Param.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2012.
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//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
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// $Maintainer: Erhan Kenar $
// $Authors:  Marc Sturm, Clemens Groepl $
// --------------------------------------------------------------------------

#ifndef OPENMS_DATASTRUCTURES_PARAM_H
#define OPENMS_DATASTRUCTURES_PARAM_H

// #include <OpenMS/APPLICATIONS/TOPPBase.h>
#include <OpenMS/CONCEPT/Exception.h>
#include <OpenMS/CONCEPT/LogStream.h>
#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/DATASTRUCTURES/DataValue.h>
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/DATASTRUCTURES/Map.h>

#include <set>
#include <iostream>


namespace OpenMS
{
  struct ParameterInformation;

  class OPENMS_DLLAPI Param
  {
public:

    struct OPENMS_DLLAPI ParamEntry
    {
      ParamEntry();
      ParamEntry(const String& n, const DataValue& v, const String& d, const StringList& t = StringList());
      ~ParamEntry();

      bool isValid(String& message) const;
      bool operator==(const ParamEntry& rhs) const;

      String name;
      String description;
      DataValue value;
      std::set<String> tags;

      DoubleReal min_float; 
      DoubleReal max_float; 
      Int min_int; 
      Int max_int; 
      std::vector<String> valid_strings; 

    };

    struct OPENMS_DLLAPI ParamNode
    {
      typedef std::vector<ParamNode>::iterator NodeIterator;
      typedef std::vector<ParamEntry>::iterator EntryIterator;
      typedef std::vector<ParamNode>::const_iterator ConstNodeIterator;
      typedef std::vector<ParamEntry>::const_iterator ConstEntryIterator;

      ParamNode();
      ParamNode(const String& n, const String& d);
      ~ParamNode();
      bool operator==(const ParamNode& rhs) const;

      EntryIterator findEntry(const String& name);
      NodeIterator findNode(const String& name);
      ParamNode* findParentOf(const String& name);
      ParamEntry* findEntryRecursive(const String& name);

      void insert(const ParamNode& node, const String& prefix = "");
      void insert(const ParamEntry& entry, const String& prefix = "");
      Size size() const;
      String suffix(const String& key) const;

      String name;
      String description;
      std::vector<ParamEntry> entries;
      std::vector<ParamNode> nodes;
    };

public:

    class OPENMS_DLLAPI ParamIterator
    {
public:
      struct OPENMS_DLLAPI TraceInfo
      {
        inline TraceInfo(const String& n, const String& d, bool o) :
          name(n),
          description(d),
          opened(o)
        {
        }

        String name;
        String description;
        bool opened;
      };

      ParamIterator();
      ParamIterator(const Param::ParamNode& root);
      ~ParamIterator();
      const Param::ParamEntry& operator*();
      const Param::ParamEntry* operator->();
      ParamIterator& operator++();
      ParamIterator operator++(int);
      bool operator==(const ParamIterator& rhs) const;
      bool operator!=(const ParamIterator& rhs) const;
      String getName() const;
      const std::vector<TraceInfo>& getTrace() const;

protected:
      const Param::ParamNode* root_;
      Int current_;
      std::vector<const Param::ParamNode*> stack_;
      std::vector<TraceInfo> trace_;

    };

    Param();

    Param(const Param& rhs);

    ~Param();

    Param& operator=(const Param& rhs);

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

    ParamIterator begin() const;

    ParamIterator end() const;



    void setValue(const String& key, const DataValue& value, const String& description = "", const StringList& tags = StringList());

    const DataValue& getValue(const String& key) const;

    const ParamEntry& getEntry(const String& key) const;

    bool exists(const String& key) const;

    ParamIterator findFirst(const String& leaf) const;

    ParamIterator findNext(const String& leaf, const ParamIterator& start_leaf) const;






    void addTag(const String& key, const String& tag);

    void addTags(const String& key, const StringList& tags);

    bool hasTag(const String& key, const String& tag) const;

    StringList getTags(const String& key) const;

    void clearTags(const String& key);




    const String& getDescription(const String& key) const;

    void setSectionDescription(const String& key, const String& description);

    const String& getSectionDescription(const String& key) const;



    Size size() const;

    bool empty() const;

    void clear();

    void insert(const String& prefix, const Param& param);

    void remove(const String& key);

    void removeAll(const String& prefix);

    Param copy(const String& prefix, bool remove_prefix = false) const;

    void update(const Param& old_version, const bool add_unknown = false, Logger::LogStream& stream = LOG_WARN);

    void merge(const Param& toMerge);





    void setDefaults(const Param& defaults, const String& prefix = "", bool showMessage = false);

    void checkDefaults(const String& name, const Param& defaults, const String& prefix = "", std::ostream& os = std::cout) const;



    void setValidStrings(const String& key, const std::vector<String>& strings);

    void setMinInt(const String& key, Int min);

    void setMaxInt(const String& key, Int max);

    void setMinFloat(const String& key, DoubleReal min);

    void setMaxFloat(const String& key, DoubleReal max);



    void parseCommandLine(const int argc, const char** argv, const String& prefix = "");
    void parseCommandLine(const int argc, const char** argv, const Map<String, String>& options_with_one_argument, const Map<String, String>& options_without_argument, const Map<String, String>& options_with_multiple_argument, const String& misc = "misc", const String& unknown = "unknown");

    void parseCommandLine(const int argc, const char** argv, const std::vector<ParameterInformation>& parameters, const String& misc = "misc", const String& unknown = "unknown");

protected:
    ParamEntry& getEntry_(const String& key) const;

    Param(const Param::ParamNode& node);

    mutable Param::ParamNode root_;
  };

  OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const Param& param);


} // namespace OpenMS

#endif // OPENMS_DATASTRUCTURES_PARAM_H