class NpSearch::Sequence
Adapted from GeneValidator's Query Class.. A class to hold sequence data
Constants
- DI_NP_CLV
- MONO_NP_CLV
Attributes
defline[R]
html_seq[R]
id[R]
potential_cleaved_nps[RW]
score[RW]
seq[R]
signalp[R]
translated_frame[R]
Public Class Methods
new(entry, sp, frame = nil)
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# File lib/npsearch/sequence.rb, line 18 def initialize(entry, sp, frame = nil) @id = entry.entry_id @defline = entry.definition sp_cleavage_site_idx = sp[:ymax_pos].to_i - 1 @signalp = sp[:orf][0..(sp_cleavage_site_idx - 1)] @seq = sp[:orf][sp_cleavage_site_idx..-1] @html_seq = format_seq_for_html @translated_frame = frame @score = 0 @potential_cleaved_nps = nil end
Public Instance Methods
format_seq_for_html()
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# File lib/npsearch/sequence.rb, line 30 def format_seq_for_html seq = @seq.gsub(/C/, '<span class=cysteine>C</span>') seq.gsub!(/#{DI_NP_CLV}/i, '<span class=np_clv>\0</span>') seq.gsub!(/#{MONO_NP_CLV}/i, '\0::NP_CLV::') # so that we can target 'R' seq.gsub!('R::NP_CLV::', '<span class=mono_np_clv>R</span>') seq.gsub!('G<span class=np_clv>', '<span class=glycine>G</span><span class=np_clv>') "<span class=signalp>#{@signalp}</span><span class=seq>#{seq}</span>" end