class Bio::Alignment::FactoryTemplate::Simple
Template class for alignment application factory. The program acts: input: stdin or file, format = fasta format output: stdout (parser should be specified by DEFAULT_PARSER)
Attributes
Last command-line string. Returns nil or an array of String. Note that filenames described in the command-line may already be removed because these files may be temporary files.
Last output to the stdout.
Last exit status
options
Last raw result of the program. Return a string (or nil).
program name
Last result object performed by the factory.
Public Class Methods
Source
# File lib/bio/alignment.rb 2215 def initialize(program = self.class::DEFAULT_PROGRAM, options = []) 2216 @program = program 2217 @options = options 2218 @command = nil 2219 @output = nil 2220 @report = nil 2221 @exit_status = nil 2222 @data_stdout = nil 2223 end
Creates a new alignment factory
Public Instance Methods
Source
# File lib/bio/alignment.rb 2265 def query(seqs) 2266 if seqs then 2267 query_alignment(seqs) 2268 else 2269 exec_local(@options) 2270 @exit_status.exitstatus == 0 ? true : false 2271 end 2272 end
Executes the program. If seqs is not nil, perform alignment for seqs. If seqs is nil, simply executes the program.
Compatibility note: When seqs is nil, returns true if the program exits normally, and returns false if the program exits abnormally.
Source
# File lib/bio/alignment.rb 2286 def query_align(seqs) 2287 #warn 'query_align is renamed to query_alignment.' 2288 query_alignment(seqs) 2289 end
alias of query_alignment.
Compatibility Note: query_align will renamed to query_alignment.
Source
# File lib/bio/alignment.rb 2276 def query_alignment(seqs) 2277 unless seqs.respond_to?(:output_fasta) then 2278 seqs = Bio::Alignment.new(seqs) 2279 end 2280 query_string(seqs.output_fasta(:width => 70)) 2281 end
Performs alignment for seqs. seqs should be Bio::Alignment or Array of sequences or nil.
Source
# File lib/bio/alignment.rb 2299 def query_by_filename(filename_in) 2300 _query_local(filename_in, @options) 2301 @report 2302 end
Performs alignment of sequences in the file named fn.
Source
# File lib/bio/alignment.rb 2293 def query_string(str) 2294 _query_string(str, @options) 2295 @report 2296 end
Performs alignment for str. The str should be a string that can be recognized by the program.
Source
# File lib/bio/alignment.rb 2250 def reset 2251 @command = nil 2252 @output = nil 2253 @report = nil 2254 @exit_status = nil 2255 @data_stdout = nil 2256 end
Clear the internal data and status, except program and options.