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#ifndef _ALI_READ_INCLUDED
#define _ALI_READ_INCLUDED
#include <ncbi.h>
/* Defined constants */
#define ALI_NUCLEOTIDE 1
#define ALI_PROTEIN 2
#define ALI_AMBIGUOUS 3
/* Data structures */
typedef struct
{
Int4 rownum;
CharPtr data;
} RowPart, PNTR RowPartPtr;
typedef struct
{
Int4 rowNum;
CharPtr sequence;
Int2 type; /* Nucleotide = 1, Protein = 2, Ambiguous = 3 */
CharPtr id;
CharPtr junk;
Boolean maybe;
Int4 firstWordLen;
} SeqLineInfo, PNTR SeqLineInfoPtr;
typedef struct
{
Int4 rowNum;
CharPtr definitions;
CharPtr id;
} DefLineInfo, PNTR DefLineInfoPtr;
typedef struct
{
Int4 rowNum;
CharPtr other;
CharPtr id;
} OtherLineInfo, PNTR OtherLineInfoPtr;
typedef struct _ErrInfo
{
Int2 errNum;
Int2 level;
Int4 rowNum;
CharPtr info;
CharPtr extraInfo;
struct _ErrInfo PNTR next;
} ErrInfo, PNTR ErrInfoPtr;
typedef struct
{
Int2 dataType;
Int2 contigOrInter;
Int4 idCount;
Int4 seqLength;
} DataInfo, PNTR DataInfoPtr;
typedef struct
{
CharPtr gapChar;
CharPtr missingChar;
CharPtr unalignedChar;
Boolean useMaybes;
Int4 readBuffSize;
Int2 debugLevel;
Int2 corruptSeqThreshold;
Int2 nuclLineMinThreshold;
Int2 nuclLineMaxThreshold;
Int2 errExpandLevel;
DataInfo declaredInfo;
} AliConfigInfo, PNTR AliConfigInfoPtr;
typedef struct
{
CharPtr missingChar;
CharPtr gapChar;
CharPtr unalignedChar;
Int2 dataType; /* ALI_DATA_NUCLEOTIDE,ALI_DATA_PROTEIN,ALI_UNKNOWN */
Int2 contigOrInter; /* ALI_INTERLEAVED, ALI_CONTIGUOUS, ALI_UNKNOWN */
} ParsedInfo, PNTR ParsedInfoPtr;
typedef struct _SeqPart
{
CharPtr sequence;
struct _SeqPart PNTR next;
} SeqPart, PNTR SeqPartPtr;
typedef struct _IdInfo
{
CharPtr id;
Int4 length;
SeqPartPtr sequence;
CharPtr defline;
struct _IdInfo PNTR next;
} IdInfo, PNTR IdInfoPtr;
typedef struct
{
IdInfoPtr sequences;
IdInfoPtr maybes;
ErrInfoPtr errors;
ParsedInfoPtr info;
} AlignFileData, PNTR AlignFileDataPtr;
/* Function prototypes */
Int2 Ali_SeqLineGetType(CharPtr seqStr,
AliConfigInfoPtr configPtr);
void Ali_ChangeRowToOther (ValNodePtr rowPtr);
ValNodePtr Ali_ReadLines (FILE PNTR alignFilePtr,
ErrInfoPtr PNTR errorListPtr,
AliConfigInfoPtr configPtr,
AlignFileDataPtr fileInfoPtr);
#endif
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