Load ncbi (6.1.20010709) into ncbi-tools6/branches/upstream/current.

11 files changed, 515 insertions, 627 deletions

diff --git a/cdromlib/accentr.c b/cdromlib/accentr.c
index 0b2219b1..d01b6a6d 100644
--- a/cdromlib/accentr.c
+++ b/cdromlib/accentr.c
@@ -23,7 +23,7 @@
  *
  * ===========================================================================
  *
- * RCS $Id: accentr.c,v 6.5 1999/01/06 14:18:35 grisha Exp $
+ * RCS $Id: accentr.c,v 6.6 2000/01/12 20:17:12 vakatov Exp $
  *
  * Author:  Ostell
  *
@@ -48,6 +48,9 @@
  *                      modification comments.
  *
  * Revision $Log: accentr.c,v $
+ * Revision Revision 6.6  2000/01/12 20:17:12  vakatov
+ * Revision Get rid of the LIBCALL specifier at EntrezSeqEntryGet()
+ * Revision
  * Revision Revision 6.5  1999/01/06 14:18:35  grisha
  * Revision add defines to switch ID0/ID1 usage
  * Revision
@@ -277,7 +280,7 @@
  * ==========================================================================
  */
 
-#define REVISION_STR "$Revision: 6.5 $"
+#define REVISION_STR "$Revision: 6.6 $"
 
 #include <accentr.h>
 #include <seqmgr.h>
@@ -2350,7 +2353,7 @@ NLM_EXTERN Int2 LIBCALL EntrezSeqEntryListGet (SeqEntryPtr PNTR result, Int2 num
 *       get one SeqEntry
 *
 *****************************************************************************/
-NLM_EXTERN SeqEntryPtr LIBCALL EntrezSeqEntryGet (Int4 uid, Int2 retcode)
+NLM_EXTERN SeqEntryPtr EntrezSeqEntryGet (Int4 uid, Int2 retcode)
 
 {
     SeqEntryPtr sep = NULL;
diff --git a/cdromlib/accentr.h b/cdromlib/accentr.h
index 9db1e773..4cf8b352 100644
--- a/cdromlib/accentr.h
+++ b/cdromlib/accentr.h
@@ -23,7 +23,7 @@
 *
 * ===========================================================================
 *
-* RCS $Id: accentr.h,v 6.0 1997/08/25 18:12:31 madden Exp $
+* RCS $Id: accentr.h,v 6.1 2000/01/12 20:17:13 vakatov Exp $
 *
 * Author:  Ostell
 *
@@ -51,90 +51,66 @@
 * 05-16-94 Schuler     Added RCS Log directive.  Comments will henceforth
 *                      be inserted automatically into the source at the
 *                      time it is checked into the system. 
-$Log: accentr.h,v $
-Revision 6.0  1997/08/25 18:12:31  madden
-Revision changed to 6.0
-
-Revision 5.10  1997/07/28 13:30:41  ostell
-Moved GetUniGeneIDForSeqId() to seqmgr.c
-
-Revision 5.9  1997/06/26 21:55:14  vakatov
-[PC] DLL'd "ncbicdr.lib", "ncbiacc.lib", "ncbinacc.lib" and "ncbicacc.lib"
-
-Revision 5.8  1996/12/02 22:20:52  brandon
-*** empty log message ***
-
- * Revision 5.7  1996/12/02  22:14:52  brandon
- * *** empty log message ***
- *
- * Revision 5.6  1996/12/02  22:10:46  brandon
- * *** empty log message ***
- *
- * Revision 5.5  1996/09/23  21:21:33  shavirin
- * Added definition for the function AccessionToFasta
- *
- * Revision 5.4  1996/08/14  19:56:09  epstein
- * add APIs for fetching pieces of biostruc annots
- *
- * Revision 5.3  1996/08/14  17:08:29  brandon
- * *** empty log message ***
- *
- * Revision 5.1  1996/08/14  15:15:05  brandon
- * added date parameter to tleval functions
- *
- * Revision 5.0  1996/05/28  13:55:34  ostell
- * Set to revision 5.0
- *
- * Revision 4.8  1996/05/14  21:02:10  epstein
- * adjust field descriptions to reflect current reality
- *
- * Revision 4.7  1996/03/29  18:52:51  epstein
- * add support for structure alignments
- *
- * Revision 4.6  1996/03/11  21:51:03  ostell
- * made GetUniGeneIDForSeqId() externally visible
- *
- * Revision 4.5  1995/10/11  13:39:29  epstein
- * add EntrezIsInited() function
- *
- * Revision 4.4  1995/10/02  02:35:50  epstein
- * add range-checking
- *
- * Revision 4.3  1995/08/28  23:20:47  kans
- * Biostruc_supported restored
- *
- * Revision 4.2  1995/08/21  19:42:16  epstein
- * add cluster analysis
- *
- * Revision 4.1  1995/08/11  20:25:53  epstein
- * add max-models support for biostrucs
- *
- * Revision 4.0  1995/07/26  13:50:32  ostell
- * force revision to 4.0
- *
- * Revision 2.44  1995/07/25  18:47:57  kans
- * revert to no Biostruc_supported
- *
- * Revision 2.43  1995/07/05  19:15:46  ostell
- * changed prototype for BiostrucAvail to be included only once
- *
- * Revision 2.42  1995/06/29  15:57:46  epstein
- * added Complexity argument when fetching structures
- *
- * Revision 2.41  95/06/26  18:07:13  kans
- * restored #define Biostruc_supported
- * 
- * Revision 2.39  1995/06/23  16:02:43  kans
- * support for accmmdbs.c stub to resolve symbols without MMDB link
- *
- * Revision 2.38  1995/06/22  21:21:22  kans
- * #define Biostruc_supported
- *
- * Revision 2.37  1995/05/16  14:12:46  schuler
- * Automatic comment insertion enabled
- *
-
-
+* $Log: accentr.h,v $
+* Revision 6.1  2000/01/12 20:17:13  vakatov
+* Get rid of the LIBCALL specifier at EntrezSeqEntryGet()
+*
+* Revision 5.10  1997/07/28 13:30:41  ostell
+* Moved GetUniGeneIDForSeqId() to seqmgr.c
+* 
+* Revision 5.9  1997/06/26 21:55:14  vakatov
+* [PC] DLL'd "ncbicdr.lib", "ncbiacc.lib", "ncbinacc.lib" and "ncbicacc.lib"
+*
+* Revision 5.5  1996/09/23  21:21:33  shavirin
+* Added definition for the function AccessionToFasta
+*
+* Revision 5.4  1996/08/14  19:56:09  epstein
+* add APIs for fetching pieces of biostruc annots
+*
+* Revision 5.1  1996/08/14  15:15:05  brandon
+* added date parameter to tleval functions
+*
+* Revision 4.8  1996/05/14  21:02:10  epstein
+* adjust field descriptions to reflect current reality
+*
+* Revision 4.7  1996/03/29  18:52:51  epstein
+* add support for structure alignments
+*
+* Revision 4.6  1996/03/11  21:51:03  ostell
+* made GetUniGeneIDForSeqId() externally visible
+*
+* Revision 4.5  1995/10/11  13:39:29  epstein
+* add EntrezIsInited() function
+*
+* Revision 4.4  1995/10/02  02:35:50  epstein
+* add range-checking
+*
+* Revision 4.3  1995/08/28  23:20:47  kans
+* Biostruc_supported restored
+*
+* Revision 4.2  1995/08/21  19:42:16  epstein
+* add cluster analysis
+*
+* Revision 4.1  1995/08/11  20:25:53  epstein
+* add max-models support for biostrucs
+*
+* Revision 2.44  1995/07/25  18:47:57  kans
+* revert to no Biostruc_supported
+*
+* Revision 2.43  1995/07/05  19:15:46  ostell
+* changed prototype for BiostrucAvail to be included only once
+*
+* Revision 2.42  1995/06/29  15:57:46  epstein
+* added Complexity argument when fetching structures
+*
+* Revision 2.41  95/06/26  18:07:13  kans
+* restored #define Biostruc_supported
+* 
+* Revision 2.39  1995/06/23  16:02:43  kans
+* support for accmmdbs.c stub to resolve symbols without MMDB link
+*
+* Revision 2.38  1995/06/22  21:21:22  kans
+* #define Biostruc_supported
 * ==========================================================================
 */
 
@@ -167,18 +143,6 @@ Revision 5.8  1996/12/02 22:20:52  brandon
 #include <mmdbapi1.h>
 #include <mmdbapi2.h>
 #include <mmdbapi3.h>
-#else
-typedef struct { int bogus; } Biostruc, *BiostrucPtr;
-
-/*****************************************************************************
-*
-*   BiostrucAvail is in the accmmdbs.c stub (returning FALSE) and in
-*      bios2ff7.c (returning TRUE).  The stub file also has BiostrucAsnRead
-*      and BiostrucAsnWrite empty functions for proper linking without MMDB.
-*
-*****************************************************************************/
-
-NLM_EXTERN Boolean LIBCALL BiostrucAvail PROTO((void));
 #endif
 
 
@@ -193,6 +157,22 @@ NLM_EXTERN Boolean LIBCALL BiostrucAvail PROTO((void));
 extern "C" {
 #endif
 
+
+#ifndef Biostruc_supported
+typedef struct { int bogus; } Biostruc, *BiostrucPtr;
+
+/*****************************************************************************
+*
+*   BiostrucAvail is in the accmmdbs.c stub (returning FALSE) and in
+*      bios2ff7.c (returning TRUE).  The stub file also has BiostrucAsnRead
+*      and BiostrucAsnWrite empty functions for proper linking without MMDB.
+*
+*****************************************************************************/
+
+NLM_EXTERN Boolean LIBCALL BiostrucAvail(void);
+#endif
+
+
 /* --- Type Definitions --- */
 
 typedef DocUid *DocUidPtr;
@@ -271,7 +251,7 @@ typedef struct FastaSeq {
 #define TERM__EXPLODE 1
 
 
-typedef Boolean (*DocSumListCallBack) PROTO((DocSumPtr dsp, DocUid uid));
+typedef Boolean (*DocSumListCallBack)(DocSumPtr dsp, DocUid uid);
 
 
 typedef struct EntrezHierarchyChild {
@@ -314,122 +294,122 @@ typedef struct EntrezNeighborText {
 
 /**** Initialize and close session *********************/
 
-/* Note:                                                                      */
-/*   The EntrezInitWithExtras() capability is provided for backwards          */
-/*   compatability until May, 1994.  This name was introduced as a temporary  */
-/*   interface to EntrezInit(), to smooth the transition for EntrezInit()'s   */
-/*   use of three parameters; previously it took no parameters.               */
-/*                                                                            */
-/*                                  - J. Epstein, 17 Feb 1994                 */
+/* Note:                                                                     */
+/*   The EntrezInitWithExtras() capability is provided for backwards         */
+/*   compatability until May, 1994.  This name was introduced as a temporary */
+/*   interface to EntrezInit(), to smooth the transition for EntrezInit()'s  */
+/*   use of three parameters; previously it took no parameters.              */
+/*                                                                           */
+/*                                  - J. Epstein, 17 Feb 1994                */
 
 #define EntrezInitWithExtras(a,b,c) EntrezInit(a,b,c)
-NLM_EXTERN Boolean LIBCALL EntrezInit PROTO((CharPtr appl_id, Boolean no_warnings, BoolPtr is_network));
-NLM_EXTERN Boolean LIBCALL EntrezIsInited PROTO((void));
-NLM_EXTERN void LIBCALL EntrezFini PROTO((void));
+NLM_EXTERN Boolean LIBCALL EntrezInit(CharPtr appl_id, Boolean no_warnings, BoolPtr is_network);
+NLM_EXTERN Boolean LIBCALL EntrezIsInited(void);
+NLM_EXTERN void LIBCALL EntrezFini(void);
 
 /**** Get names and numbers of fields and types ********/
 
-NLM_EXTERN EntrezInfoPtr LIBCALL EntrezGetInfo PROTO((void));
+NLM_EXTERN EntrezInfoPtr LIBCALL EntrezGetInfo(void);
 
 /**** Creates a term node from the uid parameter ********/
-NLM_EXTERN void LIBCALL EntrezCreateNamedUidList PROTO((CharPtr term, DocType type, DocField field, Int4 num, DocUidPtr uids));
-NLM_EXTERN void LIBCALL EntrezCreateNamedUidListX PROTO((CharPtr term, DocType type, DocField field, ByteStorePtr bsp));
+NLM_EXTERN void LIBCALL EntrezCreateNamedUidList(CharPtr term, DocType type, DocField field, Int4 num, DocUidPtr uids);
+NLM_EXTERN void LIBCALL EntrezCreateNamedUidListX(CharPtr term, DocType type, DocField field, ByteStorePtr bsp);
 
 /**** Get detailed text information about the current status *****/
-NLM_EXTERN CharPtr LIBCALL EntrezDetailedInfo PROTO((void));
+NLM_EXTERN CharPtr LIBCALL EntrezDetailedInfo(void);
 
 /**** Get Links and Neighbors **************************/
 
-NLM_EXTERN Int4 LIBCALL EntrezGetMaxLinks PROTO((void));
-NLM_EXTERN Int4 LIBCALL EntrezSetUserMaxLinks PROTO((Int4 usermax));
-NLM_EXTERN Int4 LIBCALL EntrezGetUserMaxLinks PROTO((void));
+NLM_EXTERN Int4 LIBCALL EntrezGetMaxLinks(void);
+NLM_EXTERN Int4 LIBCALL EntrezSetUserMaxLinks(Int4 usermax);
+NLM_EXTERN Int4 LIBCALL EntrezGetUserMaxLinks(void);
 
-NLM_EXTERN LinkSetPtr LIBCALL EntrezUidLinks PROTO((DocType type, DocUid uid, DocType link_to_type));
-NLM_EXTERN Int2 LIBCALL EntrezLinkUidList PROTO((LinkSetPtr PNTR result, DocType type, DocType link_to_type, Int2 numuid, Int4Ptr uids, Boolean mark_missing));
+NLM_EXTERN LinkSetPtr LIBCALL EntrezUidLinks(DocType type, DocUid uid, DocType link_to_type);
+NLM_EXTERN Int2 LIBCALL EntrezLinkUidList(LinkSetPtr PNTR result, DocType type, DocType link_to_type, Int2 numuid, Int4Ptr uids, Boolean mark_missing);
 
 /**** Get Summaries ************************************/
 
-NLM_EXTERN DocSumPtr LIBCALL EntrezDocSum PROTO((DocType type, DocUid uid));
-NLM_EXTERN DocSumPtr LIBCALL DocSumFree PROTO((DocSumPtr dsp));
-NLM_EXTERN Int2 LIBCALL EntrezDocSumListGet PROTO((Int2 numuid, DocType type, DocUidPtr uids, DocSumListCallBack callback));
-NLM_EXTERN Int2 LIBCALL EntrezMlSumListGet PROTO((DocSumPtr PNTR result, Int2 numuid, Int4Ptr uids));
-NLM_EXTERN Int2 LIBCALL EntrezSeqSumListGet PROTO((DocSumPtr PNTR result, Int2 numuid, DocType type, Int4Ptr uids));
+NLM_EXTERN DocSumPtr LIBCALL EntrezDocSum(DocType type, DocUid uid);
+NLM_EXTERN DocSumPtr LIBCALL DocSumFree(DocSumPtr dsp);
+NLM_EXTERN Int2 LIBCALL EntrezDocSumListGet(Int2 numuid, DocType type, DocUidPtr uids, DocSumListCallBack callback);
+NLM_EXTERN Int2 LIBCALL EntrezMlSumListGet(DocSumPtr PNTR result, Int2 numuid, Int4Ptr uids);
+NLM_EXTERN Int2 LIBCALL EntrezSeqSumListGet(DocSumPtr PNTR result, Int2 numuid, DocType type, Int4Ptr uids);
 
 /**** Get Term Lists ***********************************/
 
-typedef Boolean (*TermListProc) PROTO((CharPtr term, Int4 special, Int4 total));
+typedef Boolean (*TermListProc)(CharPtr term, Int4 special, Int4 total);
 
-NLM_EXTERN Int2 LIBCALL EntrezTermListByPage PROTO((DocType type, DocField field, Int2 page, Int2 numpage, TermListProc proc));
-NLM_EXTERN Int2 LIBCALL EntrezTermListByTerm PROTO((DocType type, DocField field, CharPtr term, Int2 numterms, TermListProc proc, Int2Ptr first_page));
+NLM_EXTERN Int2 LIBCALL EntrezTermListByPage(DocType type, DocField field, Int2 page, Int2 numpage, TermListProc proc);
+NLM_EXTERN Int2 LIBCALL EntrezTermListByTerm(DocType type, DocField field, CharPtr term, Int2 numterms, TermListProc proc, Int2Ptr first_page);
 
-NLM_EXTERN Boolean LIBCALL EntrezFindTerm PROTO((DocType type, DocField field, CharPtr term, Int4Ptr spcl, Int4Ptr totl));
+NLM_EXTERN Boolean LIBCALL EntrezFindTerm(DocType type, DocField field, CharPtr term, Int4Ptr spcl, Int4Ptr totl);
 
 /**** Look up terms with Boolean operations ************/
 
-NLM_EXTERN ValNodePtr LIBCALL EntrezTLNew PROTO((DocType type));
-NLM_EXTERN ValNodePtr LIBCALL EntrezTLAddTerm PROTO((ValNodePtr elst, CharPtr term, DocType type, DocField field, Boolean special));
-NLM_EXTERN ValNodePtr LIBCALL EntrezTLAddTermWithRange PROTO((ValNodePtr elst, CharPtr term, DocType type, DocField field, Boolean special, CharPtr highRange));
-NLM_EXTERN ValNodePtr LIBCALL EntrezTLAddLParen PROTO((ValNodePtr elst));
-NLM_EXTERN ValNodePtr LIBCALL EntrezTLAddRParen PROTO((ValNodePtr elst));
-NLM_EXTERN ValNodePtr LIBCALL EntrezTLAddAND PROTO((ValNodePtr elst));
-NLM_EXTERN ValNodePtr LIBCALL EntrezTLAddOR PROTO((ValNodePtr elst));
-NLM_EXTERN ValNodePtr LIBCALL EntrezTLAddBUTNOT PROTO((ValNodePtr elst));
-NLM_EXTERN ValNodePtr LIBCALL EntrezTLFree PROTO((ValNodePtr elst));
-NLM_EXTERN LinkSetPtr LIBCALL EntrezPMTLEval PROTO((ValNodePtr elst, void * edc));
-NLM_EXTERN Int4 LIBCALL EntrezPMTLEvalCount PROTO((ValNodePtr elst, void * edc));
-NLM_EXTERN ByteStorePtr LIBCALL EntrezPMTLEvalX PROTO((ValNodePtr elst, void * edc));
-NLM_EXTERN LinkSetPtr LIBCALL EntrezTLEval PROTO((ValNodePtr elst));
-NLM_EXTERN Int4 LIBCALL EntrezTLEvalCount PROTO((ValNodePtr elst));
-NLM_EXTERN ByteStorePtr LIBCALL EntrezTLEvalX PROTO((ValNodePtr elst));
+NLM_EXTERN ValNodePtr LIBCALL EntrezTLNew(DocType type);
+NLM_EXTERN ValNodePtr LIBCALL EntrezTLAddTerm(ValNodePtr elst, CharPtr term, DocType type, DocField field, Boolean special);
+NLM_EXTERN ValNodePtr LIBCALL EntrezTLAddTermWithRange(ValNodePtr elst, CharPtr term, DocType type, DocField field, Boolean special, CharPtr highRange);
+NLM_EXTERN ValNodePtr LIBCALL EntrezTLAddLParen(ValNodePtr elst);
+NLM_EXTERN ValNodePtr LIBCALL EntrezTLAddRParen(ValNodePtr elst);
+NLM_EXTERN ValNodePtr LIBCALL EntrezTLAddAND(ValNodePtr elst);
+NLM_EXTERN ValNodePtr LIBCALL EntrezTLAddOR(ValNodePtr elst);
+NLM_EXTERN ValNodePtr LIBCALL EntrezTLAddBUTNOT(ValNodePtr elst);
+NLM_EXTERN ValNodePtr LIBCALL EntrezTLFree(ValNodePtr elst);
+NLM_EXTERN LinkSetPtr LIBCALL EntrezPMTLEval(ValNodePtr elst, void * edc);
+NLM_EXTERN Int4 LIBCALL EntrezPMTLEvalCount(ValNodePtr elst, void * edc);
+NLM_EXTERN ByteStorePtr LIBCALL EntrezPMTLEvalX(ValNodePtr elst, void * edc);
+NLM_EXTERN LinkSetPtr LIBCALL EntrezTLEval(ValNodePtr elst);
+NLM_EXTERN Int4 LIBCALL EntrezTLEvalCount(ValNodePtr elst);
+NLM_EXTERN ByteStorePtr LIBCALL EntrezTLEvalX(ValNodePtr elst);
 
 
 /**** Look Up a Uid from a SeqId using the Terms list ****/
 
-NLM_EXTERN Int4 LIBCALL EntrezFindSeqId PROTO((SeqIdPtr sip));
+NLM_EXTERN Int4 LIBCALL EntrezFindSeqId(SeqIdPtr sip);
 
 /**** Look Up the source SeqId given a GI ****************/
 
-NLM_EXTERN SeqIdPtr LIBCALL EntrezSeqIdForGI PROTO ((Int4 gi));
+NLM_EXTERN SeqIdPtr LIBCALL EntrezSeqIdForGI(Int4 gi);
 
 /**** Look Up the Fasta entry given a GI or Accession ****/
 
-NLM_EXTERN FastaSeqPtr LIBCALL AccessionToFasta PROTO ((CharPtr string));
+NLM_EXTERN FastaSeqPtr LIBCALL AccessionToFasta(CharPtr string);
 
 /**** Get Sequence or MEDLINE data **********************/
 
-NLM_EXTERN Int2 LIBCALL EntrezSeqEntryListGet PROTO((SeqEntryPtr PNTR result, Int2 numuid, Int4Ptr uids, Int2 retcode, Boolean mark_missing));
-NLM_EXTERN SeqEntryPtr LIBCALL EntrezSeqEntryGet PROTO((Int4 uid, Int2 retcode));
+NLM_EXTERN Int2 LIBCALL EntrezSeqEntryListGet(SeqEntryPtr PNTR result, Int2 numuid, Int4Ptr uids, Int2 retcode, Boolean mark_missing);
+NLM_EXTERN SeqEntryPtr EntrezSeqEntryGet(Int4 uid, Int2 retcode);
 
-NLM_EXTERN Int2 LIBCALL EntrezMedlineEntryListGet PROTO((MedlineEntryPtr PNTR result, Int2 numuid, Int4Ptr uids, Boolean mark_missing));
-NLM_EXTERN MedlineEntryPtr LIBCALL EntrezMedlineEntryGet PROTO((Int4 uid));
+NLM_EXTERN Int2 LIBCALL EntrezMedlineEntryListGet(MedlineEntryPtr PNTR result, Int2 numuid, Int4Ptr uids, Boolean mark_missing);
+NLM_EXTERN MedlineEntryPtr LIBCALL EntrezMedlineEntryGet(Int4 uid);
 
 #ifdef _PMENTREZ_
-Int2 LIBCALL EntrezPubmedEntryListGet PROTO((PubmedEntryPtr PNTR result, Int2 numuid, Int4Ptr uids, Boolean mark_missing));
-PubmedEntryPtr LIBCALL EntrezPubmedEntryGet PROTO((Int4 uid));
+Int2 LIBCALL EntrezPubmedEntryListGet(PubmedEntryPtr PNTR result, Int2 numuid, Int4Ptr uids, Boolean mark_missing);
+PubmedEntryPtr LIBCALL EntrezPubmedEntryGet(Int4 uid);
 #endif
 
-NLM_EXTERN BiostrucPtr LIBCALL EntrezBiostrucGet PROTO((DocUid uid, Int4 mdlLvl, Int4 maxModels));
-NLM_EXTERN BiostrucAnnotSetPtr LIBCALL EntrezBiostrucAnnotSetGet PROTO((DocUid uid));
-NLM_EXTERN LinkSetPtr LIBCALL EntrezBiostrucFeatIds PROTO((DocUid mmdbid, Int2 feature_type, Int4 feature_set_id));
-NLM_EXTERN BiostrucAnnotSetPtr LIBCALL EntrezBiostrucAnnotSetGetByFid PROTO((DocUid mmdbid, Int4 feature_id, Int4 feature_set_id));
+NLM_EXTERN BiostrucPtr LIBCALL EntrezBiostrucGet(DocUid uid, Int4 mdlLvl, Int4 maxModels);
+NLM_EXTERN BiostrucAnnotSetPtr LIBCALL EntrezBiostrucAnnotSetGet(DocUid uid);
+NLM_EXTERN LinkSetPtr LIBCALL EntrezBiostrucFeatIds(DocUid mmdbid, Int2 feature_type, Int4 feature_set_id);
+NLM_EXTERN BiostrucAnnotSetPtr LIBCALL EntrezBiostrucAnnotSetGetByFid(DocUid mmdbid, Int4 feature_id, Int4 feature_set_id);
 
 
-NLM_EXTERN EntrezHierarchyPtr LIBCALL EntrezHierarchyGet PROTO((CharPtr term,DocType type, DocField fld));
-NLM_EXTERN EntrezHierarchyPtr LIBCALL EntrezHierarchyFree PROTO ((EntrezHierarchyPtr ehp));
+NLM_EXTERN EntrezHierarchyPtr LIBCALL EntrezHierarchyGet(CharPtr term,DocType type, DocField fld);
+NLM_EXTERN EntrezHierarchyPtr LIBCALL EntrezHierarchyFree(EntrezHierarchyPtr ehp);
 
 /***** Neighbor text on-the-fly ***********/
-NLM_EXTERN EntrezNeighborTextPtr LIBCALL EntrezNeighborTextFree PROTO ((EntrezNeighborTextPtr ));
-NLM_EXTERN EntrezNeighborTextPtr LIBCALL EntrezNeighborTextNew PROTO (( void ));
-NLM_EXTERN LinkSetPtr LIBCALL EntrezDoNeighborText PROTO((EntrezNeighborTextPtr entp));
-NLM_EXTERN Boolean LIBCALL EntrezCanNeighborText PROTO((void));
+NLM_EXTERN EntrezNeighborTextPtr LIBCALL EntrezNeighborTextFree(EntrezNeighborTextPtr );
+NLM_EXTERN EntrezNeighborTextPtr LIBCALL EntrezNeighborTextNew(void);
+NLM_EXTERN LinkSetPtr LIBCALL EntrezDoNeighborText(EntrezNeighborTextPtr entp);
+NLM_EXTERN Boolean LIBCALL EntrezCanNeighborText(void);
 
 
-NLM_EXTERN Boolean LIBCALL EntrezExpandedMedlineFeatures PROTO((void));
-NLM_EXTERN Int4 LIBCALL EntrezClusterAnalysis PROTO((DocUidPtr uids, Int4 numuids, DocField fld, Int4 minCluster, Int4 maxCluster, Int4 maxTerms, CharPtr *terms, Int4Ptr termTotals));
+NLM_EXTERN Boolean LIBCALL EntrezExpandedMedlineFeatures(void);
+NLM_EXTERN Int4 LIBCALL EntrezClusterAnalysis(DocUidPtr uids, Int4 numuids, DocField fld, Int4 minCluster, Int4 maxCluster, Int4 maxTerms, CharPtr *terms, Int4Ptr termTotals);
 
 /***** on-the-fly BLAST *****/
-NLM_EXTERN LinkSetPtr LIBCALL EntrezBlastBioseq PROTO((BioseqPtr bsp, DocType db, CharPtr program, CharPtr database, CharPtr options, Boolean usemonitor));
-NLM_EXTERN Boolean LIBCALL EntrezCanBlast PROTO((void));
+NLM_EXTERN LinkSetPtr LIBCALL EntrezBlastBioseq(BioseqPtr bsp, DocType db, CharPtr program, CharPtr database, CharPtr options, Boolean usemonitor);
+NLM_EXTERN Boolean LIBCALL EntrezCanBlast(void);
 
 /*****************************************************************************
 *
@@ -445,11 +425,12 @@ NLM_EXTERN Boolean LIBCALL EntrezCanBlast PROTO((void));
 *     call, and yours will be call AFTER entrez.
 *   
 *****************************************************************************/
-NLM_EXTERN Boolean LIBCALL EntrezBioseqFetchEnable PROTO((CharPtr progname, Boolean now));
-NLM_EXTERN void LIBCALL EntrezBioseqFetchDisable PROTO((void));
+NLM_EXTERN Boolean LIBCALL EntrezBioseqFetchEnable(CharPtr progname, Boolean now);
+NLM_EXTERN void LIBCALL EntrezBioseqFetchDisable(void);
+
 
 #ifdef __cplusplus
-}
+}  /* extern "C" */
 #endif
 
 #undef NLM_EXTERN
diff --git a/cdromlib/accmmdbs.c b/cdromlib/accmmdbs.c
index 996f48a9..ca84b092 100644
--- a/cdromlib/accmmdbs.c
+++ b/cdromlib/accmmdbs.c
@@ -38,6 +38,12 @@
  * -------  ----------  -----------------------------------------------------
  *
  * $Log: accmmdbs.c,v $
+ * Revision 6.2  2001/06/21 14:21:55  thiessen
+ * add BiostrucId... stubs
+ *
+ * Revision 6.1  1999/03/03 21:27:34  kans
+ * added stub for ClearStructures
+ *
  * Revision 6.0  1997/08/25 18:12:33  madden
  * Revision changed to 6.0
  *
@@ -134,6 +140,9 @@ NLM_EXTERN void LIBCALL FreeAModelstruc(PDNMS pdnmsThis)
 NLM_EXTERN PDNMS LIBCALL MakeAModelstruc(BiostrucPtr pbsThis)
 { return NULL; }
 
+NLM_EXTERN void LIBCALL ClearStructures(void)
+{ }
+
 NLM_EXTERN BiostrucPtr LIBCALL BiostrucAsnRead(AsnIoPtr aip, AsnTypePtr orig)
 { return NULL; }
 
@@ -208,3 +217,13 @@ NLM_EXTERN BiostrucFeatureSetPtr LIBCALL BiostrucFeatureSetNew(void)
 
 NLM_EXTERN BiostrucFeaturePtr LIBCALL BiostrucFeatureNew(void)
 { return NULL; }
+
+NLM_EXTERN BiostrucIdPtr LIBCALL BiostrucIdFree(BiostrucIdPtr ptr)
+{ return NULL; }
+
+NLM_EXTERN BiostrucIdPtr LIBCALL BiostrucIdAsnRead(AsnIoPtr io, AsnTypePtr type)
+{ return NULL; }
+
+NLM_EXTERN Boolean LIBCALL BiostrucIdAsnWrite(BiostrucIdPtr id, AsnIoPtr io, AsnTypePtr type)
+{ return FALSE; }
+
diff --git a/cdromlib/accutils.c b/cdromlib/accutils.c
index 4f433114..50c98d81 100644
--- a/cdromlib/accutils.c
+++ b/cdromlib/accutils.c
@@ -23,7 +23,7 @@
  *
  * ===========================================================================
  *
- * RCS $Id: accutils.c,v 6.7 1999/01/06 14:18:36 grisha Exp $
+ * RCS $Id: accutils.c,v 6.15 1999/04/01 13:56:34 sicotte Exp $
  *
  * Author:  J. Epstein
  *
@@ -35,6 +35,37 @@
  * Modifications:  
  * --------------------------------------------------------------------------
  * $Log: accutils.c,v $
+ * Revision 6.15  1999/04/01 13:56:34  sicotte
+ * Moved WHICH_db_accession,IS_ntdb_accession,IS_protdb_accession to
+ *   sequtil.ch
+ * Removed old static functions of Colombe (that are public in salutil.c)
+ * The only code left in accutils.c is the Entrez Access code.
+ *
+ * Revision 6.14  1999/03/31 21:13:47  sicotte
+ * Add info on N-accessions
+ *
+ * Revision 6.13  1999/03/31 13:34:18  sicotte
+ * in WHICH_ntdb_accession, swapped (C** and B** prot accession for embl/ddbj)
+ *
+ * Revision 6.12  1999/03/18 20:24:05  sicotte
+ * changed the define name for NC_ accession
+ *
+ * Revision 6.11  1999/03/18 20:18:18  sicotte
+ * added REFSEQ accession numbers and macro ACCN_IS_GENBANK()
+ *
+ * Revision 6.10  1999/03/18 15:34:04  sicotte
+ * Updated Accession List and added protein Accessions
+ * for functions IS_ntdb_accession and IS_protdb_accession.
+ * New function WHICH_db_accession with return code allowing
+ * to figure out the molecule type and the database from macros
+ * in accutils.h
+ *
+ * Revision 6.9  1999/02/24 16:48:09  kans
+ * added IS_ntdb_accession and IS_protdb_accession, removed NormalizeSeqAlignId
+ *
+ * Revision 6.8  1999/01/27 16:20:51  chappey
+ * update IS_ntdb_accession with AB, AJ
+ *
  * Revision 6.7  1999/01/06 14:18:36  grisha
  * add defines to switch ID0/ID1 usage
  *
@@ -113,7 +144,7 @@
  * ==========================================================================
  */
 
-#define REVISION_STR "$Revision: 6.7 $"
+#define REVISION_STR "$Revision: 6.15 $"
 
 #include <accutils.h>
 #ifndef _CDROMLIB_
@@ -168,444 +199,7 @@ static ValNode nextRealNode;
 static Int2 lastGood = -1;
 static Int2 lastBad = -1;
 
-/****************************COLOMBE **************************/
-
-static Int4 CCAccessionToGi (CharPtr string)
-{
-   CharPtr str;
-   LinkSetPtr lsp;
-   Int4 gi;
-
-   str = MemNew (StringLen (string) + 10);
-   sprintf (str, "\"%s\" [ACCN]", string);
-   lsp = EntrezTLEvalString (str, TYP_NT, -1, NULL, NULL);
-   MemFree (str);
-   if (lsp == NULL) return 0;
-   if (lsp->num <= 0) {
-       LinkSetFree (lsp);
-       return 0;
-   }
-   gi = lsp->uids [0];
-   LinkSetFree (lsp);
-   return gi;
-}
-
-/*****************************************************************************
-*
-*  Function:    IS_ntdb_accession
-*
-*  Description: Return TRUE if the input string is a validly formatted
-*               nucleotide database accession number (GenBank, EMBL, DDBJ)
-*
-*  Arguments:   s : CharPtr; pointer to accession number string.
-*                   Must be null terminated.
-*
-*  Author:      Mark Cavanaugh
-*  Date:        7/96
-*
-*  WARNING:     IS_ntdb_accession() does not communicate with any central
-*               resource about accession numbers. So there's no way to
-*               inform it automatically about new accession number prefixes.
-*
-*****************************************************************************/
-static Boolean IS_ntdb_accession(CharPtr s)
-{
-  Boolean retval = TRUE;
-
-  Boolean first = TRUE;
-  CharPtr temp;
-
-  if (s == NULL || ! *s)
-    return FALSE;
-
-  switch (StringLen(s)) {
-
-  case 6:                       /* Old-style 6-character accession */
-    while (*s) {
-      if (retval == FALSE)
-        break;
-
-      if (first) {
-        if (! IS_ALPHA(*s)) {
-          retval = FALSE;
-          break;
-        }
-
-      switch (TO_UPPER(*s)) {
-      case 'H': case 'N': case 'R': case 'T': case 'W': /* GenBank : EST */
-        break;
-      case 'B': case 'G': case 'I': case 'S': case 'U': /* GenBank : non-EST */
-        break;
-      case 'J': case 'K': case 'L': case 'M':      /* GenBank : before NCBI */
-        break;
-      case 'A': case 'F': case 'V': case 'X': case 'Y': case 'Z':  /* EMBL */
-        break;
-      case 'C': case 'D': case 'E':                /* DDBJ */
-        break;
-      default:
-        retval = FALSE;
-        break;
-      }
-      first = FALSE;
-      }
-      else {
-        if (! IS_DIGIT(*s)) {
-          retval = FALSE;
-        }
-      }
-      s++;
-    }  
-    break;
-    case 8: /* New 8-character accession, two letters + 6 digits */
- 
-      /* Copy the first two chars of the accession to a buffer */
- 
-      temp = (CharPtr) MemNew(3);
-
-      temp[0] = *s; s++;          
-      temp[1] = *s; s++;
-      temp[2] = '\0';
-
-      if ((StringICmp(temp,"AA") == 0) ||       /* NCBI EST */
-          (StringICmp(temp,"AC") == 0) ||       /* NCBI HTGS */
-          (StringICmp(temp,"AF") == 0) ||       /* NCBI ??? */
-          (StringICmp(temp,"AD") == 0) ) {      /* NCBI accessions assigned to GSDB entries */
-        /* No-op */
-      }
-      else if ( (StringICmp(temp,"AB") == 0) ) {        /* DDBJ */
-        /* No-op */
-      }
-      else {
-        retval = FALSE;
-        break;
-      }
-
-      while (*s) {
-        if (! IS_DIGIT(*s)) {
-          retval = FALSE;
-          break;
-        }
-        s++;
-      }  
-      break;
-       
-  default:   
-       
-    retval = FALSE;
-    break;
-  }                     /* Endswitch, StringLen(s) */
-
-  return retval;                                      
-}
-/*****************************************************************************
-*
-*  Function:    IS_protdb_accession
-*
-*  Description: Return TRUE if the input string is a validly formatted
-*               protein database accession number (SWISS-PROT)
-*
-*  Arguments:   s : CharPtr; pointer to accession number string.
-*                   Must be null terminated.
-*
-*  Author:      Mark Cavanaugh
-*  Date:        8/96
-*
-*  WARNING:     IS_protdb_accession() does not communicate with any central
-*               resource about accession numbers. So there's no way to
-*               inform it automatically about new accession number prefixes.
-*
-*****************************************************************************/
-static Boolean IS_protdb_accession(CharPtr s)
-{
-  Boolean retval = TRUE;
-  Boolean first = TRUE;
-
-  if (s == NULL || ! *s)
-    return FALSE;
- 
-  if (StringLen(s) != 6)
-    return FALSE;
-
-  while (*s) {
-    if (retval == FALSE)
-      break;
-
-    if (first) {
-      if (! IS_ALPHA(*s)) {
-        retval = FALSE;
-        break;
-      }  
-
-      switch (TO_UPPER(*s)) {
-      case 'P': case 'Q':                 /* SWISS-PROT accessions */
-        break;
-      default:
-        retval = FALSE;
-        break;
-      }  
-      first = FALSE;
-    }
-    else {
-      if (! IS_DIGIT(*s)) {
-        retval = FALSE;
-        break;
-      }  
-    }  
-    s++;
-  }
-  return retval;
-}
-
-/****************************************************
-***   Copy of Read SeqPort.bsp from SeqPort.start to stop
-***   in : spp, from + to in seq coordinates
-***   out: length of buffer + buffer
-***        compiled with -D SAP
-*****************************************************/
-static Int4 AccutReadBufferFromSep (SeqPortPtr spp, CharPtr buffer, Int4 from, Int4 to, Int4 buffsegstart)
-{
-  Uint1    residue;
-  Int4     k;
-  Int4     pos;
-
-  SeqPortSeek (spp, from, SEEK_SET);
-  k = buffsegstart;
-  pos = from;
-  residue = SeqPortGetResidue(spp);
-  while (pos < to && residue != SEQPORT_EOF)
-  {
-    if ( ! IS_residue(residue)) {
-      /*
-      switch (residue)
-      {  
-           case SEQPORT_VIRT:
-              Message(MSG_OK,"SEQPORT_VIRT [%d=%c] at %ld\n", (int)residue, (char)residue, (long)pos);
-              break;
-           case SEQPORT_EOS:
-              Message(MSG_OK,"[EOS]\n");
-              break;
-           default:
-              Message(MSG_OK,"unknown char\n");
-              break;
-      }  
-      pos++;
-      */
-    } else {
-      buffer[k] = (Char) residue;
-      k++;  
-      pos++;
-    }
-    residue = SeqPortGetResidue(spp);
-  }
-  buffer[k] = '\0';
-  return k;
-}
- 
-
-/*************************************************************
-***
-*** load_seq_data
-***    loads bioseq sequence into a string
-***    sip: SeqId of the bioseq
-***    from, to: included bondaries
-***    returns the length of the string (lenp)
-***
-***************************************************************/
-static CharPtr load_seq_data (SeqIdPtr sip, Int4 from, Int4 to, Int4 *lenp)
-{
-  BioseqPtr        bsp;
-  SeqLocPtr        slp;
-  SeqPortPtr       spp;
-  CharPtr          str = NULL;
-  Int4             lens;
-
-  if (from > -1 && to > -1 && from >= to)
-     return NULL;
-  bsp = BioseqLockById (sip);
-  if (bsp != NULL) {
-     if (from < 0 || from > bsp->length -1)
-        from = 0;
-     if (to < 0 || to > bsp->length -1)
-        to = bsp->length -1;
-     BioseqUnlock (bsp);
-     slp = SeqLocIntNew (from, to, Seq_strand_plus, sip);
-     spp = SeqPortNewByLoc (slp, Seq_code_iupacna);
-     if (spp != NULL) {
-        str = MemNew ((to-from+4) * sizeof(Char));
-        lens = AccutReadBufferFromSep (spp, str, 0, to -from +1, 0);
-        SeqPortFree (spp);
-        if (lenp != NULL)
-           *lenp = lens;
-     }   
-     SeqLocFree (slp);
-  }
-  return str;
-}
-
-static Int4 getlengthforid (SeqIdPtr sip)
-{
-  BioseqPtr        bsp;
-  Int4             lens=0;
- 
-  if (sip==NULL)
-     return 0;
-  bsp = BioseqLockById (sip);
-  if (bsp != NULL) {
-     lens = bsp->length;
-     BioseqUnlock (bsp);
-  }
-  return lens;
-}
-
-/********************************************************
-***
-*** NormalizeSeqAlignId
-***   Checks local seqid . if a seqid string contains "acc"
-***   seqid has a correspondant sequence in db.
-***   This local seqid is replaced by its gi number. 
-***
-***   The local sequence is compared to the sequence from 
-***   the db. If the local sequence is a region of the db sequence
-***   the positions in the seqalign are updaded with the offset.
-***
-***   local copy of IS_ntdb_accession & IS_protdb_accession
-***          Thanks to Mark for this useful function! 
-**********************************************************/
-NLM_EXTERN ValNodePtr NormalizeSeqAlignId (SeqAlignPtr salp, ValNodePtr vnp)
-{
-  ValNodePtr  vnptmp;
-  DenseSegPtr dsp;
-  SeqIdPtr    sip,
-              dbsip,
-              presip, 
-              next,
-              siptmp;
-  CharPtr     TmpBuff, tmp;
-  CharPtr     strlcl,
-              strdb,
-              strtmp;
-  Char        str [52];
-  Int4        gi = 0;
-  Int4        offset;
-  Int4        lenlcl, lendb;
-  Int4        totlenlcl, totlendb;
-  Int4        j, k, k1;
-  Int2        index;
-  Boolean     ok, goOn, found;
-
-  Int4        step = 1000;
-  Int4        window = 1020;
-
-  EntrezInit ("Sequin", FALSE, NULL);
-
-  if (salp!=NULL) {
-     if (salp->segtype == 2) {
-        dsp = (DenseSegPtr) salp->segs;
-        presip = NULL;
-        sip = dsp->ids;
-        index = 0;
-        while (sip != NULL) {
-           next = sip->next;
-           SeqIdWrite (sip, str, PRINTID_FASTA_LONG, 50);
-           tmp = StringStr (str, "acc");
-           if (tmp==NULL) {
-              tmp = StringStr (str, "ACC");
-           }
-           if (tmp!=NULL) {
-              tmp++; tmp++; tmp++;
-              if (*tmp == '|')
-                 tmp++;   
-              TmpBuff = tmp;
-              while (*tmp!='\0' && *tmp != '|' && *tmp!='\n')
-                 tmp++;
-              *tmp = '\0';
-
-              ok = FALSE;
-              j = StringLen (TmpBuff);
-              for(k =0; k < j; k++) {
-                 if(!isdigit(TmpBuff[k])) {
-                    break;
-                 }
-              }
-              if(k != j) {
-                 ok=(IS_ntdb_accession(TmpBuff) || IS_protdb_accession(TmpBuff));
-              }
-              if (ok) {
-                 gi = CCAccessionToGi(TmpBuff);
-                 ok = (gi>0);
-              }
-              if (ok) {
-                 dbsip = ValNodeNew (NULL);
-                 dbsip->choice = SEQID_GI;
-                 dbsip->data.intvalue = (Int4)gi;
-                 sip->next = NULL;
-                 found = FALSE;
-                 totlenlcl = getlengthforid(sip);
-                 strlcl = load_seq_data (sip, 0, MIN(totlenlcl, 20), &lenlcl); 
-                 k1=0;
-                 totlendb = getlengthforid(dbsip);
-                 k = MIN(totlendb, k1+window); 
-                 goOn = (Boolean) (strlcl!=NULL && k > 0); 
-                 while (goOn) 
-                 {
-                    strdb = load_seq_data (dbsip, k1, k, &lendb);
-                    if (strlcl != NULL && strdb != NULL) 
-                    {
-                     offset = 0;
-                     strtmp = StringStr (strdb, strlcl);
-                     if (strtmp != NULL) {
-                       offset =(Int4)abs(abs((long)strdb)-abs((long)strtmp));
-                       offset += k1;
-                       if (offset > 0) {
-                          for (j=0; j<dsp->numseg; j++) {
-                             if (dsp->starts[dsp->dim*j+index] != -1)
-                                dsp->starts[dsp->dim*j+index] += offset;
-                          }
-                       }
-                       if (presip == NULL) {
-                          dsp->ids = dbsip;
-                       } else {
-                          presip->next = dbsip;
-                       }
-                       dbsip->next = next;
-                       vnptmp=NULL;
-                       if (vnp!=NULL) {
-                          for (vnptmp=vnp; vnptmp!=NULL; vnptmp=vnptmp->next) {
-                             siptmp=(SeqIdPtr)vnptmp->data.ptrvalue;
-                             if (SeqIdForSameBioseq(sip, siptmp))
-                                break;
-                          }
-                       }
-                       if (vnptmp==NULL)
-                          ValNodeAddPointer(&vnp, 0, sip);
-                       found = TRUE;
-                       sip = dbsip;
-                     }
-                     MemFree (strdb);
-                    }
-                    goOn = (Boolean)(!found && k<totlendb);
-                    k1=k1+step;
-                    k = MIN(totlendb, k1+window);
-                 }
-                 if (!found)
-                    sip->next = next;
-                 if (strlcl != NULL)
-                    MemFree (strlcl);
-              } 
-           }
-           presip = sip;
-           sip = next;
-           index++;
-        }
-     }
-  }
-  EntrezFini ();
-  return vnp;  
-}
-/****************************COLOMBE **************************/
-
-static
-Int2 LexClassifyChar(Char c)
+static Int2 LexClassifyChar(Char c)
 {
     Int2 retval;
 
@@ -635,8 +229,7 @@ Int2 LexClassifyChar(Char c)
 }
 
 /* Returns -1 if no token available, else the position of the token */
-static Int2
-EntrezLexExpression(CharPtr str, ValNodePtr vnp)
+static Int2 EntrezLexExpression(CharPtr str, ValNodePtr vnp)
 {
     Int2 startPos;
     Int2 classChar;
@@ -841,8 +434,7 @@ static Boolean FindTermRequired(CharPtr term)
 
 /* traverse all the possible fields, and take the "union" of this term */
 /* over all the possibilities for the specified database               */
-static Boolean
-AddAllFields(ValNodePtr elst, CharPtr term, DocType db, Boolean special)
+static Boolean AddAllFields(ValNodePtr elst, CharPtr term, DocType db, Boolean special)
 {
     EntrezInfoPtr eip;
     Boolean first = TRUE;
diff --git a/cdromlib/accutils.h b/cdromlib/accutils.h
index 6576a18f..c661435b 100644
--- a/cdromlib/accutils.h
+++ b/cdromlib/accutils.h
@@ -23,7 +23,7 @@
 *
 * ===========================================================================
 *
-* RCS $Id: accutils.h,v 6.3 1997/11/14 22:13:52 vakatov Exp $
+* RCS $Id: accutils.h,v 6.8 1999/04/01 13:56:35 sicotte Exp $
 *
 * Author:  J. Epstein
 *
@@ -41,6 +41,28 @@
 *                      time it is checked into the system.
 
 $Log: accutils.h,v $
+Revision 6.8  1999/04/01 13:56:35  sicotte
+Moved WHICH_db_accession,IS_ntdb_accession,IS_protdb_accession to
+  sequtil.ch
+Removed old static functions of Colombe (that are public in salutil.c)
+The only code left in accutils.c is the Entrez Access code.
+
+Revision 6.7  1999/03/18 20:24:06  sicotte
+changed the define name for NC_ accession
+
+Revision 6.6  1999/03/18 20:18:18  sicotte
+added REFSEQ accession numbers and macro ACCN_IS_GENBANK()
+
+Revision 6.5  1999/03/18 15:34:04  sicotte
+Updated Accession List and added protein Accessions
+for functions IS_ntdb_accession and IS_protdb_accession.
+New function WHICH_db_accession with return code allowing
+to figure out the molecule type and the database from macros
+in accutils.h
+
+Revision 6.4  1999/02/24 16:48:10  kans
+added IS_ntdb_accession and IS_protdb_accession, removed NormalizeSeqAlignId
+
 Revision 6.3  1997/11/14 22:13:52  vakatov
 [WIN32,DLL]  Added NLM_EXTERN's
 
@@ -100,6 +122,11 @@ add GetFullEntrezTermList() function
 #include <tofasta.h>
 #include <lsqfetch.h>
 
+/* 4/1/99 Temporately include sequtil.h to avoid breaking code that
+   uses IS_ntdb_accession
+   */
+#include <sequtil.h>
+
 #undef NLM_EXTERN
 #ifdef NLM_IMPORT
 #define NLM_EXTERN NLM_IMPORT
@@ -111,7 +138,8 @@ add GetFullEntrezTermList() function
 extern "C" {
 #endif
 
-NLM_EXTERN ValNodePtr NormalizeSeqAlignId (SeqAlignPtr salp, ValNodePtr vnp);
+
+
 
 NLM_EXTERN CharPtr LIBCALL EntrezFieldToString PROTO((DocType db, DocField fld));
 NLM_EXTERN DocField LIBCALL EntrezStringToField PROTO((DocType db, CharPtr str));
diff --git a/cdromlib/casn.c b/cdromlib/casn.c
index 4f656eb8..a8002079 100644
--- a/cdromlib/casn.c
+++ b/cdromlib/casn.c
@@ -23,7 +23,7 @@
  *
  * ===========================================================================
  *
- * RCS $Id: casn.c,v 6.0 1997/08/25 18:12:41 madden Exp $
+ * RCS $Id: casn.c,v 6.1 2001/04/27 18:00:30 juran Exp $
  *
  * Author:  Greg Schuler
  *
@@ -47,6 +47,9 @@
  *                      modification comments.
  *
  * Revision $Log: casn.c,v $
+ * Revision Revision 6.1  2001/04/27 18:00:30  juran
+ * Revision Warnings.
+ * Revision
  * Revision Revision 6.0  1997/08/25 18:12:41  madden
  * Revision Revision changed to 6.0
  * Revision
@@ -75,7 +78,7 @@
  * ==========================================================================
  */
 
-#define REVISION_STR "$Revision: 6.0 $"
+#define REVISION_STR "$Revision: 6.1 $"
 
 
 #include <asn.h>
@@ -261,7 +264,7 @@ NLM_EXTERN SeqEntry* LIBCALL CASN_NextSeqEntry (CASN_Handle handle)
 	AsnTypePtr atp;
 
 	ASSERT(Handle_IsValid(handle));
-	if(atp = AsnReadId(handle->aio, handle->amp, handle->atp)) {
+	if ((atp = AsnReadId(handle->aio, handle->amp, handle->atp))) {
 	  SeqEntryPtr sep = SeqEntryAsnRead(handle->aio, atp);
 	  while(handle->compr != -1) {
 	    char buf[4];
diff --git a/cdromlib/cdentrez.c b/cdromlib/cdentrez.c
index 4ecbd32c..568a695b 100644
--- a/cdromlib/cdentrez.c
+++ b/cdromlib/cdentrez.c
@@ -23,7 +23,7 @@
  *
  * ===========================================================================
  *
- * RCS $Id: cdentrez.c,v 6.1 1998/08/24 18:42:15 kans Exp $
+ * RCS $Id: cdentrez.c,v 6.2 1999/03/11 23:20:07 kans Exp $
  *
  * Author:  Ostell, Kans
  *
@@ -46,6 +46,9 @@
  *                      modification comments.
  *
  * Revision $Log: cdentrez.c,v $
+ * Revision Revision 6.2  1999/03/11 23:20:07  kans
+ * Revision sprintf cast
+ * Revision
  * Revision Revision 6.1  1998/08/24 18:42:15  kans
  * Revision fixed -v -fd warnings
  * Revision
@@ -149,7 +152,7 @@
  * ==========================================================================
  */
 
-#define REVISION_STR  "$Revision: 6.1 $"
+#define REVISION_STR  "$Revision: 6.2 $"
 
 static char * _this_module = "CdEntrez";
 #define THIS_MODULE _this_module
@@ -3705,7 +3708,7 @@ NLM_EXTERN BiostrucAnnotSetPtr CdEntrezBiostrucAnnotSetGet (DocUid uid)
 	
 	if (CdMountEntrezVolume(1,fname,PATH_MAX-32))
 	{
-		sprintf(strchr(fname,0), "/vast/%ld.bas.Z", uid);
+		sprintf(strchr(fname,0), "/vast/%ld.bas.Z", (long) uid);
 		if (FileLength(fname) <= 0)
 		{
 			return NULL;
diff --git a/cdromlib/cdnewlib.c b/cdromlib/cdnewlib.c
index 7b3d9030..461292ce 100644
--- a/cdromlib/cdnewlib.c
+++ b/cdromlib/cdnewlib.c
@@ -23,7 +23,7 @@
  *
  * ===========================================================================
  *
- * RCS $Id: cdnewlib.c,v 6.1 1998/08/24 18:42:16 kans Exp $
+ * RCS $Id: cdnewlib.c,v 6.2 1999/03/12 18:44:57 kans Exp $
  *
  * Author:  Gregory Schuler
  *
@@ -91,6 +91,9 @@
  *                      modification comments.
  *
  * Revision $Log: cdnewlib.c,v $
+ * Revision Revision 6.2  1999/03/12 18:44:57  kans
+ * Revision fixed ErrPostEx problem
+ * Revision
  * Revision Revision 6.1  1998/08/24 18:42:16  kans
  * Revision fixed -v -fd warnings
  * Revision
@@ -132,7 +135,7 @@
  * ==========================================================================
  */
 
-#define REVISION_STR "$Revision: 6.1 $"
+#define REVISION_STR "$Revision: 6.2 $"
 
 
 
@@ -3694,7 +3697,7 @@ static int FileNotRecognized (const char *fname)
 {
 	ErrPostEx(SEV_ERROR,ERR_BadFile,SUB_NeedUpdate,
 				"The file %s cannot be read by this release of "
-				"the software.  Please obtain a newer version.");
+				"the software.  Please obtain a newer version.", fname);
 	return FALSE;
 }
 
diff --git a/cdromlib/ncbicdr.dsp b/cdromlib/ncbicdr.dsp
new file mode 100644
index 00000000..f7880e1e
--- /dev/null
+++ b/cdromlib/ncbicdr.dsp
@@ -0,0 +1,142 @@
+# Microsoft Developer Studio Project File - Name="ncbicdr" - Package Owner=<4>
+# Microsoft Developer Studio Generated Build File, Format Version 6.00
+# ** DO NOT EDIT **
+
+# TARGTYPE "Win32 (x86) Static Library" 0x0104
+
+CFG=ncbicdr - Win32 Release
+!MESSAGE This is not a valid makefile. To build this project using NMAKE,
+!MESSAGE use the Export Makefile command and run
+!MESSAGE 
+!MESSAGE NMAKE /f "ncbicdr.mak".
+!MESSAGE 
+!MESSAGE You can specify a configuration when running NMAKE
+!MESSAGE by defining the macro CFG on the command line. For example:
+!MESSAGE 
+!MESSAGE NMAKE /f "ncbicdr.mak" CFG="ncbicdr - Win32 Release"
+!MESSAGE 
+!MESSAGE Possible choices for configuration are:
+!MESSAGE 
+!MESSAGE "ncbicdr - Win32 Debug" (based on "Win32 (x86) Static Library")
+!MESSAGE "ncbicdr - Win32 Release" (based on "Win32 (x86) Static Library")
+!MESSAGE 
+
+# Begin Project
+# PROP AllowPerConfigDependencies 0
+# PROP Scc_ProjName ""
+# PROP Scc_LocalPath ""
+CPP=cl.exe
+RSC=rc.exe
+
+!IF  "$(CFG)" == "ncbicdr - Win32 Debug"
+
+# PROP BASE Use_MFC 0
+# PROP BASE Use_Debug_Libraries 1
+# PROP BASE Output_Dir "ncbicdr___Win32_Debug"
+# PROP BASE Intermediate_Dir "ncbicdr___Win32_Debug"
+# PROP BASE Target_Dir ""
+# PROP Use_MFC 0
+# PROP Use_Debug_Libraries 1
+# PROP Output_Dir "ncbicdr___Win32_Debug"
+# PROP Intermediate_Dir "ncbicdr___Win32_Debug"
+# PROP Target_Dir ""
+# ADD BASE CPP /nologo /W3 /Gm /GX /ZI /Od /D "WIN32" /D "_DEBUG" /D "_MBCS" /D "_LIB" /YX /FD /GZ /c
+# ADD CPP /nologo /W2 /Gm /GX /ZI /Od /I ".." /I "..\ddv" /I "..\cn3d" /I "..\access" /I "..\asnstat" /I "..\connect\lbapi" /I "..\connect" /I "..\asnlib" /I "..\vibrant" /I "..\biostruc" /I "..\object" /I "..\api" /I "..\cdromlib" /I "..\desktop" /I "..\tools" /I "..\corelib" /I "..\network\taxon1\common" /I "..\network\vibnet" /I "..\network\entrez\client" /I "..\network\nsclilib" /I "..\network\medarch\client" /I "..\network\id1arch" /I "..\network\taxon1\taxon2" /I "..\network\blast3\client" /D "WIN32" /D "_DEBUG" /D "_MBCS" /D "_LIB" /YX /FD /GZ /c
+# SUBTRACT CPP /Fr
+# ADD BASE RSC /l 0x409 /d "_DEBUG"
+# ADD RSC /l 0x409 /d "_DEBUG"
+BSC32=bscmake.exe
+# ADD BASE BSC32 /nologo
+# ADD BSC32 /nologo
+LIB32=link.exe -lib
+# ADD BASE LIB32 /nologo
+# ADD LIB32 /nologo
+
+!ELSEIF  "$(CFG)" == "ncbicdr - Win32 Release"
+
+# PROP BASE Use_MFC 0
+# PROP BASE Use_Debug_Libraries 1
+# PROP BASE Output_Dir "ncbicdr___Win32_Release"
+# PROP BASE Intermediate_Dir "ncbicdr___Win32_Release"
+# PROP BASE Target_Dir ""
+# PROP Use_MFC 0
+# PROP Use_Debug_Libraries 1
+# PROP Output_Dir "ncbicdr___Win32_Release"
+# PROP Intermediate_Dir "ncbicdr___Win32_Release"
+# PROP Target_Dir ""
+# ADD BASE CPP /nologo /W2 /Gm /GX /ZI /Od /I ".." /I "..\ddv" /I "..\cn3d" /I "..\access" /I "..\asnstat" /I "..\connect\lbapi" /I "..\connect" /I "..\asnlib" /I "..\vibrant" /I "..\biostruc" /I "..\object" /I "..\api" /I "..\cdromlib" /I "..\desktop" /I "..\tools" /I "..\corelib" /I "..\network\taxon1\common" /I "..\network\vibnet" /I "..\network\entrez\client" /I "..\network\nsclilib" /I "..\network\medarch\client" /I "..\network\id1arch" /I "..\network\taxon1\taxon2" /I "..\network\blast3\client" /D "WIN32" /D "_DEBUG" /D "_MBCS" /D "_LIB" /YX /FD /GZ /c
+# SUBTRACT BASE CPP /Fr
+# ADD CPP /nologo /W2 /Gm /GX /Zi /I ".." /I "..\ddv" /I "..\cn3d" /I "..\access" /I "..\asnstat" /I "..\connect\lbapi" /I "..\connect" /I "..\asnlib" /I "..\vibrant" /I "..\biostruc" /I "..\object" /I "..\api" /I "..\cdromlib" /I "..\desktop" /I "..\tools" /I "..\corelib" /I "..\network\taxon1\common" /I "..\network\vibnet" /I "..\network\entrez\client" /I "..\network\nsclilib" /I "..\network\medarch\client" /I "..\network\id1arch" /I "..\network\taxon1\taxon2" /I "..\network\blast3\client" /D "_LIB" /D "WIN32" /D "_MBCS" /YX /FD /c
+# ADD BASE RSC /l 0x409 /d "_DEBUG"
+# ADD RSC /l 0x409
+BSC32=bscmake.exe
+# ADD BASE BSC32 /nologo
+# ADD BSC32 /nologo
+LIB32=link.exe -lib
+# ADD BASE LIB32 /nologo
+# ADD LIB32 /nologo
+
+!ENDIF 
+
+# Begin Target
+
+# Name "ncbicdr - Win32 Debug"
+# Name "ncbicdr - Win32 Release"
+# Begin Group "Source Files"
+
+# PROP Default_Filter "cpp;c;cxx;rc;def;r;odl;idl;hpj;bat"
+# Begin Source File
+
+SOURCE=.\casn.c
+# End Source File
+# Begin Source File
+
+SOURCE=.\cdconfig.c
+# End Source File
+# Begin Source File
+
+SOURCE=.\cdentrez.c
+# End Source File
+# Begin Source File
+
+SOURCE=.\cdnewlib.c
+# End Source File
+# Begin Source File
+
+SOURCE=.\cdromlib.c
+# End Source File
+# Begin Source File
+
+SOURCE=.\objentr.c
+# End Source File
+# End Group
+# Begin Group "Header Files"
+
+# PROP Default_Filter "h;hpp;hxx;hm;inl"
+# Begin Source File
+
+SOURCE=.\casn.h
+# End Source File
+# Begin Source File
+
+SOURCE=.\cdconfig.h
+# End Source File
+# Begin Source File
+
+SOURCE=.\cdentrez.h
+# End Source File
+# Begin Source File
+
+SOURCE=.\cdnewlib.h
+# End Source File
+# Begin Source File
+
+SOURCE=.\cdromlib.h
+# End Source File
+# Begin Source File
+
+SOURCE=.\objentr.h
+# End Source File
+# End Group
+# End Target
+# End Project
diff --git a/cdromlib/ncbinacc.dsp b/cdromlib/ncbinacc.dsp
new file mode 100644
index 00000000..e3dfaa76
--- /dev/null
+++ b/cdromlib/ncbinacc.dsp
@@ -0,0 +1,111 @@
+# Microsoft Developer Studio Project File - Name="ncbinacc" - Package Owner=<4>
+# Microsoft Developer Studio Generated Build File, Format Version 6.00
+# ** DO NOT EDIT **
+
+# TARGTYPE "Win32 (x86) Static Library" 0x0104
+
+CFG=ncbinacc - Win32 Release
+!MESSAGE This is not a valid makefile. To build this project using NMAKE,
+!MESSAGE use the Export Makefile command and run
+!MESSAGE 
+!MESSAGE NMAKE /f "ncbinacc.mak".
+!MESSAGE 
+!MESSAGE You can specify a configuration when running NMAKE
+!MESSAGE by defining the macro CFG on the command line. For example:
+!MESSAGE 
+!MESSAGE NMAKE /f "ncbinacc.mak" CFG="ncbinacc - Win32 Release"
+!MESSAGE 
+!MESSAGE Possible choices for configuration are:
+!MESSAGE 
+!MESSAGE "ncbinacc - Win32 Debug" (based on "Win32 (x86) Static Library")
+!MESSAGE "ncbinacc - Win32 Release" (based on "Win32 (x86) Static Library")
+!MESSAGE 
+
+# Begin Project
+# PROP AllowPerConfigDependencies 0
+# PROP Scc_ProjName ""
+# PROP Scc_LocalPath ""
+CPP=cl.exe
+RSC=rc.exe
+
+!IF  "$(CFG)" == "ncbinacc - Win32 Debug"
+
+# PROP BASE Use_MFC 0
+# PROP BASE Use_Debug_Libraries 1
+# PROP BASE Output_Dir "Debug"
+# PROP BASE Intermediate_Dir "Debug"
+# PROP BASE Target_Dir ""
+# PROP Use_MFC 0
+# PROP Use_Debug_Libraries 1
+# PROP Output_Dir "Debug"
+# PROP Intermediate_Dir "Debug"
+# PROP Target_Dir ""
+# ADD BASE CPP /nologo /W3 /Gm /GX /ZI /Od /D "WIN32" /D "_DEBUG" /D "_MBCS" /D "_LIB" /YX /FD /GZ /c
+# ADD CPP /nologo /W2 /Gm /GX /ZI /Od /I ".." /I "..\ddv" /I "..\cn3d" /I "..\access" /I "..\asnstat" /I "..\connect\lbapi" /I "..\connect" /I "..\asnlib" /I "..\vibrant" /I "..\biostruc" /I "..\object" /I "..\api" /I "..\cdromlib" /I "..\desktop" /I "..\tools" /I "..\corelib" /I "..\network\taxon1\common" /I "..\network\vibnet" /I "..\network\entrez\client" /I "..\network\nsclilib" /I "..\network\medarch\client" /I "..\network\id1arch" /I "..\network\taxon1\taxon2" /I "..\network\blast3\client" /D "WIN32" /D "_DEBUG" /D "_MBCS" /D "_LIB" /YX /FD /GZ /c
+# SUBTRACT CPP /Fr
+# ADD BASE RSC /l 0x409 /d "_DEBUG"
+# ADD RSC /l 0x409 /d "_DEBUG"
+BSC32=bscmake.exe
+# ADD BASE BSC32 /nologo
+# ADD BSC32 /nologo
+LIB32=link.exe -lib
+# ADD BASE LIB32 /nologo
+# ADD LIB32 /nologo
+
+!ELSEIF  "$(CFG)" == "ncbinacc - Win32 Release"
+
+# PROP BASE Use_MFC 0
+# PROP BASE Use_Debug_Libraries 1
+# PROP BASE Output_Dir "ncbinacc___Win32_Release"
+# PROP BASE Intermediate_Dir "ncbinacc___Win32_Release"
+# PROP BASE Target_Dir ""
+# PROP Use_MFC 0
+# PROP Use_Debug_Libraries 1
+# PROP Output_Dir "ncbinacc___Win32_Release"
+# PROP Intermediate_Dir "ncbinacc___Win32_Release"
+# PROP Target_Dir ""
+# ADD BASE CPP /nologo /W2 /Gm /GX /ZI /Od /I ".." /I "..\ddv" /I "..\cn3d" /I "..\access" /I "..\asnstat" /I "..\connect\lbapi" /I "..\connect" /I "..\asnlib" /I "..\vibrant" /I "..\biostruc" /I "..\object" /I "..\api" /I "..\cdromlib" /I "..\desktop" /I "..\tools" /I "..\corelib" /I "..\network\taxon1\common" /I "..\network\vibnet" /I "..\network\entrez\client" /I "..\network\nsclilib" /I "..\network\medarch\client" /I "..\network\id1arch" /I "..\network\taxon1\taxon2" /I "..\network\blast3\client" /D "WIN32" /D "_DEBUG" /D "_MBCS" /D "_LIB" /YX /FD /GZ /c
+# SUBTRACT BASE CPP /Fr
+# ADD CPP /nologo /W2 /Gm /GX /Zi /I ".." /I "..\ddv" /I "..\cn3d" /I "..\access" /I "..\asnstat" /I "..\connect\lbapi" /I "..\connect" /I "..\asnlib" /I "..\vibrant" /I "..\biostruc" /I "..\object" /I "..\api" /I "..\cdromlib" /I "..\desktop" /I "..\tools" /I "..\corelib" /I "..\network\taxon1\common" /I "..\network\vibnet" /I "..\network\entrez\client" /I "..\network\nsclilib" /I "..\network\medarch\client" /I "..\network\id1arch" /I "..\network\taxon1\taxon2" /I "..\network\blast3\client" /D "_LIB" /D "WIN32" /D "_MBCS" /YX /FD /c
+# ADD BASE RSC /l 0x409 /d "_DEBUG"
+# ADD RSC /l 0x409
+BSC32=bscmake.exe
+# ADD BASE BSC32 /nologo
+# ADD BSC32 /nologo
+LIB32=link.exe -lib
+# ADD BASE LIB32 /nologo
+# ADD LIB32 /nologo
+
+!ENDIF 
+
+# Begin Target
+
+# Name "ncbinacc - Win32 Debug"
+# Name "ncbinacc - Win32 Release"
+# Begin Group "Source Files"
+
+# PROP Default_Filter "cpp;c;cxx;rc;def;r;odl;idl;hpj;bat"
+# Begin Source File
+
+SOURCE=.\accentr.c
+# ADD CPP /D "_NETENT_"
+# End Source File
+# Begin Source File
+
+SOURCE=.\accutils.c
+# End Source File
+# End Group
+# Begin Group "Header Files"
+
+# PROP Default_Filter "h;hpp;hxx;hm;inl"
+# Begin Source File
+
+SOURCE=.\accentr.h
+# End Source File
+# Begin Source File
+
+SOURCE=.\accutils.h
+# End Source File
+# End Group
+# End Target
+# End Project
diff --git a/cdromlib/objentr.h b/cdromlib/objentr.h
index 863feeaf..8b1bdc91 100644
--- a/cdromlib/objentr.h
+++ b/cdromlib/objentr.h
@@ -23,7 +23,7 @@
 *
 * ===========================================================================
 *
-* RCS $Id: objentr.h,v 6.2 1998/03/26 23:23:19 yaschenk Exp $
+* RCS $Id: objentr.h,v 6.3 1999/08/17 16:31:27 kans Exp $
 *
 * Author:  Ostell, Schuler
 *
@@ -46,6 +46,9 @@
 *                      time it is checked into the system.
 
 $Log: objentr.h,v $
+Revision 6.3  1999/08/17 16:31:27  kans
+increased field tag size to handle current data
+
 Revision 6.2  1998/03/26 23:23:19  yaschenk
 adding CdRomAsnLoad() as extern function to load Asn tree
 
@@ -172,7 +175,7 @@ EntrezTypeInfo;
 typedef struct EntrezFieldInfo
 {
 	short id;                 /* id number to pass to APIs         */
-	char  tag[6];             /* 4-letter tag (for internal use)   */
+	char  tag[7];             /* 4-letter tag (for internal use)   */
 	char *name;               /* short string to go on menu        */
 	char *descr;              /* longer, descriptive string        */
 	unsigned single_token :1; /* all terms are single-token        */