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, 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