#include <async_system_polymarker_tool.hpp>

Inheritance diagram for AsyncSystemPolymarkerTool:

Collaboration diagram for AsyncSystemPolymarkerTool:

Public Member Functions
	AsyncSystemPolymarkerTool (PolymarkerServiceJob job_p, const PolymarkerSequence seq_p, const PolymarkerServiceData *data_p)

	AsyncSystemPolymarkerTool (PolymarkerServiceJob job_p, const PolymarkerSequence seq_p, const PolymarkerServiceData data_p, const json_t root_p)

virtual	~AsyncSystemPolymarkerTool ()

virtual bool	PreRun ()
	The function that will be called before trying to run this PolymarkerTool. More...

virtual bool	PostRun ()
	The function that will be called after running this PolymarkerTool. More...

virtual char *	GetLog ()
	Get the log after the PolymarkerTool has finished running. More...

virtual char *	GetResults (PolymarkerFormatter *formatter_p)
	Get the results from the run of this PolymarkerTool. More...

virtual OperationStatus	Run ()

virtual OperationStatus	GetStatus (bool update_flag)
	Get the OperationStatus for the ServiceJob that this PolymarkerTool is running. More...

virtual bool	ParseParameters (const ParameterSet *const param_set_p)
	Parse a ParameterSet to set the variables that the PolymarkerTool's ServiceJob will run with. More...

virtual bool	AddToJSON (json_t *root_p)
	Add the required information for this PolymarkerTool to be serialised to JSON and deserialised again. More...

virtual PolymarkerToolType	GetToolType () const
	Get the PolymarkerToolType for this PolymarkerTool. More...

Public Member Functions inherited from PolymarkerTool
	PolymarkerTool (PolymarkerServiceJob job_p, const PolymarkerSequence seq_p, const PolymarkerServiceData *data_p)

	PolymarkerTool (PolymarkerServiceJob job_p, const PolymarkerSequence seq_p, const PolymarkerServiceData data_p, const json_t root_p)

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

const char *	GetName ()
	Get the name of this PolymarkerTool. More...

bool	AddSectionToResult (json_t result_p, const char const filename_s, const char const key_s, PolymarkerFormatter formatter_p)

void	SetPolymarkerSequence (const PolymarkerSequence *seq_p)
	Set the PolymarkerSequence that this PolymarkerTool will run against. More...

bool	SaveJobMetadata () const

bool	SetJobMetadata ()

bool	SetJobUUID (const uuid_t id)

void	FreePolymarkerTool (PolymarkerTool *tool_p)
	Free a given PolymarkerTool. More...

OperationStatus	RunPolymarkerTool (PolymarkerTool *tool_p)
	Run a given PolymarkerTool. More...

Protected Member Functions
bool	CreateArgs (const char input_s, char output_s, char *contigs_s)

TempFile *	GetInputFile (const char gene_id_s, const char target_chromosome_s, const char *sequence_s)

char *	GetOutputFolder ()

bool	GetStringParameter (const ParameterSet const params_p, const char param_name_s, char **param_value_ss)

void	FreeCommandLineArgs ()

bool	SetExecutable (const PolymarkerServiceData *data_p)

Protected Attributes
const char *	aspt_executable_s

char *	aspt_command_line_args_s

Protected Attributes inherited from PolymarkerTool
PolymarkerServiceJob *	pt_service_job_p
	The PolymarkerServiceJob that this PolymarkerTool will run. More...

const PolymarkerSequence *	pt_seq_p
	The PolymarkerSequence that this PolymarkerTool's ServiceJob will be running against. More...

const PolymarkerServiceData *	pt_service_data_p
	The PolymarkerServiceData for the PolymarkerService that will be running this PolymarkerTool. More...

char *	pt_job_dir_s
	The local directory where the results and logging data will be stored. More...

Additional Inherited Members
Static Protected Attributes inherited from PolymarkerTool
static const char *const	PT_JOB_DIR_S
	The key used for specifying the PolymarkerTool's job directory within and JSON-based serialisations of a PolymarkerTool. More...

Constructor & Destructor Documentation

◆ AsyncSystemPolymarkerTool() [1/2]

AsyncSystemPolymarkerTool	(	PolymarkerServiceJob *	job_p,
		const PolymarkerSequence *	seq_p,
		const PolymarkerServiceData *	data_p
	)

◆ AsyncSystemPolymarkerTool() [2/2]

AsyncSystemPolymarkerTool	(	PolymarkerServiceJob *	job_p,
		const PolymarkerSequence *	seq_p,
		const PolymarkerServiceData *	data_p,
		const json_t *	root_p
	)

◆ ~AsyncSystemPolymarkerTool()

virtual ~AsyncSystemPolymarkerTool ( )

virtual

Member Function Documentation

◆ PreRun()

virtual bool PreRun ( )

virtual

The function that will be called before trying to run this PolymarkerTool.

Returns: true if the call was successful, false otherwise

Reimplemented from PolymarkerTool.

◆ PostRun()

virtual bool PostRun ( )

virtual

The function that will be called after running this PolymarkerTool.

Returns: true if the call was successful, false otherwise

Implements PolymarkerTool.

◆ GetLog()

virtual char* GetLog ( )

virtual

Get the log after the PolymarkerTool has finished running.

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

Implements PolymarkerTool.

◆ GetResults()

virtual char* GetResults ( PolymarkerFormatter * formatter_p )

virtual

Get the results from the run of this PolymarkerTool.

Parameters

formatter_p The PolymarkerFormatter used to

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

Implements PolymarkerTool.

◆ Run()

virtual OperationStatus Run ( )

virtual

Implements PolymarkerTool.

◆ GetStatus()

virtual OperationStatus GetStatus ( bool update_flag )

virtual

Get the OperationStatus for the ServiceJob that this PolymarkerTool is running.

Parameters

update_flag If this is true, then the ServiceJob will be checked for its latest status. If this is false, then the last cached value will be used.

Returns: The OperationStatus for this PolymarkerTool's ServiceJob.

Implements PolymarkerTool.

◆ ParseParameters()

virtual bool ParseParameters ( const ParameterSet *const param_set_p )

virtual

Parse a ParameterSet to set the variables that the PolymarkerTool's ServiceJob will run with.

Parameters

param_set_p The ParameterSet that the variables will be set from.

Returns: true if the required variables were collected successfully, false otherwise

Implements PolymarkerTool.

◆ AddToJSON()

virtual bool AddToJSON ( json_t * root_p )

virtual

Add the required information for this PolymarkerTool to be serialised to JSON and deserialised again.

This is called by each child class of PolymarkerTool all the way down to the actual PolymarkerTool child object that is being used.

Parameters

root_p The JSON fragment that the required details will be added to

Returns: true if the information was added successfully, false otherwise

Reimplemented from PolymarkerTool.

◆ GetToolType()

virtual PolymarkerToolType GetToolType ( ) const

virtual

Get the PolymarkerToolType for this PolymarkerTool.

Returns: The PolymarkerToolType.

Implements PolymarkerTool.

◆ CreateArgs()

bool CreateArgs	(	const char *	input_s,
		char *	output_s,
		char *	contigs_s
	)

protected

◆ GetInputFile()

TempFile* GetInputFile	(	const char *	gene_id_s,
		const char *	target_chromosome_s,
		const char *	sequence_s
	)

protected

◆ GetOutputFolder()

char* GetOutputFolder ( )

protected

◆ GetStringParameter()

bool GetStringParameter	(	const ParameterSet *const	params_p,
		const char *	param_name_s,
		char **	param_value_ss
	)

protected

◆ FreeCommandLineArgs()

void FreeCommandLineArgs ( )

protected

◆ SetExecutable()

bool SetExecutable ( const PolymarkerServiceData * data_p )

protected

Field Documentation

◆ aspt_executable_s

const char* aspt_executable_s

protected

◆ aspt_command_line_args_s

char* aspt_command_line_args_s

protected

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

async_system_polymarker_tool.hpp

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ AsyncSystemPolymarkerTool() [1/2]

◆ AsyncSystemPolymarkerTool() [2/2]

◆ ~AsyncSystemPolymarkerTool()

Member Function Documentation

◆ PreRun()

◆ PostRun()

◆ GetLog()

◆ GetResults()

◆ Run()

◆ GetStatus()

◆ ParseParameters()

◆ AddToJSON()

◆ GetToolType()

◆ CreateArgs()

◆ GetInputFile()

◆ GetOutputFolder()

◆ GetStringParameter()

◆ FreeCommandLineArgs()

◆ SetExecutable()

Field Documentation

◆ aspt_executable_s

◆ aspt_command_line_args_s