No superclasses
Subclasses:
- Bio::EnsEMBL::GlyphSet::HSP_coverage
- Bio::EnsEMBL::GlyphSet::HSP_scalebar
- Bio::EnsEMBL::GlyphSet::Psnp_legend
- Bio::EnsEMBL::GlyphSet::TSE_transcript
- Bio::EnsEMBL::GlyphSet::Vannotation_status
- Bio::EnsEMBL::GlyphSet::Vbinned
- Bio::EnsEMBL::GlyphSet::Vbinned_bar
- Bio::EnsEMBL::GlyphSet::Vbinned_outline
- Bio::EnsEMBL::GlyphSet::Videogram_legend
- Bio::EnsEMBL::GlyphSet::Vrefseqs
- Bio::EnsEMBL::GlyphSet::Vsupercontigs
- Bio::EnsEMBL::GlyphSet::Vsynteny
- Bio::EnsEMBL::GlyphSet::alignscalebar
- Bio::EnsEMBL::GlyphSet::comparafake
- Bio::EnsEMBL::GlyphSet::coverage
- Bio::EnsEMBL::GlyphSet::fg_regulatory_features_legend
- Bio::EnsEMBL::GlyphSet::gcplot
- Bio::EnsEMBL::GlyphSet::gene_legend
- Bio::EnsEMBL::GlyphSet::gsv_domain
- Bio::EnsEMBL::GlyphSet::gsv_transcript
- Bio::EnsEMBL::GlyphSet::gsv_variations
- Bio::EnsEMBL::GlyphSet::ld2
- Bio::EnsEMBL::GlyphSet::navigation
- Bio::EnsEMBL::GlyphSet::read_coverage
- Bio::EnsEMBL::GlyphSet::scalebar
- Bio::EnsEMBL::GlyphSet::snp_fake_haplotype
- Bio::EnsEMBL::GlyphSet::text
- Bio::EnsEMBL::GlyphSet::tsv_haplotype_legend
- Bio::EnsEMBL::GlyphSet::tsv_missing
- Bio::EnsEMBL::GlyphSet::tsv_transcript
- Bio::EnsEMBL::GlyphSet::tsv_variations
- Bio::EnsEMBL::GlyphSet::variation_legend
- Sanger::Graphics::GlyphSet::scalebar
Overview
Accessor
Etc...
Method
Unknown
- Bezier
- Circle
- Composite
- Diagnostic
- Ellipse
- HASH_URL
- ID_URL
- Intron
- Line
- Poly
- Rect
- Space
- Sprite
- Text
- _c
- _colour_background
- _max_bump_row
- _pos
- _render_text
- _type
- _url
- bumpbutton
- cache
- check
- core
- das_link
- dbadaptor
- de_camel
- draw_cigar_feature
- errorTrack
- error_track_name
- gene_key
- gene_label
- get_featurestyle
- get_font_details
- get_parameter
- get_text_width
- get_textheight
- human_readable
- image_width
- init_label
- label2
- legend
- my_colour
- my_config
- new
- no_features
- readable_strand
- render
- render_normal
- scalex
- set_my_config
- slice2sr
- species
- sr2slice
- transcript_key
- transcript_label
- zoom_URL
- zoom_zmenu
- zoom_zoom_zmenu
Methods
- _init_bump
Initialize bumping - single parameter - max depth - if undefined it is "infinite"
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_threshold_update
Update parameters of the display based on the size of the slice... threshold_array contains a hash of values: 'threshold_array' => { slice_length_1 => { k=>v, .... } # hash 1 slice_length_2 => { k=>v, .... } # hash 2 }. If slice_length <= slice_length_1 - do nothing If slice_length_1 < slice_length <= slice_length_2 - update configuration values from - hash 1 If slice_length_2 < slice_length ... - update configuration values from - hash 2 Etc....
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bump_row
compute the row to bump the feature to.. parameters are start/end in drawing (pixel co-ordinates)
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commify
Puts commas into numbers over 1000
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get_featuredata
_init_bump <- initialise the bumping code to be able to pack track... moved from separate Bump module so that it can be used in an OO way!! parameter passed is the maximum number of rows to bump... (optional)
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get_gd_simple
and fontsize. GD::Text objects are cached against fontname and fontsize.Returns the GD::Text object appropriate for the given fontname
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get_gd_text
and fontsize. GD::Text objects are cached against fontname and fontsize.Returns the GD::Text object appropriate for the given fontname
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get_text_simple
Simple function which calls the get_font_details and caches the result!!
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species_defs
Accessor.
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timer_push
Helper functions to wrap round Glyphs...
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