EnsEMBL::Web::Object::Slice

Location: /modules/EnsEMBL/Web/Object/Slice.pm
Source code · Permalink

Inherits from:

No subclasses

Overview

This object is called from a Component object e.g. my ($count_snps, $filtered_snps) = $sliceObj->getVariationFeatures(); This class consists of methods for calls on a slice object.

Accessor

Deprecated

Geneseqalignview

Genesnpview

Method

Sequencealignview

Unknown

  • _availability (EnsEMBL::Web::Object)
  • _help_URL (EnsEMBL::Web::Object)
  • availability (EnsEMBL::Web::Object)
  • bp_to_nearest_unit (EnsEMBL::Web::Object)
  • can_export (EnsEMBL::Web::Object)
  • core_params (EnsEMBL::Web::Object)
  • count_alignments (EnsEMBL::Web::Object)
  • counts (EnsEMBL::Web::Object)
  • fetch_homologues_of_gene_in_species (EnsEMBL::Web::Object)
  • gene_description (EnsEMBL::Web::Object)
  • generate_query_url (EnsEMBL::Web::Object)
  • getCoordinateSystem (EnsEMBL::Web::Object)
  • get_DASCollection (EnsEMBL::Web::Object)
  • get_adaptor (EnsEMBL::Web::Object)
  • new_image (EnsEMBL::Web::Object)
  • new_karyotype_image (EnsEMBL::Web::Object)
  • new_vimage (EnsEMBL::Web::Object)
  • referer (EnsEMBL::Web::Object)
Documentation coverage: 62 %

Methods

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

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

    URL
    (%params) Returns an absolute link to another script. %params hash is used as the parameters for the link. Note keys species and script are handled differently - as these are not passed as parameters but set the species and script name respectively in the URL
    Inherited from EnsEMBL::Web::Object
    View source

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

    alternative_object_from_factory
    There may be occassions when a script needs to work with features of more than one type. in this case we create a new EnsEMBL::Web::Proxy::Factory object for the alternative data type and retrieves the data (based on the standard URL parameters for the new factory) attach it to the universal datahash __data
    Inherited from EnsEMBL::Web::Object
    View source

    command
    Command object attached to proxy object
    Inherited from EnsEMBL::Web::Object
    View source

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

    exon_display
    GeneSeqAlignView.
    View source

    filter_munged_snps
    Arg1 Web slice obj
    Arg2 arrayref of munged 'fake snps' = [ fake_s, fake_e, SNP ]
    Arg3 gene (optional)
    Example Called from within filters 'fake snps' based on source, conseq type, validation etc Returns arrayref of munged 'fake snps' = [ fake_s, fake_e, SNP ]
    Returns arrayref of munged 'fake snps' = [ fake_s, fake_e, SNP ]
    View source

    filter_snps
    Arg1 Web Proxy::Object (slice)
    Arg2 arrayref VariationFeature objects
    Example Called from within filters snps based on users' selected parameters (which are obtained from $self->valids) e.g. on source, conseq type, validation etc Returns An arrayref of VariationFeature objects
    Returns An arrayref of VariationFeature objects
    View source

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

    getFakeMungedVariationFeatures
    arrayref of munged 'fake snps' = [ fake_s, fake_e, SNP ] scalar - number of SNPs filtered out by the context filter
    Arg1 Web slice obj
    Arg2 Subslices
    Arg3 Optional: gene
    Example Called from EnsEMBL::Web::Object::Transcript.pm for TSV Gets SNPs on slice for display + counts Returns scalar - number of SNPs on slice post context filtering, prior to other filters
    Returns scalar - number of SNPs on slice post context filtering, prior to other filters
    View source

    getVariationFeatures
    Arg1 Web Proxy::Object (slice) fetches all variation features on Slice object Calls $self->filter_snps to filter these by the user's selected parameters (e.g.type, class etc) Returns scalar- total number of SNPs in the arry before filtering
    Called from SNP component
    Needed for Bio::EnsEMBL::GlyphSet::variation.pm
    Returns arrayref- of VariationFeature objects after filtering
    View source

    get_genotyped_VariationFeatures
    Arg1 Web Proxy::Object (slice) fetches all variation features on Slice object Calls $self->filter_snps to filter these by the user's selected parameters (e.g.type, class etc) Returns scalar- total number of SNPs in the arry before filtering
    Called from SNP component
    Needed for Bio::EnsEMBL::GlyphSet::genotyped_variation.pm
    Returns arrayref- of VariationFeature objects after filtering
    View source

    get_individuals
    SequenceAlignView.
    Arg (optional) Arg (optional) : type string -"default": returns samples checked by default -"reseq": returns all resequencing sames -"reference": returns the reference (golden path name) -"display": returns all samples (for dropdown list) with default ones first
    Description returns selected samples (by default) Returns list
    Returns list
    View source

    highlight_display
    GeneSeqAlignView.
    View source

    highlights
    Accessor. The highlights array is passed between web-requests to highlight selected items (e.g. Gene around which contigview had been rendered. If any data is passed this is stored in the highlights array and an arrayref of (unique) elements is returned.
    Inherited from EnsEMBL::Web::Object
    View source

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

    interface
    Data interface attached to object
    Inherited from EnsEMBL::Web::Object
    View source

    line_numbering
    GeneSeqAlignView.
    View source

    location_URL
    Parameters: $feature, $script, $contextReturns a link to a contigview style display, based on feature, with context
    Inherited from EnsEMBL::Web::Object
    View source

    mapview_link
    Parameter $feature on a "real chromosome" then this is encapsulated in a link to mapview.Returns name of seq_region $feature is on. If the passed features is
    Inherited from EnsEMBL::Web::Object
    View source

    munge_gaps
    Arg1 Proxy::Object (slice)
    Arg2 Subslices
    Arg3 bp position 1: start
    Arg4 bp position 2: end
    Description Calculates new positions based on subslice
    Example Called from within
    Needed for TranscriptSNPView, GeneSNPView

    View source

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

    seq_region_type_and_name
    Returns the type/name of seq_region in human readable form - if the coord system type is part of the name this is dropped.
    Inherited from EnsEMBL::Web::Object
    View source

    seq_region_type_human_readable
    Returns the type of seq_region in "human readable form" (in this case just first letter captialised)
    Inherited from EnsEMBL::Web::Object
    View source

    snp_display
    GeneSeqAlignView.
    View source

    sources
    Arg1 Web slice obj gets all variation sources Returns hashref with keys as valid options, value = 1
    Returns hashref with keys as valid options, value = 1
    View source

    valids
    Arg1 Web Proxy::Object (slice) Gets all the user's selected parameters from $self->params() Returns Hashref of options with keys as valid options, value = 1 if they are on
    Called from self
    Needed for Bio::EnsEMBL::GlyphSet::variation.pm, Bio::EnsEMBL::GlyphSet::genotyped_variation.pm TranscriptSNPView GeneSNPView
    Returns Hashref of options with keys as valid options, value = 1 if they are on
    View source

    variation_adaptor
    Fetches the variation adaptor and puts it on the object hash
    View source


← Home · Source code