The base class for running Blast. More...

#include <blast_tool.hpp>

Inheritance diagram for BlastTool:

Public Member Functions
	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 OperationStatus	Run ()=0
	Run this BlastTool. More...

virtual bool	ParseParameters (ParameterSet param_set_p, BlastAppParameters app_params_p)=0
	Parse a ParameterSet to configure a BlastTool prior to it being ran. More...

virtual bool	SetInputFilename (const char *const filename_s)=0
	Set the input filename for the BlastTool to use. More...

virtual bool	SetUpOutputFile ()=0
	Set the output file parameter. 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 OperationStatus	GetStatus (bool update_flag=true)
	Get the status of a BlastTool. More...

virtual char *	GetResults (BlastFormatter *formatter_p)=0
	Get the results after the ExternalBlastTool has finished running. More...

virtual char *	GetLog ()=0
	Get the log after the BlastTool has finished running. 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 Member Functions
virtual bool	AddToJSON (json_t *root_p)
	This method is used to serialise this BlastTool so that it can be recreated from another calling process when required. More...

Protected Attributes
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...

Detailed Description

The base class for running Blast.

Constructor & Destructor Documentation

◆ BlastTool() [1/2]

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.

Parameters

job_p	The ServiceJob to associate with this BlastTool.
name_s	The name to give to this BlastTool.
data_p	The BlastServiceData for the Service that will run this BlastTool.
factory_s	The name of the BlastToolFactory that created this BlastTool.
output_format	The output format that this BlastTool will produce its results in.

See also: BlastServiceJob

◆ BlastTool() [2/2]

BlastTool	(	BlastServiceJob *	job_p,
		const BlastServiceData *	data_p,
		const json_t *	json_p
	)

Create a BlastTool for a given ServiceJob.

Parameters

job_p	The ServiceJob to associate with this BlastTool.
data_p	The BlastServiceData for the Service that will run this BlastTool.
json_p	The JSON fragment representing a serialised version of the BlastTool.

See also: BlastServiceJob

◆ ~BlastTool()

virtual ~BlastTool ( )

virtual

The BlastTool destructor,.

Member Function Documentation

◆ GetOutputFormat()

uint32 GetOutputFormat ( ) const

Get the output format code that this BlastTool will produce its results in.

Returns: The output format code.

◆ Run()

virtual OperationStatus Run ( )

pure virtual

Run this BlastTool.

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

Implemented in DrmaaBlastTool, SystemBlastTool, AsyncSystemBlastTool, and ThreadedBlastTool.

◆ ParseParameters()

virtual bool ParseParameters	(	ParameterSet *	param_set_p,
		BlastAppParameters *	app_params_p
	)

pure virtual

Parse a ParameterSet to configure a BlastTool prior to it being ran.

Parameters

param_set_p	The ParameterSet to parse.
app_params_p	The BlastAppParameters to use process the values from the given ParameterSe

Returns: true if the BlastTool was configured successfully and is ready to be ran, false otherwise.

Implemented in SystemBlastTool, and ExternalBlastTool.

◆ SetInputFilename()

virtual bool SetInputFilename ( const char *const filename_s )

pure virtual

Set the input filename for the BlastTool to use.

Parameters

filename_s The filename.

Returns: true if the input filename was set successfully, false otherwise.

Implemented in ExternalBlastTool.

◆ SetUpOutputFile()

virtual bool SetUpOutputFile ( )

pure virtual

Set the output file parameter.

Returns: true if the input filename was set successfully, false otherwise.

Implemented in DrmaaBlastTool, and ExternalBlastTool.

◆ PreRun()

virtual bool PreRun ( )

virtual

Any custom functionality required before running a BlastTool.

Reimplemented in AsyncSystemBlastTool.

◆ PostRun()

virtual void PostRun ( )

virtual

Any custom functionality required after running a BlastTool.

◆ GetStatus()

virtual OperationStatus GetStatus ( bool update_flag = true )

virtual

Get the status of a BlastTool.

Parameters

update_flag if this is true then the BlastTool 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 BlastTool.

Reimplemented in DrmaaBlastTool, AsyncSystemBlastTool, SystemBlastTool, and ThreadedBlastTool.

◆ GetResults()

virtual char* GetResults ( BlastFormatter * formatter_p )

pure virtual

Get the results after the ExternalBlastTool 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.

Implemented in ExternalBlastTool, AsyncSystemBlastTool, and ThreadedBlastTool.

◆ GetLog()

virtual char* GetLog ( )

pure virtual

Get the log after the BlastTool has finished running.

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

Implemented in ExternalBlastTool.

◆ AddErrorDetails()

virtual bool AddErrorDetails ( )

virtual

◆ GetUUID()

const uuid_t& GetUUID ( ) const

Get the uuid for the ServiceJob that this BlastTool is linked with.

Returns: The uuid of the corresponding ServiceJob for this BlastTool.

◆ GetName()

const char* GetName ( ) const

Get the name asssociated with this BlastTool.

Returns: The name.

◆ GetAsJSON()

json_t* GetAsJSON ( )

Get the JSON-based persistent description of this BlastTool.

This allows the BlastTool to be recreated in another process or thread.

Returns: The json_t description of this BlastTool or 0 upon error.

◆ GetFactoryName()

const char* GetFactoryName ( ) const

Get the name of the BlastToolFactory that created this BlastTool.

Returns: The name of the BlastToolFactory.

◆ SetCustomOutputColumns()

bool SetCustomOutputColumns ( const char * custom_columns_s )

◆ AddToJSON()

virtual bool AddToJSON ( json_t * root_p )

protectedvirtual

This method is used to serialise this BlastTool so that it can be recreated from another calling process when required.

This is used to store the BlastTool in the JobsManager.

Parameters

root_p The json object to add the serialisation of this BlastTool to.

Returns: true if the BlastTool was serialised successfully, false otherwise.

Reimplemented in ExternalBlastTool, DrmaaBlastTool, and AsyncSystemBlastTool.

◆ FreeBlastTool()

void FreeBlastTool ( BlastTool * tool_p )

Free a BlastTool.

Parameters

tool_p The BlastTool to deallocate.

◆ RunBlast()

OperationStatus RunBlast ( BlastTool * tool_p )

Run Blast using the parameters that have been previously using ConvertArguments.

Parameters

tool_p The BlastTool to use.

Returns: true if the tool completed successfully, false otherwise.

◆ GetBlastStatus()

OperationStatus GetBlastStatus ( BlastTool * tool_p )

Get the current OperationStatus of a BlastTool.

Parameters

tool_p The BlastTool to check.

Returns: The current OperationStatus.

◆ IsBlastToolSynchronous()

bool IsBlastToolSynchronous ( BlastTool * tool_p )

Is the BlastTool going to run asynchronously?

Parameters

tool_p The BlastTool to check.

Returns: true if the tool will run asynchronously, false otherwise.

Field Documentation

◆ bt_output_format

uint32 bt_output_format

protected

The output format code to use.

◆ bt_custom_output_columns_s

char* bt_custom_output_columns_s

protected

Any custom columns for tabular output formats.

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

blast_tool.hpp

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ BlastTool() [1/2]

◆ BlastTool() [2/2]

◆ ~BlastTool()

Member Function Documentation

◆ GetOutputFormat()

◆ Run()

◆ ParseParameters()

◆ SetInputFilename()

◆ SetUpOutputFile()

◆ PreRun()

◆ PostRun()

◆ GetStatus()

◆ GetResults()

◆ GetLog()

◆ AddErrorDetails()

◆ GetUUID()

◆ GetName()

◆ GetAsJSON()

◆ GetFactoryName()

◆ SetCustomOutputColumns()

◆ AddToJSON()

◆ FreeBlastTool()

◆ RunBlast()

◆ GetBlastStatus()

◆ IsBlastToolSynchronous()

Field Documentation

◆ bt_output_format

◆ bt_custom_output_columns_s