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Fix mzXML precursor ion transition not being set #1908

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Oct 17, 2024
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Fix mzXML precursor ion transition not being set #1908

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43 changes: 38 additions & 5 deletions ...ipse/chemclipse/msd/converter/supplier/mzxml/internal/io/ChromatogramReaderVersion20.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -32,16 +32,18 @@
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.v20.model.MsRun;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.v20.model.ObjectFactory;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.v20.model.Peaks;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.v20.model.PrecursorMz;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.v20.model.Scan;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.v20.model.Software;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.model.IVendorChromatogram;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.model.IVendorIon;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.model.IVendorScan;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.model.VendorChromatogram;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.model.VendorIon;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.model.VendorScan;
import org.eclipse.chemclipse.msd.model.core.IChromatogramMSD;
import org.eclipse.chemclipse.msd.model.core.IIonTransition;
import org.eclipse.chemclipse.msd.model.core.Polarity;
import org.eclipse.chemclipse.msd.model.implementation.IonTransition;
import org.eclipse.chemclipse.support.history.EditInformation;
import org.eclipse.core.runtime.IProgressMonitor;
import org.w3c.dom.Document;
Expand Down Expand Up @@ -74,6 +76,8 @@ public IChromatogramMSD read(File file, IProgressMonitor monitor) throws IOExcep
MsRun msrun = (MsRun)unmarshaller.unmarshal(nodeList.item(0));
//
chromatogram = new VendorChromatogram();
boolean isTandemMeasurement = isTandemMeasurement(msrun);
int cycleNumber = isTandemMeasurement ? 1 : 0;
//
MsInstrument instrument = msrun.getMsInstrument();
if(instrument != null) {
Expand Down Expand Up @@ -110,6 +114,22 @@ public IChromatogramMSD read(File file, IProgressMonitor monitor) throws IOExcep
massSpectrum.setPolarity(Polarity.NEGATIVE);
}
}
// MS, MS/MS
short msLevel = scan.getMsLevel().shortValue();
massSpectrum.setMassSpectrometer(msLevel);
//
if(!scan.getPrecursorMz().isEmpty()) {
PrecursorMz precursor = scan.getPrecursorMz().get(0);
massSpectrum.setPrecursorIon(precursor.getValue());
}
//
if(msLevel < 2) {
cycleNumber++;
}
if(cycleNumber >= 1) {
massSpectrum.setCycleNumber(cycleNumber);
}
massSpectrum.setRetentionTime(retentionTime);
/*
* Get the ions.
*/
Expand Down Expand Up @@ -142,15 +162,19 @@ public IChromatogramMSD read(File file, IProgressMonitor monitor) throws IOExcep
values[index] = floatBuffer.get(index);
}
}
//
for(int peakIndex = 0; peakIndex < values.length - 1; peakIndex += 2) {
/*
* Get m/z and intensity (m/z-int)
*/
double mz = values[peakIndex];
float intensity = (float)values[peakIndex + 1];
IVendorIon ion = new VendorIon(mz, intensity);
massSpectrum.addIon(ion, false);
if(msLevel >= 2) {
IIonTransition ionTransition = new IonTransition(massSpectrum.getPrecursorIon(), mz, scan.getCollisionEnergy(), 1, 1, 0);
massSpectrum.addIon(new VendorIon(mz, intensity, ionTransition), false);
chromatogram.getIonTransitionSettings().getIonTransitions().add(ionTransition);
} else {
massSpectrum.addIon(new VendorIon(mz, intensity), false);
}
}
chromatogram.addScan(massSpectrum);
monitor.worked(1);
Expand All @@ -162,9 +186,18 @@ public IChromatogramMSD read(File file, IProgressMonitor monitor) throws IOExcep
} catch(ParserConfigurationException e) {
logger.warn(e);
}
//
chromatogram.setConverterId("");
chromatogram.setFile(file);
return chromatogram;
}

private boolean isTandemMeasurement(MsRun msrun) {

for(Scan scan : msrun.getScan()) {
if(scan.getMsLevel().shortValue() > 1) {
return true;
}
}
return false;
}
}
45 changes: 40 additions & 5 deletions ...ipse/chemclipse/msd/converter/supplier/mzxml/internal/io/ChromatogramReaderVersion21.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -32,16 +32,18 @@
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.v21.model.MsRun;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.v21.model.ObjectFactory;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.v21.model.Peaks;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.v21.model.PrecursorMz;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.v21.model.Scan;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.v21.model.Software;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.model.IVendorChromatogram;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.model.IVendorIon;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.model.IVendorScan;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.model.VendorChromatogram;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.model.VendorIon;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.model.VendorScan;
import org.eclipse.chemclipse.msd.model.core.IChromatogramMSD;
import org.eclipse.chemclipse.msd.model.core.IIonTransition;
import org.eclipse.chemclipse.msd.model.core.Polarity;
import org.eclipse.chemclipse.msd.model.implementation.IonTransition;
import org.eclipse.chemclipse.support.history.EditInformation;
import org.eclipse.core.runtime.IProgressMonitor;
import org.w3c.dom.Document;
Expand Down Expand Up @@ -74,6 +76,8 @@ public IChromatogramMSD read(File file, IProgressMonitor monitor) throws IOExcep
MsRun msrun = (MsRun)unmarshaller.unmarshal(nodeList.item(0));
//
chromatogram = new VendorChromatogram();
boolean isTandemMeasurement = isTandemMeasurement(msrun);
int cycleNumber = isTandemMeasurement ? 1 : 0;
//
MsInstrument instrument = msrun.getMsInstrument();
if(instrument != null) {
Expand Down Expand Up @@ -110,6 +114,22 @@ public IChromatogramMSD read(File file, IProgressMonitor monitor) throws IOExcep
massSpectrum.setPolarity(Polarity.NEGATIVE);
}
}
// MS, MS/MS
short msLevel = scan.getMsLevel().shortValue();
massSpectrum.setMassSpectrometer(msLevel);
//
if(!scan.getPrecursorMz().isEmpty()) {
PrecursorMz precursor = scan.getPrecursorMz().get(0);
massSpectrum.setPrecursorIon(precursor.getValue());
}
//
if(msLevel < 2) {
cycleNumber++;
}
if(cycleNumber >= 1) {
massSpectrum.setCycleNumber(cycleNumber);
}
massSpectrum.setRetentionTime(retentionTime);
/*
* Get the ions.
*/
Expand Down Expand Up @@ -142,13 +162,19 @@ public IChromatogramMSD read(File file, IProgressMonitor monitor) throws IOExcep
values[index] = floatBuffer.get(index);
}
}
//
for(int peakIndex = 0; peakIndex < values.length - 1; peakIndex += 2) {
/*
* Get m/z and intensity (m/z-int)
*/
IVendorIon ion = new VendorIon(values[peakIndex], (float)values[peakIndex + 1]);
massSpectrum.addIon(ion, false);
double mz = values[peakIndex];
float intensity = (float)values[peakIndex + 1];
if(msLevel >= 2) {
IIonTransition ionTransition = new IonTransition(massSpectrum.getPrecursorIon(), mz, scan.getCollisionEnergy(), 1, 1, 0);
massSpectrum.addIon(new VendorIon(mz, intensity, ionTransition), false);
chromatogram.getIonTransitionSettings().getIonTransitions().add(ionTransition);
} else {
massSpectrum.addIon(new VendorIon(mz, intensity), false);
}
}
chromatogram.addScan(massSpectrum);
monitor.worked(1);
Expand All @@ -160,9 +186,18 @@ public IChromatogramMSD read(File file, IProgressMonitor monitor) throws IOExcep
} catch(ParserConfigurationException e) {
logger.warn(e);
}
//
chromatogram.setConverterId("");
chromatogram.setFile(file);
return chromatogram;
}

private boolean isTandemMeasurement(MsRun msrun) {

for(Scan scan : msrun.getScan()) {
if(scan.getMsLevel().shortValue() > 1) {
return true;
}
}
return false;
}
}
45 changes: 40 additions & 5 deletions ...ipse/chemclipse/msd/converter/supplier/mzxml/internal/io/ChromatogramReaderVersion22.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -32,16 +32,18 @@
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.v22.model.MsRun;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.v22.model.ObjectFactory;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.v22.model.Peaks;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.v22.model.PrecursorMz;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.v22.model.Scan;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.v22.model.Software;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.model.IVendorChromatogram;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.model.IVendorIon;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.model.IVendorScan;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.model.VendorChromatogram;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.model.VendorIon;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.model.VendorScan;
import org.eclipse.chemclipse.msd.model.core.IChromatogramMSD;
import org.eclipse.chemclipse.msd.model.core.IIonTransition;
import org.eclipse.chemclipse.msd.model.core.Polarity;
import org.eclipse.chemclipse.msd.model.implementation.IonTransition;
import org.eclipse.chemclipse.support.history.EditInformation;
import org.eclipse.core.runtime.IProgressMonitor;
import org.w3c.dom.Document;
Expand Down Expand Up @@ -74,6 +76,8 @@ public IChromatogramMSD read(File file, IProgressMonitor monitor) throws IOExcep
MsRun msrun = (MsRun)unmarshaller.unmarshal(nodeList.item(0));
//
chromatogram = new VendorChromatogram();
boolean isTandemMeasurement = isTandemMeasurement(msrun);
int cycleNumber = isTandemMeasurement ? 1 : 0;
//
MsInstrument instrument = msrun.getMsInstrument();
if(instrument != null) {
Expand Down Expand Up @@ -110,6 +114,22 @@ public IChromatogramMSD read(File file, IProgressMonitor monitor) throws IOExcep
massSpectrum.setPolarity(Polarity.NEGATIVE);
}
}
// MS, MS/MS
short msLevel = scan.getMsLevel().shortValue();
massSpectrum.setMassSpectrometer(msLevel);
//
if(!scan.getPrecursorMz().isEmpty()) {
PrecursorMz precursor = scan.getPrecursorMz().get(0);
massSpectrum.setPrecursorIon(precursor.getValue());
}
//
if(msLevel < 2) {
cycleNumber++;
}
if(cycleNumber >= 1) {
massSpectrum.setCycleNumber(cycleNumber);
}
massSpectrum.setRetentionTime(retentionTime);
/*
* Get the ions.
*/
Expand Down Expand Up @@ -142,13 +162,19 @@ public IChromatogramMSD read(File file, IProgressMonitor monitor) throws IOExcep
values[index] = floatBuffer.get(index);
}
}
//
for(int peakIndex = 0; peakIndex < values.length - 1; peakIndex += 2) {
/*
* Get m/z and intensity (m/z-int)
*/
IVendorIon ion = new VendorIon(values[peakIndex], (float)values[peakIndex + 1]);
massSpectrum.addIon(ion, false);
double mz = values[peakIndex];
float intensity = (float)values[peakIndex + 1];
if(msLevel >= 2) {
IIonTransition ionTransition = new IonTransition(massSpectrum.getPrecursorIon(), mz, scan.getCollisionEnergy(), 1, 1, 0);
massSpectrum.addIon(new VendorIon(mz, intensity, ionTransition), false);
chromatogram.getIonTransitionSettings().getIonTransitions().add(ionTransition);
} else {
massSpectrum.addIon(new VendorIon(mz, intensity), false);
}
}
chromatogram.addScan(massSpectrum);
monitor.worked(1);
Expand All @@ -160,9 +186,18 @@ public IChromatogramMSD read(File file, IProgressMonitor monitor) throws IOExcep
} catch(ParserConfigurationException e) {
logger.warn(e);
}
//
chromatogram.setConverterId("");
chromatogram.setFile(file);
return chromatogram;
}

private boolean isTandemMeasurement(MsRun msrun) {

for(Scan scan : msrun.getScan()) {
if(scan.getMsLevel().shortValue() > 1) {
return true;
}
}
return false;
}
}
45 changes: 40 additions & 5 deletions ...ipse/chemclipse/msd/converter/supplier/mzxml/internal/io/ChromatogramReaderVersion30.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -34,16 +34,18 @@
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.v30.model.MsRun;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.v30.model.ObjectFactory;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.v30.model.Peaks;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.v30.model.PrecursorMz;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.v30.model.Scan;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.v30.model.Software;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.model.IVendorChromatogram;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.model.IVendorIon;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.model.IVendorScan;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.model.VendorChromatogram;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.model.VendorIon;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.model.VendorScan;
import org.eclipse.chemclipse.msd.model.core.IChromatogramMSD;
import org.eclipse.chemclipse.msd.model.core.IIonTransition;
import org.eclipse.chemclipse.msd.model.core.Polarity;
import org.eclipse.chemclipse.msd.model.implementation.IonTransition;
import org.eclipse.chemclipse.support.history.EditInformation;
import org.eclipse.core.runtime.IProgressMonitor;
import org.w3c.dom.Document;
Expand Down Expand Up @@ -78,6 +80,8 @@ public IChromatogramMSD read(File file, IProgressMonitor monitor) throws IOExcep
MsRun msrun = (MsRun)unmarshaller.unmarshal(nodeList.item(0));
//
chromatogram = new VendorChromatogram();
boolean isTandemMeasurement = isTandemMeasurement(msrun);
int cycleNumber = isTandemMeasurement ? 1 : 0;
//
for(MsInstrument instrument : msrun.getMsInstrument()) {
chromatogram.setInstrument(instrument.getMsManufacturer().getTheValue() + " " + instrument.getMsModel().getTheValue());
Expand Down Expand Up @@ -113,6 +117,22 @@ public IChromatogramMSD read(File file, IProgressMonitor monitor) throws IOExcep
massSpectrum.setPolarity(Polarity.NEGATIVE);
}
}
// MS, MS/MS
short msLevel = scan.getMsLevel().shortValue();
massSpectrum.setMassSpectrometer(msLevel);
//
if(!scan.getPrecursorMz().isEmpty()) {
PrecursorMz precursor = scan.getPrecursorMz().get(0);
massSpectrum.setPrecursorIon(precursor.getValue());
}
//
if(msLevel < 2) {
cycleNumber++;
}
if(cycleNumber >= 1) {
massSpectrum.setCycleNumber(cycleNumber);
}
massSpectrum.setRetentionTime(retentionTime);
/*
* Get the ions.
*/
Expand Down Expand Up @@ -155,13 +175,19 @@ public IChromatogramMSD read(File file, IProgressMonitor monitor) throws IOExcep
values[index] = floatBuffer.get(index);
}
}
//
for(int peakIndex = 0; peakIndex < values.length - 1; peakIndex += 2) {
/*
* Get m/z and intensity (m/z-int)
*/
IVendorIon ion = new VendorIon(values[peakIndex], (float)values[peakIndex + 1]);
massSpectrum.addIon(ion, false);
double mz = values[peakIndex];
float intensity = (float)values[peakIndex + 1];
if(msLevel >= 2) {
IIonTransition ionTransition = new IonTransition(massSpectrum.getPrecursorIon(), mz, scan.getCollisionEnergy(), 1, 1, 0);
massSpectrum.addIon(new VendorIon(mz, intensity, ionTransition), false);
chromatogram.getIonTransitionSettings().getIonTransitions().add(ionTransition);
} else {
massSpectrum.addIon(new VendorIon(mz, intensity), false);
}
}
}
chromatogram.addScan(massSpectrum);
Expand All @@ -176,9 +202,18 @@ public IChromatogramMSD read(File file, IProgressMonitor monitor) throws IOExcep
} catch(DataFormatException e) {
logger.warn(e);
}
//
chromatogram.setConverterId("");
chromatogram.setFile(file);
return chromatogram;
}

private boolean isTandemMeasurement(MsRun msrun) {

for(Scan scan : msrun.getScan()) {
if(scan.getMsLevel().shortValue() > 1) {
return true;
}
}
return false;
}
}
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