src/objects/seqcode/seqcode.asn

--$Revision: 32084 $
--  *********************************************************************
--
--  These are code and conversion tables for NCBI sequence codes
--  ASN.1 for the sequences themselves are define in seq.asn
--
--  Seq-map-table and Seq-code-table REQUIRE that codes start with 0
--    and increase continuously.  So IUPAC codes, which are upper case
--    letters will always have 65 0 cells before the codes begin.  This
--    allows all codes to do indexed lookups for things
--
--  Valid names for code tables are:
--    IUPACna
--    IUPACaa
--    IUPACeaa
--    IUPACaa3     3 letter amino acid codes : parallels IUPACeaa
--                   display only, not a data exchange type
--    NCBI2na
--    NCBI4na
--    NCBI8na
--    NCBI8aa
--    NCBIstdaa
--     probability types map to IUPAC types for display as characters

NCBI-SeqCode DEFINITIONS ::=
BEGIN

EXPORTS Seq-code-table, Seq-map-table, Seq-code-set;

Seq-code-type ::= ENUMERATED {              -- sequence representations
    iupacna (1) ,              -- IUPAC 1 letter nuc acid code
    iupacaa (2) ,              -- IUPAC 1 letter amino acid code
    ncbi2na (3) ,              -- 2 bit nucleic acid code
    ncbi4na (4) ,              -- 4 bit nucleic acid code
    ncbi8na (5) ,              -- 8 bit extended nucleic acid code
    ncbipna (6) ,              -- nucleic acid probabilities
    ncbi8aa (7) ,              -- 8 bit extended amino acid codes
    ncbieaa (8) ,              -- extended ASCII 1 letter aa codes
    ncbipaa (9) ,              -- amino acid probabilities
    iupacaa3 (10) ,            -- 3 letter code only for display
    ncbistdaa (11) }           -- consecutive codes for std aas, 0-25

Seq-map-table ::= SEQUENCE { -- for tables of sequence mappings 
    from Seq-code-type ,      -- code to map from
    to Seq-code-type ,        -- code to map to
    num INTEGER ,             -- number of rows in table
    start-at INTEGER DEFAULT 0 ,   -- index offset of first element
    table SEQUENCE OF INTEGER }  -- table of values, in from-to order

Seq-code-table ::= SEQUENCE { -- for names of coded values
    code Seq-code-type ,      -- name of code
    num INTEGER ,             -- number of rows in table
    one-letter BOOLEAN ,   -- symbol is ALWAYS 1 letter?
    start-at INTEGER DEFAULT 0 ,   -- index offset of first element
    table SEQUENCE OF
        SEQUENCE {
            symbol VisibleString ,      -- the printed symbol or letter
            name VisibleString } ,      -- an explanatory name or string
    comps SEQUENCE OF INTEGER OPTIONAL } -- pointers to complement nuc acid

Seq-code-set ::= SEQUENCE {    -- for distribution
    codes SET OF Seq-code-table OPTIONAL ,
    maps SET OF Seq-map-table OPTIONAL }

END