EnsEMBL::Web::Component::SNP

Location: /modules/EnsEMBL/Web/Component/SNP.pm
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Inherits from:

No subclasses

Overview

));

General_table_info

Individual_table

Internal_individual_table

Ld

Mapping_table

Method

Population_genotype_alleles

Population_table

Unknown

  • _attach_das (EnsEMBL::Web::Component)
  • _error (EnsEMBL::Web::Component)
  • _export (EnsEMBL::Web::Component)
  • _export_image (EnsEMBL::Web::Component)
  • _flip_URL
  • _hint (EnsEMBL::Web::Component)
  • _info (EnsEMBL::Web::Component)
  • _info_panel (EnsEMBL::Web::Component)
  • _init (EnsEMBL::Web::Component)
  • _matches (EnsEMBL::Web::Component)
  • _sort_similarity_links (EnsEMBL::Web::Component)
  • _warning (EnsEMBL::Web::Component)
  • ajaxable (EnsEMBL::Web::Component)
  • build_sequence (EnsEMBL::Web::Component)
  • cache (EnsEMBL::Web::Component)
  • cache_key (EnsEMBL::Web::Component)
  • cache_print (EnsEMBL::Web::Component)
  • cacheable (EnsEMBL::Web::Component)
  • caption (EnsEMBL::Web::Component)
  • chunked_content (EnsEMBL::Web::Component)
  • configurable (EnsEMBL::Web::Component)
  • get_sequence_data (EnsEMBL::Web::Component)
  • image_width (EnsEMBL::Web::Component)
  • markup_codons (EnsEMBL::Web::Component)
  • markup_comparisons (EnsEMBL::Web::Component)
  • markup_conservation (EnsEMBL::Web::Component)
  • markup_exons (EnsEMBL::Web::Component)
  • markup_line_numbers (EnsEMBL::Web::Component)
  • markup_variation (EnsEMBL::Web::Component)
  • modal_form (EnsEMBL::Web::Component)
  • new (EnsEMBL::Web::Component)
  • new_image (EnsEMBL::Web::Component)
  • new_karyotype_image (EnsEMBL::Web::Component)
  • new_vimage (EnsEMBL::Web::Component)
  • object (EnsEMBL::Web::Component)
  • remove_redundant_xrefs (EnsEMBL::Web::Component)
  • site_name (EnsEMBL::Web::Component)
Documentation coverage: 37 %

Methods

    _format_number
    Population_genotype_alleles.

    Arg1 null or a number Returns "unknown" if null or formats the number to 3 decimal places
    Returns "unknown" if null or formats the number to 3 decimal places
    View source

    _format_parent
    Internal_individual_table.

    Arg1 data object
    Arg2 parent data
    Description Formats output Returns string
    Example format_parent( $object->parent($object, $ind_genotype,"father") );
    Returns string
    View source

    _ld_populations
    LD.
    Arg1 object
    Description data structure with population id and name of pops with LD info for this SNP Returns hashref
    Example ld_populations()
    Returns hashref
    View source

    _pop_url
    Arg1 data object
    Arg2 Population name (to be displayed)
    Arg3 dbSNP population ID (variable to be linked to)
    Description makes pop_name into a link Returns string
    Example _pop_url($object, $pop_name, $pop_dbSNPID);
    Returns string
    View source

    _sort_extra_pops
    Population_table.
    Arg1 data object
    Arg2 hashref with population data
    Description returns string with Population name (size)
    description Returns string
    Example my $super_string = _sort_extra_pops($object, $freq_data{$pop_id}{pop_info}{"Super-Population"});
    Returns string
    View source

    _sort_start_end
    Mapping_table.

    Arg1 start and end coordinate Example : $coord = _sort_star_end($start, $end)_
    Description Returns $start-$end if they are defined, else 'n/a' Returns string
    Returns string
    View source

    _warn_block
    Simple subroutine to dump a formatted "warn" block to the error logs - useful when debugging complex data structures etc... output looks like:



    # # # TEXT. TEXT. TEXT. TEXT. # # TEXT. TEXT. TEXT. TEXT. # # TEXT. TEXT. TEXT. TEXT. # # # # TEXT. TEXT. TEXT. TEXT. # # TEXT. TEXT. TEXT. TEXT. # # #




    Inherited from EnsEMBL::Web::Component
    View source

    all_freqs
    Population_genotype_alleles.
    Arg1 panel
    Arg2 data object Example : $allele_panel->add_components( qw(all_freqs EnsEMBL::Web::Component::SNP::lal_freqs) );
    Description prints a table of allele and genotype frequencies for the variation per population Returns 1
    Returns 1
    View source

    alleles
    General_table_info.
    Arg1 panel
    Arg2 data object Example : $panel1->add_rows(qw(alleles EnsEMBL::Web::Component::SNP::alleles) );
    Description adds a label and html for the Variations alleles adds a line describing the ancestor allele if this exists Returns 1
    Returns 1
    View source

    format_frequencies
    Population_genotype_alleles.
    Arg1 panel
    Arg2 data object
    Arg3 frequency data
    Description prints a table of allele or genotype frequencies for the variation Returns 1
    Example format_frequencies($panel, $object, $freq_data);
    Returns 1
    View source

    individual
    Individual_table.

    Arg1 panel
    Arg2 data object Example : $object->outputIndGenotypeTable
    Description adds a table of Individual genotypes, their refSNP ssids, allele, sex etc. in spreadsheet format to the panel Returns 1
    Returns 1
    View source

    ld_data
    General_table_info.
    Arg1 panel
    Arg2 data object Example : $panel1->add_rows(qw(ld_data EnsEMBL::Web::Component::SNP::ld_data) );
    Description adds a label and its value to the panel: Get all the populations with LD data within 100kb of this SNP Make links from these populations to LDView Returns 1
    Returns 1
    View source

    link_to_ldview
    LD.
    Arg1 panel
    Arg2 object
    Arg3 hash ref of population data
    Description Make links from these populations to LDView Returns Table of HTML links to LDView
    Example link_to_ldview($panel, $object, \%pop_data);
    Returns Table of HTML links to LDView
    View source

    mappings
    Mapping_table.
    Arg1 panel
    Arg2 data object
    Arg3 the view name (i.e. "snpview" or "ldview") Example : $mapping_panel->add_components( qw(mappings EnsEMBL::Web::Component::SNP::mappings) );
    Description table showing Variation feature mappings to genomic locations Returns 1
    Returns 1
    View source

    moltype
    General_table_info.
    Arg1 panel
    Arg2 data object
    Description adds a label and its value to the panel: which describes the molecular type e.g. 'Genomic' Returns 1
    Returns 1
    View source

    name
    General_table_info.
    Arg1 panel
    Arg2 data object Example : $panel1->add_rows(qw(name EnsEMBL::Web::Component::SNP::name) );
    Description adds a label and the variation name, source to the panel Returns 1
    Returns 1
    View source

    seq_region
    General_table_info.

    Arg1 panel
    Arg2 data object Example : $panel1->add_rows(qw(seq_region EnsEMBL::Web::Component::SNP::seq_region) );
    Description adds a label and html to the panel the variations sequence region in two_col_table format Returns 1
    Returns 1
    View source

    snpview_image
    Image.
    Arg1 panel
    Arg2 data object
    Arg[3] Arg[3] : width (optional) Example : $image_panel->add_components(qw( menu EnsEMBL::Web::Component::SNP::snpview_image_menu image EnsEMBL::Web::Component::SNP::snpview_image ));
    Description Creates a drawable container for snpview and adds it to the panel Returns 0
    Returns 0
    View source

    snpview_image_menu
    Image.
    Arg1 panel
    Arg2 data object Example : $image_panel->add_components(qw( menu EnsEMBL::Web::Component::SNP::snpview_image_menu image EnsEMBL::Web::Component::SNP::snpview_image ));
    Description Creates a menu container for snpview and adds it to the panel Returns 0
    Returns 0
    View source

    snpview_noimage
    Image.

    Arg1 panel
    Arg2 data object Example : $image_panel->add_components(qw( no_image EnsEMBL::Web::Component::SNP::snpview_noimage ));
    Description Adds an HTML string to the panel if the SNP cannot be mapped uniquely Returns 1
    Returns 1
    View source

    status
    General_table_info.
    Arg1 panel
    Arg2 data object Example : $panel1->add_rows("status EnsEMBL::Web::Component::SNP::status");
    Description adds a label and string for the variation validation status to the panel Returns 1
    Returns 1
    View source

    synonyms
    General_table_info.
    Arg1 panel
    Arg2 data object Example : $panel1->add_rows(qw(synonyms EnsEMBL::Web::Component::SNP::synonyms) );
    Description adds a label and the variation synonyms to the panel Returns 1
    Returns 1
    View source