source: src/Parser/TremoloParser.hpp@ 70f2a1

/*
 * TremoloParser.hpp
 *
 *  Created on: Mar 2, 2010
 *      Author: metzler
 */

#ifndef TREMOLOPARSER_HPP_
#define TREMOLOPARSER_HPP_

// include config.h
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif

#include <boost/function.hpp>
#include <string>

#include "FormatParser.hpp"
#include "FormatParserTrait.hpp"
#include "FormatParserInterface.hpp"
#include "FormatParser_common.hpp"
#include "ParserTypes.hpp"

#include "TremoloKey.hpp"
#include "TremoloAtomInfoContainer.hpp"

class molecule;
class AtomDataValidator;

// declaration of specialized FormatParserTrait
template<>
struct FormatParserTrait<tremolo>
{
  //!> Name of the parser
  static const std::string name;
  //!> suffix of the files the parser understands to read and write
  static const std::string suffix;
  //!> ParserTypes enumeration for the parser
  static const enum ParserTypes type;
};

/**
 * Loads a tremolo file into the World and saves the World as a tremolo file.
 */
template <>
class FormatParser< tremolo >  : virtual public FormatParserInterface, public FormatParser_common
{
  friend class AtomDataValidator;
public:
  FormatParser();
  virtual ~FormatParser();
  void load(std::istream* file);
  void save(std::ostream* file, const std::vector<const atom *> &atoms);
  std::string getAtomData() const;
  void setAtomData(const std::string &atomdata_string);
  void resetAtomData(const std::string &atomdata_string);

  /** Save given \a atoms in tremolo's exttypes file
   *
   * \note You should have stored the atoms beforehand to give them unique
   * and sensible ids.
   *
   * @param output output stream
   * @param atoms vector of atoms whose ids to store
   * @param id id to given this exttypes group
   * @return true - all atomic ids are valid, false - one id was not set (-1)
   */
  bool saveAtomsInExttypes(
      std::ostream &output,
      const std::vector<const atom*> &atoms,
      const int id) const;

protected:
  void AtomInserted(atomId_t);
  void AtomRemoved(atomId_t);

private:
  //!> typedef for usedFields' vector of strings
  typedef std::vector<std::string> usedFields_t;

  void readAtomDataLine(
      const std::string &line,
      molecule *newmol,
      const size_t _timestep,
      atom *&_addedatoms);
  void parseAtomDataKeysLine(const std::string &line, const int offset, usedFields_t &fields);
  static bool testParseAtomDataKeysLine(const std::string &line);
  void readNeighbors(std::stringstream* line, const int numberOfNeighbors, const int atomId);
  void processNeighborInformation(const std::vector<atomId_t> &atoms);
  void adaptImprData(const std::vector<atomId_t> &atoms);
  void adaptTorsion(const std::vector<atomId_t> &atoms);
  std::string adaptIdDependentDataString(const std::string &data, const boost::function<int (const int)> &idgetter);
  bool isUsedField(const usedFields_t &fields, const std::string &fieldName) const;
  void writeNeighbors(std::ostream* file, const int numberOfNeighbors, const atom* const currentAtom);
  void saveLine(
      std::ostream* file,
      const atom* const currentAtom,
      const size_t _timestep);
  void save_AtomDataLine(std::ostream* file) const;
  void save_BoxLine(std::ostream* file) const;
  void distributeContinuousIds(const std::vector<const atom *> &AtomList);
  void makeUsedFieldsUnique(usedFields_t &fields) const;
  /**
   * Map to associate the known keys with numbers.
   */
  static std::map<std::string, TremoloKey::atomDataKey> knownKeys;

  /**
   * Inverse Map to have a name to each known keys.
   */
  std::map<TremoloKey::atomDataKey, std::string> knownKeyNames;

  /**
   * Fields used globally when storing to a tremolo file.
   */
  usedFields_t usedFields_save;

  /**
   * Fields used locally when parsing in a tremolo file.
   */
  usedFields_t usedFields_load;

  /**
   * Data which is currently not stored in atoms but was provided by the input
   * file.
   */
  std::map<const atomId_t, TremoloAtomInfoContainer> additionalAtomData;

  /**
   * Default additional atom data.
   */
  TremoloAtomInfoContainer defaultAdditionalData;

  //!> bound function to convert id to global id, stored to avoid creation many times
  const boost::function<int (const int)> idglobalizer;

  //!> bound function to convert id to local id, stored to avoid creation many times
  const boost::function<int (const int)> idlocalizer;
};

#endif /* TREMOLOPARSER_HPP_ */