Class: Bio::Alignment::SequenceHash
- 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
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