Class: ProteinGroup

Inherits:
Object
  • Object
show all
Defined in:
lib/protk/protein_group.rb

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize ⇒ ProteinGroup

Returns a new instance of ProteinGroup.



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# File 'lib/protk/protein_group.rb', line 64

def initialize()

end

Instance Attribute Details

#group_number ⇒ Object

Returns the value of attribute group_number.



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# File 'lib/protk/protein_group.rb', line 12

def group_number
  @group_number
end

#group_probability ⇒ Object

Returns the value of attribute group_probability.



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# File 'lib/protk/protein_group.rb', line 13

def group_probability
  @group_probability
end

#proteins ⇒ Object

Returns the value of attribute proteins.



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# File 'lib/protk/protein_group.rb', line 14

def proteins
  @proteins
end

Class Method Details

.from_mzid(groupnode, mzid_doc, minprob = 0) ⇒ Object

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



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# 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

Instance Method Details

#as_protxml ⇒ Object 



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# 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