remove duplicated method in BatchWizardController
@@ -248,8 +248,9 @@ public class BatchWizardController {
return;
}
- final BatchQueue q = rbTOF.isSelected() ? createTofQueue(useExport, exportPath)
- : createOrbitrapQueue(useExport, exportPath);
+// final BatchQueue q = rbTOF.isSelected() ? createQueue(useExport, exportPath)
+// : createOrbitrapQueue(useExport, exportPath);
+ final BatchQueue q = createQueue(useExport, exportPath);
BatchModeParameters batchModeParameters = (BatchModeParameters) MZmineCore.getConfiguration()
.getModuleParameters(BatchModeModule.class);
batchModeParameters.getParameter(BatchModeParameters.batchQueue).setValue(q);
@@ -262,7 +263,7 @@ public class BatchWizardController {
.setModuleParameters(BatchWizardModule.class, wizardParam.cloneParameterSet());
}
- private BatchQueue createTofQueue(boolean useExport, File exportPath) {
+ private BatchQueue createQueue(boolean useExport, File exportPath) {
final BatchQueue q = new BatchQueue();
q.add(makeImportTask(files));
q.add(makeMassDetectionStep(msParameters, 1));
@@ -286,32 +287,11 @@ public class BatchWizardController {
cbMobilityType.getValue()));
q.add(makeRowFilterStep(msParameters, hplcParameters));
q.add(makeGapFillStep(msParameters, hplcParameters));
- if (!cbIonMobility.isSelected()) {
+ if (!cbIonMobility.isSelected()) { // might filter IMS resolved isomers
q.add(makeDuplicateRowFilterStep(msParameters, hplcParameters));
}
q.add(makeMetaCorrStep(msParameters, hplcParameters));
q.add(makeIinStep(msParameters, cbPolarity.getValue()));
- return q;
- }
-
- private BatchQueue createOrbitrapQueue(boolean useExport, File exportPath) {
- final BatchQueue q = new BatchQueue();
- q.add(makeImportTask(files));
- q.add(makeMassDetectionStep(msParameters, 1));
- q.add(makeMassDetectionStep(msParameters, 2));
- q.add(makeAdapStep(msParameters, hplcParameters));
- q.add(makeSmoothingStep(hplcParameters, true, false));
- q.add(makeRtResolvingStep(msParameters, hplcParameters, false));
- q.add(makeDeisotopingStep(msParameters, hplcParameters, cbIonMobility.isSelected(),
- cbMobilityType.getValue()));
- q.add(makeIsotopeFinderStep(msParameters));
- q.add(makeAlignmentStep(msParameters, hplcParameters, cbIonMobility.isSelected(),
- cbMobilityType.getValue()));
- q.add(makeRowFilterStep(msParameters, hplcParameters));
- q.add(makeGapFillStep(msParameters, hplcParameters));
- q.add(makeDuplicateRowFilterStep(msParameters, hplcParameters));
- q.add(makeMetaCorrStep(msParameters, hplcParameters));
- q.add(makeIinStep(msParameters, cbPolarity.getValue()));
if (useExport && exportPath != null) {
q.add(makeIimnGnpsExportStep(exportPath));
q.add(makeSiriusExportStep(exportPath));
