Warning, /src/objects/seqcode/seqcode.asn is written in an unsupported language. File is not indexed.
--$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
0001 0002 0003 0004 0005 0006 0007 0008 0009 0010 0011 0012 0013 0014 0015 0016 0017 0018 0019 0020 0021 0022 0023 0024 0025 0026 0027 0028 0029 0030 0031 0032 0033 0034 0035 0036 0037 0038 0039 0040 0041 0042 0043 0044 0045 0046 0047 0048 0049 0050 0051 0052 0053 0054 0055 0056 0057 0058 0059 0060 0061 0062 0063 0064 0065 0066
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