module Bio::Blast::Remote::Information

Common methods for meta-information processing (e.g. list of databases).

Public Instance Methods

database_description(program, db) click to toggle source

Returns a short description of given database.

Note: see the note of databases method.


Arguments:

  • program (required): 'blastn', 'blastp', 'blastx', 'tblastn' or 'tblastx'

  • db (required): database name

Returns

String

   # File lib/bio/appl/blast/remote.rb
81 def database_description(program, db)
82   _parse_databases
83   h = @database_descriptions[program]
84   h ? (h[db] || '') : ''
85 end
databases(program) click to toggle source

Returns a list of available databases for given program.

Note: It parses remote sites to obtain database information (e.g. blast.genome.jp/ for Bio::Blast::Remote::GenomeNet). Thus, if the site is changed, this method can not return correct data. Please tell BioRuby developers when the site is changed.


Arguments:

  • program (required): blast program('blastn', 'blastp', 'blastx', 'tblastn' or 'tblastx')

Returns

Array containing String objects

   # File lib/bio/appl/blast/remote.rb
68 def databases(program)
69   _parse_databases
70   @databases[program] || []
71 end
nucleotide_databases() click to toggle source

Returns a list of available nucleotide databases.

Note: see the note of databases method.


Returns

Array containing String objects

   # File lib/bio/appl/blast/remote.rb
42 def nucleotide_databases
43   _parse_databases
44   @databases['blastn']
45 end
protein_databases() click to toggle source

Returns a list of available protein databases.

Note: see the note of databases method.


Returns

Array containing String objects

   # File lib/bio/appl/blast/remote.rb
52 def protein_databases
53   _parse_databases
54   @databases['blastp']
55 end
reset() click to toggle source

Resets data and clears cached data in this module.

   # File lib/bio/appl/blast/remote.rb
88 def reset
89   @parse_databases = false
90   true
91 end