class Bio::Nexus::CharactersBlock
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 ]
Constants
- GAP
- MATCHCHAR
- MISSING
Public Class Methods
Source
# File lib/bio/db/nexus.rb 952 def initialize( name ) 953 super( name ) 954 @number_of_taxa = 0 955 @number_of_characters = 0 956 @data_type = String.new 957 @gap_character = String.new 958 @missing = String.new 959 @match_character = String.new 960 @matrix = NexusMatrix.new 961 end
Creates a new CharactersBlock object named ‘name’.
Arguments:
-
(required) name: String
Bio::Nexus::GenericBlock::new
Public Instance Methods
Source
# File lib/bio/db/nexus.rb 1107 def get_characters_string( row ) 1108 get_matrix.get_row_string( row, "" ) 1109 end
Returns character data as String for matrix row ‘row’.
Arguments:
-
(required) row: Integer
- Returns
-
String
Source
# File lib/bio/db/nexus.rb 1096 def get_characters_strings_by_name( name ) 1097 get_matrix.get_row_strings_by_name( name, "" ) 1098 end
Returns character data as String Array for matrix rows named ‘name’.
Arguments:
-
(required) name: String
- Returns
-
Array of Strings
Source
# File lib/bio/db/nexus.rb 1019 def get_datatype 1020 @data_type 1021 end
Gets the “datatype” property.
- Returns
-
String
Source
# File lib/bio/db/nexus.rb 1026 def get_gap_character 1027 @gap_character 1028 end
Gets the “gap character” property.
- Returns
-
String
Source
# File lib/bio/db/nexus.rb 1040 def get_match_character 1041 @match_character 1042 end
Gets the “match character” property.
- Returns
-
String
Source
# File lib/bio/db/nexus.rb 1047 def get_matrix 1048 @matrix 1049 end
Gets the matrix.
- Returns
Source
# File lib/bio/db/nexus.rb 1033 def get_missing 1034 @missing 1035 end
Gets the “missing” property.
- Returns
-
String
Source
# File lib/bio/db/nexus.rb 1012 def get_number_of_characters 1013 @number_of_characters 1014 end
Gets the “number of characters” property.
- Returns
-
Integer
Source
# File lib/bio/db/nexus.rb 1004 def get_number_of_taxa 1005 @number_of_taxa 1006 end
Gets the “number of taxa” property.
- Returns
-
Integer
Source
# File lib/bio/db/nexus.rb 1085 def get_row_name( row ) 1086 get_matrix.get_name( row ) 1087 end
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 1073 def get_sequence( row ) 1074 create_sequence( get_characters_string( row ), get_row_name( row ) ) 1075 end
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
Source
# File lib/bio/db/nexus.rb 1057 def get_sequences_by_name( name ) 1058 seq_strs = get_characters_strings_by_name( name ) 1059 seqs = Array.new 1060 seq_strs.each do | seq_str | 1061 seqs.push( create_sequence( seq_str, name ) ) 1062 end 1063 seqs 1064 end
Returns character data as Bio::Sequence object Array for matrix rows named ‘name’.
Arguments:
-
(required) name: String
- Returns
Source
# File lib/bio/db/nexus.rb 1131 def set_datatype( data_type ) 1132 @data_type = data_type 1133 end
Sets the “data type” property.
Arguments:
-
(required) data_type: String
Source
# File lib/bio/db/nexus.rb 1139 def set_gap_character( gap_character ) 1140 @gap_character = gap_character 1141 end
Sets the “gap character” property.
Arguments:
-
(required) gap_character: String
Source
# File lib/bio/db/nexus.rb 1155 def set_match_character( match_character ) 1156 @match_character = match_character 1157 end
Sets the “match character” property.
Arguments:
-
(required) match_character: String
Source
# File lib/bio/db/nexus.rb 1163 def set_matrix( matrix ) 1164 @matrix = matrix 1165 end
Sets the matrix.
Arguments:
-
(required) matrix:
Bio::Nexus::NexusMatrix
Source
# File lib/bio/db/nexus.rb 1147 def set_missing( missing ) 1148 @missing = missing 1149 end
Sets the “missing” property.
Arguments:
-
(required) missing: String
Source
# File lib/bio/db/nexus.rb 1123 def set_number_of_characters( number_of_characters ) 1124 @number_of_characters = number_of_characters 1125 end
Sets the “number of characters” property.
Arguments:
-
(required) number_of_characters: Integer
Source
# File lib/bio/db/nexus.rb 1115 def set_number_of_taxa( number_of_taxa ) 1116 @number_of_taxa = number_of_taxa 1117 end
Sets the “number of taxa” property.
Arguments:
-
(required) number_of_taxa: Integer
Source
# File lib/bio/db/nexus.rb 967 def to_nexus 968 line_1 = String.new 969 line_1 << DIMENSIONS 970 if ( Nexus::Util::larger_than_zero( get_number_of_taxa ) ) 971 line_1 << " " << NTAX << "=" << get_number_of_taxa 972 end 973 if ( Nexus::Util::larger_than_zero( get_number_of_characters ) ) 974 line_1 << " " << NCHAR << "=" << get_number_of_characters 975 end 976 line_1 << DELIMITER 977 978 line_2 = String.new 979 line_2 << FORMAT 980 if ( Nexus::Util::longer_than_zero( get_datatype ) ) 981 line_2 << " " << DATATYPE << "=" << get_datatype 982 end 983 if ( Nexus::Util::longer_than_zero( get_missing ) ) 984 line_2 << " " << MISSING << "=" << get_missing 985 end 986 if ( Nexus::Util::longer_than_zero( get_gap_character ) ) 987 line_2 << " " << GAP << "=" << get_gap_character 988 end 989 if ( Nexus::Util::longer_than_zero( get_match_character ) ) 990 line_2 << " " << MATCHCHAR << "=" << get_match_character 991 end 992 line_2 << DELIMITER 993 994 line_3 = String.new 995 line_3 << MATRIX 996 Nexus::Util::to_nexus_helper( CHARACTERS_BLOCK, [ line_1, line_2, line_3 ] + 997 get_matrix.to_nexus_row_array ) 998 end
Returns a String describing this block as nexus formatted data.
- Returns
-
String