#include "blast_service.h"
#include "blast_service_api.h"
#include "parameter_set.h"

Include dependency graph for blast_service_params.h:

This graph shows which files directly or indirectly include this file:

Data Structures
struct	BlastTask
	This datatype is used for describing the algorithms that some of the BLAST tools allow the user to choose to optimise the search procedure. More...

Enumerations
enum	BlastOutputFormat { BOF_PAIRWISE, BOF_QUERY_ANCHORED_WITH_IDENTITIES, BOF_QUERY_ANCHORED_NO_IDENTITIES, BOF_FLAT_QUERY_ANCHORED_WITH_IDENTITIES, BOF_FLAT_QUERY_ANCHORED_NO_IDENTITIES, BOF_XML_BLAST, BOF_TABULAR, BOF_TABULAR_WITH_COMMENTS, BOF_TEXT_ASN1, BOF_BINARY_ASN1, BOF_CSV, BOF_BLAST_ASN1, BOF_JSON_SEQALIGN, BOF_MULTI_FILE_JSON_BLAST, BOF_MULTI_FILE_XML2_BLAST, BOF_SINGLE_FILE_JSON_BLAST, BOF_SINGLE_FILE_XML2_BLAST, BOF_SEQUENCE_ALIGNMENT, BOF_ORGANISM_REPORT, BOF_GRASSROOTS, BOF_NUM_TYPES }
	The different available output formats. More...

Functions
bool	AddQuerySequenceParams (BlastServiceData data_p, ParameterSet param_set_p, AddAdditionalParamsFn callback_fn, void *callback_data_p)
	Add the common query sequence parameters for a Blast Service. More...

bool	AddGeneralAlgorithmParams (BlastServiceData data_p, ParameterSet param_set_p, AddAdditionalParamsFn callback_fn, const void *callback_data_p)
	Add the common general algorithm parameters for a Blast Service. More...

bool	AddProgramSelectionParameters (BlastServiceData blast_data_p, ParameterSet param_set_p, const BlastTask tasks_p, const BlastTask default_task_p, const size_t task_mem_size, const size_t num_tasks)
	Add the program selection parameters for a Blast Service. More...

uint16	AddDatabaseParams (BlastServiceData data_p, ParameterSet param_set_p, DataResource *resource_p, const DatabaseType db_type)
	Add the database parameters for a Blast Service. More...

uint32	GetNumberOfDatabases (const BlastServiceData *data_p, const DatabaseType dt)
	Get the number of databases of a given type that this BlastService has. More...

Parameter *	SetUpPreviousJobUUIDParameter (const BlastServiceData service_data_p, ParameterSet param_set_p, ParameterGroup *group_p)
	Create the Parameter for specifying the UUIDs for any previous Blast searches. More...

Parameter *	SetUpOutputFormatParameters (const char *formats_ss, const uint32 num_formats, const uint32 default_format, const BlastServiceData service_data_p, ParameterSet param_set_p, ParameterGroup group_p)
	Create the Parameter for specifying the output format from a Blast search. More...

char *	CreateGroupName (const char *server_s)
	Create the group name to use for available databases from a given named Server. More...

int8	GetOutputFormatCodeForString (const char *output_format_s)
	Get the output format code corresponding to the given string representation. More...

bool	GetDatabaseParameterTypeForNamedParameter (BlastServiceData data_p, const char param_name_s, ParameterType *pt_p)

bool	GetQuerySequenceParameterTypeForNamedParameter (const char param_name_s, ParameterType pt_p)

bool	GetGeneralAlgorithmParameterTypeForNamedParameter (const char param_name_s, ParameterType pt_p)

bool	GetProgramSelectionParameterTypeForNamedParameter (const char param_name_s, ParameterType pt_p)

bool	GetProteinGeneralAlgorithmParameterTypeForNamedParameter (const char param_name_s, ParameterType pt_p)

char *	GetLocalDatabaseGroupName (GrassrootsServer *grassroots_p)

char *	GetFullyQualifiedDatabaseName (const char group_s, const char db_s)

const char *	GetLocalDatabaseName (const char *fully_qualified_db_s)

bool	AddProteinGeneralAlgorithmParameters (BlastServiceData data_p, ParameterSet param_set_p, ParameterGroup group_p, const void callback_data_p)

Variables
const char *	BSP_OUTPUT_FORMATS_SS [BOF_NUM_TYPES]

NamedParameterType	BS_JOB_ID { .npt_name_s = "job_id" , .npt_type = PT_STRING }
	The Blast Service NamedParameterType for specifying previous job UUIDs. More...

NamedParameterType	BS_SUBRANGE_FROM { .npt_name_s = "subrange_from" , .npt_type = PT_UNSIGNED_INT }
	The Blast Service NamedParameterType for specifying the start of a subrange. More...

NamedParameterType	BS_SUBRANGE_TO { .npt_name_s = "subrange_to" , .npt_type = PT_UNSIGNED_INT }
	The Blast Service NamedParameterType for specifying the end of a subrange. More...

NamedParameterType	BS_TASK { .npt_name_s = "task" , .npt_type = PT_STRING }
	The Blast Service NamedParameterType for specifying the algorithm-specific task to use. More...

NamedParameterType	BS_INPUT_QUERY { .npt_name_s = "query" , .npt_type = PT_FASTA }
	The Blast Service NamedParameterType for specifying the input query. More...

NamedParameterType	BS_MAX_SEQUENCES { .npt_name_s = "max_target_seqs" , .npt_type = PT_UNSIGNED_INT }
	The Blast Service NamedParameterType for specifying the maximum number of sequences to return. More...

NamedParameterType	BS_EXPECT_THRESHOLD { .npt_name_s = "evalue" , .npt_type = PT_UNSIGNED_REAL }
	The Blast Service NamedParameterType for specifying the maximum number of e-value to use. More...

NamedParameterType	BS_OUTPUT_FORMAT { .npt_name_s = "outfmt" , .npt_type = PT_UNSIGNED_INT }
	The Blast Service NamedParameterType for specifying the output format to use. More...

NamedParameterType	BS_CUSTOM_OUTPUT_FORMAT { .npt_name_s = "custom_outfmt" , .npt_type = PT_STRING }
	The Blast Service NamedParameterType for specifying any custom output format options to use. More...

NamedParameterType	BS_WORD_SIZE { .npt_name_s = "word_size" , .npt_type = PT_UNSIGNED_INT }
	The Blast Service NamedParameterType for specifying the word size to use. More...

Function Documentation

◆ GetDatabaseParameterTypeForNamedParameter()

bool GetDatabaseParameterTypeForNamedParameter	(	BlastServiceData *	data_p,
		const char *	param_name_s,
		ParameterType *	pt_p
	)

◆ GetQuerySequenceParameterTypeForNamedParameter()

bool GetQuerySequenceParameterTypeForNamedParameter	(	const char *	param_name_s,
		ParameterType *	pt_p
	)

◆ GetGeneralAlgorithmParameterTypeForNamedParameter()

bool GetGeneralAlgorithmParameterTypeForNamedParameter	(	const char *	param_name_s,
		ParameterType *	pt_p
	)

◆ GetProgramSelectionParameterTypeForNamedParameter()

bool GetProgramSelectionParameterTypeForNamedParameter	(	const char *	param_name_s,
		ParameterType *	pt_p
	)

◆ GetProteinGeneralAlgorithmParameterTypeForNamedParameter()

bool GetProteinGeneralAlgorithmParameterTypeForNamedParameter	(	const char *	param_name_s,
		ParameterType *	pt_p
	)

◆ GetLocalDatabaseGroupName()

char* GetLocalDatabaseGroupName ( GrassrootsServer * grassroots_p )

◆ GetFullyQualifiedDatabaseName()

char* GetFullyQualifiedDatabaseName	(	const char *	group_s,
		const char *	db_s
	)

◆ GetLocalDatabaseName()

const char* GetLocalDatabaseName ( const char * fully_qualified_db_s )

◆ AddProteinGeneralAlgorithmParameters()

bool AddProteinGeneralAlgorithmParameters	(	BlastServiceData *	data_p,
		ParameterSet *	param_set_p,
		ParameterGroup *	group_p,
		const void *	callback_data_p
	)

Variable Documentation

◆ BSP_OUTPUT_FORMATS_SS

const char* BSP_OUTPUT_FORMATS_SS[BOF_NUM_TYPES]

Data Structures

Enumerations

Functions

Variables