan MS/MS)
        int mslevel = paramMeta.getParameter(LibraryMetaDataParameters.MS_LEVEL).getValue();
        if (mslevel == 1)
            paramSubmit.getParameter(LibrarySubmitParameters.SUBMIT_GNPS).setValue(false);
        else {
            int adducts = countSelectedAdducts();
            // every valid selected ion needs an adduct for MS2
            if (ions != adducts) {
                MZmineCore.getDesktop().displayErrorMessage(this, "ERROR", MessageFormat.format("Not all adducts are set: {0} ion spectra selected and only {1}  adducts set", ions, adducts));
                return;
            }
        }
        // 
        if (ions == 0) {
            log.info("No MS/MS spectrum selected or valid");
            DialogLoggerUtil.showMessageDialogForTime(this, "Error", "No MS/MS spectrum selected or valid", 1500);
        } else {
            String message = ions + " MS/MS spectra were selected. Submit?";
            if (mslevel > 1) {
                message += " (" + streamSelection().filter(pn -> pn.isValidAndSelected() && pn.hasAdduct()).map(ScanSelectPanel::getAdduct).collect(Collectors.joining(", ")) + ")";
            } else {
                message += " (MS1)";
            }
            // show accept dialog
            if (DialogLoggerUtil.showDialogYesNo(this, "Submission?", message)) {
                // create library / submit to GNPS
                HashMap<LibrarySubmitIonParameters, DataPoint[]> map = new HashMap<>(ions);
                for (ScanSelectPanel ion : pnScanSelect) {
                    if (ion.isValidAndSelected()) {
                        // create ion param
                        LibrarySubmitIonParameters ionParam = createIonParameters(paramSubmit, paramMeta, ion);
                        DataPoint[] dps = ion.getFilteredDataPoints();
                        // submit and save locally
                        map.put(ionParam, dps);
                    }
                }
                // start task
                log.info("Added task to export library entries: " + ions + " MS/MS spectra were selected");
                LibrarySubmitTask task = new LibrarySubmitTask(this, map);
                MZmineCore.getTaskController().addTask(task);
            }
        }
    }
}