sequence.rb in npsearch-2.1.0

- old
+ new
@@ -1,34 +1,37 @@
+# Top level module / namespace.
 module NpSearch
+  # Adapted from GeneValidator's Query Class..
   # A class to hold sequence data
   class Sequence
-    DI_NP_CLV = 'KR|KK|RR'
-    MONO_NP_CLV = '[KRH]..R|[KRH]....R|[KRH]......R'
+    DI_NP_CLV   = 'KR|KK|RR'.freeze
+    MONO_NP_CLV = '[KRH]..R|[KRH]....R|[KRH]......R'.freeze
 
     attr_reader :id
+    attr_reader :defline
     attr_reader :signalp
     attr_reader :seq
     attr_reader :html_seq
-    attr_reader :signalp_output
     attr_reader :translated_frame
     attr_accessor :score
     attr_accessor :potential_cleaved_nps
 
-    def initialize(id, seq, signalp_output, frame = nil)
-      @id                    = id
-      sp_cleavage_site_idx   = signalp_output[:ymax_pos].to_i - 1
-      @signalp               = seq[0..(sp_cleavage_site_idx - 1)]
-      @seq                   = seq[sp_cleavage_site_idx..-1]
+    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
 
     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!(/#{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