blast_service_job_markup.h

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/*
 * blast_service_job_markup.h
 *
 *  Created on: 17 Jan 2017
 *      Author: billy
 *
 * @file
 */
 
#ifndef SERVER_SRC_SERVICES_BLAST_INCLUDE_BLAST_SERVICE_JOB_MARKUP_H_
#define SERVER_SRC_SERVICES_BLAST_INCLUDE_BLAST_SERVICE_JOB_MARKUP_H_
 
#include "blast_service.h"
#include "blast_service_api.h"
#include "typedefs.h"
#include "linked_list.h"
 
#include "jansson.h"
 
typedef enum Strand
{
  ST_NONE,   
  ST_FORWARD,
  ST_REVERSE 
} Strand;
 
 
#ifdef __cplusplus
extern "C"
{
#endif
 
 
BLAST_SERVICE_LOCAL 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);
 
 
BLAST_SERVICE_LOCAL bool AddHitLocation (json_t *parent_p, const char *child_key_s, const int32 from, const int32 to, const Strand strand);
 
BLAST_SERVICE_LOCAL LinkedList *GetScaffoldsFromHit (const json_t *hit_p, const DatabaseInfo *db_p);
 
BLAST_SERVICE_LOCAL bool MarkUpHit (const json_t *hit_p, json_t *mark_up_p, const DatabaseInfo *db_p);
 
BLAST_SERVICE_LOCAL json_t *GetInitialisedProcessedRequest (void);
 
 
 
BLAST_SERVICE_LOCAL bool AddSequence (json_t *root_p, const char *key_s, const char *query_sequence_s);
 
BLAST_SERVICE_LOCAL bool AddFaldoTerminus (json_t *parent_json_p, const char *child_key_s, const int32 position, const Strand strand);
 
BLAST_SERVICE_LOCAL bool AddIntScoreValue (json_t *parent_p, const char *key_s, int score_value);
 
BLAST_SERVICE_LOCAL bool AddDoubleScoreValue (json_t *parent_p, const char *key_s, double64 score_value);
 
 
BLAST_SERVICE_LOCAL bool GetAndAddDoubleScoreValue (json_t *marked_up_result_p, const json_t *hsps_p, const char *hsp_key_s, const char *marked_up_key_s);
 
BLAST_SERVICE_LOCAL bool GetAndAddIntScoreValue (json_t *marked_up_result_p, const json_t *hsps_p, const char *hsp_key_s, const char *marked_up_key_s);
 
BLAST_SERVICE_LOCAL bool GetAndAddSequenceValue (json_t *marked_up_result_p, const json_t *hsps_p, const char *hsp_key_s, const char *sequence_key_s);
 
BLAST_SERVICE_LOCAL bool GetAndAddDatabaseDetails (json_t *marked_up_result_p, const DatabaseInfo *database_p);
 
BLAST_SERVICE_LOCAL bool GetAndAddQueryMetadata (const json_t *blast_search_p, json_t *mark_up_p);
 
 
BLAST_SERVICE_LOCAL bool AddHitDetails (json_t *marked_up_result_p, const json_t *blast_hit_p, const DatabaseInfo *db_p);
 
 
BLAST_SERVICE_LOCAL bool AddSubsequenceMarkup (json_t *parent_p, const char *key_s, const char *subsequence_start_s, const uint32 length);
 
BLAST_SERVICE_LOCAL 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);
 
BLAST_SERVICE_LOCAL 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);
 
 
BLAST_SERVICE_LOCAL const char *GetDatabaseNameFromMarkedUpJob (const json_t *marked_up_report_p);
 
 
BLAST_SERVICE_LOCAL bool AddHsp (json_t *marked_up_hit_p, const json_t *hsp_p);
 
 
BLAST_SERVICE_LOCAL bool GetAndAddDatabaseMappedParameter (LinkedService *linked_service_p, const json_t *report_p, ParameterSet *output_params_p, const char **database_ss);
 
 
BLAST_SERVICE_LOCAL bool GetAndAddScaffoldsParameter (LinkedService *linked_service_p, json_t *hit_p, ParameterSet *output_params_p);
 
 
BLAST_SERVICE_LOCAL bool GetAndAddSequencesParameter (LinkedService *linked_service_p, json_t *hit_p, ParameterSet *output_params_p);
 
 
BLAST_SERVICE_LOCAL const json_t *GetScaffoldsForDatabaseHit (const json_t *hit_p);
 
 
BLAST_SERVICE_LOCAL json_t *MarkUpBlastResult (BlastServiceJob *job_p);
 
 
 
BLAST_SERVICE_LOCAL json_t *ConvertBlastResultToGrassrootsMarkUp (const json_t *blast_job_output_p, BlastServiceData *data_p);
 
 
 
BLAST_SERVICE_LOCAL json_t *GetMarkupReports (json_t *markup_p);
 
 
BLAST_SERVICE_LOCAL json_t *GetHitsFromMarkedUpReport (json_t *report_p);
 
 
BLAST_SERVICE_LOCAL bool GetAndAddScaffoldsFromHit (const json_t *hit_p, json_t *mark_up_p, const DatabaseInfo *db_p);
 
 
BLAST_SERVICE_LOCAL bool GetAndAddSequenceMappedParameter (LinkedService *linked_service_p, const json_t *hit_p, ParameterSet *output_params_p, json_t *request_p);
 
#ifdef __cplusplus
}
#endif
 
#endif /* SERVER_SRC_SERVICES_BLAST_INCLUDE_BLAST_SERVICE_JOB_MARKUP_H_ */