class ProteinGroup

Attributes

group_number[RW]
group_probability[RW]
proteins[RW]

Public Class Methods

from_mzid(groupnode,mzid_doc,minprob=0) click to toggle source

Note: This is hacked together to work for a specific PeptideShaker output type Refactor and properly respect cvParams for real conversion

# File lib/protk/protein_group.rb, line 38
def from_mzid(groupnode,mzid_doc,minprob=0)

        group=new()

        group.group_number=groupnode.attributes['id'].split("_").last.to_i+1
        group.group_probability=mzid_doc.get_cvParam(groupnode,"MS:1002470").attributes['value'].to_f

        # require 'byebug';byebug

        protein_nodes=mzid_doc.get_proteins_for_group(groupnode)



        group_members = protein_nodes.select do |e| 
                mzid_doc.get_protein_probability(e)>=minprob
        end

        group.proteins = group_members.collect { |e| Protein.from_mzid(e,mzid_doc) }

        group
end
new() click to toggle source
# File lib/protk/protein_group.rb, line 64
def initialize()

end

Public Instance Methods

as_protxml() click to toggle source
# File lib/protk/protein_group.rb, line 68
def as_protxml()
        node = XML::Node.new('protein_group')
node["group_number"] = self.group_number.to_s
# require 'byebug';byebug
node["group_probability"] = (self.group_probability * 0.01).to_s
self.proteins.each { |prot| node << prot.as_protxml }
node
end