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Open Activator.java and update the code with your package declaration as well as occurrences of your plug in class name. The sample code implements an annotation operation, so Activator.java registers service for Alignment, Annotation and ProbeSet means this plugin is designed only for these 3 types of annotations. Actually this SamplePlugin derives from the existing IGB plugin named OverlapAnnotationOperator which you can find it in the plugins folder.

There are also many other different types of operation for annotation and graph created as a plugin or not, such as MergeAnnotationOperator plugin and XorOperator in core folder then com.affymetrix.genometryImpl.operator package.

Your plugin class name is inserted in the file as shown in the following code, as "MyPlugin".

@Override
protected ServiceRegistration<?>[] registerService(IGBService igbService) throws Exception {
	return new ServiceRegistration[] {
		bundleContext.registerService(Operator.class, new MyPlugin(FileTypeCategory.Alignment), null),
		bundleContext.registerService(Operator.class, new MyPlugin(FileTypeCategory.Annotation), null),
		bundleContext.registerService(Operator.class, new MyPlugin(FileTypeCategory.ProbeSet), null)
	};
}

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This sample code inherits AbstractAnnotationOperator and implements Operator interface to work as a new annotation operation. For more options refer to the Extension Points section.

public class MyPlugin extends AbstractAnnotationOperator implements Operator {

	// Constructor
	MyPlugin(FileTypeCategory category){
		super(category);
	}

	// Method to determine the internal plugin name
	@Override
	public String getName() {
		return this.category.toString().toLowerCase() +"_my_plugin";
	}


	// Method to determine the display name for the operation
	@Override
	public String getDisplay() {
		return "My Operation";
	}


	// Private method to check if two symmetries are overlapped used by the operate()
	private boolean overlap(BioSeq aseq, SeqSymmetry s0, SeqSymmetry s1) {
		return s0.getSpan(aseq) != null && s1.getSpan(aseq) != null && s0.getSpan(aseq).getMax() > s1.getSpan(aseq).getMin() && s0.getSpan(aseq).getMin() < s1.getSpan(aseq).getMax();
	}


	// Core code for the operation which loops over input symmetries and return the overlapped ones
	@Override
	public SeqSymmetry operate(BioSeq aseq, List<SeqSymmetry> symList) {
		SimpleSymWithProps result = new SimpleSymWithProps();
		result.setProperties(new HashMap<String,Object>());
		TypeContainerAnnot t0 = (TypeContainerAnnot)symList.get(0);
		TypeContainerAnnot t1 = (TypeContainerAnnot)symList.get(1);
		result.setProperty("type", t0.getType() + " " + getName());

		for (int i = 0; i < t0.getChildCount(); i++) {
			SeqSymmetry s0 = t0.getChild(i);
			for (int j = 0; j < t1.getChildCount(); j++) {
				SeqSymmetry s1 = t1.getChild(j);
				if (overlap(aseq, s0, s1)) {
					result.addChild(s0);
					result.addSpan(s0.getSpan(aseq));
					break;
				}
			}
		}
		return result;
	}

*Step 7. Update* *{_}MAINFEST.BASE{_}{*}*:* Directly under the _\[MyPlugin\]_ folder, update the following highlighted fields for _MAINFEST.BASE_.

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You can refer more operations in plugins or com.affymetrix.genometryImpl.operator package in core folder.

Step 7. Update MAINFEST.BASE: Directly under the [MyPlugin] folder, update the following highlighted fields for MAINFEST.BASE.

• Bundle-Name - change to your plugin name
• Bundle-SymbolicName - change to your package path
• Bundle-Version - change to your plugin version
• Bundle-Activation - change to your Activator path (e.g. com.myorg.myplugin.Activator)
• Import-Package - include all the classes your are using in your source code

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*Step 8. Update* *{_}ant.properties{_}{*}*:* Also found under _\[MyPlugin\]_ folder, update the highlighted fields as follows.

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• name=\[your plugin name\]unmigrated-wiki-markup
• project=\[your plugin name\]
• classpath is updated with the necessary paths; refer to the project build.xml for the actual paths listed, i.e. the path for igb_service, windows_service, etc.

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• Next, using a command line prompt, navigate to IGB_HOME folder and run the following command (Enter your svn password as necessary):

Wiki Markup*Step 4. Move the .jar and .xml files to your plugin directory:* There should be 2 generated files in IGB_HOME/plugins/ext, _\[MyPlugin\].jar_ and _repository.xml_. Move these files to your plugin repository folder (local or remote HTTP server). Make sure to cut these files from from the IGB_HOME/plugins/ext folder, or delete after copying.

Step 5 (optional): Revert IGB code: You can now revert all of the code changes you have made, if you wish, or simply change the name of the plugin in all appropriate code locations to create files for another plugin.

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