class Bio::Nexus
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
Constants
- BEGIN_BLOCK
- BEGIN_COMMENT
- BEGIN_NEXUS
- CHARACTERS
- CHARACTERS_BLOCK
- DATA
- DATATYPE
- DATA_BLOCK
- DELIMITER
- DIMENSIONS
- DISTANCES
- DISTANCES_BLOCK
- DOUBLE_QUOTE
- END_BLOCK
- END_COMMENT
- END_OF_LINE
- FORMAT
- INDENTENTION
- MATRIX
- NCHAR
- NTAX
- SINGLE_QUOTE
- TAXA
- TAXA_BLOCK
- TAXLABELS
- TREES
- TREES_BLOCK
Public Class Methods
Creates a new nexus parser for ‘nexus_str’.
Arguments:
-
(required) nexus_str: String - nexus formatted data
# File lib/bio/db/nexus.rb 177 def initialize( nexus_str ) 178 @blocks = Array.new 179 @current_cmd = nil 180 @current_subcmd = nil 181 @current_block_name = nil 182 @current_block = nil 183 parse( nexus_str ) 184 end
Public Instance Methods
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
# File lib/bio/db/nexus.rb 192 def get_blocks 193 @blocks 194 end
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
# File lib/bio/db/nexus.rb 204 def get_blocks_by_name( name ) 205 found_blocks = Array.new 206 @blocks.each do | block | 207 if ( name == block.get_name ) 208 found_blocks.push( block ) 209 end 210 end 211 found_blocks 212 end
A convenience methods which returns an array of all characters blocks.
- Returns
-
Array of CharactersBlocks
# File lib/bio/db/nexus.rb 228 def get_characters_blocks 229 get_blocks_by_name( CHARACTERS_BLOCK.chomp( ";").downcase ) 230 end
A convenience methods which returns an array of all data blocks.
- Returns
-
Array of DataBlocks
# File lib/bio/db/nexus.rb 219 def get_data_blocks 220 get_blocks_by_name( DATA_BLOCK.chomp( ";").downcase ) 221 end
A convenience methods which returns an array of all distances blocks.
- Returns
-
Array of
DistancesBlock
# File lib/bio/db/nexus.rb 246 def get_distances_blocks 247 get_blocks_by_name( DISTANCES_BLOCK.chomp( ";").downcase ) 248 end
A convenience methods which returns an array of all taxa blocks.
- Returns
-
Array of TaxaBlocks
# File lib/bio/db/nexus.rb 255 def get_taxa_blocks 256 get_blocks_by_name( TAXA_BLOCK.chomp( ";").downcase ) 257 end
A convenience methods which returns an array of all trees blocks.
- Returns
-
Array of TreesBlocks
# File lib/bio/db/nexus.rb 237 def get_trees_blocks 238 get_blocks_by_name( TREES_BLOCK.chomp( ";").downcase ) 239 end
Returns a String listing how many of each blocks it parsed.
- Returns
-
String
# File lib/bio/db/nexus.rb 263 def to_s 264 str = String.new 265 if get_blocks.length < 1 266 str << "empty" 267 else 268 str << "number of blocks: " << get_blocks.length.to_s 269 if get_characters_blocks.length > 0 270 str << " [characters blocks: " << get_characters_blocks.length.to_s << "] " 271 end 272 if get_data_blocks.length > 0 273 str << " [data blocks: " << get_data_blocks.length.to_s << "] " 274 end 275 if get_distances_blocks.length > 0 276 str << " [distances blocks: " << get_distances_blocks.length.to_s << "] " 277 end 278 if get_taxa_blocks.length > 0 279 str << " [taxa blocks: " << get_taxa_blocks.length.to_s << "] " 280 end 281 if get_trees_blocks.length > 0 282 str << " [trees blocks: " << get_trees_blocks.length.to_s << "] " 283 end 284 end 285 str 286 end