Class: ProteinSummary

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

Overview

Represents the protein_summary node of a protXML document This is the root of the document

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize ⇒ ProteinSummary

Returns a new instance of ProteinSummary.



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# File 'lib/protk/protein_summary.rb', line 74

def initialize()

end

Instance Attribute Details

#analysis_time ⇒ Object

Returns the value of attribute analysis_time.



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# File 'lib/protk/protein_summary.rb', line 29

def analysis_time
  @analysis_time
end

#initial_min_peptide_prob ⇒ Object

Returns the value of attribute initial_min_peptide_prob.



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# File 'lib/protk/protein_summary.rb', line 24

def initial_min_peptide_prob
  @initial_min_peptide_prob
end

#min_peptide_probability ⇒ Object

Returns the value of attribute min_peptide_probability.



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# File 'lib/protk/protein_summary.rb', line 16

def min_peptide_probability
  @min_peptide_probability
end

#min_peptide_weight ⇒ Object

Returns the value of attribute min_peptide_weight.



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# File 'lib/protk/protein_summary.rb', line 17

def min_peptide_weight
  @min_peptide_weight
end

#num_input_1_spectra ⇒ Object

Returns the value of attribute num_input_1_spectra.



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# File 'lib/protk/protein_summary.rb', line 19

def num_input_1_spectra
  @num_input_1_spectra
end

#num_input_2_spectra ⇒ Object

Returns the value of attribute num_input_2_spectra.



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# File 'lib/protk/protein_summary.rb', line 20

def num_input_2_spectra
  @num_input_2_spectra
end

#num_input_3_spectra ⇒ Object

Returns the value of attribute num_input_3_spectra.



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# File 'lib/protk/protein_summary.rb', line 21

def num_input_3_spectra
  @num_input_3_spectra
end

#num_input_4_spectra ⇒ Object

Returns the value of attribute num_input_4_spectra.



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# File 'lib/protk/protein_summary.rb', line 22

def num_input_4_spectra
  @num_input_4_spectra
end

#num_input_5_spectra ⇒ Object

Returns the value of attribute num_input_5_spectra.



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# File 'lib/protk/protein_summary.rb', line 23

def num_input_5_spectra
  @num_input_5_spectra
end

#num_predicted_correct_prots ⇒ Object

Returns the value of attribute num_predicted_correct_prots.



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# File 'lib/protk/protein_summary.rb', line 18

def num_predicted_correct_prots
  @num_predicted_correct_prots
end

#program_name ⇒ Object

Returns the value of attribute program_name.



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# File 'lib/protk/protein_summary.rb', line 28

def program_name
  @program_name
end

#program_version ⇒ Object

Returns the value of attribute program_version.



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# File 'lib/protk/protein_summary.rb', line 30

def program_version
  @program_version
end

#reference_database ⇒ Object

Returns the value of attribute reference_database.



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

def reference_database
  @reference_database
end

#residue_substitution_list ⇒ Object

Returns the value of attribute residue_substitution_list.



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

def residue_substitution_list
  @residue_substitution_list
end

#sample_enzyme ⇒ Object

Returns the value of attribute sample_enzyme.



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# File 'lib/protk/protein_summary.rb', line 26

def sample_enzyme
  @sample_enzyme
end

#source_files ⇒ Object

Returns the value of attribute source_files.



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

def source_files
  @source_files
end

#source_files_alt ⇒ Object

Returns the value of attribute source_files_alt.



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# File 'lib/protk/protein_summary.rb', line 15

def source_files_alt
  @source_files_alt
end

#total_no_spectrum_ids ⇒ Object

Returns the value of attribute total_no_spectrum_ids.



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# File 'lib/protk/protein_summary.rb', line 25

def total_no_spectrum_ids
  @total_no_spectrum_ids
end

Class Method Details

.from_mzid(mzid_doc) ⇒ Object 



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# File 'lib/protk/protein_summary.rb', line 35

def from_mzid(mzid_doc)

	summary = new()
	# Things we cant retrieve
	summary.residue_substitution_list = ""
	summary.min_peptide_probability = ""
	summary.min_peptide_weight = ""
	summary.num_predicted_correct_prots = ""
	summary.num_input_1_spectra = ""
	summary.num_input_2_spectra = ""
	summary.num_input_3_spectra = ""
	summary.num_input_4_spectra = ""
	summary.num_input_5_spectra = ""
	summary.initial_min_peptide_prob = ""
	summary.total_no_spectrum_ids = ""			
	summary.analysis_time = ""

	db = mzid_doc.search_databases.first
	summary.reference_database = db.attributes['location']

	summary.source_files = mzid_doc.source_files.collect { |sf| sf.attributes['location'] }
	summary.source_files_alt = summary.source_files

	summary.sample_enzyme = mzid_doc.enzymes.first.attributes['name']
	if mzid_doc.enzymes.first.attributes['semiSpecific']=="true"
		summary.sample_enzyme = "semi#{summary.sample_enzyme}"
	end

	analysis_software = mzid_doc.analysis_software.first
	summary.program_name = analysis_software.attributes['name']
	summary.program_version = analysis_software.attributes['version']

	summary
end

Instance Method Details

#as_protxml ⇒ Object 



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# File 'lib/protk/protein_summary.rb', line 78

def as_protxml()
	node = XML::Node.new('protein_summary_header')
	# node.space_preserve=true
	node["reference_database"] = self.reference_database
	node["min_peptide_probability"] = self.min_peptide_probability
	node["min_peptide_weight"] = self.min_peptide_weight
	node["num_predicted_correct_prots"] = self.num_predicted_correct_prots
	node["num_input_1_spectra"] = self.num_input_1_spectra
	node["num_input_2_spectra"] = self.num_input_2_spectra
	node["num_input_3_spectra"] = self.num_input_3_spectra
	node["num_input_4_spectra"] = self.num_input_4_spectra
	node["num_input_5_spectra"] = self.num_input_5_spectra
	node["initial_min_peptide_prob"] = self.initial_min_peptide_prob
	node["total_no_spectrum_ids"] = self.total_no_spectrum_ids
	node["sample_enzyme"] = self.sample_enzyme


	cnode = XML::Node.new('program_details')
	# node.space_preserve=true
	cnode["program_name"] = self.program_name
	cnode["analysis_time"] = self.analysis_time
	cnode["program_version"] = self.program_version
#		require 'byebug';byebug

	node << cnode

	# ddnode = XML::Node.new('dataset_derivation')
	# ddnode["generation_no"]="0"

	# node << ddnode

 	node
end