NCBI C Toolkit Cross Reference

C/api/aliparse.h

  1 /*=========================================================================*/
  2 /*                                                                         */
  3 /*  aliparse.h -- Header file for aliparse.c                               */
  4 /*                                                                         */
  5 /*=========================================================================*/
  6 
  7 #ifndef _ALIPARSE_
  8 #define _ALIPARSE_
  9 
 10 /* Include files */
 11 
 12 #include <ncbi.h>
 13 #include <objalign.h>
 14 #include <sqnutils.h>
 15 #include <alignmgr.h>
 16 #include <aliread.h>
 17 
 18 #undef NLM_EXTERN
 19 #ifdef NLM_IMPORT
 20 #define NLM_EXTERN NLM_IMPORT
 21 #else
 22 #define NLM_EXTERN extern
 23 #endif
 24 
 25 #ifdef __cplusplus
 26 extern "C" {
 27 #endif
 28 
 29 /* Defined constants */
 30 
 31 #define ALI_SET_DEFAULTS       0x0000
 32 #define ALI_SET_GAP_CHAR       0x0001
 33 #define ALI_SET_MISSING_CHAR   0x0002
 34 #define ALI_SET_MAYBES         0x0004
 35 #define ALI_SET_READBUFF       0x0008
 36 #define ALI_SET_NUCL_MIN       0x0010
 37 #define ALI_SET_NUCL_MAX       0x0020
 38 #define ALI_SET_CORRUPT_MAX    0x0040
 39 #define ALI_SET_DEBUG_LEVEL    0x0080
 40 #define ALI_SET_ERRMSG_EXPAND  0x0100
 41 #define ALI_SET_ALL            0x00ff
 42 
 43 #define ALI_SHOW_NONE          0x00
 44 #define ALI_SHOW_SEQUENCES     0x01
 45 #define ALI_SHOW_DEFLINES      0x02
 46 #define ALI_SHOW_OTHERS        0x04
 47 #define ALI_SHOW_ALL           0xff
 48 
 49 #define ALI_CONTIGUOUS         1
 50 #define ALI_INTERLEAVED        2
 51 
 52 #define ALI_ERRMSG_EXPAND_ALL  1
 53 #define ALI_ERRMSG_EXPAND_SOME 2
 54 #define ALI_ERRMSG_EXPAND_NONE 3
 55 
 56 #define SEQUENCE_LINE          1
 57 #define DEFINITION_LINE        2
 58 #define OTHER_LINE             3
 59 
 60 /* The alignment file when read in is stored in a   */
 61 /* linked list of ValNodes.  These ValNodes contain */
 62 /* one of the following data types depending on the */
 63 /* choice setting.                                  */
 64 /*                                                  */
 65 /*        choice             type of data.ptrvalue  */
 66 /*        ------             ---------------------  */
 67 /*     0 (ALI_UNKNOWN)           NULL               */
 68 /*     1 (ALI_SEQLINE)           SeqLineInfoPtr     */
 69 /*     2 (ALI_DEFLINE)           DefLineInfoPtr     */
 70 /*     3 (ALI_OTHERLINE)         OtherLineInfoPtr   */
 71 
 72 #define ALI_UNKNOWN        0
 73 #define ALI_SEQLINE        1
 74 #define ALI_DEFLINE        2
 75 #define ALI_OTHERLINE      3
 76 
 77 #define ERR_SEQ_BEFORE_ID         1
 78 #define ERR_ID_WITHOUT_SEQ        2
 79 #define ERR_SEQ_WITHOUT_ID        3
 80 #define ERR_DUPLICATE_IDS         4
 81 #define ERR_SEQUENCE_TOO_SHORT    5
 82 #define ERR_SEQUENCE_TOO_LONG     6
 83 #define ERR_OUT_OF_MEMORY         7
 84 #define ERR_ID_NO_PRECEDING_SEQ   8
 85 #define ERR_DEFLINE_WITH_NO_ID    9
 86 #define ERR_ID_WITH_NO_DEFLINE    10
 87 #define ERR_NOT_INTERLEAVED       11
 88 #define ERR_NOT_CONTIGUOUS        12
 89 #define ERR_NO_SEQUENCES_FOUND    13
 90 #define ERR_ID_COUNT_MISMATCH     14
 91 #define ERR_SEQ_LENGTH_MISMATCH   15
 92 #define ERR_INVALID_DEFLINE       16
 93 #define ERR_DEFLINE_NODEFS        17
 94 #define ERR_GLOBAL_DEFLINE_NODEFS 18
 95 #define ERR_MULTI_DEFLINE_NODEFS  19
 96 
 97 #define LEVEL_MULTI    1
 98 #define LEVEL_ERROR    2
 99 #define LEVEL_WARNING  3
100 #define LEVEL_INFO     4
101 
102 /* Data structures */
103 
104 /* Function prototypes */
105 
106 SeqLineInfoPtr   SeqLineReEval (SeqLineInfoPtr seqLinePtr);
107 AlignFileDataPtr Ali_Read (FILE PNTR alignFilePtr);
108 void             Ali_Free (AlignFileDataPtr fileInfoPtr);
109 ErrInfoPtr       XAli_AddError (ErrInfoPtr PNTR errorList, Int4 iError);
110 ErrInfoPtr       Ali_AddError (ErrInfoPtr PNTR errorListPtr,
111                                Int4            iError,
112                                ...);
113 void             Ali_ChangeRowToOther (ValNodePtr rowPtr);
114 Boolean          Ali_SetConfig (AliConfigInfoPtr configPtr,
115                                        Int2             options);
116 AliConfigInfoPtr Ali_GetConfig (void);
117 
118 NLM_EXTERN SeqEntryPtr ALI_ConvertToNCBIData(AlignFileDataPtr afp);
119 
120 #ifdef __cplusplus
121 }
122 #endif
123 
124 #undef NLM_EXTERN
125 #ifdef NLM_EXPORT
126 #define NLM_EXTERN NLM_EXPORT
127 #else
128 #define NLM_EXTERN
129 #endif
130 
131 #endif /* _ALIPARSE_ */
132 
133
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