Main Page | Class Hierarchy | Class List | File List | Class Members

JIGSAW Public API Class List

Here are the classes, structs, unions and interfaces with brief descriptions:
Abstracts the notion of a "score", has ended up behaving
just like a "double", but hey how was I suppose to know!
CompareClass Compare
DataDescripDefines the mapping function that takes user supplied evidence sets and maps them into feature vectors for use in identifying and evalutating patterns by the combiner
Defines the standard interface for input data source factories
These factories are responsible for parsing input files and storing them
in apropriate datastructures (typically a list of genome coordinates so far).
Pattern: Abstract Factory (Design Patterns Gamma et
Defines the basic behavior of all input data sets, whether it be
gene prediction data, splice site site data, EST matches or some as of
yet undetermined source
DnaStrFacilitates some useful operations on a particular double stranded dna sequence (e.g
EvidenceTypeInterface specifies the requiremnts of how user defined evidence types must behave as a feature in a vector
EvidenceTypeRegistryClass ormatRegistry The purpose of this class is to prevent any format specific details from permeating the combiner application code
ExonDistrSingleton, records exon prob
FeatVecVector of EvidenceType* and is used to store a heterogenous collection evidence types
FormatRegistryClass FormatRegistry The purpose of this class is to prevent any format specific details from permeating the combiner application code
Interface - defines the behavior of an idividual exon model type
GenePredictionGenePrediction is derived from Prediction and is designed to record whole exon genes
instance of a GeneModelType
define behavior of an "initial" exon model.
instance of the GeneModelType

instantiation of GeneModelType, defines behavior
of an "internal" exon.
instance of a GeneModelType
OptionsCommand line interface
represents an individual exon and points to the exons parent genemodel
The parent gene models is what gets stored in the big scoring matrix.
This class is used as a matter of conveniance for
breaking up the genomic sequence into regions made up of unique datasets
of annotation data

sequence location
This is a general interface for dealing with specific
locations on a double stranded sequence
SeqLoc is implemented specifically with the idea of traversing through a double stranded sequence
instance of a GeneModelType
Instance of GeneModelType, defines the behavior for
a "terminal" exon type.