/usr/include/ncbi/aliparse.h is in libncbi6-dev 6.1.20110713-3ubuntu2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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/* */
/* aliparse.h -- Header file for aliparse.c */
/* */
/*=========================================================================*/
#ifndef _ALIPARSE_
#define _ALIPARSE_
/* Include files */
#include <ncbi.h>
#include <objalign.h>
#include <sqnutils.h>
#include <alignmgr.h>
#include <aliread.h>
#undef NLM_EXTERN
#ifdef NLM_IMPORT
#define NLM_EXTERN NLM_IMPORT
#else
#define NLM_EXTERN extern
#endif
#ifdef __cplusplus
extern "C" {
#endif
/* Defined constants */
#define ALI_SET_DEFAULTS 0x0000
#define ALI_SET_GAP_CHAR 0x0001
#define ALI_SET_MISSING_CHAR 0x0002
#define ALI_SET_MAYBES 0x0004
#define ALI_SET_READBUFF 0x0008
#define ALI_SET_NUCL_MIN 0x0010
#define ALI_SET_NUCL_MAX 0x0020
#define ALI_SET_CORRUPT_MAX 0x0040
#define ALI_SET_DEBUG_LEVEL 0x0080
#define ALI_SET_ERRMSG_EXPAND 0x0100
#define ALI_SET_ALL 0x00ff
#define ALI_SHOW_NONE 0x00
#define ALI_SHOW_SEQUENCES 0x01
#define ALI_SHOW_DEFLINES 0x02
#define ALI_SHOW_OTHERS 0x04
#define ALI_SHOW_ALL 0xff
#define ALI_CONTIGUOUS 1
#define ALI_INTERLEAVED 2
#define ALI_ERRMSG_EXPAND_ALL 1
#define ALI_ERRMSG_EXPAND_SOME 2
#define ALI_ERRMSG_EXPAND_NONE 3
#define SEQUENCE_LINE 1
#define DEFINITION_LINE 2
#define OTHER_LINE 3
/* The alignment file when read in is stored in a */
/* linked list of ValNodes. These ValNodes contain */
/* one of the following data types depending on the */
/* choice setting. */
/* */
/* choice type of data.ptrvalue */
/* ------ --------------------- */
/* 0 (ALI_UNKNOWN) NULL */
/* 1 (ALI_SEQLINE) SeqLineInfoPtr */
/* 2 (ALI_DEFLINE) DefLineInfoPtr */
/* 3 (ALI_OTHERLINE) OtherLineInfoPtr */
#define ALI_UNKNOWN 0
#define ALI_SEQLINE 1
#define ALI_DEFLINE 2
#define ALI_OTHERLINE 3
#define ERR_SEQ_BEFORE_ID 1
#define ERR_ID_WITHOUT_SEQ 2
#define ERR_SEQ_WITHOUT_ID 3
#define ERR_DUPLICATE_IDS 4
#define ERR_SEQUENCE_TOO_SHORT 5
#define ERR_SEQUENCE_TOO_LONG 6
#define ERR_OUT_OF_MEMORY 7
#define ERR_ID_NO_PRECEDING_SEQ 8
#define ERR_DEFLINE_WITH_NO_ID 9
#define ERR_ID_WITH_NO_DEFLINE 10
#define ERR_NOT_INTERLEAVED 11
#define ERR_NOT_CONTIGUOUS 12
#define ERR_NO_SEQUENCES_FOUND 13
#define ERR_ID_COUNT_MISMATCH 14
#define ERR_SEQ_LENGTH_MISMATCH 15
#define ERR_INVALID_DEFLINE 16
#define ERR_DEFLINE_NODEFS 17
#define ERR_GLOBAL_DEFLINE_NODEFS 18
#define ERR_MULTI_DEFLINE_NODEFS 19
#define LEVEL_MULTI 1
#define LEVEL_ERROR 2
#define LEVEL_WARNING 3
#define LEVEL_INFO 4
/* Data structures */
/* Function prototypes */
SeqLineInfoPtr SeqLineReEval (SeqLineInfoPtr seqLinePtr);
AlignFileDataPtr Ali_Read (FILE PNTR alignFilePtr);
void Ali_Free (AlignFileDataPtr fileInfoPtr);
ErrInfoPtr XAli_AddError (ErrInfoPtr PNTR errorList, Int4 iError);
ErrInfoPtr Ali_AddError (ErrInfoPtr PNTR errorListPtr,
Int4 iError,
...);
void Ali_ChangeRowToOther (ValNodePtr rowPtr);
Boolean Ali_SetConfig (AliConfigInfoPtr configPtr,
Int2 options);
AliConfigInfoPtr Ali_GetConfig (void);
NLM_EXTERN SeqEntryPtr ALI_ConvertToNCBIData(AlignFileDataPtr afp);
#ifdef __cplusplus
}
#endif
#undef NLM_EXTERN
#ifdef NLM_EXPORT
#define NLM_EXTERN NLM_EXPORT
#else
#define NLM_EXTERN
#endif
#endif /* _ALIPARSE_ */
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