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MAExplorer has a Java plugin extension facility. Plugins written for MAExplorer are called "MAEPlugins". These MAEPlugins allow investigators to extend the core capabilities of MAExplorer program themselves by writing special programs to implement new analysis methods and access data from their MAExplorer database(s). The design of this plugin extension enables users to write these new methods and have them added to the MAExplorer menus or for plugins to be invoked when MAExplorer starts up. In addition, default MAExplorer functionality could be changed by replacing existing MAExplorer methods with user defined methods. Writing a plugin to extend functionality using our Open Java API (Application Programming Interface) than to understand and modify the full MAExplorer program. This section of the Web site describes the API, describes how to write a MAEPlugin, and gives examples of various plugins. All source code is available on our CVS Repository.

The Open Java API is available as the set of MJAxxxx classes in the MAExplorer.jar file.

Keep checking this Web page for the current status of the API as well as the MAExplorer Revision Notes which gives a history of new features and changes to both MAExplorer and the API.

MAExplorer is open source with a Mozilla 1.1 general public license. However, we have made the MAEPlugins public domain (a secondary license that is even less restrictive) with no restrictions on their use. This enables the research community to modify and help improve MAExplorer and the MAEPlugins as required. We are dividing the plugins into those that are donated and those that require interaction with the supplier. We hope that most plugin developers will make them available as open source, but that is not a requirement. If you are interested in writing a plugin or working with us on this open source project please contact us.

1. The MAEPlugins home page

This Web page includes documentation, an Open Java API with javadoc documentation, open source Java source code and jar file examples for lists of MAEPlugins. It contains donated MAEPlugins and links to MAEPlugins offered at other Web sites. Typical MAEPlugins could include: normalization, distance metrics, data Filters, PCA or other visualization tools, graphic plots, clustering, classifiers, array sample I/O data conversion, client-server, Web-server functional analysis of cluster results, etc.

1.1 MAEPlugins are grouped into three types of implementations

These allow various degrees of portability and server independence.
  1. Using 100% Java code to implement the complete plugin. This means it will be portable across all systems.
  2. Accessing local programs written in any language (eg. the R-statistics package). This method may not be portable across all systems.
  3. Web-CGI or client-server to specialized genomic database plugins. This method should be portable across all systems.

2. Open Java API (Applications Programming Interface)

The MAExplorer
Open Java API (Applications Programming Interface) allows users to access all data structures without having to understand the low level internal details of the MAExplorer system.

As we noted, the Open Java API is included in the regular .jar file distributed when you download MAExplorer. The current MAExplorer jar file may be downloaded from MAExplorer.jar. You also will also automatically download the jar file when installing MAExplorer. If you have MAExplorer installed, then you can use the (File menu | Update MAExplorer from command when running MAExplorer to get the latest MAExplorer.jar file release.

3. Distribution of MAExplorer Plugins

The distribution system for MAEPlugins is very flexible. There are several options for distributing Plugins on this Web site including:
  1. MAEPlugins with Java source files, ready-to-run Jar files, and documentation. These are developed by various groups and contributed to the Open Source Web site. You may maintain these yourself or contract the authors or contact the Open Source development group for MAExplorer.
  2. Links to other Web sites where you may obtain the Jar files and (or) Java source and documentation for MAEPlugins from that provider. No MAExplugins will be kept on the this server unless the source code is included.

4. Lists of MAEPlugins being made available

5. How to write a MAEPlugin