system_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.
*/
 
/*
 * system_blast_tool.hpp
 *
 *  Created on: 22 Apr 2015
 *      Author: tyrrells
 */
 
#ifndef SYSTEM_BLAST_TOOL_HPP_
#define SYSTEM_BLAST_TOOL_HPP_
 
#include "byte_buffer_args_processor.hpp"
#include "external_blast_tool.hpp"
 
class BLAST_SERVICE_LOCAL SystemBlastTool : public ExternalBlastTool
{
public:
  SystemBlastTool (BlastServiceJob *service_job_p, const char *name_s, const char *factory_s, const BlastServiceData *data_p, const char *blast_program_name_s);
 
 
  SystemBlastTool (BlastServiceJob *job_p, const BlastServiceData *data_p, const json_t *json_p);
 
 
  virtual ~SystemBlastTool ();
 
  virtual bool ParseParameters (ParameterSet *params_p, BlastAppParameters *app_params_p);
 
 
  virtual OperationStatus Run ();
 
 
  virtual OperationStatus GetStatus (bool update_flag = true);
 
protected:
 
  ByteBufferArgsProcessor *sbt_args_processor_p;
 
  virtual ArgsProcessor *GetArgsProcessor ();
 
  bool Init (const char *prog_s);
 
  bool SaveCommandLine (const char *command_line_s);
 
};
 
 
 
 
#endif /* SYSTEM_BLAST_TOOL_HPP_ */