Inherits from:
No subclasses
Overview
E.g.
- Features (EnsEMBL::Web::Object::DAS::transcript)
Method
Unknown
- EntryPoints (EnsEMBL::Web::Object::DAS)
- FeatureIDs (EnsEMBL::Web::Object::DAS)
- FeatureTypes (EnsEMBL::Web::Object::DAS)
- Features
- GroupIDs (EnsEMBL::Web::Object::DAS)
- Locations (EnsEMBL::Web::Object::DAS)
- Stylesheet
- Stylesheet (EnsEMBL::Web::Object::DAS::transcript)
- Stylesheet (EnsEMBL::Web::Object::DAS)
- Types (EnsEMBL::Web::Object::DAS)
- _Stylesheet (EnsEMBL::Web::Object::DAS)
- _group_info (EnsEMBL::Web::Object::DAS::transcript)
- base_features (EnsEMBL::Web::Object::DAS)
- get_projections (EnsEMBL::Web::Object::DAS)
- loc (EnsEMBL::Web::Object::DAS)
- new (EnsEMBL::Web::Object::DAS)
- ori (EnsEMBL::Web::Object::DAS)
- project_onto_coord_system (EnsEMBL::Web::Object::DAS::transcript)
- real_species (EnsEMBL::Web::Object::DAS)
- slice_cache (EnsEMBL::Web::Object::DAS)
Methods
- Features
debugging - return chromosomal coordinates as well as clone coordinates when requested DO NOT use when live. Also print some warnings Return das features... structure returned is an arrayref of hashrefs, each array element refers to a different segment, the hashrefs contain segment info (seg type, seg name, seg start, seg end) and an array of feature hashes
For transcripts the format is:
> {species}.ASSEMBLY[-{coordinate_system}]/[enhanced_]transcript[-{database}[-{logicname}]*]
If database is missing assumes core, if logicname is missing assumes all transcript features
coordinate_system defines the coord system on whihc to return the features E.g..
* /das/Homo_sapiens.NCBI36-toplevel.transcript-core-ensembl
* /das/Homo_sapiens.NCBI36-clone.transcript-vega
| Part 4 | Fetch features on the segments requested... The approach is to map all requested slices onto the top level in the Factory, irrespective of their actual coord system. By retrieving features on this top level coord_system partially overlapping features can be retrieved. When features are requested to be *returned* on a different coordinate system such as clone, then this change in coordinates is done at the very end, using information in the %projection_mappings hash. |
| Part 6 | Grab and return features Now we do all the nasty stuff of retrieving features and creating DAS objects for them... |
| Part 7 | Return the reference to an array of the slice specific hashes. |
| _ Part 1 | initialize data structures... |
| _ Part 2 | parse the DSN to work out what we want to display Relevant part of DSN is stored in $ENV{'ENSEMBL_DAS_SUBTYPE'} |
| _ Part 3 | parse CGI parameters to get out feature types, group ids and feature ids * FeatureTypes - Currently ignored... * Group IDs - filter in this case transcripts * Feature IDs - filter in ths case exons |
| _ Part 5 | Fetch features based on group_id and filter_id - filter_id currently only works for exons and group_id only for transcripts |
Inherited from EnsEMBL::Web::Object::DAS::transcript
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Types
gets features on a slice, and adds to those any other features / groups requested -the format od the DSN is very similar transcripts:
> {species}.ASSEMBLY[-{coordinate_system}]/translation[-{database}[-{logicname}]*]
If database is missing assumes core, if logicname is missing assumes all
Returns a list of types served by this das source....
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Types
Returns a list of types served by this das source....
Inherited from EnsEMBL::Web::Object::DAS::transcript
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