Class | Bio::Nexus::TaxaBlock |
In: |
lib/bio/db/nexus.rb
|
Parent: | GenericBlock |
Bio::Nexus::TaxaBlock represents a taxa nexus block.
Begin Taxa;
Dimensions NTax=4; TaxLabels fish [comment] 'african frog' "rat snake" 'red mouse';
End;
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 ]
Gets the "number of taxa" property.
Returns: | Integer |
# File lib/bio/db/nexus.rb, line 878 878: def get_number_of_taxa 879: @number_of_taxa 880: end
Gets the taxa of this block.
Returns: | Array |
# File lib/bio/db/nexus.rb, line 886 886: def get_taxa 887: @taxa 888: end
Sets the "number of taxa" property.
Arguments:
# 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
Returns a String describing this block as nexus formatted data.
Returns: | String |
# 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