Bio::Alignment::PropertyMethods is a set of methods to treat the gap character and so on.
gap character
regular expression for detecting gaps.
missing character
Gap character.
# File lib/bio/alignment.rb, line 102 def gap_char ((defined? @gap_char) ? @gap_char : nil) or GAP_CHAR end
Returns regular expression for checking gap.
# File lib/bio/alignment.rb, line 95 def gap_regexp ((defined? @gap_regexp) ? @gap_regexp : nil) or GAP_REGEXP end
Returns properties defined in the object as an hash.
# File lib/bio/alignment.rb, line 129 def get_all_property ret = {} if defined? @gap_regexp ret[:gap_regexp] = @gap_regexp end if defined? @gap_char ret[:gap_char] = @gap_char end if defined? @missing_char ret[:missing_char] = @missing_char end if defined? @seqclass ret[:seqclass] = @seqclass end ret 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, line 90 def is_gap?(s) (gap_regexp =~ s) ? true : false end
Character if the site is missing or unknown.
# File lib/bio/alignment.rb, line 109 def missing_char ((defined? @missing_char) ? @missing_char : nil) or MISSING_CHAR 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 def seqclass ((defined? @seqclass) ? @seqclass : nil) or String end
Sets properties from given hash. hash would be a return value of get_character method.
# File lib/bio/alignment.rb, line 148 def set_all_property(hash) @gap_regexp = hash[:gap_regexp] if hash.has_key?(:gap_regexp) @gap_char = hash[:gap_char] if hash.has_key?(:gap_char) @missing_char = hash[:missing_char] if hash.has_key?(:missing_char) @seqclass = hash[:seqclass] if hash.has_key?(:seqclass) self end
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