Class | Bio::ClustalW::Report |
In: |
lib/bio/appl/clustalw/report.rb
|
Parent: | Bio::DB |
CLUSTAL W result data (*.aln file) parser class.
DELIMITER | = | nil | Delimiter of each entry. Bio::FlatFile uses it. In Bio::ClustalW::Report, it it nil (1 entry 1 file). |
raw | [R] | string of whole result |
seqclass | [R] | sequence class (one of Bio::Sequence, Bio::Sequence::NA, Bio::Sequence::AA, …) |
Creates new instance. str should be a CLUSTAL format string. seqclass should on of following:
# File lib/bio/appl/clustalw/report.rb, line 43 43: def initialize(str, seqclass = nil) 44: @raw = str 45: @align = nil 46: @match_line = nil 47: @header = nil 48: case seqclass 49: when /PROTEIN/i 50: @seqclass = Bio::Sequence::AA 51: when /[DR]NA/i 52: @seqclass = Bio::Sequence::NA 53: else 54: if seqclass.is_a?(Module) then 55: @seqclass = seqclass 56: else 57: @seqclass = Bio::Sequence 58: end 59: end 60: end
This will be deprecated. Instead, please use alignment.
Gets an multiple alignment. Returns a Bio::Alignment object.
# File lib/bio/appl/clustalw/report.rb, line 93 93: def align 94: warn "Bio::ClustalW#align will be deprecated. Please use \'alignment\'." 95: alignment 96: end
Gets an multiple alignment. Returns a Bio::Alignment object.
# File lib/bio/appl/clustalw/report.rb, line 84 84: def alignment 85: do_parse() unless @align 86: @align 87: end
Compatibility note: Behavior of the method will be changed in the future.
Gets an array of the sequences. Returns an array of Bio::FastaFormat objects.
# File lib/bio/appl/clustalw/report.rb, line 112 112: def to_a 113: alignment.to_fastaformat_array 114: end
This will be deprecated. Instead, please use alignment.output_fasta.
Gets an fasta-format string of the sequences. Returns a string.
# File lib/bio/appl/clustalw/report.rb, line 102 102: def to_fasta(*arg) 103: warn "Bio::ClustalW::report#to_fasta is deprecated. Please use \'alignment.output_fasta\'" 104: alignment.output_fasta(*arg) 105: end