Move File to IVendorStandaloneMassSpectrum

See: eclipse/chemclipse#919
OpenChrom · Feb 23, 2022 · 9c0d6ba · 9c0d6ba
1 parent 168aad2
commit 9c0d6ba
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Showing 6 changed files with 31 additions and 37 deletions.
diff --git a/....supplier.animl/src/net/openchrom/msd/converter/supplier/animl/io/MassSpectrumReader.java b/....supplier.animl/src/net/openchrom/msd/converter/supplier/animl/io/MassSpectrumReader.java
@@ -24,7 +24,7 @@
 import org.eclipse.chemclipse.msd.converter.io.IMassSpectraReader;
 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;
 import org.eclipse.chemclipse.msd.model.exceptions.IonLimitExceededException;
 import org.eclipse.chemclipse.msd.model.implementation.VendorMassSpectrum;
 import org.eclipse.core.runtime.IProgressMonitor;
@@ -54,7 +54,7 @@ public class MassSpectrumReader extends AbstractMassSpectraReader implements IMa
 	@Override
 	public IMassSpectra read(File file, IProgressMonitor monitor) throws IOException {
 
-		IVendorMassSpectrum massSpectrum = null;
+		IVendorStandaloneMassSpectrum massSpectrum = null;
 		//
 		try {
 			AnIMLType animl = XmlReader.getAnIML(file);
@@ -143,10 +143,10 @@ public IMassSpectra read(File file, IProgressMonitor monitor) throws IOException
 		return massSpectra;
 	}
 
-	private IVendorMassSpectrum readSample(AnIMLType animl, IVendorMassSpectrum massSpectrum) {
+	private IVendorStandaloneMassSpectrum readSample(AnIMLType animl, IVendorStandaloneMassSpectrum massSpectrum) {
 
 		SampleType sample = animl.getSampleSet().getSample().get(0);
 		massSpectrum.setIdentifier(sample.getSampleID());
 		return massSpectrum;
 	}
-}
+}
diff --git a/....supplier.animl/src/net/openchrom/msd/converter/supplier/animl/io/MassSpectrumWriter.java b/....supplier.animl/src/net/openchrom/msd/converter/supplier/animl/io/MassSpectrumWriter.java
@@ -27,6 +27,7 @@
 import org.eclipse.chemclipse.msd.model.core.IMassSpectra;
 import org.eclipse.chemclipse.msd.model.core.IScanMSD;
 import org.eclipse.chemclipse.msd.model.core.IVendorMassSpectrum;
+import org.eclipse.chemclipse.msd.model.core.IVendorStandaloneMassSpectrum;
 import org.eclipse.core.runtime.IProgressMonitor;
 
 import net.openchrom.xxd.converter.supplier.animl.internal.converter.BinaryReader;
@@ -87,13 +88,15 @@ private void writeMassSpectra(FileWriter fileWriter, IMassSpectra massSpectra, I
 	public void writeMassSpectrum(FileWriter fileWriter, IScanMSD massSpectrum, IProgressMonitor monitor) throws IOException {
 
 		try {
-			writeAnIML(fileWriter, (IVendorMassSpectrum)massSpectrum);
+			if(massSpectrum instanceof IVendorStandaloneMassSpectrum) {
+				writeAnIML(fileWriter, (IVendorStandaloneMassSpectrum)massSpectrum);
+			}
 		} catch(JAXBException e) {
 			logger.warn(e);
 		}
 	}
 
-	private void writeAnIML(FileWriter fileWriter, IVendorMassSpectrum massSpectrum) throws JAXBException {
+	private void writeAnIML(FileWriter fileWriter, IVendorStandaloneMassSpectrum massSpectrum) throws JAXBException {
 
 		JAXBContext jaxbContext = JAXBContext.newInstance(AnIMLType.class);
 		Marshaller marshaller = jaxbContext.createMarshaller();
@@ -106,7 +109,7 @@ private void writeAnIML(FileWriter fileWriter, IVendorMassSpectrum massSpectrum)
 		marshaller.marshal(anIML, fileWriter);
 	}
 
-	private SampleSetType createSampleSet(IVendorMassSpectrum massSpectrum) {
+	private SampleSetType createSampleSet(IVendorStandaloneMassSpectrum massSpectrum) {
 
 		SampleSetType sampleSet = new SampleSetType();
 		SampleType sample = new SampleType();
@@ -225,4 +228,4 @@ private AuditTrailEntrySetType createAuditTrail() {
 		auditTrail.setSoftware(Common.createSoftware());
 		return auditTrailEntrySet;
 	}
-}
+}
diff --git a/...rter.supplier.animl/src/net/openchrom/msd/converter/supplier/animl/model/IVendorScan.java b/...rter.supplier.animl/src/net/openchrom/msd/converter/supplier/animl/model/IVendorScan.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2008, 2021 Lablicate GmbH.
+ * Copyright (c) 2008, 2022 Lablicate GmbH.
  * 
  * All rights reserved.
  * This program and the accompanying materials are made available under the
@@ -11,7 +11,7 @@
  *******************************************************************************/
 package net.openchrom.msd.converter.supplier.animl.model;
 
-import org.eclipse.chemclipse.msd.model.core.IVendorMassSpectrum;
+import org.eclipse.chemclipse.msd.model.core.IVendorStandaloneMassSpectrum;
 
-public interface IVendorScan extends IVendorMassSpectrum {
-}
+public interface IVendorScan extends IVendorStandaloneMassSpectrum {
+}
diff --git a/...upplier.animl/src/net/openchrom/msd/converter/supplier/animl/model/VendorMassSpectra.java b/...upplier.animl/src/net/openchrom/msd/converter/supplier/animl/model/VendorMassSpectra.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2013, 2021 Lablicate GmbH.
+ * Copyright (c) 2013, 2022 Lablicate GmbH.
  * 
  * All rights reserved.
  * This program and the accompanying materials are made available under the
@@ -13,18 +13,18 @@
 
 import org.eclipse.chemclipse.msd.model.core.AbstractMassSpectra;
 import org.eclipse.chemclipse.msd.model.core.IScanMSD;
-import org.eclipse.chemclipse.msd.model.core.IVendorMassSpectrum;
+import org.eclipse.chemclipse.msd.model.core.IVendorStandaloneMassSpectrum;
 
 public class VendorMassSpectra extends AbstractMassSpectra implements IVendorMassSpectra {
 
 	@Override
 	public String getName() {
 
 		IScanMSD scanMSD = this.getMassSpectrum(1);
-		if(scanMSD instanceof IVendorMassSpectrum) {
-			return ((IVendorMassSpectrum)scanMSD).getName();
+		if(scanMSD instanceof IVendorStandaloneMassSpectrum) {
+			return ((IVendorStandaloneMassSpectrum)scanMSD).getName();
 		} else {
 			return super.getName();
 		}
 	}
-}
+}
diff --git a/...erter.supplier.animl/src/net/openchrom/msd/converter/supplier/animl/model/VendorScan.java b/...erter.supplier.animl/src/net/openchrom/msd/converter/supplier/animl/model/VendorScan.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2008, 2021 Lablicate GmbH.
+ * Copyright (c) 2008, 2022 Lablicate GmbH.
  * 
  * All rights reserved.
  * This program and the accompanying materials are made available under the
@@ -13,24 +13,15 @@
 
 import org.eclipse.chemclipse.logging.core.Logger;
 import org.eclipse.chemclipse.model.exceptions.AbundanceLimitExceededException;
-import org.eclipse.chemclipse.msd.model.core.AbstractVendorMassSpectrum;
+import org.eclipse.chemclipse.msd.model.core.AbstractVendorStandaloneMassSpectrum;
 import org.eclipse.chemclipse.msd.model.core.IIon;
 import org.eclipse.chemclipse.msd.model.exceptions.IonLimitExceededException;
 
-public class VendorScan extends AbstractVendorMassSpectrum implements IVendorScan {
+public class VendorScan extends AbstractVendorStandaloneMassSpectrum implements IVendorScan {
 
-	/**
-	 * Renew the serialVersionUID any time you have changed some fields or
-	 * methods.
-	 */
-	private static final long serialVersionUID = -4140714855668296421L;
+	private static final long serialVersionUID = -2505351166336940676L;
 	private static final Logger logger = Logger.getLogger(VendorScan.class);
-	/**
-	 * MAX_IONS The total amount of ions to be stored in the
-	 * cdf chromatogram.<br/>
-	 * It does not mean, that ion 65535 is the upper bound, but only 65535 mass
-	 * fragments can be stored in a mass spectrum.
-	 */
+	//
 	public static final int MAX_IONS = 65535;
 	public static final int MIN_RETENTION_TIME = 0;
 	public static final int MAX_RETENTION_TIME = Integer.MAX_VALUE;
@@ -84,4 +75,4 @@ protected Object clone() throws CloneNotSupportedException {
 
 		return makeDeepCopy();
 	}
-}
+}
diff --git a/....supplier.gaml/src/net/openchrom/msd/converter/supplier/gaml/model/VendorMassSpectra.java b/....supplier.gaml/src/net/openchrom/msd/converter/supplier/gaml/model/VendorMassSpectra.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2013, 2021 Lablicate GmbH.
+ * Copyright (c) 2013, 2022 Lablicate GmbH.
  * 
  * All rights reserved.
  * This program and the accompanying materials are made available under the
@@ -13,18 +13,18 @@
 
 import org.eclipse.chemclipse.msd.model.core.AbstractMassSpectra;
 import org.eclipse.chemclipse.msd.model.core.IScanMSD;
-import org.eclipse.chemclipse.msd.model.core.IVendorMassSpectrum;
+import org.eclipse.chemclipse.msd.model.core.IVendorStandaloneMassSpectrum;
 
 public class VendorMassSpectra extends AbstractMassSpectra implements IVendorMassSpectra {
 
 	@Override
 	public String getName() {
 
 		IScanMSD scanMSD = this.getMassSpectrum(1);
-		if(scanMSD instanceof IVendorMassSpectrum) {
-			return ((IVendorMassSpectrum)scanMSD).getName();
+		if(scanMSD instanceof IVendorStandaloneMassSpectrum) {
+			return ((IVendorStandaloneMassSpectrum)scanMSD).getName();
 		} else {
 			return super.getName();
 		}
 	}
-}
+}