Add services needed for automated multiple chromatogram segmentation

Signed-off-by: Lorenz Gerber <[email protected]>

openchrom/plugins/net.openchrom.xxd.base.ui/src/net/openchrom/xxd/base/ui/Activator.java

@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2023 Lablicate GmbH.
+ * Copyright (c) 2023, 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
@@ -17,9 +17,13 @@
 import org.osgi.util.tracker.ServiceTracker;
 
 import net.openchrom.xxd.base.ui.services.IAlignmentService;
+import net.openchrom.xxd.base.ui.services.IAnalysisSegmentService;
+import net.openchrom.xxd.base.ui.services.IAverageChromatogramService;
 import net.openchrom.xxd.base.ui.services.IDeconvolutionBatchService;
 import net.openchrom.xxd.base.ui.services.IDeconvolutionService;
 import net.openchrom.xxd.base.ui.services.IIdentificationService;
+import net.openchrom.xxd.base.ui.services.ILocalMaximaScanService;
+import net.openchrom.xxd.base.ui.services.ILocalMinimaScanService;
 
 public class Activator extends AbstractActivatorUI {
 
@@ -30,6 +34,10 @@ public class Activator extends AbstractActivatorUI {
 	private ServiceTracker<IDeconvolutionBatchService, IDeconvolutionBatchService> deconvolutionBatchServiceTracker = null;
 	private ServiceTracker<IIdentificationService, IIdentificationService> identificationServiceTracker = null;
 	private ServiceTracker<IAlignmentService, IAlignmentService> alignmentServiceTracker = null;
+	private ServiceTracker<IAverageChromatogramService, IAverageChromatogramService> averageChromatogramServiceTracker = null;
+	private ServiceTracker<ILocalMinimaScanService, ILocalMinimaScanService> localMinimaScanServiceTracker = null;
+	private ServiceTracker<ILocalMaximaScanService, ILocalMaximaScanService> localMaximaScanServiceTracker = null;
+	private ServiceTracker<IAnalysisSegmentService, IAnalysisSegmentService> analysisSegmentServiceTracker = null;
 
 	public static BundleContext getContext() {
 
@@ -77,6 +85,26 @@ public Object[] getAlignmentServices() {
 		return alignmentServiceTracker.getServices();
 	}
 
+	public Object[] getAverageChromatogramServices() {
+
+		return averageChromatogramServiceTracker.getServices();
+	}
+
+	public Object[] getLocalMinimaScanServices() {
+
+		return localMinimaScanServiceTracker.getServices();
+	}
+
+	public Object[] getLocalMaximaScanServices() {
+
+		return localMaximaScanServiceTracker.getServices();
+	}
+
+	public Object[] getAnalysisSegmentServices() {
+
+		return analysisSegmentServiceTracker.getServices();
+	}
+
 	private void startServices(BundleContext context) {
 
 		deconvolutionServiceTracker = new ServiceTracker<>(context, IDeconvolutionService.class, null);
@@ -90,6 +118,18 @@ private void startServices(BundleContext context) {
 		//
 		alignmentServiceTracker = new ServiceTracker<>(context, IAlignmentService.class, null);
 		alignmentServiceTracker.open();
+		//
+		averageChromatogramServiceTracker = new ServiceTracker<>(context, IAverageChromatogramService.class, null);
+		averageChromatogramServiceTracker.open();
+		//
+		localMinimaScanServiceTracker = new ServiceTracker<>(context, ILocalMinimaScanService.class, null);
+		localMinimaScanServiceTracker.open();
+		//
+		localMaximaScanServiceTracker = new ServiceTracker<>(context, ILocalMaximaScanService.class, null);
+		localMaximaScanServiceTracker.open();
+		//
+		analysisSegmentServiceTracker = new ServiceTracker<>(context, IAnalysisSegmentService.class, null);
+		analysisSegmentServiceTracker.open();
 	}
 
 	private void stopServices() {
@@ -98,5 +138,9 @@ private void stopServices() {
 		deconvolutionBatchServiceTracker.close();
 		identificationServiceTracker.close();
 		alignmentServiceTracker.close();
+		averageChromatogramServiceTracker.close();
+		localMinimaScanServiceTracker.close();
+		localMaximaScanServiceTracker.close();
+		analysisSegmentServiceTracker.close();
 	}
 }

openchrom/plugins/net.openchrom.xxd.base.ui/src/net/openchrom/xxd/base/ui/services/IAnalysisSegmentService.java

@@ -0,0 +1,37 @@
+/*******************************************************************************
+ * Copyright (c) 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
+ * which accompanies this distribution, and is available at
+ * http://www.eclipse.org/legal/epl-v10.html
+ * 
+ * Contributors:
+ * Lorenz Gerber - initial API and implementation
+ *******************************************************************************/
+package net.openchrom.xxd.base.ui.services;
+
+import java.util.List;
+
+import org.eclipse.chemclipse.model.core.IChromatogram;
+import org.eclipse.chemclipse.model.core.IScan;
+import org.eclipse.chemclipse.model.support.IAnalysisSegment;
+import org.eclipse.chemclipse.model.types.DataType;
+import org.eclipse.chemclipse.processing.core.IProcessingInfo;
+import org.eclipse.core.runtime.IProgressMonitor;
+import org.eclipse.ui.IWorkbenchPreferencePage;
+
+public interface IAnalysisSegmentService {
+
+	String getName();
+
+	String getDescription();
+
+	String getVersion();
+
+	DataType getDataType();
+
+	IProcessingInfo<List<IAnalysisSegment>> calculate(IChromatogram<?> chromatogram, List<? extends IScan> scans, IProgressMonitor monitor);
+
+	Class<? extends IWorkbenchPreferencePage> getPreferencePage();
+}

openchrom/plugins/net.openchrom.xxd.base.ui/src/net/openchrom/xxd/base/ui/services/IAverageChromatogramService.java

@@ -0,0 +1,35 @@
+/*******************************************************************************
+ * Copyright (c) 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
+ * which accompanies this distribution, and is available at
+ * http://www.eclipse.org/legal/epl-v10.html
+ * 
+ * Contributors:
+ * Lorenz Gerber - initial API and implementation
+ *******************************************************************************/
+package net.openchrom.xxd.base.ui.services;
+
+import java.util.List;
+
+import org.eclipse.chemclipse.model.core.IChromatogram;
+import org.eclipse.chemclipse.model.types.DataType;
+import org.eclipse.chemclipse.processing.core.IProcessingInfo;
+import org.eclipse.core.runtime.IProgressMonitor;
+import org.eclipse.ui.IWorkbenchPreferencePage;
+
+public interface IAverageChromatogramService {
+
+	String getName();
+
+	String getDescription();
+
+	String getVersion();
+
+	DataType getDataType();
+
+	IProcessingInfo<IChromatogram<?>> calculate(List<IChromatogram<?>> chromatograms, IProgressMonitor monitor);
+
+	Class<? extends IWorkbenchPreferencePage> getPreferencePage();
+}

openchrom/plugins/net.openchrom.xxd.base.ui/src/net/openchrom/xxd/base/ui/services/ILocalMaximaScanService.java

@@ -0,0 +1,36 @@
+/*******************************************************************************
+ * Copyright (c) 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
+ * which accompanies this distribution, and is available at
+ * http://www.eclipse.org/legal/epl-v10.html
+ * 
+ * Contributors:
+ * Lorenz Gerber - initial API and implementation
+ *******************************************************************************/
+package net.openchrom.xxd.base.ui.services;
+
+import java.util.List;
+
+import org.eclipse.chemclipse.model.core.IScan;
+import org.eclipse.chemclipse.model.selection.IChromatogramSelection;
+import org.eclipse.chemclipse.model.types.DataType;
+import org.eclipse.chemclipse.processing.core.IProcessingInfo;
+import org.eclipse.core.runtime.IProgressMonitor;
+import org.eclipse.ui.IWorkbenchPreferencePage;
+
+public interface ILocalMaximaScanService {
+
+	String getName();
+
+	String getDescription();
+
+	String getVersion();
+
+	DataType getDataType();
+
+	IProcessingInfo<List<? extends IScan>> calculate(IChromatogramSelection<?, ?> chromatogram, IProgressMonitor monitor);
+
+	Class<? extends IWorkbenchPreferencePage> getPreferencePage();
+}

openchrom/plugins/net.openchrom.xxd.base.ui/src/net/openchrom/xxd/base/ui/services/ILocalMinimaScanService.java

@@ -0,0 +1,36 @@
+/*******************************************************************************
+ * Copyright (c) 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
+ * which accompanies this distribution, and is available at
+ * http://www.eclipse.org/legal/epl-v10.html
+ * 
+ * Contributors:
+ * Lorenz Gerber - initial API and implementation
+ *******************************************************************************/
+package net.openchrom.xxd.base.ui.services;
+
+import java.util.List;
+
+import org.eclipse.chemclipse.model.core.IScan;
+import org.eclipse.chemclipse.model.selection.IChromatogramSelection;
+import org.eclipse.chemclipse.model.types.DataType;
+import org.eclipse.chemclipse.processing.core.IProcessingInfo;
+import org.eclipse.core.runtime.IProgressMonitor;
+import org.eclipse.ui.IWorkbenchPreferencePage;
+
+public interface ILocalMinimaScanService {
+
+	String getName();
+
+	String getDescription();
+
+	String getVersion();
+
+	DataType getDataType();
+
+	IProcessingInfo<List<? extends IScan>> calculate(IChromatogramSelection<?, ?> chromatogram, IProgressMonitor monitor);
+
+	Class<? extends IWorkbenchPreferencePage> getPreferencePage();
+}

openchrom/plugins/net.openchrom.xxd.base.ui/src/net/openchrom/xxd/base/ui/support/AnalysisSegmentSupport.java

@@ -0,0 +1,36 @@
+/*******************************************************************************
+ * Copyright (c) 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
+ * which accompanies this distribution, and is available at
+ * http://www.eclipse.org/legal/epl-v10.html
+ * 
+ * Contributors:
+ * Lorenz Gerber - initial API and implementation
+ *******************************************************************************/
+package net.openchrom.xxd.base.ui.support;
+
+import org.eclipse.chemclipse.model.types.DataType;
+
+import net.openchrom.xxd.base.ui.Activator;
+import net.openchrom.xxd.base.ui.services.IAnalysisSegmentService;
+
+public class AnalysisSegmentSupport {
+
+	public static IAnalysisSegmentService getAnalysisSegmentService(DataType dataType) {
+
+		Object[] services = Activator.getDefault().getAnalysisSegmentServices();
+		if(services != null) {
+			for(Object service : services) {
+				if(service instanceof IAnalysisSegmentService analysisSegmentService) {
+					if(dataType.equals(analysisSegmentService.getDataType())) {
+						return analysisSegmentService;
+					}
+				}
+			}
+		}
+		//
+		return null;
+	}
+}

openchrom/plugins/net.openchrom.xxd.base.ui/src/net/openchrom/xxd/base/ui/support/AverageChromatogramSupport.java

@@ -0,0 +1,36 @@
+/*******************************************************************************
+ * Copyright (c) 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
+ * which accompanies this distribution, and is available at
+ * http://www.eclipse.org/legal/epl-v10.html
+ * 
+ * Contributors:
+ * Lorenz Gerber - initial API and implementation
+ *******************************************************************************/
+package net.openchrom.xxd.base.ui.support;
+
+import org.eclipse.chemclipse.model.types.DataType;
+
+import net.openchrom.xxd.base.ui.Activator;
+import net.openchrom.xxd.base.ui.services.IAverageChromatogramService;
+
+public class AverageChromatogramSupport {
+
+	public static IAverageChromatogramService getAverageChromatogramService(DataType dataType) {
+
+		Object[] services = Activator.getDefault().getAverageChromatogramServices();
+		if(services != null) {
+			for(Object service : services) {
+				if(service instanceof IAverageChromatogramService averageChromatogramService) {
+					if(dataType.equals(averageChromatogramService.getDataType())) {
+						return averageChromatogramService;
+					}
+				}
+			}
+		}
+		//
+		return null;
+	}
+}

openchrom/plugins/net.openchrom.xxd.base.ui/src/net/openchrom/xxd/base/ui/support/LocalMaximaScanSupport.java

@@ -0,0 +1,36 @@
+/*******************************************************************************
+ * Copyright (c) 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
+ * which accompanies this distribution, and is available at
+ * http://www.eclipse.org/legal/epl-v10.html
+ * 
+ * Contributors:
+ * Lorenz Gerber - initial API and implementation
+ *******************************************************************************/
+package net.openchrom.xxd.base.ui.support;
+
+import org.eclipse.chemclipse.model.types.DataType;
+
+import net.openchrom.xxd.base.ui.Activator;
+import net.openchrom.xxd.base.ui.services.ILocalMaximaScanService;
+
+public class LocalMaximaScanSupport {
+
+	public static ILocalMaximaScanService getLocalMaximaScanService(DataType dataType) {
+
+		Object[] services = Activator.getDefault().getLocalMaximaScanServices();
+		if(services != null) {
+			for(Object service : services) {
+				if(service instanceof ILocalMaximaScanService localMaximaScanService) {
+					if(dataType.equals(localMaximaScanService.getDataType())) {
+						return localMaximaScanService;
+					}
+				}
+			}
+		}
+		//
+		return null;
+	}
+}

openchrom/plugins/net.openchrom.xxd.base.ui/src/net/openchrom/xxd/base/ui/support/LocalMinimaScanSupport.java

@@ -0,0 +1,36 @@
+/*******************************************************************************
+ * Copyright (c) 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
+ * which accompanies this distribution, and is available at
+ * http://www.eclipse.org/legal/epl-v10.html
+ * 
+ * Contributors:
+ * Lorenz Gerber - initial API and implementation
+ *******************************************************************************/
+package net.openchrom.xxd.base.ui.support;
+
+import org.eclipse.chemclipse.model.types.DataType;
+
+import net.openchrom.xxd.base.ui.Activator;
+import net.openchrom.xxd.base.ui.services.ILocalMinimaScanService;
+
+public class LocalMinimaScanSupport {
+
+	public static ILocalMinimaScanService getLocalMinimaScanService(DataType dataType) {
+
+		Object[] services = Activator.getDefault().getLocalMinimaScanServices();
+		if(services != null) {
+			for(Object service : services) {
+				if(service instanceof ILocalMinimaScanService localMinimaScanService) {
+					if(dataType.equals(localMinimaScanService.getDataType())) {
+						return localMinimaScanService;
+					}
+				}
+			}
+		}
+		//
+		return null;
+	}
+}