NCBI C Toolkit Cross Reference

C/api/aliread.h

  1 #ifndef _ALI_READ_INCLUDED
  2 #define _ALI_READ_INCLUDED
  3 
  4 #include <ncbi.h>
  5 
  6 /* Defined constants */
  7 
  8 #define ALI_NUCLEOTIDE        1
  9 #define ALI_PROTEIN           2
 10 #define ALI_AMBIGUOUS         3
 11 
 12 /* Data structures */
 13 
 14 typedef struct 
 15 {
 16   Int4    rownum;
 17   CharPtr data;
 18 } RowPart, PNTR RowPartPtr;
 19 
 20 typedef struct
 21 {
 22   Int4    rowNum;
 23   CharPtr sequence;
 24   Int2    type;         /* Nucleotide = 1, Protein = 2, Ambiguous = 3 */
 25   CharPtr id;
 26   CharPtr junk;
 27   Boolean maybe;
 28   Int4    firstWordLen;
 29 } SeqLineInfo, PNTR SeqLineInfoPtr;
 30 
 31 typedef struct
 32 {
 33   Int4    rowNum;
 34   CharPtr definitions;
 35   CharPtr id;
 36 } DefLineInfo, PNTR DefLineInfoPtr;
 37 
 38 typedef struct
 39 {
 40   Int4    rowNum;
 41   CharPtr other;
 42   CharPtr id;
 43 } OtherLineInfo, PNTR OtherLineInfoPtr;
 44 
 45 typedef struct _ErrInfo
 46 {
 47   Int2       errNum;
 48   Int2       level;
 49   Int4       rowNum;
 50   CharPtr    info;
 51   CharPtr    extraInfo;
 52   struct _ErrInfo PNTR next;
 53 } ErrInfo, PNTR ErrInfoPtr;
 54 
 55 typedef struct
 56 {
 57   Int2    dataType;
 58   Int2    contigOrInter;
 59   Int4    idCount;
 60   Int4    seqLength;
 61 } DataInfo, PNTR DataInfoPtr;
 62 
 63 typedef struct
 64 {
 65   CharPtr  gapChar;
 66   CharPtr  missingChar;
 67   CharPtr  unalignedChar;
 68   Boolean  useMaybes;
 69   Int4     readBuffSize;
 70   Int2     debugLevel;
 71   Int2     corruptSeqThreshold;
 72   Int2     nuclLineMinThreshold;
 73   Int2     nuclLineMaxThreshold;
 74   Int2     errExpandLevel;
 75   DataInfo declaredInfo;
 76 } AliConfigInfo, PNTR AliConfigInfoPtr;
 77 
 78 typedef struct
 79 {
 80   CharPtr missingChar;
 81   CharPtr gapChar;
 82   CharPtr unalignedChar;
 83   Int2    dataType;      /* ALI_DATA_NUCLEOTIDE,ALI_DATA_PROTEIN,ALI_UNKNOWN */
 84   Int2    contigOrInter; /* ALI_INTERLEAVED, ALI_CONTIGUOUS, ALI_UNKNOWN */
 85 } ParsedInfo, PNTR ParsedInfoPtr;
 86 
 87 typedef struct _SeqPart
 88 {
 89   CharPtr  sequence;
 90   struct _SeqPart PNTR next;
 91 } SeqPart, PNTR SeqPartPtr;
 92 
 93 typedef struct _IdInfo
 94 {
 95   CharPtr        id;
 96   Int4           length;
 97   SeqPartPtr     sequence;
 98   CharPtr        defline;
 99   struct _IdInfo PNTR next;
100 } IdInfo, PNTR IdInfoPtr;
101 
102 typedef struct
103 {
104   IdInfoPtr     sequences;
105   IdInfoPtr     maybes;
106   ErrInfoPtr    errors;
107   ParsedInfoPtr info;
108 } AlignFileData, PNTR AlignFileDataPtr;
109 
110 /* Function prototypes */
111 
112 Int2       Ali_SeqLineGetType(CharPtr          seqStr,
113                               AliConfigInfoPtr configPtr);
114 void       Ali_ChangeRowToOther (ValNodePtr rowPtr);
115 ValNodePtr Ali_ReadLines (FILE PNTR        alignFilePtr,
116                           ErrInfoPtr PNTR  errorListPtr,
117                           AliConfigInfoPtr configPtr,
118                           AlignFileDataPtr fileInfoPtr);
119 #endif
120
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