module Bio::Blast::Remote::Information
Common methods for meta-information processing (e.g. list of databases).
Public Instance Methods
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
# File lib/bio/appl/blast/remote.rb, line 90 def database_description(program, db) _parse_databases h = @database_descriptions[program] h ? (h[db] || '') : '' end
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 77 def databases(program) _parse_databases @databases[program] || [] end
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 51 def nucleotide_databases _parse_databases @databases['blastn'] end
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 61 def protein_databases _parse_databases @databases['blastp'] end
Resets data and clears cached data in this module.
# File lib/bio/appl/blast/remote.rb, line 97 def reset @parse_databases = false true end
Private Instance Methods
(private) parses database information and stores data
# File lib/bio/appl/blast/remote.rb, line 40 def _parse_databases raise NotImplementedError end