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 Number getX(int series, int index) {
return dataFile.getScan(scanNumbers[index]).getRetentionTime();
}
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);
}
}
}
/**
* @see org.xml.sax.helpers.DefaultHandler#endElement(java.lang.String, java.lang.String,
* java.lang.String)
*/
public void endElement(String namespaceURI, String sName, String qName) throws SAXException {
if (canceled) throw new SAXException("Parsing canceled");
// <NAME>
if (qName.equals(PeakListElementName_2_3.PEAKLIST_NAME.getElementName())) {
name = getTextOfElement();
logger.info("Loading peak list: " + name);
peakListName = name;
}
// <PEAKLIST_DATE>
if (qName.equals(PeakListElementName_2_3.PEAKLIST_DATE.getElementName())) {
dateCreated = getTextOfElement();
}
// <QUANTITY>
if (qName.equals(PeakListElementName_2_3.QUANTITY.getElementName())) {
String text = getTextOfElement();
totalRows = Integer.parseInt(text);
}
// <RAW_FILE>
if (qName.equals(PeakListElementName_2_3.RAWFILE.getElementName())) {
rawDataFileID = getTextOfElement();
RawDataFile dataFile = dataFilesIDMap.get(rawDataFileID);
if (dataFile == null) {
throw new SAXException(
"Cannot open peak list, because raw data file " + rawDataFileID + " is missing.");
}
currentPeakListDataFiles.add(dataFile);
}
// <SCAN_ID>
if (qName.equals(PeakListElementName_2_3.SCAN_ID.getElementName())) {
byte[] bytes = Base64.decodeToBytes(getTextOfElement());
// make a data input stream
DataInputStream dataInputStream = new DataInputStream(new ByteArrayInputStream(bytes));
scanNumbers = new int[numOfMZpeaks];
for (int i = 0; i < numOfMZpeaks; i++) {
try {
scanNumbers[i] = dataInputStream.readInt();
} catch (IOException ex) {
throw new SAXException(ex);
}
}
}
// <REPRESENTATIVE_SCAN>
if (qName.equals(PeakListElementName_2_3.REPRESENTATIVE_SCAN.getElementName())) {
representativeScan = Integer.valueOf(getTextOfElement());
}
// <FRAGMENT_SCAN>
if (qName.equals(PeakListElementName_2_3.FRAGMENT_SCAN.getElementName())) {
fragmentScan = Integer.valueOf(getTextOfElement());
}
// <MASS>
if (qName.equals(PeakListElementName_2_3.MZ.getElementName())) {
byte[] bytes = Base64.decodeToBytes(getTextOfElement());
// make a data input stream
DataInputStream dataInputStream = new DataInputStream(new ByteArrayInputStream(bytes));
masses = new double[numOfMZpeaks];
for (int i = 0; i < numOfMZpeaks; i++) {
try {
masses[i] = (double) dataInputStream.readFloat();
} catch (IOException ex) {
throw new SAXException(ex);
}
}
}
// <HEIGHT>
if (qName.equals(PeakListElementName_2_3.HEIGHT.getElementName())) {
byte[] bytes = Base64.decodeToBytes(getTextOfElement());
// make a data input stream
DataInputStream dataInputStream = new DataInputStream(new ByteArrayInputStream(bytes));
intensities = new double[numOfMZpeaks];
for (int i = 0; i < numOfMZpeaks; i++) {
try {
intensities[i] = (double) dataInputStream.readFloat();
} catch (IOException ex) {
throw new SAXException(ex);
}
}
}
// <PEAK>
if (qName.equals(PeakListElementName_2_3.PEAK.getElementName())) {
DataPoint[] mzPeaks = new DataPoint[numOfMZpeaks];
Range peakRTRange = null, peakMZRange = null, peakIntensityRange = null;
RawDataFile dataFile = dataFilesIDMap.get(peakColumnID);
if (dataFile == null)
throw new SAXException("Error in project: data file " + peakColumnID + " not found");
for (int i = 0; i < numOfMZpeaks; i++) {
Scan sc = dataFile.getScan(scanNumbers[i]);
double retentionTime = sc.getRetentionTime();
double mz = masses[i];
double intensity = intensities[i];
if ((peakRTRange == null) || (peakIntensityRange == null)) {
peakRTRange = new Range(retentionTime);
peakIntensityRange = new Range(intensity);
} else {
peakRTRange.extendRange(retentionTime);
peakIntensityRange.extendRange(intensity);
}
if (mz > 0.0) {
mzPeaks[i] = new SimpleDataPoint(mz, intensity);
if (peakMZRange == null) peakMZRange = new Range(mz);
else peakMZRange.extendRange(mz);
}
}
FeatureStatus status = FeatureStatus.valueOf(peakStatus);
SimpleFeature peak =
new SimpleFeature(
dataFile,
mass,
rt,
height,
area,
scanNumbers,
mzPeaks,
status,
representativeScan,
fragmentScan,
peakRTRange,
peakMZRange,
peakIntensityRange);
peak.setCharge(currentPeakCharge);
if (currentIsotopes.size() > 0) {
SimpleIsotopePattern newPattern =
new SimpleIsotopePattern(
currentIsotopes.toArray(new DataPoint[0]),
currentIsotopePatternStatus,
currentIsotopePatternDescription);
peak.setIsotopePattern(newPattern);
currentIsotopes.clear();
}
buildingRow.addPeak(dataFile, peak);
}
// <IDENTITY_PROPERTY>
if (qName.equals(PeakListElementName_2_3.IDPROPERTY.getElementName())) {
identityProperties.put(identityPropertyName, getTextOfElement());
}
// <PEAK_IDENTITY>
if (qName.equals(PeakListElementName_2_3.PEAK_IDENTITY.getElementName())) {
SimplePeakIdentity identity = new SimplePeakIdentity(identityProperties);
buildingRow.addPeakIdentity(identity, preferred);
}
// <ROW>
if (qName.equals(PeakListElementName_2_3.ROW.getElementName())) {
buildingPeakList.addRow(buildingRow);
buildingRow = null;
parsedRows++;
}
// <ISOTOPE>
if (qName.equals(PeakListElementName_2_3.ISOTOPE.getElementName())) {
String text = getTextOfElement();
String items[] = text.split(":");
double mz = Double.valueOf(items[0]);
double intensity = Double.valueOf(items[1]);
DataPoint isotope = new SimpleDataPoint(mz, intensity);
currentIsotopes.add(isotope);
}
if (qName.equals(PeakListElementName_2_3.METHOD_NAME.getElementName())) {
String appliedMethod = getTextOfElement();
appliedMethods.add(appliedMethod);
}
if (qName.equals(PeakListElementName_2_3.METHOD_PARAMETERS.getElementName())) {
String appliedMethodParam = getTextOfElement();
appliedMethodParameters.add(appliedMethodParam);
}
}
void updateTitle() {
StringBuffer title = new StringBuffer();
title.append("Time vs. m/z for precursor ions\n");
title.append(dataFile.getName());
IDAPlot.setTitle(title.toString());
}