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)

Methods

new   query   query_align   query_alignment   query_by_filename   query_string   reset  

Attributes

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.

Public Class methods

new(program = self.class::DEFAULT_PROGRAM, options = [])

Creates a new alignment factory

[Source]

      # 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

Public Instance methods

query(seqs)

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, 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
query_align(seqs)

alias of query_alignment.

Compatibility Note: query_align will renamed to query_alignment.

[Source]

      # 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
query_alignment(seqs)

Performs alignment for seqs. seqs should be Bio::Alignment or Array of sequences or nil.

[Source]

      # 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
query_by_filename(filename_in)

Performs alignment of sequences in the file named fn.

[Source]

      # File lib/bio/alignment.rb, line 2305
2305:         def query_by_filename(filename_in)
2306:           _query_local(filename_in, @options)
2307:           @report
2308:         end
query_string(str)

Performs alignment for str. The str should be a string that can be recognized by the program.

[Source]

      # File lib/bio/alignment.rb, line 2299
2299:         def query_string(str)
2300:           _query_string(str, @options)
2301:           @report
2302:         end
reset()

Clear the internal data and status, except program and options.

[Source]

      # File lib/bio/alignment.rb, line 2256
2256:         def reset
2257:           @command = nil
2258:           @output = nil
2259:           @report = nil
2260:           @exit_status = nil
2261:           @data_stdout = nil
2262:         end

[Validate]