FeatureData Class Reference

Provides a abstract feature object representing a feature, i.e. an attribute to a read. Holds its corresponding read index (recno) and geometric placement relative to its read. More...

#include <featuredata.h>

Inheritance diagram for FeatureData:

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Collaboration diagram for FeatureData:

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List of all members.

Public Member Functions

 FeatureData (db_recno_t readRec=0)
virtual ~FeatureData ()
virtual TrDb::IndexMap getIndexMap ()
void setReadRecno (db_recno_t readRec)
FeatureGui * gui ()
FeatureInfo * info ()
virtual void readStream (QDataStream &str)
virtual void writeStream (QDataStream &str)
virtual void readAttributes (const QXmlAttributes &attr)
virtual void writeXml (ostream &stream)
virtual void print_debug_info ()
db_recno_t readRecno ()
 FeatureData (db_recno_t readRecno=0, TR_DNA startPos=0, TR_DNA endPos=0)
virtual ~FeatureData ()
TrDb::IndexMap getIndexMap ()
TR_DNA startPos ()
TR_DNA endPos ()
void setStartPos (TR_DNA startPos)
void setEndPos (TR_DNA endPos)
void setReadRecno (db_recno_t readRecno)
FeatureGui * gui ()
FeatureInfo * info ()
virtual void readStream (QDataStream &str)
virtual void writeStream (QDataStream &str)
virtual void readAttributes (const QXmlAttributes &attr)
virtual void writeXml (ostream &stream)
virtual void print_debug_info ()

Static Public Member Functions

static int getSeqRecNo (Db *, const Dbt *, const Dbt *pdata, Dbt *skey)
static int bt_compare_seqRecNo (DB *db, const DBT *dbt1, const DBT *dbt2)
static int getSeqRecNo (Db *, const Dbt *, const Dbt *pdata, Dbt *skey)
static int bt_compare_seqRecNo (DB *db, const DBT *dbt1, const DBT *dbt2)

Protected Member Functions

virtual FeatureGui * makeGui ()=0
virtual FeatureInfo * makeInfo ()=0
virtual FeatureGui * makeGui ()=0
virtual FeatureInfo * makeInfo ()

Protected Attributes

db_recno_t readRecno_
 to keep the order of the data members when serializing/unserializing
FeatureGui * m_gui
FeatureInfo * m_info
StorageData s
FeatureGui * m_gui
FeatureInfo * m_info

Classes

struct  StorageData
 to keep the order of the data members when serializing/unserializing More...

Detailed Description

Provides a abstract feature object representing a feature, i.e. an attribute to a read. Holds its corresponding read index (recno) and geometric placement relative to its read.

The geometrical placement of this feature should be inside the dimensions of its read.

Definition at line 43 of file featuredata.h.

Constructor & Destructor Documentation

FeatureData::FeatureData ( db_recno_t  readRec = 0  ) 

Definition at line 24 of file featuredata.cpp.

References m_gui, m_info, and readRecno_.

00024                                             : GeneralData()
00025 {
00026   readRecno_ = readRec;
00027   m_gui = NULL;
00028   m_info = NULL;
00029 }

FeatureData::~FeatureData (  )  [virtual]

Definition at line 31 of file featuredata.cpp.

References m_gui, and m_info.

00032 {
00033   delete m_gui;
00034   delete m_info;
00035 }

FeatureData::FeatureData ( db_recno_t  readRecno = 0,
TR_DNA  startPos = 0,
TR_DNA  endPos = 0 
)

virtual FeatureData::~FeatureData (  )  [virtual]

Member Function Documentation

TrDb::IndexMap FeatureData::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.

Reimplemented in TagData, ReadMetaData, and ReadMetaData.

Definition at line 56 of file featuredata.cpp.

References QString::ascii(), bt_compare_seqRecNo(), getSeqRecNo(), and TrDb::Index::name.

Referenced by ReadMetaData::getIndexMap(), and TagData::getIndexMap().

00057 {
00058   TrDb::IndexMap iMap;
00059   TrDb::Index i = {
00060     &FeatureData::bt_compare_seqRecNo,
00061     &FeatureData::getSeqRecNo,
00062     QString("readRecno"),
00063     NULL
00064   };
00065   iMap.insert( make_pair( i.name.ascii(), i ) );//Have to use ascii function since call is otherwise ambigous...
00066   return iMap;
00067 }

void FeatureData::setReadRecno ( db_recno_t  readRec  )  [inline]

Definition at line 49 of file featuredata.h.

References readRecno_.

Referenced by Destroyer::destroy(), MacsimParser::endElement(), TrapperView::getInfo(), TrapperDoc::importChromat(), TrapperDoc::importPhd(), TrapperView::paintFeatures(), MAl_Readonly::read_feat_from_db(), TrapperView::readSelected(), TrapperDoc::saveExport(), FindMatesAlgo::start(), and TrapperParser::startElement().

00049 {  readRecno_ = readRec; }

FeatureGui * FeatureData::gui (  ) 

Definition at line 37 of file featuredata.cpp.

References m_gui, and makeGui().

Referenced by TrapperView::paintFeatures().

00038 {
00039   
00040   if ( !m_gui )
00041     m_gui = makeGui();
00042   
00043   return m_gui;
00044 }

FeatureInfo * FeatureData::info (  ) 

Definition at line 46 of file featuredata.cpp.

References m_info, and makeInfo().

Referenced by TagData::getInfo(), TagData::getInfoAssoc(), TagData::readAttributes(), TagData::readStream(), TagData::setInfo(), TagData::writeStream(), and TagData::writeXml().

00047 {
00048   
00049   if ( !m_info )
00050     m_info = makeInfo();
00051   
00052   return m_info;
00053 }

int FeatureData::getSeqRecNo ( Db *  ,
const Dbt *  ,
const Dbt *  pdata,
Dbt *  skey 
) [static]

Definition at line 84 of file featuredata.cpp.

Referenced by getIndexMap().

00085 {
00086     memset(skey, 0, sizeof(Dbt));
00087     db_recno_t * data = ( db_recno_t * ) pdata->get_data();
00088     skey->set_data( data );
00089     skey->set_size(sizeof( db_recno_t ));
00090     return(0);
00091 }

int FeatureData::bt_compare_seqRecNo ( DB *  db,
const DBT *  dbt1,
const DBT *  dbt2 
) [static]

Definition at line 69 of file featuredata.cpp.

Referenced by getIndexMap().

00070 {
00071     /* order after row and then after end position */
00072     db_recno_t * recno1  = ( db_recno_t *) dbt1->data;
00073     db_recno_t * recno2  = ( db_recno_t *) dbt2->data;
00074     if ( *recno1 > *recno2 )
00075         return 1;
00076     if ( *recno1 < *recno2 )
00077         return -1;
00078     if ( *recno1 == *recno2 )
00079         return 0;
00080     /* should never reach this point */
00081     return 0;
00082 }

void FeatureData::readStream ( QDataStream &  str  )  [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.

Reimplemented in SpatialFeatureData, DnpData, DnaStrData, ChromatData, QualityData, TagData, ReadMetaData, ReadMetaData, DnpData, DnaStrData, ChromatData, QualityData, and TagData.

Definition at line 106 of file featuredata.cpp.

References QDataStream::device(), and readRecno_.

Referenced by SpatialFeatureData::readStream().

00107 {
00108   QIODevice * dev = stream.device();
00109   Q_ASSERT( dev );
00110 //   stream.readRawBytes( ( char * ) &s, sizeof ( StorageData ) );
00111   stream>>readRecno_;
00112 }

void FeatureData::writeStream ( QDataStream &  str  )  [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.

Reimplemented in SpatialFeatureData, DnpData, DnaStrData, ChromatData, QualityData, TagData, ReadMetaData, ReadMetaData, DnpData, DnaStrData, ChromatData, QualityData, and TagData.

Definition at line 93 of file featuredata.cpp.

References QDataStream::device(), QIODevice::mode(), and readRecno_.

Referenced by SpatialFeatureData::writeStream().

00094 {
00095   QIODevice * dev = stream.device();
00096   Q_ASSERT( dev );
00097   if ( ! ( IO_WriteOnly & dev->mode() ) )
00098     {
00099       cerr << "data stream should be writeonly" << endl;
00100       exit(1);
00101     }
00102   //     stream.writeRawBytes( ( char * ) &s, sizeof ( StorageData ) );
00103   stream<<readRecno_;
00104 }

void FeatureData::readAttributes ( const QXmlAttributes &  attr  )  [virtual]

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

Implements GeneralData.

Reimplemented in SpatialFeatureData, DnpData, DnaStrData, ChromatData, QualityData, TagData, ReadMetaData, ReadMetaData, DnpData, DnaStrData, ChromatData, QualityData, and TagData.

Definition at line 114 of file featuredata.cpp.

Referenced by SpatialFeatureData::readAttributes().

00115 {
00116   
00117 }

void FeatureData::writeXml ( ostream &  stream  )  [virtual]

Reimplemented in SpatialFeatureData, DnpData, DnaStrData, ChromatData, QualityData, TagData, ReadMetaData, ReadMetaData, DnpData, DnaStrData, ChromatData, QualityData, and TagData.

Definition at line 118 of file featuredata.cpp.

References GeneralData::uniqueName().

Referenced by TrapperDoc::saveExport(), and SpatialFeatureData::writeXml().

00119 {
00120   stream<<'<'<<uniqueName()<<' ';
00121 }

void FeatureData::print_debug_info (  )  [virtual]

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

Reimplemented from GeneralData.

Reimplemented in SpatialFeatureData, ReadMetaData, and ReadMetaData.

Definition at line 123 of file featuredata.cpp.

References readRecno_.

Referenced by ReadMetaData::print_debug_info(), and SpatialFeatureData::print_debug_info().

00124 {
00125   cerr<<"readRecno: "<<readRecno_<<endl;
00126 }

db_recno_t FeatureData::readRecno (  )  [inline]

Definition at line 60 of file featuredata.h.

References readRecno_.

Referenced by TrapperView::findTag(), and ReadMetaData::ReadMetaData().

00060 { return readRecno_; }

virtual FeatureGui* FeatureData::makeGui (  )  [protected, pure virtual]

Implemented in DnpData, DnaStrData, ChromatData, QualityData, TagData, ReadMetaData, DnpData, DnaStrData, ChromatData, QualityData, and TagData.

Referenced by gui().

virtual FeatureInfo* FeatureData::makeInfo (  )  [protected, pure virtual]

Implemented in SpatialFeatureData, DnpData, DnaStrData, QualityData, TagData, ReadMetaData, DnpData, DnaStrData, QualityData, and TagData.

Referenced by info().

TrDb::IndexMap FeatureData::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.

Reimplemented in TagData, ReadMetaData, and ReadMetaData.

TR_DNA FeatureData::startPos (  )  [inline]

Reimplemented in SpatialFeatureData.

Definition at line 49 of file spatialfeaturedata.h.

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

Referenced by DnpInfo::myInfoRange(), and ChromatGui::paintMe().

00049 { return s.startPos; }

TR_DNA FeatureData::endPos (  )  [inline]

Reimplemented in SpatialFeatureData.

Definition at line 50 of file spatialfeaturedata.h.

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

Referenced by TrapperDoc::importPhd(), and ChromatGui::paintMe().

00050 { return s.endPos; }

void FeatureData::setStartPos ( TR_DNA  startPos  )  [inline]

Reimplemented in SpatialFeatureData.

Definition at line 51 of file spatialfeaturedata.h.

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

00051 { s.startPos = startPos; }

void FeatureData::setEndPos ( TR_DNA  endPos  )  [inline]

Reimplemented in SpatialFeatureData.

Definition at line 52 of file spatialfeaturedata.h.

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

00052 { s.endPos = endPos; }

void FeatureData::setReadRecno ( db_recno_t  readRecno  )  [inline]

Definition at line 53 of file spatialfeaturedata.h.

References FeatureData::StorageData::readRecno, and s.

00053 {  s.readRecno = readRecno; }

FeatureGui* FeatureData::gui (  ) 

FeatureInfo* FeatureData::info (  ) 

static int FeatureData::getSeqRecNo ( Db *  ,
const Dbt *  ,
const Dbt *  pdata,
Dbt *  skey 
) [static]

static int FeatureData::bt_compare_seqRecNo ( DB *  db,
const DBT *  dbt1,
const DBT *  dbt2 
) [static]

virtual void FeatureData::readStream ( QDataStream &  str  )  [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.

Reimplemented in SpatialFeatureData, DnpData, DnaStrData, ChromatData, QualityData, TagData, ReadMetaData, ReadMetaData, DnpData, DnaStrData, ChromatData, QualityData, and TagData.

virtual void FeatureData::writeStream ( QDataStream &  str  )  [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.

Reimplemented in SpatialFeatureData, DnpData, DnaStrData, ChromatData, QualityData, TagData, ReadMetaData, ReadMetaData, DnpData, DnaStrData, ChromatData, QualityData, and TagData.

virtual void FeatureData::readAttributes ( const QXmlAttributes &  attr  )  [virtual]

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

Implements GeneralData.

Reimplemented in SpatialFeatureData, DnpData, DnaStrData, ChromatData, QualityData, TagData, ReadMetaData, ReadMetaData, DnpData, DnaStrData, ChromatData, QualityData, and TagData.

virtual void FeatureData::writeXml ( ostream &  stream  )  [virtual]

Reimplemented in SpatialFeatureData, DnpData, DnaStrData, ChromatData, QualityData, TagData, ReadMetaData, ReadMetaData, DnpData, DnaStrData, ChromatData, QualityData, and TagData.

virtual void FeatureData::print_debug_info (  )  [virtual]

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

Reimplemented from GeneralData.

Reimplemented in SpatialFeatureData, ReadMetaData, and ReadMetaData.

virtual FeatureGui* FeatureData::makeGui (  )  [protected, pure virtual]

Implemented in DnpData, DnaStrData, ChromatData, QualityData, TagData, ReadMetaData, DnpData, DnaStrData, ChromatData, QualityData, and TagData.

virtual FeatureInfo* FeatureData::makeInfo (  )  [protected, virtual]

Reimplemented in SpatialFeatureData, DnpData, DnaStrData, QualityData, TagData, ReadMetaData, DnpData, DnaStrData, QualityData, and TagData.

Member Data Documentation

db_recno_t FeatureData::readRecno_ [protected]

to keep the order of the data members when serializing/unserializing

This might make the serializing/unserializing a bit faster ( probably not significant at all, not tested ). But the main reason for the existence of this class is that the order is kept right between serializing and unserializing. But a problem with this approach might be that the endian awareness of QDataStream might be lost, when we don't serialize the types one by one. It might be a problem when moving berkeley dbs around archictures. But berkeley db probably doesn't allow this anyway?

Definition at line 73 of file featuredata.h.

Referenced by FeatureData(), ReadMetaData::print_debug_info(), print_debug_info(), readRecno(), ReadMetaData::readStream(), readStream(), setReadRecno(), ReadMetaData::writeStream(), and writeStream().

FeatureGui* FeatureData::m_gui [protected]

Definition at line 75 of file featuredata.h.

Referenced by FeatureData(), gui(), and ~FeatureData().

FeatureInfo* FeatureData::m_info [protected]

Reimplemented in ReadMetaData, and ReadMetaData.

Definition at line 77 of file featuredata.h.

Referenced by FeatureData(), info(), and ~FeatureData().

StorageData FeatureData::s [protected]

Definition at line 83 of file spatialfeaturedata.h.

Referenced by endPos(), setEndPos(), setReadRecno(), setStartPos(), and startPos().

FeatureGui* FeatureData::m_gui [protected]

Definition at line 84 of file spatialfeaturedata.h.

FeatureInfo* FeatureData::m_info [protected]

Reimplemented in ReadMetaData, and ReadMetaData.

Definition at line 86 of file spatialfeaturedata.h.

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