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• The java standard for Plugins is OSGi (http://www.osgi.org), this is what IGB (written in java) uses.
• The OSGi term for a Plugin is Bundle, they mean the same thing.
• An OSGi bundle is a jar file. It must have a MANIFEST.MF file with the OSGi headers (see below).
• An OSGi bundle can (usually will) have a special java class called an Activator. This class must extend org.osgi.framework.BundleActivator, and implement the start() and stop() methods. The activator class is specified in the Bundle-Activator MANIFEST.MF header (see below). These methods are called when the bundle is started and stopped.
• When a program is running with OSGi, the OSGi framework dynamically handles installing / uninstalling,
  activating (starting), deactivating (stopping), and upgrading bundles.
• OSGi caches bundles, saving them to a directory on the local hard disk, so that they don't need to be downloaded every time. So you can work offline after you have loaded IGB. If, for some reason, you need to clean out the bundle cache, you can run ant cbc (clear bundle cache).
• There are several implementations of OSGi, including:
  1. Apache Felix (http://felix.apache.org/)
  2. Eclipse Equinox (http://www.eclipse.org/equinox/)
  3. Knoplerfish (http://www.knopflerfish.org/)
• The implementations are (for the most part) interchangeable and are free.
• The implementations allow the user to run OSGi from a command line tool or to start it within a program.
• IGB starts the felix implementation from within the com.affymetrix.igb.main.OSGiHandler class, but IGB can
  be run using the Felix command line tool by running ant gogo.
• there are several tutorials for OSGi, including:
  1. How to get Started with OSGi (http://www.osgi.org/About/HowOSGi)
  2. Apache Felix OSGi Tutorial (http://felix.apache.org/site/apache-felix-osgi-tutorial.html)
  3. OSGi for Beginners (http://www.theserverside.com/news/1363825/OSGi-for-Beginners)
  4. OSGi with Eclipse Equinox - Tutorial (http://www.vogella.de/articles/OSGi/article.html)
• IGB uses OBR (http://felix.apache.org/site/apache-felix-osgi-bundle-repository.html) to find and load bundles from web servers (repositories). The web servers need to use OBR to create the repository.xml file listing all the available bundles.
• Users can add / remove bundle repositories by choosing File>Preferences page, Plugin Repositories tab.
• IGB uses OSGi Services to allow bundles to add new implementations of existing IGB elements. The new implementations will show up as soon as the bundle is started. Examples include IGB tabs and graph manipulation functions.

Extension

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Points

(TODO Differentiate our use this term from Eclipse's use of this term.)

IGB has several "extension points" designed specifically for plugins. These are interfaces or abstract classes that
are implemented or extended by plugin versions. Usually the Activator for the plugin will register the plugin as a
service in the start() method:
bundleContext.registerService(<extension point>.class.getName(), <plugin implementation>, new Properties());

The current (as of when?) extension points are:

• com.affymetrix.genometryImpl.operator.Operator - operates on a selection of tracks from the GraphAdjuster tab or popup menu
• com.affymetrix.genometryImpl.parsers.FileTypeHandler - process a file type (by the file extension)
• com.affymetrix.igb.shared.TrackClickListener - called when the user clicks on the label portion of a track
• com.affymetrix.igb.shared.GlyphProcessor - called when IGB creates a glyph
• com.affymetrix.igb.shared.MapViewGlyphFactoryI - a new way to display a track
• com.affymetrix.igb.search.mode.ISearchMode - a new search method option on the Search View tab
• com.affymetrix.igb.osgi.service.IGBTabPanel - a tab in the JTabbedPane at the bottom and sides of IGB
• com.affymetrix.genometryImpl.util.ServerTypeI - a server type
• com.affymetrix.igb.osgi.service.IStopRoutine - a routine to be run when IGB terminates
• com.affymetrix.igb.prefs.IPrefEditorComponent - a Preferences window to let users enter preferences

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