Structures for BLAST messages. More...

#include <algo/blast/core/ncbi_std.h>
#include <algo/blast/core/blast_export.h>

Include dependency graph for blast_message.h:

This graph shows which files directly or indirectly include this file:

Classes
struct	SMessageOrigin
	Structure to enclose the origin of an error message or warning. More...

struct	Blast_Message
	Structure to hold the a message from the core of the BLAST engine. More...

Macros
#define	Blast_PerrorWithLocation(msg, error_code, context) Blast_PerrorEx(msg, error_code, __FILE__, __LINE__, context)
	Convenient define to call the function Blast_PerrorEx. More...

#define	BLASTERR_MEMORY 50
	System error: out of memory condition. More...

#define	BLASTERR_INVALIDPARAM 75
	Invalid parameter: possible programmer error or pre-condition not met. More...

#define	BLASTERR_IDEALSTATPARAMCALC 100
	Could not compute the ideal Karlin-Altschul parameters. More...

#define	BLASTERR_REDOALIGNMENTCORE_NOTSUPPORTED 101
	Composition based statistics/Smith-Waterman not supported for a program type. More...

#define	BLASTERR_INVALIDQUERIES 102
	All queries/contexts are determined invalid in the setup code. More...

#define	BLASTERR_INTERRUPTED 103
	BLAST search was interrupted via a user-provided callback. More...

#define	BLASTERR_NOVALIDKARLINALTSCHUL 104
	Could not calculate Karlin-Altschul statistics for any context. More...

#define	BLASTERR_OPTION_PROGRAM_INVALID 201
	The option is not supported with the specified program. More...

#define	BLASTERR_OPTION_VALUE_INVALID 202
	The value of the option is not supported (e.g., word size too small) More...

#define	BLASTERR_SUBJECT_LENGTH_INVALID 203
	Subject seqs min avg length error. More...

#define	BLASTERR_SEQSRC 300
	Blast seqsrc returns BLAST_SEQSRC_ERROR. More...

#define	BLASTERR_DB_MEMORY_MAP 400
	Database file error. More...

#define	BLASTERR_DB_OPEN_FILES 401

Typedefs
typedef struct SMessageOrigin	SMessageOrigin
	Structure to enclose the origin of an error message or warning. More...

typedef struct Blast_Message	Blast_Message
	Structure to hold the a message from the core of the BLAST engine. More...

Enumerations
enum	EBlastSeverity { eBlastSevInfo = 1 , eBlastSevWarning , eBlastSevError , eBlastSevFatal }
	Blast error message severities . More...

Functions
Blast_Message *	Blast_MessageFree (Blast_Message *blast_msg)
	Deallocates message memory. More...

Int2	Blast_MessageWrite (Blast_Message *blast_msg, EBlastSeverity severity, int context, const char message)
	Writes a message to a structure. More...

Int2	Blast_MessagePost (Blast_Message *blast_msg)
	Print a message with ErrPostEx. More...

void	Blast_Perror (Blast_Message **msg, Int2 error_code, int context)
	Analogous to perror. More...

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 the error/warning occurred. More...

Variables
const int	kBlastMessageNoContext
	Declared in blast_message.h as extern const. More...

const char *	kBlastErrMsg_CantCalculateUngappedKAParams

Detailed Description

Structures for BLAST messages.

Definition in file blast_message.h.

Macro Definition Documentation

◆ Blast_PerrorWithLocation

#define Blast_PerrorWithLocation	(	msg,
		error_code,
		context
	)	Blast_PerrorEx(msg, error_code, __FILE__, __LINE__, context)

Convenient define to call the function Blast_PerrorEx.

Definition at line 119 of file blast_message.h.

◆ BLASTERR_DB_MEMORY_MAP

#define BLASTERR_DB_MEMORY_MAP 400

Database file error.

Definition at line 177 of file blast_message.h.

◆ BLASTERR_DB_OPEN_FILES

#define BLASTERR_DB_OPEN_FILES 401

Definition at line 178 of file blast_message.h.

◆ BLASTERR_IDEALSTATPARAMCALC

#define BLASTERR_IDEALSTATPARAMCALC 100

Could not compute the ideal Karlin-Altschul parameters.

Definition at line 149 of file blast_message.h.

◆ BLASTERR_INTERRUPTED

#define BLASTERR_INTERRUPTED 103

BLAST search was interrupted via a user-provided callback.

Definition at line 159 of file blast_message.h.

◆ BLASTERR_INVALIDPARAM

#define BLASTERR_INVALIDPARAM 75

Invalid parameter: possible programmer error or pre-condition not met.

Definition at line 146 of file blast_message.h.

◆ BLASTERR_INVALIDQUERIES

#define BLASTERR_INVALIDQUERIES 102

All queries/contexts are determined invalid in the setup code.

Definition at line 156 of file blast_message.h.

◆ BLASTERR_MEMORY

#define BLASTERR_MEMORY 50

System error: out of memory condition.

Definition at line 143 of file blast_message.h.

◆ BLASTERR_NOVALIDKARLINALTSCHUL

#define BLASTERR_NOVALIDKARLINALTSCHUL 104

Could not calculate Karlin-Altschul statistics for any context.

Definition at line 162 of file blast_message.h.

◆ BLASTERR_OPTION_PROGRAM_INVALID

#define BLASTERR_OPTION_PROGRAM_INVALID 201

The option is not supported with the specified program.

Definition at line 165 of file blast_message.h.

◆ BLASTERR_OPTION_VALUE_INVALID

#define BLASTERR_OPTION_VALUE_INVALID 202

The value of the option is not supported (e.g., word size too small)

Definition at line 168 of file blast_message.h.

◆ BLASTERR_REDOALIGNMENTCORE_NOTSUPPORTED

#define BLASTERR_REDOALIGNMENTCORE_NOTSUPPORTED 101

Composition based statistics/Smith-Waterman not supported for a program type.

Definition at line 153 of file blast_message.h.

◆ BLASTERR_SEQSRC

#define BLASTERR_SEQSRC 300

Blast seqsrc returns BLAST_SEQSRC_ERROR.

Definition at line 174 of file blast_message.h.

◆ BLASTERR_SUBJECT_LENGTH_INVALID

#define BLASTERR_SUBJECT_LENGTH_INVALID 203

Subject seqs min avg length error.

Definition at line 171 of file blast_message.h.

Typedef Documentation

◆ Blast_Message

typedef struct Blast_Message Blast_Message

Structure to hold the a message from the core of the BLAST engine.

◆ SMessageOrigin

typedef struct SMessageOrigin SMessageOrigin

Structure to enclose the origin of an error message or warning.

Enumeration Type Documentation

◆ EBlastSeverity

enum EBlastSeverity

Blast error message severities .

These start with 1 to be consistent with the C toolkit severity numbers.

Enumerator
eBlastSevInfo
eBlastSevWarning
eBlastSevError
eBlastSevFatal

Definition at line 55 of file blast_message.h.

Function Documentation

◆ Blast_MessageFree()

Blast_Message* Blast_MessageFree ( Blast_Message * blast_msg )

Deallocates message memory.

Parameters

blast_msg structure to be deallocated [in]

Definition at line 80 of file blast_message.c.

References Blast_Message::message, Blast_Message::next, next(), NULL, Blast_Message::origin, sfree, and SMessageOriginFree().

Referenced by Blast_PerrorEx(), BlastErrorCode2String(), BOOST_AUTO_TEST_CASE(), s_BlastMessageToException(), s_Validate(), TestFixture::SetUpLookupTable(), LinkHspTestFixture::setupScoreBlk(), CBlastExtendTestFixture::setupStructures(), CPssmEngine::x_InitializeScoreBlock(), and CTracebackTestFixture::~CTracebackTestFixture().

◆ Blast_MessagePost()

Int2 Blast_MessagePost ( Blast_Message * blast_msg )

Print a message with ErrPostEx.

Parameters

blast_msg message to be printed [in]

Definition at line 136 of file blast_message.c.

References Blast_Message::message, and NULL.

◆ Blast_MessageWrite()

Int2 Blast_MessageWrite	(	Blast_Message **	blast_msg,
		EBlastSeverity	severity,
		int	context,
		const char *	message
	)

Writes a message to a structure.

The Blast_Message* is allocated.

Parameters

blast_msg	structure to be filled in [in]
severity	severity code [in]
context	query context to which this error applies [in]
message	User message to be saved [in]

Definition at line 102 of file blast_message.c.

References calloc(), Blast_Message::context, context, Blast_Message::message, Blast_Message::next, NULL, Blast_Message::severity, and strdup.

Referenced by Blast_GumbelBlkCalc(), Blast_KarlinBlkGappedCalc(), Blast_KarlinBlkNuclGappedCalc(), Blast_ScoreBlkKbpUngappedCalc(), Blast_SetPHIPatternInfo(), BLAST_ValidateOptions(), BlastExtensionOptionsValidate(), BlastFilteringOptionsFromString(), BlastHitSavingOptionsValidate(), BlastInitialWordOptionsValidate(), BlastKarlinReportAllowedValues(), BlastScoringOptionsValidate(), BlastSetUp_GetFilteringLocations(), LookupTableOptionsValidate(), PSIBlastOptionsValidate(), s_BlastExtensionScoringOptionsValidate(), s_DiscWordOptionsValidate(), s_GetEffectiveSearchSpaceForContext(), s_GetNuclValuesArray(), s_PHIScoreBlkFill(), SBlastFilterOptionsValidate(), and SPHIPatternSearchBlkNew().

◆ Blast_Perror()

void Blast_Perror	(	Blast_Message **	msg,
		Int2	error_code,
		int	context
	)

Analogous to perror.

Parameters

msg	object to be appended to or created [in\|out]
error_code	error code returned from BLAST function [in]
context	context number so that query or frame can be found [in]

Returns: Blast_Message structure containing error description

Definition at line 147 of file blast_message.c.

References Blast_PerrorEx(), context, msg(), and NULL.

◆ Blast_PerrorEx()

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 the error/warning occurred.

This function should be invoked via the Blast_PerrorWithLocation macro.

Parameters

msg	object to be appended to or created [in\|out]
error_code	one of the error codes defined below [in]
file_name	name of the file where the error ocurred [in]
lineno	line number where the error ocurred in the file above [in]
context	context number so that query or frame can be found [in]

Definition at line 154 of file blast_message.c.

References ASSERT, Blast_MessageFree(), BLASTERR_DB_MEMORY_MAP, BLASTERR_DB_OPEN_FILES, BLASTERR_IDEALSTATPARAMCALC, BLASTERR_INTERRUPTED, BLASTERR_INVALIDPARAM, BLASTERR_INVALIDQUERIES, BLASTERR_MEMORY, BLASTERR_NOVALIDKARLINALTSCHUL, BLASTERR_REDOALIGNMENTCORE_NOTSUPPORTED, BLASTERR_SEQSRC, BLASTERR_SUBJECT_LENGTH_INVALID, buf, calloc(), Blast_Message::context, context, eBlastSevError, eBlastSevFatal, eBlastSevInfo, file_name, kBlastErrMsg_CantCalculateUngappedKAParams, lineno, Blast_Message::message, msg(), Blast_Message::next, Blast_Message::origin, Blast_Message::severity, SMessageOriginNew(), and strdup.

Referenced by Blast_Perror().

Variable Documentation

◆ kBlastErrMsg_CantCalculateUngappedKAParams

const char* kBlastErrMsg_CantCalculateUngappedKAParams

extern

Definition at line 37 of file blast_message.c.

Referenced by Blast_PerrorEx(), Blast_ScoreBlkKbpUngappedCalc(), BlastSetupPreliminarySearchEx(), BOOST_AUTO_TEST_CASE(), and CBlastPrelimSearch::Run().

◆ kBlastMessageNoContext

const int kBlastMessageNoContext

extern

Declared in blast_message.h as extern const.

Definition at line 36 of file blast_message.c.

Referenced by TSearchMessages::AddMessageAllQueries(), Blast_GumbelBlkCalc(), Blast_KarlinBlkGappedCalc(), Blast_KarlinBlkNuclGappedCalc(), BLAST_MainSetUp(), Blast_Message2TSearchMessages(), Blast_ScoreBlkKbpUngappedCalc(), Blast_SetPHIPatternInfo(), BLAST_ValidateOptions(), BlastErrorCode2String(), BlastExtensionOptionsValidate(), BlastFilteringOptionsFromString(), BlastHitSavingOptionsValidate(), BlastInitialWordOptionsValidate(), BlastKarlinReportAllowedValues(), BlastScoringOptionsValidate(), BlastSetup_ScoreBlkInit(), CRemoteBlast::GetResultSet(), LookupTableOptionsValidate(), PSIBlastOptionsValidate(), CBlastPrelimSearch::Run(), s_BlastExtensionScoringOptionsValidate(), s_DiscWordOptionsValidate(), s_GetNuclValuesArray(), s_PHIScoreBlkFill(), SBlastFilterOptionsValidate(), and SPHIPatternSearchBlkNew().

Classes

Macros

Typedefs

Enumerations

Functions

Variables

Detailed Description

Macro Definition Documentation

◆ Blast_PerrorWithLocation

◆ BLASTERR_DB_MEMORY_MAP

◆ BLASTERR_DB_OPEN_FILES

◆ BLASTERR_IDEALSTATPARAMCALC

◆ BLASTERR_INTERRUPTED

◆ BLASTERR_INVALIDPARAM

◆ BLASTERR_INVALIDQUERIES

◆ BLASTERR_MEMORY

◆ BLASTERR_NOVALIDKARLINALTSCHUL

◆ BLASTERR_OPTION_PROGRAM_INVALID

◆ BLASTERR_OPTION_VALUE_INVALID

◆ BLASTERR_REDOALIGNMENTCORE_NOTSUPPORTED

◆ BLASTERR_SEQSRC

◆ BLASTERR_SUBJECT_LENGTH_INVALID

Typedef Documentation

◆ Blast_Message

◆ SMessageOrigin

Enumeration Type Documentation

◆ EBlastSeverity

Function Documentation

◆ Blast_MessageFree()

◆ Blast_MessagePost()

◆ Blast_MessageWrite()

◆ Blast_Perror()

◆ Blast_PerrorEx()

Variable Documentation

◆ kBlastErrMsg_CantCalculateUngappedKAParams

◆ kBlastMessageNoContext