Class: Bio::Nexus::CharactersBlock

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

Overview

DESCRIPTION

Bio::Nexus::CharactersBlock represents a characters nexus block.

Example of Characters block:

Begin Characters;

Dimensions NChar=20
           NTax=4;
Format DataType=DNA
Missing=x
Gap=- MatchChar=.;
Matrix
 fish  ACATA GAGGG TACCT CTAAG
 frog  ACTTA GAGGC TACCT CTAGC
 snake ACTCA CTGGG TACCT TTGCG
 mouse ACTCA GACGG TACCT TTGCG;

End;

USAGE

require 'bio/db/nexus'

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

# Get first characters block (same methods as Nexus::DataBlock except
# it lacks get_taxa method):   
characters_block = nexus.get_characters_blocks[ 0 ]

Direct Known Subclasses

DataBlock

Constant Summary

MISSING =
"Missing"
GAP =
"Gap"
MATCHCHAR =
"MatchChar"

Instance Method Summary (collapse)

Methods inherited from GenericBlock

#add_token, #get_name, #get_tokens, #to_s

Constructor Details

- (CharactersBlock) initialize(name)

Creates a new CharactersBlock object named 'name'.


Arguments:

  • (required) name: String



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# File 'lib/bio/db/nexus.rb', line 951

def initialize( name )
  super( name )
  @number_of_taxa = 0
  @number_of_characters = 0
  @data_type = String.new
  @gap_character = String.new
  @missing = String.new
  @match_character = String.new
  @matrix = NexusMatrix.new
end

Instance Method Details

- (Object) get_characters_string(row)

Returns character data as String for matrix row 'row'.


Arguments:

  • (required) row: Integer

Returns

String



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# File 'lib/bio/db/nexus.rb', line 1106

def get_characters_string( row )
  get_matrix.get_row_string( row, "" )
end

- (Object) get_characters_strings_by_name(name)

Returns character data as String Array for matrix rows named 'name'.


Arguments:

  • (required) name: String

Returns

Array of Strings



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# File 'lib/bio/db/nexus.rb', line 1095

def get_characters_strings_by_name( name )
  get_matrix.get_row_strings_by_name( name, "" )
end

- (Object) get_datatype

Gets the “datatype” property.


Returns

String



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# File 'lib/bio/db/nexus.rb', line 1018

def get_datatype
  @data_type
end

- (Object) get_gap_character

Gets the “gap character” property.


Returns

String



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# File 'lib/bio/db/nexus.rb', line 1025

def get_gap_character
  @gap_character
end

- (Object) get_match_character

Gets the “match character” property.


Returns

String



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# File 'lib/bio/db/nexus.rb', line 1039

def get_match_character 
  @match_character 
end

- (Object) get_matrix

Gets the matrix.


Returns

Bio::Nexus::NexusMatrix



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# File 'lib/bio/db/nexus.rb', line 1046

def get_matrix
  @matrix 
end

- (Object) get_missing

Gets the “missing” property.


Returns

String



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# File 'lib/bio/db/nexus.rb', line 1032

def get_missing
  @missing
end

- (Object) get_number_of_characters

Gets the “number of characters” property.


Returns

Integer



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# File 'lib/bio/db/nexus.rb', line 1011

def get_number_of_characters
  @number_of_characters
end

- (Object) get_number_of_taxa

Gets the “number of taxa” property.


Returns

Integer



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# File 'lib/bio/db/nexus.rb', line 1003

def get_number_of_taxa
  @number_of_taxa
end

- (Object) get_row_name(row)

Returns the String in the matrix at row 'row' and column 0, which usually is interpreted as a sequence name (if the matrix contains molecular sequence characters).


Arguments:

  • (required) row: Integer

Returns

String



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# File 'lib/bio/db/nexus.rb', line 1084

def get_row_name( row )
  get_matrix.get_name( row )
end

- (Object) get_sequence(row)

Returns the characters in the matrix at row 'row' as Bio::Sequence object. Column 0 of the matrix is set as the definition of the Bio::Sequence object.


Arguments:

  • (required) row: Integer

Returns

Bio::Sequence



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# File 'lib/bio/db/nexus.rb', line 1072

def get_sequence( row )
  create_sequence( get_characters_string( row ), get_row_name( row )  )
end

- (Object) get_sequences_by_name(name)

Returns character data as Bio::Sequence object Array for matrix rows named 'name'.


Arguments:

  • (required) name: String

Returns

Bio::Sequence



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# File 'lib/bio/db/nexus.rb', line 1056

def get_sequences_by_name( name )
  seq_strs = get_characters_strings_by_name( name )
  seqs = Array.new
  seq_strs.each do | seq_str |
    seqs.push( create_sequence( seq_str, name ) )
  end
  seqs
end

- (Object) set_datatype(data_type)

Sets the “data type” property.


Arguments:

  • (required) data_type: String



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# File 'lib/bio/db/nexus.rb', line 1130

def set_datatype( data_type )
  @data_type = data_type
end

- (Object) set_gap_character(gap_character)

Sets the “gap character” property.


Arguments:

  • (required) gap_character: String



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# File 'lib/bio/db/nexus.rb', line 1138

def set_gap_character( gap_character )
  @gap_character = gap_character
end

- (Object) set_match_character(match_character)

Sets the “match character” property.


Arguments:

  • (required) match_character: String



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# File 'lib/bio/db/nexus.rb', line 1154

def set_match_character( match_character )
  @match_character = match_character
end

- (Object) set_matrix(matrix)

Sets the matrix.


Arguments:

  • (required) matrix: Bio::Nexus::NexusMatrix



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# File 'lib/bio/db/nexus.rb', line 1162

def set_matrix( matrix )
  @matrix = matrix
end

- (Object) set_missing(missing)

Sets the “missing” property.


Arguments:

  • (required) missing: String



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# File 'lib/bio/db/nexus.rb', line 1146

def set_missing( missing )
  @missing = missing
end

- (Object) set_number_of_characters(number_of_characters)

Sets the “number of characters” property.


Arguments:

  • (required) number_of_characters: Integer



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# File 'lib/bio/db/nexus.rb', line 1122

def set_number_of_characters( number_of_characters )
  @number_of_characters = number_of_characters
end

- (Object) set_number_of_taxa(number_of_taxa)

Sets the “number of taxa” property.


Arguments:

  • (required) number_of_taxa: Integer



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# File 'lib/bio/db/nexus.rb', line 1114

def set_number_of_taxa( number_of_taxa )
  @number_of_taxa = number_of_taxa
end

- (Object) to_nexus

Returns a String describing this block as nexus formatted data.


Returns

String



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# File 'lib/bio/db/nexus.rb', line 966

def to_nexus
  line_1 = String.new
  line_1 << DIMENSIONS  
  if ( Nexus::Util::larger_than_zero( get_number_of_taxa ) )
    line_1 << " " <<  NTAX << "=" << get_number_of_taxa
  end
  if ( Nexus::Util::larger_than_zero( get_number_of_characters ) )
    line_1 << " " <<  NCHAR << "=" << get_number_of_characters
  end
  line_1 << DELIMITER
  
  line_2 = String.new
  line_2 << FORMAT  
  if ( Nexus::Util::longer_than_zero( get_datatype ) )
    line_2 << " " <<  DATATYPE << "=" << get_datatype
  end
  if ( Nexus::Util::longer_than_zero( get_missing ) )
    line_2 << " " <<  MISSING << "=" << get_missing
  end
  if ( Nexus::Util::longer_than_zero( get_gap_character ) )
    line_2 << " " <<  GAP << "=" << get_gap_character
  end
  if ( Nexus::Util::longer_than_zero( get_match_character ) )
    line_2 << " " <<  MATCHCHAR << "=" << get_match_character
  end
  line_2 << DELIMITER
  
  line_3 = String.new
  line_3 << MATRIX 
  Nexus::Util::to_nexus_helper( CHARACTERS_BLOCK, [ line_1, line_2, line_3 ] +
                                get_matrix.to_nexus_row_array  )
end