drmaa_blast_tool.hpp

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/*
** 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.
*/
 
/*
 * drmaa_blast_tool.hpp
 *
 *  Created on: 27 Apr 2015
 *      Author: billy
 */
 
#ifndef DRMAA_BLAST_TOOL_HPP_
#define DRMAA_BLAST_TOOL_HPP_
 
#include "drmaa_tool_args_processor.hpp"
#include "external_blast_tool.hpp"
#include "drmaa_tool.h"
 
 
class BLAST_SERVICE_LOCAL DrmaaBlastTool : public ExternalBlastTool
{
public:
 
  static DrmaaBlastTool *GetFromJSON (const json_t *json_p, const char *name_s, const char *program_name_s, ServiceJob *job_p, BlastServiceData *service_data_p);
 
  DrmaaBlastTool (BlastServiceJob *job_p, const char *name_s, const char *factory_s, const BlastServiceData *data_p, const char *blast_program_name_s, const char *queue_name_s, const char *const output_path_s, bool async_flag);
 
 
  DrmaaBlastTool (BlastServiceJob *job_p, const BlastServiceData *data_p, const json_t *json_p);
 
 
  void SetDrmaaOptions (DrmaaTool *drmaa_p, bool async_flag);
 
  virtual ~DrmaaBlastTool ();
 
  virtual OperationStatus Run ();
 
 
  virtual OperationStatus GetStatus (bool update_flag = true);
 
 
  void SetCoresPerSearch (uint32 cores);
 
  bool SetEmailNotifications (const char **email_addresses_ss);
 
  virtual bool SetUpOutputFile ();
 
 
protected:
 
  DrmaaToolArgsProcessor *dbt_args_processor_p;
 
 
  virtual ArgsProcessor *GetArgsProcessor ();
 
  virtual bool AddBlastArg (const char * const arg_s, const bool hyphen_flag);
 
 
 
  virtual bool AddToJSON (json_t *root_p);
 
 
private:
 
 
 
  static const char * const DBT_DRMAA_S;
 
  DrmaaTool *dbt_drmaa_tool_p;
 
  bool dbt_async_flag;
 
 
  DrmaaBlastTool (ServiceJob *job_p, DrmaaTool *drmaa_p, bool async_flag);
};
 
 
 
#endif /* DRMAA_BLAST_TOOL_HPP_ */