NCBI C++ ToolKit
blast_message.h
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1 /* $Id: blast_message.h 102523 2024-05-22 13:19:52Z fongah2 $
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29 
30 /** @file blast_message.h
31  * Structures for BLAST messages
32  */
33 
34 #ifndef ALGO_BLAST_CORE__BLAST_MESSAGE__H
35 #define ALGO_BLAST_CORE__BLAST_MESSAGE__H
36 
39 
40 #ifdef __cplusplus
41 extern "C" {
42 #endif
43 
44 /** Structure to enclose the origin of an error message or warning
45  */
46 typedef struct SMessageOrigin {
47  char* filename; /**< Name of the file */
48  int lineno; /**< Line number in the file above */
50 
51 /** Blast error message severities .
52  * These start with 1 to be consistent
53  * with the C toolkit severity numbers.
54  */
55 typedef enum {
61 
62 /*** No single context is known to cause the error (probably a setup issue). */
63 extern NCBI_XBLAST_EXPORT
64 const int kBlastMessageNoContext;
65 /*** Error message for failure to calculate ungapped Karlin-Altschul parameters */
66 extern NCBI_XBLAST_EXPORT
68 
69 /** Structure to hold the a message from the core of the BLAST engine. */
70 typedef struct Blast_Message {
71  struct Blast_Message *next; /**< next message in this list */
72  EBlastSeverity severity; /**< severity code */
73  char* message; /**< User message to be saved. */
74  SMessageOrigin* origin; /**< Optional: origin of the message */
75  int context; /**< Context, allows us to print message for query number.
76  kBlastMessageNoContext used if no context applies */
78 
79 /** Deallocates message memory.
80  * @param blast_msg structure to be deallocated [in]
81 */
82 
85 
86 
87 /** Writes a message to a structure. The Blast_Message* is allocated.
88  * @param blast_msg structure to be filled in [in]
89  * @param severity severity code [in]
90  * @param context query context to which this error applies [in]
91  * @param message User message to be saved [in]
92 */
93 
96  int context, const char *message);
97 
98 
99 /** Print a message with ErrPostEx
100  * @param blast_msg message to be printed [in]
101 */
102 
105 
106 /* FIXME: should the code below and its implementation be moved to another
107  * file, say blast_error.[hc]? */
108 
109 /** Analogous to perror
110  * @param msg object to be appended to or created [in|out]
111  * @param error_code error code returned from BLAST function [in]
112  * @param context context number so that query or frame can be found [in]
113  * @return Blast_Message structure containing error description
114  */
116 void Blast_Perror(Blast_Message* *msg, Int2 error_code, int context);
117 
118 /** Convenient define to call the function Blast_PerrorEx. */
119 #define Blast_PerrorWithLocation(msg, error_code, context) \
120 Blast_PerrorEx(msg, error_code, __FILE__, __LINE__, context)
121 
122 /** Extended version of Blast_Perror which includes parameters for the file
123  * name and line number where the error/warning occurred. This function should
124  * be invoked via the Blast_PerrorWithLocation macro.
125  * @param msg object to be appended to or created [in|out]
126  * @param error_code one of the error codes defined below [in]
127  * @param file_name name of the file where the error ocurred [in]
128  * @param lineno line number where the error ocurred in the file above [in]
129  * @param context context number so that query or frame can be found [in]
130  */
132 void Blast_PerrorEx(Blast_Message* *msg,
133  Int2 error_code,
134  const char* file_name,
135  int lineno,
136  int context);
137 
138 /* BLAST error codes: these are meant to describe errors that can occur in the
139  * core of BLAST only
140  */
141 
142 /** System error: out of memory condition */
143 #define BLASTERR_MEMORY 50
144 
145 /** Invalid parameter: possible programmer error or pre-condition not met */
146 #define BLASTERR_INVALIDPARAM 75
147 
148 /** Could not compute the ideal Karlin-Altschul parameters */
149 #define BLASTERR_IDEALSTATPARAMCALC 100
150 
151 /** Composition based statistics/Smith-Waterman not supported for a program
152  * type */
153 #define BLASTERR_REDOALIGNMENTCORE_NOTSUPPORTED 101
154 
155 /** All queries/contexts are determined invalid in the setup code */
156 #define BLASTERR_INVALIDQUERIES 102
157 
158 /** BLAST search was interrupted via a user-provided callback */
159 #define BLASTERR_INTERRUPTED 103
160 
161 /** Could not calculate Karlin-Altschul statistics for any context. */
162 #define BLASTERR_NOVALIDKARLINALTSCHUL 104
163 
164 /** The option is not supported with the specified program. */
165 #define BLASTERR_OPTION_PROGRAM_INVALID 201
166 
167  /** The value of the option is not supported (e.g., word size too small) */
168 #define BLASTERR_OPTION_VALUE_INVALID 202
169 
170  /** Subject seqs min avg length error */
171 #define BLASTERR_SUBJECT_LENGTH_INVALID 203
172 
173 /** Blast seqsrc returns BLAST_SEQSRC_ERROR */
174 #define BLASTERR_SEQSRC 300
175 
176 /** Database file error */
177 #define BLASTERR_DB_MEMORY_MAP 400
178 #define BLASTERR_DB_OPEN_FILES 401
179 
180 
181 #ifdef __cplusplus
182 }
183 #endif
184 #endif /* !ALGO_BLAST_CORE__BLAST_MESSAGE__H */
185 
Defines to provide correct exporting from BLAST DLL in Windows.
#define NCBI_XBLAST_EXPORT
NULL operations for other cases.
Definition: blast_export.h:65
const char * kBlastErrMsg_CantCalculateUngappedKAParams
Definition: blast_message.c:38
EBlastSeverity
Blast error message severities .
Definition: blast_message.h:55
@ eBlastSevError
Definition: blast_message.h:58
@ eBlastSevInfo
Definition: blast_message.h:56
@ eBlastSevFatal
Definition: blast_message.h:59
@ eBlastSevWarning
Definition: blast_message.h:57
struct SMessageOrigin SMessageOrigin
Structure to enclose the origin of an error message or warning.
void Blast_PerrorEx(Blast_Message **msg, Int2 error_code, const char *file_name, int lineno, int context)
Extended version of Blast_Perror which includes parameters for the file name and line number where th...
void Blast_Perror(Blast_Message **msg, Int2 error_code, int context)
Analogous to perror.
Int2 Blast_MessagePost(Blast_Message *blast_msg)
Print a message with ErrPostEx.
struct Blast_Message Blast_Message
Structure to hold the a message from the core of the BLAST engine.
Int2 Blast_MessageWrite(Blast_Message **blast_msg, EBlastSeverity severity, int context, const char *message)
Writes a message to a structure.
const int kBlastMessageNoContext
Declared in blast_message.h as extern const.
Definition: blast_message.c:36
Blast_Message * Blast_MessageFree(Blast_Message *blast_msg)
Deallocates message memory.
Definition: blast_message.c:80
const char * file_name[]
int16_t Int2
2-byte (16-bit) signed integer
Definition: ncbitype.h:100
static size_t lineno
Definition: mdb_load.c:28
Type and macro definitions from C toolkit that are not defined in C++ toolkit.
Structure to hold the a message from the core of the BLAST engine.
Definition: blast_message.h:70
int context
Context, allows us to print message for query number.
Definition: blast_message.h:75
EBlastSeverity severity
severity code
Definition: blast_message.h:72
SMessageOrigin * origin
Optional: origin of the message.
Definition: blast_message.h:74
char * message
User message to be saved.
Definition: blast_message.h:73
struct Blast_Message * next
next message in this list
Definition: blast_message.h:71
Structure to enclose the origin of an error message or warning.
Definition: blast_message.h:46
int lineno
Line number in the file above.
Definition: blast_message.h:48
char * filename
Name of the file.
Definition: blast_message.h:47
static CS_CONTEXT * context
Definition: will_convert.c:21
Modified on Tue May 28 05:51:34 2024 by modify_doxy.py rev. 669887