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Add a simple model for spot location and MALDI target ID.
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@Mailaender
Mailaender committed Feb 27, 2025
1 parent 5c8b58c commit aee348a
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Showing 9 changed files with 117 additions and 29 deletions.
10 changes: 5 additions & 5 deletions ...se/chemclipse/msd/converter/supplier/mzdata/internal/io/MassSpectrumReaderVersion105.java
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Expand Up @@ -48,24 +48,24 @@
public class MassSpectrumReaderVersion105 extends AbstractMassSpectraReader implements IMassSpectraReader {

public static final String VERSION = "1.05";
//

private static final Logger logger = Logger.getLogger(MassSpectrumReaderVersion105.class);

@Override
public IMassSpectra read(File file, IProgressMonitor monitor) throws IOException {

IStandaloneMassSpectrum massSpectrum = null;
//

try {
DocumentBuilderFactory documentBuilderFactory = DocumentBuilderFactory.newInstance();
DocumentBuilder documentBuilder = documentBuilderFactory.newDocumentBuilder();
Document document = documentBuilder.parse(file);
NodeList nodeList = document.getElementsByTagName(ReaderVersion105.NODE_MZ_DATA);
//

JAXBContext jaxbContext = JAXBContext.newInstance(ObjectFactory.class);
Unmarshaller unmarshaller = jaxbContext.createUnmarshaller();
MzData mzData = (MzData)unmarshaller.unmarshal(nodeList.item(0));
//

massSpectrum = new StandaloneMassSpectrum();
massSpectrum.setFile(file);
massSpectrum.setIdentifier(file.getName());
Expand All @@ -79,7 +79,7 @@ public IMassSpectra read(File file, IProgressMonitor monitor) throws IOException
} catch(ParserConfigurationException e) {
logger.warn(e);
}
//

IVendorMassSpectra massSpectra = new VendorMassSpectra();
massSpectra.setName(file.getName());
massSpectra.addMassSpectrum(massSpectrum);
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17 changes: 10 additions & 7 deletions ...c/org/eclipse/chemclipse/msd/converter/supplier/mzml/io/MassSpectrumReaderVersion110.java
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Expand Up @@ -49,15 +49,15 @@ public class MassSpectrumReaderVersion110 extends AbstractMassSpectraReader impl
public IMassSpectra read(File file, IProgressMonitor monitor) throws IOException {

IStandaloneMassSpectrum massSpectrum = null;
//

try {
//

massSpectrum = new VendorMassSpectrum();
massSpectrum.setFile(file);
massSpectrum.setIdentifier(file.getName());
//

MzMLType mzML = XmlReader110.getMzML(file);
//

FileDescriptionType fileDescription = mzML.getFileDescription();
if(fileDescription != null) {
ParamGroupType fileContent = fileDescription.getFileContent();
Expand All @@ -69,12 +69,15 @@ public IMassSpectra read(File file, IProgressMonitor monitor) throws IOException
}
}
}
//

double[] mzs = null;
double[] intensities = null;
//

RunType run = mzML.getRun();
for(SpectrumType spectrum : run.getSpectrumList().getSpectrum()) {

massSpectrum.setPosition(spectrum.getSpotID());

for(CVParamType cvParam : spectrum.getCvParam()) {
if(cvParam.getAccession().equals("MS:1000127") && cvParam.getName().equals("centroid spectrum")) {
massSpectrum.setMassSpectrumType(MassSpectrumType.CENTROID);
Expand All @@ -101,7 +104,7 @@ public IMassSpectra read(File file, IProgressMonitor monitor) throws IOException
} catch(DataFormatException e) {
logger.warn(e);
}
//

IVendorMassSpectra massSpectra = new VendorMassSpectra();
massSpectra.setName(file.getName());
massSpectra.addMassSpectrum(massSpectrum);
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5 changes: 4 additions & 1 deletion ...c/org/eclipse/chemclipse/msd/converter/supplier/mzml/io/MassSpectrumWriterVersion110.java
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Expand Up @@ -111,7 +111,7 @@ private SourceFileListType createSourceFileList(IMassSpectra massSpectra) {
for(IScanMSD massSpectrum : massSpectra.getList()) {
if(massSpectrum instanceof IStandaloneMassSpectrum standaloneMassSpectrum) {
SourceFileType sourceFile = XmlWriter110.createSourceFile(standaloneMassSpectrum.getFile());
//

if(massSpectra.getConverterId().equals("org.eclipse.chemclipse.msd.converter.supplier.mzdata.ms")) {
CVParamType cvParamFileFormat = new CVParamType();
cvParamFileFormat.setCvRef(XmlWriter110.MS);
Expand Down Expand Up @@ -243,6 +243,9 @@ private void writeScans(IMassSpectra massSpectra, SpectrumListType spectrumList)
spectrum.getCvParam().add(XmlWriter110.createSpectrumLevel(massSpectrum));
spectrum.getCvParam().add(XmlWriter110.createSpectrumType(massSpectrum));
}
if(scanMSD instanceof IStandaloneMassSpectrum standaloneMassSpectrum) {
spectrum.setSpotID(standaloneMassSpectrum.getPosition());
}
spectrum.setDefaultArrayLength(scanMSD.getNumberOfIons());
spectrumList.getSpectrum().add(spectrum);
}
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19 changes: 14 additions & 5 deletions ...ipse/chemclipse/msd/converter/supplier/mzxml/internal/io/MassSpectrumReaderVersion20.java
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@@ -1,5 +1,5 @@
/*******************************************************************************
* Copyright (c) 2015, 2024 Lablicate GmbH.
* Copyright (c) 2015, 2025 Lablicate GmbH.
*
* All rights reserved.
* This program and the accompanying materials are made available under the
Expand Down Expand Up @@ -30,6 +30,7 @@
import org.eclipse.chemclipse.msd.converter.io.AbstractMassSpectraReader;
import org.eclipse.chemclipse.msd.converter.io.IMassSpectraReader;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.v20.model.DataProcessing;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.v20.model.Maldi;
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;
Expand All @@ -54,24 +55,24 @@
public class MassSpectrumReaderVersion20 extends AbstractMassSpectraReader implements IMassSpectraReader {

public static final String VERSION = "mzXML_2.0";
//

private static final Logger logger = Logger.getLogger(MassSpectrumReaderVersion20.class);

@Override
public IMassSpectra read(File file, IProgressMonitor monitor) throws IOException {

IStandaloneMassSpectrum massSpectrum = null;
//

try {
DocumentBuilderFactory documentBuilderFactory = DocumentBuilderFactory.newInstance();
DocumentBuilder documentBuilder = documentBuilderFactory.newDocumentBuilder();
Document document = documentBuilder.parse(file);
NodeList nodeList = document.getElementsByTagName(AbstractChromatogramReaderVersion.NODE_MS_RUN);
//

JAXBContext jaxbContext = JAXBContext.newInstance(ObjectFactory.class);
Unmarshaller unmarshaller = jaxbContext.createUnmarshaller();
MsRun msrun = (MsRun)unmarshaller.unmarshal(nodeList.item(0));
//

massSpectrum = new VendorMassSpectrum();
massSpectrum.setFile(file);
massSpectrum.setIdentifier(file.getName());
Expand All @@ -96,6 +97,14 @@ public IMassSpectra read(File file, IProgressMonitor monitor) throws IOException
massSpectrum.setPolarity(Polarity.NEGATIVE);
}
}
/*
* Plate
*/
Maldi maldi = scan.getMaldi();
if(maldi != null) {
massSpectrum.setPlate(maldi.getPlateID());
massSpectrum.setPosition(maldi.getSpotID());
}
/*
* Get the ions.
*/
Expand Down
15 changes: 12 additions & 3 deletions ...ipse/chemclipse/msd/converter/supplier/mzxml/internal/io/MassSpectrumReaderVersion21.java
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Expand Up @@ -30,6 +30,7 @@
import org.eclipse.chemclipse.msd.converter.io.AbstractMassSpectraReader;
import org.eclipse.chemclipse.msd.converter.io.IMassSpectraReader;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.v21.model.DataProcessing;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.v21.model.Maldi;
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;
Expand Down Expand Up @@ -61,17 +62,17 @@ public class MassSpectrumReaderVersion21 extends AbstractMassSpectraReader imple
public IMassSpectra read(File file, IProgressMonitor monitor) throws IOException {

IStandaloneMassSpectrum massSpectrum = null;
//

try {
DocumentBuilderFactory documentBuilderFactory = DocumentBuilderFactory.newInstance();
DocumentBuilder documentBuilder = documentBuilderFactory.newDocumentBuilder();
Document document = documentBuilder.parse(file);
NodeList nodeList = document.getElementsByTagName(AbstractChromatogramReaderVersion.NODE_MS_RUN);
//

JAXBContext jaxbContext = JAXBContext.newInstance(ObjectFactory.class);
Unmarshaller unmarshaller = jaxbContext.createUnmarshaller();
MsRun msrun = (MsRun)unmarshaller.unmarshal(nodeList.item(0));
//

massSpectrum = new VendorMassSpectrum();
massSpectrum.setFile(file);
massSpectrum.setIdentifier(file.getName());
Expand All @@ -96,6 +97,14 @@ public IMassSpectra read(File file, IProgressMonitor monitor) throws IOException
massSpectrum.setPolarity(Polarity.NEGATIVE);
}
}
/*
* Plate
*/
Maldi maldi = scan.getMaldi();
if(maldi != null) {
massSpectrum.setPlate(maldi.getPlateID());
massSpectrum.setPosition(maldi.getSpotID());
}
/*
* Get the ions.
*/
Expand Down
17 changes: 13 additions & 4 deletions ...ipse/chemclipse/msd/converter/supplier/mzxml/internal/io/MassSpectrumReaderVersion22.java
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Original file line number Diff line number Diff line change
Expand Up @@ -30,6 +30,7 @@
import org.eclipse.chemclipse.msd.converter.io.AbstractMassSpectraReader;
import org.eclipse.chemclipse.msd.converter.io.IMassSpectraReader;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.v22.model.DataProcessing;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.v22.model.Maldi;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.v22.model.MsRun;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.v22.model.MzXML;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.v22.model.ObjectFactory;
Expand All @@ -55,25 +56,25 @@
public class MassSpectrumReaderVersion22 extends AbstractMassSpectraReader implements IMassSpectraReader {

public static final String VERSION = "mzXML_2.2";
//

private static final Logger logger = Logger.getLogger(MassSpectrumReaderVersion22.class);

@Override
public IMassSpectra read(File file, IProgressMonitor monitor) throws IOException {

IStandaloneMassSpectrum massSpectrum = null;
//

try {
DocumentBuilderFactory documentBuilderFactory = DocumentBuilderFactory.newInstance();
documentBuilderFactory.setNamespaceAware(true);
DocumentBuilder documentBuilder = documentBuilderFactory.newDocumentBuilder();
Document document = documentBuilder.parse(file);
NodeList nodeList = document.getElementsByTagName(AbstractChromatogramReaderVersion.NODE_MZXML);
//

JAXBContext jaxbContext = JAXBContext.newInstance(ObjectFactory.class);
Unmarshaller unmarshaller = jaxbContext.createUnmarshaller();
MzXML mzXML = (MzXML)unmarshaller.unmarshal(nodeList.item(0));
//

massSpectrum = new VendorMassSpectrum();
massSpectrum.setFile(file);
massSpectrum.setIdentifier(file.getName());
Expand All @@ -98,6 +99,14 @@ public IMassSpectra read(File file, IProgressMonitor monitor) throws IOException
massSpectrum.setPolarity(Polarity.NEGATIVE);
}
}
/*
* Plate
*/
Maldi maldi = scan.getMaldi();
if(maldi != null) {
massSpectrum.setPlate(maldi.getPlateID());
massSpectrum.setPosition(maldi.getSpotID());
}
/*
* Get the ions.
*/
Expand Down
15 changes: 15 additions & 0 deletions ...ipse/chemclipse/msd/converter/supplier/mzxml/internal/io/MassSpectrumWriterVersion22.java
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Original file line number Diff line number Diff line change
Expand Up @@ -27,6 +27,7 @@
import org.eclipse.chemclipse.msd.converter.massspectrum.MassSpectrumConverter;
import org.eclipse.chemclipse.msd.converter.massspectrum.MassSpectrumConverterSupport;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.v22.model.DataProcessing;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.v22.model.Maldi;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.v22.model.MsRun;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.v22.model.MzXML;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.internal.v22.model.ObjectFactory;
Expand All @@ -39,6 +40,7 @@
import org.eclipse.chemclipse.msd.model.core.IMassSpectra;
import org.eclipse.chemclipse.msd.model.core.IRegularMassSpectrum;
import org.eclipse.chemclipse.msd.model.core.IScanMSD;
import org.eclipse.chemclipse.msd.model.core.IStandaloneMassSpectrum;
import org.eclipse.chemclipse.msd.model.core.MassSpectrumType;
import org.eclipse.core.runtime.IProduct;
import org.eclipse.core.runtime.IProgressMonitor;
Expand Down Expand Up @@ -157,11 +159,24 @@ private Scan createScan(IScanMSD scanMSD) {
scan.setMsLevel(BigInteger.valueOf(regularMassSpectrum.getMassSpectrometer()));
scan.setCentroided(regularMassSpectrum.getMassSpectrumType() == MassSpectrumType.CENTROID);
}
if(scanMSD instanceof IStandaloneMassSpectrum standaloneMassSpectrum) {
scan.setMaldi(createMaldi(standaloneMassSpectrum));
}
scan.setPeaksCount(BigInteger.valueOf(scanMSD.getNumberOfIons()));
scan.setPeaks(createPeaks(scanMSD));
return scan;
}

private Maldi createMaldi(IStandaloneMassSpectrum standaloneMassSpectrum) {

Maldi maldi = new Maldi();
if(maldi != null) {
maldi.setPlateID(standaloneMassSpectrum.getPlate());
maldi.setSpotID(standaloneMassSpectrum.getPosition());
}
return null;
}

private Peaks createPeaks(IScanMSD scanMSD) {

Peaks peaks = new Peaks();
Expand Down
32 changes: 29 additions & 3 deletions ...e.msd.model/src/org/eclipse/chemclipse/msd/model/core/AbstractStandaloneMassSpectrum.java
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
/*******************************************************************************
* Copyright (c) 2022, 2024 Lablicate GmbH.
* Copyright (c) 2022, 2025 Lablicate GmbH.
*
* All rights reserved.
* This program and the accompanying materials are made available under the
Expand All @@ -24,9 +24,11 @@ public abstract class AbstractStandaloneMassSpectrum extends AbstractRegularMass
* Renew the serialVersionUID any time you have changed some fields or
* methods.
*/
private static final long serialVersionUID = 7180911179209208598L;
//
private static final long serialVersionUID = 7180911179209208599L;

private File file;
private String plate;
private String position;
private String sample;
private String description;
private String operator;
Expand All @@ -46,6 +48,30 @@ public void setFile(File file) {
this.file = file;
}

@Override
public String getPlate() {

return plate;
}

@Override
public void setPlate(String plate) {

this.plate = plate;
}

@Override
public String getPosition() {

return position;
}

@Override
public void setPosition(String position) {

this.position = position;
}

@Override
public String getName() {

Expand Down
16 changes: 15 additions & 1 deletion ...emclipse.msd.model/src/org/eclipse/chemclipse/msd/model/core/IStandaloneMassSpectrum.java
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
/*******************************************************************************
* Copyright (c) 2022, 2024 Lablicate GmbH.
* Copyright (c) 2022, 2025 Lablicate GmbH.
*
* All rights reserved.
* This program and the accompanying materials are made available under the
Expand Down Expand Up @@ -51,6 +51,20 @@ public interface IStandaloneMassSpectrum extends IRegularMassSpectrum {

void setSampleName(String name);

/**
* @return ID of the MALDI target
*/
String getPlate();

void setPlate(String plate);

/**
* @return location (coordinate) on the plate
*/
String getPosition();

void setPosition(String plateLocation);

String getDescription();

void setDescription(String description);
Expand Down

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