Module | Bio::Alignment::PropertyMethods |
In: |
lib/bio/alignment.rb
|
Bio::Alignment::PropertyMethods is a set of methods to treat the gap character and so on.
GAP_REGEXP | = | /[^a-zA-Z]/ | regular expression for detecting gaps. | |
GAP_CHAR | = | '-'.freeze | gap character | |
MISSING_CHAR | = | '?'.freeze | missing character |
gap_char | [W] | gap character |
gap_regexp | [W] | regular expression for checking gap |
missing_char | [W] | Character if the site is missing or unknown. |
seqclass | [W] | The class of the sequence. The value must be String or its derivatives. |
Gap character.
# File lib/bio/alignment.rb, line 102 102: def gap_char 103: ((defined? @gap_char) ? @gap_char : nil) or GAP_CHAR 104: end
Returns regular expression for checking gap.
# File lib/bio/alignment.rb, line 95 95: def gap_regexp 96: ((defined? @gap_regexp) ? @gap_regexp : nil) or GAP_REGEXP 97: end
Returns properties defined in the object as an hash.
# File lib/bio/alignment.rb, line 129 129: def get_all_property 130: ret = {} 131: if defined? @gap_regexp 132: ret[:gap_regexp] = @gap_regexp 133: end 134: if defined? @gap_char 135: ret[:gap_char] = @gap_char 136: end 137: if defined? @missing_char 138: ret[:missing_char] = @missing_char 139: end 140: if defined? @seqclass 141: ret[:seqclass] = @seqclass 142: end 143: ret 144: end
Character if the site is missing or unknown.
# File lib/bio/alignment.rb, line 109 109: def missing_char 110: ((defined? @missing_char) ? @missing_char : nil) or MISSING_CHAR 111: end
Returns class of the sequence. If instance variable @seqclass (which can be set by ‘seqclass=’ method) is set, simply returns the value. Otherwise, returns the first sequence‘s class. If no sequences are found, returns nil.
# File lib/bio/alignment.rb, line 120 120: def seqclass 121: ((defined? @seqclass) ? @seqclass : nil) or String 122: end
Sets properties from given hash. hash would be a return value of get_character method.
# File lib/bio/alignment.rb, line 148 148: def set_all_property(hash) 149: @gap_regexp = hash[:gap_regexp] if hash.has_key?(:gap_regexp) 150: @gap_char = hash[:gap_char] if hash.has_key?(:gap_char) 151: @missing_char = hash[:missing_char] if hash.has_key?(:missing_char) 152: @seqclass = hash[:seqclass] if hash.has_key?(:seqclass) 153: self 154: end