A class that will run Blast within a pthread. More...

#include <threaded_blast_tool.hpp>

Inheritance diagram for ThreadedBlastTool:

Collaboration diagram for ThreadedBlastTool:

Public Member Functions
	ThreadedBlastTool (BlastServiceJob service_job_p, const char name_s, const char factory_s, const BlastServiceData data_p, const char *blast_program_name_s)
	Create a new ThreadedBlastTool. More...

virtual	~ThreadedBlastTool ()
	The ThreadedBlastTool destructor. More...

virtual OperationStatus	Run ()
	Run this ThreadedBlastTool. More...

virtual char *	GetResults (BlastFormatter *formatter_p)
	Get the results after the ThreadedBlastTool has finished running. More...

virtual OperationStatus	GetStatus (bool update_flag=true)
	Get the status of a ThreadedBlastTool. More...

Public Member Functions inherited from SystemBlastTool
	SystemBlastTool (BlastServiceJob service_job_p, const char name_s, const char factory_s, const BlastServiceData data_p, const char *blast_program_name_s)
	Create a SystemBlastTool for a given ServiceJob. More...

	SystemBlastTool (BlastServiceJob job_p, const BlastServiceData data_p, const json_t *json_p)
	Create a SystemBlastTool for a given ServiceJob using the configuration details from a serialised JSON fragment. More...

virtual	~SystemBlastTool ()
	The SystemBlastTool destructor. More...

virtual bool	ParseParameters (ParameterSet params_p, BlastAppParameters app_params_p)
	Parse a ParameterSet to configure a BlastTool prior to it being ran. More...

Public Member Functions inherited from ExternalBlastTool
	ExternalBlastTool (BlastServiceJob job_p, const char name_s, const char factory_s, const BlastServiceData data_p, const char *blast_program_name_s, const bool async_flag)
	Create a ExternalBlastTool for a given ServiceJob. More...

	ExternalBlastTool (BlastServiceJob job_p, const BlastServiceData data_p, const json_t *json_p)
	Create a ExternalBlastTool for a given ServiceJob using the configuration details from a serialised JSON fragment. More...

virtual	~ExternalBlastTool ()
	The ExternalBlastTool destructor. More...

virtual bool	SetInputFilename (const char *const filename_s)
	Set the input filename for the BlastTool to use. More...

virtual bool	SetUpOutputFile ()
	Set the output file parameter. More...

virtual char *	GetLog ()
	Get a copy of the log data from the run of this ExternalBlastTool's run. More...

Public Member Functions inherited from BlastTool
	BlastTool (BlastServiceJob job_p, const char name_s, const char factory_s, const BlastServiceData data_p, const uint32 output_format, const char *custom_output_s)
	Create a BlastTool for a given ServiceJob. More...

	BlastTool (BlastServiceJob job_p, const BlastServiceData data_p, const json_t *json_p)
	Create a BlastTool for a given ServiceJob. More...

virtual	~BlastTool ()
	The BlastTool destructor,. More...

uint32	GetOutputFormat () const
	Get the output format code that this BlastTool will produce its results in. More...

virtual bool	PreRun ()
	Any custom functionality required before running a BlastTool. More...

virtual void	PostRun ()
	Any custom functionality required after running a BlastTool. More...

virtual bool	AddErrorDetails ()

const uuid_t &	GetUUID () const
	Get the uuid for the ServiceJob that this BlastTool is linked with. More...

const char *	GetName () const
	Get the name asssociated with this BlastTool. More...

json_t *	GetAsJSON ()
	Get the JSON-based persistent description of this BlastTool. More...

const char *	GetFactoryName () const
	Get the name of the BlastToolFactory that created this BlastTool. More...

bool	SetCustomOutputColumns (const char *custom_columns_s)

void	FreeBlastTool (BlastTool *tool_p)
	Free a BlastTool. More...

OperationStatus	RunBlast (BlastTool *tool_p)
	Run Blast using the parameters that have been previously using ConvertArguments. More...

OperationStatus	GetBlastStatus (BlastTool *tool_p)
	Get the current OperationStatus of a BlastTool. More...

bool	IsBlastToolSynchronous (BlastTool *tool_p)
	Is the BlastTool going to run asynchronously? More...

Protected Attributes
pthread_t *	tbt_thread_p
	The pthread to run this BlastTool in. More...

pthread_mutex_t *	tbt_mutex_p
	The mutex to use to moderate access to the pthread. More...

int	tbt_thread_id
	The id of the pthread to run this BlastTool in. More...

Protected Attributes inherited from SystemBlastTool
ByteBufferArgsProcessor *	sbt_args_processor_p

Protected Attributes inherited from ExternalBlastTool
char *	ebt_results_filename_s
	The filename which the Blast results will be written to if the job runs successfully. More...

char *	ebt_working_directory_s
	The working directory where all of the input, output and log files will be created. More...

char *	ebt_blast_s
	The name of the blast command line executable to use. More...

bool	ebt_async_flag
	If this is `true`, then the ExternalBlastTool will run asynchronously. More...

Protected Attributes inherited from BlastTool
uint32	bt_output_format
	The output format code to use. More...

char *	bt_custom_output_columns_s
	Any custom columns for tabular output formats. More...

Additional Inherited Members
Static Public Attributes inherited from ExternalBlastTool
static const char *const	EBT_INPUT_SUFFIX_S
	This is the string that will get appended to each input file used by the ExternalBlastTool. More...

static const char *const	EBT_ASYNC_S
	This is the string that will get appended to each log file created when an ExternalBlastTool is ran. More...

Protected Member Functions inherited from SystemBlastTool
virtual ArgsProcessor *	GetArgsProcessor ()
	Get the ArgsProcessor that this BlastTool will use to parse the input ParameterSet prior to running its job. More...

bool	Init (const char *prog_s)
	Initialise the SystemBlastTool prior to it being run. More...

bool	SaveCommandLine (const char *command_line_s)

Protected Member Functions inherited from ExternalBlastTool
virtual bool	AddBlastArg (const char *const arg_s, const bool hyphen_flag)
	Add the argument to the command line arguments that this BlastTool will run with. More...

virtual bool	AddBlastArgsPair (const char key_s, const char value_s)
	Add a pair of arguments to the command line arguments that this BlastTool will run with. More...

char *	GetJobFilename (const char const prefix_s, const char const suffix_s)
	Create the filename to use for a ServiceJob. More...

virtual bool	AddToJSON (json_t *root_p)
	This method is used to serialise this ExternalBlastTool so that it can be recreated from another calling process when required. More...

Detailed Description

A class that will run Blast within a pthread.

Constructor & Destructor Documentation

◆ ThreadedBlastTool()

ThreadedBlastTool	(	BlastServiceJob *	service_job_p,
		const char *	name_s,
		const char *	factory_s,
		const BlastServiceData *	data_p,
		const char *	blast_program_name_s
	)

Create a new ThreadedBlastTool.

Parameters

service_job_p	The ServiceJob to associate with this ExternalBlastTool.
name_s	The name to give to this ExternalBlastTool.
factory_s	The name of the BlastToolFactory that is creating this ExternalBlastTool.
data_p	The BlastServiceData for the Service that will run this ExternalBlastTool.
blast_program_name_s	The name of blast command line executable that this ExternalBlastTool will call to run its blast job.

◆ ~ThreadedBlastTool()

virtual ~ThreadedBlastTool ( )

virtual

The ThreadedBlastTool destructor.

Member Function Documentation

◆ Run()

virtual OperationStatus Run ( )

virtual

Run this ThreadedBlastTool.

Returns: The OperationStatus of this ThreadedBlastTool after it has started running.

Reimplemented from SystemBlastTool.

◆ GetResults()

virtual char* GetResults ( BlastFormatter * formatter_p )

virtual

Get the results after the ThreadedBlastTool has finished running.

Parameters

formatter_p The BlastFormatter to convert the results into a different format. If this is 0, then the results will be returned without any conversion.

Returns: The results as a c-style string or 0 upon error.

Reimplemented from ExternalBlastTool.

◆ GetStatus()

virtual OperationStatus GetStatus ( bool update_flag = true )

virtual

Get the status of a ThreadedBlastTool.

Parameters

update_flag if this is true then the ThreadedBlastTool will check the status of its running jobs if necessary, if this is false it will return the last cached value.

Returns: The OperationStatus of this ThreadedBlastTool.

Reimplemented from SystemBlastTool.

Field Documentation

◆ tbt_thread_p

pthread_t* tbt_thread_p

protected

The pthread to run this BlastTool in.

◆ tbt_mutex_p

pthread_mutex_t* tbt_mutex_p

protected

The mutex to use to moderate access to the pthread.

◆ tbt_thread_id

int tbt_thread_id

protected

The id of the pthread to run this BlastTool in.

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

threaded_blast_tool.hpp

Public Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ ThreadedBlastTool()

◆ ~ThreadedBlastTool()

Member Function Documentation

◆ Run()

◆ GetResults()

◆ GetStatus()

Field Documentation

◆ tbt_thread_p

◆ tbt_mutex_p

◆ tbt_thread_id