readmetadata.cpp

Go to the documentation of this file.

//Copyright (C) 2007 Erik Arner, erik.arner@gmail.com

#include "readmetadata.h"
// #include <map>
#include "trappervector.h"
#include <ostream>

using namespace std;



ReadMetaData::ReadMetaData( const ReadMetaData& other ) : GeneralData(other)
{
  readRecno = other.readRecno;
  name_ = other.name_;
  mate_ = other.mate_;
  matelen_ = other.matelen_;
  strand_ = other.strand_;
  beginGood_ = other.beginGood_;
  endGood_ = other.endGood_;
  tc_vec = other.tc_vec;
}


ReadMetaData::~ReadMetaData()
{}

void ReadMetaData::print_debug_info()
{
  cerr<<"This is class "<<uniqueName()<<endl;
  cerr<<"recno: "<<getRecno()<<endl;
}

void ReadMetaData::readStream( QDataStream & stream )
{
  QIODevice * dev = stream.device();
  Q_ASSERT( dev );
//   stream.readRawBytes( ( char * ) &s, sizeof ( StorageData ) );  

  stream>>readRecno;
  QString tmp;
  stream>>tmp;
  name_ = tmp.ascii();
  stream>>tmp;
  mate_ = tmp.ascii();
  stream>>matelen_;
  stream>>tmp;
  strand_ = tmp.ascii();
  stream>>beginGood_;
  stream>>endGood_;
  tc_vec.stlVector().clear();
  stream>>tc_vec;
}

void ReadMetaData::writeStream( QDataStream & stream )
{
  QIODevice * dev = stream.device();
  Q_ASSERT( dev );
  if ( ! ( IO_WriteOnly & dev->mode() ) )
    {
      cerr << "data stream should be writeonly" << endl;
      exit(1);
    }
//   stream.writeRawBytes( ( char * ) &s, sizeof ( StorageData ) );
  stream<<readRecno;

  QString tmp;
  tmp = name_;
  stream<<tmp;
  tmp = mate_;
  stream<<tmp;
  stream<<matelen_;
  tmp = strand_;
  stream<<tmp;
  stream<<beginGood_;
  stream<<endGood_;
  stream<<tc_vec;
}

void ReadMetaData::readAttributes( const QXmlAttributes& attr )
{
  if ( attr.value("name") != "" ) {
    name_ = attr.value("name").ascii();
  }
  if ( attr.value("mate") != "" ) {
    mate_ = attr.value("mate").ascii();
  }
  if ( attr.value("matelen") != "" ) {
    matelen_ = attr.value("matelen").toInt();
  }
  if ( attr.value("strand") != "" ) {
    strand_ = attr.value("strand").ascii();
  }
  if ( attr.value("beginGood") != "" ) {
    beginGood_ = attr.value("beginGood").toInt();
  }
  if ( attr.value("endGood") != "" ) {
    endGood_ = attr.value("endGood").toInt();
  }
  if ( attr.value("tc") != "" ) {
    QString str = attr.value("tc");
    tc_vec.readString(str);
  }

}

void ReadMetaData::writeXml( ostream& stream )
{
  stream<<"<ReadMetaData "
        <<"name=\""<<name_<<"\" "
        <<"mate=\""<<mate_<<"\" "
        <<"matelen=\""<<matelen_<<"\" "
        <<"strand=\""<<strand_<<"\" "
        <<"beginGood=\""<<beginGood_<<"\" "
        <<"endGood=\""<<endGood_<<"\"";
  if ( tc_vec.stlVector().size() > 0 ) {
    stream<<" tc=\"";
    for( size_t i = 0; i < tc_vec.stlVector().size(); i++ ) {
      stream<<' '<<tc_vec.stlVector()[i];
    }
    stream<<"\"";
  }
  stream<<">\n";
}

TrDb::IndexMap ReadMetaData::getIndexMap()
{

  TrDb::Index i1 = {
    &ReadMetaData::bt_compare_name,
    &ReadMetaData::getName,
    QString("name"),
    NULL
  };
  iMap.insert( make_pair( i1.name.ascii(), i1 ) );
  
  return iMap;
}

int ReadMetaData::bt_compare_name( DB * /* not used */, const DBT *dbt1, const DBT *dbt2)
{
  /* order after end position */
  
  char* seqData1 = ( char* ) dbt1->data;
  char* seqData2 = ( char* ) dbt2->data;

//   cerr<<seqData1<<'\t'<<seqData2<<'\t'<<strcmp(seqData1, seqData2)<<endl;
  
  return strcmp(seqData1, seqData2);
}

int ReadMetaData::getName(Db * /* not used */, const Dbt * /* not used */,
                        const Dbt *pdata, Dbt *skey)
{
  
  memset(skey, 0, sizeof(Dbt));

  
  ReadMetaData tmp;
  Database::setFromDbt(pdata, &tmp);
  char* name = (char*)malloc(sizeof(char)*(tmp.name().length() + 1));
  strcpy(name, tmp.name().c_str());
  assert( name[ tmp.name().length() ] == '\0' );
  skey->set_flags( DB_DBT_APPMALLOC );
  skey->set_data( (void*)name ); 
  skey->set_size(sizeof(char)*(strlen(name) + 1) );
  

  return 0;
}

---