Class: Bio::NeXML::Parser

Inherits:
Object
  • Object
show all
Defined in:
lib/bio/db/nexml/parser.rb

Overview

end

Instance Method Summary collapse

Constructor Details

#initialize(nexml, validate = false) ⇒ Parser

Returns a new instance of Parser.



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# File 'lib/bio/db/nexml/parser.rb', line 14

def initialize( nexml, validate = false )
  #initialize a cache
  @cache = {}

  #initialize a libxml cursor
  @reader = read( nexml )
  
  #validate
  validate_nexml if validate

end

Instance Method Details

#close ⇒ Object

Close the assosicated XML::Reader object and try to free other resources like @nexml



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# File 'lib/bio/db/nexml/parser.rb', line 63

def close
  @reader.close
end

#parse ⇒ Object

Is a factory method that returns an object of class Bio::NeXML::Nexml



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# File 'lib/bio/db/nexml/parser.rb', line 28

def parse
  #return a cached version if it exists
  return @nexml if @nexml

  #start at the root element
  skip_leader

  #start with a new Nexml object
  version = attribute( 'version' )
  generator = attribute( 'generator' )
  @nexml = NeXML::Nexml.new( version, generator )

  #perhaps a namespace api as well
  
  #start parsing other elements
  while next_node
    case local_name
    when "otus"
      @nexml.add_otus( parse_otus )
    when "trees"
      @nexml.add_trees( parse_trees )
    when "characters"
      @nexml.add_characters( parse_characters )
    end
  end

  #close the libxml parser object
  #close

  #return the Nexml object
  @nexml
end