Class | Bio::Nexus::DistancesBlock |
In: |
lib/bio/db/nexus.rb
|
Parent: | GenericBlock |
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 )
TRIANGLE | = | "Triangle" |
Creates a new DistancesBlock object named ‘name’.
Arguments:
# File lib/bio/db/nexus.rb, line 1332 1332: def initialize( name ) 1333: super( name ) 1334: @number_of_taxa = 0 1335: @number_of_characters = 0 1336: @triangle = String.new 1337: @matrix = NexusMatrix.new 1338: end
Gets the matrix.
Returns: | Bio::Nexus::NexusMatrix |
# File lib/bio/db/nexus.rb, line 1391 1391: def get_matrix 1392: @matrix 1393: end
Gets the "number of characters" property.
Returns: | Integer |
# File lib/bio/db/nexus.rb, line 1377 1377: def get_number_of_characters 1378: @number_of_characters 1379: end
Gets the "number of taxa" property.
Returns: | Integer |
# File lib/bio/db/nexus.rb, line 1370 1370: def get_number_of_taxa 1371: @number_of_taxa 1372: end
Sets the matrix.
Arguments:
# File lib/bio/db/nexus.rb, line 1423 1423: def set_matrix( matrix ) 1424: @matrix = matrix 1425: end
Sets the "number of characters" property.
Arguments:
# File lib/bio/db/nexus.rb, line 1407 1407: def set_number_of_characters( number_of_characters ) 1408: @number_of_characters = number_of_characters 1409: end
Sets the "number of taxa" property.
Arguments:
# File lib/bio/db/nexus.rb, line 1399 1399: def set_number_of_taxa( number_of_taxa ) 1400: @number_of_taxa = number_of_taxa 1401: end
Returns a String describing this block as nexus formatted data.
Returns: | String |
# File lib/bio/db/nexus.rb, line 1343 1343: def to_nexus 1344: line_1 = String.new 1345: line_1 << DIMENSIONS 1346: if ( Nexus::Util::larger_than_zero( get_number_of_taxa ) ) 1347: line_1 << " " << NTAX << "=" << get_number_of_taxa 1348: end 1349: if ( Nexus::Util::larger_than_zero( get_number_of_characters ) ) 1350: line_1 << " " << NCHAR << "=" << get_number_of_characters 1351: end 1352: line_1 << DELIMITER 1353: 1354: line_2 = String.new 1355: line_2 << FORMAT 1356: if ( Nexus::Util::longer_than_zero( get_triangle ) ) 1357: line_2 << " " << TRIANGLE << "=" << get_triangle 1358: end 1359: line_2 << DELIMITER 1360: 1361: line_3 = String.new 1362: line_3 << MATRIX 1363: Nexus::Util::to_nexus_helper( DISTANCES_BLOCK, [ line_1, line_2, line_3 ] + 1364: get_matrix.to_nexus_row_array( " " ) ) 1365: end