Class Bio::Nexus::GenericBlock
In: lib/bio/db/nexus.rb
Parent: Object

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

Methods

add_token   get_name   get_tokens   new   to_nexus   to_s   to_str  

Public Class methods

Creates a new GenericBlock object named ‘name’.


Arguments:

[Source]

     # File lib/bio/db/nexus.rb, line 775
775:       def initialize( name )
776:         @name = name.chomp(";") 
777:         @tokens = Array.new
778:       end

Public Instance methods

Adds a token to this.


Arguments:

[Source]

     # File lib/bio/db/nexus.rb, line 817
817:       def add_token( token )
818:         @tokens.push( token )
819:       end

Gets the name of this block.


Returns:String

[Source]

     # File lib/bio/db/nexus.rb, line 784
784:       def get_name
785:         @name
786:       end

Returns contents as Array of Strings.


Returns:Array

[Source]

     # File lib/bio/db/nexus.rb, line 792
792:       def get_tokens
793:         @tokens
794:       end

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


Returns:String

[Source]

     # File lib/bio/db/nexus.rb, line 808
808:       def to_nexus
809:         str = "generic block \"" + get_name + "\" [do not know how to write in nexus format]"
810:       end

Same as to_nexus.


Returns:String

[Source]

     # File lib/bio/db/nexus.rb, line 800
800:       def to_s
801:         to_nexus
802:       end
to_str()

Alias for to_s

[Validate]