SystemBlastFormatter Class Reference

This class calls a command line executable to convert a blast job between the available different formats. More...

#include <blast_formatter.h>

Inheritance diagram for SystemBlastFormatter:

Collaboration diagram for SystemBlastFormatter:

Public Member Functions
virtual	~SystemBlastFormatter ()
	The SystemBlastFormatter destructor. More...
virtual char *	GetConvertedOutput (const char *job_id_s, const uint32 output_format_code, const char *custom_format_s, const BlastServiceData *data_p)
	The function gets the converted output as a c-style string using its specified command line executable. More...
Public Member Functions inherited from BlastFormatter
	BlastFormatter ()
virtual	~BlastFormatter ()
	The BlastFormatter destructor. More...
virtual char *	GetConvertedOutput (const char *job_id_s, const uint32 output_format_code, const char *custom_format_s, const struct BlastServiceData *data_p)=0
	The function to get the converted output as a c-style string. More...

Static Public Member Functions
static SystemBlastFormatter *	Create (const json_t *config_p)
	Create a SystemBlastFormatter using the given configuration. More...
static char *	GetOutputFormatAsString (const uint32 output_format_code, const char *custom_output_formats_s)
Static Public Member Functions inherited from BlastFormatter
static char *	GetConvertedOutputFilename (const char *const filename_s, const uint32 output_format_code)
	Get the output filename for the converted output in a given format. More...
static bool	IsCustomisableOutputFormat (const uint32 output_format_code)

Static Public Attributes
static const char *const	SBF_LOG_SUFFIX_S

Protected Member Functions
bool	SaveCommandLine (const char *filename_s, const char *command_line_s)

Protected Attributes
const char *	sbf_blast_formatter_command_s
	The command line executable used to convert between the different formats. More...

Detailed Description

This class calls a command line executable to convert a blast job between the available different formats.

The executable used is the value specified in the global Grassroots server configuration file by the

"services" -> "Blast service" -> "system_formatter_config" -> "command"

key.

Constructor & Destructor Documentation

~SystemBlastFormatter()

virtual ~SystemBlastFormatter ( )

virtual

The SystemBlastFormatter destructor.

Member Function Documentation

Create()

static SystemBlastFormatter* Create ( const json_t *  config_p )

static

Create a SystemBlastFormatter using the given configuration.

Parameters

config_p

The JSON fragment that is the value of "system_formatter_config" from within the Blast service section of the global Server configuration file.

Returns

A new SystemBlastFormatter or 0 upon error.

GetConvertedOutput()

virtual char* GetConvertedOutput ( const char *  job_id_s, const uint32  output_format_code, const char *  custom_format_s, const BlastServiceData *  data_p  )

virtual

The function gets the converted output as a c-style string using its specified command line executable.

Parameters

input_filename_s	The file that is in "BLAST archive format (ASN.1)" format.
output_format_code	The required output code.

Returns

The converted outpur or NULL upon error.

See also

BlastFormatter::GetConvertedOutput

BlastOutputFormat

GetOutputFormatAsString()

static char* GetOutputFormatAsString ( const uint32  output_format_code, const char *  custom_output_formats_s  )

static

SaveCommandLine()

bool SaveCommandLine ( const char *  filename_s, const char *  command_line_s  )

protected

Field Documentation

SBF_LOG_SUFFIX_S

const char* const SBF_LOG_SUFFIX_S

static

sbf_blast_formatter_command_s

const char* sbf_blast_formatter_command_s

protected

The command line executable used to convert between the different formats.

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The documentation for this class was generated from the following file:

• blast_formatter.h