Class: Bio::Nexus::GenericBlock

Inherits:
Object
  • Object
show all
Defined in:
lib/bio/db/nexus.rb

Overview

DESCRIPTION

Bio::Nexus::GenericBlock represents a generic nexus block. It is mainly intended to be extended into more specific classes, although it is used for blocks not represented by more specific block classes. It has a name and a array for the tokenized content of a nexus block.

USAGE

require 'bio/db/nexus'

# Create a new parser:
nexus = Bio::Nexus.new( nexus_data_as_string )

# Get blocks for which no class exists (private blocks)
as Nexus::GenericBlock:
private_blocks = nexus.get_blocks_by_name( "my_block" )
# Get first block names "my_block":
my_block_0 = private_blocks[ 0 ]
# Get first token in first block names "my_block":
first_token = my_block_0.get_tokens[ 0 ]
# Get name of block (would return "my_block" in this case):
name = my_block_0.get_name
# Return data of block as nexus formatted String:
name = my_block_0.to_nexus

Direct Known Subclasses

CharactersBlock, DistancesBlock, TaxaBlock, TreesBlock

Instance Method Summary collapse

Constructor Details

#initialize(name) ⇒ GenericBlock

Creates a new GenericBlock object named ‘name’.

Arguments:

  • (required) name: String



775
776
777
778
 
# File 'lib/bio/db/nexus.rb', line 775

def initialize( name )
  @name = name.chomp(";") 
  @tokens = Array.new
end

Instance Method Details

#add_token(token) ⇒ Object

Adds a token to this.

Arguments:

  • (required) token: String



817
818
819
 
# File 'lib/bio/db/nexus.rb', line 817

def add_token( token )
  @tokens.push( token )
end

#get_name ⇒ Object

Gets the name of this block.

Returns

String



784
785
786
 
# File 'lib/bio/db/nexus.rb', line 784

def get_name
  @name
end

#get_tokens ⇒ Object

Returns contents as Array of Strings.

Returns

Array



792
793
794
 
# File 'lib/bio/db/nexus.rb', line 792

def get_tokens
  @tokens
end

#to_nexus ⇒ Object

Should return a String describing this block as nexus formatted data.

Returns

String



808
809
810
 
# File 'lib/bio/db/nexus.rb', line 808

def to_nexus
  str = "generic block \"" + get_name + "\" [do not know how to write in nexus format]"
end

#to_s ⇒ Object Also known as: to_str

Same as to_nexus.

Returns

String



800
801
802
 
# File 'lib/bio/db/nexus.rb', line 800

def to_s
  to_nexus
end