Inherits from:
No subclasses
Overview
';
Geneseqalignview
Geneseqview
Method
- _sort_slices
- _warn_block (EnsEMBL::Web::Component)
- add_display_name
- markupInit
- markup_and_render
- sequence_markupInit
- sort_out_snp_strand
Sequencealignview
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)
- add_text
- ajaxable (EnsEMBL::Web::Component)
- alignment_options_form
- 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)
- dump_hash
- get_sequence_data (EnsEMBL::Web::Component)
- image_width (EnsEMBL::Web::Component)
- individuals_options_form
- markupCodons
- markupConservation
- markupExons
- markupSNPs
- 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)
- sequence_markupCodons
- sequence_markupExons
- sequence_markup_options
- sequence_markup_options_form
- sequence_options_form
- site_name (EnsEMBL::Web::Component)
Methods
- _sort_slices
This method sort the values of hRef according to the _order tags if sets
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
add_display_name
View source
align_sequence_display
GeneSeqAlignView.
| Arg1 | panel |
| Arg2 | Proxy Obj of type Gene |
View source
bin_starts
GeneSeqView. Sequence markup uses a 'variable-length bin' approach. Each bin has a format. A feature can span multiple bins. Allows for feature overlaps - combined formats. Bins start at feature starts, and end at feature ends + 1 Allow for cigar strings - these split alignments into 'mini-features'.
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cigar_segments
| Arg | Bio::EnsEMBL::Feature GeneSeqView |
View source
generateHTML
';.
View source
markupInit
abbreviated name and display nameReturns arrayref of conservation
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markup_and_render
GeneSeqAlignView and SequenceAlignView
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populate_bins
GeneSeqView. Code to mark up the exons in each bin
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sequence_display2
GeneSeqView.
| Arg1 | panel |
| Arg2 | Proxy Obj of type Gene |
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sequence_generateHTML
';.
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sequence_markupInit
abbreviated name and display nameReturns arrayref of conservation
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sequence_markup_and_render
SequenceAlignView.
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sequencealignview
SequenceAlignView. Returns 1
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sort_out_snp_strand
GeneSeqView and GeneSeqAlignView
| Arg | variation object slice strand Returns the start of the snp relative to the gene |
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