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)
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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
new()
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# File lib/protk/protein_summary.rb, line 74 def initialize() end
Public Instance Methods
as_protxml()
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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