This document describes the MAEPlugins Open Java API (Applications Programming Interface) to enable researchers to write their own MAEPlugins for use with MAExplorer. The Open Java API (or API) is presented here as two javadoc trees.
The Open Java API is automatically included in the MAExplorer.jar file. Although it wastes some space, we are exporting the symbol tables with the files in MAExplorer.jar so that you could use it with a debugger (such as Forte for Java Community Edition) to develop a MAEPlugin. Forte 4.0 has been renamed "Sun One". We have prepared a document Configuring SourceForge's CVS to work with Forte on Windows for MAExplorer that describes how to set up a software development environment.
MJAxxxx Class Objects and method access ------------- ------------------------- MJAbase base class and constants used by other MJA classes MJAcluster cluster data structures and methodst MJAcondition condition lists of samples and ordered lists of condition lists MJAeval command interpreter to invoke MAExplorer commands MJAexprProfile expression profiles data MJAfilter data filters MJAgene single gene data MJAgeneList lists of genes and get sets MJAgenomicDB genomic databases on the Internet MJAgeometry array geometry, spot to gene maps, etc. MJAhelp popup browser help methods MJAhistogram histogram plots MJAmath built-in math functions MJAnormalziation normalization data and methods MJAplot scrollable 2D plot support [Future] MJAproperty get and put individual properties MJApropList get lists of properties MJAsample get and put single sample top-level data MJAsampleList get lists of samples top-level data MJAscrollablePlot scrollable 2D plot support [Future] MJAsort built-in sort methods MJAstatistics built-in statistics methods MJAstate get and save state, get additional state info MJAutil built-in utility methods