blast_service_job_markup.h File Reference

#include "blast_service.h"
#include "blast_service_api.h"
#include "typedefs.h"
#include "linked_list.h"
#include "jansson.h"

Include dependency graph for blast_service_job_markup.h:

Go to the source code of this file.

Enumerations
enum	Strand { ST_NONE, ST_FORWARD, ST_REVERSE }
	Which strand is being used to for positioning purposes. More...

Functions
bool	GetAndAddHitLocation (json_t *marked_up_result_p, const json_t *hsps_p, const char *hsp_from_key_s, const char *hsp_to_key_s, const char *strand_key_s, const char *child_key_s)
bool	AddHitLocation (json_t *parent_p, const char *child_key_s, const int32 from, const int32 to, const Strand strand)
LinkedList *	GetScaffoldsFromHit (const json_t *hit_p, const DatabaseInfo *db_p)
bool	MarkUpHit (const json_t *hit_p, json_t *mark_up_p, const DatabaseInfo *db_p)
json_t *	GetInitialisedProcessedRequest (void)
bool	AddSequence (json_t *root_p, const char *key_s, const char *query_sequence_s)
bool	AddFaldoTerminus (json_t *parent_json_p, const char *child_key_s, const int32 position, const Strand strand)
bool	AddIntScoreValue (json_t *parent_p, const char *key_s, int score_value)
bool	AddDoubleScoreValue (json_t *parent_p, const char *key_s, double64 score_value)
bool	GetAndAddDoubleScoreValue (json_t *marked_up_result_p, const json_t *hsps_p, const char *hsp_key_s, const char *marked_up_key_s)
bool	GetAndAddIntScoreValue (json_t *marked_up_result_p, const json_t *hsps_p, const char *hsp_key_s, const char *marked_up_key_s)
bool	GetAndAddSequenceValue (json_t *marked_up_result_p, const json_t *hsps_p, const char *hsp_key_s, const char *sequence_key_s)
bool	GetAndAddDatabaseDetails (json_t *marked_up_result_p, const DatabaseInfo *database_p)
bool	GetAndAddQueryMetadata (const json_t *blast_search_p, json_t *mark_up_p)
bool	AddHitDetails (json_t *marked_up_result_p, const json_t *blast_hit_p, const DatabaseInfo *db_p)
bool	AddSubsequenceMarkup (json_t *parent_p, const char *key_s, const char *subsequence_start_s, const uint32 length)
bool	GetAndAddNucleotidePolymorphisms (json_t *marked_up_hsp_p, const char *reference_sequence_s, const char *hit_sequence_s, const char *midline_s, uint32 hit_index, const int32 inc_value)
bool	AddPolymorphism (json_t *marked_up_hsp_p, const char *hit_gap_start_p, const char *reference_gap_start_p, const uint32 start_of_region, const uint32 end_of_region)
const char *	GetDatabaseNameFromMarkedUpJob (const json_t *marked_up_report_p)
bool	GetAndAddScaffoldsParameter (LinkedService *linked_service_p, json_t *hit_p, ParameterSet *output_params_p)
bool	GetAndAddSequencesParameter (LinkedService *linked_service_p, json_t *hit_p, ParameterSet *output_params_p)
json_t *	ConvertBlastResultToGrassrootsMarkUp (const json_t *blast_job_output_p, BlastServiceData *data_p)
json_t *	GetMarkupReports (json_t *markup_p)
json_t *	GetHitsFromMarkedUpReport (json_t *report_p)
bool	GetAndAddScaffoldsFromHit (const json_t *hit_p, json_t *mark_up_p, const DatabaseInfo *db_p)
bool	GetAndAddSequenceMappedParameter (LinkedService *linked_service_p, const json_t *hit_p, ParameterSet *output_params_p, json_t *request_p)

Enumeration Type Documentation

Strand

enum Strand

Which strand is being used to for positioning purposes.

Enumerator
ST_NONE	ST_NONE.
ST_FORWARD	ST_FORWARD.
ST_REVERSE	ST_REVERSE.

Function Documentation

GetAndAddHitLocation()

bool GetAndAddHitLocation	(	json_t *	marked_up_result_p,
		const json_t *	hsps_p,
		const char *	hsp_from_key_s,
		const char *	hsp_to_key_s,
		const char *	strand_key_s,
		const char *	child_key_s
	)

AddHitLocation()

bool AddHitLocation	(	json_t *	parent_p,
		const char *	child_key_s,
		const int32	from,
		const int32	to,
		const Strand	strand
	)

GetScaffoldsFromHit()

LinkedList* GetScaffoldsFromHit	(	const json_t *	hit_p,
		const DatabaseInfo *	db_p
	)

MarkUpHit()

bool MarkUpHit	(	const json_t *	hit_p,
		json_t *	mark_up_p,
		const DatabaseInfo *	db_p
	)

GetInitialisedProcessedRequest()

json_t* GetInitialisedProcessedRequest

(

void

)

AddSequence()

bool AddSequence	(	json_t *	root_p,
		const char *	key_s,
		const char *	query_sequence_s
	)

AddFaldoTerminus()

bool AddFaldoTerminus	(	json_t *	parent_json_p,
		const char *	child_key_s,
		const int32	position,
		const Strand	strand
	)

AddIntScoreValue()

bool AddIntScoreValue	(	json_t *	parent_p,
		const char *	key_s,
		int	score_value
	)

AddDoubleScoreValue()

bool AddDoubleScoreValue	(	json_t *	parent_p,
		const char *	key_s,
		double64	score_value
	)

GetAndAddDoubleScoreValue()

bool GetAndAddDoubleScoreValue	(	json_t *	marked_up_result_p,
		const json_t *	hsps_p,
		const char *	hsp_key_s,
		const char *	marked_up_key_s
	)

GetAndAddIntScoreValue()

bool GetAndAddIntScoreValue	(	json_t *	marked_up_result_p,
		const json_t *	hsps_p,
		const char *	hsp_key_s,
		const char *	marked_up_key_s
	)

GetAndAddSequenceValue()

bool GetAndAddSequenceValue	(	json_t *	marked_up_result_p,
		const json_t *	hsps_p,
		const char *	hsp_key_s,
		const char *	sequence_key_s
	)

GetAndAddDatabaseDetails()

bool GetAndAddDatabaseDetails	(	json_t *	marked_up_result_p,
		const DatabaseInfo *	database_p
	)

GetAndAddQueryMetadata()

bool GetAndAddQueryMetadata	(	const json_t *	blast_search_p,
		json_t *	mark_up_p
	)

AddHitDetails()

bool AddHitDetails	(	json_t *	marked_up_result_p,
		const json_t *	blast_hit_p,
		const DatabaseInfo *	db_p
	)

AddSubsequenceMarkup()

bool AddSubsequenceMarkup	(	json_t *	parent_p,
		const char *	key_s,
		const char *	subsequence_start_s,
		const uint32	length
	)

GetAndAddNucleotidePolymorphisms()

bool GetAndAddNucleotidePolymorphisms	(	json_t *	marked_up_hsp_p,
		const char *	reference_sequence_s,
		const char *	hit_sequence_s,
		const char *	midline_s,
		uint32	hit_index,
		const int32	inc_value
	)

AddPolymorphism()

bool AddPolymorphism	(	json_t *	marked_up_hsp_p,
		const char *	hit_gap_start_p,
		const char *	reference_gap_start_p,
		const uint32	start_of_region,
		const uint32	end_of_region
	)

GetDatabaseNameFromMarkedUpJob()

const char* GetDatabaseNameFromMarkedUpJob

(

const json_t *

marked_up_report_p

)

GetAndAddScaffoldsParameter()

bool GetAndAddScaffoldsParameter	(	LinkedService *	linked_service_p,
		json_t *	hit_p,
		ParameterSet *	output_params_p
	)

GetAndAddSequencesParameter()

bool GetAndAddSequencesParameter	(	LinkedService *	linked_service_p,
		json_t *	hit_p,
		ParameterSet *	output_params_p
	)

ConvertBlastResultToGrassrootsMarkUp()

json_t* ConvertBlastResultToGrassrootsMarkUp	(	const json_t *	blast_job_output_p,
		BlastServiceData *	data_p
	)

GetMarkupReports()

json_t* GetMarkupReports

(

json_t *

markup_p

)

GetHitsFromMarkedUpReport()

json_t* GetHitsFromMarkedUpReport

(

json_t *

report_p

)

GetAndAddScaffoldsFromHit()

bool GetAndAddScaffoldsFromHit	(	const json_t *	hit_p,
		json_t *	mark_up_p,
		const DatabaseInfo *	db_p
	)

GetAndAddSequenceMappedParameter()

bool GetAndAddSequenceMappedParameter	(	LinkedService *	linked_service_p,
		const json_t *	hit_p,
		ParameterSet *	output_params_p,
		json_t *	request_p
	)