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 void createColumns() {
// clear column groups
ColumnGroup groups[] = header.getColumnGroups();
if (groups != null) {
for (ColumnGroup group : groups) {
header.removeColumnGroup(group);
}
}
// clear the column model
while (getColumnCount() > 0) {
TableColumn col = getColumn(0);
removeColumn(col);
}
// create the "average" group
ColumnGroup averageGroup = new ColumnGroup("Average");
header.addColumnGroup(averageGroup);
JTextField editorField = new JTextField();
editorField.setFont(editFont);
DefaultCellEditor defaultEditor = new DefaultCellEditor(editorField);
ColumnSettingParameter<CommonColumnType> csPar =
parameters.getParameter(PeakListTableParameters.commonColumns);
CommonColumnType visibleCommonColumns[] = csPar.getValue();
// This is a workaround for a bug - we need to always show the ID, m/z
// and RT columns, otherwise manual editing of peak identities does not
// work.
ArrayList<CommonColumnType> commonColumnsList =
new ArrayList<>(Arrays.asList(visibleCommonColumns));
commonColumnsList.remove(CommonColumnType.ROWID);
commonColumnsList.remove(CommonColumnType.AVERAGEMZ);
commonColumnsList.remove(CommonColumnType.AVERAGERT);
commonColumnsList.add(0, CommonColumnType.ROWID);
commonColumnsList.add(1, CommonColumnType.AVERAGEMZ);
commonColumnsList.add(2, CommonColumnType.AVERAGERT);
visibleCommonColumns = commonColumnsList.toArray(visibleCommonColumns);
ColumnSettingParameter<DataFileColumnType> dfPar =
parameters.getParameter(PeakListTableParameters.dataFileColumns);
DataFileColumnType visibleDataFileColumns[] = dfPar.getValue();
for (int i = 0; i < visibleCommonColumns.length; i++) {
CommonColumnType commonColumn = visibleCommonColumns[i];
int modelIndex = Arrays.asList(CommonColumnType.values()).indexOf(commonColumn);
TableColumn newColumn = new TableColumn(modelIndex);
newColumn.setHeaderValue(commonColumn.getColumnName());
newColumn.setIdentifier(commonColumn);
switch (commonColumn) {
case AVERAGEMZ:
newColumn.setCellRenderer(mzRenderer);
break;
case AVERAGERT:
newColumn.setCellRenderer(rtRenderer);
break;
case IDENTITY:
newColumn.setCellRenderer(identityRenderer);
break;
case COMMENT:
newColumn.setCellRenderer(defaultRendererLeft);
newColumn.setCellEditor(defaultEditor);
break;
case PEAKSHAPE:
newColumn.setCellRenderer(peakShapeRenderer);
break;
default:
newColumn.setCellRenderer(defaultRenderer);
}
this.addColumn(newColumn);
newColumn.setPreferredWidth(csPar.getColumnWidth(modelIndex));
if ((commonColumn == CommonColumnType.AVERAGEMZ)
|| (commonColumn == CommonColumnType.AVERAGERT)) {
averageGroup.add(newColumn);
}
}
for (int i = 0; i < peakList.getNumberOfRawDataFiles(); i++) {
RawDataFile dataFile = peakList.getRawDataFile(i);
ColumnGroup fileGroup = new ColumnGroup(dataFile.getName());
header.addColumnGroup(fileGroup);
for (int j = 0; j < visibleDataFileColumns.length; j++) {
DataFileColumnType dataFileColumn = visibleDataFileColumns[j];
int dataFileColumnIndex =
Arrays.asList(DataFileColumnType.values()).indexOf(dataFileColumn);
int modelIndex =
CommonColumnType.values().length
+ (i * DataFileColumnType.values().length)
+ dataFileColumnIndex;
TableColumn newColumn = new TableColumn(modelIndex);
newColumn.setHeaderValue(dataFileColumn.getColumnName());
newColumn.setIdentifier(dataFileColumn);
switch (dataFileColumn) {
case MZ:
newColumn.setCellRenderer(mzRenderer);
break;
case PEAKSHAPE:
newColumn.setCellRenderer(peakShapeRenderer);
break;
case STATUS:
newColumn.setCellRenderer(peakStatusRenderer);
break;
case RT:
newColumn.setCellRenderer(rtRenderer);
break;
case RT_START:
newColumn.setCellRenderer(rtRenderer);
break;
case RT_END:
newColumn.setCellRenderer(rtRenderer);
break;
case DURATION:
newColumn.setCellRenderer(rtRenderer);
break;
case HEIGHT:
newColumn.setCellRenderer(intensityRenderer);
break;
case AREA:
newColumn.setCellRenderer(intensityRenderer);
break;
default:
newColumn.setCellRenderer(defaultRenderer);
break;
}
this.addColumn(newColumn);
newColumn.setPreferredWidth(dfPar.getColumnWidth(dataFileColumnIndex));
fileGroup.add(newColumn);
}
}
}
void updateTitle() {
StringBuffer title = new StringBuffer();
title.append("Time vs. m/z for precursor ions\n");
title.append(dataFile.getName());
IDAPlot.setTitle(title.toString());
}