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<!-- ============================================
::DATATOOL:: Generated from "seqcode.asn"
::DATATOOL:: by application DATATOOL version 1.9.0
::DATATOOL:: on 04/10/2008 16:04:22
============================================ -->
<!-- ============================================ -->
<!-- This section is mapped from module "NCBI-SeqCode"
================================================= -->
<!--
$Revision: 6.0 $
*********************************************************************
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
-->
<!-- Elements used by other modules:
Seq-code-table,
Seq-map-table,
Seq-code-set -->
<!-- ============================================ -->
<!-- sequence representations -->
<!ELEMENT Seq-code-type %ENUM;>
<!--
iupacna - IUPAC 1 letter nuc acid code
iupacaa - IUPAC 1 letter amino acid code
ncbi2na - 2 bit nucleic acid code
ncbi4na - 4 bit nucleic acid code
ncbi8na - 8 bit extended nucleic acid code
ncbipna - nucleic acid probabilities
ncbi8aa - 8 bit extended amino acid codes
ncbieaa - extended ASCII 1 letter aa codes
ncbipaa - amino acid probabilities
iupacaa3 - 3 letter code only for display
ncbistdaa - consecutive codes for std aas, 0-25
-->
<!ATTLIST Seq-code-type value (
iupacna |
iupacaa |
ncbi2na |
ncbi4na |
ncbi8na |
ncbipna |
ncbi8aa |
ncbieaa |
ncbipaa |
iupacaa3 |
ncbistdaa
) #REQUIRED >
<!-- for tables of sequence mappings -->
<!ELEMENT Seq-map-table (
Seq-map-table_from,
Seq-map-table_to,
Seq-map-table_num,
Seq-map-table_start-at?,
Seq-map-table_table)>
<!-- code to map from -->
<!ELEMENT Seq-map-table_from (Seq-code-type)>
<!-- code to map to -->
<!ELEMENT Seq-map-table_to (Seq-code-type)>
<!-- number of rows in table -->
<!ELEMENT Seq-map-table_num (%INTEGER;)>
<!-- index offset of first element -->
<!ELEMENT Seq-map-table_start-at (%INTEGER;)>
<!-- table of values, in from-to order -->
<!ELEMENT Seq-map-table_table (Seq-map-table_table_E*)>
<!ELEMENT Seq-map-table_table_E (%INTEGER;)>
<!-- for names of coded values -->
<!ELEMENT Seq-code-table (
Seq-code-table_code,
Seq-code-table_num,
Seq-code-table_one-letter,
Seq-code-table_start-at?,
Seq-code-table_table,
Seq-code-table_comps?)>
<!-- name of code -->
<!ELEMENT Seq-code-table_code (Seq-code-type)>
<!-- number of rows in table -->
<!ELEMENT Seq-code-table_num (%INTEGER;)>
<!-- symbol is ALWAYS 1 letter? -->
<!ELEMENT Seq-code-table_one-letter EMPTY>
<!ATTLIST Seq-code-table_one-letter value ( true | false ) #REQUIRED >
<!-- index offset of first element -->
<!ELEMENT Seq-code-table_start-at (%INTEGER;)>
<!-- an explanatory name or string -->
<!ELEMENT Seq-code-table_table (Seq-code-table_table_E*)>
<!ELEMENT Seq-code-table_table_E (
Seq-code-table_table_E_symbol,
Seq-code-table_table_E_name)>
<!-- the printed symbol or letter -->
<!ELEMENT Seq-code-table_table_E_symbol (#PCDATA)>
<!ELEMENT Seq-code-table_table_E_name (#PCDATA)>
<!-- pointers to complement nuc acid -->
<!ELEMENT Seq-code-table_comps (Seq-code-table_comps_E*)>
<!ELEMENT Seq-code-table_comps_E (%INTEGER;)>
<!-- for distribution -->
<!ELEMENT Seq-code-set (
Seq-code-set_codes?,
Seq-code-set_maps?)>
<!ELEMENT Seq-code-set_codes (Seq-code-table*)>
<!ELEMENT Seq-code-set_maps (Seq-map-table*)>
|
