Module Bio::Blast::Remote::Information
In: lib/bio/appl/blast/remote.rb

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

Methods

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:String

[Source]

    # File lib/bio/appl/blast/remote.rb, line 90
90:       def database_description(program, db)
91:         _parse_databases
92:         h = @database_descriptions[program]
93:         h ? (h[db] || '') : ''
94:       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

[Source]

    # File lib/bio/appl/blast/remote.rb, line 77
77:       def databases(program)
78:         _parse_databases
79:         @databases[program] || []
80:       end

Returns a list of available nucleotide databases.

Note: see the note of databases method.


Returns:Array containing String objects

[Source]

    # File lib/bio/appl/blast/remote.rb, line 51
51:       def nucleotide_databases
52:         _parse_databases
53:         @databases['blastn']
54:       end

Returns a list of available protein databases.

Note: see the note of databases method.


Returns:Array containing String objects

[Source]

    # File lib/bio/appl/blast/remote.rb, line 61
61:       def protein_databases
62:         _parse_databases
63:         @databases['blastp']
64:       end

Resets data and clears cached data in this module.

[Source]

     # File lib/bio/appl/blast/remote.rb, line 97
 97:       def reset
 98:         @parse_databases = false
 99:         true
100:       end

[Validate]