| AnnotatedFeature | A module to represent a feature mapping as
predicted by the eFG pipeline. |
| Array | A module to represent a nucleotide microarray. |
| ArrayChip | A simple module to represent the concept/template of
a chip/slide within an array, of which the physical manifestation is an ExperimentalChip. |
| CellType | A module to represent a CellType. |
| Channel | A module to represent a single channel of an ExperimentalChip |
| CoordSystem | Bio::EnsEMBL::Funcgen::CoordSystem |
| DataSet | A module to represent DataSet object. |
| DesignDefs | Bio::EnsEMBL::Funcgen::DesignDefs |
| Experiment | Bio::EnsEMBL::Funcgen::Experiment |
| ExperimentalChip | A module to represent a physical unique experimental chip. |
| ExperimentalSet(1) | A module to represent ExperimentalSet object. |
| ExperimentalSubset | A module to represent ExperimentalSubset object. |
| ExternalFeature | A module to represent an externally curated feature
mapping from an external_db. |
| FeatureSet | A module to represent FeatureSet. |
| FeatureType | A module to represent a FeatureType. i.e. the target of an experiment. |
| Importer | Bio::EnsEMBL::Funcgen::Importer |
| Probe | A module to represent a nucleotide probe. |
| ProbeFeature | A module to represent an nucleotide probe
genomic mapping. |
| ProbeSet | A module to represent a probeset. |
| RegulatoryFeature | A module to represent a regulatory feature
mapping as generated by the eFG regulatory build pipeline. |
| ResultFeature(1) | A module to represent a lightweight ResultFeature object |
| ResultSet | A module to represent ResultSet. |
| Set | A module to represent a base Set object. |
| SetFeature | Ensembl specific set feature. |
| Storable | Bio::EnsEMBL::Funcgen::Storable |
| AnnotatedFeatureAdaptor | A database adaptor for fetching and
storing AnnotatedFeature objects. |
| ArrayAdaptor | A database adaptor for fetching and
storing Funcgen Array objects. |
| ArrayChipAdaptor | A database adaptor for fetching and
storing Funcgen ArrayChip objects. |
| BaseAdaptor | Simple wrapper class for Funcgen StorableAdaptors |
| BaseFeatureAdaptor | An Base class for all
Funcgen FeatureAdaptors, redefines some methods to use the Funcgen DB |
| CellTypeAdaptor | A database adaptor for fetching and
storing Funcgen CellType objects. |
| ChannelAdaptor | A database adaptor for fetching and
storing Funcgen Channel objects. |
| CoordSystemAdaptor | Bio::EnsEMBL::Funcgen::DBSQL::CoordSystemAdaptor |
| DBAdaptor | Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor |
| DBEntryAdaptor | MySQL Database queries to load and store external object references. |
| DataSetAdaptor | A database adaptor for fetching and
storing DataSet objects. |
| ExperimentAdaptor | A database adaptor for fetching and
storing Funcgen Experiment objects. |
| ExperimentalChipAdaptor | A database adaptor for fetching and
storing Funcgen ExperimentalChip objects. |
| ExperimentalSetAdaptor | A database adaptor for fetching and
storing ExperimentalSet objects. |
| ExternalFeatureAdaptor | A database adaptor for fetching and
storing ExternalFeature objects. |
| FeatureSetAdaptor | A database adaptor for fetching and
storing Funcgen feature sets. |
| FeatureTypeAdaptor | A database adaptor for fetching and
storing Funcgen FeatureType objects. |
| MetaCoordContainer | |
| ProbeAdaptor | A database adaptor for fetching and
storing Probe objects. |
| ProbeFeatureAdaptor | A database adaptor for fetching and
storing ProbeFeature objects. |
| ProbeSetAdaptor | A database adaptor for fetching and
storing ProbeSet objects. |
| RegulatoryFeatureAdaptor | A database adaptor for fetching and
storing RegulatoryFeature objects. |
| ResultFeatureAdaptor | A hybrid/chimaeric database adaptor for fetching and
storing ResultFeature objects. This will automatically query the web optimised result_feature
table if a data is present, else it will query the underlying raw data tables.
How are we going to track the association between these two result sets? We could use the supporting_set table and DataSets, but this would require hijacking the product feature set field for a result set??!!
This is not really a DataSet, but two associated result sets.
Add type to result_set, result and result_feature. This would simply be a replicate pointing to the same cc_ids, but we can then simply test for the type and use a different table if possible.
We can healtcheck the two sets to make sure they have the same cc_ids, analysis, feaure and cell types.
How do we make the association? Query using the name, analysis, cell/feature types and different result_set type. Or we could add a parent_result_set_id
This could utilise a Binner object which would do the necessary DB compaction based on the association Feature Collection methods.
Are we going to binary pack the scores?
We should just add another table result_feature_set.
Need to left join on this table as might not be present.
Would need update_result_feature_set method? |
| ResultSetAdaptor | A database adaptor for fetching and
storing ResultSet objects. |
| SetFeatureAdaptor | A base database adaptor for SetFeature adaptors.
storing SetFeature objects. |
| SliceAdaptor | A database aware adaptor responsible for
the creation of Slices in the context of eFG objects. |