/usr/include/ncbi/util/creaders/alnread.h is in libncbi6-dev 6.1.20120620-8.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 | #ifndef UTIL_CREADERS___ALNREAD__H
#define UTIL_CREADERS___ALNREAD__H
/*
* $Id: alnread.h,v 1.8 2012/03/30 13:44:31 kazimird Exp $
*
* ===========================================================================
*
* 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.
*
* ===========================================================================
*
* Authors: Colleen Bollin
*
*/
#include <util/creaders/creaders_export.h>
#ifdef __cplusplus
extern "C" {
#endif
/* defines from ncbistd.h */
#ifndef FAR
#define FAR
#endif
#ifndef PASCAL
#define PASCAL
#endif
#ifndef EXPORT
#define EXPORT
#endif
#ifndef PASCAL
#define PASCAL
#endif
#ifndef EXPORT
#define EXPORT
#endif
#if defined (WIN32)
# define ALIGNMENT_CALLBACK __stdcall
#else
# define ALIGNMENT_CALLBACK
#endif
typedef char * (ALIGNMENT_CALLBACK *FReadLineFunction) (void * userdata);
typedef enum {
eTrue = -1,
eFalse = 0
} EBool;
typedef enum {
eAlnErr_Unknown = -1,
eAlnErr_NoError = 0,
eAlnErr_Fatal,
eAlnErr_BadData,
eAlnErr_BadFormat
} EAlnErr;
/* This structure and the accompanying functions are used for storing
* information about errors encountered while reading the alignment data.
*/
typedef struct SErrorInfo {
EAlnErr category;
int line_num;
char * id;
char * message;
struct SErrorInfo * next;
} SErrorInfo, * TErrorInfoPtr;
typedef void (ALIGNMENT_CALLBACK *FReportErrorFunction) (
TErrorInfoPtr err_ptr, /* error to report */
void * userdata /* data supplied by calling program to library */
);
NCBI_CREADERS_EXPORT
extern TErrorInfoPtr ErrorInfoNew (TErrorInfoPtr list);
NCBI_CREADERS_EXPORT
extern void ErrorInfoFree (TErrorInfoPtr eip);
typedef struct SSequenceInfo {
char * missing;
char * match;
char * beginning_gap;
char * middle_gap;
char * end_gap;
const char * alphabet;
} SSequenceInfo, * TSequenceInfoPtr;
extern NCBI_CREADERS_EXPORT TSequenceInfoPtr SequenceInfoNew (void);
extern NCBI_CREADERS_EXPORT void SequenceInfoFree (TSequenceInfoPtr sip);
typedef struct SAlignmentFile {
int num_sequences;
int num_organisms;
int num_deflines;
int num_segments;
char ** ids;
char ** sequences;
char ** organisms;
char ** deflines;
char align_format_found;
} SAlignmentFile, * TAlignmentFilePtr;
extern NCBI_CREADERS_EXPORT TAlignmentFilePtr AlignmentFileNew (void);
extern NCBI_CREADERS_EXPORT void AlignmentFileFree (TAlignmentFilePtr afp);
extern NCBI_CREADERS_EXPORT TAlignmentFilePtr ReadAlignmentFile (
FReadLineFunction readfunc, /* function for reading lines of
* alignment file
*/
void * fileuserdata, /* data to be passed back each time
* readfunc is invoked
*/
FReportErrorFunction errfunc, /* function for reporting errors */
void * erroruserdata, /* data to be passed back each time
* errfunc is invoked
*/
TSequenceInfoPtr sequence_info /* structure containing sequence
* alphabet and special characters
*/
);
extern NCBI_CREADERS_EXPORT TAlignmentFilePtr ReadAlignmentFileEx (
FReadLineFunction readfunc, /* function for reading lines of
* alignment file
*/
void * fileuserdata, /* data to be passed back each time
* readfunc is invoked
*/
FReportErrorFunction errfunc, /* function for reporting errors */
void * erroruserdata, /* data to be passed back each time
* errfunc is invoked
*/
TSequenceInfoPtr sequence_info, /* structure containing sequence
* alphabet and special characters
*/
EBool use_nexus_file_info /* set to nonzero to replace data in
* sequence_info with characters
* read from NEXUS comment in file,
* set to 0 otherwise.
*/
);
/*
* The following are to accommodate creating of local IDs to replace the IDs
* found in the actual alignment file. We are retaining the original API for
* legacy code compatibility, hence the new functions with almost the same
* signature.
*/
extern NCBI_CREADERS_EXPORT TAlignmentFilePtr ReadAlignmentFile2 (
FReadLineFunction readfunc, /* function for reading lines of
* alignment file
*/
void * fileuserdata, /* data to be passed back each time
* readfunc is invoked
*/
FReportErrorFunction errfunc, /* function for reporting errors */
void * erroruserdata, /* data to be passed back each time
* errfunc is invoked
*/
TSequenceInfoPtr sequence_info, /* structure containing sequence
* alphabet and special characters
*/
EBool gen_local_ids /* flag indicating whether input IDs
* should be replaced with unique
* local IDs
*/
);
extern NCBI_CREADERS_EXPORT TAlignmentFilePtr ReadAlignmentFileEx2 (
FReadLineFunction readfunc, /* function for reading lines of
* alignment file
*/
void * fileuserdata, /* data to be passed back each time
* readfunc is invoked
*/
FReportErrorFunction errfunc, /* function for reporting errors */
void * erroruserdata, /* data to be passed back each time
* errfunc is invoked
*/
TSequenceInfoPtr sequence_info, /* structure containing sequence
* alphabet and special characters
*/
EBool use_nexus_file_info, /* set to nonzero to replace data in
* sequence_info with characters
* read from NEXUS comment in file,
* set to 0 otherwise.
*/
EBool gen_local_ids /* flag indicating whether input IDs
* should be replaced with unique
* local IDs
*/
);
#ifdef __cplusplus
}
#endif
#endif /* UTIL_CREADERS___ALNREAD__H */
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