external_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.
*/
 
/*
 * external_blast_tool.hpp
 *
 *  Created on: 22 Apr 2015
 *      Author: tyrrells
 */
 
#ifndef EXTERNAL_BLAST_TOOL_HPP_
#define EXTERNAL_BLAST_TOOL_HPP_
 
#include "blast_tool.hpp"
#include "byte_buffer.h"
#include "temp_file.hpp"
 
 
class BLAST_SERVICE_LOCAL ExternalBlastTool : public BlastTool
{
public:
  static const char * const EBT_INPUT_SUFFIX_S;
 
//  static const char * const EBT_LOG_SUFFIX_S;
 
  static const char * const EBT_ASYNC_S;
 
 
  ExternalBlastTool (BlastServiceJob *job_p, const char *name_s, const char *factory_s, const BlastServiceData *data_p, const char *blast_program_name_s, const bool async_flag);
 
 
  ExternalBlastTool (BlastServiceJob *job_p, const BlastServiceData *data_p, const json_t *json_p);
 
 
  virtual ~ExternalBlastTool ();
 
  virtual bool ParseParameters (ParameterSet *param_set_p, BlastAppParameters *app_params_p);
 
 
  virtual bool SetInputFilename (const char * const filename_s);
 
 
  virtual bool SetUpOutputFile ();
 
 
  virtual char *GetResults (BlastFormatter *formatter_p);
 
 
  virtual char *GetLog ();
 
 
protected:
 
  char *ebt_results_filename_s;
 
  char *ebt_working_directory_s;
 
  char *ebt_blast_s;
 
 
  bool ebt_async_flag;
 
 
  virtual ArgsProcessor *GetArgsProcessor () = 0;
 
 
  virtual bool AddBlastArg (const char * const arg_s, const bool hyphen_flag);
 
 
  virtual bool AddBlastArgsPair (const char *key_s, const char *value_s);
 
 
 
  char *GetJobFilename (const char * const prefix_s, const char * const suffix_s);
 
 
  virtual bool AddToJSON (json_t *root_p);
 
 
 
private:
  static const char * const EBT_COMMAND_LINE_EXECUTABLE_S;
  static const char * const EBT_WORKING_DIR_S;
  static const char * const EBT_RESULTS_FILE_S;
};
#endif /* EXTERNAL_BLAST_TOOL_HPP_ */