NCBI C Toolkit Cross Reference

C/api/fastadl.asn

  1 --$Id: fastadl.asn,v 6.6 2008/04/28 15:55:43 kazimird Exp $
  2 --
  3 -- Notes:
  4 --
  5 -- taxonomy: an integer is proposed, which would require some sort of 
  6 -- table (or network connection) to do the conversions from integer 
  7 -- to various names.  This could save quite a bit of space for databases 
  8 -- that are predominantly of one organism (e.g., human in htgs).
  9 -- I've proposed here that table contain scientific-, common-, and 
 10 -- blast-names at the advice of Scott Federhen.  Scott also was in 
 11 -- favor of having the complete lineage in the file, but it seems like 
 12 -- this would be seldom used and we could have a view with a link back 
 13 -- to the taxonomy page for anyone needing it. Since one file would 
 14 -- suffice for all blast databases, it seems like this should be a new file.
 15 --
 16 -- memberships: a sequence of integers is proposed.  Each bit of an integer 
 17 -- would indicate membership in some (virtual) blast database (e.g., pdb, 
 18 -- swissprot) or some classification (e.g., mRNA, genomic).
 19 --
 20 -- links: a sequence of integers is proposed.  Each bit of an integer would 
 21 -- indicate a link that could be established based upon the gi of the 
 22 -- database sequence.
 23 --
 24 
 25 NCBI-BlastDL DEFINITIONS ::=
 26 BEGIN
 27 
 28 EXPORTS Blast-def-line-set, Blast-def-line;
 29         
 30 IMPORTS Seq-id, Seq-loc FROM NCBI-Seqloc;
 31 
 32 Blast-def-line-set ::= SEQUENCE OF Blast-def-line  -- all deflines for an entry
 33 
 34 Blast-def-line ::= SEQUENCE {
 35         title VisibleString OPTIONAL,             -- simple title
 36         seqid SEQUENCE OF Seq-id,                 -- Regular NCBI Seq-Id
 37         taxid  INTEGER OPTIONAL,                  -- taxonomy id
 38         memberships SEQUENCE OF INTEGER OPTIONAL, -- bit arrays
 39         links SEQUENCE OF INTEGER OPTIONAL,       -- bit arrays
 40         other-info SEQUENCE OF INTEGER OPTIONAL   -- for future use (probably genomic sequences)
 41 }
 42 
 43 -- This defines the possible sequence filtering algorithms to be used in a
 44 -- BLAST database
 45 Blast-filter-program ::= INTEGER {
 46     not-set             (0),
 47     dust                (10),
 48     seg                 (20),
 49     windowmasker        (30),
 50     repeat              (40),
 51     other               (100),
 52     max                 (255)
 53 }
 54 
 55 Blast-mask-list ::= SEQUENCE {
 56     masks SEQUENCE OF Seq-loc,
 57     more BOOLEAN
 58 }
 59 
 60 Blast-db-mask-info ::= SEQUENCE {
 61     algo-id      INTEGER,
 62     algo-program Blast-filter-program,
 63     algo-options VisibleString,
 64     masks        Blast-mask-list
 65 }
 66 
 67 END
 68
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