Inherits from:
No subclasses
Overview
));
General_table_info
Individual_table
Internal_individual_table
Ld
Mapping_table
Method
- _pop_url
- _warn_block (EnsEMBL::Web::Component)
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)
Methods
- _format_number
Population_genotype_alleles.
| Arg1 | null or a number 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, $ind_genotype,"father") ); |
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_ld_populations
LD.
| Arg1 | object |
| Description | data structure with population id and name of pops with LD info for this SNP Returns hashref |
| Example | ld_populations() |
View source
_pop_url
| Arg1 | data object |
| Arg2 | Population name (to be displayed) |
| Arg3 | dbSNP population ID (variable to be linked to) |
| Description | makes pop_name into a link Returns string |
| Example | _pop_url($object, $pop_name, $pop_dbSNPID); |
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"}); |
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 |
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 |
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alleles
General_table_info.
| Arg1 | panel |
| Arg2 | data object Example : $panel1->add_rows(qw(alleles EnsEMBL::Web::Component::SNP::alleles) ); |
| Description | adds a label and html for the Variations alleles adds a line describing the ancestor allele if this exists Returns 1 |
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format_frequencies
Population_genotype_alleles.
| Arg1 | panel |
| Arg2 | data object |
| Arg3 | frequency data |
| Description | prints a table of allele or genotype frequencies for the variation Returns 1 |
| Example | format_frequencies($panel, $object, $freq_data); |
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 |
View source
ld_data
General_table_info.
| Arg1 | panel |
| Arg2 | data object Example : $panel1->add_rows(qw(ld_data EnsEMBL::Web::Component::SNP::ld_data) ); |
| Description | adds a label and its value to the panel: Get all the populations with LD data within 100kb of this SNP Make links from these populations to LDView Returns 1 |
View source
link_to_ldview
LD.
| Arg1 | panel |
| Arg2 | object |
| Arg3 | hash ref of population data |
| Description | Make links from these populations to LDView Returns Table of HTML links to LDView |
| Example | link_to_ldview($panel, $object, \%pop_data); |
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 |
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 |
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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 |
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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 |
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 |
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 |
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 |
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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 |
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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 |
View source