class Ms::Ident::Pepxml::SearchDatabase
Attributes
database_name[RW]
optional
database_release_date[RW]
optional
database_release_identifier[RW]
optional
local_path[RW]
required! the local, full path to the protein sequence database
orig_database_url[RW]
optional
seq_type[RW]
required! ‘AA’ or ‘NA’
size_of_residues[RW]
optional
Public Class Methods
new(hash={}, get_size_of_residues=false)
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takes a hash to fill in values
# File lib/ms/ident/pepxml/search_database.rb, line 26 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
Public Instance Methods
set_size_of_residues!()
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returns self for chaining
# File lib/ms/ident/pepxml/search_database.rb, line 34 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
to_xml(builder)
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# File lib/ms/ident/pepxml/search_database.rb, line 42 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