libopenms-dev 1.11.1-3 / usr / include / OpenMS / DATASTRUCTURES / ToolDescription.h

// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2013.
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// $Maintainer: $
// $Authors: Chris Bielow, Mathias Walzer $
// --------------------------------------------------------------------------

#ifndef OPENMS_DATASTRUCTURES_TOOLDESCRIPTION_H
#define OPENMS_DATASTRUCTURES_TOOLDESCRIPTION_H

#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/DATASTRUCTURES/StringList.h>
#include <OpenMS/DATASTRUCTURES/Param.h>
#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/CONCEPT/Exception.h>
#include <OpenMS/CONCEPT/LogStream.h>



namespace OpenMS
{

  namespace Internal
  {
    /**
      @brief Maps input/output files to filenames for the external program

    */
    struct FileMapping
    {
      String location; // a regex/macro mix; to be expanded by tool;
      String target;   // TOPP parameter that determines the desired name
      // thus: move location -> target

      FileMapping & operator=(const FileMapping & rhs)
      {
        if (this == &rhs) return *this;

        location = rhs.location;
        target = rhs.target;
        return *this;
      }

    };

    /**
      @brief Filename mappings for all input/output files

    */
    struct MappingParam
    {
      std::map<Int, String> mapping;
      std::vector<FileMapping> pre_moves;
      std::vector<FileMapping> post_moves;

      MappingParam & operator=(const MappingParam & rhs)
      {
        if (this == &rhs) return *this;

        mapping = rhs.mapping;
        pre_moves = rhs.pre_moves;
        post_moves = rhs.post_moves;
        return *this;
      }

    };

    /**
        @brief ToolDescription Class.

        This class represents a ToolDescription.

        @ingroup Datastructures
    */
    struct OPENMS_DLLAPI ToolDescriptionInternal
    {
      bool is_internal;
      String name;
      String category;
      StringList types; // -types of the tool (if any, e.g. ['centroided','wavelet'])

      // default C'Tor
      ToolDescriptionInternal();

      // C'Tor with arguments
      ToolDescriptionInternal(const bool p_is_internal, const String & p_name, const String & p_category, const StringList & p_types);

      // short C'Tor
      ToolDescriptionInternal(const String & p_name, const StringList & p_types);

      ToolDescriptionInternal & operator=(const ToolDescriptionInternal & rhs);

      bool operator==(const ToolDescriptionInternal & rhs) const;

      bool operator<(const ToolDescriptionInternal & rhs) const;
    };

    struct OPENMS_DLLAPI ToolExternalDetails
    {
      String text_startup;
      String text_fail;
      String text_finish;
      String category;
      String commandline;
      String path; //< filename to external tool
      String working_directory; //< folder where the command will be executed from
      MappingParam tr_table;
      Param param;
    };

    /**
      Used for internal and external tools
    */
    struct OPENMS_DLLAPI ToolDescription :
      ToolDescriptionInternal
    {
      // additional details for external tools (one entry for each 'type')
      std::vector<ToolExternalDetails> external_details;

      // default CTor
      ToolDescription();

      // C'Tor for internal TOPP tools
      ToolDescription(const String & p_name, const String & p_category, const StringList & p_types = StringList());

      void addExternalType(const String & type, const ToolExternalDetails & details);

      void append(const ToolDescription & other);

      ToolDescription & operator=(const ToolDescription & rhs);
    };

  } // namespace Internal

} // namespace OPENMS

#endif // OPENMS_DATASTRUCTURES_TOOLDESCRIPTION_H