class Bio::Nexus::DistancesBlock
DESCRIPTION¶ ↑
Bio::Nexus::DistancesBlock represents a distances nexus block.
Example of Distances 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;
USAGE¶ ↑
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 )
Constants
- TRIANGLE
Public Class Methods
Source
# File lib/bio/db/nexus.rb 1333 def initialize( name ) 1334 super( name ) 1335 @number_of_taxa = 0 1336 @number_of_characters = 0 1337 @triangle = String.new 1338 @matrix = NexusMatrix.new 1339 end
Creates a new DistancesBlock object named ‘name’.
Arguments:
-
(required) name: String
Calls superclass method
Bio::Nexus::GenericBlock::new
Public Instance Methods
Source
# File lib/bio/db/nexus.rb 1392 def get_matrix 1393 @matrix 1394 end
Gets the matrix.
- Returns
Source
# File lib/bio/db/nexus.rb 1378 def get_number_of_characters 1379 @number_of_characters 1380 end
Gets the “number of characters” property.
- Returns
-
Integer
Source
# File lib/bio/db/nexus.rb 1371 def get_number_of_taxa 1372 @number_of_taxa 1373 end
Gets the “number of taxa” property.
- Returns
-
Integer
Source
# File lib/bio/db/nexus.rb 1385 def get_triangle 1386 @triangle 1387 end
Gets the “triangle” property.
- Returns
-
String
Source
# File lib/bio/db/nexus.rb 1424 def set_matrix( matrix ) 1425 @matrix = matrix 1426 end
Sets the matrix.
Arguments:
-
(required) matrix:
Bio::Nexus::NexusMatrix
Source
# File lib/bio/db/nexus.rb 1408 def set_number_of_characters( number_of_characters ) 1409 @number_of_characters = number_of_characters 1410 end
Sets the “number of characters” property.
Arguments:
-
(required) number_of_characters: Integer
Source
# File lib/bio/db/nexus.rb 1400 def set_number_of_taxa( number_of_taxa ) 1401 @number_of_taxa = number_of_taxa 1402 end
Sets the “number of taxa” property.
Arguments:
-
(required) number_of_taxa: Integer
Source
# File lib/bio/db/nexus.rb 1416 def set_triangle( triangle ) 1417 @triangle = triangle 1418 end
Sets the “triangle” property.
Arguments:
-
(required) triangle: String
Source
# File lib/bio/db/nexus.rb 1344 def to_nexus 1345 line_1 = String.new 1346 line_1 << DIMENSIONS 1347 if ( Nexus::Util::larger_than_zero( get_number_of_taxa ) ) 1348 line_1 << " " << NTAX << "=" << get_number_of_taxa 1349 end 1350 if ( Nexus::Util::larger_than_zero( get_number_of_characters ) ) 1351 line_1 << " " << NCHAR << "=" << get_number_of_characters 1352 end 1353 line_1 << DELIMITER 1354 1355 line_2 = String.new 1356 line_2 << FORMAT 1357 if ( Nexus::Util::longer_than_zero( get_triangle ) ) 1358 line_2 << " " << TRIANGLE << "=" << get_triangle 1359 end 1360 line_2 << DELIMITER 1361 1362 line_3 = String.new 1363 line_3 << MATRIX 1364 Nexus::Util::to_nexus_helper( DISTANCES_BLOCK, [ line_1, line_2, line_3 ] + 1365 get_matrix.to_nexus_row_array( " " ) ) 1366 end
Returns a String describing this block as nexus formatted data.
- Returns
-
String