Class Bio::TMHMM::Report
In: lib/bio/appl/tmhmm/report.rb
Parent: Object

TMHMM report parser class.

Methods

helix   new   to_s  

External Aliases

query_len -> length

Attributes

entry_id  [R]  Returns
exp_aas_in_tmhs  [R]  Returns
exp_first_60aa  [R]  Returns
predicted_tmhs  [R]  Returns
query_len  [R]  Returns
tmhs  [R]  Returns an Array of Bio::TMHMM::TMH.
total_prob_of_N_in  [R]  Returns

Public Class methods

new(entry = nil)

[Source]

    # File lib/bio/appl/tmhmm/report.rb, line 85
85:       def initialize(entry = nil)
86:         begin
87:           str = entry.to_str
88:         rescue NoMethodError
89:         end
90:         if str then
91:           entry = str.enum_for(:each_line)
92:         end
93:         parse_header(entry)
94:         @tmhs = parse_tmhs(entry)
95:       end

Public Instance methods

helix()

Returns an Array of Bio::TMHMM::TMH including only "TMhelix".

[Source]

     # File lib/bio/appl/tmhmm/report.rb, line 98
 98:       def helix
 99:         @tmhs.map {|t| t if t.status == 'TMhelix' }.compact
100:       end
to_s()

[Source]

     # File lib/bio/appl/tmhmm/report.rb, line 103
103:       def to_s
104:         [
105:           [
106:             ["Length:",                    @query_len],
107:             ["Number of predicted TMHs:",  @predicted_tmhs],
108:             ["Exp number of AAs in THMs:", @exp_aas_in_tmhs],
109:             ["Exp number, first 60 AAs:",  @exp_first_60aa],
110:             ["Total prob of N-in:",        @total_prob_of_N_in]
111:           ].map {|e| "\# " + [@entry_id, e].flatten.join("\t") },
112:           tmhs.map {|ent| ent.to_s }
113:         ].flatten.join("\n")
114:       end

[Validate]