@Override
public String toString() {
final FeatureTable df = getFeatureTable();
if (df != null) return df.getName();
return "Unnamed item";
}
@SuppressWarnings("null")
@Test
public void testOrbitrap() throws MSDKException {
// Create the data structures
final DataPointStore dataStore = DataPointStoreFactory.getMemoryDataStore();
// Import the file
File inputFile = new File(TEST_DATA_PATH + "orbitrap_300-600mz.mzML");
Assert.assertTrue("Cannot read test data", inputFile.canRead());
MzMLFileImportMethod importer = new MzMLFileImportMethod(inputFile);
RawDataFile rawFile = importer.execute();
Assert.assertNotNull(rawFile);
Assert.assertEquals(1.0, importer.getFinishedPercentage(), 0.0001);
// Ion 1
List<IonAnnotation> ionAnnotations = new ArrayList<IonAnnotation>();
IonAnnotation ion1 = MSDKObjectBuilder.getSimpleIonAnnotation();
ion1.setExpectedMz(332.56);
ion1.setAnnotationId("Feature 332.56");
ion1.setChromatographyInfo(
MSDKObjectBuilder.getChromatographyInfo1D(SeparationType.LC, (float) 772.8));
ionAnnotations.add(ion1);
// Ion 2
IonAnnotation ion2 = MSDKObjectBuilder.getSimpleIonAnnotation();
ion2.setExpectedMz(508.004);
ion2.setAnnotationId("Feature 508.004");
ion2.setChromatographyInfo(
MSDKObjectBuilder.getChromatographyInfo1D(SeparationType.LC, (float) 868.8));
ionAnnotations.add(ion2);
// Ion 3
IonAnnotation ion3 = MSDKObjectBuilder.getSimpleIonAnnotation();
ion3.setExpectedMz(362.102);
ion3.setAnnotationId("Feature 362.102");
ion3.setChromatographyInfo(
MSDKObjectBuilder.getChromatographyInfo1D(SeparationType.LC, (float) 643.2));
ionAnnotations.add(ion3);
// Variables
final MZTolerance mzTolerance = new MZTolerance(0.003, 5.0);
final RTTolerance rtTolerance = new RTTolerance(3, false);
final Double intensityTolerance = 0.10d;
final Double noiseLevel = 5000d;
TargetedDetectionMethod chromBuilder =
new TargetedDetectionMethod(
ionAnnotations,
rawFile,
dataStore,
mzTolerance,
rtTolerance,
intensityTolerance,
noiseLevel);
final List<Chromatogram> chromatograms = chromBuilder.execute();
Assert.assertEquals(1.0, chromBuilder.getFinishedPercentage(), 0.0001);
Assert.assertNotNull(chromatograms);
Assert.assertEquals(3, chromatograms.size());
// Create a new feature table
FeatureTable featureTable = MSDKObjectBuilder.getFeatureTable("orbitrap_300-600mz", dataStore);
Sample sample = MSDKObjectBuilder.getSimpleSample("orbitrap_300-600mz");
ChromatogramToFeatureTableMethod tableBuilder =
new ChromatogramToFeatureTableMethod(chromatograms, featureTable, sample);
tableBuilder.execute();
// 1. Filter parameters
boolean filterByMz = true;
boolean filterByRt = true;
boolean filterByDuration = true;
boolean filterByCount = true;
boolean filterByIsotopes = true;
boolean filterByIonAnnotation = true;
boolean requireAnnotation = false;
boolean removeDuplicates = false;
boolean duplicateRequireSameID = true;
Range<Double> mzRange = Range.closed(300.0, 600.0);
Range<Double> rtRange = Range.closed(600.0, 900.0); // Seconds
Range<Double> durationRange = Range.closed(0.0, 47.0); // Seconds
final MZTolerance duplicateMzTolerance = new MZTolerance(0.003, 5.0);
final RTTolerance duplicateRtTolerance = new RTTolerance(0.2, false);
int minCount = 1;
int minIsotopes = 1;
String ionAnnotation = null;
String nameSuffix = "-rowFiltered";
// 1. Filter the rows
RowFilterMethod filterMethod =
new RowFilterMethod(
featureTable,
dataStore,
nameSuffix,
filterByMz,
filterByRt,
filterByDuration,
filterByCount,
filterByIsotopes,
filterByIonAnnotation,
requireAnnotation,
mzRange,
rtRange,
durationRange,
minCount,
minIsotopes,
ionAnnotation,
removeDuplicates,
duplicateMzTolerance,
duplicateRtTolerance,
duplicateRequireSameID);
filterMethod.execute();
Assert.assertEquals(1.0, filterMethod.getFinishedPercentage(), 0.0001);
// 1. Verify data
FeatureTable filteredTable = filterMethod.getResult();
Assert.assertNotNull(filteredTable);
Assert.assertEquals(3, filteredTable.getRows().size());
// 2. Filter parameters
mzRange = Range.closed(350.0, 600.0);
durationRange = Range.closed(46.0, 47.0); // Seconds
// 2. Filter the features
filterMethod =
new RowFilterMethod(
featureTable,
dataStore,
nameSuffix,
filterByMz,
filterByRt,
filterByDuration,
filterByCount,
filterByIsotopes,
filterByIonAnnotation,
requireAnnotation,
mzRange,
rtRange,
durationRange,
minCount,
minIsotopes,
ionAnnotation,
removeDuplicates,
duplicateMzTolerance,
duplicateRtTolerance,
duplicateRequireSameID);
filterMethod.execute();
Assert.assertEquals(1.0, filterMethod.getFinishedPercentage(), 0.0001);
// 2. Verify data
filteredTable = filterMethod.getResult();
Assert.assertNotNull(filteredTable);
Assert.assertEquals(1, filteredTable.getRows().size());
// 3. Filter parameters
minCount = 2;
// 3. Filter the features
filterMethod =
new RowFilterMethod(
filteredTable,
dataStore,
nameSuffix,
filterByMz,
filterByRt,
filterByDuration,
filterByCount,
filterByIsotopes,
filterByIonAnnotation,
requireAnnotation,
mzRange,
rtRange,
durationRange,
minCount,
minIsotopes,
ionAnnotation,
removeDuplicates,
duplicateMzTolerance,
duplicateRtTolerance,
duplicateRequireSameID);
filterMethod.execute();
Assert.assertEquals(1.0, filterMethod.getFinishedPercentage(), 0.0001);
// 3. Verify data
filteredTable = filterMethod.getResult();
Assert.assertNotNull(filteredTable);
Assert.assertEquals(0, filteredTable.getRows().size());
featureTable.dispose();
filteredTable.dispose();
}
@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);
}
}