Add an Isotope Distribution Calculator

openchrom/features/net.openchrom.msd.extensions.cdk.feature/.project

@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>net.openchrom.msd.extensions.cdk.feature</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.pde.FeatureBuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.eclipse.pde.FeatureNature</nature>
+	</natures>
+</projectDescription>

openchrom/features/net.openchrom.msd.extensions.cdk.feature/.settings/org.eclipse.core.resources.prefs

@@ -0,0 +1,2 @@
+eclipse.preferences.version=1
+encoding/<project>=UTF-8

openchrom/features/net.openchrom.msd.extensions.cdk.feature/build.properties

@@ -0,0 +1 @@
+bin.includes = feature.xml

openchrom/features/net.openchrom.msd.extensions.cdk.feature/feature.xml

@@ -0,0 +1,30 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<feature
+      id="net.openchrom.msd.extensions.cdk.feature"
+      label="CDK Mass Spectrometry"
+      version="1.5.3.qualifier"
+      provider-name="OpenChrom"
+      license-feature="org.eclipse.license"
+      license-feature-version="1.0.0.qualifier">
+
+   <description url="https://www.openchrom.net">
+      CDK Mass Spectrometry Extension
+   </description>
+
+   <copyright url="https://www.lablicate.net">
+      Copyright (c) 2025 Lablicate GmbH.
+   </copyright>
+
+   <license url="%licenseURL">
+      %license
+   </license>
+
+   <plugin
+         id="net.openchrom.msd.extensions.cdk.ui"
+         version="0.0.0"/>
+
+   <plugin
+         id="net.openchrom.msd.extensions.cdk"
+         version="0.0.0"/>
+
+</feature>

openchrom/features/net.openchrom.platform.feature/feature.xml

@@ -143,6 +143,10 @@
          id="net.openchrom.chromatogram.xxd.report.supplier.pdf.ui.feature"
          version="0.0.0"/>
 
+   <includes
+         id="net.openchrom.msd.extensions.cdk.feature"
+         version="0.0.0"/>
+
    <plugin
          id="net.openchrom.rcp.compilation.community.ui"
          version="0.0.0"/>

openchrom/plugins/net.openchrom.msd.extensions.cdk.ui/.classpath

@@ -0,0 +1,7 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-21"/>
+	<classpathentry kind="con" path="org.eclipse.pde.core.requiredPlugins"/>
+	<classpathentry kind="src" path="src"/>
+	<classpathentry kind="output" path="bin"/>
+</classpath>

openchrom/plugins/net.openchrom.msd.extensions.cdk.ui/.gitignore

@@ -0,0 +1,2 @@
+/bin
+

openchrom/plugins/net.openchrom.msd.extensions.cdk.ui/.project

@@ -0,0 +1,33 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>net.openchrom.msd.extensions.cdk.ui</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.jdt.core.javabuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.pde.ManifestBuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.pde.SchemaBuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.pde.ds.core.builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.eclipse.pde.PluginNature</nature>
+		<nature>org.eclipse.jdt.core.javanature</nature>
+	</natures>
+</projectDescription>

openchrom/plugins/net.openchrom.msd.extensions.cdk.ui/.settings/org.eclipse.core.resources.prefs

@@ -0,0 +1,2 @@
+eclipse.preferences.version=1
+encoding/<project>=UTF-8

openchrom/plugins/net.openchrom.msd.extensions.cdk.ui/.settings/org.eclipse.jdt.core.prefs

@@ -0,0 +1,9 @@
+eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=21
+org.eclipse.jdt.core.compiler.compliance=21
+org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
+org.eclipse.jdt.core.compiler.problem.enablePreviewFeatures=disabled
+org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
+org.eclipse.jdt.core.compiler.problem.reportPreviewFeatures=warning
+org.eclipse.jdt.core.compiler.release=enabled
+org.eclipse.jdt.core.compiler.source=21

openchrom/plugins/net.openchrom.msd.extensions.cdk.ui/.settings/org.eclipse.pde.ds.annotations.prefs

@@ -0,0 +1,6 @@
+eclipse.preferences.version=1
+enabled=true
+generateBundleActivationPolicyLazy=true
+path=OSGI-INF
+validationErrorLevel=error
+validationErrorLevel.missingImplicitUnbindMethod=error

openchrom/plugins/net.openchrom.msd.extensions.cdk.ui/META-INF/MANIFEST.MF

@@ -0,0 +1,28 @@
+Manifest-Version: 1.0
+Bundle-ManifestVersion: 2
+Bundle-Name: CDK Mass Spectrometry UI
+Bundle-SymbolicName: net.openchrom.msd.extensions.cdk.ui;singleton:=true
+Bundle-Version: 1.5.3.qualifier
+Bundle-Activator: net.openchrom.msd.extensions.cdk.ui.Activator
+Bundle-Vendor: OpenChrom
+Require-Bundle: org.eclipse.ui;bundle-version="3.207.100",
+ org.eclipse.core.runtime;bundle-version="3.33.0",
+ org.eclipse.ui.views;bundle-version="3.6.0",
+ org.eclipse.chemclipse.logging;bundle-version="0.9.0",
+ org.eclipse.chemclipse.support;bundle-version="0.9.0",
+ org.eclipse.chemclipse.support.ui;bundle-version="0.9.0",
+ net.openchrom.thirdparty.cdk;bundle-version="2.10.0",
+ net.openchrom.msd.extensions.cdk;bundle-version="1.5.3",
+ org.eclipse.chemclipse.ux.extension.ui;bundle-version="0.9.0",
+ org.eclipse.chemclipse.rcp.ui.icons;bundle-version="0.9.0",
+ org.eclipse.chemclipse.ux.extension.xxd.ui;bundle-version="0.9.0",
+ org.eclipse.chemclipse.model;bundle-version="0.9.0",
+ org.eclipse.chemclipse.msd.model;bundle-version="0.9.0",
+ org.eclipse.chemclipse.msd.swt.ui;bundle-version="0.9.0",
+ org.eclipse.swtchart.extensions;bundle-version="1.1.0",
+ org.eclipse.chemclipse.chromatogram.msd.filter.supplier.xpass;bundle-version="0.9.0"
+Bundle-RequiredExecutionEnvironment: JavaSE-21
+Bundle-ActivationPolicy: lazy
+Automatic-Module-Name: net.openchrom.msd.extensions.cdk.ui
+Model-Fragment: fragment.e4xmi
+Import-Package: jakarta.inject;version="[2.0.0,3.0.0)"

openchrom/plugins/net.openchrom.msd.extensions.cdk.ui/OSGI-INF/l10n/bundle_en.properties

@@ -0,0 +1 @@
+#Properties file

openchrom/plugins/net.openchrom.msd.extensions.cdk.ui/build.properties

@@ -0,0 +1,7 @@
+bin.includes = META-INF/,\
+               .,\
+               OSGI-INF/,\
+               plugin.xml,\
+               fragment.e4xmi
+source.. = src/
+output.. = bin/

openchrom/plugins/net.openchrom.msd.extensions.cdk.ui/fragment.e4xmi

@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="ASCII"?>
+<fragment:ModelFragments xmi:version="2.0" xmlns:xmi="http://www.omg.org/XMI" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:basic="http://www.eclipse.org/ui/2010/UIModel/application/descriptor/basic" xmlns:fragment="http://www.eclipse.org/ui/2010/UIModel/fragment" xmi:id="_3IeOkDG_Ee6Tv4Js7LTvsw">
+  <fragments xsi:type="fragment:StringModelFragment" xmi:id="_1wpoEDzYEe6hp9DJU-acIA" featurename="descriptors" parentElementId="xpath:/">
+    <elements xsi:type="basic:PartDescriptor" xmi:id="_4LerwDzYEe6hp9DJU-acIA" elementId="net.openchrom.msd.extensions.cdk.ui.partdescriptor.isotopeDistributionCalculatorPart" label="Isotope Distribution Calculator" iconURI="platform:/plugin/org.eclipse.chemclipse.rcp.ui.icons/icons/16x16/info.png" tooltip="Calculate isotopic patterns from molecular formulas." closeable="true" contributionURI="bundleclass://net.openchrom.msd.extensions.cdk.ui/net.openchrom.msd.extensions.cdk.ui.parts.IsotopeDistributionCalculatorPart"/>
+  </fragments>
+</fragment:ModelFragments>

openchrom/plugins/net.openchrom.msd.extensions.cdk.ui/plugin.xml

@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<plugin>
+   <extension
+         point="org.eclipse.ui.preferencePages">
+      <page
+            name="Chemistry Development Kit (CDK) MS Tools"
+            category="org.eclipse.chemclipse.rcp.app.ui.preferences.settingsPreferencePage"
+            class="net.openchrom.msd.extensions.cdk.ui.preferences.PreferencePage"
+            id="net.openchrom.msd.extensions.cdk.ui.preferences.preferencePage">
+      </page>
+   </extension>
+</plugin>

openchrom/plugins/net.openchrom.msd.extensions.cdk.ui/src/net/openchrom/msd/extensions/cdk/ui/Activator.java

@@ -0,0 +1,42 @@
+/*******************************************************************************
+ * Copyright (c) 2025 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:
+ * Philip Wenig - initial API and implementation
+ *******************************************************************************/
+package net.openchrom.msd.extensions.cdk.ui;
+
+import org.eclipse.chemclipse.support.ui.activator.AbstractActivatorUI;
+import org.osgi.framework.BundleContext;
+
+import net.openchrom.msd.extensions.cdk.preferences.PreferenceSupplier;
+
+public class Activator extends AbstractActivatorUI {
+
+	private static Activator plugin;
+
+	@Override
+	public void start(BundleContext context) throws Exception {
+
+		super.start(context);
+		plugin = this;
+		initializePreferenceStore(PreferenceSupplier.INSTANCE());
+	}
+
+	@Override
+	public void stop(BundleContext context) throws Exception {
+
+		plugin = null;
+		super.stop(context);
+	}
+
+	public static Activator getDefault() {
+
+		return plugin;
+	}
+}

openchrom/plugins/net.openchrom.msd.extensions.cdk.ui/src/net/openchrom/msd/extensions/cdk/ui/parts/IsotopeDistributionCalculatorPart.java

@@ -0,0 +1,28 @@
+/*******************************************************************************
+ * Copyright (c) 2025 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:
+ * Matthias Mailänder - initial API and implementation
+ *******************************************************************************/
+package net.openchrom.msd.extensions.cdk.ui.parts;
+
+import org.eclipse.swt.SWT;
+import org.eclipse.swt.widgets.Composite;
+
+import net.openchrom.msd.extensions.cdk.ui.swt.ExtendedIsotopeDistributionCalculatorUI;
+
+import jakarta.inject.Inject;
+
+public class IsotopeDistributionCalculatorPart {
+
+	@Inject
+	public IsotopeDistributionCalculatorPart(Composite parent) {
+
+		new ExtendedIsotopeDistributionCalculatorUI(parent, SWT.NONE);
+	}
+}

openchrom/plugins/net.openchrom.msd.extensions.cdk.ui/src/net/openchrom/msd/extensions/cdk/ui/preferences/PreferencePage.java

@@ -0,0 +1,42 @@
+/*******************************************************************************
+ * Copyright (c) 2025 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:
+ * Matthias Mailänder - initial API and implementation
+ *******************************************************************************/
+package net.openchrom.msd.extensions.cdk.ui.preferences;
+
+import org.eclipse.chemclipse.support.ui.preferences.fieldeditors.DoubleFieldEditor;
+import org.eclipse.jface.preference.FieldEditorPreferencePage;
+import org.eclipse.ui.IWorkbench;
+import org.eclipse.ui.IWorkbenchPreferencePage;
+
+import net.openchrom.msd.extensions.cdk.preferences.PreferenceSupplier;
+import net.openchrom.msd.extensions.cdk.ui.Activator;
+
+public class PreferencePage extends FieldEditorPreferencePage implements IWorkbenchPreferencePage {
+
+	public PreferencePage() {
+
+		super(GRID);
+		setPreferenceStore(Activator.getDefault().getPreferenceStore());
+		setTitle("CDK");
+		setDescription("Mass Spectometry using the Chemistry Development Kit");
+	}
+
+	@Override
+	public void createFieldEditors() {
+
+		addField(new DoubleFieldEditor(PreferenceSupplier.P_MIN_INTENSITY, "Minimum Isotope Intensity", getFieldEditorParent()));
+	}
+
+	@Override
+	public void init(IWorkbench workbench) {
+
+	}
+}