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

- (GenericBlock) initialize(name)

Creates a new GenericBlock object named 'name'.


Arguments:

  • (required) name: String



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

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

Instance Method Details

- (Object) add_token(token)

Adds a token to this.


Arguments:

  • (required) token: String



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

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

- (Object) get_name

Gets the name of this block.


Returns

String



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

def get_name
  @name
end

- (Object) get_tokens

Returns contents as Array of Strings.


Returns

Array



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

def get_tokens
  @tokens
end

- (Object) to_nexus

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


Returns

String



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# 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]"
  str
end

- (Object) to_s Also known as: to_str

Same as to_nexus.


Returns

String



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

def to_s
  to_nexus
end