NCBI C Toolkit Cross Reference

C/cdromlib/cdentrez.h

  1 /*   cdentrez.h
  2 * ===========================================================================
  3 *
  4 *                            PUBLIC DOMAIN NOTICE                          
  5 *               National Center for Biotechnology Information
  6 *                                                                          
  7 *  This software/database is a "United States Government Work" under the   
  8 *  terms of the United States Copyright Act.  It was written as part of    
  9 *  the author's official duties as a United States Government employee and 
 10 *  thus cannot be copyrighted.  This software/database is freely available 
 11 *  to the public for use. The National Library of Medicine and the U.S.    
 12 *  Government have not placed any restriction on its use or reproduction.  
 13 *                                                                          
 14 *  Although all reasonable efforts have been taken to ensure the accuracy  
 15 *  and reliability of the software and data, the NLM and the U.S.          
 16 *  Government do not and cannot warrant the performance or results that    
 17 *  may be obtained by using this software or data. The NLM and the U.S.    
 18 *  Government disclaim all warranties, express or implied, including       
 19 *  warranties of performance, merchantability or fitness for any particular
 20 *  purpose.                                                                
 21 *                                                                          
 22 *  Please cite the author in any work or product based on this material.   
 23 *
 24 * ===========================================================================
 25 *
 26 * RCS $Id: cdentrez.h,v 6.0 1997/08/25 18:12:58 madden Exp $
 27 *
 28 * Author:  Ostell, Kans
 29 *
 30 * Version Creation Date:   10/15/91
 31 *
 32 * File Description: 
 33 *       entrez index access library for Entrez CDROM
 34 *
 35 * Modifications:  
 36 * --------------------------------------------------------------------------
 37 * Date     Name        Description of modification
 38 * -------  ----------  -----------------------------------------------------
 39 * July'94  Schuler     Multiple changes to support new CD-ROM formats
 40 * 1/24/95  Kans        Define _NEW_CdEntrez_
 41 * 05-16-94 Schuler     Added RCS Log directive.  Comments will henceforth
 42 *                      be inserted automatically into the source at the
 43 *                      time it is checked into the system.
 44 
 45 $Log: cdentrez.h,v $
 46 Revision 6.0  1997/08/25 18:12:58  madden
 47 Revision changed to 6.0
 48 
 49 Revision 5.2  1997/06/26 21:55:35  vakatov
 50 [PC] DLL'd "ncbicdr.lib", "ncbiacc.lib", "ncbinacc.lib" and "ncbicacc.lib"
 51 
 52 Revision 5.1  1996/08/14 19:57:08  epstein
 53 add APIs for fetching pieces of biostruc annots
 54 
 55  * Revision 5.0  1996/05/28  13:55:34  ostell
 56  * Set to revision 5.0
 57  *
 58  * Revision 4.3  1996/03/29  18:52:30  epstein
 59  * add support for structure alignments
 60  *
 61  * Revision 4.2  1995/10/02  02:35:42  epstein
 62  * add range-checking
 63  *
 64  * Revision 4.1  1995/08/11  20:26:11  epstein
 65  * add max-models support for biostrucs
 66  *
 67  * Revision 4.0  1995/07/26  13:50:32  ostell
 68  * force revision to 4.0
 69  *
 70  * Revision 2.24  1995/06/29  15:57:13  epstein
 71  * added Complexity argument when fetching structures
 72  *
 73  * Revision 2.23  95/06/23  16:02:43  kans
 74  * support for accmmdbs.c stub to resolve symbols without MMDB link
 75  * 
 76  * Revision 2.22  1995/06/23  13:22:25  kans
 77  * Biostruc_CD_supported symbol needed for local MMDB access
 78  *
 79  * Revision 2.21  1995/05/16  14:12:46  schuler
 80  * Automatic comment insertion enabled
 81  *
 82 
 83 
 84 
 85 * ==========================================================================
 86 */
 87 
 88 #ifndef _CDENTREZ_
 89 #define _CDENTREZ_
 90 
 91 #ifndef _NEW_CdEntrez_
 92 /* only use new symbol */
 93 #define _NEW_CdEntrez_
 94 #endif
 95 
 96 #if !defined(_NEW_CdEntrez_) && !defined(_OLD_CdEntrez_)
 97 /* if neither symbol defined, default to using both */
 98 #define _OLD_CdEntrez_
 99 #define _NEW_CdEntrez_
100 #endif
101 
102 #ifndef _ACCENTR_
103 #include <accentr.h>
104 #endif
105 #ifndef _CDROMLIB_
106 #include <cdromlib.h>
107 #endif
108 
109 #undef NLM_EXTERN
110 #ifdef NLM_IMPORT
111 #define NLM_EXTERN NLM_IMPORT
112 #else
113 #define NLM_EXTERN extern
114 #endif
115 
116 #ifdef __cplusplus
117 extern "C" {
118 #endif
119 
120 /**** Initialize and close session *********************/
121 
122 NLM_EXTERN Boolean  CdEntrezInit PROTO((Boolean no_warnings));
123 NLM_EXTERN void  CdEntrezFini PROTO((void));
124 
125 /**** Get Types and Terms ******************************/
126 /**** prototypes are in cdromlib.h *********************/
127 
128 NLM_EXTERN EntrezInfo* CdEntrezGetInfo PROTO((void));
129 NLM_EXTERN char* CdEntrezDetailedInfo PROTO((void));
130 /*#define CdEntrezGetInfo CdGetInfo*/
131 /*#define CdEntrezDetailedInfo CdDetailedInfo*/
132 
133 /**** Get Links and Neighbors **************************/
134 
135 NLM_EXTERN Int4 CdEntGetMaxLinks PROTO((void));
136 
137 NLM_EXTERN LinkSetPtr  CdUidLinks PROTO((DocType type, DocUid uid, DocType link_to_type));
138 NLM_EXTERN Int2  CdLinkUidList PROTO((LinkSetPtr PNTR result, DocType type,
139                 DocType link_to_type, Int2 numuid, Int4Ptr uids, Boolean mark_missing));
140 
141 /**** Get Summaries ************************************/
142 
143 NLM_EXTERN DocSumPtr  CdDocSum PROTO((DocType type, DocUid uid));
144 NLM_EXTERN Int2  CdEntMlSumListGet PROTO((DocSumPtr PNTR result, Int2 numuid, Int4Ptr uids));
145 NLM_EXTERN Int2  CdEntSeqSumListGet PROTO((DocSumPtr PNTR result, Int2 numuid, DocType db, Int4Ptr uids));
146 #ifdef _NEW_CdEntrez_
147 NLM_EXTERN int  CdDocSumListGet PROTO((DocSum **result, int numuid, DocType type, const DocUid *uids));
148 #endif
149 
150 /**** Get Term List ************************************/
151 
152 NLM_EXTERN Int2  CdTermListByPage PROTO((DocType type, DocField field,
153                                 Int2 page, Int2 numpage, TermListProc proc));
154 NLM_EXTERN Int2  CdTermListByTerm PROTO((DocType type, DocField field,
155                                 CharPtr term, Int2 numterms, TermListProc proc, Int2Ptr first_page));
156 
157 NLM_EXTERN Boolean  CdEntrezFindTerm PROTO((DocType type, DocField field, CharPtr term, Int4Ptr spcl, Int4Ptr totl));
158 
159 /**** Creates a term node from the uid parameter ********/
160 NLM_EXTERN void  CdEntrezCreateNamedUidList PROTO((CharPtr term, DocType type, DocField field, Int4 num, DocUidPtr uids));
161 NLM_EXTERN void  CdEntrezCreateNamedUidListX PROTO((CharPtr term, DocType type, DocField field, ByteStorePtr bsp));
162 
163 /**** Look up terms with Boolean operations ************/
164 
165 NLM_EXTERN ValNodePtr  CdEntTLNew PROTO((DocType type));
166 NLM_EXTERN ValNodePtr  CdEntTLAddTerm PROTO((ValNodePtr elst, CharPtr term, DocType type, DocField field, Boolean special, CharPtr highRange));
167 NLM_EXTERN ValNodePtr  CdEntTLFree PROTO((ValNodePtr elst));
168 NLM_EXTERN LinkSetPtr  CdEntTLEval PROTO((ValNodePtr elst));
169 NLM_EXTERN Int4  CdEntTLEvalCount PROTO((ValNodePtr elst));
170 
171 NLM_EXTERN ByteStorePtr  CdEntTLEvalX PROTO((ValNodePtr elst));
172 
173 /**** Retrieve Data ***********************************/
174 
175 NLM_EXTERN Int2  CdEntMedlineEntryListGet PROTO((MedlineEntryPtr PNTR result, Int2 numuid,
176                 Int4Ptr uids, Boolean mark_missing));
177 NLM_EXTERN Int2  CdEntSeqEntryListGet PROTO((SeqEntryPtr PNTR result, Int2 numuid,
178                 Int4Ptr uids, Int2 retcode, Boolean mark_missing));
179 
180 /* may be called by Network Entrez server */
181 NLM_EXTERN DocSumPtr CdSeqSumAsnRead PROTO((AsnIoPtr aip, DocUid uid));
182 
183 /**** Get a SeqId for a GI ***************************/
184 
185 NLM_EXTERN SeqIdPtr CdSeqIdForGI PROTO((Int4 gi));
186 NLM_EXTERN Int4  CdEntrezFindSeqId PROTO((SeqIdPtr sip));
187 
188 /**** get a 3-d structure *********************/
189 #ifdef Biostruc_supported
190 NLM_EXTERN BiostrucPtr CdEntrezBiostrucGet PROTO((DocUid uid, Int4 mdlLvl, Int4 maxModels));
191 NLM_EXTERN BiostrucAnnotSetPtr CdEntrezBiostrucAnnotSetGet PROTO((DocUid uid));
192 NLM_EXTERN LinkSetPtr LIBCALL CdEntrezBiostrucFeatIds PROTO((DocUid mmdbid, Int2 feature_type, Int4 feature_set_id));
193 NLM_EXTERN BiostrucAnnotSetPtr LIBCALL CdEntrezBiostrucAnnotSetGetByFid PROTO((DocUid mmdbid, Int4 feature_id, Int4 feature_set_id));
194 #endif /* Biostruc_supported */
195 
196 #ifdef __cplusplus
197 }
198 #endif
199 
200 #undef NLM_EXTERN
201 #ifdef NLM_EXPORT
202 #define NLM_EXTERN NLM_EXPORT
203 #else
204 #define NLM_EXTERN
205 #endif
206 
207 #endif
208 
209 
210
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