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_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.

Public Instance Methods

gap_char ()

Source

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

Gap character.

gap_regexp ()

Source

   # File lib/bio/alignment.rb
95 def gap_regexp
96   ((defined? @gap_regexp) ? @gap_regexp : nil) or GAP_REGEXP
97 end

Returns regular expression for checking gap.

get_all_property ()

Source

    # 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

Returns properties defined in the object as an hash.

is_gap? (s)

Source

   # File lib/bio/alignment.rb
90 def is_gap?(s)
91   (gap_regexp =~ s) ? true : false
92 end

If given character is a gap, returns true. Otherwise, return false. Note that s must be a String which contain a single character.

missing_char ()

Source

    # File lib/bio/alignment.rb
109 def missing_char
110   ((defined? @missing_char) ? @missing_char : nil) or MISSING_CHAR
111 end

Character if the site is missing or unknown.

seqclass ()

Source

    # File lib/bio/alignment.rb
120 def seqclass
121   ((defined? @seqclass) ? @seqclass : nil) or String
122 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.

set_all_property (hash)

Source

    # 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

Sets properties from given hash. hash would be a return value of get_character method.