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;
}
}