EnsEMBL::Web::Object::Translation

Location: /modules/EnsEMBL/Web/Object/Translation.pm
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Inherits from:

No subclasses

Overview

Accessor

Deprecated

Method

Unknown

  • _availability (EnsEMBL::Web::Object)
  • _help_URL (EnsEMBL::Web::Object)
  • analysis
  • availability (EnsEMBL::Web::Object)
  • bp_to_nearest_unit (EnsEMBL::Web::Object)
  • can_export (EnsEMBL::Web::Object)
  • coord_system
  • core_params (EnsEMBL::Web::Object)
  • count_alignments (EnsEMBL::Web::Object)
  • counts (EnsEMBL::Web::Object)
  • db_type
  • display_xref
  • feature_length
  • feature_type
  • fetch_homologues_of_gene_in_species (EnsEMBL::Web::Object)
  • gene
  • gene_description
  • gene_description (EnsEMBL::Web::Object)
  • gene_type
  • generate_query_url (EnsEMBL::Web::Object)
  • getCoordinateSystem (EnsEMBL::Web::Object)
  • get_DASCollection (EnsEMBL::Web::Object)
  • get_Slice
  • get_adaptor (EnsEMBL::Web::Object)
  • get_all_ProteinFeatures
  • get_alternative_locations
  • get_archive_object
  • get_author_email
  • get_author_name
  • get_contig_location
  • get_das_factories
  • get_das_features_by_name
  • get_das_features_by_slice
  • get_database_matches
  • get_db
  • get_family_links
  • get_family_object
  • get_interpro_links
  • get_interpro_object
  • get_pep_seq
  • get_pepstats
  • get_prediction_method
  • get_protein_domains
  • get_similarity_hash
  • get_transcript_object
  • logic_name
  • modified
  • new_image (EnsEMBL::Web::Object)
  • new_karyotype_image (EnsEMBL::Web::Object)
  • new_vimage (EnsEMBL::Web::Object)
  • pep_snps
  • pep_splice_site
  • protein
  • referer (EnsEMBL::Web::Object)
  • seq_region_end
  • seq_region_name
  • seq_region_start
  • seq_region_strand
  • seq_region_type
  • source
  • stable_id
  • transcript
  • translation
  • translation_object
  • type_name
  • vega_projection
  • version
Documentation coverage: 21 %

Methods

    EnsemblObject
    Deprecated. Sets/gets the underlying Ensembl object wrapped by the web object
    Inherited from EnsEMBL::Web::Object
    View source

    Obj
    Accessor. Gets the underlying Ensembl object wrapped by the web object
    Inherited from EnsEMBL::Web::Object
    View source

    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
    View source

    _URL
    Returns either a full link or absolute link to a script
    Inherited from EnsEMBL::Web::Object
    View source

    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
    View source

    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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    full_URL
    Returns a full (http://...) link to another script. Wrapper around _URL function
    Inherited from EnsEMBL::Web::Object
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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
    View source

    highlights_string
    Returns the highlights area as a | separated list for passing in URLs.
    Inherited from EnsEMBL::Web::Object
    View source

    history





    View source

    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
    View source

    location_string





    View source

    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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    prefix
    Accessor.
    Inherited from EnsEMBL::Web::Object
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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
    View source

    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
    View source


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