/** @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);
}