| AnnotationScore | Purpose: Abstracts the notion of a "score", has ended up behaving just like a "double", but hey how was I suppose to know! |
| Compare | Class Compare |
| DataDescrip | Defines 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 |
| DataSetAbstractFactory | Purpose: 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 |
| DataSetAbstractProduct | Responsibilities: 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 |
| DnaStr | Facilitates some useful operations on a particular double stranded dna sequence (e.g |
| EvidenceType | Interface specifies the requiremnts of how user defined evidence types must behave as a feature in a vector |
| EvidenceTypeRegistry | Class ormatRegistry The purpose of this class is to prevent any format specific details from permeating the combiner application code |
| ExonDistr | Singleton, records exon prob |
| FeatVec | Vector of EvidenceType* and is used to store a heterogenous collection evidence types |
| FormatRegistry | Class FormatRegistry The purpose of this class is to prevent any format specific details from permeating the combiner application code |
| GeneModelType | Purpose: Interface - defines the behavior of an idividual exon model type |
| GenePrediction | GenePrediction is derived from Prediction and is designed to record whole exon genes |
| Igr | Responsibilities: instance of a GeneModelType |
| Initial | Responsibilities: define behavior of an "initial" exon model. instance of the GeneModelType Collaborators: GeneModelType |
| Internal | Responsibilities: instantiation of GeneModelType, defines behavior of an "internal" exon. |
| Intron | Responsibilities: instance of a GeneModelType |
| Options | Command line interface |
| PlaceHolder | Responsibilities: 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 Collaborators: Prediction |
| Prediction | Responsibilities: sequence location |
| SeqLoc | Responsibilities: 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 |
| Single | Responsibilities: instance of a GeneModelType |
| Terminal | Responsibilities: Instance of GeneModelType, defines the behavior for a "terminal" exon type. Collaborators: GeneModelType |