Class: Bio::Nexus

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

Overview

DESCRIPTION

Bio::Nexus is a parser for nexus formatted data. It contains classes and constants enabling the representation and processing of nexus data.

USAGE

# Parsing a nexus formatted string str:
nexus = Bio::Nexus.new( nexus_str )

# Obtaining of the nexus blocks as array of GenericBlock or
# any of its subclasses (such as DistancesBlock):
blocks = nexus.get_blocks

# Getting a block by name:
my_blocks = nexus.get_blocks_by_name( "my_block" )

# Getting distance blocks:
distances_blocks = nexus.get_distances_blocks

# Getting trees blocks:
trees_blocks = nexus.get_trees_blocks

# Getting data blocks:
data_blocks = nexus.get_data_blocks

# Getting characters blocks: 
character_blocks = nexus.get_characters_blocks

# Getting taxa blocks: 
taxa_blocks = nexus.get_taxa_blocks

Defined Under Namespace

Classes: CharactersBlock, DataBlock, DistancesBlock, GenericBlock, NexusMatrix, NexusParseError, TaxaBlock, TreesBlock, Util

Constant Summary

END_OF_LINE =
"\n"
INDENTENTION =
" "
DOUBLE_QUOTE =
"\""
SINGLE_QUOTE =
"'"
BEGIN_NEXUS =
"#NEXUS"
DELIMITER =
";"
BEGIN_BLOCK =
"Begin"
END_BLOCK =
"End" + DELIMITER
BEGIN_COMMENT =
"["
END_COMMENT =
"]"
TAXA =
"Taxa"
CHARACTERS =
"Characters"
DATA =
"Data"
DISTANCES =
"Distances"
TREES =
"Trees"
TAXA_BLOCK =
TAXA + DELIMITER
CHARACTERS_BLOCK =
CHARACTERS + DELIMITER
DATA_BLOCK =
DATA + DELIMITER
DISTANCES_BLOCK =
DISTANCES + DELIMITER
TREES_BLOCK =
TREES + DELIMITER
DIMENSIONS =
"Dimensions"
FORMAT =
"Format"
NTAX =
"NTax"
NCHAR =
"NChar"
DATATYPE =
"DataType"
TAXLABELS =
"TaxLabels"
MATRIX =
"Matrix"

Instance Method Summary collapse

Constructor Details

#initialize(nexus_str) ⇒ Nexus

Creates a new nexus parser for 'nexus_str'.


Arguments:

  • (required) nexus_str: String - nexus formatted data



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# File 'lib/bio/db/nexus.rb', line 177

def initialize( nexus_str )
  @blocks             = Array.new
  @current_cmd        = nil
  @current_subcmd     = nil
  @current_block_name = nil
  @current_block      = nil
  parse( nexus_str )
end

Instance Method Details

#get_blocksObject

Returns an Array of all blocks found in the String 'nexus_str' set via Bio::Nexus.new( nexus_str ).


Returns

Array of GenericBlocks or any of its subclasses



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# File 'lib/bio/db/nexus.rb', line 192

def get_blocks
  @blocks
end

#get_blocks_by_name(name) ⇒ Object

A convenience methods which returns an array of all nexus blocks for which the name equals 'name' found in the String 'nexus_str' set via Bio::Nexus.new( nexus_str ).


Arguments:

  • (required) name: String

Returns

Array of GenericBlocks or any of its subclasses



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# File 'lib/bio/db/nexus.rb', line 204

def get_blocks_by_name( name )
  found_blocks = Array.new
  @blocks.each do | block |
    if ( name == block.get_name )
      found_blocks.push( block )
    end
  end
  found_blocks
end

#get_characters_blocksObject

A convenience methods which returns an array of all characters blocks.


Returns

Array of CharactersBlocks



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# File 'lib/bio/db/nexus.rb', line 228

def get_characters_blocks
  get_blocks_by_name( CHARACTERS_BLOCK.chomp( ";").downcase )
end

#get_data_blocksObject

A convenience methods which returns an array of all data blocks.


Returns

Array of DataBlocks



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# File 'lib/bio/db/nexus.rb', line 219

def get_data_blocks
  get_blocks_by_name( DATA_BLOCK.chomp( ";").downcase )
end

#get_distances_blocksObject

A convenience methods which returns an array of all distances blocks.


Returns

Array of DistancesBlock



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# File 'lib/bio/db/nexus.rb', line 246

def get_distances_blocks
  get_blocks_by_name( DISTANCES_BLOCK.chomp( ";").downcase )
end

#get_taxa_blocksObject

A convenience methods which returns an array of all taxa blocks.


Returns

Array of TaxaBlocks



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# File 'lib/bio/db/nexus.rb', line 255

def get_taxa_blocks
  get_blocks_by_name( TAXA_BLOCK.chomp( ";").downcase )
end

#get_trees_blocksObject

A convenience methods which returns an array of all trees blocks.


Returns

Array of TreesBlocks



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# File 'lib/bio/db/nexus.rb', line 237

def get_trees_blocks
  get_blocks_by_name( TREES_BLOCK.chomp( ";").downcase )
end

#to_sObject Also known as: to_str

Returns a String listing how many of each blocks it parsed.


Returns

String



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# File 'lib/bio/db/nexus.rb', line 263

def to_s
  str = String.new
  if get_blocks.length < 1
    str << "empty"
  else 
    str << "number of blocks: " << get_blocks.length.to_s
    if get_characters_blocks.length > 0
      str << " [characters blocks: " << get_characters_blocks.length.to_s << "] "
    end  
    if get_data_blocks.length > 0
      str << " [data blocks: " << get_data_blocks.length.to_s << "] "
    end
    if get_distances_blocks.length > 0
      str << " [distances blocks: " << get_distances_blocks.length.to_s << "] "
    end  
    if get_taxa_blocks.length > 0
      str << " [taxa blocks: " << get_taxa_blocks.length.to_s << "] "
    end    
    if get_trees_blocks.length > 0
      str << " [trees blocks: " << get_trees_blocks.length.to_s << "] "
    end        
  end
  str
end