JIGSAW Application Development Class List

Here are the classes, structs, unions and interfaces with brief descriptions:

Annotation	Purpose: Holds all possible gene annotations given a set of input annotations This structure will be used by the dynamic prog. algorithm to record the optimal annotation with respect to the scoring system. This class is mainly a wrapper around the AnnotationMatrix object and is responsible for inserting into the matrix and extracting the optimal parse from the matrix Collaborators: AnnotationMatrix, AnnotationItem, AnnotationScore, Combine
AnnotationItem	Purpose: The annotation matrix is made up of a linked list of this object One instance of this class records all the necessary information for one unique genomic region
AnnotationMatrix	Purpose: A glorified linked list of AnnotationItem objects class acts as a wrapper container class
Combine	Purpose: Initiates the main combiner algorithm
CustomScore	Interface, defines the behavior of the scoring function for the client application
InputData	Responsibilities: Stores all data input information, in sorted 5' -> 3' order. Collaborators: DataSetAbstractFactory, GenePredDataSetFactory, NapDataSetConcreteFactory, SpliceSiteDataSetConcreteFactory, Prediction, Combine
Main	Interface to the "main" function runs combiner
RegionPrediction	Responsibilities: Manage all available evidence for a given sequence region Collaborators: DataSetAbstractProduct, SpliceSite, AnnotationScore