Inherits from:
No subclasses
Overview
Accessor
- Obj (EnsEMBL::Web::Object)
- dataobj (EnsEMBL::Web::Object)
- highlights (EnsEMBL::Web::Object)
- prefix (EnsEMBL::Web::Object)
Deprecated
- EnsemblObject (EnsEMBL::Web::Object)
Method
- URL (EnsEMBL::Web::Object)
- _URL (EnsEMBL::Web::Object)
- alternative_object_from_factory (EnsEMBL::Web::Object)
- command (EnsEMBL::Web::Object)
- full_URL (EnsEMBL::Web::Object)
- get_Slice
- get_alignment
- get_families
- highlights_string (EnsEMBL::Web::Object)
- history
- interface (EnsEMBL::Web::Object)
- location_URL (EnsEMBL::Web::Object)
- mapview_link (EnsEMBL::Web::Object)
- munge_gaps
- seq_region_type_and_name (EnsEMBL::Web::Object)
- seq_region_type_human_readable (EnsEMBL::Web::Object)
Tsv
- ambig_code
- extent
- generate_query_hash
- getFakeMungedVariationsOnSlice
- get_samples
- get_source
- get_transcript_Slice
- get_transcript_slices
- munge_gaps_split
- munge_read_coverage
- read_coverage
- valids
- var_class
Tsv/tse
Unknown
- _availability (EnsEMBL::Web::Object)
- _filename
- _help_URL (EnsEMBL::Web::Object)
- analysis
- availability
- availability (EnsEMBL::Web::Object)
- bp_to_nearest_unit (EnsEMBL::Web::Object)
- can_export
- can_export (EnsEMBL::Web::Object)
- caption
- coord_system
- core_params (EnsEMBL::Web::Object)
- count_alignments (EnsEMBL::Web::Object)
- count_go
- count_oligos
- count_prot_domains
- count_prot_variations
- count_similarity_matches
- count_supporting_evidence
- count_supporting_evidence_old
- counts
- counts (EnsEMBL::Web::Object)
- created_date
- date_format
- db_type
- default_track_by_gene
- determine_sequence_type
- display_label
- display_xref
- feature_length
- feature_type
- fetch_homologues_of_gene_in_species (EnsEMBL::Web::Object)
- gene
- gene_description (EnsEMBL::Web::Object)
- gene_stat_and_biotype
- gene_type
- generate_query_url (EnsEMBL::Web::Object)
- getAllelesConsequencesOnSlice
- getCoordinateSystem (EnsEMBL::Web::Object)
- get_DASCollection (EnsEMBL::Web::Object)
- get_adaptor (EnsEMBL::Web::Object)
- get_alternative_locations
- get_archive_object
- get_author_email
- get_author_name
- get_contig_location
- get_database_matches
- get_db
- get_domain_genes
- get_exon
- get_go_list
- get_hit
- get_int_seq
- get_interpro
- get_latest_incarnation
- get_markedup_trans_seq
- get_prediction_method
- get_sf_hit_db_name
- get_similarity_hash
- get_supporting_evidence
- get_trans_seq
- location_string
- logic_name
- mod_date
- modified
- new_image (EnsEMBL::Web::Object)
- new_karyotype_image (EnsEMBL::Web::Object)
- new_vimage (EnsEMBL::Web::Object)
- referer (EnsEMBL::Web::Object)
- rna_notation
- save_seq
- seq_region_end
- seq_region_name
- seq_region_start
- seq_region_strand
- seq_region_type
- short_caption
- source
- split60
- stable_id
- status
- trans_description
- transcript
- transcript_class
- transcript_type
- translation_object
- type_name
- vega_projection
- version
Methods
- EnsemblObject
Deprecated. Sets/gets the underlying Ensembl object wrapped by the web object
Inherited from EnsEMBL::Web::Object
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Obj
Accessor. Gets the underlying Ensembl object wrapped by the web object
Inherited from EnsEMBL::Web::Object
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URL
(%params) Returns an absolute link to another script. %params hash is used as the parameters for the link. Note keys species and script are handled differently - as these are not passed as parameters but set the species and script name respectively in the URL
Inherited from EnsEMBL::Web::Object
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_URL
Returns either a full link or absolute link to a script
Inherited from EnsEMBL::Web::Object
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alternative_object_from_factory
There may be occassions when a script needs to work with features of more than one type. in this case we create a new EnsEMBL::Web::Proxy::Factory object for the alternative data type and retrieves the data (based on the standard URL parameters for the new factory) attach it to the universal datahash __data
Inherited from EnsEMBL::Web::Object
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ambig_code
TSV.
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command
Command object attached to proxy object
Inherited from EnsEMBL::Web::Object
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dataobj
Deprecated. Accessor. Gets the underlying Ensembl object wrapped by the web object
Inherited from EnsEMBL::Web::Object
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extent
TSV.
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full_URL
Returns a full (http://...) link to another script. Wrapper around _URL function
Inherited from EnsEMBL::Web::Object
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generate_query_hash
TSV.
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getFakeMungedVariationsOnSlice
TSV.
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get_Slice
should this be called on gene?
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get_alignment
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get_families
Returns a hash of family information and associated (API) Gene objects
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get_munged_slice
TSV/TSE.
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get_samples
TSV.
| Arg (optional) | Arg (optional) : type string -"default": returns samples checked by default -"display": returns samples for dropdown list with default ones first |
| Description | returns selected samples (by default) Returns type list |
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get_source
TSV.
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get_transcript_Slice
TSV.
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get_transcript_slices
TSV.
| Args | Web user config, arrayref of slices (see example) |
| Description | Gets slices for transcript sample view Returns hash ref of slices |
| Example | my $slice = $object->get_Slice( $wuc, ['context', 'normal', '500%'] ); |
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highlights
Accessor. The highlights array is passed between web-requests to highlight selected items (e.g. Gene around which contigview had been rendered. If any data is passed this is stored in the highlights array and an arrayref of (unique) elements is returned.
Inherited from EnsEMBL::Web::Object
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highlights_string
Returns the highlights area as a | separated list for passing in URLs.
Inherited from EnsEMBL::Web::Object
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history
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interface
Data interface attached to object
Inherited from EnsEMBL::Web::Object
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location_URL
Parameters: $feature, $script, $contextReturns a link to a contigview style display, based on feature, with context
Inherited from EnsEMBL::Web::Object
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mapview_link
Parameter $feature on a "real chromosome" then this is encapsulated in a link to mapview.Returns name of seq_region $feature is on. If the passed features is
Inherited from EnsEMBL::Web::Object
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munge_gaps
TSV and SE
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munge_gaps_split
TSV.
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munge_read_coverage
TSV.
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prefix
Accessor.
Inherited from EnsEMBL::Web::Object
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read_coverage
TSV.
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seq_region_type_and_name
Returns the type/name of seq_region in human readable form - if the coord system type is part of the name this is dropped.
Inherited from EnsEMBL::Web::Object
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seq_region_type_human_readable
Returns the type of seq_region in "human readable form" (in this case just first letter captialised)
Inherited from EnsEMBL::Web::Object
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valids
TSV.
| Description | Valid user selections Returns hashref |
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var_class
TSV.
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