@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); } }