Load /tmp/.../ncbi-tools6-6.1.20060301 into

branches/upstream/current.

1 files changed, 98 insertions, 34 deletions

diff --git a/asn/asn.all b/asn/asn.all
index b6cf3ea4..660f7999 100644
--- a/asn/asn.all
+++ b/asn/asn.all
@@ -740,7 +740,7 @@ Seq-loc-equiv ::= SET OF Seq-loc      -- for a set of equivalent locations
 END
     
 
---$Revision: 6.11 $
+--$Revision: 6.12 $
 --**********************************************************************
 --
 --  NCBI Sequence elements
@@ -752,8 +752,9 @@ END
 NCBI-Sequence DEFINITIONS ::=
 BEGIN
 
-EXPORTS Annotdesc, Bioseq, GIBB-mol, Heterogen, Numbering, Pubdesc,
-        Seq-annot, Seq-descr, Seq-hist, Seq-literal, Seqdesc;
+EXPORTS Annotdesc, Annot-descr, Bioseq, GIBB-mol, Heterogen, Numbering, Pubdesc,
+        Seq-annot, Seq-data, Seq-descr, Seq-ext, Seq-hist, Seq-inst,Seq-literal, 
+        Seqdesc;
 
 IMPORTS Date, Int-fuzz, Dbtag, Object-id, User-object FROM NCBI-General
         Seq-align FROM NCBI-Seqalign
@@ -2889,11 +2890,12 @@ PrintFormText ::= SEQUENCE {
     
 END
 
---$Revision: 6.5 $
+--$Revision: 6.6 $
 --*********************************************************
 --
 -- ASN.1 and XML for the components of a GenBank format sequence
 -- J.Ostell 2002
+-- Updated 14 December 2005
 --
 --*********************************************************
 
@@ -2977,28 +2979,12 @@ BEGIN
 GBSeq ::= SEQUENCE {
 	locus VisibleString ,
 	length INTEGER ,
-	strandedness INTEGER {
-		not-set (0) ,
-		single-stranded (1) ,
-		double-stranded (2) ,
-		mixed-stranded (3) } DEFAULT not-set ,
-	moltype INTEGER {
-		nucleic-acid (0) ,
-		dna (1) ,
-		rna (2) ,
-		trna (3) ,
-		rrna (4) ,
-		mrna (5) ,
-		urna (6) ,
-		snrna (7) ,
-		snorna (8) ,
-		peptide (9) } DEFAULT nucleic-acid ,
-	topology INTEGER {
-		linear (1) ,
-		circular (2) } DEFAULT linear ,
+	strandedness VisibleString OPTIONAL ,
+	moltype VisibleString ,
+	topology VisibleString OPTIONAL ,
 	division VisibleString ,
 	update-date VisibleString ,
-	create-date VisibleString ,
+	create-date VisibleString OPTIONAL ,
 	update-release VisibleString OPTIONAL ,
 	create-release VisibleString OPTIONAL ,
 	definition VisibleString ,
@@ -3007,12 +2993,13 @@ GBSeq ::= SEQUENCE {
 	accession-version VisibleString OPTIONAL ,
 	other-seqids SEQUENCE OF GBSeqid OPTIONAL ,
 	secondary-accessions SEQUENCE OF GBSecondary-accn OPTIONAL,
+	project VisibleString OPTIONAL ,
 	keywords SEQUENCE OF GBKeyword OPTIONAL ,
 	segment VisibleString OPTIONAL ,
-	source VisibleString ,
-	organism VisibleString ,
-	taxonomy VisibleString ,
-	references SEQUENCE OF GBReference ,
+	source VisibleString OPTIONAL ,
+	organism VisibleString OPTIONAL ,
+	taxonomy VisibleString OPTIONAL ,
+	references SEQUENCE OF GBReference OPTIONAL ,
 	comment VisibleString OPTIONAL ,
 	primary VisibleString OPTIONAL ,
 	source-db VisibleString OPTIONAL ,
@@ -3029,26 +3016,36 @@ GBSeq ::= SEQUENCE {
 
 	GBReference ::= SEQUENCE {
 		reference VisibleString ,
+		position VisibleString OPTIONAL ,
 		authors SEQUENCE OF GBAuthor OPTIONAL ,
 		consortium VisibleString OPTIONAL ,
 		title VisibleString OPTIONAL ,
 		journal VisibleString ,
-		medline INTEGER OPTIONAL ,
+		xref SET OF GBXref OPTIONAL ,
 		pubmed INTEGER OPTIONAL ,
 		remark VisibleString OPTIONAL }
 
 	GBAuthor ::= VisibleString
 
+    GBXref ::= SEQUENCE {
+		dbname VisibleString ,
+		id VisibleString }
+
 	GBFeature ::= SEQUENCE {
 		key VisibleString ,
 		location VisibleString ,
 		intervals SEQUENCE OF GBInterval OPTIONAL ,
+		operator VisibleString OPTIONAL ,
+		partial5 BOOLEAN OPTIONAL ,
+		partial3 BOOLEAN OPTIONAL ,
 		quals SEQUENCE OF GBQualifier OPTIONAL }
 
 	GBInterval ::= SEQUENCE {
 		from INTEGER OPTIONAL ,
 		to INTEGER OPTIONAL ,
 		point INTEGER OPTIONAL ,
+		iscomp BOOLEAN OPTIONAL ,
+		interbp BOOLEAN OPTIONAL ,
 		accession VisibleString }
 
 	GBQualifier ::= SEQUENCE {
@@ -3059,12 +3056,12 @@ GBSeq ::= SEQUENCE {
 		
 END
 
---$Revision: 1.5 $
+--$Revision: 1.6 $
 --************************************************************************
 --
 -- ASN.1 and XML for the components of a GenBank/EMBL/DDBJ sequence record
 -- The International Nucleotide Sequence Database (INSD) collaboration
--- Version 1.3, 1 June 2004
+-- Version 1.4, 19 September 2005
 --
 --************************************************************************
 
@@ -3089,7 +3086,7 @@ BEGIN
 --    http://www.ncbi.nlm.nih.gov/projects/collab/FT/index.html
 --
 --    URLs for DDBJ, EMBL, and GenBank Release Notes :
---    http://www.ddbj.nig.ac.jp/ddbjnew/ddbj_relnote.html
+--    ftp://ftp.ddbj.nig.ac.jp/database/ddbj/ddbjrel.txt
 --    http://www.ebi.ac.uk/embl/Documentation/Release_notes/current/relnotes.html
 --    ftp://ftp.ncbi.nih.gov/genbank/gbrel.txt
 --
@@ -3157,7 +3154,7 @@ INSDSeq ::= SEQUENCE {
 	topology VisibleString OPTIONAL ,
 	division VisibleString ,
 	update-date VisibleString ,
-	create-date VisibleString ,
+	create-date VisibleString OPTIONAL ,
 	update-release VisibleString OPTIONAL ,
 	create-release VisibleString OPTIONAL ,
 	definition VisibleString ,
@@ -3166,6 +3163,7 @@ INSDSeq ::= SEQUENCE {
 	accession-version VisibleString OPTIONAL ,
 	other-seqids SEQUENCE OF INSDSeqid OPTIONAL ,
 	secondary-accessions SEQUENCE OF INSDSecondary-accn OPTIONAL,
+	project VisibleString OPTIONAL ,
 	keywords SEQUENCE OF INSDKeyword OPTIONAL ,
 	segment VisibleString OPTIONAL ,
 	source VisibleString OPTIONAL ,
@@ -3186,28 +3184,94 @@ INSDSeq ::= SEQUENCE {
 
 	INSDKeyword ::= VisibleString
 
+-- INSDReference_position contains a string value indicating the
+-- basepair span(s) to which a reference applies. The allowable
+-- formats are:
+-- 
+--   X..Y  : Where X and Y are integers separated by two periods,
+--           X >= 1 , Y <= sequence length, and X <= Y 
+--
+--           Multiple basepair spans can exist, separated by a
+--           semi-colon and a space. For example : 10..20; 100..500
+--             
+--   sites : The string literal 'sites', indicating that a reference
+--           provides sequence annotation information, but the specific
+--           basepair spans are either not captured, or were too numerous
+--           to record.
+-- 
+--           The 'sites' literal string is singly occuring, and
+--            cannot be used in conjunction with any X..Y basepair spans.
+-- 
+--   References that lack an INSDReference_position element apply
+--   to the entire sequence.
+
 	INSDReference ::= SEQUENCE {
 		reference VisibleString ,
+		position VisibleString OPTIONAL ,
 		authors SEQUENCE OF INSDAuthor OPTIONAL ,
 		consortium VisibleString OPTIONAL ,
 		title VisibleString OPTIONAL ,
 		journal VisibleString ,
-		medline INTEGER OPTIONAL ,
+		xref SET OF INSDXref OPTIONAL ,
 		pubmed INTEGER OPTIONAL ,
 		remark VisibleString OPTIONAL }
 
 	INSDAuthor ::= VisibleString
 
+-- INSDXref provides a method for referring to records in
+-- other databases. INSDXref_dbname is a string value that
+-- provides the name of the database, and INSDXref_dbname
+-- is a string value that provides the record's identifier
+-- in that database.
+
+    INSDXref ::= SEQUENCE {
+		dbname VisibleString ,
+		id VisibleString }
+
+-- INSDFeature_operator contains a string value describing
+-- the relationship among a set of INSDInterval within
+-- INSDFeature_intervals. The allowable formats are:
+-- 
+--   join :  The string literal 'join' indicates that the
+--           INSDInterval intervals are biologically joined
+--           together into a contiguous molecule.
+-- 
+--   order : The string literal 'order' indicates that the
+--           INSDInterval intervals are in the presented
+--           order, but they are not necessarily contiguous.
+-- 
+--   Either 'join' or 'order' is required if INSDFeature_intervals
+--   is comprised of more than one INSDInterval .
+
 	INSDFeature ::= SEQUENCE {
 		key VisibleString ,
 		location VisibleString ,
 		intervals SEQUENCE OF INSDInterval OPTIONAL ,
+		operator VisibleString OPTIONAL ,
+		partial5 BOOLEAN OPTIONAL ,
+		partial3 BOOLEAN OPTIONAL ,
 		quals SEQUENCE OF INSDQualifier OPTIONAL }
 
+-- INSDInterval_iscomp is a boolean indicating whether
+-- an INSDInterval_from / INSDInterval_to location
+-- represents a location on the complement strand.
+-- When INSDInterval_iscomp is TRUE, it essentially
+-- confirms that a 'from' value which is greater than
+-- a 'to' value is intentional, because the location
+-- is on the opposite strand of the presented sequence.
+
+-- INSDInterval_interbp is a boolean indicating whether
+-- a feature (such as a restriction site) is located
+-- between two adjacent basepairs. When INSDInterval_iscomp
+-- is TRUE, the 'from' and 'to' values must differ by
+-- exactly one base.
+
 	INSDInterval ::= SEQUENCE {
 		from INTEGER OPTIONAL ,
 		to INTEGER OPTIONAL ,
 		point INTEGER OPTIONAL ,
+		iscomp BOOLEAN OPTIONAL ,
+		interbp BOOLEAN OPTIONAL ,
 		accession VisibleString }
 
 	INSDQualifier ::= SEQUENCE {