Class: Bio::Alignment::SequenceHash

Inherits:
Hash show all
Includes:
HashExtension
Defined in:
lib/bio/alignment.rb

Overview

Bio::Alignment::SequenceHash is a container class of multiple sequence alignment. Since it inherits Hash, it acts completely same as Hash. In addition, methods defined in HashExtension 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 HashExtension

#alignment_collect, #alignment_concat, #each_seq, #number_of_sequences, #sequence_names

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