class Bio::AAindex
Description¶ ↑
Bio::AAindex is the super class of Bio::AAindex1 and Bio::AAindex2, parser classes for AAindex Amino Acid Index Database.
Except Bio::AAindex.auto, do not use this class directly. Methods of this super class is used from AAindex1 and AAindex2 classes.
Examples¶ ↑
# auto-detection of data format aax1 = Bio::AAindex.auto("PRAM900102.aaindex1") aax2 = Bio::AAindex.auto("DAYM780301.aaindex2") # Example of Bio::AAindex1 class aax1 = Bio::AAindex1.new("PRAM900102.aaindex1") aax1.entry_id aax1.index # Example of Bio::AAindex2 class aax2 = Bio::AAindex2.new("DAYM780301.aaindex2") aax2.entry_id aax2.matrix aax2.matrix[2,2] aax2.matrix('R', 'A') aax2['R', 'A']
References¶ ↑
Constants
- DELIMITER
-
Delimiter
- RS
-
Delimiter
- TAGSIZE
-
Bio::DBAPI
Public Class Methods
Source
# File lib/bio/db/aaindex.rb 87 def self.auto(str) 88 case str 89 when /^I /m 90 Bio::AAindex1.new(str) 91 when /^M /m 92 Bio::AAindex2.new(str) 93 else 94 raise 95 end 96 end
Auto detecter for two AAindex formats. returns a Bio::AAindex1 object or a Bio::AAindex2 object.
Source
# File lib/bio/db/aaindex.rb 99 def initialize(entry) 100 super(entry, TAGSIZE) 101 end
Calls superclass method
Bio::NCBIDB::new
Public Instance Methods
Source
# File lib/bio/db/aaindex.rb 159 def comment 160 if @data['comment'] 161 @data['comment'] 162 else 163 @data['comment'] = field_fetch('*') 164 end 165 end
Returns comment (if any).
Source
# File lib/bio/db/aaindex.rb 123 def dblinks 124 if @data['ref'] 125 @data['ref'] 126 else 127 @data['ref'] = field_fetch('R').split(' ') 128 end 129 end
Returns database links in the R line. cf.) [‘LIT:123456’, ‘PMID:12345678’]
Source
# File lib/bio/db/aaindex.rb 113 def definition 114 if @data['definition'] 115 @data['definition'] 116 else 117 @data['definition'] = field_fetch('D') 118 end 119 end
Returns definition in the D line.
Source
# File lib/bio/db/aaindex.rb 104 def entry_id 105 if @data['entry_id'] 106 @data['entry_id'] 107 else 108 @data['entry_id'] = field_fetch('H') 109 end 110 end
Returns entry_id in the H line.
Source
# File lib/bio/db/aaindex.rb 150 def journal 151 if @data['journal'] 152 @data['journal'] 153 else 154 @data['journal'] = field_fetch('J') 155 end 156 end
Returns journal name in the J line.
Source
# File lib/bio/db/aaindex.rb 141 def title 142 if @data['title'] 143 @data['title'] 144 else 145 @data['title'] = field_fetch('T') 146 end 147 end
Returns title in the T line.