@Override
public void loadValueFromXML(Element xmlElement) {
PeakList[] currentDataPeakLists =
MZmineCore.getProjectManager().getCurrentProject().getPeakLists();
PeakListsSelectionType selectionType;
final String attrValue = xmlElement.getAttribute("type");
if (Strings.isNullOrEmpty(attrValue))
selectionType = PeakListsSelectionType.GUI_SELECTED_PEAKLISTS;
else selectionType = PeakListsSelectionType.valueOf(xmlElement.getAttribute("type"));
ArrayList<Object> newValues = new ArrayList<Object>();
NodeList items = xmlElement.getElementsByTagName("specific_peak_list");
for (int i = 0; i < items.getLength(); i++) {
String itemString = items.item(i).getTextContent();
for (PeakList df : currentDataPeakLists) {
if (df.getName().equals(itemString)) newValues.add(df);
}
}
PeakList specificPeakLists[] = newValues.toArray(new PeakList[0]);
String namePattern = null;
items = xmlElement.getElementsByTagName("name_pattern");
for (int i = 0; i < items.getLength(); i++) {
namePattern = items.item(i).getTextContent();
}
this.value = new PeakListsSelection();
this.value.setSelectionType(selectionType);
this.value.setSpecificPeakLists(specificPeakLists);
this.value.setNamePattern(namePattern);
}
/** Returns a peak list with the peaks which intensity is above the parameter "intensity" */
PeakList getIntensityThresholdPeakList(double intensity) {
PeakList selectedPeakList = (PeakList) peakListSelector.getSelectedItem();
if (selectedPeakList == null) return null;
SimplePeakList newList =
new SimplePeakList(selectedPeakList.getName(), selectedPeakList.getRawDataFiles());
for (PeakListRow peakRow : selectedPeakList.getRows()) {
Feature peak = peakRow.getPeak(dataFile);
if (peak == null) continue;
if (peak.getRawDataPointsIntensityRange().upperEndpoint() > intensity) {
newList.addRow(peakRow);
}
}
return newList;
}
@Override
public void saveValueToXML(Element xmlElement) {
if (value == null) return;
Document parentDocument = xmlElement.getOwnerDocument();
xmlElement.setAttribute("type", value.getSelectionType().name());
if (value.getSpecificPeakLists() != null) {
for (PeakList item : value.getSpecificPeakLists()) {
Element newElement = parentDocument.createElement("specific_peak_list");
newElement.setTextContent(item.getName());
xmlElement.appendChild(newElement);
}
}
if (value.getNamePattern() != null) {
Element newElement = parentDocument.createElement("name_pattern");
newElement.setTextContent(value.getNamePattern());
xmlElement.appendChild(newElement);
}
}
/** @see java.awt.event.MouseListener#mouseReleased(java.awt.event.MouseEvent) */
public void mouseReleased(MouseEvent e) {
if (columnBeingResized == null) return;
ColumnSettingParameter<CommonColumnType> csPar =
parameters.getParameter(PeakListTableParameters.commonColumns);
ColumnSettingParameter<DataFileColumnType> dfPar =
parameters.getParameter(PeakListTableParameters.dataFileColumns);
final int modelIndex = columnBeingResized.getModelIndex();
final int newWidth = columnBeingResized.getPreferredWidth();
final int numOfCommonColumns = CommonColumnType.values().length;
final int numOfDataFileColumns = DataFileColumnType.values().length;
if (modelIndex < numOfCommonColumns) {
csPar.setColumnWidth(modelIndex, newWidth);
} else {
int dataFileColumnIndex = (modelIndex - numOfCommonColumns) % numOfDataFileColumns;
dfPar.setColumnWidth(dataFileColumnIndex, newWidth);
// set same width to other data file columns of this type
for (int dataFileIndex = peakList.getNumberOfRawDataFiles() - 1;
dataFileIndex >= 0;
dataFileIndex--) {
int columnIndex =
numOfCommonColumns + (dataFileIndex * numOfDataFileColumns) + dataFileColumnIndex;
TableColumn col = this.getColumnByModelIndex(columnIndex);
int currentWidth = col.getPreferredWidth();
if (currentWidth != newWidth) {
col.setPreferredWidth(newWidth);
}
}
}
}
/** Returns a peak list with the top peaks defined by the parameter "threshold" */
PeakList getTopThresholdPeakList(int threshold) {
PeakList selectedPeakList = (PeakList) peakListSelector.getSelectedItem();
if (selectedPeakList == null) return null;
SimplePeakList newList =
new SimplePeakList(selectedPeakList.getName(), selectedPeakList.getRawDataFiles());
Vector<PeakListRow> peakRows = new Vector<PeakListRow>();
Range<Double> mzRange = selectedPeakList.getRowsMZRange();
Range<Double> rtRange = selectedPeakList.getRowsRTRange();
PeakThresholdMode selectedPeakOption = (PeakThresholdMode) thresholdCombo.getSelectedItem();
if (selectedPeakOption == PeakThresholdMode.TOP_PEAKS_AREA) {
XYPlot xyPlot = masterFrame.getPlot().getXYPlot();
org.jfree.data.Range yAxis = xyPlot.getRangeAxis().getRange();
org.jfree.data.Range xAxis = xyPlot.getDomainAxis().getRange();
rtRange = Range.closed(xAxis.getLowerBound(), xAxis.getUpperBound());
mzRange = Range.closed(yAxis.getLowerBound(), yAxis.getUpperBound());
}
for (PeakListRow peakRow : selectedPeakList.getRows()) {
if (mzRange.contains(peakRow.getAverageMZ()) && rtRange.contains(peakRow.getAverageRT())) {
peakRows.add(peakRow);
}
}
Collections.sort(
peakRows, new PeakListRowSorter(SortingProperty.Intensity, SortingDirection.Descending));
if (threshold > peakRows.size()) threshold = peakRows.size();
for (int i = 0; i < threshold; i++) {
newList.addRow(peakRows.elementAt(i));
}
return newList;
}
/** @see Runnable#run() */
public void run() {
if ((mzWeight == 0) && (rtWeight == 0)) {
setStatus(TaskStatus.ERROR);
errorMessage = "Cannot run alignment, all the weight parameters are zero";
return;
}
setStatus(TaskStatus.PROCESSING);
logger.info("Running join aligner");
// Remember how many rows we need to process. Each row will be processed
// 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 peak list
if (allDataFiles.contains(dataFile)) {
setStatus(TaskStatus.ERROR);
errorMessage =
"Cannot run alignment, because file "
+ dataFile
+ " is present in multiple peak lists";
return;
}
allDataFiles.add(dataFile);
}
}
// Create a new aligned peak list
alignedPeakList = new SimplePeakList(peakListName, allDataFiles.toArray(new RawDataFile[0]));
// Iterate source peak 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 mzRange = mzTolerance.getToleranceRange(row.getAverageMZ());
Range 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;
}
}
}
RowVsRowScore score =
new RowVsRowScore(
row, candidate, mzRange.getSize() / 2, mzWeight, rtRange.getSize() / 2, 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 peak list
// Add new aligned peak list to the project
MZmineProject currentProject = MZmineCore.getCurrentProject();
currentProject.addPeakList(alignedPeakList);
// Add task description to peakList
alignedPeakList.addDescriptionOfAppliedTask(
new SimplePeakListAppliedMethod("Join aligner", parameters));
logger.info("Finished join aligner");
setStatus(TaskStatus.FINISHED);
}
/**
* Filter the peak list.
*
* @param peakList peak list to filter.
* @return a new peak list with entries of the original peak list that pass the filtering.
*/
private PeakList filterPeakList(final PeakList peakList) {
// Make a copy of the peakList
final PeakList newPeakList =
new SimplePeakList(
peakList.getName()
+ ' '
+ parameters.getParameter(RowsFilterParameters.SUFFIX).getValue(),
peakList.getRawDataFiles());
// Get parameters - which filters are active
final boolean filterByDuration =
parameters.getParameter(PeakFilterParameters.PEAK_DURATION).getValue();
final boolean filterByArea = parameters.getParameter(PeakFilterParameters.PEAK_AREA).getValue();
final boolean filterByHeight =
parameters.getParameter(PeakFilterParameters.PEAK_HEIGHT).getValue();
final boolean filterByDatapoints =
parameters.getParameter(PeakFilterParameters.PEAK_DATAPOINTS).getValue();
final boolean filterByFWHM = parameters.getParameter(PeakFilterParameters.PEAK_FWHM).getValue();
final boolean filterByTailingFactor =
parameters.getParameter(PeakFilterParameters.PEAK_TAILINGFACTOR).getValue();
final boolean filterByAsymmetryFactor =
parameters.getParameter(PeakFilterParameters.PEAK_ASYMMETRYFACTOR).getValue();
// Loop through all rows in peak list
final PeakListRow[] rows = peakList.getRows();
totalRows = rows.length;
for (processedRows = 0; !isCanceled() && processedRows < totalRows; processedRows++) {
final PeakListRow row = rows[processedRows];
final RawDataFile[] rawdatafiles = row.getRawDataFiles();
int totalRawDataFiles = rawdatafiles.length;
boolean[] keepPeak = new boolean[totalRawDataFiles];
for (int i = 0; i < totalRawDataFiles; i++) {
// Peak values
keepPeak[i] = true;
final Feature peak = row.getPeak(rawdatafiles[i]);
final double peakDuration =
peak.getRawDataPointsRTRange().upperEndpoint()
- peak.getRawDataPointsRTRange().lowerEndpoint();
final double peakArea = peak.getArea();
final double peakHeight = peak.getHeight();
final int peakDatapoints = peak.getScanNumbers().length;
Double peakFWHM = peak.getFWHM();
Double peakTailingFactor = peak.getTailingFactor();
Double peakAsymmetryFactor = peak.getAsymmetryFactor();
if (peakFWHM == null) {
peakFWHM = -1.0;
}
if (peakTailingFactor == null) {
peakTailingFactor = -1.0;
}
if (peakAsymmetryFactor == null) {
peakAsymmetryFactor = -1.0;
}
// Check Duration
if (filterByDuration) {
final Range<Double> durationRange =
parameters
.getParameter(PeakFilterParameters.PEAK_DURATION)
.getEmbeddedParameter()
.getValue();
if (!durationRange.contains(peakDuration)) {
// Mark peak to be removed
keepPeak[i] = false;
}
}
// Check Area
if (filterByArea) {
final Range<Double> areaRange =
parameters
.getParameter(PeakFilterParameters.PEAK_AREA)
.getEmbeddedParameter()
.getValue();
if (!areaRange.contains(peakArea)) {
// Mark peak to be removed
keepPeak[i] = false;
}
}
// Check Height
if (filterByHeight) {
final Range<Double> heightRange =
parameters
.getParameter(PeakFilterParameters.PEAK_HEIGHT)
.getEmbeddedParameter()
.getValue();
if (!heightRange.contains(peakHeight)) {
// Mark peak to be removed
keepPeak[i] = false;
}
}
// Check # Data Points
if (filterByDatapoints) {
final Range<Integer> datapointsRange =
parameters
.getParameter(PeakFilterParameters.PEAK_DATAPOINTS)
.getEmbeddedParameter()
.getValue();
if (!datapointsRange.contains(peakDatapoints)) {
// Mark peak to be removed
keepPeak[i] = false;
}
}
// Check FWHM
if (filterByFWHM) {
final Range<Double> fwhmRange =
parameters
.getParameter(PeakFilterParameters.PEAK_FWHM)
.getEmbeddedParameter()
.getValue();
if (!fwhmRange.contains(peakFWHM)) {
// Mark peak to be removed
keepPeak[i] = false;
}
}
// Check Tailing Factor
if (filterByTailingFactor) {
final Range<Double> tailingRange =
parameters
.getParameter(PeakFilterParameters.PEAK_TAILINGFACTOR)
.getEmbeddedParameter()
.getValue();
if (!tailingRange.contains(peakTailingFactor)) {
// Mark peak to be removed
keepPeak[i] = false;
}
}
// Check height
if (filterByAsymmetryFactor) {
final Range<Double> asymmetryRange =
parameters
.getParameter(PeakFilterParameters.PEAK_ASYMMETRYFACTOR)
.getEmbeddedParameter()
.getValue();
if (!asymmetryRange.contains(peakAsymmetryFactor)) {
// Mark peak to be removed
keepPeak[i] = false;
}
}
}
newPeakList.addRow(copyPeakRow(row, keepPeak));
}
return newPeakList;
}
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);
}
}
}