datatypes_AMOS.hh

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#ifndef __datatypes_AMOS_HH
#define __datatypes_AMOS_HH 1

#include "Message_AMOS.hh"
#include <vector>
#include <string>





//-- Miscellaneous types and definitions
namespace AMOS {

//================================================ Distribution_t ==============
//==============================================================================
struct Distribution_t : public IMessagable_t
{

  Pos_t mean;           
  SD_t sd;              


  static const NCode_t NCODE;


  //--------------------------------------------------- Distribution_t ---------
  Distribution_t ( )
  {
    clear( );
  }


  //--------------------------------------------------- ~Distribution_t --------
  ~Distribution_t ( )
  {

  }


  //--------------------------------------------------- clear ------------------
  void clear ( )
  {
    mean = 0; sd = 0;
  }


  //--------------------------------------------------- getNCode ---------------
  virtual NCode_t getNCode ( ) const
  {
    return Distribution_t::NCODE;
  }


  //--------------------------------------------------- readMessage ------------
  virtual void readMessage (const Message_t & msg);


  //--------------------------------------------------- readRecord -------------
  void readRecord (std::istream & in);


  //--------------------------------------------------- writeMessage -----------
  virtual void writeMessage (Message_t & msg) const;


  //--------------------------------------------------- writeRecord ------------
  void writeRecord (std::ostream & out) const;

};




//================================================ Range_t =====================
//==============================================================================
struct Range_t
{

  Pos_t begin;              
  Pos_t end;                


  //--------------------------------------------------- Range_t ----------------
  Range_t ( )
  {
    clear( );
  }


  //--------------------------------------------------- Range_t ----------------
  Range_t (const Range_t & source)
  {
    *this = source;
  }


  //--------------------------------------------------- Range_t ----------------
  Range_t (Pos_t b, Pos_t e)
  {
    begin = b;
    end = e;
  }


  //--------------------------------------------------- ~Range_t ---------------
  ~Range_t ( )
  {

  }


  //--------------------------------------------------- clear ------------------
  void clear ( )
  {
    begin = end = 0;
  }


  //--------------------------------------------------- getBegin ---------------
  Pos_t getBegin ( ) const
  {
    return begin;
  }


  //--------------------------------------------------- getLo ------------------
  Pos_t getLo ( ) const
  {
    return (begin < end ? begin : end);
  }


  //--------------------------------------------------- getHi ------------------
  Pos_t getHi ( ) const
  {
    return (begin > end ? begin : end);
  }


  //--------------------------------------------------- getEnd -----------------
  Pos_t getEnd ( ) const
  {
    return end;
  }


  //--------------------------------------------------- getLength --------------
  Size_t getLength ( ) const
  {
    return labs (end - begin);
  }


  //--------------------------------------------------- isReverse --------------
  bool isReverse ( ) const
  {
    return begin > end;
  }


  //--------------------------------------------------- setBegin ---------------
  void setBegin (Pos_t b)
  {
    begin = b;
  }


  //--------------------------------------------------- setEnd -----------------
  void setEnd (Pos_t e)
  {
    end = e;
  }


  //--------------------------------------------------- setRange ---------------
  void setRange (Pos_t b, Pos_t e)
  {
    begin = b;
    end = e;
  }


  //--------------------------------------------------- swap -------------------
  void swap ( )
  {
   Pos_t save = begin;
   begin = end;
   end = save;
  }

};




//================================================ Tile_t ======================
//==============================================================================
struct Tile_t : public IMessagable_t
{
  ID_t source;                
  std::vector<Pos_t> gaps;    
  Pos_t offset;               
  Range_t range;              


  static const NCode_t NCODE;


  //--------------------------------------------------- Tile_t -----------------
  Tile_t ( )
  {
    source = NULL_ID;
    offset = 0;
  }


  //--------------------------------------------------- ~Tile_t ----------------
  ~Tile_t ( )
  {

  }


  //--------------------------------------------------- clear ------------------
  void clear ( );


  //--------------------------------------------------- getGappedLength --------
  Size_t getGappedLength ( ) const
  {
    return (range . getLength( ) + gaps . size( ));
  }


  //--------------------------------------------------- getNCode ---------------
  virtual NCode_t getNCode ( ) const
  {
    return Tile_t::NCODE;
  }


  //--------------------------------------------------- getRightOffset --------

  Pos_t getRightOffset() const
  {
    return offset + range.getLength() + gaps.size() - 1;
  }


  //--------------------------------------------------- readMessage ------------
  virtual void readMessage (const Message_t & msg);


  //--------------------------------------------------- readRecord -------------
  void readRecord (std::istream & in);


  //--------------------------------------------------- writeMessage -----------
  virtual void writeMessage (Message_t & msg) const;


  //--------------------------------------------------- writeRecord ------------
  void writeRecord (std::ostream & out) const;

};


//================================================ Helper Functions ============
//----------------------------------------------------- operator& --------------
Range_t operator& (Range_t a, Range_t b);


//----------------------------------------------------- operator| --------------
Range_t operator| (Range_t a, Range_t b);


//----------------------------------------------------- operator== -------------
bool operator== (const Range_t & a, const Range_t & b);
bool operator!= (const Range_t & a, const Range_t & b);


//----------------------------------------------------- operator== -------------
bool operator== (const Distribution_t & a, const Distribution_t & b);
bool operator!= (const Distribution_t & a, const Distribution_t & b);


//----------------------------------------------------- operator== -------------
bool operator== (const Tile_t & a, const Tile_t & b);
bool operator!= (const Tile_t & a, const Tile_t & b);


//----------------------------------------------------- WrapStirng -------------
void WrapString (std::ostream & out, const std::string & s, int per);


//--TEMPORARY
typedef Range_t Ordered_Range_t;

} // namespace AMOS

#endif // #ifndef __datatypes_AMOS_HH

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