EnsEMBL::Web::ImageConfig::thjviewbottom

Location: /modules/EnsEMBL/Web/ImageConfig/thjviewbottom.pm
Source code · Permalink

Inherits from:

No subclasses

Overview

Accessor

Add_dna_align_feature...

Add_gene...

Add_protein_align_feature...

Method

Unknown

  • TRIM
  • TRIM (EnsEMBL::Web::ImageConfig)
  • _add_flat_file_track (EnsEMBL::Web::ImageConfig)
  • _check_menus (EnsEMBL::Web::ImageConfig)
  • _merge (EnsEMBL::Web::ImageConfig)
  • _set (EnsEMBL::Web::ImageConfig)
  • _set_core (EnsEMBL::Web::ImageConfig)
  • _update_missing (EnsEMBL::Web::ImageConfig)
  • add_alignments (EnsEMBL::Web::ImageConfig)
  • add_artefacts (EnsEMBL::Web::ImageConfig)
  • add_das_track (EnsEMBL::Web::ImageConfig)
  • add_decorations (EnsEMBL::Web::ImageConfig)
  • add_gene (EnsEMBL::Web::ImageConfig)
  • add_marker_feature (EnsEMBL::Web::ImageConfig)
  • add_misc_feature (EnsEMBL::Web::ImageConfig)
  • add_oligo_probe (EnsEMBL::Web::ImageConfig)
  • add_option (EnsEMBL::Web::ImageConfig)
  • add_options (EnsEMBL::Web::ImageConfig)
  • add_prediction_transcript (EnsEMBL::Web::ImageConfig)
  • add_protein_align_feature (EnsEMBL::Web::ImageConfig)
  • add_protein_feature (EnsEMBL::Web::ImageConfig)
  • add_qtl_feature (EnsEMBL::Web::ImageConfig)
  • add_regulation_feature (EnsEMBL::Web::ImageConfig)
  • add_repeat_feature (EnsEMBL::Web::ImageConfig)
  • add_settings (EnsEMBL::Web::ImageConfig)
  • add_simple_feature (EnsEMBL::Web::ImageConfig)
  • add_synteny (EnsEMBL::Web::ImageConfig)
  • add_track (EnsEMBL::Web::ImageConfig)
  • add_tracks (EnsEMBL::Web::ImageConfig)
  • add_variation_feature (EnsEMBL::Web::ImageConfig)
  • artefacts (EnsEMBL::Web::ImageConfig)
  • cache (EnsEMBL::Web::ImageConfig)
  • container_width (EnsEMBL::Web::ImageConfig)
  • core_objects (EnsEMBL::Web::ImageConfig)
  • create_option (EnsEMBL::Web::ImageConfig)
  • create_submenu (EnsEMBL::Web::ImageConfig)
  • create_track (EnsEMBL::Web::ImageConfig)
  • get_node (EnsEMBL::Web::ImageConfig)
  • get_parameter (EnsEMBL::Web::ImageConfig)
  • get_parameters (EnsEMBL::Web::ImageConfig)
  • get_track_key (EnsEMBL::Web::ImageConfig)
  • get_user_settings (EnsEMBL::Web::ImageConfig)
  • glyphset_configs (EnsEMBL::Web::ImageConfig)
  • image_width (EnsEMBL::Web::ImageConfig)
  • init
  • load_configured_das (EnsEMBL::Web::ImageConfig)
  • load_tracks (EnsEMBL::Web::ImageConfig)
  • load_user_vert_tracks (EnsEMBL::Web::ImageConfig)
  • modify_configs (EnsEMBL::Web::ImageConfig)
  • mult
  • remove_artefacts (EnsEMBL::Web::ImageConfig)
  • reset (EnsEMBL::Web::ImageConfig)
  • reset_subsection (EnsEMBL::Web::ImageConfig)
  • save (EnsEMBL::Web::ImageConfig)
  • scalex (EnsEMBL::Web::ImageConfig)
  • set_parameter (EnsEMBL::Web::ImageConfig)
  • set_parameters (EnsEMBL::Web::ImageConfig)
  • set_species (EnsEMBL::Web::ImageConfig)
  • set_width (EnsEMBL::Web::ImageConfig)
  • slice_number (EnsEMBL::Web::ImageConfig)
  • subsections (EnsEMBL::Web::ImageConfig)
  • title (EnsEMBL::Web::ImageConfig)
  • transform (EnsEMBL::Web::ImageConfig)
  • turn_off (EnsEMBL::Web::ImageConfig)
  • turn_on (EnsEMBL::Web::ImageConfig)
  • update_config_from_parameter (EnsEMBL::Web::ImageConfig)
  • update_from_input (EnsEMBL::Web::ImageConfig)
Documentation coverage: 18 %

Methods

    add_assemblies
    Add_dna_align_feature.... loop through all core databases - and attach the dna align features from the dna_align_feature tables... these are added to one of four menus: cdna/mrna, est, rna, other depending whats in the web_data column in the database
    Inherited from EnsEMBL::Web::ImageConfig
    View source

    add_ditag_feature
    Add_gene.... loop through all core databases - and attach the gene features from the gene tables... there are a number of menus sub-types these are added to: * gene # genes * transcript # ordinary transcripts * alignslice_transcript # transcripts in align slice co-ordinates * tse_transcript # transcripts in collapsed intro co-ords * tsv_transcript # transcripts in collapsed intro co-ords * gsv_transcript # transcripts in collapsed gene co-ords depending on which menus are configured
    Inherited from EnsEMBL::Web::ImageConfig
    View source

    add_dna_align_feature
    Add_protein_align_feature.... loop through all core databases - and attach the protein align features from the protein_align_feature tables...
    Inherited from EnsEMBL::Web::ImageConfig
    View source

    altered
    Accessor. Set to one if the configuration has been updated...
    Inherited from EnsEMBL::Web::ImageConfig
    View source

    bgcolor
    Accessor.
    Inherited from EnsEMBL::Web::ImageConfig
    View source

    bgcolour
    Accessor.
    Inherited from EnsEMBL::Web::ImageConfig
    View source

    colourmap
    Accessor.
    Inherited from EnsEMBL::Web::ImageConfig
    View source

    create_menus
    load_tracks - loads in various database derived tracks; loop through core like dbs, compara like dbs, funcgen like dbs; variation like dbs
    Inherited from EnsEMBL::Web::ImageConfig
    View source

    image_height
    Accessor.
    Inherited from EnsEMBL::Web::ImageConfig
    View source

    load_user_tracks
    Get the tracks that are temporarily stored - as "files" not in the DB....
    Inherited from EnsEMBL::Web::ImageConfig
    View source

    new





    Inherited from EnsEMBL::Web::ImageConfig
    View source

    species_defs
    Accessor.
    Inherited from EnsEMBL::Web::ImageConfig
    View source

    storable
    Accessor. Set whether this ViewConfig is changeable by the User, and hence needs to access the database to set storable do $view_config->storable = 1; in SC code...
    Inherited from EnsEMBL::Web::ImageConfig
    View source

    texthelper
    Accessor.
    Inherited from EnsEMBL::Web::ImageConfig
    View source

    tree
    create_menus - takes an "associate array" i.e. ordered key value pairs to configure the menus to be seen on the display.. key and value pairs are the code and the text of the menu...
    Inherited from EnsEMBL::Web::ImageConfig
    View source


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