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Contents
require 'mspire/fasta'
require 'merge'
module Mspire ; end
module Mspire::Ident ; end
class Mspire::Ident::Pepxml
class SearchDatabase
include Merge
# required! the local, full path to the protein sequence database
attr_accessor :local_path
# required! 'AA' or 'NA'
attr_accessor :seq_type
# optional
attr_accessor :database_name
# optional
attr_accessor :orig_database_url
# optional
attr_accessor :database_release_date
# optional
attr_accessor :database_release_identifier
# optional
attr_accessor :size_of_residues
# takes a hash to fill in values
def initialize(hash={}, get_size_of_residues=false)
merge!(hash)
if get_size_of_residues && File.exist?(@local_path)
set_size_of_residues!
end
end
# returns self for chaining
def set_size_of_residues!
@size_of_residues = 0
Mspire::Fasta.foreach(@local_path) do |entry|
@size_of_residues += entry.sequence.size
end
self
end
def to_xml(builder)
attrs = [:local_path, :seq_type, :database_name, :orig_database_url, :database_release_date, :database_release_identifier, :size_of_residues].map {|k| v=send(k) ; [k, v] if v }.compact
builder.search_database(Hash[attrs])
builder
end
end
end
Version data entries
39 entries across 39 versions & 1 rubygems