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, line 81
def database_description(program, db)
  _parse_databases
  h = @database_descriptions[program]
  h ? (h[db] || '') : ''
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, line 68
def databases(program)
  _parse_databases
  @databases[program] || []
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, line 42
def nucleotide_databases
  _parse_databases
  @databases['blastn']
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, line 52
def protein_databases
  _parse_databases
  @databases['blastp']
end
reset() click to toggle source

Resets data and clears cached data in this module.

# File lib/bio/appl/blast/remote.rb, line 88
def reset
  @parse_databases = false
  true
end