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 )

Methods

get_matrix get_number_of_characters get_number_of_taxa get_triangle new set_matrix set_number_of_characters set_number_of_taxa set_triangle to_nexus

Constants

TRIANGLE = "Triangle"

Public Class methods

new( name )

Creates a new DistancesBlock object named ‘name’.

Arguments:

(required) name: String

[Source]

      # 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

Public Instance methods

get_matrix()

Gets the matrix.

Returns:

Bio::Nexus::NexusMatrix

[Source]

      # File lib/bio/db/nexus.rb, line 1391
1391:       def get_matrix
1392:         @matrix
1393:       end

get_number_of_characters()

Gets the "number of characters" property.

Returns:

Integer

[Source]

      # File lib/bio/db/nexus.rb, line 1377
1377:       def get_number_of_characters
1378:         @number_of_characters
1379:       end

get_number_of_taxa()

Gets the "number of taxa" property.

Returns:

Integer

[Source]

      # File lib/bio/db/nexus.rb, line 1370
1370:       def get_number_of_taxa
1371:         @number_of_taxa
1372:       end

get_triangle()

Gets the "triangle" property.

Returns:

String

[Source]

      # File lib/bio/db/nexus.rb, line 1384
1384:       def get_triangle
1385:         @triangle
1386:       end

set_matrix( matrix )

Sets the matrix.

Arguments:

(required) matrix: Bio::Nexus::NexusMatrix

[Source]

      # File lib/bio/db/nexus.rb, line 1423
1423:       def set_matrix( matrix )
1424:         @matrix = matrix
1425:       end

set_number_of_characters( number_of_characters )

Sets the "number of characters" property.

Arguments:

(required) number_of_characters: Integer

[Source]

      # 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

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 1399
1399:       def set_number_of_taxa( number_of_taxa )
1400:         @number_of_taxa = number_of_taxa
1401:       end

set_triangle( triangle )

Sets the "triangle" property.

Arguments:

(required) triangle: String

[Source]

      # File lib/bio/db/nexus.rb, line 1415
1415:       def set_triangle( triangle )
1416:         @triangle = triangle
1417:       end

to_nexus()

Returns a String describing this block as nexus formatted data.

Returns:

String

[Source]

      # 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