/usr/include/ncbi/cddapi.h is in libncbi6-dev 6.1.20120620-8.
This file is owned by root:root, with mode 0o644.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 | /* cddapi.h
* ===========================================================================
*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information (NCBI)
*
* 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 do not place any restriction on its use or reproduction.
* We would, however, appreciate having the NCBI and the author cited in
* any work or product based on this material
*
* 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.
*
* ===========================================================================
*
* File Name: cddapi.h
*
* Author: Jonathan Kans
*
* Version Creation Date: 8/16/00
*
* $Revision: 1.5 $
*
* File Description:
*
* Modifications:
* --------------------------------------------------------------------------
* Date Name Description of modification
* ------- ---------- -----------------------------------------------------
*
*
* ==========================================================================
*/
#ifndef _CDDAPI_
#define _CDDAPI_
#include <ncbi.h>
#include <asn.h>
#include <objseq.h>
#include <urlquery.h>
#undef NLM_EXTERN
#ifdef NLM_IMPORT
#define NLM_EXTERN NLM_IMPORT
#else
#define NLM_EXTERN extern
#endif
#ifdef __cplusplus
extern "C" {
#endif
/* See synchronous and asynchronous code examples at bottom of this header */
/*
Parameters are as follows:
BioseqPtr bsp - Query sequence
FloatHi expectValue - Expectation value
Boolean findBest - Return only non-redundant CDs
Boolean doFilter - Filter out low sequence complexity
Boolean makeFeats - Return features (T) or alignments (F)
CharPtr dataLib - RPS-BLAST database
Boolean precalc - Use DART to avoid search
*/
/* low-level connection functions */
NLM_EXTERN CONN CddOpenConnection (
BioseqPtr bsp,
FloatHi expectValue,
Boolean findBest,
Boolean doFilter,
Boolean makeFeats,
CharPtr dataLib,
Boolean precalc
);
NLM_EXTERN SeqAnnotPtr CddWaitForReply (
CONN conn
);
/*
CddSynchronousQuery opens connection, sends a
uid request, and waits for a reply
*/
NLM_EXTERN SeqAnnotPtr CddSynchronousQuery (
BioseqPtr bsp,
FloatHi expectValue,
Boolean findBest,
Boolean doFilter,
Boolean makeFeats,
CharPtr dataLib,
Boolean precalc
);
/*
CddAsynchronousQuery opens connection, send request,
and queues completion routine using urlquery queueing
mechanism.
CddCheckQueue should be called several times a second with
a timer. It calls QUERY_CheckQueue to poll connection,
which calls completion routine when result is available,
cleaning up connection afterwards.
CddReadReply take conns and status parameters from completion
routine and reads SeqAnnotPtr.
*/
NLM_EXTERN Boolean CddAsynchronousQuery (
BioseqPtr bsp,
FloatHi expectValue,
Boolean findBest,
Boolean doFilter,
Boolean makeFeats,
CharPtr dataLib,
Boolean precalc,
QUEUE* queue,
QueryResultProc resultproc,
VoidPtr userdata
);
NLM_EXTERN Int4 CddCheckQueue (
QUEUE* queue
);
NLM_EXTERN SeqAnnotPtr CddReadReply (
CONN conn,
EIO_Status status
);
/*
CddCorrectIDs should be called after the result is read
in order to replace the temporary Seq-ids on the returned
Seq-annot.
*/
NLM_EXTERN void CddCorrectIDs (
BioseqPtr bsp,
SeqAnnotPtr sap
);
#ifdef __cplusplus
}
#endif
#undef NLM_EXTERN
#ifdef NLM_EXPORT
#define NLM_EXTERN NLM_EXPORT
#else
#define NLM_EXTERN
#endif
#endif /* _CDDAPI_ */
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