Class: Bio::Nexus::GenericBlock

Inherits:

Object

• Object
• Bio::Nexus::GenericBlock

show all

Defined in:

lib/bio/db/nexus.rb

Overview

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

Instance Method Summary (collapse)

• - (Object) add_token(token)

  Adds a token to this.

• - (Object) get_name

  Gets the name of this block.

• - (Object) get_tokens

  Returns contents as Array of Strings.

• - (GenericBlock) initialize(name) constructor

  Creates a new GenericBlock object named 'name'.

• - (Object) to_nexus

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

• - (Object) to_s (also: #to_str)

  Same as to_nexus.

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

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

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

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

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

def get_name
  @name
end

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

def get_tokens
  @tokens
end

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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]"
end

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

def to_s
  to_nexus
end