PeakListTableColumnModel( GroupableTableHeader header, PeakListTableModel tableModel, ParameterSet parameters, PeakList peakList) { this.parameters = parameters; this.peakList = peakList; this.header = header; header.addMouseListener(this); // prepare formatters NumberFormat mzFormat = MZmineCore.getConfiguration().getMZFormat(); NumberFormat rtFormat = MZmineCore.getConfiguration().getRTFormat(); NumberFormat intensityFormat = MZmineCore.getConfiguration().getIntensityFormat(); // prepare cell renderers mzRenderer = new FormattedCellRenderer(mzFormat); rtRenderer = new FormattedCellRenderer(rtFormat); intensityRenderer = new FormattedCellRenderer(intensityFormat); peakShapeRenderer = new PeakShapeCellRenderer(peakList, parameters); identityRenderer = new CompoundIdentityCellRenderer(); peakStatusRenderer = new PeakStatusCellRenderer(); defaultRenderer = new DefaultTableCellRenderer(); defaultRenderer.setHorizontalAlignment(SwingConstants.CENTER); defaultRendererLeft = new DefaultTableCellRenderer(); defaultRendererLeft.setHorizontalAlignment(SwingConstants.LEFT); }
public FragmentIdentity(final PeakListRow mainPeakListRow) { super( "Fragment of " + MZmineCore.getConfiguration().getMZFormat().format(mainPeakListRow.getAverageMZ()) + " m/z"); setPropertyValue(PROPERTY_METHOD, "Fragment search"); }
/** * Search for a peak-list row's mass spectrum. * * @param peakList the peak-list. * @param row the peak-list row. */ public static void singleRowSearch(final PeakList peakList, final PeakListRow row) { final ParameterSet parameters = MZmineCore.getConfiguration().getModuleParameters(NistMsSearchModule.class); if (parameters.showSetupDialog() == ExitCode.OK) { MZmineCore.getTaskController().addTask(new NistMsSearchTask(row, peakList, parameters)); } }
public MsMsVisualizerWindow( RawDataFile dataFile, Range<Double> rtRange, Range<Double> mzRange, IntensityType intensityType, NormalizationType normalizationType, Double minPeakInt, ParameterSet parameters) { super("MS/MS visualizer: [" + dataFile.getName() + "]"); setDefaultCloseOperation(DISPOSE_ON_CLOSE); setBackground(Color.white); this.dataFile = dataFile; this.tooltipMode = true; dataset = new MsMsDataSet( dataFile, rtRange, mzRange, intensityType, normalizationType, minPeakInt, this); toolBar = new MsMsToolBar(this); add(toolBar, BorderLayout.EAST); IDAPlot = new MsMsPlot(this, dataFile, this, dataset, rtRange, mzRange); add(IDAPlot, BorderLayout.CENTER); bottomPanel = new MsMsBottomPanel(this, dataFile, parameters); add(bottomPanel, BorderLayout.SOUTH); updateTitle(); // After we have constructed everything, load the peak lists into the // bottom panel bottomPanel.rebuildPeakListSelector(); MZmineCore.getDesktop().addPeakListTreeListener(bottomPanel); // Add the Windows menu JMenuBar menuBar = new JMenuBar(); menuBar.add(new WindowsMenu()); setJMenuBar(menuBar); pack(); // get the window settings parameter ParameterSet paramSet = MZmineCore.getConfiguration().getModuleParameters(MsMsVisualizerModule.class); WindowSettingsParameter settings = paramSet.getParameter(MsMsParameters.windowSettings); // update the window and listen for changes settings.applySettingsToWindow(this); this.addComponentListener(settings); }
public static void setupNewTICVisualizer( final RawDataFile[] allFiles, final RawDataFile[] selectedFiles, final ChromatographicPeak[] allPeaks, final ChromatographicPeak[] selectedPeaks, final Map<ChromatographicPeak, String> peakLabels, final Range rtRange, final Range mzRange) { assert allFiles != null; final TICVisualizerModule myInstance = MZmineCore.getModuleInstance(TICVisualizerModule.class); final TICVisualizerParameters myParameters = (TICVisualizerParameters) MZmineCore.getConfiguration().getModuleParameters(TICVisualizerModule.class); myParameters.getParameter(TICVisualizerParameters.MS_LEVEL).setValue(1); myParameters.getParameter(TICVisualizerParameters.PLOT_TYPE).setValue(PlotType.BASEPEAK); if (rtRange != null) { myParameters.getParameter(TICVisualizerParameters.RT_RANGE).setValue(rtRange); } if (mzRange != null) { myParameters.getParameter(TICVisualizerParameters.MZ_RANGE).setValue(mzRange); } if (myParameters.showSetupDialog(allFiles, selectedFiles, allPeaks, selectedPeaks) == ExitCode.OK) { final TICVisualizerParameters p = (TICVisualizerParameters) myParameters.cloneParameter(); if (peakLabels != null) { p.setPeakLabelMap(peakLabels); } myInstance.runModule(p, new ArrayList<Task>()); } }
/** * Parameters used by CentWaveDetector. * * @author $Author: cpudney $ * @version $Revision: 3153 $ */ public class CentWaveDetectorParameters extends SimpleParameterSet { /** Peak integration methods. */ public enum PeakIntegrationMethod { UseSmoothedData("Use smoothed data", 1), UseRawData("Use raw data", 2); private final String name; private final int index; /** * Create the method. * * @param aName name * @param anIndex index (as used by findPeaks.centWave) */ PeakIntegrationMethod(final String aName, final int anIndex) { name = aName; index = anIndex; } @Override public String toString() { return name; } public int getIndex() { return index; } } public static final RangeParameter PEAK_DURATION = new RangeParameter( "Peak duration range", "Range of acceptable peak lengths", MZmineCore.getConfiguration().getRTFormat(), new Range(0.0, 10.0)); public static final RangeParameter PEAK_SCALES = new RangeParameter( "Wavelet scales", "Range wavelet widths (smallest, largest) in minutes", MZmineCore.getConfiguration().getRTFormat(), new Range(0.25, 5.0)); public static final DoubleParameter SN_THRESHOLD = new DoubleParameter( "S/N threshold", "Signal to noise ratio threshold", NumberFormat.getNumberInstance(), 10.0, 0.0, null); public static final ComboParameter<PeakIntegrationMethod> INTEGRATION_METHOD = new ComboParameter<PeakIntegrationMethod>( "Peak integration method", "Method used to determine RT extents of detected peaks", PeakIntegrationMethod.values(), PeakIntegrationMethod.UseSmoothedData); public CentWaveDetectorParameters() { super(new Parameter[] {SN_THRESHOLD, PEAK_SCALES, PEAK_DURATION, INTEGRATION_METHOD}); } @Override public ExitCode showSetupDialog() { final PeakResolverSetupDialog dialog = new PeakResolverSetupDialog(this, CentWaveDetector.class); dialog.setVisible(true); return dialog.getExitCode(); } }
public class PeakSummaryTableModel extends AbstractTableModel { private static NumberFormat mzFormat = MZmineCore.getConfiguration().getMZFormat(); private static NumberFormat rtFormat = MZmineCore.getConfiguration().getRTFormat(); private static NumberFormat intensityFormat = MZmineCore.getConfiguration().getIntensityFormat(); private Vector<ChromatographicPeak> peaks = new Vector<ChromatographicPeak>(); private Vector<Color> peakColors = new Vector<Color>(); private static String[] columnNames = {"File Name", "Mass", "RT", "Height", "Area"}; public String getColumnName(int col) { return columnNames[col].toString(); } public int getRowCount() { return peaks.size(); } public int getColumnCount() { return columnNames.length; } public Object getValueAt(int row, int col) { Object value = null; ChromatographicPeak peak = peaks.get(row); switch (col) { case (0): value = peak.getDataFile().getName(); break; case (1): value = mzFormat.format(peak.getMZ()); break; case (2): value = rtFormat.format(peak.getRT()); break; case (3): value = intensityFormat.format(peak.getHeight()); break; case (4): value = intensityFormat.format(peak.getArea()); break; } return value; } public ChromatographicPeak getElementAt(int row) { return peaks.get(row); } public boolean isCellEditable(int row, int col) { return false; } public Color getPeakColor(int row) { return peakColors.get(row); } public void addElement(ChromatographicPeak peak, Color peakColor) { peaks.add(peak); peakColors.add(peakColor); fireTableRowsInserted(0, peaks.size() - 1); } public void setValueAt(Object value, int row, int col) {} public int getIndexRow(String fileName) { String localFileName; int index = -1; for (int i = 0; i < peaks.size(); i++) { localFileName = peaks.get(i).getDataFile().getName(); if (localFileName.equals(fileName)) { index = i; } } return index; } }