EnsEMBL::Web::Component::LD

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

No subclasses

Overview

Description: This class consists of methods which output chunks of XHTML for LD based displays. The page is based on a slice created round a gene or SNP This object is called from a Configuration object e.g. from package EnsEMBL::Web::Configuration::Location For each component to be displayed, you need to create an appropriate panel object and then add the component. See EnsEMBL::Web::Configuration::Location Args : Except where indicated, all methods take the same two arguments a EnsEMBL::Web::Document::Panel object and a EnsEMBL::Web::Proxy::Object object (data). Returns : In general components return true on completion. If true is returned and the components are chained (see notes in Ensembl::Web::Configuration) then the subsequence components are ignored. if false is returned any subsequent components are executed. Note: Variation objects have all the data (flanks, alleles) but no position Note: VariationFeature objects have position (but also short cut calls to allele etc.) for contigview

Dumping_form

Image_panel

Information_panel

Internal_call

Method

Unknown

  • _attach_das (EnsEMBL::Web::Component)
  • _error (EnsEMBL::Web::Component)
  • _export (EnsEMBL::Web::Component)
  • _export_image (EnsEMBL::Web::Component)
  • _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: 27 %

Methods

    _pop_url
    Internal_call.
    Arg 1 Proxy object
    Arg 2 Population name (to be displayed)
    Arg 3 dbSNP population ID (variable to be linked to)
    Description makes pop_name into a link Returns HTML string of link to population in dbSNP
    Example _pop_url($pop_name, $pop_dbSNPID);
    Returns HTML string of link to population in dbSNP
    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

    focus
    Information_panel.
    Description adds pair of values (type of focus e.g gene or snp and the ID) to panel if the paramater "gene" or "snp" is defined
    Purpose outputs focus of page e.g.. gene, SNP (rs5050)or slice

    View source

    ldview_image
    Image_panel.
    Description Gets the slice, creates the user config Creates the image, imagemap and renders the image Returns 0
    Returns 0
    View source

    ldview_image_menu
    Image_panel. Example : $image_panel->add_components(qw( menu EnsEMBL::Web::Component::LD::ldview_image_menu image EnsEMBL::Web::Component::LD::ldview_image ));
    Description Creates a menu container for ldview and adds it to the panel Returns 0
    Returns 0
    View source

    ldview_noimage
    Image_panel.

    Description Adds an HTML string to the panel if the LD cannot be mapped uniquely

    View source

    mappings
    Use this if there is more than one mapping for SNP

    Description table showing Variation feature mappings to genomic locations. May only display when a SNP maps to more than one location

    View source

    options
    Dumping_form.
    Description Adds text to the page instructing user how to navigate round page

    View source

    options_form
    Dumping_form.



    Description Creates a new form to dump LD data in different formats (html, text, excel and haploview) Returns $form
    Returns $form
    View source

    population_info
    Information_panel.
    Description Returns information about the population. Calls helper function print_pop_info to get population data (name, size, description, whether the SNP is tagged)
    Purpose outputs name, size, description of population and super/sub population info if exists

    View source

    prediction_method
    Information_panel.
    Description Adds text information about the prediction method
    Purpose standard blurb about calculation of LD

    View source

    print_pop_info
    Internal_call.
    Arg1 population object
    Arg2 label (e.g. "Super-Population" or "Sub-Population")
    Description Returns information about the population: name, size, description and whether it is a tagged SNP Returns HTML string with population data
    Example print_pop_info($super_pop, "Super-Population").
    Returns HTML string with population data
    View source

    tagged_snp
    Arg1 object
    Arg2 population name (string)
    Description Gets the EnsEMBL::Web::Object::SNP object off the proxy object and checks if SNP is tagged in the current population. Returns 0 if no SNP.
    returns no
    View source


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