class ProteinSummary

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

Attributes

analysis_time[RW]
initial_min_peptide_prob[RW]
min_peptide_probability[RW]
min_peptide_weight[RW]
num_input_1_spectra[RW]
num_input_2_spectra[RW]
num_input_3_spectra[RW]
num_input_4_spectra[RW]
num_input_5_spectra[RW]
num_predicted_correct_prots[RW]
program_name[RW]
program_version[RW]
reference_database[RW]
residue_substitution_list[RW]
sample_enzyme[RW]
source_files[RW]
source_files_alt[RW]
total_no_spectrum_ids[RW]

Public Class Methods

from_mzid(mzid_doc) click to toggle source
# 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
new() click to toggle source
# File lib/protk/protein_summary.rb, line 74
def initialize()

end

Public Instance Methods

as_protxml() click to toggle source
# 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