A class that will run Blast using an external application such as blastn rather than calling Blast library routines directly. More...

#include <external_blast_tool.hpp>

Inheritance diagram for ExternalBlastTool:

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Collaboration diagram for ExternalBlastTool:

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Public Member Functions
	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	ParseParameters (ParameterSet param_set_p, BlastAppParameters app_params_p)
	Parse a ParameterSet to configure a ExternalBlastTool prior to it being ran. 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 *	GetResults (BlastFormatter *formatter_p)
	Get the results after the ExternalBlastTool has finished running. 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 OperationStatus	Run ()=0
	Run this BlastTool. 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 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...

Static Public Attributes
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
virtual ArgsProcessor *	GetArgsProcessor ()=0
	Get the ArgsProcessor that this BlastTool will use to parse the input ParameterSet prior to running its job. More...

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...

Protected Attributes
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...

Detailed Description

A class that will run Blast using an external application such as blastn rather than calling Blast library routines directly.

Constructor & Destructor Documentation

◆ ExternalBlastTool() [1/2]

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.

Parameters

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.

◆ ExternalBlastTool() [2/2]

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.

Parameters

job_p	The ServiceJob to associate with this ExternalBlastTool.
data_p	The BlastServiceData for the Service that will run this ExternalBlastTool.
json_p	The JSON fragment to fill in the serialised values such as job name, etc.

◆ ~ExternalBlastTool()

virtual ~ExternalBlastTool ( )

virtual

The ExternalBlastTool destructor.

Member Function Documentation

◆ ParseParameters()

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

virtual

Parse a ParameterSet to configure a ExternalBlastTool 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 ParameterSet.

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

See also: BlastTool::ParseParameters

Implements BlastTool.

Reimplemented in SystemBlastTool.

◆ SetInputFilename()

virtual bool SetInputFilename ( const char *const filename_s )

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.

Implements BlastTool.

◆ SetUpOutputFile()

virtual bool SetUpOutputFile ( )

virtual

Set the output file parameter.

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

Implements BlastTool.

Reimplemented in DrmaaBlastTool.

◆ GetResults()

virtual char* GetResults ( BlastFormatter * formatter_p )

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.

Implements BlastTool.

Reimplemented in AsyncSystemBlastTool, and ThreadedBlastTool.

◆ GetLog()

virtual char* GetLog ( )

virtual

Get a copy of the log data from the run of this ExternalBlastTool's run.

Returns: The log data or 0 upon error. If a valid value is returned, this will need to be freed by FreeCopiedString to avoid a memory leak.

See also: FreeCopiedString

Implements BlastTool.

◆ GetArgsProcessor()

virtual ArgsProcessor* GetArgsProcessor ( )

protectedpure virtual

Get the ArgsProcessor that this BlastTool will use to parse the input ParameterSet prior to running its job.

Returns: The ArgsProcessor for this BlastTool or 0 upon error.

Implemented in DrmaaBlastTool, and SystemBlastTool.

◆ AddBlastArg()

virtual bool AddBlastArg	(	const char *const	arg_s,
		const bool	hyphen_flag
	)

protectedvirtual

Add the argument to the command line arguments that this BlastTool will run with.

Parameters

arg_s	The argument to add.
hyphen_flag	If this is `true` then a hyphen will be prefixed the given value e.g. turning "foo" into "-foo" before being added, if this is `false` then the argument is added unaltered.

Returns: true if the argument was added successfully, false otherwise.

Reimplemented in DrmaaBlastTool.

◆ AddBlastArgsPair()

virtual bool AddBlastArgsPair	(	const char *	key_s,
		const char *	value_s
	)

protectedvirtual

Add a pair of arguments to the command line arguments that this BlastTool will run with.

Parameters

key_s	The first argument to add.
value_s	The second argument to add.

Returns: true if the arguments were added successfully, false otherwise.

◆ GetJobFilename()

char* GetJobFilename	(	const char *const	prefix_s,
		const char *const	suffix_s
	)

protected

Create the filename to use for a ServiceJob.

Parameters

prefix_s	The prefix to use for the filename.
suffix_s	The suffix to use from a set of constants.

Returns: The filename or 0 upon error.

See also: EBT_INPUT_SUFFIX_S; EBT_LOG_SUFFIX_S; BS_OUTPUT_SUFFIX_S

◆ AddToJSON()

virtual bool AddToJSON ( json_t * root_p )

protectedvirtual

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

This is used to store the ExternalBlastTool in the JobsManager.

Parameters

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

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

Reimplemented from BlastTool.

Reimplemented in DrmaaBlastTool, and AsyncSystemBlastTool.

Field Documentation

◆ EBT_INPUT_SUFFIX_S

const char* const EBT_INPUT_SUFFIX_S

static

This is the string that will get appended to each input file used by the ExternalBlastTool.

◆ EBT_ASYNC_S

const char* const EBT_ASYNC_S

static

This is the string that will get appended to each log file created when an ExternalBlastTool is ran.

This is the string identifier to use to set whether the ExternalBlastTool will run synchronously or asynchronously.

◆ ebt_results_filename_s

char* ebt_results_filename_s

protected

The filename which the Blast results will be written to if the job runs successfully.

◆ ebt_working_directory_s

char* ebt_working_directory_s

protected

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

◆ ebt_blast_s

char* ebt_blast_s

protected

The name of the blast command line executable to use.

◆ ebt_async_flag

bool ebt_async_flag

protected

If this is true, then the ExternalBlastTool will run asynchronously.

If it is false, then the ExternalBlastTool will run synchronously.

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

external_blast_tool.hpp

Public Member Functions

Static Public Attributes

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ ExternalBlastTool() [1/2]

◆ ExternalBlastTool() [2/2]

◆ ~ExternalBlastTool()

Member Function Documentation

◆ ParseParameters()

◆ SetInputFilename()

◆ SetUpOutputFile()

◆ GetResults()

◆ GetLog()

◆ GetArgsProcessor()

◆ AddBlastArg()

◆ AddBlastArgsPair()

◆ GetJobFilename()

◆ AddToJSON()

Field Documentation

◆ EBT_INPUT_SUFFIX_S

◆ EBT_ASYNC_S

◆ ebt_results_filename_s

◆ ebt_working_directory_s

◆ ebt_blast_s

◆ ebt_async_flag