ReadData Class Reference

Representing a read stored in the berkeley db. Holds its name and geometric placement in the contig. More...

#include <readdata.h>

Inheritance diagram for ReadData:

[legend]Collaboration diagram for ReadData:

[legend]List of all members.

Public Member Functions
	ReadData (TR_DNA row=0, TR_DNA startPos=0, TR_DNA endPos=0)
	ReadData (const ReadData &other)
	~ReadData ()
void	print_debug_info ()
std::string	uniqueName ()
TrDb::IndexMap	getIndexMap ()
void	setRow (TR_DNA row)
void	setStartPos (TR_DNA startPos)
void	setEndPos (TR_DNA endPos)
TR_DNA	row ()
TR_DNA	startPos ()
TR_DNA	endPos ()
void	writeXml (std::ostream &stream)
void	readStream (QDataStream &stream)
void	writeStream (QDataStream &stream)
void	readAttributes (const QXmlAttributes &attr)
Static Public Member Functions
static int	getRowPos (Db *dbp, const Dbt *pkey, const Dbt *pdata, Dbt *skey)
static int	bt_compare_rowPos (DB *db, const DBT *a, const DBT *b)
static int	bt_compare_end (DB *db, const DBT *dbt1, const DBT *dbt2)
static int	bt_compare_start (DB *db, const DBT *dbt1, const DBT *dbt2)
Protected Attributes
StorageData	s
Classes
struct	StorageData
	to keep the order of the data members when serializing/unserializing More...

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Detailed Description

Representing a read stored in the berkeley db. Holds its name and geometric placement in the contig.

The index value of this read, m_recno, is used as a secondary search index for subclasses of FeatureData.

Definition at line 32 of file readdata.h.

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Constructor & Destructor Documentation

ReadData::ReadData	(	TR_DNA	row = 0,
		TR_DNA	startPos = 0,
		TR_DNA	endPos = 0
	)			[inline]

Definition at line 48 of file readdata.h.

References endPos(), ReadData::StorageData::endPos, row(), ReadData::StorageData::row, s, startPos(), and ReadData::StorageData::startPos.

                                                                     : GeneralData()
  {
    s.row = row;
    s.startPos = startPos;
    s.endPos = endPos;
  }

ReadData::ReadData

(

const ReadData &

other

)

Definition at line 21 of file readdata.cpp.

References s.

                                          : GeneralData(other)
{
  s = other.s;//Works since StorageData is trivial

//   name_ = other.name_;
//   mate_ = other.mate_;
//   matelen_ = other.matelen_;
//   strand_ = other.strand_;
//   beginGood_ = other.beginGood_;
//   endGood_ = other.endGood_;
//   tc_vec = other.tc_vec;
}

ReadData::~ReadData

(

)

Definition at line 35 of file readdata.cpp.

{}

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Member Function Documentation

void ReadData::print_debug_info

(

)

[virtual]

Prints some info for debugging, this should be removed in release version!

Reimplemented from GeneralData.

Definition at line 38 of file readdata.cpp.

References endPos(), GeneralData::getRecno(), row(), startPos(), and uniqueName().

{
  cerr<<"This is class "<<uniqueName()<<endl;
  cerr<<"recno: "<<getRecno()<<endl;
  cerr<<"row: "<<row()<<endl;
  cerr<<"startPos: "<<startPos()<<endl;
  cerr<<"endPos: "<<endPos()<<endl;
}

std::string ReadData::uniqueName

(

)

[inline, virtual]

Specifies a name that uniquely should identify this class. It will be used for lookups in the GeneralMaker class.

Implements GeneralData.

Definition at line 57 of file readdata.h.

Referenced by print_debug_info().

{ return std::string("ReadData"); }

TrDb::IndexMap ReadData::getIndexMap

(

)

[virtual]

Returns a TrDb::IndexMap that specifies which secondary indexes should be generated for stored data objects of this class in the Berkeley Db backend. Each record in the TrDb::IndexMap generates a secondary index built as a btree ( a DB_BTREE in Berkeley Db wording ). The secondary index is sorted which makes it possible to do queries like "Give me the object that has the smallest value, bigger or equal than x".

And about speed performance, a quote from Berkeley Db documentation says: "Searches take O(log base_b N) time, where base_b is the average number of keys per page, and N is the total number of keys stored"

Implements GeneralData.

Definition at line 154 of file readdata.cpp.

References QString::ascii(), bt_compare_end(), bt_compare_rowPos(), bt_compare_start(), getRowPos(), and TrDb::Index::name.

{
  TrDb::IndexMap iMap;
  TrDb::Index i = {
    &ReadData::bt_compare_rowPos,
    &ReadData::getRowPos,
    QString("pos"),
    NULL
  };
  iMap.insert( make_pair( i.name.ascii(), i ) );
  
  TrDb::Index i2 = {
    &ReadData::bt_compare_end,
    &ReadData::getRowPos,
    QString("end"),
    NULL
  };
  iMap.insert( make_pair( i2.name.ascii(), i2 ) );

//   TrDb::Index i3 = {
//     &ReadData::bt_compare_name,
//     &ReadData::getName,
//     QString("name"),
//     NULL
//   };
//   iMap.insert( make_pair( i3.name.ascii(), i3 ) );
  
  TrDb::Index i4 = {
    &ReadData::bt_compare_start,
    &ReadData::getRowPos,
    QString("start"),
    NULL
  };
  iMap.insert( make_pair( i4.name.ascii(), i4 ) );

  return iMap;
}

void ReadData::setRow

(

TR_DNA

row

)

[inline]

Set the row where this "read" is placed in the contig

Definition at line 60 of file readdata.h.

References ReadData::StorageData::row, and s.

Referenced by MacsimParser::endElement(), ReadsInRect::find(), optimize_layout(), TrapperView::selectCols(), TrapperView::selectRows(), MoveAlgo::start(), and TrapperParser::startElement().

{ s.row = row; }

void ReadData::setStartPos

(

TR_DNA

startPos

)

[inline]

Set the start position in DNA coordinates where this "read" is placed in the contig

Definition at line 62 of file readdata.h.

References s, and ReadData::StorageData::startPos.

Referenced by TrapperView::scrollToNextCluster(), TrapperView::selectRows(), and MoveAlgo::start().

{ s.startPos = startPos; }

void ReadData::setEndPos

(

TR_DNA

endPos

)

[inline]

Set the end position in DNA coordinates where this "read" is placed in the contig

Definition at line 64 of file readdata.h.

References ReadData::StorageData::endPos, and s.

Referenced by ReadsInRect::find(), TrapperView::selectCols(), and MoveAlgo::start().

{ s.endPos = endPos; }

TR_DNA ReadData::row

(

)

[inline]

Returns the row where this "read" is placed in the contig

Definition at line 72 of file readdata.h.

References ReadData::StorageData::row, and s.

Referenced by ReadsInRect::find(), TrapperView::fitContentsizeToData(), ReadsInRect::hasAnythingInsideWindow(), optimize_layout(), print_debug_info(), MAl_Readonly::read_seq_from_db(), ReadData(), TrapperView::selectRows(), MoveAlgo::start(), and TrapperParser::startElement().

{ return s.row; }

TR_DNA ReadData::startPos

(

)

[inline]

Returns the start position in DNA coordinates where this "read" is placed in the contig

Definition at line 74 of file readdata.h.

References s, and ReadData::StorageData::startPos.

Referenced by TrapperView::getInfo(), ReadsInRect::hasAnythingInsideWindow(), optimize_layout(), print_debug_info(), MAl_Readonly::read_seq_from_db(), ReadData(), TrapperView::scrollToNextCluster(), TrapperView::selectCols(), and MoveAlgo::start().

{ return s.startPos; }

TR_DNA ReadData::endPos

(

)

[inline]

Returns the end position in DNA coordinates where this "read" is placed in the contig

Definition at line 76 of file readdata.h.

References ReadData::StorageData::endPos, and s.

Referenced by ReadsInRect::find(), TrapperView::fitContentsizeToData(), TrapperView::getInfo(), ReadsInRect::hasAnythingInsideWindow(), ReadsInRect::hasRightEndInsideWindow(), optimize_layout(), print_debug_info(), MAl_Readonly::read_seq_from_db(), ReadData(), and TrapperView::selectCols().

{ return s.endPos; }

int ReadData::getRowPos	(	Db *	dbp,
		const Dbt *	pkey,
		const Dbt *	pdata,
		Dbt *	skey
	)			[static]

Definition at line 259 of file readdata.cpp.

Referenced by getIndexMap().

{
  //  memset(skey, 0, sizeof(Dbt));
  //  ReadData::StorageData * data = ( ReadData::StorageData * ) pdata->get_data();
  //  skey->set_data( ( u_int8_t * ) (& (data->readRecno)) );
  // skey->set_size(sizeof( db_recno_t ));
  
  memset(skey, 0, sizeof(Dbt));
  skey->set_data( pdata->get_data() );
  skey->set_size(sizeof( struct ReadData::StorageData ));
  return(0);
}

int ReadData::bt_compare_rowPos	(	DB *	db,
		const DBT *	a,
		const DBT *	b
	)			[static]

Definition at line 192 of file readdata.cpp.

References ReadData::StorageData::endPos, and ReadData::StorageData::row.

Referenced by getIndexMap().

{
  /* order after row and then after end position */
  
  ReadData::StorageData * seqData1 = ( ReadData::StorageData *) dbt1->data;
  ReadData::StorageData * seqData2 = ( ReadData::StorageData *) dbt2->data;
  if ( seqData1->row > seqData2->row )
    return 1;
  if ( seqData1->row < seqData2->row )
    return -1;
  if ( seqData1->endPos == seqData2->endPos )
    return 0;
  if ( seqData1->endPos > seqData2->endPos )
    return 1;
  if ( seqData1->endPos < seqData2->endPos )
    return -1;
  
  /* should never reach this point */
  return 0;
}

int ReadData::bt_compare_end	(	DB *	db,
		const DBT *	dbt1,
		const DBT *	dbt2
	)			[static]

Definition at line 213 of file readdata.cpp.

References ReadData::StorageData::endPos.

Referenced by getIndexMap().

{
  /* order after end position */
  
  ReadData::StorageData * seqData1 = ( ReadData::StorageData *) dbt1->data;
  ReadData::StorageData * seqData2 = ( ReadData::StorageData *) dbt2->data;
  if ( seqData1->endPos > seqData2->endPos )
    return 1;
  if ( seqData1->endPos < seqData2->endPos )
    return -1;
  if ( seqData1->endPos == seqData2->endPos )
    return 0;
  
  /* should never reach this point */
  return 0;
}

int ReadData::bt_compare_start	(	DB *	db,
		const DBT *	dbt1,
		const DBT *	dbt2
	)			[static]

Definition at line 230 of file readdata.cpp.

References ReadData::StorageData::startPos.

Referenced by getIndexMap().

{
  /* order after end position */
  
  ReadData::StorageData * seqData1 = ( ReadData::StorageData *) dbt1->data;
  ReadData::StorageData * seqData2 = ( ReadData::StorageData *) dbt2->data;
  if ( seqData1->startPos > seqData2->startPos )
    return 1;
  if ( seqData1->startPos < seqData2->startPos )
    return -1;
  if ( seqData1->startPos == seqData2->startPos )
    return 0;
  
  /* should never reach this point */
  return 0;
}

void ReadData::writeXml

(

std::ostream &

stream

)

[virtual]

Writes the state of this object to a stream as an XML entry. This method is used for exporting

Implements GeneralData.

Referenced by TrapperDoc::saveExport().

void ReadData::readStream

(

QDataStream &

stream

)

[virtual]

Loads the state of this object from a byte stream. Or in other words reads and unserializes a byte stream to set the values of this class object. This method is used for loading a GeneralData object from Berkeley Db.

Implements GeneralData.

Definition at line 47 of file readdata.cpp.

References QDataStream::device(), QDataStream::readRawBytes(), and s.

{
  QIODevice * dev = stream.device();
  Q_ASSERT( dev );
  stream.readRawBytes( ( char * ) &s, sizeof ( StorageData ) );  

//   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 ReadData::writeStream

(

QDataStream &

stream

)

[virtual]

Saves the state of this object to a byte stream. Or in other words serializes and writes the internal data held in this class object to a byte stream. This method is used for storing a GeneralData object into Berkeley Db.

Implements GeneralData.

Definition at line 67 of file readdata.cpp.

References QDataStream::device(), QIODevice::mode(), s, and QDataStream::writeRawBytes().

Referenced by TrapperView::writeSelected().

{
  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 ) );

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

void ReadData::readAttributes

(

const QXmlAttributes &

attr

)

[virtual]

Loads the state of this object from QXmlAttributes.This method is used for importing.

Implements GeneralData.

Definition at line 91 of file readdata.cpp.

References ReadData::StorageData::endPos, ReadData::StorageData::row, s, ReadData::StorageData::startPos, and QXmlAttributes::value().

Referenced by MacsimParser::endElement().

{
  if ( attr.value("row") != "" ) {
    QString rowPosStr = attr.value("row");
    s.row = rowPosStr.toLong();
  }
  if ( attr.value("startPos") != "" ) {
    QString startPosStr = attr.value("startPos");
    s.startPos = startPosStr.toLong();
  }
  if ( attr.value("endPos") != "" ) {
    QString endPosStr = attr.value("endPos");
    s.endPos = endPosStr.toLong();
//     endGood_ = s.endPos - s.startPos;
  }
//   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);
//   }

}

---

Member Data Documentation

StorageData ReadData::s [protected]

Definition at line 112 of file readdata.h.

Referenced by endPos(), readAttributes(), ReadData(), readStream(), row(), setEndPos(), setRow(), setStartPos(), startPos(), and writeStream().

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The documentation for this class was generated from the following files:

• readdata.h
• readdata.cpp

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