From 75359d8556aed8e0a909a169fea2242091c83bb8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Matthias=20Mail=C3=A4nder?= Date: Sun, 1 Sep 2024 10:23:27 +0200 Subject: [PATCH] Don't round raw data input. --- .../mmass/internal/io/MassSpectrumReaderVersion22.java | 5 +---- .../mzdata/internal/io/MassSpectrumReaderVersion105.java | 7 +------ .../supplier/mzml/internal/converter/XmlReader.java | 9 +-------- .../mzxml/internal/io/ChromatogramReaderVersion21.java | 6 +----- .../mzxml/internal/io/ChromatogramReaderVersion22.java | 6 +----- .../mzxml/internal/io/ChromatogramReaderVersion30.java | 6 +----- .../mzxml/internal/io/ChromatogramReaderVersion31.java | 6 +----- .../mzxml/internal/io/MassSpectrumReaderVersion20.java | 7 +------ 8 files changed, 8 insertions(+), 44 deletions(-) diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mmass/src/org/eclipse/chemclipse/msd/converter/supplier/mmass/internal/io/MassSpectrumReaderVersion22.java b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mmass/src/org/eclipse/chemclipse/msd/converter/supplier/mmass/internal/io/MassSpectrumReaderVersion22.java index c90ac81733..9a25622963 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mmass/src/org/eclipse/chemclipse/msd/converter/supplier/mmass/internal/io/MassSpectrumReaderVersion22.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mmass/src/org/eclipse/chemclipse/msd/converter/supplier/mmass/internal/io/MassSpectrumReaderVersion22.java @@ -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; @@ -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); } } diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzdata/src/org/eclipse/chemclipse/msd/converter/supplier/mzdata/internal/io/MassSpectrumReaderVersion105.java b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzdata/src/org/eclipse/chemclipse/msd/converter/supplier/mzdata/internal/io/MassSpectrumReaderVersion105.java index 41738a2cda..b51da37ee6 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzdata/src/org/eclipse/chemclipse/msd/converter/supplier/mzdata/internal/io/MassSpectrumReaderVersion105.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzdata/src/org/eclipse/chemclipse/msd/converter/supplier/mzdata/internal/io/MassSpectrumReaderVersion105.java @@ -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; @@ -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); diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/converter/XmlReader.java b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/converter/XmlReader.java index 840833e5ae..a9f5a933ba 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/converter/XmlReader.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzml/src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/converter/XmlReader.java @@ -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; @@ -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])); } } } diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzxml/src/org/eclipse/chemclipse/msd/converter/supplier/mzxml/internal/io/ChromatogramReaderVersion21.java b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzxml/src/org/eclipse/chemclipse/msd/converter/supplier/mzxml/internal/io/ChromatogramReaderVersion21.java index 4a1af6a32a..d6430695fb 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzxml/src/org/eclipse/chemclipse/msd/converter/supplier/mzxml/internal/io/ChromatogramReaderVersion21.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzxml/src/org/eclipse/chemclipse/msd/converter/supplier/mzxml/internal/io/ChromatogramReaderVersion21.java @@ -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; @@ -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 { @@ -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); diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzxml/src/org/eclipse/chemclipse/msd/converter/supplier/mzxml/internal/io/ChromatogramReaderVersion22.java b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzxml/src/org/eclipse/chemclipse/msd/converter/supplier/mzxml/internal/io/ChromatogramReaderVersion22.java index a0f0c49c62..0178f34453 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzxml/src/org/eclipse/chemclipse/msd/converter/supplier/mzxml/internal/io/ChromatogramReaderVersion22.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzxml/src/org/eclipse/chemclipse/msd/converter/supplier/mzxml/internal/io/ChromatogramReaderVersion22.java @@ -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; @@ -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 { @@ -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); diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzxml/src/org/eclipse/chemclipse/msd/converter/supplier/mzxml/internal/io/ChromatogramReaderVersion30.java b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzxml/src/org/eclipse/chemclipse/msd/converter/supplier/mzxml/internal/io/ChromatogramReaderVersion30.java index af543c363a..4edff9096f 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzxml/src/org/eclipse/chemclipse/msd/converter/supplier/mzxml/internal/io/ChromatogramReaderVersion30.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzxml/src/org/eclipse/chemclipse/msd/converter/supplier/mzxml/internal/io/ChromatogramReaderVersion30.java @@ -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; @@ -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 { @@ -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); } } diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzxml/src/org/eclipse/chemclipse/msd/converter/supplier/mzxml/internal/io/ChromatogramReaderVersion31.java b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzxml/src/org/eclipse/chemclipse/msd/converter/supplier/mzxml/internal/io/ChromatogramReaderVersion31.java index 2998ebf271..0ac8e4d958 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzxml/src/org/eclipse/chemclipse/msd/converter/supplier/mzxml/internal/io/ChromatogramReaderVersion31.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzxml/src/org/eclipse/chemclipse/msd/converter/supplier/mzxml/internal/io/ChromatogramReaderVersion31.java @@ -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; @@ -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 { @@ -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); } } diff --git a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzxml/src/org/eclipse/chemclipse/msd/converter/supplier/mzxml/internal/io/MassSpectrumReaderVersion20.java b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzxml/src/org/eclipse/chemclipse/msd/converter/supplier/mzxml/internal/io/MassSpectrumReaderVersion20.java index 52511d5bfb..4264b2e2f8 100644 --- a/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzxml/src/org/eclipse/chemclipse/msd/converter/supplier/mzxml/internal/io/MassSpectrumReaderVersion20.java +++ b/chemclipse/plugins/org.eclipse.chemclipse.msd.converter.supplier.mzxml/src/org/eclipse/chemclipse/msd/converter/supplier/mzxml/internal/io/MassSpectrumReaderVersion20.java @@ -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; @@ -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); }