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Deduplicate
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@Mailaender @eselmeister
Mailaender authored and eselmeister committed Oct 14, 2024
1 parent 0d34ff0 commit 9067d62
Showing 1 changed file with 8 additions and 69 deletions.
77 changes: 8 additions & 69 deletions ....supplier.mzmlb/src/net/openchrom/msd/converter/supplier/mzmlb/io/ChromatogramWriter.java
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,6 @@
import org.eclipse.chemclipse.converter.exceptions.FileIsNotWriteableException;
import org.eclipse.chemclipse.converter.io.AbstractChromatogramWriter;
import org.eclipse.chemclipse.logging.core.Logger;
import org.eclipse.chemclipse.model.core.IChromatogramOverview;
import org.eclipse.chemclipse.model.core.IScan;
import org.eclipse.chemclipse.msd.converter.io.IChromatogramMSDWriter;
import org.eclipse.chemclipse.msd.model.core.IChromatogramMSD;
Expand Down Expand Up @@ -131,9 +130,9 @@ private SpectrumType createSpectrum(IScanMSD scanMSD, int offset) {
SpectrumType spectrum = new SpectrumType();
spectrum.setId("scan=" + scanMSD.getScanNumber());
spectrum.setIndex(BigInteger.valueOf((scanMSD.getScanNumber() - 1)));
spectrum.getCvParam().add(createTotalIonCurrentType(scanMSD));
spectrum.getCvParam().add(XmlWriter110.createTotalIonCurrentType(scanMSD));
if(scanMSD instanceof IRegularMassSpectrum massSpectrum) {
spectrum.getCvParam().add(createSpectrumLevel(massSpectrum));
spectrum.getCvParam().add(XmlWriter110.createSpectrumLevel(massSpectrum));
}
spectrum.setScanList(createScanList(scanMSD));
spectrum.setBinaryDataArrayList(createBinaryDataArrayList(scanMSD, offset));
Expand All @@ -153,8 +152,8 @@ private BinaryDataArrayType mzArrayType(IScanMSD scanMSD, int offset) {

BinaryDataArrayType mzArrayType = new BinaryDataArrayType();
mzArrayType.getCvParam().add(createMzArrayType());
mzArrayType.getCvParam().add(createZlibCompressionParamType());
mzArrayType.getCvParam().add(createDoubleParamType());
mzArrayType.getCvParam().add(XmlWriter110.createZlibCompressionParamType());
mzArrayType.getCvParam().add(XmlWriter110.createDoubleParamType());
mzArrayType.getCvParam().add(createExternalHdf5MzDataset());
mzArrayType.getCvParam().add(createExternalArrayLength(scanMSD));
mzArrayType.getCvParam().add(createExternalOffset(offset));
Expand All @@ -176,42 +175,15 @@ private CVParamType createMzArrayType() {
private BinaryDataArrayType createIntensityArrayType(IScanMSD scanMSD, int offset) {

BinaryDataArrayType intensityArrayType = new BinaryDataArrayType();
intensityArrayType.getCvParam().add(XmlWriter110.createIntensityArrayType()); // TODO rename
intensityArrayType.getCvParam().add(createZlibCompressionParamType());
intensityArrayType.getCvParam().add(createFloatParamType());
intensityArrayType.getCvParam().add(XmlWriter110.createIntensityArrayType());
intensityArrayType.getCvParam().add(XmlWriter110.createZlibCompressionParamType());
intensityArrayType.getCvParam().add(XmlWriter110.createFloatParamType());
intensityArrayType.getCvParam().add(createExternalHdf5IntensityDataset());
intensityArrayType.getCvParam().add(createExternalArrayLength(scanMSD));
intensityArrayType.getCvParam().add(createExternalOffset(offset));
return intensityArrayType;
}

private CVParamType createZlibCompressionParamType() { // TODO: deduplicate

CVParamType cvParamCompression = new CVParamType();
cvParamCompression.setCvRef(XmlWriter110.MS);
cvParamCompression.setAccession("MS:1000574");
cvParamCompression.setName("zlib compression");
return cvParamCompression;
}

private CVParamType createFloatParamType() { // TODO: deduplicate

CVParamType cvParamData = new CVParamType();
cvParamData.setCvRef(XmlWriter110.MS);
cvParamData.setAccession("MS:1000521");
cvParamData.setName("32-bit float");
return cvParamData;
}

private CVParamType createDoubleParamType() { // TODO: deduplicate

CVParamType cvParamData = new CVParamType();
cvParamData.setCvRef(XmlWriter110.MS);
cvParamData.setAccession("MS:1000523");
cvParamData.setName("64-bit float");
return cvParamData;
}

private CVParamType createExternalHdf5MzDataset() {

CVParamType cvParamExternalHdf5Datase = new CVParamType();
Expand Down Expand Up @@ -268,40 +240,7 @@ private ScanListType createScanList(IScan scan) {
private ScanType createScanType(IScan scan) {

ScanType scanType = new ScanType();
scanType.getCvParam().add(createScanStartTimeType(scan));
scanType.getCvParam().add(XmlWriter110.createScanStartTimeType(scan));
return scanType;
}

private CVParamType createScanStartTimeType(IScan scan) { // TODO: deduplicate

CVParamType cvParamScanStartTime = new CVParamType();
cvParamScanStartTime.setCvRef(XmlWriter110.MS);
cvParamScanStartTime.setAccession("MS:1000016");
cvParamScanStartTime.setName("scan start time");
cvParamScanStartTime.setUnitCvRef(XmlWriter110.UO);
cvParamScanStartTime.setUnitAccession("UO:0000031");
cvParamScanStartTime.setUnitName("minute");
cvParamScanStartTime.setValue(String.valueOf(scan.getRetentionTime() / IChromatogramOverview.MINUTE_CORRELATION_FACTOR));
return cvParamScanStartTime;
}

private CVParamType createTotalIonCurrentType(IScan scan) { // TODO: deduplicate

CVParamType cvParamTotalIonCurrent = new CVParamType();
cvParamTotalIonCurrent.setCvRef(XmlWriter110.MS);
cvParamTotalIonCurrent.setAccession("MS:1000285");
cvParamTotalIonCurrent.setName("total ion current");
cvParamTotalIonCurrent.setValue(String.valueOf(scan.getTotalSignal()));
return cvParamTotalIonCurrent;
}

private CVParamType createSpectrumLevel(IRegularMassSpectrum massSpectrum) { // TODO: deduplicate

CVParamType cvParamLevel = new CVParamType();
cvParamLevel.setCvRef(XmlWriter110.MS);
cvParamLevel.setAccession("MS:1000511");
cvParamLevel.setName("ms level");
cvParamLevel.setValue(String.valueOf(massSpectrum.getMassSpectrometer()));
return cvParamLevel;
}
}

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