@Override
public String toString() {
final FeatureTable df = getFeatureTable();
if (df != null) return df.getName();
return "Unnamed item";
}
@Override
public void runModule(
@Nonnull MZmineProject project,
@Nonnull ParameterSet parameters,
@Nonnull Collection<Task<?>> tasks) {
// Boolean values
Boolean filterByDuration = parameters.getParameter(FeatureFilterParameters.duration).getValue();
Boolean filterByArea = parameters.getParameter(FeatureFilterParameters.area).getValue();
Boolean filterByHeight = parameters.getParameter(FeatureFilterParameters.height).getValue();
Boolean filterByDataPoints =
parameters.getParameter(FeatureFilterParameters.dataPoints).getValue();
Boolean filterByFWHM = parameters.getParameter(FeatureFilterParameters.fwhm).getValue();
Boolean filterByTailingFactor =
parameters.getParameter(FeatureFilterParameters.tailingFactor).getValue();
Boolean filterByAsymmetryFactor =
parameters.getParameter(FeatureFilterParameters.asymmetryFactor).getValue();
// Default values
if (filterByDuration == null) filterByDuration = false;
if (filterByArea == null) filterByArea = false;
if (filterByHeight == null) filterByHeight = false;
if (filterByDataPoints == null) filterByDataPoints = false;
if (filterByFWHM == null) filterByFWHM = false;
if (filterByTailingFactor == null) filterByTailingFactor = false;
if (filterByAsymmetryFactor == null) filterByAsymmetryFactor = false;
// Embedded values
final Range<Double> durationRange =
parameters.getParameter(FeatureFilterParameters.duration).getEmbeddedParameter().getValue();
final Range<Double> areaRange =
parameters.getParameter(FeatureFilterParameters.area).getEmbeddedParameter().getValue();
final Range<Double> heightRange =
parameters.getParameter(FeatureFilterParameters.height).getEmbeddedParameter().getValue();
final Range<Integer> dataPointsRange =
parameters
.getParameter(FeatureFilterParameters.dataPoints)
.getEmbeddedParameter()
.getValue();
final Range<Double> fwhmRange =
parameters.getParameter(FeatureFilterParameters.fwhm).getEmbeddedParameter().getValue();
final Range<Double> tailingFactorRange =
parameters
.getParameter(FeatureFilterParameters.tailingFactor)
.getEmbeddedParameter()
.getValue();
final Range<Double> asymmetryFactorRange =
parameters
.getParameter(FeatureFilterParameters.asymmetryFactor)
.getEmbeddedParameter()
.getValue();
// Other values
final FeatureTablesSelection featureTables =
parameters.getParameter(FeatureFilterParameters.featureTables).getValue();
final Boolean removeOldTable =
parameters.getParameter(FeatureFilterParameters.removeOldTable).getValue();
final String nameSuffix =
parameters.getParameter(FeatureFilterParameters.nameSuffix).getValue();
if (featureTables == null || featureTables.getMatchingFeatureTables().isEmpty()) {
MZmineGUI.displayMessage("Feature filter module started with no feature table selected.");
logger.warn("Feature filter module started with no feature table selected.");
return;
}
// Check if at least one filter is selected
if (!filterByDuration
&& !filterByArea
&& !filterByHeight
&& !filterByDataPoints
&& !filterByFWHM
&& !filterByTailingFactor
&& !filterByAsymmetryFactor) {
MZmineGUI.displayMessage("Feature filter module started with no filter selected.");
logger.warn("Feature filter module started with no filter selected.");
return;
}
// Add a task for each feature table
for (FeatureTable featureTable : featureTables.getMatchingFeatureTables()) {
// Create the data structures
DataPointStore dataStore = DataPointStoreFactory.getMemoryDataStore();
// New feature filter task
FeatureFilterMethod method =
new FeatureFilterMethod(
featureTable,
dataStore,
filterByDuration,
filterByArea,
filterByHeight,
filterByDataPoints,
filterByFWHM,
filterByTailingFactor,
filterByAsymmetryFactor,
durationRange,
areaRange,
heightRange,
dataPointsRange,
fwhmRange,
tailingFactorRange,
asymmetryFactorRange,
nameSuffix);
MSDKTask newTask =
new MSDKTask("Filtering features in tables", featureTable.getName(), method);
// Add the feature table to the project
newTask.setOnSucceeded(
e -> {
FeatureTable newFeatureTable = method.getResult();
project.addFeatureTable(newFeatureTable);
// If selected, remove old feature table
if (removeOldTable != null && removeOldTable) {
project.removeFeatureTable(featureTable);
}
});
// Add the task to the queue
tasks.add(newTask);
}
}
