NCBI C Toolkit Cross Reference

C/access/cddapi.h

  1 /*   cddapi.h
  2 * ===========================================================================
  3 *
  4 *                            PUBLIC DOMAIN NOTICE
  5 *            National Center for Biotechnology Information (NCBI)
  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 do not place any restriction on its use or reproduction.
 13 *  We would, however, appreciate having the NCBI and the author cited in
 14 *  any work or product based on this material
 15 *
 16 *  Although all reasonable efforts have been taken to ensure the accuracy
 17 *  and reliability of the software and data, the NLM and the U.S.
 18 *  Government do not and cannot warrant the performance or results that
 19 *  may be obtained by using this software or data. The NLM and the U.S.
 20 *  Government disclaim all warranties, express or implied, including
 21 *  warranties of performance, merchantability or fitness for any particular
 22 *  purpose.
 23 *
 24 * ===========================================================================
 25 *
 26 * File Name:  cddapi.h
 27 *
 28 * Author:  Jonathan Kans
 29 *
 30 * Version Creation Date:   8/16/00
 31 *
 32 * $Revision: 1.5 $
 33 *
 34 * File Description: 
 35 *
 36 * Modifications:  
 37 * --------------------------------------------------------------------------
 38 * Date     Name        Description of modification
 39 * -------  ----------  -----------------------------------------------------
 40 *
 41 *
 42 * ==========================================================================
 43 */
 44 
 45 
 46 #ifndef _CDDAPI_
 47 #define _CDDAPI_
 48 
 49 #include <ncbi.h>
 50 #include <asn.h>
 51 #include <objseq.h>
 52 #include <urlquery.h>
 53 
 54 #undef NLM_EXTERN
 55 #ifdef NLM_IMPORT
 56 #define NLM_EXTERN NLM_IMPORT
 57 #else
 58 #define NLM_EXTERN extern
 59 #endif
 60 
 61 
 62 #ifdef __cplusplus
 63 extern "C" {
 64 #endif
 65 
 66 
 67 /* See synchronous and asynchronous code examples at bottom of this header */
 68 
 69 /*
 70    Parameters are as follows:
 71 
 72    BioseqPtr bsp       - Query sequence
 73    FloatHi expectValue - Expectation value
 74    Boolean findBest    - Return only non-redundant CDs
 75    Boolean doFilter    - Filter out low sequence complexity
 76    Boolean makeFeats   - Return features (T) or alignments (F)
 77    CharPtr dataLib     - RPS-BLAST database
 78    Boolean precalc     - Use DART to avoid search
 79 */
 80 
 81 /* low-level connection functions */
 82 
 83 NLM_EXTERN CONN CddOpenConnection (
 84   BioseqPtr bsp,
 85   FloatHi expectValue,
 86   Boolean findBest,
 87   Boolean doFilter,
 88   Boolean makeFeats,
 89   CharPtr dataLib,
 90   Boolean precalc
 91 );
 92 
 93 NLM_EXTERN SeqAnnotPtr CddWaitForReply (
 94   CONN conn
 95 );
 96 
 97 /*
 98  CddSynchronousQuery opens connection, sends a
 99  uid request, and waits for a reply
100 */
101 
102 NLM_EXTERN SeqAnnotPtr CddSynchronousQuery (
103   BioseqPtr bsp,
104   FloatHi expectValue,
105   Boolean findBest,
106   Boolean doFilter,
107   Boolean makeFeats,
108   CharPtr dataLib,
109   Boolean precalc
110 );
111 
112 /*
113  CddAsynchronousQuery opens connection, send request,
114  and queues completion routine using urlquery queueing
115  mechanism.
116 
117  CddCheckQueue should be called several times a second with
118  a timer.  It calls QUERY_CheckQueue to poll connection,
119  which calls completion routine when result is available,
120  cleaning up connection afterwards.
121 
122  CddReadReply take conns and status parameters from completion
123  routine and reads SeqAnnotPtr.
124 */
125 
126 NLM_EXTERN Boolean CddAsynchronousQuery (
127   BioseqPtr bsp,
128   FloatHi expectValue,
129   Boolean findBest,
130   Boolean doFilter,
131   Boolean makeFeats,
132   CharPtr dataLib,
133   Boolean precalc,
134   QUEUE* queue,
135   QueryResultProc resultproc,
136   VoidPtr userdata
137 );
138 
139 NLM_EXTERN Int4 CddCheckQueue (
140   QUEUE* queue
141 );
142 
143 NLM_EXTERN SeqAnnotPtr CddReadReply (
144   CONN conn,
145   EIO_Status status
146 );
147 
148 /*
149  CddCorrectIDs should be called after the result is read
150  in order to replace the temporary Seq-ids on the returned
151  Seq-annot.
152 */
153 
154 NLM_EXTERN void CddCorrectIDs (
155   BioseqPtr bsp,
156   SeqAnnotPtr sap
157 );
158 
159 
160 #ifdef __cplusplus
161 }
162 #endif
163 
164 #undef NLM_EXTERN
165 #ifdef NLM_EXPORT
166 #define NLM_EXTERN NLM_EXPORT
167 #else
168 #define NLM_EXTERN
169 #endif
170 
171 #endif /* _CDDAPI_ */
172 
173
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