Class Bio::ClustalW::Report
In: lib/bio/appl/clustalw/report.rb
Parent: Bio::DB

CLUSTAL W result data (*.aln file) parser class.

Methods

align   alignment   header   match_line   new   to_a   to_fasta  

Constants

DELIMITER = nil   Delimiter of each entry. Bio::FlatFile uses it. In Bio::ClustalW::Report, it it nil (1 entry 1 file).

Attributes

raw  [R]  string of whole result
seqclass  [R]  sequence class (one of Bio::Sequence, Bio::Sequence::NA, Bio::Sequence::AA, …)

Public Class methods

new(str, seqclass = nil)

Creates new instance. str should be a CLUSTAL format string. seqclass should on of following:

[Source]

    # 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

Public Instance methods

align()

This will be deprecated. Instead, please use alignment.

Gets an multiple alignment. Returns a Bio::Alignment object.

[Source]

    # 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
alignment()

Gets an multiple alignment. Returns a Bio::Alignment object.

[Source]

    # File lib/bio/appl/clustalw/report.rb, line 84
84:       def alignment
85:         do_parse() unless @align
86:         @align
87:       end
header()

Shows first line of the result data, for example, ‘CLUSTAL W (1.82) multiple sequence alignment’. Returns a string.

[Source]

    # File lib/bio/appl/clustalw/report.rb, line 71
71:       def header
72:         @header or (do_parse or @header)
73:       end
match_line()

Shows "match line" of CLUSTAL‘s alignment result, for example, ’:* :* .* * .*::*. ** :* . * . ’. Returns a string.

[Source]

    # File lib/bio/appl/clustalw/report.rb, line 78
78:       def match_line
79:         @match_line or (do_parse or @match_line)
80:       end
to_a()

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.

[Source]

     # File lib/bio/appl/clustalw/report.rb, line 112
112:       def to_a
113:         alignment.to_fastaformat_array
114:       end
to_fasta(*arg)

This will be deprecated. Instead, please use alignment.output_fasta.

Gets an fasta-format string of the sequences. Returns a string.

[Source]

     # 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

[Validate]