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

Example 1 with LibrarySubmitIonParameters

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

the class LibrarySubmitTask method run.

@Override
public void run() {
    setStatus(TaskStatus.PROCESSING);
    for (Entry<LibrarySubmitIonParameters, DataPoint[]> e : map.entrySet()) {
        LibrarySubmitIonParameters param = e.getKey();
        DataPoint[] dps = e.getValue();
        // at least 2 data points
        if (dps != null && dps.length > 2) {
            // export / submit json?
            if (fileJson != null || submitGNPS) {
                String json = GnpsJsonGenerator.generateJSON(param, dps);
                log.info(json);
                if (saveLocal && fileJson != null) {
                    if (writeToLocalGnpsJsonFile(fileJson, json))
                        writeResults("GNPS json entry successfully writen" + fileJson.getAbsolutePath(), Result.SUCCED);
                    else
                        writeResults("Error while writing GNPS json entry to " + fileJson.getAbsolutePath(), Result.ERROR);
                }
                if (submitGNPS)
                    submitGNPS(json);
            }
            // export msp?
            if (fileMSP != null) {
                if (writeToLocalMSPFIle(fileMSP, param, dps))
                    writeResults("MSP entry successfully writen to " + fileMSP.getAbsolutePath(), Result.SUCCED);
                else
                    writeResults("Error while writing msp entry to " + fileMSP.getAbsolutePath(), Result.ERROR);
            }
        }
        done++;
    }
    setStatus(TaskStatus.FINISHED);
}

Example 2 with LibrarySubmitIonParameters

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

the class MSMSLibrarySubmissionWindow method createIonParameters.

/**
 * The full set of parameters for the submission/creation of one library entry
 *
 * @param paramSubmit
 * @param paramMeta
 * @param ion
 * @return
 */
private LibrarySubmitIonParameters createIonParameters(LibrarySubmitParameters paramSubmit, LibraryMetaDataParameters paramMeta, ScanSelectPanel ion) {
    LibrarySubmitIonParameters ionParam = new LibrarySubmitIonParameters();
    ionParam.getParameter(LibrarySubmitIonParameters.META_PARAM).setValue(paramMeta);
    ionParam.getParameter(LibrarySubmitIonParameters.SUBMIT_PARAM).setValue(paramSubmit);
    if (isFragmentScan) {
        String adduct = ion.getAdduct();
        double precursorMZ = ion.getPrecursorMZ();
        int charge = ion.getPrecursorCharge();
        ionParam.getParameter(LibrarySubmitIonParameters.ADDUCT).setValue(adduct == null || adduct.isEmpty() ? null : adduct);
        ionParam.getParameter(LibrarySubmitIonParameters.CHARGE).setValue(charge == 0 ? null : charge);
        ionParam.getParameter(LibrarySubmitIonParameters.MZ).setValue(precursorMZ == 0d ? null : precursorMZ);
    } else {
        // MS1
        ionParam.getParameter(LibrarySubmitIonParameters.ADDUCT).setValue(null);
        ionParam.getParameter(LibrarySubmitIonParameters.CHARGE).setValue(null);
        ionParam.getParameter(LibrarySubmitIonParameters.MZ).setValue(null);
    }
    return (LibrarySubmitIonParameters) ionParam.cloneParameterSet();
}

Example 3 with LibrarySubmitIonParameters

use of net.sf.mzmine.modules.peaklistmethods.io.spectraldbsubmit.param.LibrarySubmitIonParameters 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);
            }
        }
    }
}