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

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 ]

Methods

get_characters_string   get_characters_strings_by_name   get_datatype   get_gap_character   get_match_character   get_matrix   get_missing   get_number_of_characters   get_number_of_taxa   get_row_name   get_sequence   get_sequences_by_name   new   set_datatype   set_gap_character   set_match_character   set_matrix   set_missing   set_number_of_characters   set_number_of_taxa   to_nexus  

Constants

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

Public Class methods

new( name )

Creates a new CharactersBlock object named ‘name’.

Arguments:

[Source]

     # File lib/bio/db/nexus.rb, line 951
951:       def initialize( name )
952:         super( name )
953:         @number_of_taxa = 0
954:         @number_of_characters = 0
955:         @data_type = String.new
956:         @gap_character = String.new
957:         @missing = String.new
958:         @match_character = String.new
959:         @matrix = NexusMatrix.new
960:       end

Public Instance methods

get_characters_string( row )

Returns character data as String for matrix row ‘row’.

Arguments:

  • (required) row: Integer
Returns:String

[Source]

      # File lib/bio/db/nexus.rb, line 1106
1106:       def get_characters_string( row )
1107:         get_matrix.get_row_string( row, "" )
1108:       end
get_characters_strings_by_name( name )

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

Arguments:

Returns:Array of Strings

[Source]

      # File lib/bio/db/nexus.rb, line 1095
1095:       def get_characters_strings_by_name( name )
1096:         get_matrix.get_row_strings_by_name( name, "" )
1097:       end
get_datatype()

Gets the "datatype" property.

Returns:String

[Source]

      # File lib/bio/db/nexus.rb, line 1018
1018:       def get_datatype
1019:         @data_type
1020:       end
get_gap_character()

Gets the "gap character" property.

Returns:String

[Source]

      # File lib/bio/db/nexus.rb, line 1025
1025:       def get_gap_character
1026:         @gap_character
1027:       end
get_match_character()

Gets the "match character" property.

Returns:String

[Source]

      # File lib/bio/db/nexus.rb, line 1039
1039:       def get_match_character 
1040:         @match_character 
1041:       end
get_matrix()

Gets the matrix.

Returns:Bio::Nexus::NexusMatrix

[Source]

      # File lib/bio/db/nexus.rb, line 1046
1046:       def get_matrix
1047:         @matrix 
1048:       end
get_missing()

Gets the "missing" property.

Returns:String

[Source]

      # File lib/bio/db/nexus.rb, line 1032
1032:       def get_missing
1033:         @missing
1034:       end
get_number_of_characters()

Gets the "number of characters" property.

Returns:Integer

[Source]

      # File lib/bio/db/nexus.rb, line 1011
1011:       def get_number_of_characters
1012:         @number_of_characters
1013:       end
get_number_of_taxa()

Gets the "number of taxa" property.

Returns:Integer

[Source]

      # File lib/bio/db/nexus.rb, line 1003
1003:       def get_number_of_taxa
1004:         @number_of_taxa
1005:       end
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

[Source]

      # File lib/bio/db/nexus.rb, line 1084
1084:       def get_row_name( row )
1085:         get_matrix.get_name( row )
1086:       end
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

[Source]

      # File lib/bio/db/nexus.rb, line 1072
1072:       def get_sequence( row )
1073:         create_sequence( get_characters_string( row ), get_row_name( row )  )
1074:       end
get_sequences_by_name( name )

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

Arguments:

Returns:Bio::Sequence

[Source]

      # File lib/bio/db/nexus.rb, line 1056
1056:       def get_sequences_by_name( name )
1057:         seq_strs = get_characters_strings_by_name( name )
1058:         seqs = Array.new
1059:         seq_strs.each do | seq_str |
1060:           seqs.push( create_sequence( seq_str, name ) )
1061:         end
1062:         seqs
1063:       end
set_datatype( data_type )

Sets the "data type" property.

Arguments:

  • (required) data_type: String

[Source]

      # File lib/bio/db/nexus.rb, line 1130
1130:       def set_datatype( data_type )
1131:         @data_type = data_type
1132:       end
set_gap_character( gap_character )

Sets the "gap character" property.

Arguments:

  • (required) gap_character: String

[Source]

      # File lib/bio/db/nexus.rb, line 1138
1138:       def set_gap_character( gap_character )
1139:         @gap_character = gap_character
1140:       end
set_match_character( match_character )

Sets the "match character" property.

Arguments:

  • (required) match_character: String

[Source]

      # File lib/bio/db/nexus.rb, line 1154
1154:       def set_match_character( match_character )
1155:         @match_character = match_character
1156:       end
set_matrix( matrix )

Sets the matrix.

Arguments:

[Source]

      # File lib/bio/db/nexus.rb, line 1162
1162:       def set_matrix( matrix )
1163:         @matrix = matrix
1164:       end
set_missing( missing )

Sets the "missing" property.

Arguments:

[Source]

      # File lib/bio/db/nexus.rb, line 1146
1146:       def set_missing( missing )
1147:         @missing = missing
1148:       end
set_number_of_characters( number_of_characters )

Sets the "number of characters" property.

Arguments:

  • (required) number_of_characters: Integer

[Source]

      # File lib/bio/db/nexus.rb, line 1122
1122:       def set_number_of_characters( number_of_characters )
1123:         @number_of_characters = number_of_characters
1124:       end
set_number_of_taxa( number_of_taxa )

Sets the "number of taxa" property.

Arguments:

  • (required) number_of_taxa: Integer

[Source]

      # File lib/bio/db/nexus.rb, line 1114
1114:       def set_number_of_taxa( number_of_taxa )
1115:         @number_of_taxa = number_of_taxa
1116:       end
to_nexus()

Returns a String describing this block as nexus formatted data.

Returns:String

[Source]

     # File lib/bio/db/nexus.rb, line 966
966:       def to_nexus
967:         line_1 = String.new
968:         line_1 << DIMENSIONS  
969:         if ( Nexus::Util::larger_than_zero( get_number_of_taxa ) )
970:           line_1 << " " <<  NTAX << "=" << get_number_of_taxa
971:         end
972:         if ( Nexus::Util::larger_than_zero( get_number_of_characters ) )
973:           line_1 << " " <<  NCHAR << "=" << get_number_of_characters
974:         end
975:         line_1 << DELIMITER
976:         
977:         line_2 = String.new
978:         line_2 << FORMAT  
979:         if ( Nexus::Util::longer_than_zero( get_datatype ) )
980:           line_2 << " " <<  DATATYPE << "=" << get_datatype
981:         end
982:         if ( Nexus::Util::longer_than_zero( get_missing ) )
983:           line_2 << " " <<  MISSING << "=" << get_missing
984:         end
985:         if ( Nexus::Util::longer_than_zero( get_gap_character ) )
986:           line_2 << " " <<  GAP << "=" << get_gap_character
987:         end
988:         if ( Nexus::Util::longer_than_zero( get_match_character ) )
989:           line_2 << " " <<  MATCHCHAR << "=" << get_match_character
990:         end
991:         line_2 << DELIMITER
992:         
993:         line_3 = String.new
994:         line_3 << MATRIX 
995:         Nexus::Util::to_nexus_helper( CHARACTERS_BLOCK, [ line_1, line_2, line_3 ] +
996:                                       get_matrix.to_nexus_row_array  )
997:       end

[Validate]