Module: Bio::Alignment::ArrayExtension

Includes:

EnumerableExtension

Included in:

SequenceArray

Defined in:

lib/bio/alignment.rb

Overview

Bio::Alignment::ArrayExtension is a set of useful methods for multiple sequence alignment. It is designed to be extended to array objects or included in your own classes which inherit Array. (It can also be included in Array, though not recommended.)

It possesses all methods defined in EnumerableExtension. For usage of methods, please refer to EnumerableExtension.

Constant Summary

Constants included from PropertyMethods

PropertyMethods::GAP_CHAR, PropertyMethods::GAP_REGEXP, PropertyMethods::MISSING_CHAR

Instance Attribute Summary

Attributes included from PropertyMethods

#gap_char, #gap_regexp, #missing_char, #seqclass

Instance Method Summary

• #each_seq(&block) ⇒ Object

  Iterates over each sequences.

• #number_of_sequences ⇒ Object

  Returns number of sequences in this alignment.

Methods included from EnumerableExtension

#alignment_collect, #alignment_concat, #alignment_length, #alignment_lstrip!, #alignment_normalize!, #alignment_rstrip!, #alignment_site, #alignment_slice, #alignment_strip!, #alignment_subseq, #alignment_window, #collect_each_site, #consensus_each_site, #consensus_iupac, #consensus_string, #convert_match, #convert_unmatch, #each_site, #each_site_step, #each_window, #match_line, #match_line_amino, #match_line_nuc, #remove_all_gaps!, #seqclass, #sequence_names

Methods included from Output

#__output_phylip_common, #output, #output_clustal, #output_fasta, #output_molphy, #output_msf, #output_phylip, #output_phylipnon, #to_clustal

Methods included from PropertyMethods

#get_all_property, #is_gap?, #set_all_property

Instance Method Details

#each_seq(&block) ⇒ Object

Iterates over each sequences. Yields a sequence.

It works the same as Array#each.

# File 'lib/bio/alignment.rb', line 1343

def each_seq(&block) #:yields: seq
  each(&block)
end

#number_of_sequences ⇒ Object

Returns number of sequences in this alignment.

# File 'lib/bio/alignment.rb', line 1348

def number_of_sequences
  self.size
end