e! doc

Methods

ALIGNMENT_FORMATS
ALIGN_CENTER
ALIGN_LEFT
ALIGN_RIGHT
ALTERNATING_BACKGROUND
AUTOLOAD (Bio::EnsEMBL::Glyph)
AUTOLOAD (Sanger::Graphics::Glyph)
AUTOLOAD (EnsEMBL::Web::Proxy)
AUTOLOAD (EnsEMBL::Web::SpeciesDefs)
AUTOLOAD (EnsEMBL::Web::BlastView::Meta)
AUTOLOAD (EnsEMBL::Web::Input::Options)
AUTOLOAD (EnsEMBL::Web::Input::Parameters)
BUILD (EnsEMBL::Web::Filter)
BUILD (EnsEMBL::Web::Mailer)
BUILD (EnsEMBL::Web::Session)
BUILD (EnsEMBL::Web::Interface)
BUILD (EnsEMBL::Web::Command::Help::DoSearch)
BUILD (EnsEMBL::Web::Command::Help::Feedback)
BUILD (EnsEMBL::Web::Command::Help::MovieEmail)
BUILD (EnsEMBL::Web::Command::Help::SendEmail)
BUILD (EnsEMBL::Web::Command::UserData::CheckShare)
BUILD (EnsEMBL::Web::Command::UserData::DeleteRemote)
BUILD (EnsEMBL::Web::Command::UserData::DeleteUpload)
BUILD (EnsEMBL::Web::Command::UserData::UploadFile)
BUILD (EnsEMBL::Web::Command::UserData::ValidateDAS)
BUILD (EnsEMBL::Web::Command::UserData::AttachDAS)
BUILD (EnsEMBL::Web::Data::Field)
BUILD (EnsEMBL::Web::Filter::Activation)
BUILD (EnsEMBL::Web::Filter::Admin)
BUILD (EnsEMBL::Web::Filter::DAS)
BUILD (EnsEMBL::Web::Filter::Data)
BUILD (EnsEMBL::Web::Filter::DuplicateUser)
BUILD (EnsEMBL::Web::Filter::EmailAddress)
BUILD (EnsEMBL::Web::Filter::Invitation)
BUILD (EnsEMBL::Web::Filter::LoggedIn)
BUILD (EnsEMBL::Web::Filter::Member)
BUILD (EnsEMBL::Web::Filter::PasswordSecure)
BUILD (EnsEMBL::Web::Filter::PasswordValid)
BUILD (EnsEMBL::Web::Filter::Sanitize)
BUILD (EnsEMBL::Web::Filter::Shareable)
BUILD (EnsEMBL::Web::Filter::Sources)
BUILD (EnsEMBL::Web::Filter::Spam)
BUILD (EnsEMBL::Web::Filter::UserData)
BUILD (EnsEMBL::Web::Filter::Owner)
BUILD (EnsEMBL::Web::Interface::Element)
Bezier
Circle
Composite
DBConnection
DESTROY (EnsEMBL::Web::Proxy)
DESTROY (EnsEMBL::Web::SpeciesDefs)
DESTROY (EnsEMBL::Web::BlastView::Meta)
DESTROY (EnsEMBL::Web::Document::WebPage)
DESTROY (EnsEMBL::Web::Document::Renderer::File)
DESTROY (EnsEMBL::Web::Document::Renderer::GzFile)
DESTROY (EnsEMBL::Web::Input::Options)
DESTROY (EnsEMBL::Web::Input::Parameters)
DESTROY (EnsEMBL::Web::Tools::Document)
DESTROY (EnsEMBL::Web::Tools::DocumentView)
DESTROY (EnsEMBL::Web::Tools::PluginLocator)
DESTROY (EnsEMBL::Web::Tools::URL)
DESTROY (EnsEMBL::Web::Tools::Document::Method)
DESTROY (EnsEMBL::Web::Tools::Document::Module)
DNA
DataObjects
Diagnostic
EC_URL (EnsEMBL::Web::Component::Gene)
EC_URL (EnsEMBL::Web::Component::Transcript)
Ellipse
EnsemblObject
EntryPoints (EnsEMBL::Web::Object::DAS)
EntryPoints (EnsEMBL::Web::Object::DAS::reference)
ExtURL
FAMILY_EXTERNAL
FORMATS
FORMAT_BOLD
FORMAT_BOLDITALIC
FORMAT_ITALIC
FORMAT_NDP
FORMAT_THOUSANDIFY
FeatureIDs
FeatureTypes
Features (EnsEMBL::Web::Object::DAS::cagetags)
Features (EnsEMBL::Web::Object::DAS::ditags)
Features (EnsEMBL::Web::Object::DAS::ditags_rr)
Features (EnsEMBL::Web::Object::DAS::dna_align)
Features (EnsEMBL::Web::Object::DAS::gene)
Features (EnsEMBL::Web::Object::DAS::karyotype)
Features (EnsEMBL::Web::Object::DAS::marker)
Features (EnsEMBL::Web::Object::DAS::prediction_transcript)
Features (EnsEMBL::Web::Object::DAS::protein_align)
Features (EnsEMBL::Web::Object::DAS::reference)
Features (EnsEMBL::Web::Object::DAS::repeat)
Features (EnsEMBL::Web::Object::DAS::simple)
Features (EnsEMBL::Web::Object::DAS::transcript)
Features (EnsEMBL::Web::Object::DAS::translation)
GENERAL_MARKUP_OPTIONS
GENE_MARKUP_OPTIONS
Gene
GroupIDs
H
HASH_URL
HOMOLOGY_TYPES (EnsEMBL::Web::Constants)
HOMOLOGY_TYPES (EnsEMBL::Web::Component::Alignment)
ID_URL
Intron
Line
Location
Locations (EnsEMBL::Web::Object::DAS)
Locations (EnsEMBL::Web::Object::MultipleLocation)
MESSAGE_PRIORITY
NEWICK_OPTIONS
NHX_OPTIONS
OTHER_MARKUP_OPTIONS
Obj (EnsEMBL::Web::Object)
Obj (EnsEMBL::Web::Object::MultipleLocation)
Poly
PrimaryLocation
RENDERER
Rect
SIMPLEALIGN_DEFAULT (EnsEMBL::Web::Constants)
SIMPLEALIGN_DEFAULT (EnsEMBL::Web::Component::Alignment)
SIMPLEALIGN_FORMATS
Server
Space
Sprite
Stylesheet (EnsEMBL::Web::Object::DAS)
Stylesheet (EnsEMBL::Web::Object::DAS::cagetags)
Stylesheet (EnsEMBL::Web::Object::DAS::ditags)
Stylesheet (EnsEMBL::Web::Object::DAS::ditags_rr)
Stylesheet (EnsEMBL::Web::Object::DAS::dna_align)
Stylesheet (EnsEMBL::Web::Object::DAS::gene)
Stylesheet (EnsEMBL::Web::Object::DAS::karyotype)
Stylesheet (EnsEMBL::Web::Object::DAS::prediction_transcript)
Stylesheet (EnsEMBL::Web::Object::DAS::protein_align)
Stylesheet (EnsEMBL::Web::Object::DAS::reference)
Stylesheet (EnsEMBL::Web::Object::DAS::transcript)
Stylesheet (EnsEMBL::Web::Object::DAS::translation)
TREE_FORMATS
TRIM (EnsEMBL::Web::ImageConfig)
TRIM (EnsEMBL::Web::ImageConfig::thjviewbottom)
Text
Transcript
Types (EnsEMBL::Web::Object::DAS)
Types (EnsEMBL::Web::Object::DAS::cagetags)
Types (EnsEMBL::Web::Object::DAS::ditags)
Types (EnsEMBL::Web::Object::DAS::ditags_rr)
Types (EnsEMBL::Web::Object::DAS::dna_align)
Types (EnsEMBL::Web::Object::DAS::gene)
Types (EnsEMBL::Web::Object::DAS::karyotype)
Types (EnsEMBL::Web::Object::DAS::marker)
Types (EnsEMBL::Web::Object::DAS::prediction_transcript)
Types (EnsEMBL::Web::Object::DAS::protein_align)
Types (EnsEMBL::Web::Object::DAS::reference)
Types (EnsEMBL::Web::Object::DAS::repeat)
Types (EnsEMBL::Web::Object::DAS::simple)
Types (EnsEMBL::Web::Object::DAS::transcript)
Types (EnsEMBL::Web::Object::DAS::translation)
URL (EnsEMBL::Web::Object)
URL (EnsEMBL::Web::Object::Link)
URL (ExaLead::Hit)
URL (ExaLead::Link)
VARIATION_OPTIONS
Variation
Vpx2bp
W
X
XY
Y
_Stylesheet
_URL
__children
__coord_systems
__data (EnsEMBL::Web::Proxiable)
__data (EnsEMBL::Web::Proxy)
__error
__gene_databases
__golden_path
__level
__meta
__objecttype
__set_default_otherspecies
__set_species
__species
__species_hash
__status
__supertype
__timeout
_access_ok
_adaptor
_add_bookmark
_add_command
_add_element
_add_flat_file_track
_add_legend_entry
_add_module
_ajax_content
_ajax_zmenu
_ajax_zmenu_alignment
_ajax_zmenu_av
_ajax_zmenu_change_reference
_ajax_zmenu_compara_tree_node
_ajax_zmenu_ga
_ajax_zmenu_marker
_ajax_zmenu_misc_feature
_ajax_zmenu_protein_feature
_ajax_zmenu_region
_ajax_zmenu_regulation (EnsEMBL::Web::Configuration::Location)
_ajax_zmenu_regulation (EnsEMBL::Web::Configuration::Gene)
_ajax_zmenu_synteny
_ajax_zmenu_transcript_variation
_ajax_zmenu_view
_archive
_archive_link (EnsEMBL::Web::Configuration)
_archive_link (EnsEMBL::Web::Component::ArchiveStableId)
_archive_link (EnsEMBL::Web::Component::Gene::HistoryReport)
_attach_das
_availability
_bar
_basic_HTML
_best_guess
_blast_adaptor
_bool
_build_conf
_c
_caption_with_helplink
_centre_point
_check_data_row
_check_if_snp_unique_location
_check_menus
_class (EnsEMBL::Web::Form::Element::Age)
_class (EnsEMBL::Web::Form::Element::Email)
_class (EnsEMBL::Web::Form::Element::Float)
_class (EnsEMBL::Web::Form::Element::Html)
_class (EnsEMBL::Web::Form::Element::Int)
_class (EnsEMBL::Web::Form::Element::NonNegFloat)
_class (EnsEMBL::Web::Form::Element::NonNegInt)
_class (EnsEMBL::Web::Form::Element::Password)
_class (EnsEMBL::Web::Form::Element::PosFloat)
_class (EnsEMBL::Web::Form::Element::PosInt)
_class (EnsEMBL::Web::Form::Element::String)
_class (EnsEMBL::Web::Form::Element::Text)
_class (EnsEMBL::Web::Form::Element::URL)
_clear_defaults
_collapsed_nodes
_colour (Bio::EnsEMBL::GlyphSet_generic)
_colour (Sanger::Graphics::Renderer::eps)
_colour (Sanger::Graphics::Renderer::postscript)
_colour_background (Bio::EnsEMBL::GlyphSet)
_colour_background (Bio::EnsEMBL::GlyphSet::draggable)
_colour_points
_command_string
_common_HTML
_compara_tree_jalview_html
_configurator
_configure_blast
_configure_display
_content (EnsEMBL::Web::Component::Gene::GeneSNPImage)
_content (EnsEMBL::Web::Component::Transcript::SupportingEvidence)
_content (EnsEMBL::Web::Document::Panel)
_content (EnsEMBL::Web::Document::HTML::GlobalContext)
_content (EnsEMBL::Web::Document::HTML::LocalContext)
_content_panel
_context_panel
_convert_date
_coord_system_adaptor
_createObjects
_create_DnaAlignFeature
_create_Gene
_create_OligoFeature
_create_ProteinAlignFeature
_create_RegulatoryFactor
_create_Xref
_create_XrefArray
_create_datasource
_create_from_slice (EnsEMBL::Web::Factory::DAS)
_create_from_slice (EnsEMBL::Web::Factory::Location)
_create_idhistory_tree (EnsEMBL::Web::Component::ArchiveStableId)
_create_idhistory_tree (EnsEMBL::Web::Component::Gene::HistoryMap)
_create_label
_create_object_from_core
_das_link (Bio::EnsEMBL::GlyphSet::_alignment)
_das_link (Bio::EnsEMBL::GlyphSet::_blast)
_das_link (Bio::EnsEMBL::GlyphSet::_flat_file)
_das_link (Bio::EnsEMBL::GlyphSet::_user_data)
_das_query_object (EnsEMBL::Web::Component::Gene::TextDAS)
_das_query_object (EnsEMBL::Web::Component::Transcript::TextDAS)
_das_type (Bio::EnsEMBL::GlyphSet::_prediction_transcript)
_das_type (Bio::EnsEMBL::GlyphSet::_qtl)
_das_type (Bio::EnsEMBL::GlyphSet::_simple)
_debug
_decode_and_validate
_delete_datasource
_delete_datasource_features
_display_alignment_table
_dna_align_feature_adaptor
_draw_alignment
_draw_features
_draw_karyotype
_draw_key
_dump
_dump_tree_as_text
_embed_jalview
_end (EnsEMBL::Web::Document::Panel)
_end (EnsEMBL::Web::Document::HTML::Content)
_end (EnsEMBL::Web::Document::Panel::Ajax)
_end (EnsEMBL::Web::Document::Panel::AjaxMenu)
_end (EnsEMBL::Web::Document::Panel::Configurator)
_end (EnsEMBL::Web::Document::Panel::Image)
_end (EnsEMBL::Web::Document::Panel::Information)
_end (EnsEMBL::Web::Document::Panel::InformationImage)
_end (EnsEMBL::Web::Document::Panel::SpreadSheet)
_end (EnsEMBL::Web::Document::Panel::Summary)
_error (EnsEMBL::Web::Component)
_error (EnsEMBL::Web::Document::Panel)
_error (EnsEMBL::Web::Document::Panel::Ajax)
_error (EnsEMBL::Web::Document::Panel::AjaxMenu)
_error (EnsEMBL::Web::Document::Panel::Configurator)
_error (EnsEMBL::Web::Document::Panel::Information)
_error (EnsEMBL::Web::Document::Panel::Navigation)
_error (EnsEMBL::Web::Document::Panel::SpreadSheet)
_error (EnsEMBL::Web::Document::Panel::Summary)
_exon_adaptor
_expand_database_templates
_export
_export_configurator
_export_image
_extent
_extra (EnsEMBL::Web::Component::Location::Compara_AlignSliceTop)
_extra (EnsEMBL::Web::Component::Location::ViewTop)
_extra (EnsEMBL::Web::Form::Element)
_extra (EnsEMBL::Web::Form::Element::File)
_feature (EnsEMBL::Web::Object::DAS::base_align)
_feature (EnsEMBL::Web::Object::DAS::marker)
_feature (EnsEMBL::Web::Object::DAS::repeat)
_feature (EnsEMBL::Web::Object::DAS::simple)
_fetch
_fetch_results
_filename (EnsEMBL::Web::Object::Gene)
_filename (EnsEMBL::Web::Object::Location)
_filename (EnsEMBL::Web::Object::Transcript)
_filename (EnsEMBL::Web::Object::Variation)
_flip_URL (EnsEMBL::Web::Component::ArchiveStableId)
_flip_URL (EnsEMBL::Web::Component::SNP)
_flip_URL (EnsEMBL::Web::Component::Transcript)
_flip_URL (EnsEMBL::Web::Component::Translation)
_flip_URL (EnsEMBL::Web::Component::Variation::FlankingSequence)
_flip_URL_gene
_flush_tree
_format_error
_format_number (EnsEMBL::Web::Component::SNP)
_format_number (EnsEMBL::Web::Component::Variation)
_format_number (EnsEMBL::Web::Component::Variation::PopulationGenotypes)
_format_parent (EnsEMBL::Web::Component::SNP)
_format_parent (EnsEMBL::Web::Component::Variation)
_format_parent (EnsEMBL::Web::Component::Variation::IndividualGenotypes)
_formats
_gen_base_form
_gen_element
_gen_radio
_gen_select
_gen_specified_group
_gen_specified_group_vertical
_gen_text
_gen_textarea
_gen_type_with_select
_gene_adaptor
_generate_objects
_generate_objects_Gene
_generate_objects_Location
_generate_objects_Transcript
_generate_objects_Variation
_generate_objects_lw
_generate_unique_key
_generic_create
_get
_getHref (Bio::EnsEMBL::VRenderer::imagemap)
_getHref (Sanger::Graphics::Renderer::imagemap)
_get_blast_database
_get_colour_gradient
_get_compara_database
_get_core_database
_get_database
_get_database_info
_get_databases_common
_get_db_with_dnadb
_get_defaults
_get_details
_get_fasta_database
_get_favourites
_get_formatted_pep_seq (EnsEMBL::Web::Component::ArchiveStableId)
_get_formatted_pep_seq (EnsEMBL::Web::Component::Gene::HistoryLinked)
_get_gene_location_from_transcript
_get_gene_transcript_from_location
_get_go_database
_get_help_database
_get_input_parameters (EnsEMBL::Web::Input::CGI)
_get_input_parameters (EnsEMBL::Web::Input::CommandLine)
_get_loads
_get_location_from_gene
_get_pops_from_param
_get_seq
_get_server (Bio::Tools::Run::Search::blat_gfclient)
_get_server (Bio::Tools::Run::Search::ssaha2_client)
_get_unique_source_name
_get_userdata_database
_get_valid_action (EnsEMBL::Web::Configuration)
_get_valid_action (EnsEMBL::Web::Configuration::DAS)
_get_valid_action (EnsEMBL::Web::Configuration::Search)
_get_valid_action (EnsEMBL::Web::Configuration::Account)
_give_snp_unique_identifier
_glob
_global_context
_group_info (EnsEMBL::Web::Object::DAS::enhanced_transcript)
_group_info (EnsEMBL::Web::Object::DAS::transcript)
_guess_views
_help (EnsEMBL::Web::Factory)
_help (EnsEMBL::Web::Factory::Gene)
_help (EnsEMBL::Web::Factory::Location)
_help (EnsEMBL::Web::Factory::Transcript)
_help (EnsEMBL::Web::Factory::Variation)
_help_URL
_hint
_html_path_from_package
_idhistoryview_link (EnsEMBL::Web::Component::ArchiveStableId)
_idhistoryview_link (EnsEMBL::Web::Component::History)
_idhistoryview_link (EnsEMBL::Web::Component::Gene::HistoryLinked)
_info
_info_line
_info_log
_info_panel
_init (Bio::EnsEMBL::DrawableContainer)
_init (Bio::EnsEMBL::GlyphSet_transcript)
_init (Bio::EnsEMBL::GlyphSet_simple)
_init (Bio::EnsEMBL::GlyphSet::HSP_coverage)
_init (Bio::EnsEMBL::GlyphSet::codons)
_init (Bio::EnsEMBL::GlyphSet::HSP_plot)
_init (Bio::EnsEMBL::GlyphSet::comparafake)
_init (Bio::EnsEMBL::GlyphSet::contig)
_init (Bio::EnsEMBL::GlyphSet::HSP_scalebar)
_init (Bio::EnsEMBL::GlyphSet::P_domain)
_init (Bio::EnsEMBL::GlyphSet::geneexon_bgtrack)
_init (Bio::EnsEMBL::GlyphSet::P_feature)
_init (Bio::EnsEMBL::GlyphSet::P_protdas)
_init (Bio::EnsEMBL::GlyphSet::genetree)
_init (Bio::EnsEMBL::GlyphSet::P_protein)
_init (Bio::EnsEMBL::GlyphSet::P_scalebar)
_init (Sanger::Graphics::GlyphSet::gradient_key)
_init (Bio::EnsEMBL::GlyphSet::P_separator)
_init (Bio::EnsEMBL::GlyphSet::gsv_domain)
_init (Bio::EnsEMBL::GlyphSet::P_variation)
_init (Bio::EnsEMBL::GlyphSet::gsv_transcript)
_init (Bio::EnsEMBL::GlyphSet::Psnp_legend)
_init (Bio::EnsEMBL::GlyphSet::gsv_variations)
_init (Bio::EnsEMBL::GlyphSet::SE_generic_match)
_init (Bio::EnsEMBL::GlyphSet::SE_generic_match_label)
_init (Bio::EnsEMBL::GlyphSet::ideogram)
_init (Bio::EnsEMBL::GlyphSet::TSE_background_exon)
_init (Bio::EnsEMBL::GlyphSet::info)
_init (Bio::EnsEMBL::GlyphSet::TSE_generic_match)
_init (Bio::EnsEMBL::GlyphSet::ld)
_init (Bio::EnsEMBL::GlyphSet::TSE_generic_match_label)
_init (Bio::EnsEMBL::GlyphSet::ld2)
_init (Bio::EnsEMBL::GlyphSet::TSE_legend)
_init (Bio::EnsEMBL::GlyphSet::missing)
_init (Bio::EnsEMBL::GlyphSet::TSE_transcript)
_init (Bio::EnsEMBL::GlyphSet::mod)
_init (Bio::EnsEMBL::GlyphSet::Vannotation_status)
_init (Bio::EnsEMBL::GlyphSet::navigation)
_init (Bio::EnsEMBL::GlyphSet::Vbinned)
_init (Bio::EnsEMBL::GlyphSet::non_can_intron)
_init (Bio::EnsEMBL::GlyphSet::Vbinned_bar)
_init (Bio::EnsEMBL::GlyphSet::preliminary)
_init (Bio::EnsEMBL::GlyphSet::Vbinned_outline)
_init (Bio::EnsEMBL::GlyphSet::read_coverage)
_init (Bio::EnsEMBL::GlyphSet::Vdensity)
_init (Bio::EnsEMBL::GlyphSet::ruler)
_init (Bio::EnsEMBL::GlyphSet::Vgeneric)
_init (Bio::EnsEMBL::GlyphSet::restrict)
_init (Bio::EnsEMBL::GlyphSet::Videogram)
_init (Bio::EnsEMBL::GlyphSet::scalebar)
_init (Bio::EnsEMBL::GlyphSet::Videogram_legend)
_init (Bio::EnsEMBL::GlyphSet::Vrefseqs)
_init (Bio::EnsEMBL::GlyphSet::snp_fake)
_init (Bio::EnsEMBL::GlyphSet::Vsupercontigs)
_init (Bio::EnsEMBL::GlyphSet::snp_fake_haplotype)
_init (Bio::EnsEMBL::GlyphSet::Vsynteny)
_init (Bio::EnsEMBL::GlyphSet::snp_join)
_init (Bio::EnsEMBL::GlyphSet::spacer)
_init (Bio::EnsEMBL::GlyphSet::text)
_init (Bio::EnsEMBL::GlyphSet::tsv_missing)
_init (Bio::EnsEMBL::GlyphSet::tsv_transcript)
_init (Bio::EnsEMBL::GlyphSet::_gene)
_init (Bio::EnsEMBL::GlyphSet::tsv_variations)
_init (Bio::EnsEMBL::GlyphSet::_marker)
_init (Bio::EnsEMBL::GlyphSet::variation_legend)
_init (Bio::EnsEMBL::GlyphSet::_text)
_init (Bio::EnsEMBL::GlyphSet::alignscalebar)
_init (Bio::EnsEMBL::GlyphSet::chr_band)
_init (Bio::EnsEMBL::GlyphSet::coverage)
_init (Bio::EnsEMBL::GlyphSet::draggable)
_init (Bio::EnsEMBL::GlyphSet::fg_regulatory_features_legend)
_init (Bio::EnsEMBL::GlyphSet::gcplot)
_init (Bio::EnsEMBL::GlyphSet::gene_legend)
_init (Bio::EnsEMBL::GlyphSet::transcriptexon_bgtrack)
_init (Bio::EnsEMBL::GlyphSet::tsv_haplotype_legend)
_init (Sanger::Graphics::DrawableContainer)
_init (Sanger::Graphics::GlyphSet)
_init (Sanger::Graphics::GlyphSet::generic_das_feature)
_init (Sanger::Graphics::GlyphSet::ruler)
_init (Sanger::Graphics::GlyphSet::scalebar)
_init (EnsEMBL::Web::Component)
_init (EnsEMBL::Web::Component::CommandMessage)
_init (EnsEMBL::Web::Component::Compara_AlignSliceSelector)
_init (EnsEMBL::Web::Component::Compara_Alignments)
_init (EnsEMBL::Web::Component::Configurator)
_init (EnsEMBL::Web::Component::Messages)
_init (EnsEMBL::Web::Component::UnderConstruction)
_init (EnsEMBL::Web::Component::Account::ActivationSent)
_init (EnsEMBL::Web::Component::Account::AdimnDetails)
_init (EnsEMBL::Web::Component::Account::AdminGroups)
_init (EnsEMBL::Web::Component::Account::Configurations)
_init (EnsEMBL::Web::Component::Account::Details)
_init (EnsEMBL::Web::Component::Account::Links)
_init (EnsEMBL::Web::Component::Account::Login)
_init (EnsEMBL::Web::Component::Account::LostPassword)
_init (EnsEMBL::Web::Component::Account::ManageGroup)
_init (EnsEMBL::Web::Component::Account::MemberDetails)
_init (EnsEMBL::Web::Component::Account::MemberGroups)
_init (EnsEMBL::Web::Component::Account::NewsFilters)
_init (EnsEMBL::Web::Component::Account::Password)
_init (EnsEMBL::Web::Component::Account::RegistrationFailed)
_init (EnsEMBL::Web::Component::Account::SelectGroup)
_init (EnsEMBL::Web::Component::Account::UpdateFailed)
_init (EnsEMBL::Web::Component::Account::Interface::AnnotationList)
_init (EnsEMBL::Web::Component::Account::Interface::BookmarkList)
_init (EnsEMBL::Web::Component::Account::Interface::GroupList)
_init (EnsEMBL::Web::Component::Account::Interface::NewsfilterList)
_init (EnsEMBL::Web::Component::Account::Interface::UserDisplay)
_init (EnsEMBL::Web::Component::Blast::Alignment)
_init (EnsEMBL::Web::Component::Blast::Alignment)
_init (EnsEMBL::Web::Component::Blast::Alignment)
_init (EnsEMBL::Web::Component::Blast::Retrieve)
_init (EnsEMBL::Web::Component::Blast::Search)
_init (EnsEMBL::Web::Component::Blast::Ticket)
_init (EnsEMBL::Web::Component::Blast::View)
_init (EnsEMBL::Web::Component::Gene::ComparaAlignmentsOptions)
_init (EnsEMBL::Web::Component::Gene::ComparaOrthologs)
_init (EnsEMBL::Web::Component::Gene::ComparaParalogs)
_init (EnsEMBL::Web::Component::Gene::ComparaTree)
_init (EnsEMBL::Web::Component::Gene::ExternalData)
_init (EnsEMBL::Web::Component::Gene::Family)
_init (EnsEMBL::Web::Component::Gene::FamilyAlignments)
_init (EnsEMBL::Web::Component::Gene::FamilyGenes)
_init (EnsEMBL::Web::Component::Gene::FamilyProteins)
_init (EnsEMBL::Web::Component::Gene::GeneSNPImage)
_init (EnsEMBL::Web::Component::Gene::GeneSNPInfo)
_init (EnsEMBL::Web::Component::Gene::GeneSNPTable)
_init (EnsEMBL::Web::Component::Gene::GeneSeq)
_init (EnsEMBL::Web::Component::Gene::GeneSpliceImage)
_init (EnsEMBL::Web::Component::Gene::GeneSummary)
_init (EnsEMBL::Web::Component::Gene::HistoryLinked)
_init (EnsEMBL::Web::Component::Gene::HistoryMap)
_init (EnsEMBL::Web::Component::Gene::HistoryReport)
_init (EnsEMBL::Web::Component::Gene::HomologAlignment)
_init (EnsEMBL::Web::Component::Gene::RegulationImage)
_init (EnsEMBL::Web::Component::Gene::RegulationTable)
_init (EnsEMBL::Web::Component::Gene::SimilarityMatches)
_init (EnsEMBL::Web::Component::Gene::Summary)
_init (EnsEMBL::Web::Component::Gene::SupportingEvidence)
_init (EnsEMBL::Web::Component::Gene::TextDAS)
_init (EnsEMBL::Web::Component::Gene::TranscriptsImage)
_init (EnsEMBL::Web::Component::Gene::UnderConstruction)
_init (EnsEMBL::Web::Component::Gene::UserAnnotation)
_init (EnsEMBL::Web::Component::Help::ArchiveList)
_init (EnsEMBL::Web::Component::Help::Contact)
_init (EnsEMBL::Web::Component::Help::EmailSent)
_init (EnsEMBL::Web::Component::Help::Faq)
_init (EnsEMBL::Web::Component::Help::FeedbackPreview)
_init (EnsEMBL::Web::Component::Help::Glossary)
_init (EnsEMBL::Web::Component::Help::Movie)
_init (EnsEMBL::Web::Component::Help::MovieFeedback)
_init (EnsEMBL::Web::Component::Help::Permalink)
_init (EnsEMBL::Web::Component::Help::Preview)
_init (EnsEMBL::Web::Component::Help::Results)
_init (EnsEMBL::Web::Component::Help::Search)
_init (EnsEMBL::Web::Component::Help::View)
_init (EnsEMBL::Web::Component::Info::Content)
_init (EnsEMBL::Web::Component::Info::IPtop40)
_init (EnsEMBL::Web::Component::Info::IPtop500)
_init (EnsEMBL::Web::Component::Info::Index)
_init (EnsEMBL::Web::Component::Info::SpeciesBlurb)
_init (EnsEMBL::Web::Component::Info::SpeciesBurp)
_init (EnsEMBL::Web::Component::Info::SpeciesStats)
_init (EnsEMBL::Web::Component::Info::Summary)
_init (EnsEMBL::Web::Component::Info::WhatsNew)
_init (EnsEMBL::Web::Component::Interface::Add)
_init (EnsEMBL::Web::Component::Interface::ConfirmDelete)
_init (EnsEMBL::Web::Component::Interface::Display)
_init (EnsEMBL::Web::Component::Interface::Edit)
_init (EnsEMBL::Web::Component::Interface::List)
_init (EnsEMBL::Web::Component::Interface::OnFailure)
_init (EnsEMBL::Web::Component::Interface::OnSuccess)
_init (EnsEMBL::Web::Component::Interface::Preview)
_init (EnsEMBL::Web::Component::Interface::Problem)
_init (EnsEMBL::Web::Component::Interface::SelectToDelete)
_init (EnsEMBL::Web::Component::Interface::SelectToEdit)
_init (EnsEMBL::Web::Component::Interface::Account::Add)
_init (EnsEMBL::Web::Component::Interface::Account::FailedRegistration)
_init (EnsEMBL::Web::Component::Location::ChangeChromosome)
_init (EnsEMBL::Web::Component::Location::ChangeSpecies)
_init (EnsEMBL::Web::Component::Location::ChromosomeImage)
_init (EnsEMBL::Web::Component::Location::ChromosomeStats)
_init (EnsEMBL::Web::Component::Location::ComparaGenomicAlignment)
_init (EnsEMBL::Web::Component::Location::Compara_AlignSliceBottom)
_init (EnsEMBL::Web::Component::Location::Compara_AlignSliceTop)
_init (EnsEMBL::Web::Component::Location::Genome)
_init (EnsEMBL::Web::Component::Location::Ideogram)
_init (EnsEMBL::Web::Component::Location::LD)
_init (EnsEMBL::Web::Component::Location::LDImage)
_init (EnsEMBL::Web::Component::Location::MarkerDetails)
_init (EnsEMBL::Web::Component::Location::NavigateHomology)
_init (EnsEMBL::Web::Component::Location::Region)
_init (EnsEMBL::Web::Component::Location::RegionNav)
_init (EnsEMBL::Web::Component::Location::SequenceAlignment)
_init (EnsEMBL::Web::Component::Location::Summary)
_init (EnsEMBL::Web::Component::Location::SyntenyImage)
_init (EnsEMBL::Web::Component::Location::SyntenyMatches)
_init (EnsEMBL::Web::Component::Location::UnderConstruction)
_init (EnsEMBL::Web::Component::Location::ViewBottom)
_init (EnsEMBL::Web::Component::Location::ViewBottomNav)
_init (EnsEMBL::Web::Component::Location::ViewTop)
_init (EnsEMBL::Web::Component::Location::ViewZoom)
_init (EnsEMBL::Web::Component::Search::Summary)
_init (EnsEMBL::Web::Component::Server::ColourMap)
_init (EnsEMBL::Web::Component::Server::Information)
_init (EnsEMBL::Web::Component::Server::Summary)
_init (EnsEMBL::Web::Component::Transcript::DomainGenes)
_init (EnsEMBL::Web::Component::Transcript::DomainSpreadsheet)
_init (EnsEMBL::Web::Component::Transcript::ExonsSpreadsheet)
_init (EnsEMBL::Web::Component::Transcript::ExternalData)
_init (EnsEMBL::Web::Component::Transcript::ExternalRecordAlignment)
_init (EnsEMBL::Web::Component::Transcript::Go)
_init (EnsEMBL::Web::Component::Transcript::ID)
_init (EnsEMBL::Web::Component::Transcript::OligoArrays)
_init (EnsEMBL::Web::Component::Transcript::PepStats)
_init (EnsEMBL::Web::Component::Transcript::ProteinSeq)
_init (EnsEMBL::Web::Component::Transcript::ProteinVariations)
_init (EnsEMBL::Web::Component::Transcript::SNPView)
_init (EnsEMBL::Web::Component::Transcript::SimilarityMatches)
_init (EnsEMBL::Web::Component::Transcript::Summary)
_init (EnsEMBL::Web::Component::Transcript::SupportingEvidence)
_init (EnsEMBL::Web::Component::Transcript::SupportingEvidenceAlignment)
_init (EnsEMBL::Web::Component::Transcript::TranscriptImage)
_init (EnsEMBL::Web::Component::Transcript::TranscriptNeighbourhood)
_init (EnsEMBL::Web::Component::Transcript::TranscriptSNPInfo)
_init (EnsEMBL::Web::Component::Transcript::TranscriptSNPTable)
_init (EnsEMBL::Web::Component::Transcript::TranscriptSeq)
_init (EnsEMBL::Web::Component::Transcript::TranscriptSummary)
_init (EnsEMBL::Web::Component::Transcript::TranslationImage)
_init (EnsEMBL::Web::Component::Transcript::UnderConstruction)
_init (EnsEMBL::Web::Component::Transcript::UserAnnotation)
_init (EnsEMBL::Web::Component::UniSearch::Summary)
_init (EnsEMBL::Web::Component::UserData::DasCoords)
_init (EnsEMBL::Web::Component::UserData::DasFeedback)
_init (EnsEMBL::Web::Component::UserData::DasSources)
_init (EnsEMBL::Web::Component::UserData::DasSpecies)
_init (EnsEMBL::Web::Component::UserData::)
_init (EnsEMBL::Web::Component::UserData::ManageData)
_init (EnsEMBL::Web::Component::UserData::MoreInput)
_init (EnsEMBL::Web::Component::UserData::RenameRecord)
_init (EnsEMBL::Web::Component::UserData::RenameTempData)
_init (EnsEMBL::Web::Component::UserData::SelectFile)
_init (EnsEMBL::Web::Component::UserData::SelectServer)
_init (EnsEMBL::Web::Component::UserData::SelectShare)
_init (EnsEMBL::Web::Component::UserData::SelectURL)
_init (EnsEMBL::Web::Component::UserData::ShareURL)
_init (EnsEMBL::Web::Component::UserData::ShowRemote)
_init (EnsEMBL::Web::Component::UserData::TempDasSaved)
_init (EnsEMBL::Web::Component::UserData::UploadFeedback)
_init (EnsEMBL::Web::Component::UserData::UrlFeedback)
_init (EnsEMBL::Web::Component::Variation::Context)
_init (EnsEMBL::Web::Component::Variation::FlankingSequence)
_init (EnsEMBL::Web::Component::Variation::IndividualGenotypes)
_init (EnsEMBL::Web::Component::Variation::Mappings)
_init (EnsEMBL::Web::Component::Variation::PopulationGenotypes)
_init (EnsEMBL::Web::Component::Variation::Summary)
_init (EnsEMBL::Web::Component::Variation::VariationSummary)
_init (EnsEMBL::Web::Component::Variation::ExternalData)
_init (EnsEMBL::Web::Document::Page)
_init_bump
_init_command_string
_init_non_assembled_contig
_initialise_parameter
_initialise_search
_initialize
_initialize_DAS (EnsEMBL::Web::Document::Component)
_initialize_DAS (EnsEMBL::Web::Document::Dynamic)
_initialize_Excel (EnsEMBL::Web::Document::Component)
_initialize_Excel (EnsEMBL::Web::Document::Dynamic)
_initialize_HTML (EnsEMBL::Web::Document::Component)
_initialize_HTML (EnsEMBL::Web::Document::Dynamic)
_initialize_HTML (EnsEMBL::Web::Document::Popup)
_initialize_Text (EnsEMBL::Web::Document::Component)
_initialize_Text (EnsEMBL::Web::Document::Dynamic)
_initialize_TextGz (EnsEMBL::Web::Document::Component)
_initialize_TextGz (EnsEMBL::Web::Document::Dynamic)
_initialize_XML (EnsEMBL::Web::Document::Component)
_initialize_XML (EnsEMBL::Web::Document::Dynamic)
_is_ajax_request
_is_available_artefact
_is_valid (EnsEMBL::Web::Form::Element)
_is_valid (EnsEMBL::Web::Form::Element::Age)
_is_valid (EnsEMBL::Web::Form::Element::Email)
_is_valid (EnsEMBL::Web::Form::Element::Float)
_is_valid (EnsEMBL::Web::Form::Element::Html)
_is_valid (EnsEMBL::Web::Form::Element::Int)
_is_valid (EnsEMBL::Web::Form::Element::NonNegFloat)
_is_valid (EnsEMBL::Web::Form::Element::NonNegInt)
_is_valid (EnsEMBL::Web::Form::Element::Password)
_is_valid (EnsEMBL::Web::Form::Element::PosFloat)
_is_valid (EnsEMBL::Web::Form::Element::PosInt)
_is_valid (EnsEMBL::Web::Form::Element::String)
_is_valid (EnsEMBL::Web::Form::Element::URL)
_jalview_link
_key
_known_feature
_ld_populations (EnsEMBL::Web::Component::SNP)
_ld_populations (EnsEMBL::Web::Component::Variation)
_ld_populations (EnsEMBL::Web::Component::Variation::VariationSummary)
_line
_link
_load_command_alpha
_load_command_linux
_load_command_null
_load_in_webtree
_local_context
_local_genes
_local_tools
_location_from_Band
_location_from_Exon
_location_from_Gene
_location_from_Marker
_location_from_MiscFeature
_location_from_Peptide
_location_from_RegFeature
_location_from_SeqRegion (EnsEMBL::Web::Factory::DAS)
_location_from_SeqRegion (EnsEMBL::Web::Factory::Location)
_location_from_Transcript
_location_from_Variation
_make_gene
_marker_adaptor
_matches
_max_bump_row
_merge
_merge_db_tree
_merge_in_dhtml
_meta_info
_munge_alignment
_munge_colours
_munge_config_tree
_munge_config_tree_multi
_munge_das
_munge_databases
_munge_databases_multi
_munge_meta
_munge_variation
_munge_website
_munge_website_multi
_nav_url
_next_id (EnsEMBL::Web::Form)
_next_id (EnsEMBL::Web::Form::FieldSet)
_node (EnsEMBL::Web::OrderedTree)
_node (EnsEMBL::Web::OrderedTree::Node)
_nodes (EnsEMBL::Web::OrderedTree)
_nodes (EnsEMBL::Web::OrderedTree::Node)
_object_template (EnsEMBL::Web::BlastView::Meta)
_object_template (EnsEMBL::Web::BlastView::MetaBlock)
_object_template (EnsEMBL::Web::BlastView::MetaForm)
_object_template (EnsEMBL::Web::BlastView::MetaFormEntry)
_object_template (EnsEMBL::Web::BlastView::MetaHyperlink)
_object_template (EnsEMBL::Web::BlastView::MetaStage)
_offset
_outline
_output_bookmark
_output_config
_output_link
_output_story
_package_name
_parse (EnsEMBL::Web::SpeciesDefs)
_parse (ExaLead)
_parse_category_tree
_parse_das_server
_parse_hit_category_tree
_parse_package_file
_parse_referer
_pop_url (EnsEMBL::Web::Component::LD)
_pop_url (EnsEMBL::Web::Component::SNP)
_pop_url (EnsEMBL::Web::Component::Variation)
_pop_url (EnsEMBL::Web::Component::Location::LD)
_pop_url (EnsEMBL::Web::Component::Variation::IndividualGenotypes)
_pop_url (EnsEMBL::Web::Component::Variation::PopulationGenotypes)
_populate_base_forms
_pos
_predtranscript_adaptor
_prob
_process
_process_method
_process_query
_promote_general
_push_unshift
_read_in_ini_file
_remove_defaults
_render
_render_ajax_reorder_list
_render_buttons
_render_category (ExaLead::Renderer::HTML)
_render_category (ExaLead::Renderer::Text)
_render_close_body_tag
_render_content
_render_element
_render_group (ExaLead::Renderer::HTML)
_render_group (ExaLead::Renderer::Text)
_render_head_and_body_tag
_render_hit (ExaLead::Renderer::HTML)
_render_hit (ExaLead::Renderer::Text)
_render_hitcats (ExaLead::Renderer::HTML)
_render_hitcats (ExaLead::Renderer::Text)
_render_hits_end
_render_hits_start
_render_species_dropdown
_render_species_list
_render_text (Bio::EnsEMBL::GlyphSet)
_render_text (ExaLead::Renderer::HTML)
_render_with_images
_reorder_nodes
_repeatmask
_reset_config_panel
_retrieve_alignments
_row
_run_blast_no_ticket
_run_blast_ticket
_sample_configs
_sanitize
_save_genomic_features
_save_protein_features
_script_HTML
_se
_search_all
_send_invitation
_seq_region_ (EnsEMBL::Web::Object::Marker)
_seq_region_ (EnsEMBL::Web::Object::SNP)
_seq_region_ (EnsEMBL::Web::Object::Variation)
_seqname (EnsEMBL::Web::Text::Feature::BED)
_seqname (EnsEMBL::Web::Text::Feature::DAS)
_seqname (EnsEMBL::Web::Text::Feature::GBrowse)
_seqname (EnsEMBL::Web::Text::Feature::GFF)
_seqname (EnsEMBL::Web::Text::Feature::PSL)
_seqname (EnsEMBL::Web::Text::Feature::WIG)
_set
_set_core
_set_defaults
_setup_species_descriptions
_short_das_desc
_show_group_details
_slice_adaptor
_sort_extra_pops (EnsEMBL::Web::Component::SNP)
_sort_extra_pops (EnsEMBL::Web::Component::Variation)
_sort_extra_pops (EnsEMBL::Web::Component::Variation::PopulationGenotypes)
_sort_scores
_sort_similarity_links (EnsEMBL::Web::Component)
_sort_similarity_links (EnsEMBL::Web::Component::Translation)
_sort_slices
_sort_start_end (EnsEMBL::Web::Component::SNP)
_sort_start_end (EnsEMBL::Web::Component::Variation)
_sort_start_end (EnsEMBL::Web::Component::Variation::Mappings)
_sorted_keys (EnsEMBL::Web::OrderedTree)
_sorted_keys (EnsEMBL::Web::OrderedTree::Node)
_species_label
_spreadsheet_miscset
_start (EnsEMBL::Web::Document::Panel)
_start (EnsEMBL::Web::Document::HTML::Content)
_start (EnsEMBL::Web::Document::Panel::Ajax)
_start (EnsEMBL::Web::Document::Panel::AjaxMenu)
_start (EnsEMBL::Web::Document::Panel::Configurator)
_start (EnsEMBL::Web::Document::Panel::Image)
_start (EnsEMBL::Web::Document::Panel::Information)
_start (EnsEMBL::Web::Document::Panel::InformationImage)
_start (EnsEMBL::Web::Document::Panel::SpreadSheet)
_start (EnsEMBL::Web::Document::Panel::Summary)
_store_user_track
_strand
_summarise_ancestral_db
_summarise_compara_db
_summarise_core_tables
_summarise_dasregistry
_summarise_funcgen_db
_summarise_generic
_summarise_go_db
_summarise_variation_db
_summarise_website_db
_symbol_bg
_symbol_init
_table_exists
_temp_store
_threshold_update
_transcript_adaptor
_traverse_tree
_tree_info
_type
_update_datasource
_update_missing
_url (Bio::EnsEMBL::GlyphSet)
_url (EnsEMBL::Web::Proxiable)
_user_context
_user_tools
_validate (EnsEMBL::Web::Component::Gene::TextDAS)
_validate (EnsEMBL::Web::Form::Element)
_validate (EnsEMBL::Web::Form::Element::DropDown)
_validate (EnsEMBL::Web::Form::Element::DropDownAndString)
_validate (EnsEMBL::Web::Form::Element::DropDownAndSubmit)
_variation_adaptor
_variation_feature_adaptor
_vhost_cache
_view (EnsEMBL::Web::ViewConfig::Gene::ExternalData)
_view (EnsEMBL::Web::ViewConfig::Transcript::ExternalData)
_warn
_warn_block
_warning
acc_id
accession
accessor_name_for
action (EnsEMBL::Web::Configuration)
action (EnsEMBL::Web::Proxiable)
action (EnsEMBL::Web::Proxy)
active (EnsEMBL::Web::Document::HTML::GlobalContext)
active (EnsEMBL::Web::Document::HTML::LocalContext)
adaptor (EnsEMBL::Web::Fake)
adaptor (EnsEMBL::Web::Object::Blast)
adaptor (EnsEMBL::Web::Object::Help)
adaptor (EnsEMBL::Web::Object::News)
add (EnsEMBL::Web::Configuration::Interface)
add (EnsEMBL::Web::Document::HTML::HTML_Block)
add (EnsEMBL::Web::Document::HTML::Meta)
add (EnsEMBL::Web::Document::HTML::RSS)
add (EnsEMBL::Web::Document::HTML::Stylesheet)
addChildren (ExaLead::Category)
addChildren (ExaLead::Group)
addChildren (ExaLead::HitCategory)
addChildren (ExaLead::HitGroup)
addContext
addField
addGroup (ExaLead)
addGroup (ExaLead::Hit)
addHit (ExaLead)
addHit (ExaLead::Hits)
addKeyword
addLink (ExaLead::Category)
addLink (ExaLead::Group)
addLink (ExaLead::HitCategory)
addLink (ExaLead::HitGroup)
addLink (ExaLead::Keyword)
addParameter
addPart
addSpellingSuggestion
addTerm
add_after
add_alignment_links
add_alignments
add_arrows
add_artefacts
add_assemblies
add_attribute
add_before
add_block (EnsEMBL::Web::Configuration)
add_block (EnsEMBL::Web::BlastView::Panel)
add_block_header
add_body_attr
add_body_element
add_body_element_after
add_body_element_before
add_body_element_first
add_body_element_last
add_body_elements
add_button
add_canvas_frame (Bio::EnsEMBL::VRenderer::gif)
add_canvas_frame (Bio::EnsEMBL::VRenderer::imagemap)
add_canvas_frame (Sanger::Graphics::Renderer::eps)
add_canvas_frame (Sanger::Graphics::Renderer::gif)
add_canvas_frame (Sanger::Graphics::Renderer::imagemap)
add_canvas_frame (Sanger::Graphics::Renderer::pdf)
add_canvas_frame (Sanger::Graphics::Renderer::postscript)
add_canvas_frame (Sanger::Graphics::Renderer::svg)
add_canvas_frame (Sanger::Graphics::Renderer::test)
add_child
add_class
add_colour
add_columns (EnsEMBL::Web::Document::SpreadSheet)
add_columns (EnsEMBL::Web::Document::Panel::SpreadSheet)
add_component
add_component_after
add_component_before
add_component_first
add_component_last
add_components
add_content
add_das (EnsEMBL::Web::Session)
add_das (EnsEMBL::Web::Data::User)
add_das_from_string
add_das_source
add_das_sources
add_das_track
add_data
add_decorations
add_description
add_display_name
add_ditag_feature
add_div
add_dna_align_feature
add_element (EnsEMBL::Web::Form)
add_element (EnsEMBL::Web::Form::FieldSet)
add_entry (EnsEMBL::Web::Configuration)
add_entry (EnsEMBL::Web::BlastView::Panel)
add_entry (EnsEMBL::Web::Document::HTML::GlobalContext)
add_entry (EnsEMBL::Web::Document::HTML::LocalTools)
add_entry (EnsEMBL::Web::Document::Panel::AjaxMenu)
add_entry_footer
add_entry_header
add_error_panels
add_evidence_links
add_fields
add_fieldset (EnsEMBL::Web::Form)
add_fieldset (EnsEMBL::Web::ViewConfig)
add_file
add_form (EnsEMBL::Web::Configuration)
add_form (EnsEMBL::Web::BlastView::Panel)
add_form (EnsEMBL::Web::Component::Interface::Account)
add_form (EnsEMBL::Web::Document::Panel::SpreadSheet)
add_form_element
add_form_entries
add_format
add_gene
add_has_many
add_hasa_relations
add_hasmany_relations
add_head_element_after
add_head_element_before
add_head_element_first
add_head_element_last
add_head_elements
add_hex
add_hidden
add_html
add_image
add_image_configs
add_index
add_info (EnsEMBL::Web::BlastView::PanelMain)
add_info (EnsEMBL::Web::BlastView::PanelStatus)
add_link
add_marker_feature
add_method
add_misc_feature
add_notes
add_oligo_probe
add_option (EnsEMBL::Web::ImageConfig)
add_option (EnsEMBL::Web::Document::Panel)
add_option (EnsEMBL::Web::Document::SpreadSheet)
add_option (EnsEMBL::Web::Document::Panel::SpreadSheet)
add_options
add_owner
add_panel (EnsEMBL::Web::Configuration)
add_panel (EnsEMBL::Web::Document::Excel::Content)
add_panel (EnsEMBL::Web::Document::HTML::Content)
add_panel (EnsEMBL::Web::Document::Text::Content)
add_panel (EnsEMBL::Web::Document::TextGz::Content)
add_panel (EnsEMBL::Web::Document::XML::Content)
add_panel_after
add_panel_before
add_panel_button
add_panel_first
add_panel_header
add_panel_image
add_panel_last
add_panel_text
add_pointers
add_prediction_transcript
add_protein_align_feature
add_protein_feature
add_qtl_feature
add_queriable_fields
add_regulation_feature
add_repeat_feature
add_result
add_rgb
add_row (EnsEMBL::Web::Document::SpreadSheet)
add_row (EnsEMBL::Web::Document::HTML::TwoCol)
add_row (EnsEMBL::Web::Document::Panel::Ajax)
add_row (EnsEMBL::Web::Document::Panel::Configurator)
add_row (EnsEMBL::Web::Document::Panel::Information)
add_row (EnsEMBL::Web::Document::Panel::InformationFragment)
add_row (EnsEMBL::Web::Document::Panel::InformationImage)
add_row (EnsEMBL::Web::Document::Panel::SpreadSheet)
add_row (EnsEMBL::Web::Document::Panel::Summary)
add_script (EnsEMBL::Web::Document::HTML::BodyJavascript)
add_script (EnsEMBL::Web::Document::HTML::Javascript)
add_settings
add_sheet
add_simple_feature
add_source (EnsEMBL::Web::Document::HTML::BodyJavascript)
add_source (EnsEMBL::Web::Document::HTML::Javascript)
add_spanning_headers
add_string (Sanger::Graphics::Renderer::eps)
add_string (Sanger::Graphics::Renderer::postscript)
add_string (Sanger::Graphics::Renderer::svg)
add_style
add_subclass
add_superclass
add_synteny
add_tags
add_text
add_tie_relations
add_to_component
add_to_release
add_top_form
add_track
add_tracks (EnsEMBL::Web::ImageConfig)
add_tracks (EnsEMBL::Web::Document::Image)
add_trigger
add_user
add_variation_feature (EnsEMBL::Web::ImageConfig)
add_variation_feature (EnsEMBL::Web::Object::SNP)
add_variation_feature (EnsEMBL::Web::Object::Variation)
add_warning (EnsEMBL::Web::BlastView::Panel)
add_warning (EnsEMBL::Web::BlastView::PanelMain)
addequiv
aggregate_coverage
ajax_content (EnsEMBL::Web::Configuration::Blast)
ajax_content (EnsEMBL::Web::Configuration::Help)
ajax_content (EnsEMBL::Web::Configuration::Info)
ajax_content (EnsEMBL::Web::Configuration::Location)
ajax_content (EnsEMBL::Web::Configuration::Search)
ajax_content (EnsEMBL::Web::Configuration::Server)
ajax_content (EnsEMBL::Web::Configuration::Transcript)
ajax_content (EnsEMBL::Web::Configuration::UniSearch)
ajax_content (EnsEMBL::Web::Configuration::UserData)
ajax_content (EnsEMBL::Web::Configuration::Variation)
ajax_content (EnsEMBL::Web::Configuration::Gene)
ajax_content (EnsEMBL::Web::Configuration::Account)
ajax_is_available
ajax_params
ajax_redirect (EnsEMBL::Web::Command)
ajax_redirect (EnsEMBL::Web::Document::Page)
ajax_zmenu (EnsEMBL::Web::Configuration::Location)
ajax_zmenu (EnsEMBL::Web::Configuration::Transcript)
ajax_zmenu (EnsEMBL::Web::Configuration::Variation)
ajax_zmenu (EnsEMBL::Web::Configuration::Gene)
ajax_zmenu_id_history_tree_branch
ajax_zmenu_id_history_tree_label
ajax_zmenu_id_history_tree_node
ajax_zmenu_read_coverage
ajax_zmenu_variation
ajax_zmenu_variation_protein
ajax_zmenu_variation_transcript
ajaxable
algorithm (Bio::Tools::Run::Search::blat_gfclient)
algorithm (Bio::Tools::Run::Search::ssaha2_client)
align_gap
align_interval
align_sequence_display
align_species
alignment_options_form
alignsliceview
alignsliceviewbottom
alignsliceviewbottom_menu
alignsliceviewbottom_text
alignsliceviewtop
alignsliceviewzoom
alignview
alignview_AlignSlice
alignview_DnaDnaAlignFeature
alignview_External
alignview_Family
alignview_GeneTree
alignview_Homology
alignview_Supporting
all_cats
all_chromosomes
all_freqs (EnsEMBL::Web::Component::SNP)
all_freqs (EnsEMBL::Web::Component::Variation)
all_items
all_methods
all_search_indexes
all_species
all_spp
alleles (EnsEMBL::Web::Component::SNP)
alleles (EnsEMBL::Web::Object::SNP)
alleles (EnsEMBL::Web::Object::Variation)
alt (EnsEMBL::Web::Document::HTML::Logo)
alt (EnsEMBL::Web::Form::Element)
altered (EnsEMBL::Web::ImageConfig)
altered (EnsEMBL::Web::ViewConfig)
alternative_object_from_factory
ambig_code
amend_source
analyse
analyse_row
analysis (EnsEMBL::Web::Object::Gene)
analysis (EnsEMBL::Web::Object::Transcript)
analysis (EnsEMBL::Web::Object::Translation)
analysis_logic_name (Bio::EnsEMBL::GlyphSet::_transcript)
analysis_logic_name (Bio::EnsEMBL::GlyphSet::_transcript)
ancestor (EnsEMBL::Web::Object::SNP)
ancestor (EnsEMBL::Web::Object::Variation)
anyother_species
apache_handle
append
artefacts
as_compact_init
as_expanded_init
assembly
assign_level_to_user
assign_status_to_user
associated_ids
asynchronously_load
attachImageConfig
attach_image_config
attach_slice (EnsEMBL::Web::Object::Location)
attach_slice (EnsEMBL::Web::Object::MultipleLocation)
author
availability (EnsEMBL::Web::Object)
availability (EnsEMBL::Web::Document::HTML::LocalContext)
availability (EnsEMBL::Web::Object::Gene)
availability (EnsEMBL::Web::Object::Location)
availability (EnsEMBL::Web::Object::Transcript)
availability (EnsEMBL::Web::Object::Variation)
base_align_features
base_features
base_url
basepairs_per_pixel
bases_match
bg
bgcolor (Sanger::Graphics::WebUserConfig)
bgcolor (EnsEMBL::Web::ImageConfig)
bgcolour (Sanger::Graphics::WebUserConfig)
bgcolour (EnsEMBL::Web::ImageConfig)
bin_size
bin_starts
biomart (EnsEMBL::Web::Document::HTML::CloseCP)
biomart (EnsEMBL::Web::Document::HTML::ToolLinks)
biomart (EnsEMBL::Web::Document::HTML::ToolLinks)
blast (EnsEMBL::Web::Document::HTML::CloseCP)
blast (EnsEMBL::Web::Document::HTML::ToolLinks)
blast (EnsEMBL::Web::Document::HTML::ToolLinks)
blast_adaptor
block_features_zmenu (Bio::EnsEMBL::GlyphSet::ctcf)
block_features_zmenu (Bio::EnsEMBL::GlyphSet::histone_modifications)
body_elements
body_order
bp2px
bp_to_nearest_unit (Bio::EnsEMBL::GlyphSet::HSP_scalebar)
bp_to_nearest_unit (Bio::EnsEMBL::GlyphSet::ruler)
bp_to_nearest_unit (Bio::EnsEMBL::GlyphSet::scalebar)
bp_to_nearest_unit (Bio::EnsEMBL::GlyphSet::alignscalebar)
bp_to_nearest_unit (Sanger::Graphics::GlyphSet::ruler)
bp_to_nearest_unit (Sanger::Graphics::GlyphSet::scalebar)
bp_to_nearest_unit (EnsEMBL::Web::Object)
bp_to_nearest_unit_by_divs (Bio::EnsEMBL::GlyphSet::HSP_scalebar)
bp_to_nearest_unit_by_divs (Bio::EnsEMBL::GlyphSet::scalebar)
bp_to_nearest_unit_by_divs (Bio::EnsEMBL::GlyphSet::alignscalebar)
bp_to_nearest_unit_by_divs (Sanger::Graphics::GlyphSet::scalebar)
brightness
buffer
build_linear_gradient
build_sequence
bump
bump_row (Bio::EnsEMBL::GlyphSet)
bump_row (Sanger::Graphics::Bump)
bumpbutton
bumped (Bio::EnsEMBL::GlyphSet::urlfeature)
bumped (Sanger::Graphics::GlyphSet)
button_idlvalue
button_namelvalue
button_titlelvalue
button_value
buttonlvalue
cache (Bio::EnsEMBL::GlyphSet)
cache (EnsEMBL::Web::Component)
cache (EnsEMBL::Web::ImageConfig)
cache (EnsEMBL::Web::Document::Renderer)
cache_key
cache_print
cacheable
call
call_child_functions
can
can_export (EnsEMBL::Web::Object)
can_export (EnsEMBL::Web::Object::Gene)
can_export (EnsEMBL::Web::Object::Location)
can_export (EnsEMBL::Web::Object::Transcript)
can_upload
canset
canvas (Bio::EnsEMBL::Renderer)
canvas (Bio::EnsEMBL::VRenderer)
canvas (Bio::EnsEMBL::VRenderer::gif)
canvas (Bio::EnsEMBL::VRenderer::png)
canvas (Sanger::Graphics::Renderer)
canvas (Sanger::Graphics::Renderer::eps)
canvas (Sanger::Graphics::Renderer::gif)
canvas (Sanger::Graphics::Renderer::pdf)
canvas (Sanger::Graphics::Renderer::png)
canvas (Sanger::Graphics::Renderer::postscript)
canvas (Sanger::Graphics::Renderer::svg)
canvas (Sanger::Graphics::Renderer::test)
canvas (Sanger::Graphics::Renderer::wmf)
caption (EnsEMBL::Web::Component)
caption (EnsEMBL::Web::DASConfig)
caption (EnsEMBL::Web::Interface)
caption (EnsEMBL::Web::Component::CommandMessage)
caption (EnsEMBL::Web::Component::Compara_Alignments)
caption (EnsEMBL::Web::Component::Messages)
caption (EnsEMBL::Web::Component::Account::ActivationSent)
caption (EnsEMBL::Web::Component::Account::AdimnDetails)
caption (EnsEMBL::Web::Component::Account::AdminGroups)
caption (EnsEMBL::Web::Component::Account::Configurations)
caption (EnsEMBL::Web::Component::Account::Details)
caption (EnsEMBL::Web::Component::Account::Links)
caption (EnsEMBL::Web::Component::Account::Login)
caption (EnsEMBL::Web::Component::Account::LostPassword)
caption (EnsEMBL::Web::Component::Account::ManageGroup)
caption (EnsEMBL::Web::Component::Account::MemberDetails)
caption (EnsEMBL::Web::Component::Account::MemberGroups)
caption (EnsEMBL::Web::Component::Account::NewsFilters)
caption (EnsEMBL::Web::Component::Account::Password)
caption (EnsEMBL::Web::Component::Account::RegistrationFailed)
caption (EnsEMBL::Web::Component::Account::SelectGroup)
caption (EnsEMBL::Web::Component::Account::UpdateFailed)
caption (EnsEMBL::Web::Component::Account::Interface::AnnotationList)
caption (EnsEMBL::Web::Component::Account::Interface::BookmarkList)
caption (EnsEMBL::Web::Component::Account::Interface::GroupList)
caption (EnsEMBL::Web::Component::Account::Interface::NewsfilterList)
caption (EnsEMBL::Web::Component::Account::Interface::UserDisplay)
caption (EnsEMBL::Web::Component::Gene::ComparaOrthologs)
caption (EnsEMBL::Web::Component::Gene::ComparaParalogs)
caption (EnsEMBL::Web::Component::Gene::ComparaTree)
caption (EnsEMBL::Web::Component::Gene::ExternalData)
caption (EnsEMBL::Web::Component::Gene::GeneSNPImage)
caption (EnsEMBL::Web::Component::Gene::GeneSNPInfo)
caption (EnsEMBL::Web::Component::Gene::GeneSNPTable)
caption (EnsEMBL::Web::Component::Gene::GeneSeq)
caption (EnsEMBL::Web::Component::Gene::GeneSpliceImage)
caption (EnsEMBL::Web::Component::Gene::HistoryLinked)
caption (EnsEMBL::Web::Component::Gene::HistoryMap)
caption (EnsEMBL::Web::Component::Gene::HistoryReport)
caption (EnsEMBL::Web::Component::Gene::HomologAlignment)
caption (EnsEMBL::Web::Component::Gene::RegulationTable)
caption (EnsEMBL::Web::Component::Gene::SimilarityMatches)
caption (EnsEMBL::Web::Component::Gene::TextDAS)
caption (EnsEMBL::Web::Component::Gene::TranscriptsImage)
caption (EnsEMBL::Web::Component::Interface::Add)
caption (EnsEMBL::Web::Component::Interface::ConfirmDelete)
caption (EnsEMBL::Web::Component::Interface::Display)
caption (EnsEMBL::Web::Component::Interface::Edit)
caption (EnsEMBL::Web::Component::Interface::List)
caption (EnsEMBL::Web::Component::Interface::OnFailure)
caption (EnsEMBL::Web::Component::Interface::OnSuccess)
caption (EnsEMBL::Web::Component::Interface::Preview)
caption (EnsEMBL::Web::Component::Interface::Problem)
caption (EnsEMBL::Web::Component::Interface::SelectToDelete)
caption (EnsEMBL::Web::Component::Interface::SelectToEdit)
caption (EnsEMBL::Web::Component::Interface::Account::Add)
caption (EnsEMBL::Web::Component::Interface::Account::FailedRegistration)
caption (EnsEMBL::Web::Component::Location::ComparaGenomicAlignment)
caption (EnsEMBL::Web::Component::Location::LDImage)
caption (EnsEMBL::Web::Component::Location::SequenceAlignment)
caption (EnsEMBL::Web::Component::Location::SyntenyMatches)
caption (EnsEMBL::Web::Component::Transcript::DomainGenes)
caption (EnsEMBL::Web::Component::Transcript::DomainSpreadsheet)
caption (EnsEMBL::Web::Component::Transcript::ExonsSpreadsheet)
caption (EnsEMBL::Web::Component::Transcript::ExternalData)
caption (EnsEMBL::Web::Component::Transcript::ExternalRecordAlignment)
caption (EnsEMBL::Web::Component::Transcript::Go)
caption (EnsEMBL::Web::Component::Transcript::ID)
caption (EnsEMBL::Web::Component::Transcript::OligoArrays)
caption (EnsEMBL::Web::Component::Transcript::ProteinSeq)
caption (EnsEMBL::Web::Component::Transcript::ProteinVariations)
caption (EnsEMBL::Web::Component::Transcript::SNPView)
caption (EnsEMBL::Web::Component::Transcript::SimilarityMatches)
caption (EnsEMBL::Web::Component::Transcript::SupportingEvidence)
caption (EnsEMBL::Web::Component::Transcript::SupportingEvidenceAlignment)
caption (EnsEMBL::Web::Component::Transcript::TranscriptNeighbourhood)
caption (EnsEMBL::Web::Component::Transcript::TranscriptSNPInfo)
caption (EnsEMBL::Web::Component::Transcript::TranscriptSNPTable)
caption (EnsEMBL::Web::Component::Transcript::TranscriptSeq)
caption (EnsEMBL::Web::Component::UserData::DasCoords)
caption (EnsEMBL::Web::Component::UserData::DasFeedback)
caption (EnsEMBL::Web::Component::UserData::DasSources)
caption (EnsEMBL::Web::Component::UserData::DasSpecies)
caption (EnsEMBL::Web::Component::UserData::)
caption (EnsEMBL::Web::Component::UserData::MoreInput)
caption (EnsEMBL::Web::Component::UserData::RenameRecord)
caption (EnsEMBL::Web::Component::UserData::RenameTempData)
caption (EnsEMBL::Web::Component::UserData::SelectFile)
caption (EnsEMBL::Web::Component::UserData::SelectServer)
caption (EnsEMBL::Web::Component::UserData::SelectShare)
caption (EnsEMBL::Web::Component::UserData::SelectURL)
caption (EnsEMBL::Web::Component::UserData::ShareURL)
caption (EnsEMBL::Web::Component::UserData::ShowRemote)
caption (EnsEMBL::Web::Component::UserData::TempDasSaved)
caption (EnsEMBL::Web::Component::UserData::UploadFeedback)
caption (EnsEMBL::Web::Component::UserData::UrlFeedback)
caption (EnsEMBL::Web::Document::Panel)
caption (EnsEMBL::Web::Document::HTML::LocalContext)
caption (EnsEMBL::Web::Object::Account)
caption (EnsEMBL::Web::Object::Blast)
caption (EnsEMBL::Web::Object::Gene)
caption (EnsEMBL::Web::Object::Help)
caption (EnsEMBL::Web::Object::Info)
caption (EnsEMBL::Web::Object::Location)
caption (EnsEMBL::Web::Object::Search)
caption (EnsEMBL::Web::Object::Server)
caption (EnsEMBL::Web::Object::Transcript)
caption (EnsEMBL::Web::Object::UniSearch)
caption (EnsEMBL::Web::Object::UserData)
caption (EnsEMBL::Web::Object::Variation)
captionlvalue
carpet
catch (EnsEMBL::Web::Filter)
catch (EnsEMBL::Web::Filter::Activation)
catch (EnsEMBL::Web::Filter::Admin)
catch (EnsEMBL::Web::Filter::DAS)
catch (EnsEMBL::Web::Filter::Data)
catch (EnsEMBL::Web::Filter::DuplicateUser)
catch (EnsEMBL::Web::Filter::EmailAddress)
catch (EnsEMBL::Web::Filter::Invitation)
catch (EnsEMBL::Web::Filter::LoggedIn)
catch (EnsEMBL::Web::Filter::Member)
catch (EnsEMBL::Web::Filter::PasswordSecure)
catch (EnsEMBL::Web::Filter::PasswordValid)
catch (EnsEMBL::Web::Filter::Sanitize)
catch (EnsEMBL::Web::Filter::Shareable)
catch (EnsEMBL::Web::Filter::Sources)
catch (EnsEMBL::Web::Filter::Spam)
catch (EnsEMBL::Web::Filter::UserData)
catch (EnsEMBL::Web::Filter::Owner)
category
centre (Bio::EnsEMBL::Glyph)
centre (Sanger::Graphics::Glyph)
centre (Sanger::Graphics::Glyph::Circle)
centrepoint (EnsEMBL::Web::Object::Location)
centrepoint (EnsEMBL::Web::Object::MultipleLocation)
cgi_populate
check (Bio::EnsEMBL::GlyphSet)
check (Bio::EnsEMBL::GlyphSet::urlfeature)
check (Sanger::Graphics::GlyphSet)
check (EnsEMBL::Web::Filter::Spam)
check_ajax
check_for_errors
check_source
check_species
checkdrawable
checked (EnsEMBL::Web::Form::Element::CheckBox)
checked (EnsEMBL::Web::Form::Element::RadioButton)
checksum
child (EnsEMBL::Web::Object::SNP)
child (EnsEMBL::Web::Object::Variation)
childExitHandler
childInitHandler
children (EnsEMBL::Web::Tools::PluginLocator)
children (ExaLead::Category)
children (ExaLead::Group)
children (ExaLead::HitCategory)
children (ExaLead::HitGroup)
chr_list
chr_name
chr_sort
chromosome (EnsEMBL::Web::Object::Gene)
chromosome (EnsEMBL::Web::Object::Location)
chromosome (EnsEMBL::Web::Object::Marker)
chunked_content
cigar_segments
cigar_string (EnsEMBL::Web::Text::Feature::BED)
cigar_string (EnsEMBL::Web::Text::Feature::GFF)
cigar_string (EnsEMBL::Web::Text::Feature::PSL)
class (Sanger::Graphics::Renderer::svg)
class (EnsEMBL::Web::Document::HTML::LocalContext)
class (EnsEMBL::Web::Object::Alignment)
class_attrib
classes
clean
cleanURI
cleanupHandler
cleanupHandler_blast
cleanupHandler_script
clear
clearDataObjects
clear_body_attr
clear_components
clear_option (EnsEMBL::Web::Document::Panel)
clear_option (EnsEMBL::Web::Document::Panel::SpreadSheet)
clear_options (EnsEMBL::Web::Document::Panel)
clear_options (EnsEMBL::Web::Document::Panel::SpreadSheet)
clear_problems (EnsEMBL::Web::Proxiable)
clear_problems (EnsEMBL::Web::Proxy)
clear_times
clone
close (EnsEMBL::Web::Document::Renderer)
close (EnsEMBL::Web::Document::Renderer::Assembler)
close (EnsEMBL::Web::Document::Renderer::File)
close (EnsEMBL::Web::Document::Renderer::GzFile)
close (EnsEMBL::Web::Document::Renderer::Stdout)
code
coldist (EnsEMBL::Web::Component::Server)
coldist (EnsEMBL::Web::Component::Server::ColourMap)
colour (Bio::EnsEMBL::GlyphSet_transcript)
colour (Bio::EnsEMBL::GlyphSet::genetree)
colour (Bio::EnsEMBL::GlyphSet::_alignment_multiple)
colour (Bio::EnsEMBL::GlyphSet::_alignment_pairwise)
colour (Bio::EnsEMBL::GlyphSet::urlfeature)
colour (Bio::EnsEMBL::GlyphSet::vegaclones)
colour (Bio::EnsEMBL::GlyphSet::_transcript)
colour (Bio::EnsEMBL::GlyphSet::annotation_status)
colour (Bio::EnsEMBL::GlyphSet::ensemblclones)
colour (Bio::EnsEMBL::GlyphSet::regulatory_search_regions)
colour (Bio::EnsEMBL::VRenderer::gif)
colour (Sanger::Graphics::Renderer::gif)
colour (EnsEMBL::Web::SpeciesDefs)
colour_array
colour_key (Bio::EnsEMBL::GlyphSet_simple)
colour_key (Bio::EnsEMBL::GlyphSet::regulatory_regions)
colour_key (Bio::EnsEMBL::GlyphSet::sequence)
colour_key (Bio::EnsEMBL::GlyphSet::_alignment)
colour_key (Bio::EnsEMBL::GlyphSet::_clone)
colour_key (Bio::EnsEMBL::GlyphSet::_flat_file)
colour_key (Bio::EnsEMBL::GlyphSet::_qtl)
colour_key (Bio::EnsEMBL::GlyphSet::_repeat)
colour_key (Bio::EnsEMBL::GlyphSet::_simple)
colour_key (Bio::EnsEMBL::GlyphSet::_user_data)
colour_key (Bio::EnsEMBL::GlyphSet::_variation)
colour_key (Bio::EnsEMBL::GlyphSet::assemblyexception)
colour_key (Bio::EnsEMBL::GlyphSet::fg_regulatory_features)
colour_key (Bio::EnsEMBL::GlyphSet::regulatory_search_regions)
colourmap (Sanger::Graphics::WebUserConfig)
colourmap (EnsEMBL::Web::ImageConfig)
colourmap (EnsEMBL::Web::Session)
colourmap (EnsEMBL::Web::Configuration::Server)
colourmap_usage
colours (Bio::EnsEMBL::GlyphSet_transcript)
colours (Bio::EnsEMBL::GlyphSet::_transcript)
cols
command (EnsEMBL::Web::Object)
command (EnsEMBL::Web::Document::WebPage)
command (Bio::Tools::Run::Search::EnsemblBlast)
command (Bio::Tools::Run::Search::blat_gfclient)
command (Bio::Tools::Run::Search::ssaha2_client)
command_bsub
comment
commify (Bio::EnsEMBL::GlyphSet)
commify (Sanger::Graphics::GlyphSet)
common_menu_items
common_page_elements
compact_init
compara_db
compara_like_databases
completed_jobs
component
components
composite_extent_gradient
composite_extent_histogram
composite_extent_lineplot
composite_extent_tiling
composite_gradient
composite_histogram
composite_lineplot
composite_tiling
config (Bio::EnsEMBL::DrawableContainer)
config (Bio::EnsEMBL::VDrawableContainer)
config (Sanger::Graphics::DrawableContainer)
config (Sanger::Graphics::Renderer)
config (Sanger::Graphics::VDrawableContainer)
config (EnsEMBL::Web::BlastView::MetaDataBlast)
config_info
configurable (EnsEMBL::Web::Component)
configurable (EnsEMBL::Web::Configuration)
configurator (EnsEMBL::Web::Magic)
configurator (EnsEMBL::Web::Configuration::Location)
configurator (EnsEMBL::Web::Configuration::Server)
configurator (EnsEMBL::Web::Configuration::Gene)
configure (EnsEMBL::Web::Interface)
configure (EnsEMBL::Web::Document::WebPage)
configure (EnsEMBL::Web::Tools::Registry)
configure_das_views
configure_gene
confirm_delete
connect
consequence_type
contact
container_width (Sanger::Graphics::WebUserConfig)
container_width (EnsEMBL::Web::ImageConfig)
content (EnsEMBL::Web::TmpFile)
content (EnsEMBL::Web::Component::CommandMessage)
content (EnsEMBL::Web::Component::Compara_AlignSliceSelector)
content (EnsEMBL::Web::Component::Compara_Alignments)
content (EnsEMBL::Web::Component::Configurator)
content (EnsEMBL::Web::Component::Messages)
content (EnsEMBL::Web::Component::UnderConstruction)
content (EnsEMBL::Web::Component::Account::ActivationSent)
content (EnsEMBL::Web::Component::Account::AdimnDetails)
content (EnsEMBL::Web::Component::Account::AdminGroups)
content (EnsEMBL::Web::Component::Account::Configurations)
content (EnsEMBL::Web::Component::Account::Details)
content (EnsEMBL::Web::Component::Account::Links)
content (EnsEMBL::Web::Component::Account::Login)
content (EnsEMBL::Web::Component::Account::LostPassword)
content (EnsEMBL::Web::Component::Account::ManageGroup)
content (EnsEMBL::Web::Component::Account::MemberDetails)
content (EnsEMBL::Web::Component::Account::MemberGroups)
content (EnsEMBL::Web::Component::Account::NewsFilters)
content (EnsEMBL::Web::Component::Account::Password)
content (EnsEMBL::Web::Component::Account::RegistrationFailed)
content (EnsEMBL::Web::Component::Account::SelectGroup)
content (EnsEMBL::Web::Component::Account::UpdateFailed)
content (EnsEMBL::Web::Component::Account::Interface::AnnotationList)
content (EnsEMBL::Web::Component::Account::Interface::BookmarkList)
content (EnsEMBL::Web::Component::Account::Interface::GroupList)
content (EnsEMBL::Web::Component::Account::Interface::NewsfilterList)
content (EnsEMBL::Web::Component::Account::Interface::UserDisplay)
content (EnsEMBL::Web::Component::Blast::Alignment)
content (EnsEMBL::Web::Component::Blast::Alignment)
content (EnsEMBL::Web::Component::Blast::Alignment)
content (EnsEMBL::Web::Component::Blast::Retrieve)
content (EnsEMBL::Web::Component::Blast::Search)
content (EnsEMBL::Web::Component::Blast::Ticket)
content (EnsEMBL::Web::Component::Blast::View)
content (EnsEMBL::Web::Component::Gene::ComparaAlignmentsOptions)
content (EnsEMBL::Web::Component::Gene::ComparaOrthologs)
content (EnsEMBL::Web::Component::Gene::ComparaParalogs)
content (EnsEMBL::Web::Component::Gene::ComparaTree)
content (EnsEMBL::Web::Component::Gene::ExternalData)
content (EnsEMBL::Web::Component::Gene::Family)
content (EnsEMBL::Web::Component::Gene::FamilyAlignments)
content (EnsEMBL::Web::Component::Gene::FamilyGenes)
content (EnsEMBL::Web::Component::Gene::GeneSNPImage)
content (EnsEMBL::Web::Component::Gene::GeneSNPInfo)
content (EnsEMBL::Web::Component::Gene::GeneSNPTable)
content (EnsEMBL::Web::Component::Gene::GeneSeq)
content (EnsEMBL::Web::Component::Gene::GeneSpliceImage)
content (EnsEMBL::Web::Component::Gene::GeneSummary)
content (EnsEMBL::Web::Component::Gene::HistoryLinked)
content (EnsEMBL::Web::Component::Gene::HistoryMap)
content (EnsEMBL::Web::Component::Gene::HistoryReport)
content (EnsEMBL::Web::Component::Gene::HomologAlignment)
content (EnsEMBL::Web::Component::Gene::RegulationImage)
content (EnsEMBL::Web::Component::Gene::RegulationTable)
content (EnsEMBL::Web::Component::Gene::SimilarityMatches)
content (EnsEMBL::Web::Component::Gene::Summary)
content (EnsEMBL::Web::Component::Gene::SupportingEvidence)
content (EnsEMBL::Web::Component::Gene::TextDAS)
content (EnsEMBL::Web::Component::Gene::TranscriptsImage)
content (EnsEMBL::Web::Component::Gene::UnderConstruction)
content (EnsEMBL::Web::Component::Gene::UserAnnotation)
content (EnsEMBL::Web::Component::Help::ArchiveList)
content (EnsEMBL::Web::Component::Help::Contact)
content (EnsEMBL::Web::Component::Help::EmailSent)
content (EnsEMBL::Web::Component::Help::Faq)
content (EnsEMBL::Web::Component::Help::FeedbackPreview)
content (EnsEMBL::Web::Component::Help::Glossary)
content (EnsEMBL::Web::Component::Help::Movie)
content (EnsEMBL::Web::Component::Help::MovieFeedback)
content (EnsEMBL::Web::Component::Help::Permalink)
content (EnsEMBL::Web::Component::Help::Preview)
content (EnsEMBL::Web::Component::Help::Results)
content (EnsEMBL::Web::Component::Help::Search)
content (EnsEMBL::Web::Component::Help::View)
content (EnsEMBL::Web::Component::Info::Content)
content (EnsEMBL::Web::Component::Info::IPtop40)
content (EnsEMBL::Web::Component::Info::IPtop500)
content (EnsEMBL::Web::Component::Info::Index)
content (EnsEMBL::Web::Component::Info::SpeciesBlurb)
content (EnsEMBL::Web::Component::Info::SpeciesBurp)
content (EnsEMBL::Web::Component::Info::SpeciesStats)
content (EnsEMBL::Web::Component::Info::Summary)
content (EnsEMBL::Web::Component::Info::WhatsNew)
content (EnsEMBL::Web::Component::Interface::Add)
content (EnsEMBL::Web::Component::Interface::ConfirmDelete)
content (EnsEMBL::Web::Component::Interface::Display)
content (EnsEMBL::Web::Component::Interface::Edit)
content (EnsEMBL::Web::Component::Interface::List)
content (EnsEMBL::Web::Component::Interface::OnFailure)
content (EnsEMBL::Web::Component::Interface::OnSuccess)
content (EnsEMBL::Web::Component::Interface::Preview)
content (EnsEMBL::Web::Component::Interface::Problem)
content (EnsEMBL::Web::Component::Interface::SelectToDelete)
content (EnsEMBL::Web::Component::Interface::SelectToEdit)
content (EnsEMBL::Web::Component::Interface::Account::Add)
content (EnsEMBL::Web::Component::Interface::Account::FailedRegistration)
content (EnsEMBL::Web::Component::Location::ChangeChromosome)
content (EnsEMBL::Web::Component::Location::ChangeSpecies)
content (EnsEMBL::Web::Component::Location::ChromosomeImage)
content (EnsEMBL::Web::Component::Location::ChromosomeStats)
content (EnsEMBL::Web::Component::Location::ComparaGenomicAlignment)
content (EnsEMBL::Web::Component::Location::Compara_AlignSliceBottom)
content (EnsEMBL::Web::Component::Location::Genome)
content (EnsEMBL::Web::Component::Location::Ideogram)
content (EnsEMBL::Web::Component::Location::LD)
content (EnsEMBL::Web::Component::Location::LDImage)
content (EnsEMBL::Web::Component::Location::MarkerDetails)
content (EnsEMBL::Web::Component::Location::NavigateHomology)
content (EnsEMBL::Web::Component::Location::Region)
content (EnsEMBL::Web::Component::Location::RegionNav)
content (EnsEMBL::Web::Component::Location::SequenceAlignment)
content (EnsEMBL::Web::Component::Location::Summary)
content (EnsEMBL::Web::Component::Location::SyntenyImage)
content (EnsEMBL::Web::Component::Location::SyntenyMatches)
content (EnsEMBL::Web::Component::Location::UnderConstruction)
content (EnsEMBL::Web::Component::Location::ViewBottom)
content (EnsEMBL::Web::Component::Location::ViewBottomNav)
content (EnsEMBL::Web::Component::Location::ViewTop)
content (EnsEMBL::Web::Component::Location::ViewZoom)
content (EnsEMBL::Web::Component::Search::Summary)
content (EnsEMBL::Web::Component::Server::ColourMap)
content (EnsEMBL::Web::Component::Server::Information)
content (EnsEMBL::Web::Component::Server::Summary)
content (EnsEMBL::Web::Component::Server::tree)
content (EnsEMBL::Web::Component::Transcript::DomainGenes)
content (EnsEMBL::Web::Component::Transcript::DomainSpreadsheet)
content (EnsEMBL::Web::Component::Transcript::ExonsSpreadsheet)
content (EnsEMBL::Web::Component::Transcript::ExternalData)
content (EnsEMBL::Web::Component::Transcript::ExternalRecordAlignment)
content (EnsEMBL::Web::Component::Transcript::Go)
content (EnsEMBL::Web::Component::Transcript::ID)
content (EnsEMBL::Web::Component::Transcript::OligoArrays)
content (EnsEMBL::Web::Component::Transcript::PepStats)
content (EnsEMBL::Web::Component::Transcript::ProteinSeq)
content (EnsEMBL::Web::Component::Transcript::ProteinVariations)
content (EnsEMBL::Web::Component::Transcript::SNPView)
content (EnsEMBL::Web::Component::Transcript::SimilarityMatches)
content (EnsEMBL::Web::Component::Transcript::Summary)
content (EnsEMBL::Web::Component::Transcript::SupportingEvidence)
content (EnsEMBL::Web::Component::Transcript::SupportingEvidenceAlignment)
content (EnsEMBL::Web::Component::Transcript::TranscriptImage)
content (EnsEMBL::Web::Component::Transcript::TranscriptNeighbourhood)
content (EnsEMBL::Web::Component::Transcript::TranscriptSNPInfo)
content (EnsEMBL::Web::Component::Transcript::TranscriptSNPTable)
content (EnsEMBL::Web::Component::Transcript::TranscriptSeq)
content (EnsEMBL::Web::Component::Transcript::TranscriptSummary)
content (EnsEMBL::Web::Component::Transcript::TranslationImage)
content (EnsEMBL::Web::Component::Transcript::UnderConstruction)
content (EnsEMBL::Web::Component::Transcript::UserAnnotation)
content (EnsEMBL::Web::Component::UniSearch::Summary)
content (EnsEMBL::Web::Component::UserData::DasCoords)
content (EnsEMBL::Web::Component::UserData::DasFeedback)
content (EnsEMBL::Web::Component::UserData::DasSources)
content (EnsEMBL::Web::Component::UserData::DasSpecies)
content (EnsEMBL::Web::Component::UserData::)
content (EnsEMBL::Web::Component::UserData::ManageData)
content (EnsEMBL::Web::Component::UserData::MoreInput)
content (EnsEMBL::Web::Component::UserData::RenameRecord)
content (EnsEMBL::Web::Component::UserData::RenameTempData)
content (EnsEMBL::Web::Component::UserData::SelectFile)
content (EnsEMBL::Web::Component::UserData::SelectServer)
content (EnsEMBL::Web::Component::UserData::SelectShare)
content (EnsEMBL::Web::Component::UserData::SelectURL)
content (EnsEMBL::Web::Component::UserData::ShareURL)
content (EnsEMBL::Web::Component::UserData::ShowRemote)
content (EnsEMBL::Web::Component::UserData::TempDasSaved)
content (EnsEMBL::Web::Component::UserData::UploadFeedback)
content (EnsEMBL::Web::Component::UserData::UrlFeedback)
content (EnsEMBL::Web::Component::Variation::Compara_Alignments)
content (EnsEMBL::Web::Component::Variation::Context)
content (EnsEMBL::Web::Component::Variation::FlankingSequence)
content (EnsEMBL::Web::Component::Variation::IndividualGenotypes)
content (EnsEMBL::Web::Component::Variation::Mappings)
content (EnsEMBL::Web::Component::Variation::PopulationGenotypes)
content (EnsEMBL::Web::Component::Variation::Summary)
content (EnsEMBL::Web::Component::Variation::VariationSummary)
content (EnsEMBL::Web::Component::Variation::ExternalData)
content (EnsEMBL::Web::Document::Panel)
content (EnsEMBL::Web::Document::Renderer)
content (EnsEMBL::Web::Document::Panel::AjaxMenu)
content (EnsEMBL::Web::Document::Renderer::Assembler)
content (EnsEMBL::Web::Document::Renderer::GzFile)
content (EnsEMBL::Web::Document::Renderer::String)
content (EnsEMBL::Web::TmpFile::Image)
content_Excel
content_Text (EnsEMBL::Web::Document::Panel)
content_Text (EnsEMBL::Web::Document::Panel::SpreadSheet)
content_align
content_ensembl
content_export (EnsEMBL::Web::Component::Gene)
content_export (EnsEMBL::Web::Component::Location)
content_export (EnsEMBL::Web::Component::Transcript)
content_other
content_panel (EnsEMBL::Web::Configuration::Blast)
content_panel (EnsEMBL::Web::Configuration::Help)
content_panel (EnsEMBL::Web::Configuration::Info)
content_panel (EnsEMBL::Web::Configuration::Location)
content_panel (EnsEMBL::Web::Configuration::SNP)
content_panel (EnsEMBL::Web::Configuration::Search)
content_panel (EnsEMBL::Web::Configuration::Server)
content_panel (EnsEMBL::Web::Configuration::Transcript)
content_panel (EnsEMBL::Web::Configuration::UniSearch)
content_panel (EnsEMBL::Web::Configuration::UserData)
content_panel (EnsEMBL::Web::Configuration::Variation)
content_panel (EnsEMBL::Web::Configuration::Gene)
content_panel (EnsEMBL::Web::Configuration::Account)
content_protein (EnsEMBL::Web::Component::Gene::HistoryLinked)
content_protein (EnsEMBL::Web::Component::Gene::HistoryMap)
content_protein (EnsEMBL::Web::Component::Gene::HistoryReport)
content_region
content_sub_slice
content_text
context (ExaLead::Link)
context (ExaLead::Query)
context_historyview
context_menu (EnsEMBL::Web::Configuration::Alignment)
context_menu (EnsEMBL::Web::Configuration::ArchiveStableId)
context_menu (EnsEMBL::Web::Configuration::Go)
context_menu (EnsEMBL::Web::Configuration::Marker)
context_menu (EnsEMBL::Web::Configuration::MultipleLocation)
context_menu (EnsEMBL::Web::Configuration::Server)
context_menu (EnsEMBL::Web::Configuration::Translation)
context_menu (EnsEMBL::Sanger::Configuration::Server)
context_panel (EnsEMBL::Web::Configuration::Blast)
context_panel (EnsEMBL::Web::Configuration::Help)
context_panel (EnsEMBL::Web::Configuration::Info)
context_panel (EnsEMBL::Web::Configuration::Location)
context_panel (EnsEMBL::Web::Configuration::SNP)
context_panel (EnsEMBL::Web::Configuration::Search)
context_panel (EnsEMBL::Web::Configuration::Server)
context_panel (EnsEMBL::Web::Configuration::Transcript)
context_panel (EnsEMBL::Web::Configuration::UniSearch)
context_panel (EnsEMBL::Web::Configuration::UserData)
context_panel (EnsEMBL::Web::Configuration::Variation)
context_panel (EnsEMBL::Web::Configuration::Gene)
context_panel (EnsEMBL::Web::Configuration::Account)
contrast
convert_keyword
coord_system (EnsEMBL::Web::Object::Gene)
coord_system (EnsEMBL::Web::Object::Transcript)
coord_system (EnsEMBL::Web::Object::Translation)
coord_systems (EnsEMBL::Web::Object::Feature)
coord_systems (EnsEMBL::Web::Object::Location)
copy_support_files
core
core_objects (EnsEMBL::Web::ImageConfig)
core_objects (EnsEMBL::Web::Proxiable)
core_params
count (EnsEMBL::Web::Factory::UniSearch)
count (ExaLead::Category)
count (ExaLead::Group)
count (ExaLead::Keyword)
count_alignments
count_ega
count_gene_supporting_evidence
count_genes
count_go
count_individuals
count_oligos
count_populations
count_prot_domains
count_prot_variations
count_records
count_similarity_matches
count_supporting_evidence
count_supporting_evidence_old
count_transcripts
count_xrefs
counts (EnsEMBL::Web::Object)
counts (EnsEMBL::Web::Document::HTML::LocalContext)
counts (EnsEMBL::Web::Object::Account)
counts (EnsEMBL::Web::Object::Blast)
counts (EnsEMBL::Web::Object::Gene)
counts (EnsEMBL::Web::Object::Help)
counts (EnsEMBL::Web::Object::Info)
counts (EnsEMBL::Web::Object::Location)
counts (EnsEMBL::Web::Object::Search)
counts (EnsEMBL::Web::Object::Server)
counts (EnsEMBL::Web::Object::Transcript)
counts (EnsEMBL::Web::Object::UniSearch)
counts (EnsEMBL::Web::Object::UserData)
counts (EnsEMBL::Web::Object::Variation)
counts (EnsEMBL::Web::Text::DensityFeatureParser)
coverage
create (EnsEMBL::Web::Cookie)
create (EnsEMBL::Web::Tools::MartRegistry)
create (EnsEMBL::Web::Tools::OpenSearchDescription)
create (EnsEMBL::Web::Tools::RobotsTxt)
createGenesByDomain
createGenesByFamily
createObjects (EnsEMBL::Web::Factory::Account)
createObjects (EnsEMBL::Web::Factory::Alignment)
createObjects (EnsEMBL::Web::Factory::ArchiveStableId)
createObjects (EnsEMBL::Web::Factory::Blast)
createObjects (EnsEMBL::Web::Factory::DAS)
createObjects (EnsEMBL::Web::Factory::DASCollection)
createObjects (EnsEMBL::Web::Factory::Gene)
createObjects (EnsEMBL::Web::Factory::Go)
createObjects (EnsEMBL::Web::Factory::Help)
createObjects (EnsEMBL::Web::Factory::Info)
createObjects (EnsEMBL::Web::Factory::Link)
createObjects (EnsEMBL::Web::Factory::Location)
createObjects (EnsEMBL::Web::Factory::MartLink)
createObjects (EnsEMBL::Web::Factory::MultipleLocation)
createObjects (EnsEMBL::Web::Factory::News)
createObjects (EnsEMBL::Web::Factory::SNP)
createObjects (EnsEMBL::Web::Factory::Search)
createObjects (EnsEMBL::Web::Factory::Sequence)
createObjects (EnsEMBL::Web::Factory::Server)
createObjects (EnsEMBL::Web::Factory::Static)
createObjects (EnsEMBL::Web::Factory::Transcript)
createObjects (EnsEMBL::Web::Factory::Translation)
createObjects (EnsEMBL::Web::Factory::UniSearch)
createObjects (EnsEMBL::Web::Factory::UserData)
createObjects (EnsEMBL::Web::Factory::Variation)
createObjects (EnsEMBL::Web::Factory::Search::AltaVista)
createObjects (EnsEMBL::Web::Factory::Search::Unisearch)
createObjectsGene
createObjectsLocation
createObjects_AlignSlice
createObjects_DnaDnaAlignFeature
createObjects_Family
createObjects_GeneTree
create_UserData
create_UserDataFeature
create_alignment
create_all
create_family
create_features
create_hsp
create_hsp_and_alignments
create_menus
create_node (EnsEMBL::Web::Configuration)
create_node (EnsEMBL::Web::OrderedTree)
create_option
create_select_values
create_sequence
create_session_id (EnsEMBL::Web::Session)
create_session_id (EnsEMBL::Web::Data::Session)
create_submenu (EnsEMBL::Web::Configuration)
create_submenu (EnsEMBL::Web::ImageConfig)
create_subnode
create_tempdata_pointers
create_ticket
create_track
create_user_set
create_userdata_pointers
created_at_pretty
created_date (EnsEMBL::Web::Object::Gene)
created_date (EnsEMBL::Web::Object::Transcript)
current_key
current_pop_name
current_spp
current_version
das
das_annotation
das_link (Bio::EnsEMBL::GlyphSet)
das_link (Bio::EnsEMBL::GlyphSet::generic_simplest)
das_tree
data (EnsEMBL::Web::Interface)
data (EnsEMBL::Web::OrderedTree::Node)
dataObjects
data_form
data_species
data_typelvalue
database (EnsEMBL::Web::CoreObjects)
database (EnsEMBL::Web::Proxiable)
database (EnsEMBL::Web::Component::Go)
database (EnsEMBL::Web::Component::Server)
database (EnsEMBL::Web::Container::HSPContainer)
database (Bio::Tools::Run::Search::ssaha2_client)
database_labels
database_processing_callback
databases_species
datadump
datalvalue (EnsEMBL::Web::Object::Feature)
datalvalue (EnsEMBL::Web::Object::UserData)
dataobj
date_format (EnsEMBL::Web::Object::Gene)
date_format (EnsEMBL::Web::Object::Transcript)
db (EnsEMBL::Web::IndexSupport)
db (EnsEMBL::Web::DBSQL::BlastAdaptor)
dbID
db_connect
db_connect_multi_species
db_details
db_entry_adaptor
db_multi_tree
db_name
db_tree
db_type (EnsEMBL::Web::Object::Transcript)
db_type (EnsEMBL::Web::Object::Translation)
dbadaptor
dbh (EnsEMBL::Web::IndexSupport)
dbh (EnsEMBL::Sanger::WebStats)
dblinks (EnsEMBL::Web::Object::SNP)
dblinks (EnsEMBL::Web::Object::Variation)
de_camel
de_romanize
debug (EnsEMBL::Web::IndexSupport)
debug (EnsEMBL::Web::Document::HTML::BodyJavascript)
decode
decrypt_value
dedupe
deepcopy
default
default_action
default_config
default_database
default_method
default_otherspecies
default_search_code (EnsEMBL::Web::Document::HTML::HomeSearch)
default_search_code (EnsEMBL::Web::Document::HTML::SearchBox)
default_species (EnsEMBL::Web::BlastView::BlastDefs)
default_species (EnsEMBL::Web::DBSQL::DBConnection)
default_track_by_gene
default_type
delete (EnsEMBL::Web::Cache)
delete (EnsEMBL::Web::TmpFile)
delete (EnsEMBL::Web::ViewConfig)
delete (EnsEMBL::Web::Configuration::Interface)
delete (EnsEMBL::Web::TmpFile::Driver::Disk)
delete (EnsEMBL::Web::TmpFile::Driver::Memcached)
delete_block
delete_by_tags
delete_das_source
delete_link
delete_node
delete_param
delete_remote
delete_submenu
delete_upload
descendants
description (EnsEMBL::Web::Fake)
description (EnsEMBL::Web::Problem)
destroy
detect_error
determine_sequence_type
dice
directory
disabled (EnsEMBL::Web::Form::Element::CheckBox)
disabled (EnsEMBL::Web::Form::Element::RadioButton)
disconnect
discover
dispatch_bsub
display
display_label
display_node (EnsEMBL::Web::Component::Server)
display_node (EnsEMBL::Web::Component::Server::tree)
display_xref (EnsEMBL::Web::Object::Gene)
display_xref (EnsEMBL::Web::Object::Transcript)
display_xref (EnsEMBL::Web::Object::Translation)
dna (EnsEMBL::Web::Component::DAS::Reference)
dna (EnsEMBL::Web::Configuration::DAS)
do_SE_align_menu
do_glyphs
do_markedup_pep_seq
do_query
doc_type
documentation
domain_list
dotterview
draw_block_features
draw_chromosome
draw_cigar_feature
draw_error
draw_error_tracks (Bio::EnsEMBL::GlyphSet::ctcf)
draw_error_tracks (Bio::EnsEMBL::GlyphSet::histone_modifications)
draw_features (Bio::EnsEMBL::GlyphSet::read_coverage)
draw_features (Bio::EnsEMBL::GlyphSet::_alignment_multiple)
draw_features (Bio::EnsEMBL::GlyphSet::ctcf)
draw_features (Bio::EnsEMBL::GlyphSet::histone_modifications)
draw_glyphs
draw_space_glyph
draw_track_name
draw_wiggle_plot
drawable_containerlvalue
drivers
dropdown
dump (Sanger::Graphics::WebUserConfig)
dump (EnsEMBL::Web::OrderedTree)
dump (EnsEMBL::Web::SeqDumper)
dump (EnsEMBL::Web::SpeciesDefs)
dump (EnsEMBL::Web::ViewConfig)
dump_data
dump_hash
duplicate
dynamic_use (Bio::EnsEMBL::VDrawableContainer)
dynamic_use (Sanger::Graphics::Root)
dynamic_use (EnsEMBL::Web::Root)
dynamic_use (EnsEMBL::Web::DBSQL::DBConnection)
dynamic_use_failure
edit
edit_fields
edit_link
element
element_count_from_package
element_features
element_order
elements
email_URL
email_footer
encode
encryptPassword
encrypt_value
end (Bio::EnsEMBL::Glyph)
end (Sanger::Graphics::Glyph)
end (EnsEMBL::Web::Timer)
end (EnsEMBL::Web::Container::HSPContainer)
end (EnsEMBL::Web::Text::Feature)
end (ExaLead)
end (ExaLead::Hits)
engineURL
ens_ID
ens_avs_buildmode_ex
ens_avs_close
ens_avs_commit
ens_avs_finalize
ens_avs_getindexversion
ens_avs_indexdoc
ens_avs_open
ens_avs_querymode
ens_avs_version
entries (EnsEMBL::Web::Document::HTML::GlobalContext)
entries (EnsEMBL::Web::Document::HTML::LocalTools)
entry_points (EnsEMBL::Web::Component::DAS::Reference)
entry_points (EnsEMBL::Web::Configuration::DAS)
error
errorTrack (Bio::EnsEMBL::GlyphSet)
errorTrack (Sanger::Graphics::GlyphSet)
error_code
error_message
error_track_name (Bio::EnsEMBL::GlyphSet)
error_track_name (Bio::EnsEMBL::GlyphSet::gsv_transcript)
error_track_name (Bio::EnsEMBL::GlyphSet::gsv_variations)
error_track_name (Bio::EnsEMBL::GlyphSet::tsv_transcript)
error_track_name (Bio::EnsEMBL::GlyphSet::tsv_variations)
error_track_name (Bio::EnsEMBL::GlyphSet::_transcript)
error_track_name (Bio::EnsEMBL::GlyphSet::coverage)
escape_quotes
estimated (ExaLead)
estimated (ExaLead::Hits)
evaluate_bp
exalead
excel_lddata
exists (EnsEMBL::Web::TmpFile)
exists (EnsEMBL::Web::Document::Renderer::GzFile)
exists (EnsEMBL::Web::TmpFile::Driver::Disk)
exists (EnsEMBL::Web::TmpFile::Driver::Memcached)
exon_display
exon_information
exons_markup
expand
expanded_init
export
export_configurator (EnsEMBL::Web::Configuration::Location)
export_configurator (EnsEMBL::Web::Configuration::Transcript)
export_configurator (EnsEMBL::Web::Configuration::Gene)
export_feature (Bio::EnsEMBL::GlyphSet::_alignment_multiple)
export_feature (Bio::EnsEMBL::GlyphSet::_clone)
export_feature (Bio::EnsEMBL::GlyphSet::_das)
export_feature (Bio::EnsEMBL::GlyphSet::_oligo)
export_feature (Bio::EnsEMBL::GlyphSet::_prediction_transcript)
export_feature (Bio::EnsEMBL::GlyphSet::_repeat)
export_feature (Bio::EnsEMBL::GlyphSet::_simple)
export_feature (Bio::EnsEMBL::GlyphSet::_transcript)
export_feature (Bio::EnsEMBL::GlyphSet::_variation)
export_feature (Bio::EnsEMBL::GlyphSet::alternative_assembly)
export_feature (Bio::EnsEMBL::GlyphSet::assemblyexception)
export_feature (Bio::EnsEMBL::GlyphSet::fg_regulatory_features)
export_file
export_step1
exportview
extent
extent_anchored_arrow
extent_arrow
extent_box
extent_cross
extent_dot
extent_ex
extent_hidden
extent_line
extent_text
extent_triangle
external_information
extra
extraHTML
extraStyle
extra_buttons
extra_data (EnsEMBL::Web::Interface)
extra_data (EnsEMBL::Web::Text::Feature)
extra_data (EnsEMBL::Web::Text::Feature::GFF)
extra_pop (EnsEMBL::Web::Object::Location)
extra_pop (EnsEMBL::Web::Object::SNP)
extra_pop (EnsEMBL::Web::Object::Variation)
exturl
factory
failure
families
family
family_adaptor
fastCreateObjects (EnsEMBL::Web::Factory)
fastCreateObjects (EnsEMBL::Web::Factory::Location)
fastCreateObjects (EnsEMBL::Web::Factory::Transcript)
fasta
fastaview
feature
featureIDs
featureIds
featureTypes
feature_callback
feature_group (Bio::EnsEMBL::GlyphSet::_alignment)
feature_group (Bio::EnsEMBL::GlyphSet::_blast)
feature_group (Bio::EnsEMBL::GlyphSet::_flat_file)
feature_group (Bio::EnsEMBL::GlyphSet::_oligo)
feature_group (Bio::EnsEMBL::GlyphSet::_user_data)
feature_idlvalue
feature_label (Bio::EnsEMBL::GlyphSet_simple)
feature_label (Bio::EnsEMBL::GlyphSet::sequence)
feature_label (Bio::EnsEMBL::GlyphSet::_alignment)
feature_label (Bio::EnsEMBL::GlyphSet::_clone)
feature_label (Bio::EnsEMBL::GlyphSet::_flat_file)
feature_label (Bio::EnsEMBL::GlyphSet::_oligo)
feature_label (Bio::EnsEMBL::GlyphSet::_qtl)
feature_label (Bio::EnsEMBL::GlyphSet::_simple)
feature_label (Bio::EnsEMBL::GlyphSet::_synteny)
feature_label (Bio::EnsEMBL::GlyphSet::_user_data)
feature_label (Bio::EnsEMBL::GlyphSet::_variation)
feature_label (Bio::EnsEMBL::GlyphSet::alternative_assembly)
feature_label (Bio::EnsEMBL::GlyphSet::annotation_status)
feature_label (Bio::EnsEMBL::GlyphSet::assemblyexception)
feature_length (EnsEMBL::Web::Object::Gene)
feature_length (EnsEMBL::Web::Object::Transcript)
feature_length (EnsEMBL::Web::Object::Translation)
feature_mapped
feature_sets
feature_tables
feature_title (Bio::EnsEMBL::GlyphSet::_alignment)
feature_title (Bio::EnsEMBL::GlyphSet::_blast)
feature_title (Bio::EnsEMBL::GlyphSet::_flat_file)
feature_title (Bio::EnsEMBL::GlyphSet::_oligo)
feature_title (Bio::EnsEMBL::GlyphSet::_user_data)
feature_type (EnsEMBL::Web::Object::Gene)
feature_type (EnsEMBL::Web::Object::Transcript)
feature_type (EnsEMBL::Web::Object::Translation)
feature_typelvalue
feature_types
features (Bio::EnsEMBL::GlyphSet_transcript)
features (Bio::EnsEMBL::GlyphSet_generic)
features (Bio::EnsEMBL::GlyphSet_simple)
features (Bio::EnsEMBL::GlyphSet_transcript)
features (Bio::EnsEMBL::GlyphSet::codonseq)
features (Bio::EnsEMBL::GlyphSet::generic_simple)
features (Bio::EnsEMBL::GlyphSet::generic_simplest)
features (Bio::EnsEMBL::GlyphSet::genetree)
features (Bio::EnsEMBL::GlyphSet::regulatory_regions)
features (Bio::EnsEMBL::GlyphSet::sequence)
features (Bio::EnsEMBL::GlyphSet::_alignment)
features (Bio::EnsEMBL::GlyphSet::_alignment_pairwise)
features (Bio::EnsEMBL::GlyphSet::tagged_snp)
features (Bio::EnsEMBL::GlyphSet::_blast)
features (Bio::EnsEMBL::GlyphSet::_clone)
features (Bio::EnsEMBL::GlyphSet::_das)
features (Bio::EnsEMBL::GlyphSet::_flat_file)
features (Bio::EnsEMBL::GlyphSet::_gene)
features (Bio::EnsEMBL::GlyphSet::urlfeature)
features (Bio::EnsEMBL::GlyphSet::_oligo)
features (Bio::EnsEMBL::GlyphSet::_prediction_transcript)
features (Bio::EnsEMBL::GlyphSet::_qtl)
features (Bio::EnsEMBL::GlyphSet::vegaclones)
features (Bio::EnsEMBL::GlyphSet::_repeat)
features (Bio::EnsEMBL::GlyphSet::_simple)
features (Bio::EnsEMBL::GlyphSet::_synteny)
features (Bio::EnsEMBL::GlyphSet::_tmp_user_data)
features (Bio::EnsEMBL::GlyphSet::_transcript)
features (Bio::EnsEMBL::GlyphSet::_user_data)
features (Bio::EnsEMBL::GlyphSet::_variation)
features (Bio::EnsEMBL::GlyphSet::_transcript)
features (Bio::EnsEMBL::GlyphSet::alternative_assembly)
features (Bio::EnsEMBL::GlyphSet::annotation_status)
features (Bio::EnsEMBL::GlyphSet::assemblyexception)
features (Bio::EnsEMBL::GlyphSet::ensemblclones)
features (Bio::EnsEMBL::GlyphSet::fg_regulatory_features)
features (Bio::EnsEMBL::GlyphSet::regulatory_search_regions)
features (EnsEMBL::Web::Component::DAS)
features (EnsEMBL::Web::Component::Export)
features (EnsEMBL::Web::Component::DAS::Annotation)
features (EnsEMBL::Web::Configuration::DAS)
features (EnsEMBL::Web::Object::Gene)
features_of_type
fertilize_data (EnsEMBL::Web::Data)
fertilize_data (EnsEMBL::Web::Data::Session)
fetch_assembly_segments
fetch_coord_systems
fetch_das_assembly_features
fetch_das_clone_features
fetch_fastaData
fetch_fastaMeta
fetch_features (Bio::EnsEMBL::GlyphSet::_variation)
fetch_features (Bio::EnsEMBL::GlyphSet::fg_regulatory_features)
fetch_features_by_tracktype
fetch_grouped_das_clone_features
fetch_homologues_of_gene_in_species
fetch_homology_species_hash
fetch_index_list
fetch_mfetch_server
fetch_news_items
fetch_pfetch_server
fetch_sorted
fetch_species
fh (EnsEMBL::Web::Document::Renderer)
fh (EnsEMBL::Web::Document::Renderer::Apache)
fh (EnsEMBL::Web::Document::Renderer::File)
fh (EnsEMBL::Web::Document::Renderer::Stdout)
fh (EnsEMBL::Web::Document::Renderer::String)
field
fields
filename
fill
fillcolor
filter
filter_code
filter_module
filter_munged_snps
filter_snps
filters (EnsEMBL::Web::Command)
filters (EnsEMBL::Web::Root)
find
find_administratable_groups
find_all
find_available_anchor_points
find_available_features
find_location (EnsEMBL::Web::Object::SNP)
find_location (EnsEMBL::Web::Object::Variation)
find_methods
find_modules
find_nonadmin_groups
find_user_by_user_id
first (Sanger::Graphics::Glyph::Composite)
first (EnsEMBL::Web::Document::Excel::Content)
first (EnsEMBL::Web::Document::HTML::Content)
first (EnsEMBL::Web::Document::Text::Content)
first (EnsEMBL::Web::Document::TextGz::Content)
first (EnsEMBL::Web::Document::XML::Content)
firstline
fix_session
fixed (Bio::EnsEMBL::GlyphSet::genetree)
fixed (Bio::EnsEMBL::GlyphSet::sequence)
flags
flanking_seq (EnsEMBL::Web::Object::SNP)
flanking_seq (EnsEMBL::Web::Object::Variation)
flat
flush_user (EnsEMBL::Web::OrderedTree)
flush_user (EnsEMBL::Web::OrderedTree::Node)
focus (EnsEMBL::Web::Component::LD)
focus (EnsEMBL::Web::Component::Location::LD)
focus (EnsEMBL::Web::Object::Location)
form (EnsEMBL::Web::ViewConfig)
form (EnsEMBL::Web::Document::Excel::Content)
form (EnsEMBL::Web::Document::HTML::Content)
form (EnsEMBL::Web::Document::Text::Content)
form (EnsEMBL::Web::Document::TextGz::Content)
form (EnsEMBL::Web::Document::XML::Content)
form (EnsEMBL::Web::Form::Element)
form (EnsEMBL::Web::ViewConfig::Export)
form (EnsEMBL::Web::ViewConfig::Gene::Compara_Alignments)
form (EnsEMBL::Web::ViewConfig::Gene::Compara_Ortholog)
form (EnsEMBL::Web::ViewConfig::Gene::Compara_Paralog)
form (EnsEMBL::Web::ViewConfig::Gene::Compara_Tree)
form (EnsEMBL::Web::ViewConfig::Gene::ExternalData)
form (EnsEMBL::Web::ViewConfig::Gene::Family)
form (EnsEMBL::Web::ViewConfig::Gene::Idhistory)
form (EnsEMBL::Web::ViewConfig::Gene::Sequence)
form (EnsEMBL::Web::ViewConfig::geneseqalignview)
form (EnsEMBL::Web::ViewConfig::Gene::Splice)
form (EnsEMBL::Web::ViewConfig::Gene::Summary)
form (EnsEMBL::Web::ViewConfig::Gene::Variation_Gene)
form (EnsEMBL::Web::ViewConfig::Location::Align)
form (EnsEMBL::Web::ViewConfig::Location::AlignSequence)
form (EnsEMBL::Web::ViewConfig::Location::Compara_Alignments)
form (EnsEMBL::Web::ViewConfig::Location::Compara_Compare)
form (EnsEMBL::Web::ViewConfig::dotterview)
form (EnsEMBL::Web::ViewConfig::Location::Genome)
form (EnsEMBL::Web::ViewConfig::Location::LD)
form (EnsEMBL::Web::ViewConfig::Location::Overview)
form (EnsEMBL::Web::ViewConfig::Location::SequenceAlignment)
form (EnsEMBL::Web::ViewConfig::Location::View)
form (EnsEMBL::Web::ViewConfig::Transcript::Exons)
form (EnsEMBL::Web::ViewConfig::Transcript::Idhistory)
form (EnsEMBL::Web::ViewConfig::Transcript::Population)
form (EnsEMBL::Web::ViewConfig::transcriptsnpdataview)
form (EnsEMBL::Web::ViewConfig::Transcript::ProteinSummary)
form (EnsEMBL::Web::ViewConfig::Transcript::Sequence_Protein)
form (EnsEMBL::Web::ViewConfig::Transcript::Sequence_cDNA)
form (EnsEMBL::Web::ViewConfig::Transcript::SupportingEvidence)
form (EnsEMBL::Web::ViewConfig::Variation::Context)
form (EnsEMBL::Web::ViewConfig::ldview)
format (EnsEMBL::Web::Component::Alignment)
format (EnsEMBL::Web::Document::WebPage)
format (EnsEMBL::Web::Text::FeatureParser)
format (Bio::Tools::Run::Search::blat_gfclient)
format (Bio::Tools::Run::Search::ssaha2_client)
format_date (EnsEMBL::Web::Interface)
format_date (EnsEMBL::Web::Form::Element::Date)
format_form
format_frequencies (EnsEMBL::Web::Component::SNP)
format_frequencies (EnsEMBL::Web::Component::Variation)
format_frequencies (EnsEMBL::Web::Component::Variation::PopulationGenotypes)
format_pop
format_time
format_vega_name
formatlvalue
freqs (EnsEMBL::Web::Object::SNP)
freqs (EnsEMBL::Web::Object::Variation)
freqs_hack
full_URL
full_db_tree
full_tree
function (EnsEMBL::Web::Proxiable)
function (EnsEMBL::Web::Proxy)
gcount
gen_1col_group
gen_2col_group
gen_2control_group
gen_4control_group
gen_button_group
gen_check_with_check
gen_check_with_label
gen_check_with_label_and_select
gen_check_with_label_text_and_select
gen_check_with_radio
gen_check_with_radio_group
gen_check_with_select
gen_check_with_select_and_radio
gen_check_with_select_and_text
gen_check_with_select_and_textarea
gen_check_with_select_textarea_and_file
gen_check_with_select_textarea_and_file_and_check
gen_check_with_select_textarea_and_file_snp
gen_check_with_text
gen_check_with_text_and_hidden
gen_check_with_text_and_text
gen_check_with_text_button_and_radio
gen_check_with_textarea
gen_check_with_texts
gen_check_with_two_text
gen_checkbox_group
gen_checkbox_with_label
gen_chrom_start_end_filter
gen_chrom_start_end_filter_lots
gen_experiment_type_group
gen_expression_ontology
gen_feature
gen_gene_ontology
gen_hidden
gen_hidden_list
gen_href
gen_href_tmpl
gen_hyperlink
gen_label
gen_label_and_file
gen_label_with_file
gen_label_with_radiogroup
gen_label_with_select
gen_label_with_text
gen_label_with_text_and_button
gen_label_with_text_and_submit
gen_label_with_textarea
gen_master_jscript
gen_narrow_broad_radios
gen_ontology_filter
gen_proteome_gene_ontology
gen_proteome_region_filter
gen_proteome_sequence_atts
gen_proteome_species
gen_radio_group
gen_radio_group_vertical
gen_radio_group_with_checkbox_group
gen_radio_with_label
gen_radio_with_select
gen_radio_with_select_and_range
gen_radio_with_select_and_range_select
gen_radio_with_two_buttons
gen_radio_with_two_text
gen_select_and_select
gen_select_with_buttons
gen_select_with_text
gen_select_with_text_and_select
gen_seq_type_group
gen_sequence_type_group
gen_sequence_type_snp
gen_snp_filter_group_new
gen_snp_filter_group_original
gen_start_select
gen_tab_group
gen_text_and_submit
gen_text_box_with_info
gen_textarea_file_text_and_radio
gen_textarea_file_text_text_and_radio
gen_warn_placeholder
gene (EnsEMBL::Web::CoreObjects)
gene (EnsEMBL::Web::Object::ArchiveStableId)
gene (EnsEMBL::Web::Object::Gene)
gene (EnsEMBL::Web::Object::Transcript)
gene (EnsEMBL::Web::Object::Translation)
geneSNPViewOptions
gene_acc
gene_adaptor
gene_col
gene_colour (Bio::EnsEMBL::GlyphSet_transcript)
gene_colour (Bio::EnsEMBL::GlyphSet::_transcript)
gene_description (EnsEMBL::Web::Object)
gene_description (EnsEMBL::Web::Object::Translation)
gene_href (Bio::EnsEMBL::GlyphSet_transcript)
gene_href (Bio::EnsEMBL::GlyphSet_transcript)
gene_href (Bio::EnsEMBL::GlyphSet::gsv_transcript)
gene_href (Bio::EnsEMBL::GlyphSet::_transcript)
gene_href (Bio::EnsEMBL::GlyphSet::_transcript)
gene_key
gene_label (Bio::EnsEMBL::GlyphSet)
gene_label (Bio::EnsEMBL::GlyphSet::evega_gene)
gene_links
gene_long_caption
gene_name
gene_short_caption
gene_stat_and_biotype
gene_text_label (Bio::EnsEMBL::GlyphSet_transcript)
gene_text_label (Bio::EnsEMBL::GlyphSet_transcript)
gene_text_label (Bio::EnsEMBL::GlyphSet::_transcript)
gene_text_label (Bio::EnsEMBL::GlyphSet::_transcript)
gene_title (Bio::EnsEMBL::GlyphSet_transcript)
gene_title (Bio::EnsEMBL::GlyphSet_transcript)
gene_type (EnsEMBL::Web::Object::Gene)
gene_type (EnsEMBL::Web::Object::Transcript)
gene_type (EnsEMBL::Web::Object::Translation)
gene_zmenu (Bio::EnsEMBL::GlyphSet_transcript)
gene_zmenu (Bio::EnsEMBL::GlyphSet::_transcript)
generateHTML
generate_dotter_bin_file
generate_html
generate_query_hash (EnsEMBL::Web::Object::Gene)
generate_query_hash (EnsEMBL::Web::Object::Location)
generate_query_hash (EnsEMBL::Web::Object::MultipleLocation)
generate_query_hash (EnsEMBL::Web::Object::SNP)
generate_query_hash (EnsEMBL::Web::Object::Transcript)
generate_query_hash (EnsEMBL::Web::Object::Variation)
generate_query_url
generate_rows
generic_items
generic_search (EnsEMBL::Web::Factory::Search::AltaVista)
generic_search (EnsEMBL::Web::Factory::Search::Exalead)
geneseqalignview
geneseqview
genetic_variation
genetic_variation_values
genome_locations
get (Sanger::Graphics::WebUserConfig)
get (EnsEMBL::Web::Cache)
get (EnsEMBL::Web::ViewConfig)
get (EnsEMBL::Web::Document::HTML::Title)
get (EnsEMBL::Web::Input::Options)
get (EnsEMBL::Web::Input::Parameters)
get (EnsEMBL::Web::OrderedTree::Node)
get (EnsEMBL::Web::TmpFile::Driver::Disk)
get (EnsEMBL::Web::TmpFile::Driver::Memcached)
getAllelesConsequencesOnSlice
getConfigs
getCoordinateSystem
getEnsemblMapping (EnsEMBL::Web::Factory::DASCollection)
getEnsemblMapping (EnsEMBL::Web::Object::DASCollection)
getFakeMungedVariationFeatures
getFakeMungedVariationsOnSlice
getHighlighted (ExaLead::TextSeg)
getHighlighted (ExaLead::Value)
getHits
getImageConfig
getParts
getRegistrySources (EnsEMBL::Web::Factory::DASCollection)
getRegistrySources (EnsEMBL::Web::Object::DASCollection)
getServerSources
getSourceData
getString (ExaLead::TextSeg)
getString (ExaLead::Value)
getVariationFeatures
getVariationsOnSlice (EnsEMBL::Web::Object::Gene)
getVariationsOnSlice (EnsEMBL::Web::Object::Location)
getViewConfig
get_DASAdaptor_attributes_by_method
get_DASCollection (EnsEMBL::Web::Object)
get_DASCollection (EnsEMBL::Web::Object::DASCollection)
get_DASSeqFeatures_by_source_name
get_DBAdaptor
get_ExtURL
get_ExtURL_link
get_ImageConfig
get_ProteinTree
get_Slice (EnsEMBL::Web::Object::Gene)
get_Slice (EnsEMBL::Web::Object::Transcript)
get_Slice (EnsEMBL::Web::Object::Translation)
get_adaptor (EnsEMBL::Web::Object)
get_adaptor (EnsEMBL::Web::Object::Chromosome)
get_alignment (EnsEMBL::Web::Object::Alignment)
get_alignment (EnsEMBL::Web::Object::Transcript)
get_alignments
get_all_ProteinFeatures
get_all_associated_archived (EnsEMBL::Web::Object::ArchiveStableId)
get_all_associated_archived (EnsEMBL::Web::Object::Gene)
get_all_das (EnsEMBL::Web::Registry)
get_all_das (EnsEMBL::Web::Session)
get_all_das (EnsEMBL::Web::SpeciesDefs)
get_all_das (EnsEMBL::Web::Data::User)
get_all_families
get_all_fields
get_all_genotypes
get_all_misc_sets
get_all_packed_files
get_all_species
get_all_tracks
get_all_transcripts
get_alternative_locations (EnsEMBL::Web::Object::Gene)
get_alternative_locations (EnsEMBL::Web::Object::Transcript)
get_alternative_locations (EnsEMBL::Web::Object::Translation)
get_archive_object (EnsEMBL::Web::Object::Gene)
get_archive_object (EnsEMBL::Web::Object::Transcript)
get_archive_object (EnsEMBL::Web::Object::Translation)
get_archive_redirect
get_assemblies
get_assoc
get_author_email (EnsEMBL::Web::Object::Transcript)
get_author_email (EnsEMBL::Web::Object::Translation)
get_author_name (EnsEMBL::Web::Object::Gene)
get_author_name (EnsEMBL::Web::Object::Transcript)
get_author_name (EnsEMBL::Web::Object::Translation)
get_block_features (Bio::EnsEMBL::GlyphSet::ctcf)
get_block_features (Bio::EnsEMBL::GlyphSet::histone_modifications)
get_by_type
get_cached
get_cached_data
get_cgi_name
get_colours (Bio::EnsEMBL::GlyphSet_simple)
get_colours (Bio::EnsEMBL::GlyphSet::_clone)
get_colours (Bio::EnsEMBL::GlyphSet::_synteny)
get_compara_Member
get_config (EnsEMBL::Web::SpeciesDefs)
get_config (EnsEMBL::Web::BlastView::Tool)
get_config (EnsEMBL::Web::Data::Session)
get_contig_location (EnsEMBL::Web::Object::Gene)
get_contig_location (EnsEMBL::Web::Object::Transcript)
get_contig_location (EnsEMBL::Web::Object::Translation)
get_das_by_logic_name
get_das_factories (EnsEMBL::Web::Object::Gene)
get_das_factories (EnsEMBL::Web::Object::Translation)
get_das_feature_by_id
get_das_features
get_das_features_by_name (EnsEMBL::Web::Object::Gene)
get_das_features_by_name (EnsEMBL::Web::Object::Translation)
get_das_features_by_slice (EnsEMBL::Web::Object::Gene)
get_das_features_by_slice (EnsEMBL::Web::Object::Translation)
get_das_parser
get_das_servers
get_das_sources
get_data
get_database_matches (EnsEMBL::Web::Object::Gene)
get_database_matches (EnsEMBL::Web::Object::Transcript)
get_database_matches (EnsEMBL::Web::Object::Translation)
get_databases (EnsEMBL::Web::Proxiable)
get_databases (EnsEMBL::Web::DBSQL::DBConnection)
get_databases_species
get_date
get_db (EnsEMBL::Web::Object::Gene)
get_db (EnsEMBL::Web::Object::Transcript)
get_db (EnsEMBL::Web::Object::Translation)
get_default_pop_name (EnsEMBL::Web::Object::Location)
get_default_pop_name (EnsEMBL::Web::Object::SNP)
get_default_pop_name (EnsEMBL::Web::Object::Variation)
get_defaults
get_disease_matches
get_domain_genes
get_entry_result
get_exon
get_ext_seq
get_external_data
get_external_dbs
get_external_id
get_extra
get_families
get_family_links
get_family_object
get_faminfo
get_feature_sets
get_featuredata
get_featurestyle
get_fg_db
get_first_header
get_font_details
get_form
get_form_label
get_format (EnsEMBL::Web::Configuration::Location)
get_format (EnsEMBL::Web::Text::FeatureParser)
get_gd_simple
get_gd_text
get_gene_length
get_gene_slices
get_gene_supporting_evidence
get_geneinfo
get_genes (EnsEMBL::Web::Object::SNP)
get_genes (EnsEMBL::Web::Object::Variation)
get_genotyped_VariationFeatures
get_genotyped_VariationsOnSlice
get_go_list
get_hit
get_homologous_gene_ids (Bio::EnsEMBL::GlyphSet_transcript)
get_homologous_gene_ids (Bio::EnsEMBL::GlyphSet_transcript)
get_homologous_peptide_ids (Bio::EnsEMBL::GlyphSet_transcript)
get_homologous_peptide_ids (Bio::EnsEMBL::GlyphSet_transcript)
get_homologous_peptide_ids_from_gene (Bio::EnsEMBL::GlyphSet_transcript)
get_homologous_peptide_ids_from_gene (Bio::EnsEMBL::GlyphSet_transcript)
get_homology_matches
get_imageconfig
get_indexer
get_individuals
get_individuals_pops (EnsEMBL::Web::Object::SNP)
get_individuals_pops (EnsEMBL::Web::Object::Variation)
get_info
get_int_seq
get_interpro
get_interpro_links
get_interpro_object
get_key
get_latest_incarnation (EnsEMBL::Web::Object::ArchiveStableId)
get_latest_incarnation (EnsEMBL::Web::Object::Gene)
get_latest_incarnation (EnsEMBL::Web::Object::Transcript)
get_lookup_values (EnsEMBL::Web::Data)
get_lookup_values (EnsEMBL::Web::Data::NewsCategory)
get_lookup_values (EnsEMBL::Web::Data::Species)
get_markedup_trans_seq
get_meta_index
get_meta_navigation
get_meta_order
get_munged_slice (EnsEMBL::Web::Object::Gene)
get_munged_slice (EnsEMBL::Web::Object::Transcript)
get_node (EnsEMBL::Web::Configuration)
get_node (EnsEMBL::Web::ImageConfig)
get_node (EnsEMBL::Web::OrderedTree)
get_node (EnsEMBL::Web::OrderedTree::Node)
get_page_data
get_panel_warning
get_parameter (Bio::EnsEMBL::GlyphSet)
get_parameter (Sanger::Graphics::WebUserConfig)
get_parameter (EnsEMBL::Web::ImageConfig)
get_parameters
get_params
get_pep_seq
get_pepstats
get_peptide
get_prediction_method (EnsEMBL::Web::Object::Transcript)
get_prediction_method (EnsEMBL::Web::Object::Translation)
get_primary_key
get_problem_type (EnsEMBL::Web::Proxiable)
get_problem_type (EnsEMBL::Web::Proxy)
get_projections
get_protein_domains
get_redirect
get_row
get_samples
get_seq_by_acc (EnsEMBL::Web::ExtIndex)
get_seq_by_acc (EnsEMBL::Web::ExtIndex::EFETCH)
get_seq_by_acc (EnsEMBL::Web::ExtIndex::MFETCH)
get_seq_by_acc (EnsEMBL::Web::ExtIndex::NULL)
get_seq_by_acc (EnsEMBL::Web::ExtIndex::PFETCH)
get_seq_by_acc (EnsEMBL::Web::ExtIndex::SRS)
get_seq_by_acc (EnsEMBL::Web::ExtIndex::WEBSRS)
get_seq_by_acc (EnsEMBL::Web::ExtIndex::bioperl)
get_seq_by_acc (EnsEMBL::Web::ExtIndex::biosql)
get_seq_by_id (EnsEMBL::Web::ExtIndex)
get_seq_by_id (EnsEMBL::Web::ExtIndex::EFETCH)
get_seq_by_id (EnsEMBL::Web::ExtIndex::ENSEMBL_RETRIEVE)
get_seq_by_id (EnsEMBL::Web::ExtIndex::MFETCH)
get_seq_by_id (EnsEMBL::Web::ExtIndex::NULL)
get_seq_by_id (EnsEMBL::Web::ExtIndex::PFETCH)
get_seq_by_id (EnsEMBL::Web::ExtIndex::SRS)
get_seq_by_id (EnsEMBL::Web::ExtIndex::WEBSRS)
get_seq_by_id (EnsEMBL::Web::ExtIndex::bioperl)
get_seq_by_id (EnsEMBL::Web::ExtIndex::biosql)
get_sequence_data (EnsEMBL::Web::Component)
get_sequence_data (EnsEMBL::Web::Component::Transcript::ProteinSeq)
get_sequence_data (EnsEMBL::Web::Component::Transcript::TranscriptSeq)
get_sequence_data (EnsEMBL::Web::Component::Variation::Compara_Alignments)
get_session
get_sf_hit_db_name
get_similarity_hash (EnsEMBL::Web::Object::Gene)
get_similarity_hash (EnsEMBL::Web::Object::Transcript)
get_similarity_hash (EnsEMBL::Web::Object::Translation)
get_site
get_slice_object
get_slice_table
get_slices
get_snp
get_snps
get_source (EnsEMBL::Web::Object::Gene)
get_source (EnsEMBL::Web::Object::Location)
get_source (EnsEMBL::Web::Object::SNP)
get_source (EnsEMBL::Web::Object::Transcript)
get_source (EnsEMBL::Web::Object::Variation)
get_sources
get_status
get_supporting_evidence
get_synonyms
get_synteny_local_genes (EnsEMBL::Web::Object::Chromosome)
get_synteny_local_genes (EnsEMBL::Web::Object::Location)
get_synteny_matches (EnsEMBL::Web::Object::Chromosome)
get_synteny_matches (EnsEMBL::Web::Object::Location)
get_synteny_nav
get_table_size
get_text_simple
get_text_width
get_textheight
get_title
get_track_key
get_trans_seq
get_transcript_Slice
get_transcript_object
get_transcript_slices
get_url
get_url_content
get_url_filesize
get_user_id
get_user_settings (EnsEMBL::Web::ImageConfig)
get_user_settings (EnsEMBL::Web::ViewConfig)
get_valid
get_value
get_values
get_variation_features (EnsEMBL::Web::Object::Location)
get_variation_features (EnsEMBL::Web::Object::SNP)
get_variation_features (EnsEMBL::Web::Object::Variation)
get_view_config_as_string
get_viewconfig
glob_bp
global_context (EnsEMBL::Web::Configuration::Blast)
global_context (EnsEMBL::Web::Configuration::Help)
global_context (EnsEMBL::Web::Configuration::Info)
global_context (EnsEMBL::Web::Configuration::Location)
global_context (EnsEMBL::Web::Configuration::SNP)
global_context (EnsEMBL::Web::Configuration::Search)
global_context (EnsEMBL::Web::Configuration::Server)
global_context (EnsEMBL::Web::Configuration::Transcript)
global_context (EnsEMBL::Web::Configuration::UniSearch)
global_context (EnsEMBL::Web::Configuration::UserData)
global_context (EnsEMBL::Web::Configuration::Variation)
global_context (EnsEMBL::Web::Configuration::Gene)
global_context (EnsEMBL::Web::Configuration::Account)
glossary
glyph_anchored_arrow
glyph_arrow
glyph_box
glyph_cross
glyph_dot
glyph_ex
glyph_hidden
glyph_line
glyph_primers
glyph_span
glyph_text
glyph_toomany
glyph_triangle
glyphs (Sanger::Graphics::GlyphSet)
glyphs (Sanger::Graphics::Glyph::Composite)
glyphset_configs
glyphsets (Bio::EnsEMBL::DrawableContainer)
glyphsets (Bio::EnsEMBL::VDrawableContainer)
glyphsets (Sanger::Graphics::DrawableContainer)
glyphsets (Sanger::Graphics::GlyphSetManager)
glyphsets (Sanger::Graphics::VDrawableContainer)
gmenu
goview
groupIDs
group_members
group_notes
groups (EnsEMBL::Web::Data::User)
groups (EnsEMBL::Web::Document::WebPage)
groups (ExaLead)
groups (ExaLead::Hit)
hack
hack_escape
handler (EnsEMBL::Web::Apache::Error)
handler (EnsEMBL::Web::Apache::Rss)
handler (EnsEMBL::Web::Apache::SendDecPage)
handler (EnsEMBL::Web::Apache::ServerError)
handler (EnsEMBL::Web::Apache::Static)
haploview_dump
haploview_files (EnsEMBL::Web::Component::LDtable)
haploview_files (EnsEMBL::Web::Configuration::Location)
has_a (EnsEMBL::Web::Data)
has_a (EnsEMBL::Web::DBSQL::MySQLAdaptor)
has_a_problem (EnsEMBL::Web::Proxiable)
has_a_problem (EnsEMBL::Web::Proxy)
has_a_problem (EnsEMBL::Web::Document::WebPage)
has_fatal_error
has_fatal_problem (EnsEMBL::Web::Proxiable)
has_fatal_problem (EnsEMBL::Web::Proxy)
has_fatal_problem (EnsEMBL::Web::Document::WebPage)
has_form
has_image_config
has_image_configs
has_images
has_many
has_non_fatal_error
has_problem_type (EnsEMBL::Web::Proxiable)
has_problem_type (EnsEMBL::Web::Proxy)
has_problem_type (EnsEMBL::Web::Document::WebPage)
head_elements
head_order
headerParserHandler
height (Sanger::Graphics::GlyphSet)
height (Sanger::Graphics::TextHelper)
height (Sanger::Graphics::Glyph::Circle)
height (Sanger::Graphics::Glyph::Poly)
height (EnsEMBL::Web::Document::HTML::Logo)
height (EnsEMBL::Web::Form::Element)
help_feedback
hend (EnsEMBL::Web::Text::Feature)
hend (EnsEMBL::Web::Text::Feature::GFF)
hend (EnsEMBL::Web::Text::Feature::PSL)
hex_by_name
hex_by_rgb
hidden_label
hide
highlight (Bio::EnsEMBL::GlyphSet_simple)
highlight (Bio::EnsEMBL::GlyphSet::_variation)
highlight_bowtie
highlight_box
highlight_display
highlight_filledwidebox
highlight_labelline
highlight_lharrow
highlight_lhbox
highlight_outbox
highlight_rharrow
highlight_rhbox
highlight_strandedbox
highlight_text
highlight_widebox
highlight_wideline
highlights (Sanger::Graphics::GlyphSet)
highlights (EnsEMBL::Web::Object)
highlights_string
history (EnsEMBL::Web::Object::ArchiveStableId)
history (EnsEMBL::Web::Object::Gene)
history (EnsEMBL::Web::Object::Transcript)
history (EnsEMBL::Web::Object::Translation)
history_fields
history_info
historypanel
historyview
hit_type
hits (EnsEMBL::Web::Container::HSPContainer)
hits (ExaLead)
hls (EnsEMBL::Web::Component::Server)
hls (EnsEMBL::Web::Component::Server::ColourMap)
home_url (EnsEMBL::Web::Document::HTML)
home_url (EnsEMBL::Web::Document::HTML::HomeSearch)
honeypots
href (Bio::EnsEMBL::GlyphSet_transcript)
href (Bio::EnsEMBL::GlyphSet_simple)
href (Bio::EnsEMBL::GlyphSet_transcript)
href (Bio::EnsEMBL::GlyphSet::HSP_plot)
href (Bio::EnsEMBL::GlyphSet::generic_simple)
href (Bio::EnsEMBL::GlyphSet::generic_simplest)
href (Bio::EnsEMBL::GlyphSet::gsv_transcript)
href (Bio::EnsEMBL::GlyphSet::regulatory_regions)
href (Bio::EnsEMBL::GlyphSet::sequence)
href (Bio::EnsEMBL::GlyphSet::snp_fake)
href (Bio::EnsEMBL::GlyphSet::_alignment)
href (Bio::EnsEMBL::GlyphSet::_blast)
href (Bio::EnsEMBL::GlyphSet::_clone)
href (Bio::EnsEMBL::GlyphSet::tsv_transcript)
href (Bio::EnsEMBL::GlyphSet::_flat_file)
href (Bio::EnsEMBL::GlyphSet::urlfeature)
href (Bio::EnsEMBL::GlyphSet::_oligo)
href (Bio::EnsEMBL::GlyphSet::_prediction_transcript)
href (Bio::EnsEMBL::GlyphSet::_qtl)
href (Bio::EnsEMBL::GlyphSet::vegaclones)
href (Bio::EnsEMBL::GlyphSet::_simple)
href (Bio::EnsEMBL::GlyphSet::_synteny)
href (Bio::EnsEMBL::GlyphSet::_transcript)
href (Bio::EnsEMBL::GlyphSet::_user_data)
href (Bio::EnsEMBL::GlyphSet::_variation)
href (Bio::EnsEMBL::GlyphSet::_transcript)
href (Bio::EnsEMBL::GlyphSet::alternative_assembly)
href (Bio::EnsEMBL::GlyphSet::annotation_status)
href (Bio::EnsEMBL::GlyphSet::assemblyexception)
href (Bio::EnsEMBL::GlyphSet::ensemblclones)
href (Bio::EnsEMBL::GlyphSet::fg_regulatory_features)
href (Bio::EnsEMBL::GlyphSet::regulatory_search_regions)
href (EnsEMBL::Web::Document::HTML::Logo)
hsp
hsps
hstart (EnsEMBL::Web::Text::Feature)
hstart (EnsEMBL::Web::Text::Feature::GFF)
hstart (EnsEMBL::Web::Text::Feature::PSL)
hstrand (EnsEMBL::Web::Text::Feature)
hstrand (EnsEMBL::Web::Text::Feature::GFF)
hstrand (EnsEMBL::Web::Text::Feature::PSL)
html (EnsEMBL::Web::Document::Panel::Fragment)
html (EnsEMBL::Web::Document::Panel::InformationFragment)
html_collapse_expand_control
html_footer (EnsEMBL::Web::Document::Panel::Fragment)
html_footer (EnsEMBL::Web::Tools::DocumentView)
html_header (EnsEMBL::Web::Document::Panel::Fragment)
html_header (EnsEMBL::Web::Tools::DocumentView)
html_lddata
html_line
html_loading_status
human_readable
hybrid
id (EnsEMBL::Web::Component::Sequence)
id (EnsEMBL::Web::Form::Element)
id (EnsEMBL::Web::Text::Feature)
id (EnsEMBL::Web::Text::Feature::BED)
id (EnsEMBL::Web::Text::Feature::DAS)
id (EnsEMBL::Web::Text::Feature::GBrowse)
id (EnsEMBL::Web::Text::Feature::GFF)
id (EnsEMBL::Web::Text::Feature::PSL)
id (EnsEMBL::Web::Text::Feature::WIG)
id (EnsEMBL::Web::Text::Feature::generic)
id_by_name
identifier (EnsEMBL::Web::Tools::Document)
identifier (EnsEMBL::Web::Tools::Document::Module)
ideogram
ideogram_old
idhistoryview
image (EnsEMBL::Web::Component::Translation)
image (EnsEMBL::Web::Document::HTML::Logo)
image_config_hash
image_configs
image_height (Sanger::Graphics::WebUserConfig)
image_height (EnsEMBL::Web::ImageConfig)
image_idlvalue
image_label (Bio::EnsEMBL::GlyphSet::genetree)
image_label (Bio::EnsEMBL::GlyphSet::vegaclones)
image_label (Bio::EnsEMBL::GlyphSet::_repeat)
image_label (Bio::EnsEMBL::GlyphSet::ensemblclones)
image_namelvalue
image_typelvalue
image_width (Bio::EnsEMBL::GlyphSet)
image_width (Sanger::Graphics::WebUserConfig)
image_width (EnsEMBL::Web::Component)
image_width (EnsEMBL::Web::ImageConfig)
image_width (EnsEMBL::Web::Document::Image)
imagemaplvalue
img_url
import (EnsEMBL::Web::DBSQL::UserDBConnection)
import (EnsEMBL::Web::DBSQL::WebDBConnection)
in_error
in_release
include
include_javascript
include_navigation
include_stylesheet
incr
index
individual (EnsEMBL::Web::Component::SNP)
individual (EnsEMBL::Web::Component::Variation)
individual_description (EnsEMBL::Web::Object::SNP)
individual_description (EnsEMBL::Web::Object::Variation)
individual_genotype (EnsEMBL::Web::Object::SNP)
individual_genotype (EnsEMBL::Web::Object::Variation)
individual_genotypes
individual_genotypes_obj (EnsEMBL::Web::Object::SNP)
individual_genotypes_obj (EnsEMBL::Web::Object::Variation)
individual_table (EnsEMBL::Web::Object::SNP)
individual_table (EnsEMBL::Web::Object::Variation)
individuals_options_form
info
information
ingredient
inheritance
init (EnsEMBL::Web::ImageConfig::Vblastview)
init (EnsEMBL::Web::ImageConfig::Vkar2view)
init (EnsEMBL::Web::ImageConfig::Vkaryoblast)
init (EnsEMBL::Web::ImageConfig::Vkaryotype)
init (EnsEMBL::Web::ImageConfig::Vkaryotype2)
init (EnsEMBL::Web::ImageConfig::Vmap2view)
init (EnsEMBL::Web::ImageConfig::Vmapview)
init (EnsEMBL::Web::ImageConfig::Vsynteny)
init (EnsEMBL::Web::ImageConfig::alignsliceviewbottom)
init (EnsEMBL::Web::ImageConfig::alignsliceviewtop)
init (EnsEMBL::Web::ImageConfig::chromosome)
init (EnsEMBL::Web::ImageConfig::contigviewbottom)
init (EnsEMBL::Web::ImageConfig::contigviewtop)
init (EnsEMBL::Web::ImageConfig::cytoview)
init (EnsEMBL::Web::ImageConfig::fake)
init (EnsEMBL::Web::ImageConfig::gene_summary)
init (EnsEMBL::Web::ImageConfig::generegview)
init (EnsEMBL::Web::ImageConfig::genesnpview_context)
init (EnsEMBL::Web::ImageConfig::genesnpview_gene)
init (EnsEMBL::Web::ImageConfig::genesnpview_snps)
init (EnsEMBL::Web::ImageConfig::genesnpview_transcript)
init (EnsEMBL::Web::ImageConfig::genesnpview_transcripts_bottom)
init (EnsEMBL::Web::ImageConfig::genesnpview_transcripts_top)
init (EnsEMBL::Web::ImageConfig::genetreeview)
init (EnsEMBL::Web::ImageConfig::geneview)
init (EnsEMBL::Web::ImageConfig::hsp_query_plot)
init (EnsEMBL::Web::ImageConfig::idhistoryview)
init (EnsEMBL::Web::ImageConfig::ld_population)
init (EnsEMBL::Web::ImageConfig::ldview)
init (EnsEMBL::Web::ImageConfig::primerview)
init (EnsEMBL::Web::ImageConfig::protview)
init (EnsEMBL::Web::ImageConfig::single_transcript)
init (EnsEMBL::Web::ImageConfig::snpview)
init (EnsEMBL::Web::ImageConfig::supporting_evidence_transcript)
init (EnsEMBL::Web::ImageConfig::thjviewbottom)
init (EnsEMBL::Web::ImageConfig::thjviewchrom)
init (EnsEMBL::Web::ImageConfig::thjviewtop)
init (EnsEMBL::Web::ImageConfig::transview)
init (EnsEMBL::Web::ImageConfig::tsv_context)
init (EnsEMBL::Web::ImageConfig::tsv_sampletranscript)
init (EnsEMBL::Web::ImageConfig::tsv_transcript)
init (EnsEMBL::Web::ImageConfig::tsv_transcripts_bottom)
init (EnsEMBL::Web::ImageConfig::tsv_transcripts_top)
init (EnsEMBL::Web::Text::FeatureParser)
init (EnsEMBL::Web::ViewConfig::Export)
init (EnsEMBL::Web::ViewConfig::familyview)
init (EnsEMBL::Web::ViewConfig::idhistoryview)
init (EnsEMBL::Web::ViewConfig::sequencealignview)
init (EnsEMBL::Web::ViewConfig::status)
init (EnsEMBL::Web::ViewConfig::Gene::Compara_Alignments)
init (EnsEMBL::Web::ViewConfig::Gene::Compara_Ortholog)
init (EnsEMBL::Web::ViewConfig::Gene::Compara_Paralog)
init (EnsEMBL::Web::ViewConfig::Gene::Compara_Tree)
init (EnsEMBL::Web::ViewConfig::Gene::ExternalData)
init (EnsEMBL::Web::ViewConfig::Gene::Family)
init (EnsEMBL::Web::ViewConfig::Gene::Idhistory)
init (EnsEMBL::Web::ViewConfig::Gene::Regulation)
init (EnsEMBL::Web::ViewConfig::Gene::Sequence)
init (EnsEMBL::Web::ViewConfig::geneseqalignview)
init (EnsEMBL::Web::ViewConfig::Gene::Splice)
init (EnsEMBL::Web::ViewConfig::Gene::Summary)
init (EnsEMBL::Web::ViewConfig::Gene::Variation_Gene)
init (EnsEMBL::Web::ViewConfig::Location::Align)
init (EnsEMBL::Web::ViewConfig::Location::AlignSequence)
init (EnsEMBL::Web::ViewConfig::Location::Compara_Alignments)
init (EnsEMBL::Web::ViewConfig::Location::Compara_Compare)
init (EnsEMBL::Web::ViewConfig::dotterview)
init (EnsEMBL::Web::ViewConfig::Location::Genome)
init (EnsEMBL::Web::ViewConfig::Location::LD)
init (EnsEMBL::Web::ViewConfig::Location::Overview)
init (EnsEMBL::Web::ViewConfig::Location::SequenceAlignment)
init (EnsEMBL::Web::ViewConfig::Location::View)
init (EnsEMBL::Web::ViewConfig::Transcript::Exons)
init (EnsEMBL::Web::ViewConfig::Transcript::Idhistory)
init (EnsEMBL::Web::ViewConfig::Transcript::Population)
init (EnsEMBL::Web::ViewConfig::transcriptsnpdataview)
init (EnsEMBL::Web::ViewConfig::Transcript::ProteinSummary)
init (EnsEMBL::Web::ViewConfig::Transcript::Sequence_Protein)
init (EnsEMBL::Web::ViewConfig::Transcript::Sequence_cDNA)
init (EnsEMBL::Web::ViewConfig::Transcript::SupportingEvidence)
init (EnsEMBL::Web::ViewConfig::Variation::Context)
init (EnsEMBL::Web::ViewConfig::ldview)
init_canvas (Bio::EnsEMBL::VRenderer::gif)
init_canvas (Bio::EnsEMBL::VRenderer::imagemap)
init_canvas (Bio::EnsEMBL::VRenderer::png)
init_canvas (Sanger::Graphics::Renderer::eps)
init_canvas (Sanger::Graphics::Renderer::gif)
init_canvas (Sanger::Graphics::Renderer::imagemap)
init_canvas (Sanger::Graphics::Renderer::pdf)
init_canvas (Sanger::Graphics::Renderer::png)
init_canvas (Sanger::Graphics::Renderer::postscript)
init_canvas (Sanger::Graphics::Renderer::svg)
init_canvas (Sanger::Graphics::Renderer::test)
init_canvas (Sanger::Graphics::Renderer::wmf)
init_label (Bio::EnsEMBL::GlyphSet)
init_label (Bio::EnsEMBL::GlyphSet::text)
init_label (Sanger::Graphics::GlyphSet::generic_das_feature)
init_label (Sanger::Graphics::GlyphSet::ruler)
init_user
initialise_parameters
initialize_session
initialize_user
input (EnsEMBL::Web::Proxiable)
input (EnsEMBL::Web::Session)
input_param
insert_blessed
interface
interface_panel
intersect (Bio::EnsEMBL::GlyphSet::ld)
intersect (Bio::EnsEMBL::GlyphSet::ld2)
interval (Bio::EnsEMBL::GlyphSet::HSP_scalebar)
interval (Bio::EnsEMBL::GlyphSet::scalebar)
interval (Bio::EnsEMBL::GlyphSet::alignscalebar)
interval (Sanger::Graphics::GlyphSet::scalebar)
intro
introduction
introductionlvalue
invalidate_cache (EnsEMBL::Web::Data)
invalidate_cache (EnsEMBL::Web::Data::Group)
invalidate_cache (EnsEMBL::Web::Data::Membership)
invalidate_cache (EnsEMBL::Web::Data::Record)
invalidate_cache (EnsEMBL::Web::Data::Session)
invalidate_cache (EnsEMBL::Web::Data::User)
isFatal
isMappedId
isMultipleMatches
isNoMatch
isNonFatal
isRedirect
is_administrator_of
is_all_asynchronous
is_altered
is_ancestor_of
is_asynchronous (EnsEMBL::Web::Document::Panel)
is_asynchronous (EnsEMBL::Web::Document::Panel::Fragment)
is_available (EnsEMBL::Web::Root)
is_available (EnsEMBL::Web::BlastView::Meta)
is_available_artefact
is_child_of
is_configurable (EnsEMBL::Web::Component::UserData)
is_configurable (EnsEMBL::Web::Configuration::UserData)
is_current
is_defined
is_deleted
is_descendant_of
is_external
is_golden_path
is_group
is_leaf
is_linked
is_member_of
is_on
is_option
is_parent_of
is_queriable
is_session
is_user
is_valid_module_name
iterator
job_with_ticket
jobs_with_status
join_tag
js_init
js_menu
js_menu_div
js_menu_header
js_popup
js_tooltip
js_tooltip_div
js_tooltip_header
json
json_components
json_options
json_params
karyotype
key
keywords (EnsEMBL::Web::Tools::Document)
keywords (EnsEMBL::Web::Tools::Document::Module)
keywords (ExaLead)
kw_hilite
label (Sanger::Graphics::GlyphSet)
label (Sanger::Graphics::GlyphSetManager)
label (EnsEMBL::Web::Form::Element)
label (EnsEMBL::Web::Interface::Element)
label2
last (Sanger::Graphics::Glyph::Composite)
last (ExaLead)
last (ExaLead::Hits)
last_inserted_id
latest_version
layout
ld_data (EnsEMBL::Web::Component::SNP)
ld_data (EnsEMBL::Web::Component::Variation)
ld_dump
ld_export_configurator
ld_for_slice
ld_pops_for_snp (EnsEMBL::Web::Object::SNP)
ld_pops_for_snp (EnsEMBL::Web::Object::Variation)
ld_values (EnsEMBL::Web::Component::LDtable)
ld_values (EnsEMBL::Web::Component::Location)
ldview_image
ldview_image_menu
ldview_nav
ldview_noimage
leaf_codes
leaves (EnsEMBL::Web::OrderedTree)
leaves (EnsEMBL::Web::OrderedTree::Node)
left
legend (Bio::EnsEMBL::GlyphSet)
legend (Bio::EnsEMBL::GlyphSet::_gene)
legend (Bio::EnsEMBL::GlyphSet::_transcript)
legend (Bio::EnsEMBL::GlyphSet::_transcript)
legend (Bio::EnsEMBL::GlyphSet::evega_gene)
legend (EnsEMBL::Web::Form::FieldSet)
length (Sanger::Graphics::GlyphSet)
length (EnsEMBL::Web::Container::HSPContainer)
length (EnsEMBL::Web::Object::Chromosome)
length (EnsEMBL::Web::Object::Location)
length (EnsEMBL::Web::Object::MultipleLocation)
level
library
line
line_numbering
lines
linestyle
link (Sanger::Graphics::GlyphSet::generic_das_feature)
link (EnsEMBL::Web::Text::Feature)
link (EnsEMBL::Web::Text::Feature::GBrowse)
link (ExaLead::Category)
link (ExaLead::Group)
link (ExaLead::HitCategory)
link (ExaLead::HitGroup)
link (ExaLead::Keyword)
link_for_method
link_for_package
link_to_ldview (EnsEMBL::Web::Component::SNP)
link_to_ldview (EnsEMBL::Web::Component::Variation)
link_to_ldview (EnsEMBL::Web::Component::Variation::VariationSummary)
links (ExaLead::Category)
links (ExaLead::Group)
links (ExaLead::HitCategory)
links (ExaLead::HitGroup)
links (ExaLead::Keyword)
load
load_asynchronously
load_configuration
load_configured_das
load_genes
load_tracks
load_user_tracks
load_user_vert_tracks
loading_animation
loc
local_context (EnsEMBL::Web::Configuration::Blast)
local_context (EnsEMBL::Web::Configuration::Help)
local_context (EnsEMBL::Web::Configuration::Info)
local_context (EnsEMBL::Web::Configuration::Location)
local_context (EnsEMBL::Web::Configuration::SNP)
local_context (EnsEMBL::Web::Configuration::Search)
local_context (EnsEMBL::Web::Configuration::Server)
local_context (EnsEMBL::Web::Configuration::Transcript)
local_context (EnsEMBL::Web::Configuration::UniSearch)
local_context (EnsEMBL::Web::Configuration::UserData)
local_context (EnsEMBL::Web::Configuration::Variation)
local_context (EnsEMBL::Web::Configuration::Gene)
local_context (EnsEMBL::Web::Configuration::Account)
local_tools (EnsEMBL::Web::Configuration::Blast)
local_tools (EnsEMBL::Web::Configuration::Help)
local_tools (EnsEMBL::Web::Configuration::Info)
local_tools (EnsEMBL::Web::Configuration::Location)
local_tools (EnsEMBL::Web::Configuration::Search)
local_tools (EnsEMBL::Web::Configuration::Server)
local_tools (EnsEMBL::Web::Configuration::Transcript)
local_tools (EnsEMBL::Web::Configuration::UniSearch)
local_tools (EnsEMBL::Web::Configuration::UserData)
local_tools (EnsEMBL::Web::Configuration::Variation)
local_tools (EnsEMBL::Web::Configuration::Gene)
local_tools (EnsEMBL::Web::Configuration::Account)
location (EnsEMBL::Web::CoreObjects)
location (EnsEMBL::Web::Component::Marker)
location (EnsEMBL::Web::Object::Location)
location (EnsEMBL::Web::Object::MultipleLocation)
location (EnsEMBL::Web::Object::SNP)
location (EnsEMBL::Web::Object::Variation)
location (EnsEMBL::Web::Tools::DocumentView)
location (EnsEMBL::Web::Tools::Document::Module)
location_URL
location_long_caption
location_short_caption
location_string (EnsEMBL::Web::Object::Gene)
location_string (EnsEMBL::Web::Object::Marker)
location_string (EnsEMBL::Web::Object::SNP)
location_string (EnsEMBL::Web::Object::Transcript)
location_string (EnsEMBL::Web::Object::Translation)
location_string (EnsEMBL::Web::Object::Variation)
locations
logHandler
logic_name (EnsEMBL::Web::Object::Gene)
logic_name (EnsEMBL::Web::Object::Transcript)
logic_name (EnsEMBL::Web::Object::Translation)
logins (EnsEMBL::Web::Document::HTML::CloseCP)
logins (EnsEMBL::Web::Document::HTML::Empty)
logins (EnsEMBL::Web::Document::HTML::ToolLinks)
logins (EnsEMBL::Web::Document::HTML::ToolLinks)
logo_img
logo_print
magic
make_directory
make_up_filename
managed_name (Bio::EnsEMBL::GlyphSet::P_protdas)
managed_name (Bio::EnsEMBL::GlyphSet::P_separator)
managed_name (Bio::EnsEMBL::GlyphSet::urlfeature)
map
map_AS_Exons
map_alias_to_species
map_locations
mappings (EnsEMBL::Web::Component::LD)
mappings (EnsEMBL::Web::Component::SNP)
mappings (EnsEMBL::Web::Component::Variation)
mapview_link
mapview_possible
mark_altered
mark_clean
mark_deleted
marked_up_seq
marked_up_seq_form
marker
markerFeatures
markerMapLocations
markerSynonym
markerSynonyms (EnsEMBL::Web::Component::Location::MarkerDetails)
markerSynonyms (EnsEMBL::Web::Object::Marker)
markerview
markupCodons
markupConservation
markupExons
markupInit
markupSNPs
markup_and_render
markup_codons
markup_comparisons
markup_conservation (EnsEMBL::Web::Component)
markup_conservation (EnsEMBL::Web::Component::Variation::Compara_Alignments)
markup_documentation
markup_embedded_table
markup_exons
markup_line_numbers
markup_links
markup_method_table
markup_variation (EnsEMBL::Web::Component)
markup_variation (EnsEMBL::Web::Component::Transcript)
markup_variation (EnsEMBL::Web::Component::Variation::Compara_Alignments)
marts
max_chr_length
max_values
maxx
maxy
md5
member_by_source
memd
menu
menu_containerlvalue
merge (EnsEMBL::Web::Document::DHTMLmerge)
merge (EnsEMBL::Web::Factory::Location)
merge_all
meta_credits
meta_description
meta_links
meta_methods
method (Bio::EnsEMBL::Renderer)
method (Bio::EnsEMBL::VRenderer)
method (Sanger::Graphics::Renderer)
method (EnsEMBL::Web::Tools::PluginLocator)
method_processing_callback
methods (EnsEMBL::Web::Tools::Document)
methods (EnsEMBL::Web::Tools::Document::Module)
methods_html
methods_of_type
mime_type
minx
miny
misc_set (EnsEMBL::Web::Component::Export)
misc_set (EnsEMBL::Web::Component::Location)
misc_set_code
misc_set_form
misc_set_genes
miscsetview
mix
mod_date (EnsEMBL::Web::Object::Gene)
mod_date (EnsEMBL::Web::Object::Transcript)
modal_form
modal_stuff
modified (EnsEMBL::Web::Object::Transcript)
modified (EnsEMBL::Web::Object::Translation)
modified_at_pretty
modify_configs
modify_element
module
module_by_name
module_coverage
modules
moltype (EnsEMBL::Web::Component::SNP)
moltype (EnsEMBL::Web::Component::Variation)
moltype (EnsEMBL::Web::Object::SNP)
moltype (EnsEMBL::Web::Object::Variation)
move
move_to_user
movie
movie_list
mult
multi
multiX
multi_bottom
multi_bottom_menu
multi_hash
multi_ideogram
multi_species_list
multi_top
multi_val
multicontigview
multidb
munge_gaps (EnsEMBL::Web::Object::Gene)
munge_gaps (EnsEMBL::Web::Object::Slice)
munge_gaps (EnsEMBL::Web::Object::Transcript)
munge_gaps_split
munge_read_coverage
mushroom
mutator_name_for
my_colour (Bio::EnsEMBL::GlyphSet)
my_colour (Bio::EnsEMBL::GlyphSet::_flat_file)
my_colour (Bio::EnsEMBL::GlyphSet::_user_data)
my_config
my_description (Bio::EnsEMBL::GlyphSet::generic_simple)
my_description (Bio::EnsEMBL::GlyphSet::generic_simplest)
my_description (Bio::EnsEMBL::GlyphSet::regulatory_search_regions)
my_helplink (Bio::EnsEMBL::GlyphSet::generic_simple)
my_helplink (Bio::EnsEMBL::GlyphSet::generic_simplest)
my_helplink (Bio::EnsEMBL::GlyphSet::read_coverage)
my_helplink (Bio::EnsEMBL::GlyphSet::_ditag)
my_helplink (Bio::EnsEMBL::GlyphSet::ctcf)
my_helplink (Bio::EnsEMBL::GlyphSet::regulatory_search_regions)
my_label (Bio::EnsEMBL::GlyphSet_transcript)
my_label (Bio::EnsEMBL::GlyphSet::generic_simple)
my_label (Bio::EnsEMBL::GlyphSet::generic_simplest)
my_label (Bio::EnsEMBL::GlyphSet::tagged_snp)
my_label (Bio::EnsEMBL::GlyphSet::urlfeature)
my_label (Bio::EnsEMBL::GlyphSet::vegaclones)
my_label (Bio::EnsEMBL::GlyphSet::_variation)
my_label (Bio::EnsEMBL::GlyphSet::_transcript)
my_label (Bio::EnsEMBL::GlyphSet::ensemblclones)
my_label (Bio::EnsEMBL::GlyphSet::evega_gene)
my_label (Bio::EnsEMBL::GlyphSet::fg_regulatory_features)
my_label (Bio::EnsEMBL::GlyphSet::regulatory_search_regions)
mysql_db
name (EnsEMBL::Web::Fake)
name (EnsEMBL::Web::Filter)
name (EnsEMBL::Web::Problem)
name (EnsEMBL::Web::SpeciesDefs)
name (EnsEMBL::Web::Component::ArchiveStableId)
name (EnsEMBL::Web::Component::Location)
name (EnsEMBL::Web::Component::Marker)
name (EnsEMBL::Web::Component::SNP)
name (EnsEMBL::Web::Component::Server)
name (EnsEMBL::Web::Container::HSPContainer)
name (EnsEMBL::Web::Form::Element)
name (EnsEMBL::Web::Input::Parameter)
name (EnsEMBL::Web::Interface::Element)
name (EnsEMBL::Web::Object::Go)
name (EnsEMBL::Web::Object::Location)
name (EnsEMBL::Web::Object::Marker)
name (EnsEMBL::Web::Object::MultipleLocation)
name (EnsEMBL::Web::Object::SNP)
name (EnsEMBL::Web::Object::Variation)
name (EnsEMBL::Web::Tools::Document::Method)
name (EnsEMBL::Web::Tools::Document::Module)
name (ExaLead::Category)
name (ExaLead::Group)
name (ExaLead::HitCategory)
name (ExaLead::HitGroup)
name (ExaLead::Keyword)
name (ExaLead::QueryParameter)
named_element
names
neat_sr_name
new (Bio::EnsEMBL::ColourMap)
new (Bio::EnsEMBL::DrawableContainer)
new (Bio::EnsEMBL::Glyph)
new (Bio::EnsEMBL::Renderer)
new (Bio::EnsEMBL::VDrawableContainer)
new (Bio::EnsEMBL::VRenderer)
new (Bio::EnsEMBL::GlyphSet)
new (Sanger::Graphics::ColourMap)
new (Sanger::Graphics::DrawableContainer)
new (Sanger::Graphics::Glyph)
new (Sanger::Graphics::GlyphSet)
new (Sanger::Graphics::GlyphSetManager)
new (Sanger::Graphics::Renderer)
new (Sanger::Graphics::TextHelper)
new (Sanger::Graphics::VDrawableContainer)
new (Sanger::Graphics::WebUserConfig)
new (Sanger::Graphics::Glyph::Circle)
new (EnsEMBL::Web::Cache)
new (EnsEMBL::Web::Component)
new (EnsEMBL::Web::ConfigPacker_base)
new (EnsEMBL::Web::Configuration)
new (EnsEMBL::Web::CoreObjects)
new (EnsEMBL::Web::ExtIndex)
new (EnsEMBL::Web::ExtURL)
new (EnsEMBL::Web::ExternalDAS)
new (EnsEMBL::Web::Factory)
new (EnsEMBL::Web::Fake)
new (EnsEMBL::Web::Form)
new (EnsEMBL::Web::ImageConfig)
new (EnsEMBL::Web::IndexSupport)
new (EnsEMBL::Web::OldLinks)
new (EnsEMBL::Web::OrderedTree)
new (EnsEMBL::Web::Problem)
new (EnsEMBL::Web::Proxiable)
new (EnsEMBL::Web::Proxy)
new (EnsEMBL::Web::Root)
new (EnsEMBL::Web::SpeciesDefs)
new (EnsEMBL::Web::TmpFile)
new (EnsEMBL::Web::ViewConfig)
new (EnsEMBL::Web::Data)
new (EnsEMBL::Web::BlastView::BlastDefs)
new (EnsEMBL::Web::BlastView::Meta)
new (EnsEMBL::Web::BlastView::Panel)
new (EnsEMBL::Web::BlastView::PanelCache)
new (EnsEMBL::Web::BlastView::PanelMain)
new (EnsEMBL::Web::BlastView::PanelStatus)
new (EnsEMBL::Web::BlastView::PanelTop)
new (EnsEMBL::Web::Container::HSPContainer)
new (EnsEMBL::Web::DBSQL::BlastAdaptor)
new (EnsEMBL::Web::DBSQL::DBConnection)
new (EnsEMBL::Web::Data::Record)
new (EnsEMBL::Web::Document::DAS)
new (EnsEMBL::Web::Document::Excel)
new (EnsEMBL::Web::Document::HTML)
new (EnsEMBL::Web::Document::Image)
new (EnsEMBL::Web::Document::Page)
new (EnsEMBL::Web::Document::Panel)
new (EnsEMBL::Web::Document::Renderer)
new (EnsEMBL::Web::Document::SpreadSheet)
new (EnsEMBL::Web::Document::Text)
new (EnsEMBL::Web::Document::TextGz)
new (EnsEMBL::Web::Document::WebPage)
new (EnsEMBL::Web::Document::XML)
new (EnsEMBL::Web::Document::Excel::Content)
new (EnsEMBL::Web::Document::HTML::BodyJavascript)
new (EnsEMBL::Web::Document::HTML::CloseCP)
new (EnsEMBL::Web::Document::HTML::Content)
new (EnsEMBL::Web::Document::HTML::Copyright)
new (EnsEMBL::Web::Document::HTML::HTML_Block)
new (EnsEMBL::Web::Document::HTML::HomeSearch)
new (EnsEMBL::Web::Document::HTML::Javascript)
new (EnsEMBL::Web::Document::HTML::JavascriptDiv)
new (EnsEMBL::Web::Document::HTML::Links)
new (EnsEMBL::Web::Document::HTML::LocalContext)
new (EnsEMBL::Web::Document::HTML::LocalTools)
new (EnsEMBL::Web::Document::HTML::Meta)
new (EnsEMBL::Web::Document::HTML::RSS)
new (EnsEMBL::Web::Document::HTML::SearchBox)
new (EnsEMBL::Web::Document::HTML::Stylesheet)
new (EnsEMBL::Web::Document::HTML::Title)
new (EnsEMBL::Web::Document::HTML::ToolLinks)
new (EnsEMBL::Web::Document::HTML::TwoCol)
new (EnsEMBL::Web::Document::Panel::Fragment)
new (EnsEMBL::Web::Document::Panel::InformationFragment)
new (EnsEMBL::Web::Document::Panel::InformationImage)
new (EnsEMBL::Web::Document::Panel::SpreadSheet)
new (EnsEMBL::Web::Document::Renderer::Apache)
new (EnsEMBL::Web::Document::Renderer::Assembler)
new (EnsEMBL::Web::Document::Renderer::File)
new (EnsEMBL::Web::Document::Renderer::GzCacheFile)
new (EnsEMBL::Web::Document::Renderer::GzFile)
new (EnsEMBL::Web::Document::Renderer::Stdout)
new (EnsEMBL::Web::Document::Renderer::String)
new (EnsEMBL::Web::Document::Text::Content)
new (EnsEMBL::Web::Document::TextGz::Content)
new (EnsEMBL::Web::Document::XML::Content)
new (EnsEMBL::Web::ExtIndex::EFETCH)
new (EnsEMBL::Web::ExtIndex::ENSEMBL_RETRIEVE)
new (EnsEMBL::Web::ExtIndex::MFETCH)
new (EnsEMBL::Web::ExtIndex::NULL)
new (EnsEMBL::Web::ExtIndex::PFETCH)
new (EnsEMBL::Web::ExtIndex::SRS)
new (EnsEMBL::Web::ExtIndex::WEBSRS)
new (EnsEMBL::Web::ExtIndex::bioperl)
new (EnsEMBL::Web::ExtIndex::biosql)
new (EnsEMBL::Web::Factory::DAS)
new (EnsEMBL::Web::Factory::Info)
new (EnsEMBL::Web::Factory::Location)
new (EnsEMBL::Web::Factory::MultipleLocation)
new (EnsEMBL::Web::Form::Element)
new (EnsEMBL::Web::Form::FieldSet)
new (EnsEMBL::Web::Form::Element::Age)
new (EnsEMBL::Web::Form::Element::Button)
new (EnsEMBL::Web::Form::Element::CheckBox)
new (EnsEMBL::Web::Form::Element::ComboBox)
new (EnsEMBL::Web::Form::Element::DASCheckBox)
new (EnsEMBL::Web::Form::Element::DropDown)
new (EnsEMBL::Web::Form::Element::DropDownAndString)
new (EnsEMBL::Web::Form::Element::DropDownAndSubmit)
new (EnsEMBL::Web::Form::Element::File)
new (EnsEMBL::Web::Form::Element::Float)
new (EnsEMBL::Web::Form::Element::ForceReload)
new (EnsEMBL::Web::Form::Element::Header)
new (EnsEMBL::Web::Form::Element::Html)
new (EnsEMBL::Web::Form::Element::Image)
new (EnsEMBL::Web::Form::Element::Information)
new (EnsEMBL::Web::Form::Element::Int)
new (EnsEMBL::Web::Form::Element::MultiSelect)
new (EnsEMBL::Web::Form::Element::NoEdit)
new (EnsEMBL::Web::Form::Element::NonNegFloat)
new (EnsEMBL::Web::Form::Element::NonNegInt)
new (EnsEMBL::Web::Form::Element::Password)
new (EnsEMBL::Web::Form::Element::PosFloat)
new (EnsEMBL::Web::Form::Element::PosInt)
new (EnsEMBL::Web::Form::Element::RadioButton)
new (EnsEMBL::Web::Form::Element::RadioGroup)
new (EnsEMBL::Web::Form::Element::SubHeader)
new (EnsEMBL::Web::Form::Element::Submit)
new (EnsEMBL::Web::Form::Element::YesNo)
new (EnsEMBL::Web::Input::Options)
new (EnsEMBL::Web::Input::Parameter)
new (EnsEMBL::Web::Input::Parameters)
new (EnsEMBL::Web::Object::DAS)
new (EnsEMBL::Web::OrderedTree::Node)
new (EnsEMBL::Web::Proxy::Factory)
new (EnsEMBL::Web::Proxy::Object)
new (EnsEMBL::Web::Text::Feature)
new (EnsEMBL::Web::Text::FeatureParser)
new (EnsEMBL::Web::Text::Feature::BED)
new (EnsEMBL::Web::Text::Feature::DAS)
new (EnsEMBL::Web::Text::Feature::GBrowse)
new (EnsEMBL::Web::Text::Feature::GFF)
new (EnsEMBL::Web::Text::Feature::GTF)
new (EnsEMBL::Web::Text::Feature::PSL)
new (EnsEMBL::Web::TmpFile::Image)
new (EnsEMBL::Web::TmpFile::Tar)
new (EnsEMBL::Web::TmpFile::Text)
new (EnsEMBL::Web::TmpFile::Driver::Disk)
new (EnsEMBL::Web::TmpFile::Driver::Memcached)
new (EnsEMBL::Web::Tools::Document)
new (EnsEMBL::Web::Tools::DocumentView)
new (EnsEMBL::Web::Tools::PluginLocator)
new (EnsEMBL::Web::Tools::Registry)
new (EnsEMBL::Web::Tools::URL)
new (EnsEMBL::Web::Tools::Document::Method)
new (EnsEMBL::Web::Tools::Document::Module)
new (ExaLead)
new (ExaLead::Category)
new (ExaLead::Group)
new (ExaLead::Hit)
new (ExaLead::HitCategory)
new (ExaLead::HitGroup)
new (ExaLead::Hits)
new (ExaLead::Keyword)
new (ExaLead::Link)
new (ExaLead::Query)
new (ExaLead::QueryParameter)
new (ExaLead::QueryTerm)
new (ExaLead::Renderer)
new (ExaLead::SpellingSuggestion)
new (ExaLead::TextSeg)
new (ExaLead::Value)
new (EnsEMBL::Web::Document::HTML::Copyright)
new (EnsEMBL::Sanger::WebStats)
new (EnsEMBL::Web::Document::HTML::ToolLinks)
new_MultipleLocation
new_cell_format
new_child
new_from_URL
new_from_hashref
new_hsp_image
new_image (EnsEMBL::Web::Component)
new_image (EnsEMBL::Web::Object)
new_karyotype_image (EnsEMBL::Web::Component)
new_karyotype_image (EnsEMBL::Web::Object)
new_panel
new_table_renderer (EnsEMBL::Web::Document::Renderer::Apache)
new_table_renderer (EnsEMBL::Web::Document::Renderer::String)
new_vimage (EnsEMBL::Web::Component)
new_vimage (EnsEMBL::Web::Object)
next
next_leaf
nhits (ExaLead)
nhits (ExaLead::Hits)
nmatches (ExaLead)
nmatches (ExaLead::Hits)
no_features
no_of_bins
no_preview
no_results
nodes (EnsEMBL::Web::OrderedTree)
nodes (EnsEMBL::Web::OrderedTree::Node)
noescape
nohistory
non_coding_error
non_fatal_error
not_allowed
note (EnsEMBL::Web::Text::Feature)
note (EnsEMBL::Web::Text::Feature::GBrowse)
notes (EnsEMBL::Web::Form::Element)
notes (EnsEMBL::Web::Form::FieldSet)
object (EnsEMBL::Web::Command)
object (EnsEMBL::Web::Component)
object (EnsEMBL::Web::Configuration)
object (EnsEMBL::Web::Filter)
objectlvalue
on
on_failure
on_success
option (EnsEMBL::Web::Document::Panel)
option (EnsEMBL::Web::Document::Panel::SpreadSheet)
option (EnsEMBL::Web::Interface::Element)
option_columns
option_order
options (Sanger::Graphics::WebUserConfig)
options (EnsEMBL::Web::ViewConfig)
options (EnsEMBL::Web::Component::LD)
options (EnsEMBL::Web::Document::Panel)
options (EnsEMBL::Web::Document::Panel::SpreadSheet)
options (EnsEMBL::Web::Interface::Element)
options_form
ori
other_feature_list
other_species
output (EnsEMBL::Web::BlastView::Panel)
output (EnsEMBL::Web::BlastView::PanelMain)
output (EnsEMBL::Web::BlastView::PanelStatus)
output_AlignSlice
output_DnaDnaAlignFeature
output_External
output_External_exon_al
output_External_trans_al
output_Family
output_GeneTree
output_Homology
output_das_text
output_lddata
output_simple
overview
overview_documentation
owner
package (Sanger::Graphics::GlyphSet::generic_das_feature)
package (EnsEMBL::Web::Tools::Document::Method)
package_prefix
page
panel (EnsEMBL::Web::Document::Excel::Content)
panel (EnsEMBL::Web::Document::HTML::Content)
panel (EnsEMBL::Web::Document::Text::Content)
panel (EnsEMBL::Web::Document::TextGz::Content)
panel (EnsEMBL::Web::Document::XML::Content)
panel_is_closed
panellvalue
panels
param (EnsEMBL::Web::CoreObjects)
param (EnsEMBL::Web::Proxiable)
param (ExaLead::Link)
param_list
parameter_options (Bio::Tools::Run::Search::blat_gfclient)
parameter_options (Bio::Tools::Run::Search::ssaha2_client)
parameters (EnsEMBL::Web::Tools::PluginLocator)
parameters (ExaLead::Query)
params
parent (EnsEMBL::Web::Proxy)
parent (EnsEMBL::Web::Object::Location)
parent (EnsEMBL::Web::Object::SNP)
parent (EnsEMBL::Web::Object::Variation)
parent_key
parse (EnsEMBL::Web::IndexSupport)
parse (EnsEMBL::Web::SpeciesDefs)
parse (EnsEMBL::Web::Document::Panel)
parse (EnsEMBL::Web::Text::FeatureParser)
parse (EnsEMBL::Web::Tools::URL)
parse (ExaLead)
parseHTML
parse_URL
parse_file
parse_old
parse_row (EnsEMBL::Web::Text::FeatureParser)
parse_row (EnsEMBL::Web::Text::FeatureParser::BED)
parse_row (EnsEMBL::Web::Text::FeatureParser::DAS)
parse_row (EnsEMBL::Web::Text::FeatureParser::GBrowse)
parse_row (EnsEMBL::Web::Text::FeatureParser::GFF)
parse_row (EnsEMBL::Web::Text::FeatureParser::GTF)
parse_row (EnsEMBL::Web::Text::FeatureParser::PSL)
parse_row (EnsEMBL::Web::Text::FeatureParser::WIG)
parse_row (EnsEMBL::Web::Text::FeatureParser::generic)
parse_user_data
parsed_jobs
pass_fields
path_from_package
pending_jobs
pep_snps
pep_splice_site
pep_stats
peptide
perl
permit_delete
pip_anno_file
pip_anno_file_pipmaker
pip_anno_file_vista
pip_seq_file
pixelcentre (Sanger::Graphics::Glyph)
pixelcentre (Sanger::Graphics::Glyph::Circle)
placeholder
plugin_locator
pointer_default
points
pop
pop_description (EnsEMBL::Web::Object::Location)
pop_description (EnsEMBL::Web::Object::SNP)
pop_description (EnsEMBL::Web::Object::Variation)
pop_export_configurator
pop_genotype_obj (EnsEMBL::Web::Object::SNP)
pop_genotype_obj (EnsEMBL::Web::Object::Variation)
pop_genotypes (EnsEMBL::Web::Object::SNP)
pop_genotypes (EnsEMBL::Web::Object::Variation)
pop_id (EnsEMBL::Web::Object::SNP)
pop_id (EnsEMBL::Web::Object::Variation)
pop_info (EnsEMBL::Web::Object::SNP)
pop_info (EnsEMBL::Web::Object::Variation)
pop_links (EnsEMBL::Web::Object::Location)
pop_links (EnsEMBL::Web::Object::SNP)
pop_links (EnsEMBL::Web::Object::Variation)
pop_name (EnsEMBL::Web::Object::Location)
pop_name (EnsEMBL::Web::Object::SNP)
pop_name (EnsEMBL::Web::Object::Variation)
pop_name_from_id
pop_obj_from_id (EnsEMBL::Web::Object::SNP)
pop_obj_from_id (EnsEMBL::Web::Object::Variation)
pop_obj_from_name
pop_size (EnsEMBL::Web::Object::Location)
pop_size (EnsEMBL::Web::Object::SNP)
pop_size (EnsEMBL::Web::Object::Variation)
pops_for_slice
populate_bins
populate_tree (EnsEMBL::Web::Configuration)
populate_tree (EnsEMBL::Web::Configuration::Blast)
populate_tree (EnsEMBL::Web::Configuration::Help)
populate_tree (EnsEMBL::Web::Configuration::Info)
populate_tree (EnsEMBL::Web::Configuration::Location)
populate_tree (EnsEMBL::Web::Configuration::SNP)
populate_tree (EnsEMBL::Web::Configuration::Search)
populate_tree (EnsEMBL::Web::Configuration::Server)
populate_tree (EnsEMBL::Web::Configuration::Transcript)
populate_tree (EnsEMBL::Web::Configuration::UniSearch)
populate_tree (EnsEMBL::Web::Configuration::UserData)
populate_tree (EnsEMBL::Web::Configuration::Variation)
populate_tree (EnsEMBL::Web::Configuration::Gene)
populate_tree (EnsEMBL::Web::Configuration::Account)
population_info (EnsEMBL::Web::Component::LD)
population_info (EnsEMBL::Web::Component::Location::LD)
postReadRequestHandler
predecessor_history
predecessors
prediction_method (EnsEMBL::Web::Component::LD)
prediction_method (EnsEMBL::Web::Component::Location::LD)
prefix (EnsEMBL::Web::Object)
prefix (EnsEMBL::Web::Document::Image)
prefix (EnsEMBL::Web::Document::Panel)
prepare
prepend
prepend_to_component
pretty_date (EnsEMBL::Web::Root)
pretty_date (EnsEMBL::Web::Tools::Misc)
preview (EnsEMBL::Web::Configuration::Interface)
preview (EnsEMBL::Web::Interface::Element)
preview_fields
previous
previous_leaf
primers
print (EnsEMBL::Web::SeqDumper)
print (EnsEMBL::Web::TmpFile)
print (EnsEMBL::Web::Document::DAS)
print (EnsEMBL::Web::Document::Excel)
print (EnsEMBL::Web::Document::HTML)
print (EnsEMBL::Web::Document::Page)
print (EnsEMBL::Web::Document::Panel)
print (EnsEMBL::Web::Document::Renderer)
print (EnsEMBL::Web::Document::Text)
print (EnsEMBL::Web::Document::TextGz)
print (EnsEMBL::Web::Document::XML)
print (EnsEMBL::Web::Document::Panel::Fragment)
print (EnsEMBL::Web::Document::Renderer::Apache)
print (EnsEMBL::Web::Document::Renderer::Assembler)
print (EnsEMBL::Web::Document::Renderer::File)
print (EnsEMBL::Web::Document::Renderer::GzFile)
print (EnsEMBL::Web::Document::Renderer::Stdout)
print (EnsEMBL::Web::Document::Renderer::String)
print_image
print_next
print_pop_info (EnsEMBL::Web::Component::LD)
print_pop_info (EnsEMBL::Web::Component::Location::LD)
printf (EnsEMBL::Web::Document::DAS)
printf (EnsEMBL::Web::Document::Excel)
printf (EnsEMBL::Web::Document::HTML)
printf (EnsEMBL::Web::Document::Page)
printf (EnsEMBL::Web::Document::Panel)
printf (EnsEMBL::Web::Document::Renderer)
printf (EnsEMBL::Web::Document::Text)
printf (EnsEMBL::Web::Document::TextGz)
printf (EnsEMBL::Web::Document::XML)
printf (EnsEMBL::Web::Document::Renderer::Apache)
printf (EnsEMBL::Web::Document::Renderer::Assembler)
printf (EnsEMBL::Web::Document::Renderer::File)
printf (EnsEMBL::Web::Document::Renderer::GzFile)
printf (EnsEMBL::Web::Document::Renderer::Stdout)
printf (EnsEMBL::Web::Document::Renderer::String)
problem (EnsEMBL::Web::Proxiable)
problem (EnsEMBL::Web::Proxy)
problem (EnsEMBL::Web::Document::WebPage)
process (EnsEMBL::Web::Command::ShareRecord)
process (EnsEMBL::Web::Command::Wizard)
process (EnsEMBL::Web::Command::Account::AcceptInvitation)
process (EnsEMBL::Web::Command::Account::ChangeLevel)
process (EnsEMBL::Web::Command::Account::ChangeStatus)
process (EnsEMBL::Web::Command::Account::Invite)
process (EnsEMBL::Web::Command::Account::LoadConfig)
process (EnsEMBL::Web::Command::Account::LogOut)
process (EnsEMBL::Web::Command::Account::RemoveInvitation)
process (EnsEMBL::Web::Command::Account::RemoveMember)
process (EnsEMBL::Web::Command::Account::ResetFavourites)
process (EnsEMBL::Web::Command::Account::SaveDas)
process (EnsEMBL::Web::Command::Account::SaveFavourites)
process (EnsEMBL::Web::Command::Account::SavePassword)
process (EnsEMBL::Web::Command::Account::SendActivation)
process (EnsEMBL::Web::Command::Account::SetConfig)
process (EnsEMBL::Web::Command::Account::SetCookie)
process (EnsEMBL::Web::Command::Account::ShareRecord)
process (EnsEMBL::Web::Command::Account::Unsubscribe)
process (EnsEMBL::Web::Command::Account::UseBookmark)
process (EnsEMBL::Web::Command::Account::Interface::Annotation)
process (EnsEMBL::Web::Command::Account::Interface::AnnotationSave)
process (EnsEMBL::Web::Command::Account::Interface::Bookmark)
process (EnsEMBL::Web::Command::Account::Interface::Configuration)
process (EnsEMBL::Web::Command::Account::Interface::Group)
process (EnsEMBL::Web::Command::Account::Interface::GroupSave)
process (EnsEMBL::Web::Command::Account::Interface::Newsfilter)
process (EnsEMBL::Web::Command::Account::Interface::User)
process (EnsEMBL::Web::Command::Account::Interface::UserSave)
process (EnsEMBL::Web::Command::Help::DoSearch)
process (EnsEMBL::Web::Command::Help::Feedback)
process (EnsEMBL::Web::Command::Help::MovieEmail)
process (EnsEMBL::Web::Command::Help::SendEmail)
process (EnsEMBL::Web::Command::Interface::Delete)
process (EnsEMBL::Web::Command::Interface::Save)
process (EnsEMBL::Web::Command::UserData::AttachURL)
process (EnsEMBL::Web::Command::UserData::CheckShare)
process (EnsEMBL::Web::Command::UserData::DeleteRemote)
process (EnsEMBL::Web::Command::UserData::DeleteUpload)
process (EnsEMBL::Web::Command::UserData::SaveRecord)
process (EnsEMBL::Web::Command::UserData::SaveRemote)
process (EnsEMBL::Web::Command::UserData::SaveTempData)
process (EnsEMBL::Web::Command::UserData::SaveUpload)
process (EnsEMBL::Web::Command::UserData::UploadFile)
process (EnsEMBL::Web::Command::UserData::ValidateDAS)
process (EnsEMBL::Web::Command::UserData::AttachDAS)
process (EnsEMBL::Web::Document::Interface)
process (EnsEMBL::Web::Document::Renderer::Assembler)
program_name (Bio::Tools::Run::Search::blat_gfclient)
program_name (Bio::Tools::Run::Search::ssaha2_client)
project_onto_coord_system
propagate_cache_tags (EnsEMBL::Web::Data)
propagate_cache_tags (EnsEMBL::Web::Data::Group)
propagate_cache_tags (EnsEMBL::Web::Data::Record)
propagate_cache_tags (EnsEMBL::Web::Data::Session)
propagate_cache_tags (EnsEMBL::Web::Data::User)
protein
protview
proxy
ps_rgb_by_id (Sanger::Graphics::Renderer::eps)
ps_rgb_by_id (Sanger::Graphics::Renderer::postscript)
purge_data
push (Sanger::Graphics::GlyphSet)
push (Sanger::Graphics::Glyph::Composite)
push (EnsEMBL::Web::Timer)
push_class
push_endscr_line
push_primary
push_script_line
push_secondary
px2bp
query (ExaLead)
query (ExaLead::SpellingSuggestion)
query_processing_callback
query_server
query_string
queue_length
queue_pending_blast_jobs
r
random_string
raw
raw_component
raw_content
raw_feature_strand (EnsEMBL::Web::Object::Location)
raw_feature_strand (EnsEMBL::Web::Object::MultipleLocation)
rawend (EnsEMBL::Web::Text::Feature::BED)
rawend (EnsEMBL::Web::Text::Feature::DAS)
rawend (EnsEMBL::Web::Text::Feature::GBrowse)
rawend (EnsEMBL::Web::Text::Feature::GFF)
rawend (EnsEMBL::Web::Text::Feature::PSL)
rawend (EnsEMBL::Web::Text::Feature::WIG)
rawend (EnsEMBL::Web::Text::Feature::generic)
rawstart (EnsEMBL::Web::Text::Feature::BED)
rawstart (EnsEMBL::Web::Text::Feature::DAS)
rawstart (EnsEMBL::Web::Text::Feature::GBrowse)
rawstart (EnsEMBL::Web::Text::Feature::GFF)
rawstart (EnsEMBL::Web::Text::Feature::PSL)
rawstart (EnsEMBL::Web::Text::Feature::WIG)
rawstart (EnsEMBL::Web::Text::Feature::generic)
rcc_features
read_coverage (Bio::EnsEMBL::GlyphSet::read_coverage)
read_coverage (EnsEMBL::Web::Object::Transcript)
read_tree
readable_strand
real
real_location
real_px2bp
real_species (EnsEMBL::Web::Object::DAS)
real_species (EnsEMBL::Web::Object::Location)
real_species (EnsEMBL::Web::Object::MultipleLocation)
rebuild_das
receive_shared_data
record_filter
record_list
record_select
records
rect
redirect (EnsEMBL::Web::Filter)
redirect (EnsEMBL::Web::Proxiable)
redirect (EnsEMBL::Web::Document::WebPage)
ref
referer (EnsEMBL::Web::Object)
referer (EnsEMBL::Web::Document::HTML::CloseCP)
referer (EnsEMBL::Web::Document::HTML::ToolLinks)
referer (EnsEMBL::Web::Document::HTML::ToolLinks)
reg_factors
reg_features
regexp
region (Bio::EnsEMBL::GlyphSet::HSP_plot)
region (Bio::EnsEMBL::GlyphSet::HSP_query_plot)
region_name (EnsEMBL::Web::Object::SNP)
region_name (EnsEMBL::Web::Object::Variation)
region_type (EnsEMBL::Web::Object::SNP)
region_type (EnsEMBL::Web::Object::Variation)
relational_element
release
release_id
release_month
releases
remap_feature
remove
remove_artefacts
remove_body_element
remove_component
remove_head_element
remove_node
remove_panel
remove_redundant_xrefs
remove_subtree
render (Bio::EnsEMBL::DrawableContainer)
render (Bio::EnsEMBL::Renderer)
render (Bio::EnsEMBL::VDrawableContainer)
render (Bio::EnsEMBL::VRenderer)
render (Bio::EnsEMBL::GlyphSet)
render (Sanger::Graphics::DrawableContainer)
render (Sanger::Graphics::Renderer)
render (Sanger::Graphics::VDrawableContainer)
render (EnsEMBL::Web::Form)
render (EnsEMBL::Web::Timer)
render (EnsEMBL::Web::Document::Image)
render (EnsEMBL::Web::Document::Page)
render (EnsEMBL::Web::Document::Panel)
render (EnsEMBL::Web::Document::SpreadSheet)
render (EnsEMBL::Web::Document::WebPage)
render (EnsEMBL::Web::Document::Excel::Content)
render (EnsEMBL::Web::Document::HTML::Blog)
render (EnsEMBL::Web::Document::HTML::BodyJavascript)
render (EnsEMBL::Web::Document::HTML::BreadCrumbs)
render (EnsEMBL::Web::Document::HTML::CloseCP)
render (EnsEMBL::Web::Document::HTML::Content)
render (EnsEMBL::Web::Document::HTML::Copyright)
render (EnsEMBL::Web::Document::HTML::DocsMenu)
render (EnsEMBL::Web::Document::HTML::Empty)
render (EnsEMBL::Web::Document::HTML::FTPtable)
render (EnsEMBL::Web::Document::HTML::FooterLinks)
render (EnsEMBL::Web::Document::HTML::GlobalContext)
render (EnsEMBL::Web::Document::HTML::Glossary)
render (EnsEMBL::Web::Document::HTML::HTML_Block)
render (EnsEMBL::Web::Document::HTML::HomeSearch)
render (EnsEMBL::Web::Document::HTML::Javascript)
render (EnsEMBL::Web::Document::HTML::JavascriptDiv)
render (EnsEMBL::Web::Document::HTML::Links)
render (EnsEMBL::Web::Document::HTML::LocalContext)
render (EnsEMBL::Web::Document::HTML::LocalTools)
render (EnsEMBL::Web::Document::HTML::LoggedIn)
render (EnsEMBL::Web::Document::HTML::Logo)
render (EnsEMBL::Web::Document::HTML::Meta)
render (EnsEMBL::Web::Document::HTML::MovieList)
render (EnsEMBL::Web::Document::HTML::News)
render (EnsEMBL::Web::Document::HTML::RSS)
render (EnsEMBL::Web::Document::HTML::SearchBox)
render (EnsEMBL::Web::Document::HTML::SpeciesList)
render (EnsEMBL::Web::Document::HTML::SpeciesPage)
render (EnsEMBL::Web::Document::HTML::Stylesheet)
render (EnsEMBL::Web::Document::HTML::TOC)
render (EnsEMBL::Web::Document::HTML::Title)
render (EnsEMBL::Web::Document::HTML::ToolLinks)
render (EnsEMBL::Web::Document::HTML::TopFAQs)
render (EnsEMBL::Web::Document::HTML::TwoCol)
render (EnsEMBL::Web::Document::HTML::UserLinks)
render (EnsEMBL::Web::Document::HTML::WhatsNew)
render (EnsEMBL::Web::Document::Panel::Ajax)
render (EnsEMBL::Web::Document::Panel::AjaxMenu)
render (EnsEMBL::Web::Document::Panel::Configurator)
render (EnsEMBL::Web::Document::Panel::Fragment)
render (EnsEMBL::Web::Document::Text::Content)
render (EnsEMBL::Web::Document::TextGz::Content)
render (EnsEMBL::Web::Document::XML::Content)
render (EnsEMBL::Web::Form::FieldSet)
render (EnsEMBL::Web::Form::Element::Button)
render (EnsEMBL::Web::Form::Element::CheckBox)
render (EnsEMBL::Web::Form::Element::DASCheckBox)
render (EnsEMBL::Web::Form::Element::Date)
render (EnsEMBL::Web::Form::Element::DropDown)
render (EnsEMBL::Web::Form::Element::DropDownAndString)
render (EnsEMBL::Web::Form::Element::DropDownAndSubmit)
render (EnsEMBL::Web::Form::Element::ForceReload)
render (EnsEMBL::Web::Form::Element::Header)
render (EnsEMBL::Web::Form::Element::Hidden)
render (EnsEMBL::Web::Form::Element::Honeypot)
render (EnsEMBL::Web::Form::Element::Image)
render (EnsEMBL::Web::Form::Element::Information)
render (EnsEMBL::Web::Form::Element::MultiSelect)
render (EnsEMBL::Web::Form::Element::NoEdit)
render (EnsEMBL::Web::Form::Element::RadioButton)
render (EnsEMBL::Web::Form::Element::RadioGroup)
render (EnsEMBL::Web::Form::Element::Range)
render (EnsEMBL::Web::Form::Element::String)
render (EnsEMBL::Web::Form::Element::SubHeader)
render (EnsEMBL::Web::Form::Element::Submit)
render (EnsEMBL::Web::Form::Element::Text)
render (EnsEMBL::Ensembl::Document::HTML::ArchiveList)
render (EnsEMBL::Ensembl::Document::HTML::AssemblyTable)
render (EnsEMBL::Ensembl::Document::HTML::FlashTutorials)
render (EnsEMBL::Web::Document::HTML::Copyright)
render (EnsEMBL::Web::Document::HTML::FooterLinks)
render (EnsEMBL::Sanger::Document::HTML::DumpTable)
render (EnsEMBL::Sanger::Document::HTML::GoogleAnalytics)
render (EnsEMBL::Web::Document::HTML::ToolLinks)
render_AjaxMenu
render_Blank
render_Circle (Bio::EnsEMBL::VRenderer::gif)
render_Circle (Bio::EnsEMBL::VRenderer::imagemap)
render_Circle (Sanger::Graphics::Renderer::eps)
render_Circle (Sanger::Graphics::Renderer::gif)
render_Circle (Sanger::Graphics::Renderer::imagemap)
render_Circle (Sanger::Graphics::Renderer::pdf)
render_Circle (Sanger::Graphics::Renderer::postscript)
render_Circle (Sanger::Graphics::Renderer::svg)
render_Circle (Sanger::Graphics::Renderer::test)
render_Composite (Bio::EnsEMBL::Renderer)
render_Composite (Bio::EnsEMBL::VRenderer)
render_Composite (Bio::EnsEMBL::VRenderer::gif)
render_Composite (Bio::EnsEMBL::VRenderer::imagemap)
render_Composite (Sanger::Graphics::Renderer)
render_Composite (Sanger::Graphics::Renderer::eps)
render_Composite (Sanger::Graphics::Renderer::gif)
render_Composite (Sanger::Graphics::Renderer::imagemap)
render_Composite (Sanger::Graphics::Renderer::pdf)
render_Composite (Sanger::Graphics::Renderer::postscript)
render_Composite (Sanger::Graphics::Renderer::svg)
render_Composite (Sanger::Graphics::Renderer::test)
render_DAS
render_Diagnostic (Sanger::Graphics::Renderer)
render_Diagnostic (Sanger::Graphics::Renderer::test)
render_Ellipse (Bio::EnsEMBL::VRenderer::gif)
render_Ellipse (Bio::EnsEMBL::VRenderer::imagemap)
render_Ellipse (Sanger::Graphics::Renderer::eps)
render_Ellipse (Sanger::Graphics::Renderer::gif)
render_Ellipse (Sanger::Graphics::Renderer::imagemap)
render_Ellipse (Sanger::Graphics::Renderer::pdf)
render_Ellipse (Sanger::Graphics::Renderer::postscript)
render_Ellipse (Sanger::Graphics::Renderer::svg)
render_Ellipse (Sanger::Graphics::Renderer::test)
render_Excel (EnsEMBL::Web::Document::Page)
render_Excel (EnsEMBL::Web::Document::Panel)
render_Intron (Bio::EnsEMBL::VRenderer::gif)
render_Intron (Bio::EnsEMBL::VRenderer::imagemap)
render_Intron (Sanger::Graphics::Renderer::eps)
render_Intron (Sanger::Graphics::Renderer::gif)
render_Intron (Sanger::Graphics::Renderer::imagemap)
render_Intron (Sanger::Graphics::Renderer::pdf)
render_Intron (Sanger::Graphics::Renderer::postscript)
render_Intron (Sanger::Graphics::Renderer::svg)
render_Intron (Sanger::Graphics::Renderer::test)
render_Line (Bio::EnsEMBL::VRenderer::gif)
render_Line (Bio::EnsEMBL::VRenderer::imagemap)
render_Line (Sanger::Graphics::Renderer::eps)
render_Line (Sanger::Graphics::Renderer::gif)
render_Line (Sanger::Graphics::Renderer::imagemap)
render_Line (Sanger::Graphics::Renderer::pdf)
render_Line (Sanger::Graphics::Renderer::postscript)
render_Line (Sanger::Graphics::Renderer::svg)
render_Line (Sanger::Graphics::Renderer::test)
render_Poly (Bio::EnsEMBL::VRenderer::gif)
render_Poly (Bio::EnsEMBL::VRenderer::imagemap)
render_Poly (Sanger::Graphics::Renderer::eps)
render_Poly (Sanger::Graphics::Renderer::gif)
render_Poly (Sanger::Graphics::Renderer::imagemap)
render_Poly (Sanger::Graphics::Renderer::pdf)
render_Poly (Sanger::Graphics::Renderer::postscript)
render_Poly (Sanger::Graphics::Renderer::svg)
render_Poly (Sanger::Graphics::Renderer::test)
render_Poly (Sanger::Graphics::Renderer::wmf)
render_Rect (Bio::EnsEMBL::VRenderer::gif)
render_Rect (Bio::EnsEMBL::VRenderer::imagemap)
render_Rect (Sanger::Graphics::Renderer::eps)
render_Rect (Sanger::Graphics::Renderer::gif)
render_Rect (Sanger::Graphics::Renderer::imagemap)
render_Rect (Sanger::Graphics::Renderer::pdf)
render_Rect (Sanger::Graphics::Renderer::postscript)
render_Rect (Sanger::Graphics::Renderer::svg)
render_Rect (Sanger::Graphics::Renderer::test)
render_Space (Bio::EnsEMBL::Renderer)
render_Space (Bio::EnsEMBL::VRenderer::gif)
render_Space (Bio::EnsEMBL::VRenderer::imagemap)
render_Space (Sanger::Graphics::Renderer)
render_Space (Sanger::Graphics::Renderer::imagemap)
render_Space (Sanger::Graphics::Renderer::test)
render_Sprite (Sanger::Graphics::Renderer)
render_Sprite (Sanger::Graphics::Renderer::gif)
render_Sprite (Sanger::Graphics::Renderer::pdf)
render_Sprite (Sanger::Graphics::Renderer::png)
render_Text (Bio::EnsEMBL::VRenderer::gif)
render_Text (Bio::EnsEMBL::VRenderer::imagemap)
render_Text (Sanger::Graphics::Renderer::eps)
render_Text (Sanger::Graphics::Renderer::gif)
render_Text (Sanger::Graphics::Renderer::imagemap)
render_Text (Sanger::Graphics::Renderer::pdf)
render_Text (Sanger::Graphics::Renderer::postscript)
render_Text (Sanger::Graphics::Renderer::svg)
render_Text (Sanger::Graphics::Renderer::test)
render_Text (Sanger::Graphics::Renderer::wmf)
render_Text (EnsEMBL::Web::Document::Page)
render_Text (EnsEMBL::Web::Document::Panel)
render_Text (EnsEMBL::Web::Document::SpreadSheet)
render_TextGz
render_XML (EnsEMBL::Web::Document::Page)
render_XML (EnsEMBL::Web::Document::Panel)
render_as
render_assembly_table
render_category
render_collapsed
render_collapsed_label
render_collapsed_nolabel
render_colourgradient
render_compact (Bio::EnsEMBL::GlyphSet_wiggle_and_block)
render_compact (Bio::EnsEMBL::GlyphSet::_alignment_pairwise)
render_density_bar
render_density_line
render_density_outline
render_end
render_error_page
render_form (ExaLead::Renderer)
render_form (ExaLead::Renderer::HTML)
render_gene_label (Bio::EnsEMBL::GlyphSet_transcript)
render_gene_label (Bio::EnsEMBL::GlyphSet::_gene)
render_gene_nolabel (Bio::EnsEMBL::GlyphSet_transcript)
render_gene_nolabel (Bio::EnsEMBL::GlyphSet::_gene)
render_genes
render_grouped
render_half_height
render_histogram
render_hits
render_image
render_image_button
render_image_map
render_image_tag
render_keywords
render_labels (Bio::EnsEMBL::GlyphSet_generic)
render_labels (Bio::EnsEMBL::GlyphSet::_alignment)
render_location
render_marker_details
render_marker_features
render_modal (EnsEMBL::Web::Document::HTML::GlobalContext)
render_modal (EnsEMBL::Web::Document::HTML::LocalContext)
render_navigation (ExaLead::Renderer)
render_navigation (ExaLead::Renderer::HTML)
render_nolabels
render_normal (Bio::EnsEMBL::GlyphSet_generic)
render_normal (Bio::EnsEMBL::GlyphSet_transcript)
render_normal (Bio::EnsEMBL::GlyphSet)
render_normal (Bio::EnsEMBL::GlyphSet::genetree_legend)
render_normal (Bio::EnsEMBL::GlyphSet::idhistorytree)
render_normal (Bio::EnsEMBL::GlyphSet::Vdraggable)
render_normal (Bio::EnsEMBL::GlyphSet::_alignment)
render_normal (Bio::EnsEMBL::GlyphSet::_alignment_pairwise)
render_popup
render_signal_feature
render_signal_map
render_spelling (ExaLead::Renderer)
render_spelling (ExaLead::Renderer::HTML)
render_stack
render_start
render_summary
render_text (Bio::EnsEMBL::GlyphSet_generic)
render_text (Bio::EnsEMBL::GlyphSet_simple)
render_text (Bio::EnsEMBL::GlyphSet_wiggle_and_block)
render_text (Bio::EnsEMBL::GlyphSet_transcript)
render_text (Bio::EnsEMBL::GlyphSet::contig)
render_text (Bio::EnsEMBL::GlyphSet::P_domain)
render_text (Bio::EnsEMBL::GlyphSet::P_protein)
render_text (Bio::EnsEMBL::GlyphSet::P_variation)
render_text (Bio::EnsEMBL::GlyphSet::_alignment)
render_text (Bio::EnsEMBL::GlyphSet::_alignment_pairwise)
render_text (Bio::EnsEMBL::GlyphSet::_marker)
render_text (Bio::EnsEMBL::GlyphSet::chr_band)
render_text (Bio::EnsEMBL::GlyphSet::ctcf)
render_tilingarray
render_transcript
render_transcript_label
render_transcript_nolabel
render_transcripts
render_tree
render_ungrouped
render_ungrouped_labels
render_unlimited
render_webtree
renderer (EnsEMBL::Web::Document::DAS)
renderer (EnsEMBL::Web::Document::Excel)
renderer (EnsEMBL::Web::Document::HTML)
renderer (EnsEMBL::Web::Document::Page)
renderer (EnsEMBL::Web::Document::Panel)
renderer (EnsEMBL::Web::Document::Text)
renderer (EnsEMBL::Web::Document::TextGz)
renderer (EnsEMBL::Web::Document::XML)
renderer_type (EnsEMBL::Web::Component::Alignment)
renderer_type (EnsEMBL::Web::Component::Gene::HomologAlignment)
repeat
replace_body_element
replace_component
replace_head_element
replace_panel
required
required_string
required_value
reset (EnsEMBL::Web::ImageConfig)
reset (EnsEMBL::Web::ViewConfig)
reset_buffer
reset_config (EnsEMBL::Web::Session)
reset_config (EnsEMBL::Web::Data::Session)
reset_subsection
restrict
result
result_for
results (EnsEMBL::Web::Component::Search)
results (EnsEMBL::Web::Object::Help)
results (EnsEMBL::Web::Tools::PluginLocator)
retrieve (EnsEMBL::Web::Cookie)
retrieve (EnsEMBL::Web::SpeciesDefs)
retrieve (EnsEMBL::Web::TmpFile)
retrieve_DnaAlignFeature (EnsEMBL::Web::Object::Feature)
retrieve_DnaAlignFeature (EnsEMBL::Web::Object::Location)
retrieve_Gene (EnsEMBL::Web::Object::Feature)
retrieve_Gene (EnsEMBL::Web::Object::Location)
retrieve_OligoProbe (EnsEMBL::Web::Object::Feature)
retrieve_OligoProbe (EnsEMBL::Web::Object::Location)
retrieve_ProteinAlignFeature (EnsEMBL::Web::Object::Feature)
retrieve_ProteinAlignFeature (EnsEMBL::Web::Object::Location)
retrieve_RegulatoryFactor (EnsEMBL::Web::Object::Feature)
retrieve_RegulatoryFactor (EnsEMBL::Web::Object::Location)
retrieve_Transcript
retrieve_Xref (EnsEMBL::Web::Object::Feature)
retrieve_Xref (EnsEMBL::Web::Object::Location)
retrieve_data
retrieve_features (EnsEMBL::Web::Object::Feature)
retrieve_features (EnsEMBL::Web::Object::Go)
retrieve_features (EnsEMBL::Web::Object::Location)
retrieve_hit
retrieve_hsp
retrieve_runnable
retrieve_ticket
retrieve_userdata
rgb_by_hex
rgb_by_id
rgb_by_name
right
rna_notation
rootURL (ExaLead)
rootURL (ExaLead::Link)
round_bp
rows
run
run_blast
run_cgi_processing
run_jobs
running_jobs
save (EnsEMBL::Web::ImageConfig)
save (EnsEMBL::Web::TmpFile)
save (EnsEMBL::Web::ViewConfig)
save (EnsEMBL::Web::Data)
save (EnsEMBL::Web::Configuration::Interface)
save (EnsEMBL::Web::TmpFile::Image)
save (EnsEMBL::Web::TmpFile::Tar)
save (EnsEMBL::Web::TmpFile::Driver::Disk)
save (EnsEMBL::Web::TmpFile::Driver::Memcached)
save_das
save_data
save_seq (EnsEMBL::Web::Object::Alignment)
save_seq (EnsEMBL::Web::Object::Transcript)
save_sources
save_to_db
scalex (Bio::EnsEMBL::GlyphSet)
scalex (Sanger::Graphics::TextHelper)
scalex (Sanger::Graphics::WebUserConfig)
scalex (EnsEMBL::Web::ImageConfig)
scaley
score (EnsEMBL::Web::Text::Feature)
score (EnsEMBL::Web::Text::Feature::GBrowse)
score (EnsEMBL::Web::Text::Feature::WIG)
score (ExaLead::Hit)
score_features
script (Sanger::Graphics::WebUserConfig)
script (EnsEMBL::Web::Proxiable)
script (EnsEMBL::Web::Proxy)
script_name (EnsEMBL::Web::Command)
script_name (EnsEMBL::Web::Interface)
script_name (EnsEMBL::Web::Component::Interface)
script_name (EnsEMBL::Web::Document::Common)
search (EnsEMBL::Web::Component::Go)
search (EnsEMBL::Web::Data::Help)
search_ALL (EnsEMBL::Web::Factory::UniSearch)
search_ALL (EnsEMBL::Web::Factory::Search::AltaVista)
search_ALL (EnsEMBL::Web::Factory::Search::Unisearch)
search_DOMAIN (EnsEMBL::Web::Factory::UniSearch)
search_DOMAIN (EnsEMBL::Web::Factory::Search::AltaVista)
search_DOMAIN (EnsEMBL::Web::Factory::Search::Unisearch)
search_FAMILY
search_GENE (EnsEMBL::Web::Factory::UniSearch)
search_GENE (EnsEMBL::Web::Factory::Search::AltaVista)
search_GENE (EnsEMBL::Web::Factory::Search::Unisearch)
search_GENOMICALIGNMENT
search_MARKER (EnsEMBL::Web::Factory::UniSearch)
search_MARKER (EnsEMBL::Web::Factory::Search::AltaVista)
search_MARKER (EnsEMBL::Web::Factory::Search::Unisearch)
search_OLIGOPROBE
search_QTL
search_SEQUENCE
search_SNP
search_articles
search_form
search_instructions
search_url (EnsEMBL::Web::Document::HTML::HomeSearch)
search_url (EnsEMBL::Web::Document::HTML::SearchBox)
segment_callback
select_to_delete
select_to_edit
selectall_arrayref (EnsEMBL::Web::IndexSupport)
selectall_arrayref (EnsEMBL::Web::Factory::Search::Unisearch)
selectrow_array
self_compara
send
send_activation_email
send_invitation_email
send_welcome_email
seq_region
seq_region_data (EnsEMBL::Web::Object::SNP)
seq_region_data (EnsEMBL::Web::Object::Variation)
seq_region_end (EnsEMBL::Web::Object::Gene)
seq_region_end (EnsEMBL::Web::Object::Location)
seq_region_end (EnsEMBL::Web::Object::Marker)
seq_region_end (EnsEMBL::Web::Object::MultipleLocation)
seq_region_end (EnsEMBL::Web::Object::SNP)
seq_region_end (EnsEMBL::Web::Object::Transcript)
seq_region_end (EnsEMBL::Web::Object::Translation)
seq_region_end (EnsEMBL::Web::Object::Variation)
seq_region_end (EnsEMBL::Web::Text::Feature)
seq_region_length (EnsEMBL::Web::Object::Location)
seq_region_length (EnsEMBL::Web::Object::MultipleLocation)
seq_region_name (EnsEMBL::Web::Object::Chromosome)
seq_region_name (EnsEMBL::Web::Object::Gene)
seq_region_name (EnsEMBL::Web::Object::Location)
seq_region_name (EnsEMBL::Web::Object::Marker)
seq_region_name (EnsEMBL::Web::Object::MultipleLocation)
seq_region_name (EnsEMBL::Web::Object::SNP)
seq_region_name (EnsEMBL::Web::Object::Transcript)
seq_region_name (EnsEMBL::Web::Object::Translation)
seq_region_name (EnsEMBL::Web::Object::Variation)
seq_region_sort
seq_region_start (EnsEMBL::Web::Object::Gene)
seq_region_start (EnsEMBL::Web::Object::Location)
seq_region_start (EnsEMBL::Web::Object::Marker)
seq_region_start (EnsEMBL::Web::Object::MultipleLocation)
seq_region_start (EnsEMBL::Web::Object::SNP)
seq_region_start (EnsEMBL::Web::Object::Transcript)
seq_region_start (EnsEMBL::Web::Object::Translation)
seq_region_start (EnsEMBL::Web::Object::Variation)
seq_region_start (EnsEMBL::Web::Text::Feature)
seq_region_strand (EnsEMBL::Web::Object::Gene)
seq_region_strand (EnsEMBL::Web::Object::Location)
seq_region_strand (EnsEMBL::Web::Object::Marker)
seq_region_strand (EnsEMBL::Web::Object::MultipleLocation)
seq_region_strand (EnsEMBL::Web::Object::SNP)
seq_region_strand (EnsEMBL::Web::Object::Transcript)
seq_region_strand (EnsEMBL::Web::Object::Translation)
seq_region_strand (EnsEMBL::Web::Object::Variation)
seq_region_strand (EnsEMBL::Web::Text::Feature)
seq_region_type (EnsEMBL::Web::Object::Chromosome)
seq_region_type (EnsEMBL::Web::Object::Gene)
seq_region_type (EnsEMBL::Web::Object::Location)
seq_region_type (EnsEMBL::Web::Object::Marker)
seq_region_type (EnsEMBL::Web::Object::MultipleLocation)
seq_region_type (EnsEMBL::Web::Object::SNP)
seq_region_type (EnsEMBL::Web::Object::Transcript)
seq_region_type (EnsEMBL::Web::Object::Translation)
seq_region_type (EnsEMBL::Web::Object::Variation)
seq_region_type_and_name
seq_region_type_human_readable
seqname (EnsEMBL::Web::Text::Feature)
seqname (EnsEMBL::Web::Text::Feature::generic)
sequence (EnsEMBL::Web::Component::Sequence)
sequence (EnsEMBL::Web::Component::DAS::Reference)
sequence (EnsEMBL::Web::Configuration::DAS)
sequence_display2
sequence_generateHTML
sequence_markupCodons
sequence_markupExons
sequence_markupInit
sequence_markup_and_render
sequence_markup_options
sequence_markup_options_form
sequence_options_form
sequencealignview (EnsEMBL::Web::Component::Slice)
sequencealignview (EnsEMBL::Web::Configuration::Location)
sequencealignview (EnsEMBL::Web::Configuration::Gene)
server_root (EnsEMBL::Web::Tools::Document)
server_root (EnsEMBL::Web::Tools::DocumentView)
server_stats
session (EnsEMBL::Web::Proxiable)
session (EnsEMBL::Web::Document::Renderer)
set (Sanger::Graphics::WebUserConfig)
set (EnsEMBL::Web::Cache)
set (EnsEMBL::Web::ViewConfig)
set (EnsEMBL::Web::Document::HTML::Title)
set (EnsEMBL::Web::Input::Options)
set (EnsEMBL::Web::OrderedTree::Node)
setCentrePoint
setLength
set_action
set_avail
set_button
set_complete_status_for_job
set_config (EnsEMBL::Web::SpeciesDefs)
set_config (EnsEMBL::Web::Data::Session)
set_content
set_data
set_default_action (EnsEMBL::Web::Configuration)
set_default_action (EnsEMBL::Web::Configuration::Blast)
set_default_action (EnsEMBL::Web::Configuration::Help)
set_default_action (EnsEMBL::Web::Configuration::Info)
set_default_action (EnsEMBL::Web::Configuration::Location)
set_default_action (EnsEMBL::Web::Configuration::SNP)
set_default_action (EnsEMBL::Web::Configuration::Transcript)
set_default_action (EnsEMBL::Web::Configuration::UniSearch)
set_default_action (EnsEMBL::Web::Configuration::UserData)
set_default_action (EnsEMBL::Web::Configuration::Variation)
set_default_action (EnsEMBL::Web::Configuration::Gene)
set_default_action (EnsEMBL::Web::Configuration::Account)
set_doc_type
set_extra
set_filter
set_my_config
set_parameter (Sanger::Graphics::WebUserConfig)
set_parameter (EnsEMBL::Web::ImageConfig)
set_parameters
set_parsed_status_for_job
set_pending_status_for_job
set_primary_key
set_running_status_for_job
set_species (EnsEMBL::Web::ExtURL)
set_species (EnsEMBL::Web::ImageConfig)
set_status_for_job
set_title (EnsEMBL::Web::Configuration)
set_title (EnsEMBL::Web::Document::Common)
set_title (EnsEMBL::Web::Document::Component)
set_title (EnsEMBL::Web::Document::Dynamic)
set_tmp_message
set_type
set_user
set_user_settings
set_view_config_from_string
set_width
set_write_access
share
share_link
shift
short_caption (EnsEMBL::Web::Object::Account)
short_caption (EnsEMBL::Web::Object::Blast)
short_caption (EnsEMBL::Web::Object::Gene)
short_caption (EnsEMBL::Web::Object::Help)
short_caption (EnsEMBL::Web::Object::Info)
short_caption (EnsEMBL::Web::Object::Location)
short_caption (EnsEMBL::Web::Object::Search)
short_caption (EnsEMBL::Web::Object::Server)
short_caption (EnsEMBL::Web::Object::Transcript)
short_caption (EnsEMBL::Web::Object::UniSearch)
short_caption (EnsEMBL::Web::Object::UserData)
short_caption (EnsEMBL::Web::Object::Variation)
short_codes
short_id_history
shout
show_history
show_karyotype
similarity_matches
simple
site_logo
site_name
sitename (EnsEMBL::Web::Document::HTML::Copyright)
sitename (EnsEMBL::Web::Document::HTML::Empty)
sitename (EnsEMBL::Web::Document::HTML::Copyright)
size
slice (EnsEMBL::Web::Object::Location)
slice (EnsEMBL::Web::Object::MultipleLocation)
slice2sr
slice_cache (EnsEMBL::Web::Object::DAS)
slice_cache (EnsEMBL::Web::Object::Location)
slice_number
slide (EnsEMBL::Web::Text::Feature::BED)
slide (EnsEMBL::Web::Text::Feature::GFF)
slide (EnsEMBL::Web::Text::Feature::PSL)
snp_display
snp_list
snps_markup
snpview_image
snpview_image_menu (EnsEMBL::Web::Component::SNP)
snpview_image_menu (EnsEMBL::Web::Component::Variation)
snpview_noimage
sort_out_snp_strand
sort_table_values
sortby (EnsEMBL::Web::Component::Server)
sortby (EnsEMBL::Web::Component::Server::ColourMap)
sortby_hls (EnsEMBL::Web::Component::Server)
sortby_hls (EnsEMBL::Web::Component::Server::ColourMap)
sortnames
source (EnsEMBL::Web::Object::Gene)
source (EnsEMBL::Web::Object::Marker)
source (EnsEMBL::Web::Object::SNP)
source (EnsEMBL::Web::Object::Transcript)
source (EnsEMBL::Web::Object::Translation)
source (EnsEMBL::Web::Object::Variation)
source_code_link
source_link
source_version (EnsEMBL::Web::Object::SNP)
source_version (EnsEMBL::Web::Object::Variation)
sources
sp_array
space2nbsp (EnsEMBL::Web::Component::Server)
space2nbsp (EnsEMBL::Web::Component::Server::ColourMap)
species (Bio::EnsEMBL::GlyphSet)
species (EnsEMBL::Web::ConfigPacker_base)
species (EnsEMBL::Web::Configuration)
species (EnsEMBL::Web::IndexSupport)
species (EnsEMBL::Web::Proxiable)
species (EnsEMBL::Web::Proxy)
species (EnsEMBL::Web::ViewConfig)
species_and_seq_region_list
species_defs (Bio::EnsEMBL::DrawableContainer)
species_defs (Bio::EnsEMBL::GlyphSetManager)
species_defs (Bio::EnsEMBL::GlyphSet)
species_defs (EnsEMBL::Web::ImageConfig)
species_defs (EnsEMBL::Web::Proxiable)
species_defs (EnsEMBL::Web::Proxy)
species_defs (EnsEMBL::Web::Registry)
species_defs (EnsEMBL::Web::ViewConfig)
species_defs (EnsEMBL::Web::BlastView::Tool)
species_defs (EnsEMBL::Web::Document::Page)
species_defs (EnsEMBL::Web::Document::WebPage)
species_defs (EnsEMBL::Web::Text::FeatureParser)
species_dropdown
species_full_name
species_items
species_label (EnsEMBL::Web::SpeciesDefs)
species_label (EnsEMBL::Web::ViewConfig)
species_list
species_processing_callback
spell
spellingsuggestions
split60
split_evidence_and_munge_gaps
spreadsheet
spreadsheet_Colours
spreadsheet_Species
spreadsheet_Stats
spreadsheet_markerMapLocations (EnsEMBL::Web::Component::Marker)
spreadsheet_markerMapLocations (EnsEMBL::Web::Object::Marker)
spreadsheet_miscset_all
spreadsheet_miscset_genes
spreadsheet_miscset_set
spreadsheet_miscset_slice
squish (Bio::EnsEMBL::GlyphSet::generic_simple)
squish (Bio::EnsEMBL::GlyphSet::generic_simplest)
squish (Bio::EnsEMBL::GlyphSet::regulatory_regions)
squish (Bio::EnsEMBL::GlyphSet::assemblyexception)
squish (Bio::EnsEMBL::GlyphSet::regulatory_search_regions)
sr2slice
src
stable_id (EnsEMBL::Web::Fake)
stable_id (EnsEMBL::Web::Object::ArchiveStableId)
stable_id (EnsEMBL::Web::Object::Gene)
stable_id (EnsEMBL::Web::Object::Transcript)
stable_id (EnsEMBL::Web::Object::Translation)
stage1
stage1_form
start (EnsEMBL::Web::Timer)
start (EnsEMBL::Web::Container::HSPContainer)
start (EnsEMBL::Web::Object::SNP)
start (EnsEMBL::Web::Object::Variation)
start (EnsEMBL::Web::Text::Feature)
start (ExaLead)
start (ExaLead::Hits)
static_components
static_links
statsview
status (EnsEMBL::Web::Component::ArchiveStableId)
status (EnsEMBL::Web::Component::SNP)
status (EnsEMBL::Web::Configuration::Server)
status (EnsEMBL::Web::Document::Panel)
status (EnsEMBL::Web::Object::SNP)
status (EnsEMBL::Web::Object::Transcript)
status (EnsEMBL::Web::Object::Variation)
status_complete
status_parsed
status_pending
status_running
storable (EnsEMBL::Web::ImageConfig)
storable (EnsEMBL::Web::ViewConfig)
storable_data
storage (Bio::EnsEMBL::DrawableContainer)
storage (Sanger::Graphics::DrawableContainer)
store (EnsEMBL::Web::Session)
store (EnsEMBL::Web::SpeciesDefs)
store_TransformedDomains
store_TransformedSNPS
store_TransformedTranscripts
store_data
store_feature (EnsEMBL::Web::Text::DensityFeatureParser)
store_feature (EnsEMBL::Web::Text::FeatureParser)
strain_name_text
strand (Sanger::Graphics::GlyphSet)
strand (EnsEMBL::Web::Object::Location)
strand (EnsEMBL::Web::Object::MultipleLocation)
strand (EnsEMBL::Web::Text::Feature)
strand (EnsEMBL::Web::Text::Feature::BED)
strand (EnsEMBL::Web::Text::Feature::DAS)
strand (EnsEMBL::Web::Text::Feature::GBrowse)
strand (EnsEMBL::Web::Text::Feature::GFF)
strand (EnsEMBL::Web::Text::Feature::PSL)
strand (EnsEMBL::Web::Text::Feature::WIG)
string
string_label
string_name
string_value
strip_HTML (EnsEMBL::Web::Document::Panel)
strip_HTML (EnsEMBL::Web::Document::SpreadSheet)
stroke
strokecolor
study_link
stuff
style (Sanger::Graphics::Renderer::svg)
style (EnsEMBL::Web::Form::Element)
style_attrib
style_by_filesize
styles
stylesheet (EnsEMBL::Web::Component::DAS)
stylesheet (EnsEMBL::Web::Component::DAS::Annotation)
stylesheet (EnsEMBL::Web::Configuration::DAS)
stylesheet_callback
sub_type
subclasses
submit_query
subsections (Sanger::Graphics::WebUserConfig)
subsections (EnsEMBL::Web::ImageConfig)
subslice
success
successor_history
successors
suffix
summary_stats
superclass
support
svg_rgb_by_id
svg_rgb_by_name
synonym (EnsEMBL::Web::Object::Location)
synonym (EnsEMBL::Web::Object::MultipleLocation)
synonyms (EnsEMBL::Web::Component::Marker)
synonyms (EnsEMBL::Web::Component::SNP)
table
table_data
table_info (EnsEMBL::Web::Proxiable)
table_info (EnsEMBL::Web::SpeciesDefs)
table_info_other
tag (Bio::EnsEMBL::GlyphSet_simple)
tag (Bio::EnsEMBL::GlyphSet::sequence)
tag (Bio::EnsEMBL::GlyphSet::_clone)
tag (Bio::EnsEMBL::GlyphSet::_qtl)
tag (Bio::EnsEMBL::GlyphSet::_repeat)
tag (Bio::EnsEMBL::GlyphSet::_simple)
tag (Bio::EnsEMBL::GlyphSet::_synteny)
tag (Bio::EnsEMBL::GlyphSet::_variation)
tag (Bio::EnsEMBL::GlyphSet::annotation_status)
tag (Bio::EnsEMBL::GlyphSet::assemblyexception)
tag (Bio::EnsEMBL::GlyphSet::fg_regulatory_features)
tagged_snp (EnsEMBL::Web::Component::LD)
tagged_snp (EnsEMBL::Web::Component::Location::LD)
tagged_snp (EnsEMBL::Web::Object::SNP)
tagged_snp (EnsEMBL::Web::Object::Variation)
tailnote
tailnotelvalue
temp_file_create
temp_file_name
template_INCLUDE
template_LINK
template_PAGE
template_RELEASE
template_SCRIPT
template_SPECIES
template_SPECIESDEFS
template_SPECIESINFO
templatize
terms (EnsEMBL::Web::Factory::UniSearch)
terms (ExaLead::Query)
text_haploview
text_label (Bio::EnsEMBL::GlyphSet_transcript)
text_label (Bio::EnsEMBL::GlyphSet_transcript)
text_label (Bio::EnsEMBL::GlyphSet::_transcript)
text_label (Bio::EnsEMBL::GlyphSet::_transcript)
text_lddata
texthelper (Sanger::Graphics::WebUserConfig)
texthelper (EnsEMBL::Web::ImageConfig)
textstyle
thousandify
ticket
tie_a
tile
timer (EnsEMBL::Web::Proxy)
timer (EnsEMBL::Web::Registry)
timer (EnsEMBL::Web::SpeciesDefs)
timer (EnsEMBL::Web::Document::WebPage)
timer_push (Bio::EnsEMBL::DrawableContainer)
timer_push (Bio::EnsEMBL::GlyphSet)
timer_push (EnsEMBL::Web::CoreObjects)
timer_push (EnsEMBL::Web::Magic)
timer_push (EnsEMBL::Web::Proxiable)
timer_push (EnsEMBL::Web::Proxy)
timer_push (EnsEMBL::Web::Registry)
timer_push (EnsEMBL::Web::SpeciesDefs)
timer_push (EnsEMBL::Web::Document::Page)
timer_push (EnsEMBL::Web::Document::Panel)
timer_push (EnsEMBL::Web::Document::WebPage)
timer_push (EnsEMBL::Web::Document::HTML::Content)
tint_by_hex
tint_by_rgb
title (Bio::EnsEMBL::GlyphSet_transcript)
title (Bio::EnsEMBL::GlyphSet_simple)
title (Bio::EnsEMBL::GlyphSet_transcript)
title (Bio::EnsEMBL::GlyphSet::sequence)
title (Bio::EnsEMBL::GlyphSet::tsv_variations)
title (Bio::EnsEMBL::GlyphSet::_qtl)
title (Bio::EnsEMBL::GlyphSet::_repeat)
title (Bio::EnsEMBL::GlyphSet::_simple)
title (Bio::EnsEMBL::GlyphSet::_synteny)
title (Bio::EnsEMBL::GlyphSet::_variation)
title (Bio::EnsEMBL::GlyphSet::alternative_assembly)
title (Bio::EnsEMBL::GlyphSet::annotation_status)
title (Bio::EnsEMBL::GlyphSet::assemblyexception)
title (Bio::EnsEMBL::GlyphSet::fg_regulatory_features)
title (EnsEMBL::Web::ImageConfig)
title (EnsEMBL::Web::ViewConfig)
toc_html
top_level
top_start_end
transHandler
transHandler_das
transHandler_no_species
transHandler_species
trans_description
transcript (EnsEMBL::Web::CoreObjects)
transcript (EnsEMBL::Web::Object::ArchiveStableId)
transcript (EnsEMBL::Web::Object::Transcript)
transcript (EnsEMBL::Web::Object::Translation)
transcript_class
transcript_key
transcript_label
transcript_long_caption
transcript_short_caption
transcript_type (Bio::EnsEMBL::GlyphSet_transcript)
transcript_type (EnsEMBL::Web::Object::Transcript)
transcript_variation (EnsEMBL::Web::Object::SNP)
transcript_variation (EnsEMBL::Web::Object::Variation)
transform (Bio::EnsEMBL::Glyph)
transform (Sanger::Graphics::Glyph)
transform (Sanger::Graphics::GlyphSet)
transform (Sanger::Graphics::WebUserConfig)
transform (Sanger::Graphics::Glyph::Circle)
transform (Sanger::Graphics::Glyph::Composite)
transform (Sanger::Graphics::Glyph::Poly)
transform (EnsEMBL::Web::ImageConfig)
translate
translation
translation_object (EnsEMBL::Web::Object::Transcript)
translation_object (EnsEMBL::Web::Object::Translation)
tree (EnsEMBL::Web::ConfigPacker_base)
tree (EnsEMBL::Web::Configuration)
tree (EnsEMBL::Web::ImageConfig)
tree (EnsEMBL::Web::Component::ArchiveStableId)
tree (EnsEMBL::Web::Component::Go)
tree (EnsEMBL::Web::Component::Server)
tree (EnsEMBL::Web::Configuration::Server)
tree (EnsEMBL::Web::Document::HTML::LocalContext)
tree_cache_key (EnsEMBL::Web::Configuration)
tree_cache_key (EnsEMBL::Web::Configuration::Search)
tree_cache_key (EnsEMBL::Web::Configuration::UserData)
tree_cache_key (EnsEMBL::Web::Configuration::Account)
tree_form (EnsEMBL::Web::Component::Server)
tree_form (EnsEMBL::Web::Component::Server::tree)
tsv_extent (EnsEMBL::Web::Component::Transcript::SNPView)
tsv_extent (EnsEMBL::Web::Component::Transcript::TranscriptSNPTable)
turn_off
turn_on
type (EnsEMBL::Web::Configuration)
type (EnsEMBL::Web::Fake)
type (EnsEMBL::Web::Problem)
type (EnsEMBL::Web::Proxiable)
type (EnsEMBL::Web::Form::Element)
type (EnsEMBL::Web::Interface::Element)
type (EnsEMBL::Web::Object::ArchiveStableId)
type (EnsEMBL::Web::Object::MultipleLocation)
type (EnsEMBL::Web::Text::Feature)
type (EnsEMBL::Web::Text::Feature::GBrowse)
type (EnsEMBL::Web::Tools::Document::Method)
type_name (EnsEMBL::Web::Object::Gene)
type_name (EnsEMBL::Web::Object::Transcript)
type_name (EnsEMBL::Web::Object::Translation)
types (EnsEMBL::Web::Component::DAS)
types (EnsEMBL::Web::Configuration::DAS)
types (EnsEMBL::Web::Tools::Document::Module)
uncomp
unique_variation_feature (EnsEMBL::Web::Object::SNP)
unique_variation_feature (EnsEMBL::Web::Object::Variation)
unmapped_detail
unmapped_object (EnsEMBL::Web::Object::Feature)
unmapped_object (EnsEMBL::Web::Object::Location)
unpack_db_tree
unshift (Sanger::Graphics::GlyphSet)
unshift (Sanger::Graphics::Glyph::Composite)
update_cache
update_config_from_parameter (EnsEMBL::Web::ImageConfig)
update_config_from_parameter (EnsEMBL::Web::ViewConfig)
update_configs_from_parameter
update_from_config_strings
update_from_input (EnsEMBL::Web::ImageConfig)
update_from_input (EnsEMBL::Web::ViewConfig)
update_invitations
url (EnsEMBL::Web::Root)
url (EnsEMBL::Web::ViewConfig)
url (EnsEMBL::Web::Component::Server)
url (EnsEMBL::Web::Tools::URL)
urlsource (EnsEMBL::Web::Component::Server)
urlsource (EnsEMBL::Web::Configuration::Server)
urlsource_form
usage_AlignSlice
usage_DnaDnaAlignFeature
usage_External
usage_Family
usage_GeneTree
usage_Homology
user
user_context
user_data (EnsEMBL::Web::OrderedTree)
user_data (EnsEMBL::Web::OrderedTree::Node)
user_details
user_notes
user_populate_tree (EnsEMBL::Web::Configuration::Transcript)
user_populate_tree (EnsEMBL::Web::Configuration::Gene)
user_populate_tree (EnsEMBL::Web::Configuration::Account)
valid (EnsEMBL::Web::Document::Renderer)
valid (EnsEMBL::Web::Document::Renderer::Apache)
valid (EnsEMBL::Web::Document::Renderer::File)
valid (EnsEMBL::Web::Document::Renderer::GzFile)
valid (EnsEMBL::Web::Document::Renderer::Stdout)
valid_rels
valid_species
valid_spp
validate (EnsEMBL::Web::Form::Element)
validate (EnsEMBL::Web::Form::Element::CheckBox)
validate (EnsEMBL::Web::Form::Element::DropDownAndString)
validate (EnsEMBL::Web::Form::Element::File)
validate (EnsEMBL::Web::Form::Element::MultiSelect)
validate (EnsEMBL::Web::Form::Element::RadioButton)
validate (EnsEMBL::Web::Form::Element::RadioGroup)
validate (EnsEMBL::Web::Form::Element::String)
validate (EnsEMBL::Web::Form::Element::Text)
validate_checksum
validate_types
valids (EnsEMBL::Web::Object::Gene)
valids (EnsEMBL::Web::Object::Slice)
valids (EnsEMBL::Web::Object::Transcript)
value (EnsEMBL::Web::Document::Renderer)
value (EnsEMBL::Web::Form::Element)
value (EnsEMBL::Web::Input::Parameter)
value (ExaLead::QueryParameter)
value (ExaLead::Value)
values (Sanger::Graphics::WebUserConfig)
values (EnsEMBL::Web::Form::Element)
var_class
var_location
vari (EnsEMBL::Web::Object::SNP)
vari (EnsEMBL::Web::Object::Variation)
vari_class (EnsEMBL::Web::Object::SNP)
vari_class (EnsEMBL::Web::Object::Variation)
variation
variationTable
variation_adaptor
variation_feature_mapping (EnsEMBL::Web::Object::SNP)
variation_feature_mapping (EnsEMBL::Web::Object::Variation)
variation_link
variation_long_caption
variation_short_caption
variations_missing
vega_projection (EnsEMBL::Web::Object::Gene)
vega_projection (EnsEMBL::Web::Object::Transcript)
vega_projection (EnsEMBL::Web::Object::Translation)
version (EnsEMBL::Web::Component::Server)
version (EnsEMBL::Web::Component::Translation)
version (EnsEMBL::Web::Object::ArchiveStableId)
version (EnsEMBL::Web::Object::Gene)
version (EnsEMBL::Web::Object::Transcript)
version (EnsEMBL::Web::Object::Translation)
version_check
version_info
vhost
vhost_id
vhosts
view
views
wait_time
wanted
warning
warnings
web_usage
web_user_db
webpage
webserver
weeks_in_month
weeks_in_year
widget
widget_type
width (Sanger::Graphics::GlyphSet)
width (Sanger::Graphics::TextHelper)
width (Sanger::Graphics::Glyph::Poly)
width (EnsEMBL::Web::Document::HTML::Logo)
width (EnsEMBL::Web::Form::Element)
wiggle_plot
withdraw_data (EnsEMBL::Web::Data)
withdraw_data (EnsEMBL::Web::Data::Session)
wrap_ad
write_base_frame
write_frameset
write_hierarchy
write_info_page
write_method_frame
write_module_page
write_module_pages
write_package_frame
x (Sanger::Graphics::GlyphSet)
x (Sanger::Graphics::Glyph::Circle)
x (Sanger::Graphics::Glyph::Poly)
xsearch_FAMILY (EnsEMBL::Web::Factory::Search::AltaVista)
xsearch_FAMILY (EnsEMBL::Web::Factory::Search::Unisearch)
xsearch_SNP (EnsEMBL::Web::Factory::Search::AltaVista)
xsearch_SNP (EnsEMBL::Web::Factory::Search::Unisearch)
y (Sanger::Graphics::GlyphSet)
y (Sanger::Graphics::Glyph::Circle)
y (Sanger::Graphics::Glyph::Poly)
y_transform
year
zmenu (Bio::EnsEMBL::GlyphSet_transcript)
zmenu (Bio::EnsEMBL::GlyphSet::HSP_plot)
zmenu (Bio::EnsEMBL::GlyphSet::generic_simple)
zmenu (Bio::EnsEMBL::GlyphSet::generic_simplest)
zmenu (Bio::EnsEMBL::GlyphSet::P_protdas)
zmenu (Bio::EnsEMBL::GlyphSet::urlfeature)
zmenu (Bio::EnsEMBL::GlyphSet::vegaclones)
zmenu (Bio::EnsEMBL::GlyphSet::_transcript)
zmenu (Bio::EnsEMBL::GlyphSet::ensemblclones)
zoom_URL (Bio::EnsEMBL::GlyphSet)
zoom_URL (Bio::EnsEMBL::GlyphSet::HSP_scalebar)
zoom_URL (Bio::EnsEMBL::GlyphSet::alignscalebar)
zoom_URL (Sanger::Graphics::GlyphSet::scalebar)
zoom_interval (Bio::EnsEMBL::GlyphSet::HSP_scalebar)
zoom_interval (Bio::EnsEMBL::GlyphSet::scalebar)
zoom_interval (Sanger::Graphics::GlyphSet::scalebar)
zoom_zmenu (Bio::EnsEMBL::GlyphSet)
zoom_zmenu (Bio::EnsEMBL::GlyphSet::alignscalebar)
zoom_zoom_zmenu