How To Write a MAEPlugin using the Open java API

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This document briefly describes how to write MAEPlugins using the MJA Open Java API (Application Programming Interface). It discusses key issues to be addressed when writing a MAEPlugin and describes in sufficient detail to enable researchers to write their own MAEPlugins for use with MAExplorer. Note that there are basically two types of plugins: those which are one-shot plugins (e.g., popup a window with its own user interface or perform an operation one time), and pipeline operations. The latter include FilterPlugins and NormalizationPlugins. These are inserted by MAExplorer into the gene filtering chained intersection analysis and the normalization analysis. See examples of existing plugins to help understand the differences.

1. Using a Java development environment to develop and debug a Plugin

We have designed the MAExplorer.jar file so that it contains both MAExplorer and the Open Java API. All MAExplorer classes are compiled with the symbol table so that it may be used in a debugger. We use the Sun's Forte for Java (Community Edition) which is a free development environment (IDE) available over the Internet. Forte (now known as "SunONE" and most other IDEs) allows you "mount" a jar file. So to create a new plugin you would:
  1. Create a new project directory (e.g., see the ExamplePlugin source code example and discussion).
  2. Copy some example MAExplugin code into this project and rename the modules and classes to correspond to the names of your new plugin.
  3. Mount the MAExplorer.jar file (you can mount it from the directory where you installed MAExplorer (eg. typically C:/Program Files/MAExplorer/MAExplorer.jar for Windows, etc.)
  4. After you have compiled your plugin and want to test it, you create a new Jar file with the name of the plugin (e.g. ExamplePlugin.jar) from the file browser. Forte lets you create jar files with with a jar packager tool.
  5. To test it, you first open the MAExplorer.jar file tree you have mounted. Then you select "MAExplorer". At this point you can execute MAExplorer or run the debugger.
  6. After MAExplorer is running, you select "Load Plugin" from the MAExplorer Plugins pull-down menu, and then enter the name of the plugin (e.g. ExamplePlugin.jar).
  7. At this point you may run the plugin by going back to the Plugins menu and select the entry corresponding to your plugin.
  8. If you want to make a change in your plugin and try again, you do not need to restart MAExplorer. Instead first unload your plugin using the "Unload Plugin" command in the Plugins menu. Then rebuild your plugin, use "Load Plugin", and try again.

2. Installing your MAEPlugin in a working MAExplorer environment

  1. After you are happy (or somewhat happy) with your plugin, copy the plugin jar file (e.g. ExamplePlugin.jar) to the installation Plugins/ directory where you can access on any of your MAExplorer database(s) (e.g., C:/Program Files/MAExplorer/Plugins for Windows, etc.)
  2. To use the plugin on any database, just start MAExplorer and then load and run the plugin as above.