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objneten.h
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1996-07-05
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/* objneten.h
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
*
* This software/database is a "United States Government Work" under the
* terms of the United States Copyright Act. It was written as part of
* the author's official duties as a United States Government employee and
* thus cannot be copyrighted. This software/database is freely available
* to the public for use. The National Library of Medicine and the U.S.
* Government have not placed any restriction on its use or reproduction.
*
* Although all reasonable efforts have been taken to ensure the accuracy
* and reliability of the software and data, the NLM and the U.S.
* Government do not and cannot warrant the performance or results that
* may be obtained by using this software or data. The NLM and the U.S.
* Government disclaim all warranties, express or implied, including
* warranties of performance, merchantability or fitness for any particular
* purpose.
*
* Please cite the author in any work or product based on this material.
*
* ===========================================================================
*
* File Name: objneten.h
*
* Author: Epstein
*
* Version Creation Date: 6/3/92
*
* $Revision: 4.0 $
*
* File Description: Object loader interface for module NCBI-Entrez
*
* Modifications:
* --------------------------------------------------------------------------
* Date Name Description of modification
* ------- ---------- -----------------------------------------------------
* 8-16-94 Brylawski Added declarations for EntrezNeighborText and
* EntrezHierarchy loaders and structures.
*
* 11-20-94 Brylawski Moved the EntrezNeighborText structure to accentr.h
* to permit its use in chosen.c and netentr.c .
* ==========================================================================
*
*
* RCS Modification History:
* $Log: objneten.h,v $
* Revision 4.0 1995/07/26 13:54:59 ostell
* force revision to 4.0
*
* Revision 1.14 1995/07/11 12:30:30 epstein
* change CDECLs to LIBCALLs
*
* Revision 1.13 1995/07/10 19:39:04 epstein
* add docsumX
*
* Revision 1.12 1995/06/23 13:21:16 kans
* include <accentr.h> to pull in Biostruc_supported symbol
*
* Revision 1.11 1995/05/17 17:53:35 epstein
* add RCS log revision history
*
*/
#ifndef _NCBI_NetEntrez_
#define _NCBI_NetEntrez_
#ifndef _ASNTOOL_
#include <asn.h>
#endif
/* accentr.h is included to define Biostruc_supported */
#ifndef _ACCENTR_
#include <accentr.h>
#endif
/*****************************************************************************
*
* loader
*
*****************************************************************************/
extern Boolean NetEntAsnLoad PROTO((void));
/*****************************************************************************
*
* internal structures for NCBI-Entrez objects
*
*****************************************************************************/
/*****************************************************************************
*
* Entrez-ids
*
*****************************************************************************/
typedef struct {
Int4 numid;
DocUidPtr ids;
} EntrezIds, PNTR EntrezIdsPtr;
extern EntrezIdsPtr LIBCALL EntrezIdsNew PROTO((void));
extern EntrezIdsPtr LIBCALL EntrezIdsFree PROTO(( EntrezIdsPtr ufp));
extern EntrezIdsPtr LIBCALL EntrezIdsAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp));
extern Boolean LIBCALL EntrezIdsAsnWrite PROTO((EntrezIdsPtr ufp, AsnIoPtr aip, AsnTypePtr atp));
/*****************************************************************************
*
* Marked-link-set
*
*****************************************************************************/
typedef struct {
LinkSetPtr link_set;
Int4 uids_processed;
EntrezIdsPtr marked_missing;
} MarkedLinkSet, PNTR MarkedLinkSetPtr;
extern MarkedLinkSetPtr LIBCALL MarkedLinkSetNew PROTO((void));
extern MarkedLinkSetPtr LIBCALL MarkedLinkSetFree PROTO(( MarkedLinkSetPtr ufp));
extern MarkedLinkSetPtr LIBCALL MarkedLinkSetAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp));
extern Boolean LIBCALL MarkedLinkSetAsnWrite PROTO((MarkedLinkSetPtr ufp, AsnIoPtr aip, AsnTypePtr atp));
/*****************************************************************************
*
* Named-List
*
*****************************************************************************/
typedef struct {
DocType type;
DocField fld;
CharPtr term;
EntrezIdsPtr uids;
} NamedList, PNTR NamedListPtr;
extern NamedListPtr LIBCALL NamedListNew PROTO((void));
extern NamedListPtr LIBCALL NamedListFree PROTO(( NamedListPtr ufp));
extern NamedListPtr LIBCALL NamedListAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp));
extern Boolean LIBCALL NamedListAsnWrite PROTO((NamedListPtr ufp, AsnIoPtr aip, AsnTypePtr atp));
/*****************************************************************************
*
* Term-by-Page
*
*****************************************************************************/
typedef struct {
DocType type;
DocField fld;
Int4 page;
Int4 num_pages;
} TermByPage, PNTR TermByPagePtr;
extern TermByPagePtr LIBCALL TermByPageNew PROTO((void));
extern TermByPagePtr LIBCALL TermByPageFree PROTO(( TermByPagePtr ufp));
extern TermByPagePtr LIBCALL TermByPageAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp));
extern Boolean LIBCALL TermByPageAsnWrite PROTO((TermByPagePtr ufp, AsnIoPtr aip, AsnTypePtr atp));
/*****************************************************************************
*
* Term-by-Term
*
*****************************************************************************/
typedef struct {
DocType type;
DocField fld;
CharPtr term;
Int4 num_terms;
} TermByTerm, PNTR TermByTermPtr;
extern TermByTermPtr LIBCALL TermByTermNew PROTO((void));
extern TermByTermPtr LIBCALL TermByTermFree PROTO(( TermByTermPtr ufp));
extern TermByTermPtr LIBCALL TermByTermAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp));
extern Boolean LIBCALL TermByTermAsnWrite PROTO((TermByTermPtr ufp, AsnIoPtr aip, AsnTypePtr atp));
/*****************************************************************************
*
* Term-Lookup
*
*****************************************************************************/
typedef struct {
DocType type;
DocField fld;
CharPtr term;
} TermLookup, PNTR TermLookupPtr;
extern TermLookupPtr LIBCALL TermLookupNew PROTO((void));
extern TermLookupPtr LIBCALL TermLookupFree PROTO(( TermLookupPtr ufp));
extern TermLookupPtr LIBCALL TermLookupAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp));
extern Boolean LIBCALL TermLookupAsnWrite PROTO((TermLookupPtr ufp, AsnIoPtr aip, AsnTypePtr atp));
/*****************************************************************************
*
* Term-Page-Info
*
*****************************************************************************/
typedef struct {
CharPtr term;
Int4 spec_count;
Int4 tot_count;
} TermPageInfo, PNTR TermPageInfoPtr;
extern TermPageInfoPtr LIBCALL TermPageInfoNew PROTO((void));
extern TermPageInfoPtr LIBCALL TermPageInfoFree PROTO(( TermPageInfoPtr ufp));
extern TermPageInfoPtr LIBCALL TermPageInfoAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp));
extern Boolean LIBCALL TermPageInfoAsnWrite PROTO((TermPageInfoPtr ufp, AsnIoPtr aip, AsnTypePtr atp));
/*****************************************************************************
*
* Term-Counts
*
*****************************************************************************/
typedef struct {
Boolean found;
Int4 spec_count;
Int4 tot_count;
} TermCounts, PNTR TermCountsPtr;
extern TermCountsPtr LIBCALL TermCountsNew PROTO((void));
extern TermCountsPtr LIBCALL TermCountsFree PROTO(( TermCountsPtr ufp));
extern TermCountsPtr LIBCALL TermCountsAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp));
extern Boolean LIBCALL TermCountsAsnWrite PROTO((TermCountsPtr ufp, AsnIoPtr aip, AsnTypePtr atp));
/*****************************************************************************
*
* Link-SetGet
*
*****************************************************************************/
typedef struct {
Int4 max; /* maximum Ids to return */
DocType link_to_cls;
DocType query_cls;
Boolean mark_missing;
Int4 query_size;
DocUidPtr query;
} LinkSetGet, PNTR LinkSetGetPtr;
extern LinkSetGetPtr LIBCALL LinkSetGetNew PROTO((void));
extern LinkSetGetPtr LIBCALL LinkSetGetFree PROTO(( LinkSetGetPtr ufp));
extern LinkSetGetPtr LIBCALL LinkSetGetAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp));
extern Boolean LIBCALL LinkSetGetAsnWrite PROTO((LinkSetGetPtr ufp, AsnIoPtr aip, AsnTypePtr atp));
extern DocSumPtr LIBCALL MlSumNew PROTO((void));
extern DocSumPtr LIBCALL MlSumFree PROTO(( DocSumPtr ufp));
extern DocSumPtr LIBCALL MlSumAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp));
extern Boolean LIBCALL MlSumAsnWrite PROTO((DocSumPtr ufp, AsnIoPtr aip, AsnTypePtr atp));
extern DocSumPtr LIBCALL SeqSumNew PROTO((void));
extern DocSumPtr LIBCALL SeqSumFree PROTO(( DocSumPtr ufp));
extern DocSumPtr LIBCALL SeqSumAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp));
extern Boolean LIBCALL SeqSumAsnWrite PROTO((DocSumPtr ufp, AsnIoPtr aip, AsnTypePtr atp));
/*****************************************************************************
*
* EntrezDocGet
*
*****************************************************************************/
typedef struct {
DocType cls;
Boolean mark_missing;
EntrezIdsPtr ids;
Int4 defer_count;
} EntrezDocGet, PNTR EntrezDocGetPtr;
extern EntrezDocGetPtr LIBCALL EntrezDocGetNew PROTO((void));
extern EntrezDocGetPtr LIBCALL EntrezDocGetFree PROTO(( EntrezDocGetPtr ufp));
extern EntrezDocGetPtr LIBCALL EntrezDocGetAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp));
extern Boolean LIBCALL EntrezDocGetAsnWrite PROTO((EntrezDocGetPtr ufp, AsnIoPtr aip, AsnTypePtr atp));
/*****************************************************************************
*
* Medline-list
*
*****************************************************************************/
typedef struct {
Int4 num;
MedlineEntryPtr PNTR data; /* vector */
EntrezIdsPtr marked_missing; /* marked UIDs, optional */
} MedlineEntryList, PNTR MedlineEntryListPtr;
extern MedlineEntryListPtr LIBCALL MedlineEntryListNew PROTO((void));
extern MedlineEntryListPtr LIBCALL MedlineEntryListFree PROTO(( MedlineEntryListPtr ufp));
extern MedlineEntryListPtr LIBCALL MedlineEntryListAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp));
extern Boolean LIBCALL MedlineEntryListAsnWrite PROTO((MedlineEntryListPtr ufp, AsnIoPtr aip, AsnTypePtr atp));
/*****************************************************************************
*
* Ml-summary-list
*
*****************************************************************************/
typedef struct {
Int4 num;
DocSumPtr PNTR data; /* vector */
} MlSummaryList, PNTR MlSummaryListPtr;
extern MlSummaryListPtr LIBCALL MlSummaryListNew PROTO((void));
extern MlSummaryListPtr LIBCALL MlSummaryListFree PROTO(( MlSummaryListPtr ufp));
extern MlSummaryListPtr LIBCALL MlSummaryListAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp));
extern Boolean LIBCALL MlSummaryListAsnWrite PROTO((MlSummaryListPtr ufp, AsnIoPtr aip, AsnTypePtr atp));
/*****************************************************************************
*
* SeqEntryGet
*
*****************************************************************************/
typedef struct {
EntrezIdsPtr ids;
Int4 retype;
Boolean mark_missing;
} EntrezSeqGet, PNTR EntrezSeqGetPtr;
extern EntrezSeqGetPtr LIBCALL EntrezSeqGetNew PROTO((void));
extern EntrezSeqGetPtr LIBCALL EntrezSeqGetFree PROTO(( EntrezSeqGetPtr ufp));
extern EntrezSeqGetPtr LIBCALL EntrezSeqGetAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp));
extern Boolean LIBCALL EntrezSeqGetAsnWrite PROTO((EntrezSeqGetPtr ufp, AsnIoPtr aip, AsnTypePtr atp));
/*****************************************************************************
*
* Seq-summary-list
*
*****************************************************************************/
typedef struct {
Int4 num;
DocSumPtr PNTR data; /* vector */
} SeqSummaryList, PNTR SeqSummaryListPtr;
extern SeqSummaryListPtr LIBCALL SeqSummaryListNew PROTO((void));
extern SeqSummaryListPtr LIBCALL SeqSummaryListFree PROTO(( SeqSummaryListPtr ufp));
extern SeqSummaryListPtr LIBCALL SeqSummaryListAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp));
extern Boolean LIBCALL SeqSummaryListAsnWrite PROTO((SeqSummaryListPtr ufp, AsnIoPtr aip, AsnTypePtr atp));
/*****************************************************************************
*
* Seq-entry-list
*
*****************************************************************************/
typedef struct {
Int4 num;
SeqEntryPtr PNTR data; /* vector */
EntrezIdsPtr marked_missing; /* marked UIDs, optional */
} PNTR SeqEntryListPtr;
/* note that SeqEntryList is not provided because the name conflicted with */
/* the name of a function on sequtil.c; the typedef was not needed anyhow */
extern SeqEntryListPtr LIBCALL SeqEntryListNew PROTO((void));
extern SeqEntryListPtr LIBCALL SeqEntryListFree PROTO(( SeqEntryListPtr ufp));
extern SeqEntryListPtr LIBCALL SeqEntryListAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp));
extern Boolean LIBCALL SeqEntryListAsnWrite PROTO((SeqEntryListPtr ufp, AsnIoPtr aip, AsnTypePtr atp));
#ifdef Biostruc_supported
/*****************************************************************************
*
* Biostruc-list
*
*****************************************************************************/
typedef struct {
Int4 num;
BiostrucPtr PNTR data; /* vector */
EntrezIdsPtr marked_missing; /* marked UIDs, optional */
} BiostrucList, PNTR BiostrucListPtr;
extern BiostrucListPtr LIBCALL BiostrucListNew PROTO((void));
extern BiostrucListPtr LIBCALL BiostrucListFree PROTO(( BiostrucListPtr ufp));
extern BiostrucListPtr LIBCALL BiostrucListAsnRead PROTO((AsnIoPtr aip, AsnTypePtr atp));
extern Boolean LIBCALL BiostrucListAsnWrite PROTO((BiostrucListPtr ufp, AsnIoPtr aip, AsnTypePtr atp));
#endif /* Biostruc_supported */
/**************************************************
*
* EntrezNeighborText
*
**************************************************/
EntrezNeighborTextPtr LIBCALL EntrezNeighborTextAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
Boolean LIBCALL EntrezNeighborTextAsnWrite PROTO (( EntrezNeighborTextPtr , AsnIoPtr, AsnTypePtr));
/**************************************************
*
* ChildLink
*
*************************************************/
typedef struct struct_Child_Link {
struct struct_Child_Link PNTR next;
CharPtr name;
Boolean isLeafNode;
Int4 special;
Int4 total;
} ChildLink, PNTR ChildLinkPtr;
EntrezHierarchyChildPtr LIBCALL EntrezHierarchyChildFree PROTO ((EntrezHierarchyChildPtr ));
EntrezHierarchyChildPtr LIBCALL EntrezHierarchyChildNew PROTO (( void ));
EntrezHierarchyChildPtr LIBCALL EntrezHierarchyChildAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
Boolean LIBCALL EntrezHierarchyChildAsnWrite PROTO (( EntrezHierarchyChildPtr ,AsnIoPtr, AsnTypePtr));
EntrezHierarchyPtr LIBCALL EntrezHierarchyFree PROTO ((EntrezHierarchyPtr ));
EntrezHierarchyPtr LIBCALL EntrezHierarchyNew PROTO (( void ));
EntrezHierarchyPtr LIBCALL EntrezHierarchyAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
Boolean LIBCALL EntrezHierarchyAsnWrite PROTO (( EntrezHierarchyPtr ,
AsnIoPtr, AsnTypePtr));
/**************************************************
*
* EntrezBlastreq
*
**************************************************/
typedef struct struct_Entrez_blastreq {
Uint4 OBbits__;
BioseqPtr bsp;
DocType bsp_database;
CharPtr program;
CharPtr database;
CharPtr options;
Uint1 showprogress;
} EntrezBlastreq, PNTR EntrezBlastreqPtr;
EntrezBlastreqPtr LIBCALL EntrezBlastreqFree PROTO ((EntrezBlastreqPtr ));
EntrezBlastreqPtr LIBCALL EntrezBlastreqNew PROTO (( void ));
EntrezBlastreqPtr LIBCALL EntrezBlastreqAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
Boolean LIBCALL EntrezBlastreqAsnWrite PROTO (( EntrezBlastreqPtr , AsnIoPtr, AsnTypePtr));
/**************************************************
*
* EntrezExtraInfo
*
**************************************************/
typedef struct struct_Entrez_extra_info {
Uint4 OBbits__;
Int4 maxlinks;
Uint1 canneighbortext;
Uint1 expanded_medline;
Uint1 canblast;
} EntrezExtraInfo, PNTR EntrezExtraInfoPtr;
EntrezExtraInfoPtr LIBCALL EntrezExtraInfoFree PROTO ((EntrezExtraInfoPtr ));
EntrezExtraInfoPtr LIBCALL EntrezExtraInfoNew PROTO (( void ));
EntrezExtraInfoPtr LIBCALL EntrezExtraInfoAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
Boolean LIBCALL EntrezExtraInfoAsnWrite PROTO (( EntrezExtraInfoPtr , AsnIoPtr, AsnTypePtr));
typedef struct struct_New_summary_List {
Int4 num;
DocType type;
DocSumPtr PNTR data;
} NewSummaryList, PNTR NewSummaryListPtr;
NewSummaryListPtr LIBCALL NewSummaryListFree PROTO ((NewSummaryListPtr ));
NewSummaryListPtr LIBCALL NewSummaryListNew PROTO (( void ));
NewSummaryListPtr LIBCALL NewSummaryListAsnRead PROTO (( AsnIoPtr, AsnTypePtr));
Boolean LIBCALL NewSummaryListAsnWrite PROTO (( NewSummaryListPtr , AsnIoPtr, AsnTypePtr));
#endif