Class Bio::Nexus::DataBlock
In: lib/bio/db/nexus.rb
Parent: CharactersBlock

DESCRIPTION

Bio::Nexus::DataBlock represents a data nexus block. A data block is a Bio::Nexus::CharactersBlock with the added capability to store taxa names.

Example of Data block:

Begin Data; 

 Dimensions ntax=5 nchar=14;
 Format Datatype=RNA gap=# MISSING=x MatchChar=^;
 TaxLabels ciona cow [comment] ape 'purple urchin' "green lizard";
 Matrix
  taxon_1 A- CCGTCGA-GTTA
  taxon_2 T- CCG-CGA-GATA
  taxon_3 A- C-GTCGA-GATA
  taxon_4 A- CCTCGA--GTTA
  taxon_5 T- CGGTCGT-CTTA;

End;

USAGE

  require 'bio/db/nexus'

  # Create a new parser:
  nexus = Bio::Nexus.new( nexus_data_as_string )

  # Get first data block:
  data_block = nexus.get_data_blocks[ 0 ]
  # Get first characters name:
  seq_name = data_block.get_row_name( 0 )
  # Get first characters row named "taxon_2" as Bio::Sequence sequence:
  seq_tax_2 = data_block.get_sequences_by_name( "taxon_2" )[ 0 ]
  # Get third characters row as Bio::Sequence sequence:
  seq_2 = data_block.get_sequence( 2 )
  # Get first characters row named "taxon_3" as String:
  string_tax_3 = data_block.get_characters_strings_by_name( "taxon_3" )
  # Get name of first taxon:
  taxon_0 = data_block.get_taxa[ 0 ]
  # Get characters matrix as Bio::Nexus::NexusMatrix (names are in column 0)
  characters_matrix = data_block.get_matrix

Methods

add_taxon   get_taxa   new   to_nexus  

Public Class methods

new( name )

Creates a new DataBlock object named ‘name’.

Arguments:

[Source]

      # File lib/bio/db/nexus.rb, line 1232
1232:       def initialize( name )
1233:         super( name )
1234:         @taxa = Array.new
1235:       end

Public Instance methods

add_taxon( taxon )

Adds a taxon name to this block.

Arguments:

[Source]

      # File lib/bio/db/nexus.rb, line 1288
1288:       def add_taxon( taxon )
1289:         @taxa.push( taxon )
1290:       end
get_taxa()

Gets the taxa of this block.

Returns:Array

[Source]

      # File lib/bio/db/nexus.rb, line 1280
1280:       def get_taxa
1281:         @taxa
1282:       end
to_nexus()

Returns a String describing this block as nexus formatted data.

Returns:String

[Source]

      # File lib/bio/db/nexus.rb, line 1240
1240:       def to_nexus
1241:         line_1 = String.new
1242:         line_1 << DIMENSIONS  
1243:         if ( Nexus::Util::larger_than_zero( get_number_of_taxa ) )
1244:           line_1 << " " <<  NTAX << "=" << get_number_of_taxa
1245:         end
1246:         if ( Nexus::Util::larger_than_zero( get_number_of_characters ) )
1247:           line_1 << " " <<  NCHAR << "=" << get_number_of_characters
1248:         end
1249:         line_1 << DELIMITER
1250:         
1251:         line_2 = String.new
1252:         line_2 << FORMAT  
1253:         if ( Nexus::Util::longer_than_zero( get_datatype ) )
1254:           line_2 << " " <<  DATATYPE << "=" << get_datatype
1255:         end
1256:         if ( Nexus::Util::longer_than_zero( get_missing ) )
1257:           line_2 << " " <<  MISSING << "=" << get_missing
1258:         end
1259:         if ( Nexus::Util::longer_than_zero( get_gap_character ) )
1260:           line_2 << " " <<  GAP << "=" << get_gap_character
1261:         end
1262:         if ( Nexus::Util::longer_than_zero( get_match_character ) )
1263:           line_2 << " " <<  MATCHCHAR << "=" << get_match_character
1264:         end
1265:         line_2 << DELIMITER
1266:         
1267:         line_3 = String.new
1268:         line_3 << TAXLABELS << " " << Nexus::Util::array_to_string( get_taxa )
1269:         line_3 << DELIMITER
1270:         
1271:         line_4 = String.new
1272:         line_4 << MATRIX 
1273:         Nexus::Util::to_nexus_helper( DATA_BLOCK, [ line_1, line_2, line_3, line_4 ] +
1274:                                       get_matrix.to_nexus_row_array  )
1275:       end

[Validate]