Class: Bio::Alignment::SequenceArray

Inherits:
Array
  • Object
show all
Includes:
ArrayExtension
Defined in:
lib/bio/alignment.rb

Overview

Bio::Alignment::SequenceArray is a container class of multiple sequence alignment. Since it inherits Array, it acts completely same as Array. In addition, methods defined in ArrayExtension and EnumerableExtension can be used.

Constant Summary

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

Method Summary

Methods included from ArrayExtension

#each_seq, #number_of_sequences

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_seq, #each_site, #each_site_step, #each_window, #match_line, #match_line_amino, #match_line_nuc, #number_of_sequences, #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