Add ion transitions to mz5 and fix MSn display

openchrom/plugins/net.openchrom.msd.converter.supplier.mz5/src/net/openchrom/msd/converter/supplier/mz5/io/ChromatogramReader.java

@@ -123,6 +123,7 @@ private void readScanProxies(IHDF5SimpleReader reader, CVReference[] cvReference
 		int[] retentionTimes = new int[spectrumIndex.length];
 		String[] spectrumTitles = new String[spectrumIndex.length];
 		short[] msLevels = new short[spectrumIndex.length];
+		double[] selectedIon = new double[spectrumIndex.length];
 		int p = 0;
 		for(CVParam cvParam : cvParams) {
 			if(cvParam.cvRefID == getScanStartTimeReference(cvReferences)) {
@@ -136,11 +137,15 @@ private void readScanProxies(IHDF5SimpleReader reader, CVReference[] cvReference
 			if(cvParam.cvRefID == getMassSpectrumLevelReference(cvReferences)) {
 				msLevels[p] = Short.parseShort(cvParam.value);
 			}
+			if(cvParam.cvRefID == getSelectedIonReference(cvReferences)) {
+				selectedIon[p] = Double.parseDouble(cvParam.value);
+			}
 		}
 		try {
 			double[] mzs = reader.readDoubleArray(Mz5.SPECTRUM_MZ);
 			float[] spectrumIntensity = reader.readFloatArray(Mz5.SPECTRUM_INTENSITY);
 			int start = 0;
+			int cycleNumber = isMultiStageMassSpectrum(cvParams, cvReferences) ? 1 : 0;
 			for(int i = 0; i < spectrumIndex.length; i++) {
 				int offset = spectrumIndex[i];
 				IScanMarker scanMarker = new ScanMarker(start, offset);
@@ -149,6 +154,14 @@ private void readScanProxies(IHDF5SimpleReader reader, CVReference[] cvReference
 				scanProxy.setIdentifier(spectrumTitles[i]);
 				scanProxy.setRetentionTime(retentionTimes[i]);
 				scanProxy.setMassSpectrometer(msLevels[i]);
+				if(scanProxy.getMassSpectrometer() < 2) {
+					cycleNumber++;
+				} else {
+					scanProxy.setPrecursorIon(selectedIon[i]);
+				}
+				if(cycleNumber >= 1) {
+					scanProxy.setCycleNumber(cycleNumber);
+				}
 				float totalSignal = 0;
 				for(int o = start; o < offset; o++) {
 					totalSignal = totalSignal + spectrumIntensity[o];
@@ -229,4 +242,27 @@ private int getTimeMultiplicator(CVReference unit) {
 		}
 		return multiplicator;
 	}
+
+	private boolean isMultiStageMassSpectrum(CVParam[] cvParams, CVReference[] cvReferences) {
+
+		for(CVParam cvParam : cvParams) {
+			if(cvParam.cvRefID == getMassSpectrumLevelReference(cvReferences)) {
+				if(Short.parseShort(cvParam.value) > 1) {
+					return true;
+				}
+			}
+		}
+		return false;
+	}
+
+	private int getSelectedIonReference(CVReference[] cvReferences) {
+
+		int selectedIonRef = 0;
+		for(int c = 0; c < cvReferences.length; c++) {
+			if(cvReferences[c].accession == 1000744 && cvReferences[c].name.equals("selected ion m/z")) {
+				selectedIonRef = c;
+			}
+		}
+		return selectedIonRef;
+	}
 }

openchrom/plugins/net.openchrom.msd.converter.supplier.mz5/src/net/openchrom/msd/converter/supplier/mz5/io/ReaderProxy.java

@@ -15,6 +15,8 @@
 import java.io.IOException;
 
 import org.eclipse.chemclipse.logging.core.Logger;
+import org.eclipse.chemclipse.msd.model.core.IIonTransition;
+import org.eclipse.chemclipse.msd.model.implementation.IonTransition;
 import org.eclipse.core.runtime.IProgressMonitor;
 
 import net.openchrom.msd.converter.supplier.mz5.io.support.IScanMarker;
@@ -36,7 +38,13 @@ public void readMassSpectrum(double[] mzs, float[] spectrumIntensity, IScanMarke
 			for(int o = start; o < offset; o++) {
 				float intensity = spectrumIntensity[o];
 				mz += mzs[o]; // first m/z value and then deltas
-				IVendorIon ion = new VendorIon(mz, intensity);
+				IVendorIon ion = null;
+				if(massSpectrum.getPrecursorIon() != 0) {
+					IIonTransition ionTransition = new IonTransition(massSpectrum.getPrecursorIon(), mz, 0, 1, 1, 0);
+					ion = new VendorIon(mz, intensity, ionTransition);
+				} else {
+					ion = new VendorIon(mz, intensity);
+				}
 				massSpectrum.addIon(ion);
 			}
 		} catch(OutOfMemoryError e) {

openchrom/plugins/net.openchrom.msd.converter.supplier.mz5/src/net/openchrom/msd/converter/supplier/mz5/model/VendorScanProxy.java

@@ -70,7 +70,7 @@ public IVendorScan makeDeepCopy() throws CloneNotSupportedException {
 		 * Make a deep copy of all ions.
 		 */
 		for(IIon ion : getIons()) {
-			IVendorIon vendorIon = new VendorIon(ion.getIon(), ion.getAbundance());
+			IVendorIon vendorIon = new VendorIon(ion.getIon(), ion.getAbundance(), ion.getIonTransition());
 			massSpectrum.addIon(vendorIon);
 		}
 		return massSpectrum;

openchrom/tests/net.openchrom.msd.converter.supplier.mz5.fragment.test/src/net/openchrom/msd/converter/supplier/mz5/fragment/test/ChromatogramImportConverter_ITest.java

@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2022 Lablicate GmbH.
+ * Copyright (c) 2022, 2024 Lablicate GmbH.
  *
  * All rights reserved. This program and the accompanying materials
  * are made available under the terms of the Eclipse Public License v1.0
@@ -14,13 +14,16 @@
 import java.io.File;
 
 import org.eclipse.chemclipse.msd.model.core.IChromatogramMSD;
+import org.eclipse.chemclipse.msd.model.core.IIon;
+import org.eclipse.chemclipse.msd.model.core.IRegularMassSpectrum;
 import org.eclipse.chemclipse.processing.core.IProcessingInfo;
 import org.eclipse.core.runtime.NullProgressMonitor;
 
-import junit.framework.TestCase;
 import net.openchrom.msd.converter.supplier.mz5.PathResolver;
 import net.openchrom.msd.converter.supplier.mz5.converter.ChromatogramImportConverter;
 
+import junit.framework.TestCase;
+
 public class ChromatogramImportConverter_ITest extends TestCase {
 
 	private IChromatogramMSD chromatogram;
@@ -49,8 +52,17 @@ public void testLoading() {
 
 	public void testScans() {
 
-		assertEquals(chromatogram.getNumberOfScans(), 26);
-		assertEquals(chromatogram.getScan(10).getTotalSignal(), 105525.87f);
-		assertEquals(chromatogram.getScan(26).getRetentionTime(), 16639);
+		assertEquals(26, chromatogram.getNumberOfScans());
+		assertEquals(105525.87f, chromatogram.getScan(10).getTotalSignal());
+		assertEquals(16639, chromatogram.getScan(26).getRetentionTime());
+	}
+
+	public void testIonTransitions() {
+
+		IRegularMassSpectrum massSpectrum = (IRegularMassSpectrum)chromatogram.getScan(3);
+		assertEquals(367.201873779297, massSpectrum.getPrecursorIon());
+		IIon ion = massSpectrum.getIons().get(0);
+		assertEquals(367, ion.getIonTransition().getQ1Ion());
+		assertEquals(112.1d, ion.getIonTransition().getQ3Ion());
 	}
 }