class Proph::ProtSummary::Parser
Attributes
prot_groups[RW]
Public Class Methods
new(file=nil, with_peps=false, tp='axml')
click to toggle source
# File lib/ms/ident/pepxml/prot_summary.rb, line 74 def initialize(file=nil, with_peps=false, tp='axml') if file @prot_groups = parse_file(file, with_peps, tp) end end
Public Instance Methods
_parse_for_prot_groups(stream, with_peps=false, tp='axml')
click to toggle source
returns an array of ProtGroup
objects
# File lib/ms/ident/pepxml/prot_summary.rb, line 89 def _parse_for_prot_groups(stream, with_peps=false, tp='axml') prtgrps = [] case tp when 'axml' root = AXML.parse(stream) root.protein_group.each do |protein_group| pg = ProtGroup.new(protein_group.attrs) do protein_group.map do |protein| Prot.new(protein.attrs) end end prtgrps << pg end end prtgrps end
parse_file(file, with_peps=false, tp='axml')
click to toggle source
returns an array of protein_groups
# File lib/ms/ident/pepxml/prot_summary.rb, line 81 def parse_file(file, with_peps=false, tp='axml') File.open(file) do |fh| @prot_groups = _parse_for_prot_groups(fh, with_peps, tp) end @prot_groups end