Examples with ParameterSet net.sf.mzmine.parameters.ParameterSet used on opensource projects

Example 21 with ParameterSet

use of net.sf.mzmine.parameters.ParameterSet in project mzmine2 by mzmine.

the class TwoDVisualizerModule method show2DVisualizerSetupDialog.

public static void show2DVisualizerSetupDialog(RawDataFile dataFile, Range<Double> mzRange, Range<Double> rtRange) {
    ParameterSet parameters = MZmineCore.getConfiguration().getModuleParameters(TwoDVisualizerModule.class);
    parameters.getParameter(TwoDVisualizerParameters.dataFiles).setValue(RawDataFilesSelectionType.SPECIFIC_FILES, new RawDataFile[] { dataFile });
    if (rtRange != null)
        parameters.getParameter(TwoDVisualizerParameters.scanSelection).setValue(new ScanSelection(rtRange, 1));
    if (mzRange != null)
        parameters.getParameter(TwoDVisualizerParameters.mzRange).setValue(mzRange);
    ExitCode exitCode = parameters.showSetupDialog(MZmineCore.getDesktop().getMainWindow(), true);
    if (exitCode != ExitCode.OK)
        return;
    ScanSelection scanSel = parameters.getParameter(TwoDVisualizerParameters.scanSelection).getValue();
    Scan[] scans = scanSel.getMatchingScans(dataFile);
    rtRange = ScanUtils.findRtRange(scans);
    mzRange = parameters.getParameter(TwoDVisualizerParameters.mzRange).getValue();
    TwoDVisualizerWindow newWindow = new TwoDVisualizerWindow(dataFile, scans, rtRange, mzRange, parameters);
    newWindow.setVisible(true);
}

Example 22 with ParameterSet

use of net.sf.mzmine.parameters.ParameterSet in project mzmine2 by mzmine.

the class ModuleComboComponent method actionPerformed.

public void actionPerformed(ActionEvent event) {
    Object src = event.getSource();
    MZmineProcessingStep<?> selected = (MZmineProcessingStep<?>) comboBox.getSelectedItem();
    if (src == comboBox) {
        if (selected == null) {
            setButton.setEnabled(false);
            return;
        }
        ParameterSet parameterSet = selected.getParameterSet();
        int numOfParameters = parameterSet.getParameters().length;
        setButton.setEnabled(numOfParameters > 0);
    }
    if (src == setButton) {
        if (selected == null)
            return;
        ParameterSetupDialog dialog = (ParameterSetupDialog) SwingUtilities.getAncestorOfClass(ParameterSetupDialog.class, this);
        if (dialog == null)
            return;
        ParameterSet parameterSet = selected.getParameterSet();
        parameterSet.showSetupDialog(dialog, dialog.isValueCheckRequired());
    }
}

Example 23 with ParameterSet

use of net.sf.mzmine.parameters.ParameterSet in project mzmine2 by mzmine.

the class ModuleComboParameter method loadValueFromXML.

@Override
public void loadValueFromXML(Element xmlElement) {
    NodeList items = xmlElement.getElementsByTagName("module");
    for (int i = 0; i < items.getLength(); i++) {
        Element moduleElement = (Element) items.item(i);
        String name = moduleElement.getAttribute("name");
        for (int j = 0; j < modulesWithParams.length; j++) {
            if (modulesWithParams[j].getModule().getName().equals(name)) {
                ParameterSet moduleParameters = modulesWithParams[j].getParameterSet();
                if (moduleParameters == null)
                    continue;
                moduleParameters.loadValuesFromXML((Element) items.item(i));
            }
        }
    }
    String selectedAttr = xmlElement.getAttribute("selected");
    for (int j = 0; j < modulesWithParams.length; j++) {
        if (modulesWithParams[j].getModule().getName().equals(selectedAttr)) {
            value = modulesWithParams[j];
        }
    }
}

Example 24 with ParameterSet

use of net.sf.mzmine.parameters.ParameterSet in project mzmine2 by mzmine.

the class ModuleComboParameter method saveValueToXML.

@Override
public void saveValueToXML(Element xmlElement) {
    if (value != null)
        xmlElement.setAttribute("selected", value.toString());
    Document parentDocument = xmlElement.getOwnerDocument();
    for (MZmineProcessingStep<?> item : modulesWithParams) {
        Element newElement = parentDocument.createElement("module");
        newElement.setAttribute("name", item.getModule().getName());
        ParameterSet moduleParameters = item.getParameterSet();
        if (moduleParameters != null)
            moduleParameters.saveValuesToXML(newElement);
        xmlElement.appendChild(newElement);
    }
}

Example 25 with ParameterSet

use of net.sf.mzmine.parameters.ParameterSet in project mzmine2 by mzmine.

the class JoinAlignerTask method run.

/**
 * @see Runnable#run()
 */
@Override
public void run() {
    if ((mzWeight == 0) && (rtWeight == 0)) {
        setStatus(TaskStatus.ERROR);
        setErrorMessage("Cannot run alignment, all the weight parameters are zero");
        return;
    }
    setStatus(TaskStatus.PROCESSING);
    logger.info("Running join aligner");
    // twice, first for score calculation, second for actual alignment.
    for (int i = 0; i < peakLists.length; i++) {
        totalRows += peakLists[i].getNumberOfRows() * 2;
    }
    // Collect all data files
    Vector<RawDataFile> allDataFiles = new Vector<RawDataFile>();
    for (PeakList peakList : peakLists) {
        for (RawDataFile dataFile : peakList.getRawDataFiles()) {
            // Each data file can only have one column in aligned feature list
            if (allDataFiles.contains(dataFile)) {
                setStatus(TaskStatus.ERROR);
                setErrorMessage("Cannot run alignment, because file " + dataFile + " is present in multiple feature lists");
                return;
            }
            allDataFiles.add(dataFile);
        }
    }
    // Create a new aligned feature list
    alignedPeakList = new SimplePeakList(peakListName, allDataFiles.toArray(new RawDataFile[0]));
    // Iterate source feature lists
    for (PeakList peakList : peakLists) {
        // Create a sorted set of scores matching
        TreeSet<RowVsRowScore> scoreSet = new TreeSet<RowVsRowScore>();
        PeakListRow[] allRows = peakList.getRows();
        // Calculate scores for all possible alignments of this row
        for (PeakListRow row : allRows) {
            if (isCanceled())
                return;
            // Calculate limits for a row with which the row can be aligned
            Range<Double> mzRange = mzTolerance.getToleranceRange(row.getAverageMZ());
            Range<Double> rtRange = rtTolerance.getToleranceRange(row.getAverageRT());
            // Get all rows of the aligned peaklist within parameter limits
            PeakListRow[] candidateRows = alignedPeakList.getRowsInsideScanAndMZRange(rtRange, mzRange);
            // Calculate scores and store them
            for (PeakListRow candidate : candidateRows) {
                if (sameChargeRequired) {
                    if (!PeakUtils.compareChargeState(row, candidate))
                        continue;
                }
                if (sameIDRequired) {
                    if (!PeakUtils.compareIdentities(row, candidate))
                        continue;
                }
                if (compareIsotopePattern) {
                    IsotopePattern ip1 = row.getBestIsotopePattern();
                    IsotopePattern ip2 = candidate.getBestIsotopePattern();
                    if ((ip1 != null) && (ip2 != null)) {
                        ParameterSet isotopeParams = parameters.getParameter(JoinAlignerParameters.compareIsotopePattern).getEmbeddedParameters();
                        if (!IsotopePatternScoreCalculator.checkMatch(ip1, ip2, isotopeParams)) {
                            continue;
                        }
                    }
                }
                // compare the similarity of spectra mass lists on MS1 or MS2 level
                if (compareSpectraSimilarity) {
                    DataPoint[] rowDPs = null;
                    DataPoint[] candidateDPs = null;
                    SpectralSimilarity sim = null;
                    // get data points of mass list of the representative scans
                    if (msLevel == 1) {
                        rowDPs = row.getBestPeak().getRepresentativeScan().getMassList(massList).getDataPoints();
                        candidateDPs = candidate.getBestPeak().getRepresentativeScan().getMassList(massList).getDataPoints();
                    }
                    // get data points of mass list of the best fragmentation scans
                    if (msLevel == 2) {
                        if (row.getBestFragmentation() != null && candidate.getBestFragmentation() != null) {
                            rowDPs = row.getBestFragmentation().getMassList(massList).getDataPoints();
                            candidateDPs = candidate.getBestFragmentation().getMassList(massList).getDataPoints();
                        } else
                            continue;
                    }
                    // compare mass list data points of selected scans
                    if (rowDPs != null && candidateDPs != null) {
                        // calculate similarity using SimilarityFunction
                        sim = createSimilarity(rowDPs, candidateDPs);
                        // user set threshold
                        if (sim == null) {
                            continue;
                        }
                    }
                }
                RowVsRowScore score = new RowVsRowScore(row, candidate, RangeUtils.rangeLength(mzRange) / 2.0, mzWeight, RangeUtils.rangeLength(rtRange) / 2.0, rtWeight);
                scoreSet.add(score);
            }
            processedRows++;
        }
        // Create a table of mappings for best scores
        Hashtable<PeakListRow, PeakListRow> alignmentMapping = new Hashtable<PeakListRow, PeakListRow>();
        // Iterate scores by descending order
        Iterator<RowVsRowScore> scoreIterator = scoreSet.iterator();
        while (scoreIterator.hasNext()) {
            RowVsRowScore score = scoreIterator.next();
            // Check if the row is already mapped
            if (alignmentMapping.containsKey(score.getPeakListRow()))
                continue;
            // Check if the aligned row is already filled
            if (alignmentMapping.containsValue(score.getAlignedRow()))
                continue;
            alignmentMapping.put(score.getPeakListRow(), score.getAlignedRow());
        }
        // Align all rows using mapping
        for (PeakListRow row : allRows) {
            PeakListRow targetRow = alignmentMapping.get(row);
            // If we have no mapping for this row, add a new one
            if (targetRow == null) {
                targetRow = new SimplePeakListRow(newRowID);
                newRowID++;
                alignedPeakList.addRow(targetRow);
            }
            // Add all peaks from the original row to the aligned row
            for (RawDataFile file : row.getRawDataFiles()) {
                targetRow.addPeak(file, row.getPeak(file));
            }
            // Add all non-existing identities from the original row to the
            // aligned row
            PeakUtils.copyPeakListRowProperties(row, targetRow);
            processedRows++;
        }
    }
    // Next feature list
    // Add new aligned feature list to the project
    project.addPeakList(alignedPeakList);
    // Add task description to peakList
    alignedPeakList.addDescriptionOfAppliedTask(new SimplePeakListAppliedMethod("Join aligner", parameters));
    logger.info("Finished join aligner");
    setStatus(TaskStatus.FINISHED);
}