remove comments, set feature type
@@ -321,41 +321,6 @@ public class ImageBuilderTask extends AbstractTask {
image.setMzRange(rawDataPointsMZRange);
image.setIntensityRange(rawDataPointsIntensityRange);
image.setMaximumIntensity(maximumIntensity);
- // logger.info("Ion Trace results:\n" + "Scan numbers: " + ionTrace.getScanNumbers() + "\n" + //
- // "Mobility range: " + ionTrace.getMobilityRange() + "\n" + //
- // "m/z range: " + ionTrace.getMzRange() + "\n" + //
- // "rt range: " + ionTrace.getRetentionTimeRange() + "\n" + //
- // "intensity range: " + ionTrace.getIntensityRange() + "\n" + //
- // "Max intensity : " + ionTrace.getMaximumIntensity() + "\n" + //
- // "Retention time : " + ionTrace.getRetentionTime() + "\n" + //
- // "Mobility : " + ionTrace.getMobility()//
- // );
- // TODO calc area
- // Update area
- // double area = 0;
- // for (int i = 1; i < allScanNumbers.length; i++) {
- // // For area calculation, we use retention time in seconds
- // double previousRT = dataFile.getScan(allScanNumbers[i - 1]).getRetentionTime() * 60d;
- // double currentRT = dataFile.getScan(allScanNumbers[i]).getRetentionTime() * 60d;
- // double previousHeight = dataPointsMap.get(allScanNumbers[i - 1]).getIntensity();
- // double currentHeight = dataPointsMap.get(allScanNumbers[i]).getIntensity();
- // area += (currentRT - previousRT) * (currentHeight + previousHeight) / 2;
- // }
-
- // TODO
- // Update fragment scan
- // fragmentScan =
- // ScanUtils.findBestFragmentScan(dataFile, dataFile.getDataRTRange(1), rawDataPointsMZRange);
-
- // allMS2FragmentScanNumbers = ScanUtils.findAllMS2FragmentScans(dataFile,
- // dataFile.getDataRTRange(1), rawDataPointsMZRange);
-
- // if (fragmentScan > 0) {
- // Scan fragmentScanObject = dataFile.getScan(fragmentScan);
- // int precursorCharge = fragmentScanObject.getPrecursorCharge();
- // if (precursorCharge > 0)
- // this.charge = precursorCharge;
- // }
return image;
}
@@ -363,24 +328,13 @@ public class ImageBuilderTask extends AbstractTask {
private void buildModularFeatureList(SortedSet<IImage> images) {
taskDescription = "Build feature list";
- // featureList.addRowType(new FeatureShapeIonMobilityRetentionTimeType());
- // featureList.addRowType(new FeatureShapeIonMobilityRetentionTimeHeatMapType());
- // featureList.addRowType(new FeatureShapeMobilogramType());
- // featureList.addRowType(new MobilityType());
- featureList.addRowType(new ImageType());
+ featureList.addFeatureType(new ImageType());
int featureId = 1;
for (IImage image : images) {
image.setFeatureList(featureList);
ModularFeature modular = FeatureConvertors.ImageToModularFeature(image, rawDataFile);
- modular.set(ImageType.class, false);
ModularFeatureListRow newRow =
new ModularFeatureListRow(featureList, featureId, rawDataFile, modular);
-// newRow.set(ImageType.class, newRow.getFeaturesProperty());
- // newRow.set(MobilityType.class, image.getMobility());
- // newRow.set(FeatureShapeIonMobilityRetentionTimeType.class, newRow.getFeaturesProperty());
- // newRow.set(FeatureShapeMobilogramType.class, newRow.getFeaturesProperty());
- // newRow.set(FeatureShapeIonMobilityRetentionTimeHeatMapType.class,
- // newRow.getFeaturesProperty());
featureList.addRow(newRow);
featureId++;
}
