Fixed #346 - Support for LC-Raman and GC-FTIR models

OpenChrom · Feb 23, 2023 · c5fcc82 · c5fcc82
1 parent aebe2ec
commit c5fcc82
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Showing 7 changed files with 57 additions and 54 deletions.
diff --git a/...ier.gaml/src/net/openchrom/xir/converter/supplier/gaml/converter/ScanExportConverter.java b/...ier.gaml/src/net/openchrom/xir/converter/supplier/gaml/converter/ScanExportConverter.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2021 Lablicate GmbH.
+ * Copyright (c) 2021, 2023 Lablicate GmbH.
  *
  * All rights reserved. This program and the accompanying materials
  * are made available under the terms of the Eclipse Public License v1.0
@@ -17,14 +17,14 @@
 import org.eclipse.chemclipse.processing.core.ProcessingInfo;
 import org.eclipse.chemclipse.xir.converter.core.AbstractScanExportConverter;
 import org.eclipse.chemclipse.xir.converter.core.IScanExportConverter;
-import org.eclipse.chemclipse.xir.model.core.IScanXIR;
+import org.eclipse.chemclipse.xir.model.core.ISpectrumXIR;
 import org.eclipse.core.runtime.IProgressMonitor;
 
 @SuppressWarnings("rawtypes")
 public class ScanExportConverter extends AbstractScanExportConverter implements IScanExportConverter {
 
 	@Override
-	public IProcessingInfo<?> convert(File file, IScanXIR scan, IProgressMonitor monitor) {
+	public IProcessingInfo<?> convert(File file, ISpectrumXIR scan, IProgressMonitor monitor) {
 
 		IProcessingInfo<?> processingInfo = new ProcessingInfo<>();
 		processingInfo.addInfoMessage("GAML", "Export is not available");

diff --git a/...ier.gaml/src/net/openchrom/xir/converter/supplier/gaml/converter/ScanImportConverter.java b/...ier.gaml/src/net/openchrom/xir/converter/supplier/gaml/converter/ScanImportConverter.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2021 Lablicate GmbH.
+ * Copyright (c) 2021, 2023 Lablicate GmbH.
  *
  * All rights reserved. This program and the accompanying materials
  * are made available under the terms of the Eclipse Public License v1.0
@@ -26,7 +26,7 @@
 import net.openchrom.xir.converter.supplier.gaml.io.ScanReaderVersion100;
 import net.openchrom.xir.converter.supplier.gaml.io.ScanReaderVersion110;
 import net.openchrom.xir.converter.supplier.gaml.io.ScanReaderVersion120;
-import net.openchrom.xir.converter.supplier.gaml.model.IVendorScanXIR;
+import net.openchrom.xir.converter.supplier.gaml.model.IVendorSpectrumXIR;
 import net.openchrom.xxd.converter.supplier.gaml.internal.io.IConstants;
 
 @SuppressWarnings("rawtypes")
@@ -35,9 +35,9 @@ public class ScanImportConverter extends AbstractScanImportConverter implements
 	private static final Logger logger = Logger.getLogger(ScanImportConverter.class);
 
 	@Override
-	public IProcessingInfo<IVendorScanXIR> convert(File file, IProgressMonitor monitor) {
+	public IProcessingInfo<IVendorSpectrumXIR> convert(File file, IProgressMonitor monitor) {
 
-		IProcessingInfo<IVendorScanXIR> processingInfo = new ProcessingInfo<>();
+		IProcessingInfo<IVendorSpectrumXIR> processingInfo = new ProcessingInfo<>();
 		try {
 			final FileReader fileReader = new FileReader(file);
 			final char[] charBuffer = new char[100];
@@ -47,15 +47,15 @@ public IProcessingInfo<IVendorScanXIR> convert(File file, IProgressMonitor monit
 			final String header = new String(charBuffer);
 			if(header.contains(IConstants.GAML_V_100)) {
 				ScanReaderVersion100 scanReader = new ScanReaderVersion100();
-				IVendorScanXIR vendorScan = scanReader.read(file, monitor);
+				IVendorSpectrumXIR vendorScan = scanReader.read(file, monitor);
 				processingInfo.setProcessingResult(vendorScan);
 			} else if(header.contains(IConstants.GAML_V_110)) {
 				ScanReaderVersion110 scanReader = new ScanReaderVersion110();
-				IVendorScanXIR vendorScan = scanReader.read(file, monitor);
+				IVendorSpectrumXIR vendorScan = scanReader.read(file, monitor);
 				processingInfo.setProcessingResult(vendorScan);
 			} else if(header.contains(IConstants.GAML_V_120)) {
 				ScanReaderVersion120 scanReader = new ScanReaderVersion120();
-				IVendorScanXIR vendorScan = scanReader.read(file, monitor);
+				IVendorSpectrumXIR vendorScan = scanReader.read(file, monitor);
 				processingInfo.setProcessingResult(vendorScan);
 			} else {
 				throw new UnknownVersionException();

diff --git a/....supplier.gaml/src/net/openchrom/xir/converter/supplier/gaml/io/ScanReaderVersion100.java b/....supplier.gaml/src/net/openchrom/xir/converter/supplier/gaml/io/ScanReaderVersion100.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2021, 2022 Lablicate GmbH.
+ * Copyright (c) 2021, 2023 Lablicate GmbH.
  *
  * All rights reserved. This program and the accompanying materials
  * are made available under the terms of the Eclipse Public License v1.0
@@ -20,17 +20,14 @@
 import javax.xml.parsers.ParserConfigurationException;
 
 import org.eclipse.chemclipse.logging.core.Logger;
-import org.eclipse.chemclipse.xir.model.core.SignalXIR;
+import org.eclipse.chemclipse.xir.model.implementation.SignalXIR;
 import org.eclipse.core.runtime.IProgressMonitor;
 import org.w3c.dom.Document;
 import org.w3c.dom.NodeList;
 import org.xml.sax.SAXException;
 
-import jakarta.xml.bind.JAXBContext;
-import jakarta.xml.bind.JAXBException;
-import jakarta.xml.bind.Unmarshaller;
-import net.openchrom.xir.converter.supplier.gaml.model.IVendorScanXIR;
-import net.openchrom.xir.converter.supplier.gaml.model.VendorScanXIR;
+import net.openchrom.xir.converter.supplier.gaml.model.IVendorSpectrumXIR;
+import net.openchrom.xir.converter.supplier.gaml.model.VendorSpectrumXIR;
 import net.openchrom.xxd.converter.supplier.gaml.internal.io.IConstants;
 import net.openchrom.xxd.converter.supplier.gaml.internal.v100.model.Experiment;
 import net.openchrom.xxd.converter.supplier.gaml.internal.v100.model.GAML;
@@ -41,13 +38,17 @@
 import net.openchrom.xxd.converter.supplier.gaml.internal.v100.model.Ydata;
 import net.openchrom.xxd.converter.supplier.gaml.io.Reader100;
 
+import jakarta.xml.bind.JAXBContext;
+import jakarta.xml.bind.JAXBException;
+import jakarta.xml.bind.Unmarshaller;
+
 public class ScanReaderVersion100 {
 
 	private static final Logger logger = Logger.getLogger(ScanReaderVersion100.class);
 
-	public IVendorScanXIR read(File file, IProgressMonitor monitor) throws IOException {
+	public IVendorSpectrumXIR read(File file, IProgressMonitor monitor) throws IOException {
 
-		IVendorScanXIR vendorScan = null;
+		IVendorSpectrumXIR vendorScan = null;
 		try {
 			DocumentBuilderFactory documentBuilderFactory = DocumentBuilderFactory.newInstance();
 			DocumentBuilder documentBuilder = documentBuilderFactory.newDocumentBuilder();
@@ -57,7 +58,7 @@ public IVendorScanXIR read(File file, IProgressMonitor monitor) throws IOExcepti
 			Unmarshaller unmarshaller = jaxbContext.createUnmarshaller();
 			GAML gaml = (GAML)unmarshaller.unmarshal(nodeList.item(0));
 			for(Experiment experiment : gaml.getExperiment()) {
-				vendorScan = new VendorScanXIR();
+				vendorScan = new VendorSpectrumXIR();
 				vendorScan.setDataName(experiment.getName());
 				XMLGregorianCalendar collectDate = experiment.getCollectdate();
 				if(collectDate != null) {
@@ -79,7 +80,7 @@ public IVendorScanXIR read(File file, IProgressMonitor monitor) throws IOExcepti
 					}
 					int scans = Math.min(waveNumbers.length, absorbance.length);
 					for(int i = 0; i < scans; i++) {
-						vendorScan.getProcessedSignals().add(new SignalXIR(waveNumbers[i], absorbance[i], 0));
+						vendorScan.getScanXIR().getProcessedSignals().add(new SignalXIR(waveNumbers[i], absorbance[i], 0));
 					}
 				}
 			}
@@ -94,4 +95,4 @@ public IVendorScanXIR read(File file, IProgressMonitor monitor) throws IOExcepti
 		}
 		return vendorScan;
 	}
-}
+}
diff --git a/....supplier.gaml/src/net/openchrom/xir/converter/supplier/gaml/io/ScanReaderVersion110.java b/....supplier.gaml/src/net/openchrom/xir/converter/supplier/gaml/io/ScanReaderVersion110.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2021, 2022 Lablicate GmbH.
+ * Copyright (c) 2021, 2023 Lablicate GmbH.
  *
  * All rights reserved. This program and the accompanying materials
  * are made available under the terms of the Eclipse Public License v1.0
@@ -20,17 +20,14 @@
 import javax.xml.parsers.ParserConfigurationException;
 
 import org.eclipse.chemclipse.logging.core.Logger;
-import org.eclipse.chemclipse.xir.model.core.SignalXIR;
+import org.eclipse.chemclipse.xir.model.implementation.SignalXIR;
 import org.eclipse.core.runtime.IProgressMonitor;
 import org.w3c.dom.Document;
 import org.w3c.dom.NodeList;
 import org.xml.sax.SAXException;
 
-import jakarta.xml.bind.JAXBContext;
-import jakarta.xml.bind.JAXBException;
-import jakarta.xml.bind.Unmarshaller;
-import net.openchrom.xir.converter.supplier.gaml.model.IVendorScanXIR;
-import net.openchrom.xir.converter.supplier.gaml.model.VendorScanXIR;
+import net.openchrom.xir.converter.supplier.gaml.model.IVendorSpectrumXIR;
+import net.openchrom.xir.converter.supplier.gaml.model.VendorSpectrumXIR;
 import net.openchrom.xxd.converter.supplier.gaml.internal.io.IConstants;
 import net.openchrom.xxd.converter.supplier.gaml.internal.v110.model.Experiment;
 import net.openchrom.xxd.converter.supplier.gaml.internal.v110.model.GAML;
@@ -41,13 +38,17 @@
 import net.openchrom.xxd.converter.supplier.gaml.internal.v110.model.Ydata;
 import net.openchrom.xxd.converter.supplier.gaml.io.Reader110;
 
+import jakarta.xml.bind.JAXBContext;
+import jakarta.xml.bind.JAXBException;
+import jakarta.xml.bind.Unmarshaller;
+
 public class ScanReaderVersion110 {
 
 	private static final Logger logger = Logger.getLogger(ScanReaderVersion110.class);
 
-	public IVendorScanXIR read(File file, IProgressMonitor monitor) throws IOException {
+	public IVendorSpectrumXIR read(File file, IProgressMonitor monitor) throws IOException {
 
-		IVendorScanXIR vendorScan = null;
+		IVendorSpectrumXIR vendorScan = null;
 		try {
 			DocumentBuilderFactory documentBuilderFactory = DocumentBuilderFactory.newInstance();
 			DocumentBuilder documentBuilder = documentBuilderFactory.newDocumentBuilder();
@@ -57,7 +58,7 @@ public IVendorScanXIR read(File file, IProgressMonitor monitor) throws IOExcepti
 			Unmarshaller unmarshaller = jaxbContext.createUnmarshaller();
 			GAML gaml = (GAML)unmarshaller.unmarshal(nodeList.item(0));
 			for(Experiment experiment : gaml.getExperiment()) {
-				vendorScan = new VendorScanXIR();
+				vendorScan = new VendorSpectrumXIR();
 				vendorScan.setDataName(experiment.getName());
 				XMLGregorianCalendar collectDate = experiment.getCollectdate();
 				if(collectDate != null) {
@@ -79,7 +80,7 @@ public IVendorScanXIR read(File file, IProgressMonitor monitor) throws IOExcepti
 					}
 					int scans = Math.min(waveNumbers.length, absorbance.length);
 					for(int i = 0; i < scans; i++) {
-						vendorScan.getProcessedSignals().add(new SignalXIR(waveNumbers[i], absorbance[i], 0));
+						vendorScan.getScanXIR().getProcessedSignals().add(new SignalXIR(waveNumbers[i], absorbance[i], 0));
 					}
 				}
 			}
@@ -94,4 +95,4 @@ public IVendorScanXIR read(File file, IProgressMonitor monitor) throws IOExcepti
 		}
 		return vendorScan;
 	}
-}
+}
diff --git a/....supplier.gaml/src/net/openchrom/xir/converter/supplier/gaml/io/ScanReaderVersion120.java b/....supplier.gaml/src/net/openchrom/xir/converter/supplier/gaml/io/ScanReaderVersion120.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2021, 2022 Lablicate GmbH.
+ * Copyright (c) 2021, 2023 Lablicate GmbH.
  *
  * All rights reserved. This program and the accompanying materials
  * are made available under the terms of the Eclipse Public License v1.0
@@ -20,17 +20,14 @@
 import javax.xml.parsers.ParserConfigurationException;
 
 import org.eclipse.chemclipse.logging.core.Logger;
-import org.eclipse.chemclipse.xir.model.core.SignalXIR;
+import org.eclipse.chemclipse.xir.model.implementation.SignalXIR;
 import org.eclipse.core.runtime.IProgressMonitor;
 import org.w3c.dom.Document;
 import org.w3c.dom.NodeList;
 import org.xml.sax.SAXException;
 
-import jakarta.xml.bind.JAXBContext;
-import jakarta.xml.bind.JAXBException;
-import jakarta.xml.bind.Unmarshaller;
-import net.openchrom.xir.converter.supplier.gaml.model.IVendorScanXIR;
-import net.openchrom.xir.converter.supplier.gaml.model.VendorScanXIR;
+import net.openchrom.xir.converter.supplier.gaml.model.IVendorSpectrumXIR;
+import net.openchrom.xir.converter.supplier.gaml.model.VendorSpectrumXIR;
 import net.openchrom.xxd.converter.supplier.gaml.internal.io.IConstants;
 import net.openchrom.xxd.converter.supplier.gaml.internal.v120.model.Experiment;
 import net.openchrom.xxd.converter.supplier.gaml.internal.v120.model.GAML;
@@ -41,13 +38,17 @@
 import net.openchrom.xxd.converter.supplier.gaml.internal.v120.model.Ydata;
 import net.openchrom.xxd.converter.supplier.gaml.io.Reader120;
 
+import jakarta.xml.bind.JAXBContext;
+import jakarta.xml.bind.JAXBException;
+import jakarta.xml.bind.Unmarshaller;
+
 public class ScanReaderVersion120 {
 
 	private static final Logger logger = Logger.getLogger(ScanReaderVersion120.class);
 
-	public IVendorScanXIR read(File file, IProgressMonitor monitor) throws IOException {
+	public IVendorSpectrumXIR read(File file, IProgressMonitor monitor) throws IOException {
 
-		IVendorScanXIR vendorScan = null;
+		IVendorSpectrumXIR vendorScan = null;
 		try {
 			DocumentBuilderFactory documentBuilderFactory = DocumentBuilderFactory.newInstance();
 			DocumentBuilder documentBuilder = documentBuilderFactory.newDocumentBuilder();
@@ -57,7 +58,7 @@ public IVendorScanXIR read(File file, IProgressMonitor monitor) throws IOExcepti
 			Unmarshaller unmarshaller = jaxbContext.createUnmarshaller();
 			GAML gaml = (GAML)unmarshaller.unmarshal(nodeList.item(0));
 			for(Experiment experiment : gaml.getExperiment()) {
-				vendorScan = new VendorScanXIR();
+				vendorScan = new VendorSpectrumXIR();
 				vendorScan.setDataName(experiment.getName());
 				XMLGregorianCalendar collectDate = experiment.getCollectdate();
 				if(collectDate != null) {
@@ -79,7 +80,7 @@ public IVendorScanXIR read(File file, IProgressMonitor monitor) throws IOExcepti
 					}
 					int scans = Math.min(waveNumbers.length, absorbance.length);
 					for(int i = 0; i < scans; i++) {
-						vendorScan.getProcessedSignals().add(new SignalXIR(waveNumbers[i], absorbance[i], 0));
+						vendorScan.getScanXIR().getProcessedSignals().add(new SignalXIR(waveNumbers[i], absorbance[i], 0));
 					}
 				}
 			}
@@ -94,4 +95,4 @@ public IVendorScanXIR read(File file, IProgressMonitor monitor) throws IOExcepti
 		}
 		return vendorScan;
 	}
-}
+}
diff --git a/...r/supplier/gaml/model/IVendorScanXIR.java → ...pplier/gaml/model/IVendorSpectrumXIR.java b/...r/supplier/gaml/model/IVendorScanXIR.java → ...pplier/gaml/model/IVendorSpectrumXIR.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2021 Lablicate GmbH.
+ * Copyright (c) 2021, 2023 Lablicate GmbH.
  *
  * All rights reserved. This program and the accompanying materials
  * are made available under the terms of the Eclipse Public License v1.0
@@ -11,7 +11,7 @@
  *******************************************************************************/
 package net.openchrom.xir.converter.supplier.gaml.model;
 
-import org.eclipse.chemclipse.xir.model.core.IScanXIR;
+import org.eclipse.chemclipse.xir.model.core.ISpectrumXIR;
 
-public interface IVendorScanXIR extends IScanXIR {
-}
+public interface IVendorSpectrumXIR extends ISpectrumXIR {
+}
diff --git a/...er/supplier/gaml/model/VendorScanXIR.java → ...upplier/gaml/model/VendorSpectrumXIR.java b/...er/supplier/gaml/model/VendorScanXIR.java → ...upplier/gaml/model/VendorSpectrumXIR.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2021 Lablicate GmbH.
+ * Copyright (c) 2021, 2023 Lablicate GmbH.
  *
  * All rights reserved. This program and the accompanying materials
  * are made available under the terms of the Eclipse Public License v1.0
@@ -11,9 +11,9 @@
  *******************************************************************************/
 package net.openchrom.xir.converter.supplier.gaml.model;
 
-import org.eclipse.chemclipse.xir.model.core.ScanXIR;
+import org.eclipse.chemclipse.xir.model.implementation.SpectrumXIR;
 
-public class VendorScanXIR extends ScanXIR implements IVendorScanXIR {
+public class VendorSpectrumXIR extends SpectrumXIR implements IVendorSpectrumXIR {
 
 	private static final long serialVersionUID = 925295618346515442L;
-}
+}