Class: Bio::Alignment::SequenceArray
- 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
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