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)
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.
Creates a new alignment factory
# File lib/bio/alignment.rb, line 2221 def initialize(program = self.class::DEFAULT_PROGRAM, options = []) @program = program @options = options @command = nil @output = nil @report = nil @exit_status = nil @data_stdout = nil 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.
# File lib/bio/alignment.rb, line 2271 def query(seqs) if seqs then query_alignment(seqs) else exec_local(@options) @exit_status.exitstatus == 0 ? true : false end end
alias of query_alignment.
Compatibility Note: query_align will renamed to query_alignment.
# File lib/bio/alignment.rb, line 2292 def query_align(seqs) #warn 'query_align is renamed to query_alignment.' query_alignment(seqs) end
Performs alignment for seqs. seqs should be Bio::Alignment or Array of sequences or nil.
# File lib/bio/alignment.rb, line 2282 def query_alignment(seqs) unless seqs.respond_to?(:output_fasta) then seqs = Bio::Alignment.new(seqs) end query_string(seqs.output_fasta(:width => 70)) end
Performs alignment of sequences in the file named fn.
# File lib/bio/alignment.rb, line 2305 def query_by_filename(filename_in) _query_local(filename_in, @options) @report end
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