@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();
}
/**
* {@inheritDoc}
*
* <p>endElement()
*/
@SuppressWarnings("null")
public void endElement(String namespaceURI, String sName, String qName) throws SAXException {
if (canceled) throw new SAXException("Parsing Cancelled");
// <spectrumInstrument>
if (qName.equalsIgnoreCase("spectrumInstrument")) {
spectrumInstrumentFlag = false;
}
// <precursor>
if (qName.equalsIgnoreCase("precursor")) {
precursorFlag = false;
}
// <spectrum>
if (qName.equalsIgnoreCase("spectrum")) {
spectrumInstrumentFlag = false;
// Auto-detect whether this scan is centroided
MsSpectrumType spectrumType =
SpectrumTypeDetectionAlgorithm.detectSpectrumType(mzBuffer, intensityBuffer, peaksCount);
// Create a new scan
MsFunction msFunction = MSDKObjectBuilder.getMsFunction(msLevel);
MsScan newScan = MSDKObjectBuilder.getMsScan(dataStore, scanNumber, msFunction);
newScan.setDataPoints(mzBuffer, intensityBuffer, peaksCount);
newScan.setSpectrumType(spectrumType);
newScan.setPolarity(polarity);
if (retentionTime != null) {
ChromatographyInfo chromInfo =
MSDKObjectBuilder.getChromatographyInfo1D(SeparationType.UNKNOWN, retentionTime);
newScan.setChromatographyInfo(chromInfo);
}
if (precursorMz != null) {
IsolationInfo isolation =
MSDKObjectBuilder.getIsolationInfo(
Range.singleton(precursorMz), null, precursorMz, precursorCharge, null);
newScan.getIsolations().add(isolation);
}
// Add the scan to the file
newRawFile.addScan(newScan);
parsedScans++;
}
// <mzArrayBinary>
if (qName.equalsIgnoreCase("mzArrayBinary")) {
mzArrayBinaryFlag = false;
// Allocate space for the whole array
if (mzBuffer.length < peaksCount) mzBuffer = new double[peaksCount * 2];
byte[] peakBytes = Base64.decodeBase64(charBuffer.toString().getBytes());
ByteBuffer currentMzBytes = ByteBuffer.wrap(peakBytes);
if (endian.equals("big")) {
currentMzBytes = currentMzBytes.order(ByteOrder.BIG_ENDIAN);
} else {
currentMzBytes = currentMzBytes.order(ByteOrder.LITTLE_ENDIAN);
}
for (int i = 0; i < peaksCount; i++) {
if (precision == null || precision.equals("32"))
mzBuffer[i] = (double) currentMzBytes.getFloat();
else mzBuffer[i] = currentMzBytes.getDouble();
}
}
// <intenArrayBinary>
if (qName.equalsIgnoreCase("intenArrayBinary")) {
intenArrayBinaryFlag = false;
// Allocate space for the whole array
if (intensityBuffer.length < peaksCount) intensityBuffer = new float[peaksCount * 2];
byte[] peakBytes = Base64.decodeBase64(charBuffer.toString().getBytes());
ByteBuffer currentIntensityBytes = ByteBuffer.wrap(peakBytes);
if (endian.equals("big")) {
currentIntensityBytes = currentIntensityBytes.order(ByteOrder.BIG_ENDIAN);
} else {
currentIntensityBytes = currentIntensityBytes.order(ByteOrder.LITTLE_ENDIAN);
}
for (int i = 0; i < peaksCount; i++) {
if (precision == null || precision.equals("32"))
intensityBuffer[i] = currentIntensityBytes.getFloat();
else intensityBuffer[i] = (float) currentIntensityBytes.getDouble();
}
}
}