Sha256: f9c99393e9e73ac1d826fc2a457cfdca9951787ed3a3109f90d6ca27e6968d28
Contents?: true
Size: 1.26 KB
Versions: 8
Compression:
Stored size: 1.26 KB
Contents
require 'ms/fasta'
require 'merge'
module Ms ; end
module Ms::Ident ; end
class Ms::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
Ms::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
8 entries across 8 versions & 1 rubygems