readmetadata.h

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//Copyright (C) 2007 Erik Arner, erik.arner@gmail.com
 
#ifndef READMETADATA_H
#define READMETADATA_H

#include <db_cxx.h>

// #include <qcstring.h>
// #include <qvaluelist.h>
#include "generaldata.h"

#include "trappertypes.h"
#include "trdb.h"
// #include "featuregui.h"
#include "trappervector.h"
// #include <vector>
#include "featureinfo.h"
// #include <iosfwd>

class QDataStream;
class QString;

/** \brief Provides non-spatial attributes to a read. 
  * Holds its corresponding read index (recno).
  */ 

class ReadMetaData : public FeatureData
{
public:
  ReadMetaData( db_recno_t rec = 0) : FeatureData(rec), beginGood_(0), endGood_(0) {}
  ReadMetaData( const ReadMetaData& other );
  virtual ~ReadMetaData();

  virtual void print_debug_info();

  virtual void readStream( QDataStream & str );
  virtual void writeStream( QDataStream & str );

  virtual void readAttributes( const QXmlAttributes& attr );
  virtual void writeXml( ostream& stream );

  TrDb::IndexMap getIndexMap();
  //Associate functions for secondary indices
  static int getName(Db *dbp, const Dbt *pkey, const Dbt *pdata, Dbt *skey);
  //Compare functions for secondary indices
  static int bt_compare_name( DB * db, const DBT *dbt1, const DBT *dbt2);

//   FeatureInfo* info();
  std::string uniqueName() { return std::string("ReadMetaData"); }

  void setName( const std::string& n ) { name_ = n; }
  void setMate( const std::string& m ) { mate_ = m; }
  void setMateLength( const std::size_t& l ) { matelen_ = l; }
  void setStrand( const std::string& m ) { strand_ = m; }
  void setBeginGood( TR_DNA index ) { beginGood_ = index; }
  void setEndGood( TR_DNA index ) { endGood_ = index; }

  std::string name() { return name_; }
  std::string mate() { return mate_; }
  std::size_t mateLength() { return matelen_; }
  std::string strand() { return strand_; }
  TR_DNA beginGood() { return beginGood_; }
  TR_DNA endGood() { return endGood_; }




protected:
//   virtual FeatureInfo* makeInfo();
  
  db_recno_t readRecno;
  
  FeatureInfo* m_info;
  std::string name_;
  std::string mate_;
  std::size_t matelen_;
  std::string strand_;
  TR_DNA beginGood_;
  TR_DNA endGood_;
public:
  TrapperVector<double> tc_vec;
  
};
#endif READMETADATA_H

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