|
Class Summary |
| BiosegIndexTask |
A task to create a bioseg GIST index on the location table to help with overlap queries. |
| CalculateLocations |
Calculate additional mappings between annotation after loading into genomic ObjectStore. |
| CreateFlankingRegions |
Create features to represent flanking regions of configurable distance either side of gene
featues. |
| CreateReferences |
Fill in additional references/collections in genomic model |
| FlyBaseUniProtRefsTask |
Task to read a file mapping cds identifiers to UniProt accession numbers and create a protein
reference in the CDSs. |
| GoPostprocess |
Take any GOAnnotation objects assigned to proteins and copy them to corresponding genes. |
| IntergenicRegionUtil |
Methods for creating feature for intergenic regions. |
| IntronUtil |
Methods for creating feature for introns. |
| OverlapUtil |
Utility methods for finding overlaps. |
| OverlapViewTask |
A task the replace the locatedsequencefeatureoverlappingfeatures table with a view that uses the
bioseg type to calculate the overlaps. |
| PostProcessOperationsTask |
Run operations on genomic model database after DataLoading |
| PostProcessUtil |
Common operations for post processing. |
| SetCollectionCounts |
SetCollectionCounts class |
| SynonymUpdater |
This post-process sets the isPrimary field on all Synonyms that have a value field that matches
the corresponding BioEntity. |
| TransferSequences |
Transfer sequences from the Assembly objects to the other objects that are located on the
Assemblys and to the objects that the Assemblys are located on (eg. |
| UpdateOrthologues |
Orthologues from INPARANOID are attched to Proteins not Genes, this class
finds all Orthologues and Paralogues on Proteins and creates references to
to corresponding Genes, duplicating the [Orth|Para]logues if the Protein
references multiple Genes. |