Don't round raw data input.

eclipse · Sep 1, 2024 · 56aadac · 56aadac
1 parent a759a92
commit 56aadac
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Showing 8 changed files with 9 additions and 43 deletions.
diff --git a/...ipse/chemclipse/msd/converter/supplier/mmass/internal/io/MassSpectrumReaderVersion22.java b/...ipse/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/...se/chemclipse/msd/converter/supplier/mzdata/internal/io/MassSpectrumReaderVersion105.java b/...se/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/.../src/org/eclipse/chemclipse/msd/converter/supplier/mzml/internal/converter/XmlReader.java b/.../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;
 
@@ -43,11 +41,8 @@ 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);
+			if(intensities[i] >= Float.MIN_VALUE && intensities[i] <= Float.MAX_VALUE) {
+				massSpectrum.addIon(new VendorIon(mzs[i], (float)intensities[i]));
 			}
 		}
 	}

diff --git a/...ipse/chemclipse/msd/converter/supplier/mzxml/internal/io/ChromatogramReaderVersion21.java b/...ipse/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/...ipse/chemclipse/msd/converter/supplier/mzxml/internal/io/ChromatogramReaderVersion22.java b/...ipse/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/...ipse/chemclipse/msd/converter/supplier/mzxml/internal/io/ChromatogramReaderVersion30.java b/...ipse/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/...ipse/chemclipse/msd/converter/supplier/mzxml/internal/io/ChromatogramReaderVersion31.java b/...ipse/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/...ipse/chemclipse/msd/converter/supplier/mzxml/internal/io/MassSpectrumReaderVersion20.java b/...ipse/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);
 			}