blast_service_params.h

Go to the documentation of this file.

/*
** Copyright 2014-2016 The Earlham Institute
**
** Licensed under the Apache License, Version 2.0 (the "License");
** you may not use this file except in compliance with the License.
** You may obtain a copy of the License at
**
**     http://www.apache.org/licenses/LICENSE-2.0
**
** Unless required by applicable law or agreed to in writing, software
** distributed under the License is distributed on an "AS IS" BASIS,
** WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
** See the License for the specific language governing permissions and
** limitations under the License.
*/
 
/*
 * blast_service_params.h
 *
 *  Created on: 13 Feb 2016
 *      Author: billy
 */
 
#ifndef SERVICES_BLAST_INCLUDE_BLAST_SERVICE_PARAMS_H_
#define SERVICES_BLAST_INCLUDE_BLAST_SERVICE_PARAMS_H_
 
 
#include "blast_service.h"
#include "blast_service_api.h"
#include "parameter_set.h"
 
 
typedef 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
} BlastOutputFormat;
 
 
 
extern const char *BSP_OUTPUT_FORMATS_SS [BOF_NUM_TYPES];
 
 
 
/* Grassroots params */
 
BLAST_SERVICE_PREFIX NamedParameterType BS_JOB_ID BLAST_SERVICE_STRUCT_VAL ("job_id", PT_STRING);
 
/*
 * These become the -query_loc parameter with the value "<subrange_from>-<subrange_to>"
 */
BLAST_SERVICE_PREFIX NamedParameterType BS_SUBRANGE_FROM BLAST_SERVICE_STRUCT_VAL ("subrange_from", PT_UNSIGNED_INT);
 
BLAST_SERVICE_PREFIX NamedParameterType BS_SUBRANGE_TO BLAST_SERVICE_STRUCT_VAL ("subrange_to", PT_UNSIGNED_INT);
 
/* General Blast params */
BLAST_SERVICE_PREFIX NamedParameterType BS_TASK BLAST_SERVICE_STRUCT_VAL ("task", PT_STRING);
 
BLAST_SERVICE_PREFIX NamedParameterType BS_INPUT_QUERY BLAST_SERVICE_STRUCT_VAL ("query", PT_FASTA);
 
BLAST_SERVICE_PREFIX NamedParameterType BS_MAX_SEQUENCES BLAST_SERVICE_STRUCT_VAL ("max_target_seqs", PT_UNSIGNED_INT);
 
 
BLAST_SERVICE_PREFIX NamedParameterType BS_EXPECT_THRESHOLD BLAST_SERVICE_STRUCT_VAL ("evalue", PT_UNSIGNED_REAL);
 
BLAST_SERVICE_PREFIX NamedParameterType BS_OUTPUT_FORMAT BLAST_SERVICE_STRUCT_VAL ("outfmt", PT_UNSIGNED_INT);
 
BLAST_SERVICE_PREFIX NamedParameterType BS_CUSTOM_OUTPUT_FORMAT BLAST_SERVICE_STRUCT_VAL ("custom_outfmt", PT_STRING);
 
 
BLAST_SERVICE_PREFIX NamedParameterType BS_WORD_SIZE BLAST_SERVICE_STRUCT_VAL ("word_size", PT_UNSIGNED_INT);
 
 
typedef struct BlastTask
{
  const char *bt_name_s;
 
  const char *bt_description_s;
 
} BlastTask;
 
 
 
 
 
#ifdef __cplusplus
extern "C"
{
#endif
 
BLAST_SERVICE_LOCAL bool AddQuerySequenceParams (BlastServiceData *data_p, ParameterSet *param_set_p, AddAdditionalParamsFn callback_fn, void *callback_data_p);
 
 
BLAST_SERVICE_LOCAL bool AddGeneralAlgorithmParams (BlastServiceData *data_p, ParameterSet *param_set_p, AddAdditionalParamsFn callback_fn, const void *callback_data_p);
 
 
BLAST_SERVICE_LOCAL 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);
 
 
BLAST_SERVICE_LOCAL uint16 AddDatabaseParams (BlastServiceData *data_p, ParameterSet *param_set_p, DataResource *resource_p, const DatabaseType db_type);
 
 
BLAST_SERVICE_LOCAL uint32 GetNumberOfDatabases (const BlastServiceData *data_p, const DatabaseType dt);
 
 
 
BLAST_SERVICE_LOCAL Parameter *SetUpPreviousJobUUIDParameter (const BlastServiceData *service_data_p, ParameterSet *param_set_p, ParameterGroup *group_p);
 
 
BLAST_SERVICE_LOCAL 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);
 
 
BLAST_SERVICE_LOCAL char *CreateGroupName (const char *server_s);
 
 
BLAST_SERVICE_LOCAL int8 GetOutputFormatCodeForString (const char *output_format_s);
 
 
 
BLAST_SERVICE_LOCAL bool GetDatabaseParameterTypeForNamedParameter (BlastServiceData *data_p, const char *param_name_s, ParameterType *pt_p);
 
 
BLAST_SERVICE_LOCAL bool GetQuerySequenceParameterTypeForNamedParameter (const char *param_name_s, ParameterType *pt_p);
 
 
BLAST_SERVICE_LOCAL bool GetGeneralAlgorithmParameterTypeForNamedParameter (const char *param_name_s, ParameterType *pt_p);
 
 
BLAST_SERVICE_LOCAL bool GetProgramSelectionParameterTypeForNamedParameter (const char *param_name_s, ParameterType *pt_p);
 
 
BLAST_SERVICE_LOCAL bool GetProteinGeneralAlgorithmParameterTypeForNamedParameter (const char *param_name_s, ParameterType *pt_p);
 
 
BLAST_SERVICE_LOCAL char *GetLocalDatabaseGroupName (GrassrootsServer *grassroots_p);
 
 
BLAST_SERVICE_LOCAL char *GetFullyQualifiedDatabaseName (const char *group_s, const char *db_s);
 
 
BLAST_SERVICE_LOCAL const char *GetLocalDatabaseName (const char *fully_qualified_db_s);
 
 
BLAST_SERVICE_LOCAL bool AddProteinGeneralAlgorithmParameters (BlastServiceData *data_p, ParameterSet *param_set_p, ParameterGroup *group_p, const void *callback_data_p);
 
 
 
 
#ifdef __cplusplus
}
#endif
 
#endif /* SERVICES_BLAST_INCLUDE_BLAST_SERVICE_PARAMS_H_ */