Class | Bio::Alignment::FactoryTemplate::Simple |
In: |
lib/bio/alignment.rb
|
Parent: | Object |
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)
command | [R] | 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. |
data_stdout | [RW] | Last output to the stdout. |
exit_status | [R] | Last exit status |
options | [RW] | options |
output | [R] | Last raw result of the program. Return a string (or nil). |
program | [RW] | program name |
report | [R] | Last result object performed by the factory. |
Creates a new alignment factory
# File lib/bio/alignment.rb, line 2221 2221: def initialize(program = self.class::DEFAULT_PROGRAM, options = []) 2222: @program = program 2223: @options = options 2224: @command = nil 2225: @output = nil 2226: @report = nil 2227: @exit_status = nil 2228: @data_stdout = nil 2229: 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 2271: def query(seqs) 2272: if seqs then 2273: query_alignment(seqs) 2274: else 2275: exec_local(@options) 2276: @exit_status.exitstatus == 0 ? true : false 2277: end 2278: end
alias of query_alignment.
Compatibility Note: query_align will renamed to query_alignment.
# File lib/bio/alignment.rb, line 2292 2292: def query_align(seqs) 2293: #warn 'query_align is renamed to query_alignment.' 2294: query_alignment(seqs) 2295: end
Performs alignment for seqs. seqs should be Bio::Alignment or Array of sequences or nil.
# File lib/bio/alignment.rb, line 2282 2282: def query_alignment(seqs) 2283: unless seqs.respond_to?(:output_fasta) then 2284: seqs = Bio::Alignment.new(seqs) 2285: end 2286: query_string(seqs.output_fasta(:width => 70)) 2287: end
Performs alignment of sequences in the file named fn.
# File lib/bio/alignment.rb, line 2305 2305: def query_by_filename(filename_in) 2306: _query_local(filename_in, @options) 2307: @report 2308: end