Class Bio::Nexus::TaxaBlock
In: lib/bio/db/nexus.rb
Parent: GenericBlock

DESCRIPTION

Bio::Nexus::TaxaBlock represents a taxa nexus block.

Example of Taxa block:

Begin Taxa; 

 Dimensions NTax=4;
 TaxLabels fish [comment] 'african frog' "rat snake" 'red mouse';

End;

USAGE

  require 'bio/db/nexus'

  # Create a new parser:
  nexus = Bio::Nexus.new( nexus_data_as_string )

  # Get first taxa block:
  taxa_block = nexus.get_taxa_blocks[ 0 ]
  # Get number of taxa:
  number_of_taxa = taxa_block.get_number_of_taxa.to_i
  # Get name of first taxon:
  first_taxon = taxa_block.get_taxa[ 0 ]

Methods

add_taxon   get_number_of_taxa   get_taxa   new   set_number_of_taxa   to_nexus  

Public Class methods

new( name )

Creates a new TaxaBlock object named ‘name’.

Arguments:

[Source]

     # File lib/bio/db/nexus.rb, line 853
853:       def initialize( name )
854:         super( name )
855:         @number_of_taxa = 0
856:         @taxa = Array.new
857:       end

Public Instance methods

add_taxon( taxon )

Adds a taxon name to this block.

Arguments:

[Source]

     # File lib/bio/db/nexus.rb, line 904
904:       def add_taxon( taxon )
905:         @taxa.push( taxon )
906:       end
get_number_of_taxa()

Gets the "number of taxa" property.

Returns:Integer

[Source]

     # File lib/bio/db/nexus.rb, line 878
878:       def get_number_of_taxa
879:         @number_of_taxa
880:       end
get_taxa()

Gets the taxa of this block.

Returns:Array

[Source]

     # File lib/bio/db/nexus.rb, line 886
886:       def get_taxa
887:         @taxa
888:       end
set_number_of_taxa( number_of_taxa )

Sets the "number of taxa" property.

Arguments:

  • (required) number_of_taxa: Integer

[Source]

     # File lib/bio/db/nexus.rb, line 895
895:       def set_number_of_taxa( number_of_taxa )
896:         @number_of_taxa = number_of_taxa
897:       end
to_nexus()

Returns a String describing this block as nexus formatted data.

Returns:String

[Source]

     # File lib/bio/db/nexus.rb, line 862
862:       def to_nexus
863:         line_1 = String.new
864:         line_1 << DIMENSIONS 
865:         if ( Nexus::Util::larger_than_zero( get_number_of_taxa  ) )
866:           line_1 << " " <<  NTAX << "=" << get_number_of_taxa
867:         end
868:         line_1 << DELIMITER
869:         line_2 = String.new
870:         line_2 << TAXLABELS << " " << Nexus::Util::array_to_string( get_taxa ) << DELIMITER
871:         Nexus::Util::to_nexus_helper( TAXA_BLOCK, [ line_1, line_2 ] )
872:       end

[Validate]