module Bio::Alignment::PropertyMethods
Bio::Alignment::PropertyMethods
is a set of methods to treat the gap character and so on.
Constants
- GAP_CHAR
gap character
- GAP_REGEXP
regular expression for detecting gaps.
- MISSING_CHAR
missing character
Attributes
gap character
regular expression for checking gap
Character if the site is missing or unknown.
The class of the sequence. The value must be String or its derivatives.
Public Instance Methods
Gap character.
# File lib/bio/alignment.rb 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 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 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
If given character is a gap, returns true. Otherwise, return false. Note that s must be a String which contain a single character.
# File lib/bio/alignment.rb 90 def is_gap?(s) 91 (gap_regexp =~ s) ? true : false 92 end
Character if the site is missing or unknown.
# File lib/bio/alignment.rb 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 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 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