Cinema-MX modules in use

The MX architecture works best if the individual Module's are relatively small. To give some idea of how this works in Cinema-MX, the Module's are described in Table 6.1. Some of these are very small (100 lines or so), and some quite a bit larger, and use several other specialised classes.

Table: The modules in use within the Cinema-MX application. The modules are organized by their super class, either the CinemaModule, the CinemaGuiModule, or Others, which are extended from some other module.

CinemaModule	Function
CinemaColorFactory	Generates ColorMap instances, and menu items for their selection.
CinemaCommandLineParser	Parses the command line, and acts on it.
CinemaConsensus	Provides calculation of consensus sequences
CinemaGroupModule	Group sequences, for editing, viewing, and analysis.
CinemaMenuBuilder	Generate menu items on the basis of the XML configurations
CinemaMotifModule	The MotifManager dialog, and output
CinemaMultipleConsensusViewer	View consensus sequences of groups, and there variance.
CinemaPersist	Save information between instantiations of Cinema-MX
CinemaRegexp	Regular Expression searches down sequences
CinemaResizeElements	Resize sequence cells
CinemaSlaveViewerModule	Generate viewer frames for use by other modules.
CinemaSplash	Adds massive functionality in the form of a Splash screen.
FormGroupsByPrints	Experimental! Queries the PRINTS_S database to display the PRINTS motifs.
PhylipInvoker	Experimental! Displays a phylogenetic tree.
CinemaGuiModule
AbstractSequenceInput	Input sequence by some route.
AbstractSequenceOutput	Output sequence by some route.
CinemaColorSelector	Select ColorMap.
CinemaConsensusDisplay	Displays the consensus sequences.
CinemaCoreView	Support for CinemaModule class
CinemaGo	Well everybody hacks some times
CinemaHackMenu	More professionally displayed as ``in development'' in the menu system. Its quicker to add here than through XML.
CineamMenuSystem	Uses CinemaMenuBuilder to build menu, then displays it
CinemaSequenceMenu	Right click on sequence button menu.
CinemaStatusInformation	Prints ``cursor here'' information in status bar.
Others
CinemaCoreGui	Extends directly from the Module class, and provides support for the CinemaGuiModule class.
XMLBootModule	Extends from directly from Module. Loads1 parsers for reading XML configuration.
CinemaBoot	Extends from XMLBootModule. Additional support for Cinema-MX XML loading.
CinemaFilePersist	Extends from CinemaPersist. Save persistence data to file.
FileSequenceInput	Extends from AbstractSequenceInput. Load from file.
FileSequenceOutput	Extends from AbstractSequenceOutput. Save to file.