module Bio::Alignment::PropertyMethods

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


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_char() click to toggle source

Gap character.

    # File lib/bio/alignment.rb
102 def gap_char
103   ((defined? @gap_char) ? @gap_char : nil) or GAP_CHAR
104 end
gap_regexp() click to toggle source

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
get_all_property() click to toggle source

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
is_gap?(s) click to toggle source

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
missing_char() click to toggle source

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
seqclass() click to toggle source

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
set_all_property(hash) click to toggle source

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