Module | Bio::Blast::Remote::DDBJ
In: | lib/bio/appl/blast/ddbj.rb

Remote BLAST factory using DDBJ Web API for Biology (xml.nig.ac.jp/).

### Methods

exec_ddbj new

### Classes and Modules

Module Bio::Blast::Remote::DDBJ::Information

### Public Class methods

new(program, db, options = [])

Creates a remote BLAST factory using DDBJ. Returns Bio::Blast object.

Note for future improvement: In the future, it might return Bio::Blast::Remote::DDBJ or other object.

[Source]

        # File lib/bio/appl/blast/ddbj.rb, line 26
    26:     def self.new(program, db, options = [])
    27:       Bio::Blast.new(program, db, options, 'ddbj')
    28:     end

### Public Instance methods

exec_ddbj(query)

executes BLAST and returns result as a string

[Source]

         # File lib/bio/appl/blast/ddbj.rb, line 106
    106:     def exec_ddbj(query)
    107:       options = make_command_line_options
    108:       opt = Bio::Blast::NCBIOptions.new(options)
    109:
    110:       # REST objects are cached
    111:       @ddbj_remote_blast ||= Bio::DDBJ::REST::Blast.new
    112:       @ddbj_request_manager ||= Bio::DDBJ::REST::RequestManager.new
    113:
    114:       program = opt.delete('-p')
    115:       db = opt.delete('-d')
    116:       optstr = Bio::Command.make_command_line_unix(opt.options)
    117:
    118:       # using searchParamAsync
    119:       qid = @ddbj_remote_blast.searchParamAsync(program, db, query, optstr)
    120:       @output = qid
    121:
    122:       result = @ddbj_request_manager.wait_getAsyncResult(qid)
    123:
    124:       @output = result
    125:       return @output
    126:     end

[Validate]