2.6 Plugins menu

MAExplorer may be extended by users to use new analysis methods using Java plugins. We call these new methods MAEPlugins which are small Java programs written by users that may be dynamically loaded into MAExplorer and then applied to their data. These plugins will include plugins written by LECB, those written by academic or commercial groups. See the
MAEplugins for details. If you have a Java compiled plugin in the form of either a Java .class or .jar file, you may load it at run time using the "Load plugin" command in the Plugins menu. If specified in the MAEPlugin, it will be added to the appropriate menu in the MAExplorer menu tree at the end of the specified submenu (see Appendix C. Table C.5.7). If this submenu "stub" is not specified, it will place in the list of plugins in the Plugins menu (e.g. plugin #1, ..., plugin #n).

MAEPlugin paradigm

Figure 2.6 MAEPlugins paradigm. If you have a MAEPlugin .jar file, then it may be specified using the "Load plugin" command. When you invoke the command from the menus (or other methods), it accesses data from the current MAExplorer database it may need from the Open Java API.

The Plugins menu includes:

RLO methods menu

This contains a list of executable R analyses methods (called R LayOuts or RLOs created with the RtestPlugin) for evaluating MAExplorer data with R analysis scripts. It is only available if you have installed the R language program (www.r-project.org) on your computer. An RLO analysis allows you to automatically export data from MAExplorer, execute it with the associated R program, and import the R results back into MAExplorer. [This is under development and is alpha-level.] A recent poster on Extending MAExplorer with R is available as a PDF file.

The Save RLO reports in time-stamped Report/ folder [CB] options puts files generated by R from successive executions of the same RLO into separate sub-folders in the Report/ folder with names "RLOname-YYMMDD-HHMMSS/" to peep the data separate. This is useful when you want to compare results from the same RLO method but with different MAExplorer preprocessing.

You may download the latest versions of all plugins using the (File | Update Plugins from maexplorer.sourceforge.net) menu command. Similarly, you can update your versions of the RLO methods using (File | Update RLO methods from maexplorer.sourceforge.net

2.6.1 Example of using a Plugin

This shows a short demonstration of what is involved in using a MAEPlugin. The user first load the plugin from the disk. Generally the plugins .jar or .class files are stored in the Plugins/ directory where you have installed MAExplorer. Then they load a particular plugin which installs it in the Plugins pull-down menu. Then they revisit that menu to invoke the particular plugin. You may load any number of plugins (until you run out of computer memory if that should occur).

Loading a Plugin from the Plugins 'Load plugin' menu

Figure 2.6.1 Loading a MAEPlugin from your file system using the Load Plugins command in the Plugins pull down menu. If you have a plugin .jar or .class file, it may be specified using the "Load plugin" command. This pops up a file browser to let you specify the plugin file.

Selecting the loaded plugin command from the Plugin menu

Figure 2.6.2 Executing the new command previously loaded in the Plugin menu. Selecting the new "Show List Active Filters" command that now appears in the Plugins menu invokes the plugin. This pops up a report shown in the next figure.

Popup window from executing the MAEPlugin

Figure 2.6.3 Popup window from executing the MAEPlugin. This plugin gives a full report on the data Filter status in a new pop up window.

Selecting a previously loaded plugin from the Plugins menu

Figure 2.6.2 Plugins menu - executing a previously loaded plugin. Plugins that do not go into particular MAExplorer submenus go into the Plugins menu. Selecting the command will invoke that MAEPlugin.