Bio::Nexus::DistancesBlock represents a distances nexus block.
Begin Distances;
Dimensions nchar=20 ntax=5; Format Triangle=Upper; Matrix taxon_1 0.0 1.0 2.0 4.0 7.0 taxon_2 1.0 0.0 3.0 5.0 8.0 taxon_3 3.0 4.0 0.0 6.0 9.0 taxon_4 7.0 3.0 1.0 0.0 9.5 taxon_5 1.2 1.3 1.4 1.5 0.0;
End;
require 'bio/db/nexus' # Create a new parser: nexus = Bio::Nexus.new( nexus_data_as_string ) # Get distances block(s): distances_blocks = nexus.get_distances_blocks # Get matrix as Bio::Nexus::NexusMatrix object: matrix = distances_blocks[ 0 ].get_matrix # Get value (column 0 are names): val = matrix.get_value( 1, 5 )
Creates a new DistancesBlock object named ‘name’.
Arguments:
(required) name: String
# File lib/bio/db/nexus.rb, line 1332 def initialize( name ) super( name ) @number_of_taxa = 0 @number_of_characters = 0 @triangle = String.new @matrix = NexusMatrix.new end
Gets the matrix.
Returns |
# File lib/bio/db/nexus.rb, line 1391 def get_matrix @matrix end
Gets the “number of characters” property.
Returns |
Integer |
# File lib/bio/db/nexus.rb, line 1377 def get_number_of_characters @number_of_characters end
Gets the “number of taxa” property.
Returns |
Integer |
# File lib/bio/db/nexus.rb, line 1370 def get_number_of_taxa @number_of_taxa end
Gets the “triangle” property.
Returns |
# File lib/bio/db/nexus.rb, line 1384 def get_triangle @triangle end
Sets the matrix.
Arguments:
(required) matrix: Bio::Nexus::NexusMatrix
# File lib/bio/db/nexus.rb, line 1423 def set_matrix( matrix ) @matrix = matrix end
Sets the “number of characters” property.
Arguments:
(required) number_of_characters: Integer
# File lib/bio/db/nexus.rb, line 1407 def set_number_of_characters( number_of_characters ) @number_of_characters = number_of_characters end
Sets the “number of taxa” property.
Arguments:
(required) number_of_taxa: Integer
# File lib/bio/db/nexus.rb, line 1399 def set_number_of_taxa( number_of_taxa ) @number_of_taxa = number_of_taxa end
Sets the “triangle” property.
Arguments:
(required) triangle: String
# File lib/bio/db/nexus.rb, line 1415 def set_triangle( triangle ) @triangle = triangle end
Returns a String describing this block as nexus formatted data.
Returns |
# File lib/bio/db/nexus.rb, line 1343 def to_nexus line_1 = String.new line_1 << DIMENSIONS if ( Nexus::Util::larger_than_zero( get_number_of_taxa ) ) line_1 << " " << NTAX << "=" << get_number_of_taxa end if ( Nexus::Util::larger_than_zero( get_number_of_characters ) ) line_1 << " " << NCHAR << "=" << get_number_of_characters end line_1 << DELIMITER line_2 = String.new line_2 << FORMAT if ( Nexus::Util::longer_than_zero( get_triangle ) ) line_2 << " " << TRIANGLE << "=" << get_triangle end line_2 << DELIMITER line_3 = String.new line_3 << MATRIX Nexus::Util::to_nexus_helper( DISTANCES_BLOCK, [ line_1, line_2, line_3 ] + get_matrix.to_nexus_row_array( " " ) ) end
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