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Remove accidental XML m/z rounding #1846

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Sep 2, 2024
Merged

Remove accidental XML m/z rounding #1846

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5 changes: 1 addition & 4 deletions ...ipse/chemclipse/msd/converter/supplier/mmass/internal/io/MassSpectrumReaderVersion22.java
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Expand Up @@ -35,7 +35,6 @@
import org.eclipse.chemclipse.msd.converter.supplier.mmass.converter.model.IVendorMassSpectra;
import org.eclipse.chemclipse.msd.converter.supplier.mmass.converter.model.VendorIon;
import org.eclipse.chemclipse.msd.converter.supplier.mmass.converter.model.VendorMassSpectra;
import org.eclipse.chemclipse.msd.model.core.AbstractIon;
import org.eclipse.chemclipse.msd.model.core.IMassSpectra;
import org.eclipse.chemclipse.msd.model.core.IVendorMassSpectrum;
import org.eclipse.chemclipse.msd.model.core.IVendorStandaloneMassSpectrum;
Expand Down Expand Up @@ -146,9 +145,7 @@ private void readSpectrum(Element element, IVendorMassSpectrum massSpectrum) thr
}
}
for(int i = 0; i < points; i++) {
float intensity = intensities[i];
double mz = AbstractIon.getIon(mzs[i]);
IVendorIon ion = new VendorIon(mz, intensity);
IVendorIon ion = new VendorIon(mzs[i], intensities[i]);
massSpectrum.addIon(ion);
}
}
Expand Down
7 changes: 1 addition & 6 deletions ...se/chemclipse/msd/converter/supplier/mzdata/internal/io/MassSpectrumReaderVersion105.java
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Expand Up @@ -27,11 +27,9 @@
import org.eclipse.chemclipse.msd.converter.supplier.mzdata.internal.v105.model.ObjectFactory;
import org.eclipse.chemclipse.msd.converter.supplier.mzdata.internal.v105.model.ParamType;
import org.eclipse.chemclipse.msd.converter.supplier.mzdata.internal.v105.model.PersonType;
import org.eclipse.chemclipse.msd.converter.supplier.mzdata.model.IVendorIon;
import org.eclipse.chemclipse.msd.converter.supplier.mzdata.model.IVendorMassSpectra;
import org.eclipse.chemclipse.msd.converter.supplier.mzdata.model.VendorIon;
import org.eclipse.chemclipse.msd.converter.supplier.mzdata.model.VendorMassSpectra;
import org.eclipse.chemclipse.msd.model.core.AbstractIon;
import org.eclipse.chemclipse.msd.model.core.IMassSpectra;
import org.eclipse.chemclipse.msd.model.core.IVendorStandaloneMassSpectrum;
import org.eclipse.chemclipse.msd.model.implementation.VendorStandaloneMassSpectrum;
Expand Down Expand Up @@ -98,10 +96,7 @@ public IMassSpectra read(File file, IProgressMonitor monitor) throws IOException
double[] intensities = ReaderVersion105.parseData(spectrum.getIntenArrayBinary().getData());
int length = Math.min(mzs.length, intensities.length);
for(int i = 0; i < length; i++) {
double mz = AbstractIon.getIon(mzs[i]);
float intensity = (float)intensities[i];
IVendorIon ion = new VendorIon(mz, intensity);
massSpectrum.addIon(ion);
massSpectrum.addIon(new VendorIon(mzs[i], (float)intensities[i]));
}
} catch(SAXException e) {
logger.warn(e);
Expand Down
9 changes: 1 addition & 8 deletions .../src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/converter/XmlReader.java
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Expand Up @@ -12,10 +12,8 @@
package org.eclipse.chemclipse.msd.converter.supplier.mzml.internal.converter;

import org.eclipse.chemclipse.msd.converter.supplier.mzml.converter.model.IVendorChromatogram;
import org.eclipse.chemclipse.msd.converter.supplier.mzml.converter.model.IVendorIon;
import org.eclipse.chemclipse.msd.converter.supplier.mzml.converter.model.VendorIon;
import org.eclipse.chemclipse.msd.converter.supplier.mzml.converter.model.VendorScan;
import org.eclipse.chemclipse.msd.model.core.AbstractIon;
import org.eclipse.chemclipse.msd.model.core.IIon;
import org.eclipse.chemclipse.msd.model.core.IVendorMassSpectrum;

Expand Down Expand Up @@ -43,12 +41,7 @@ public static void addIons(double[] intensities, double[] mzs, IVendorMassSpectr

int ions = Math.min(mzs.length, intensities.length);
for(int i = 0; i < ions; i++) {
double intensity = intensities[i];
double mz = AbstractIon.getIon(mzs[i]);
if(intensity >= Float.MIN_VALUE && intensity <= Float.MAX_VALUE) {
IVendorIon ion = new VendorIon(mz, (float)intensity);
massSpectrum.addIon(ion);
}
massSpectrum.addIon(new VendorIon(mzs[i], (float)intensities[i]));
}
}
}
6 changes: 1 addition & 5 deletions ...ipse/chemclipse/msd/converter/supplier/mzxml/internal/io/ChromatogramReaderVersion21.java
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Expand Up @@ -39,7 +39,6 @@
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.AbstractIon;
import org.eclipse.chemclipse.msd.model.core.IChromatogramMSD;
import org.eclipse.chemclipse.msd.model.core.Polarity;
import org.eclipse.chemclipse.support.history.EditInformation;
Expand All @@ -57,7 +56,6 @@ public class ChromatogramReaderVersion21 extends AbstractChromatogramReaderVersi
public static final String VERSION = "mzXML_2.1";
//
private static final Logger logger = Logger.getLogger(ChromatogramReaderVersion21.class);
private static final int ION_PRECISION = 6;

@Override
public IChromatogramMSD read(File file, IProgressMonitor monitor) throws IOException {
Expand Down Expand Up @@ -145,9 +143,7 @@ public IChromatogramMSD read(File file, IProgressMonitor monitor) throws IOExcep
/*
* Get m/z and intensity (m/z-int)
*/
double mz = AbstractIon.getIon(values[peakIndex], ION_PRECISION);
float intensity = (float)values[peakIndex + 1];
IVendorIon ion = new VendorIon(mz, intensity);
IVendorIon ion = new VendorIon(values[peakIndex], (float)values[peakIndex + 1]);
massSpectrum.addIon(ion);
}
chromatogram.addScan(massSpectrum);
Expand Down
6 changes: 1 addition & 5 deletions ...ipse/chemclipse/msd/converter/supplier/mzxml/internal/io/ChromatogramReaderVersion22.java
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Original file line number Diff line number Diff line change
Expand Up @@ -39,7 +39,6 @@
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.AbstractIon;
import org.eclipse.chemclipse.msd.model.core.IChromatogramMSD;
import org.eclipse.chemclipse.msd.model.core.Polarity;
import org.eclipse.chemclipse.support.history.EditInformation;
Expand All @@ -57,7 +56,6 @@ public class ChromatogramReaderVersion22 extends AbstractChromatogramReaderVersi
public static final String VERSION = "mzXML_2.2";
//
private static final Logger logger = Logger.getLogger(ChromatogramReaderVersion22.class);
private static final int ION_PRECISION = 6;

@Override
public IChromatogramMSD read(File file, IProgressMonitor monitor) throws IOException {
Expand Down Expand Up @@ -145,9 +143,7 @@ public IChromatogramMSD read(File file, IProgressMonitor monitor) throws IOExcep
/*
* Get m/z and intensity (m/z-int)
*/
double mz = AbstractIon.getIon(values[peakIndex], ION_PRECISION);
float intensity = (float)values[peakIndex + 1];
IVendorIon ion = new VendorIon(mz, intensity);
IVendorIon ion = new VendorIon(values[peakIndex], (float)values[peakIndex + 1]);
massSpectrum.addIon(ion);
}
chromatogram.addScan(massSpectrum);
Expand Down
6 changes: 1 addition & 5 deletions ...ipse/chemclipse/msd/converter/supplier/mzxml/internal/io/ChromatogramReaderVersion30.java
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Original file line number Diff line number Diff line change
Expand Up @@ -41,7 +41,6 @@
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.AbstractIon;
import org.eclipse.chemclipse.msd.model.core.IChromatogramMSD;
import org.eclipse.chemclipse.msd.model.core.Polarity;
import org.eclipse.chemclipse.support.history.EditInformation;
Expand All @@ -59,7 +58,6 @@ public class ChromatogramReaderVersion30 extends AbstractChromatogramReaderVersi
public static final String VERSION = "mzXML_3.0";
//
private static final Logger logger = Logger.getLogger(ChromatogramReaderVersion30.class);
private static final int ION_PRECISION = 6;

@Override
public IChromatogramMSD read(File file, IProgressMonitor monitor) throws IOException {
Expand Down Expand Up @@ -156,9 +154,7 @@ public IChromatogramMSD read(File file, IProgressMonitor monitor) throws IOExcep
/*
* Get m/z and intensity (m/z-int)
*/
double mz = AbstractIon.getIon(values[peakIndex], ION_PRECISION);
float intensity = (float)values[peakIndex + 1];
IVendorIon ion = new VendorIon(mz, intensity);
IVendorIon ion = new VendorIon(values[peakIndex], (float)values[peakIndex + 1]);
massSpectrum.addIon(ion);
}
}
Expand Down
6 changes: 1 addition & 5 deletions ...ipse/chemclipse/msd/converter/supplier/mzxml/internal/io/ChromatogramReaderVersion31.java
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Expand Up @@ -41,7 +41,6 @@
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.AbstractIon;
import org.eclipse.chemclipse.msd.model.core.IChromatogramMSD;
import org.eclipse.chemclipse.msd.model.core.Polarity;
import org.eclipse.chemclipse.support.history.EditInformation;
Expand All @@ -59,7 +58,6 @@ public class ChromatogramReaderVersion31 extends AbstractChromatogramReaderVersi
public static final String VERSION = "mzXML_3.1";
//
private static final Logger logger = Logger.getLogger(ChromatogramReaderVersion31.class);
private static final int ION_PRECISION = 6;

@Override
public IChromatogramMSD read(File file, IProgressMonitor monitor) throws IOException {
Expand Down Expand Up @@ -156,9 +154,7 @@ public IChromatogramMSD read(File file, IProgressMonitor monitor) throws IOExcep
/*
* Get m/z and intensity (m/z-int)
*/
double mz = AbstractIon.getIon(values[peakIndex], ION_PRECISION);
float intensity = (float)values[peakIndex + 1];
IVendorIon ion = new VendorIon(mz, intensity);
IVendorIon ion = new VendorIon(values[peakIndex], (float)values[peakIndex + 1]);
massSpectrum.addIon(ion);
}
}
Expand Down
7 changes: 1 addition & 6 deletions ...ipse/chemclipse/msd/converter/supplier/mzxml/internal/io/MassSpectrumReaderVersion20.java
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Expand Up @@ -33,11 +33,9 @@
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.Scan;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.model.IVendorIon;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.model.IVendorMassSpectra;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.model.VendorIon;
import org.eclipse.chemclipse.msd.converter.supplier.mzxml.model.VendorMassSpectra;
import org.eclipse.chemclipse.msd.model.core.AbstractIon;
import org.eclipse.chemclipse.msd.model.core.IMassSpectra;
import org.eclipse.chemclipse.msd.model.core.IVendorStandaloneMassSpectrum;
import org.eclipse.chemclipse.msd.model.implementation.VendorMassSpectrum;
Expand Down Expand Up @@ -117,10 +115,7 @@ public IMassSpectra read(File file, IProgressMonitor monitor) throws IOException
/*
* Get m/z and intensity (m/z-int)
*/
double mz = AbstractIon.getIon(values[peakIndex]);
float intensity = (float)values[peakIndex + 1];
IVendorIon ion = new VendorIon(mz, intensity);
massSpectrum.addIon(ion);
massSpectrum.addIon(new VendorIon(values[peakIndex], (float)values[peakIndex + 1]));
}
monitor.worked(1);
}
Expand Down