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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 readRecno=0, TR_DNA startPos=0, TR_DNA endPos=0)
virtual ~FeatureData ()
virtual void readDom (QDomElement &elem)
virtual void writeDom (QDomElement &elem)
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)

Protected Member Functions

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

Protected Attributes

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  readRecno = 0,
TR_DNA  startPos = 0,
TR_DNA  endPos = 0
) 
 

Definition at line 24 of file featuredata.cpp.

References FeatureData::StorageData::endPos, m_gui, m_info, FeatureData::StorageData::readRecno, s, and FeatureData::StorageData::startPos.

00024                                                                               : GeneralData()
00025 {
00026     s.readRecno = readRecno;
00027     s.startPos = startPos;
00028     s.endPos = endPos;
00029     m_gui = NULL;
00030     m_info = NULL;
00031 }

FeatureData::~FeatureData (   )  [virtual]
 

Definition at line 33 of file featuredata.cpp.

References m_gui, and m_info.

00034 {
00035   delete m_gui;
00036   delete m_info;
00037 }

Member Function Documentation

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

Definition at line 435 of file featuredata.cpp.

Referenced by getIndexMap().

00436 {
00437     /* order after row and then after end position */
00438     db_recno_t * recno1  = ( db_recno_t *) dbt1->data;
00439     db_recno_t * recno2  = ( db_recno_t *) dbt2->data;
00440     if ( *recno1 > *recno2 )
00441         return 1;
00442     if ( *recno1 < *recno2 )
00443         return -1;
00444     if ( *recno1 == *recno2 )
00445         return 0;
00446     /* should never reach this point */
00447     return 0;
00448 }

TR_DNA FeatureData::endPos (   )  [inline]
 

Definition at line 52 of file featuredata.h.

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

Referenced by FeatureInfo::getPosInfo(), FeatureInfo::getRangeInfo(), TrapperDoc::importPhd(), FeatureGui::paint(), and ChromatGui::paintMe().

00052 { return s.endPos; }

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 DnpData.

Definition at line 63 of file featuredata.cpp.

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

Referenced by DnpData::getIndexMap().

00064 {
00065     TrDb::IndexMap iMap;
00066     TrDb::Index i = {
00067                         &FeatureData::bt_compare_seqRecNo,
00068                         &FeatureData::getSeqRecNo,
00069                         QString("readRecno"),
00070                         NULL
00071                     };
00072     iMap.insert( make_pair( i.name.ascii(), i ) );//Have to use ascii function since call is otherwise ambigous...
00073     return iMap;
00074 }

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

Definition at line 450 of file featuredata.cpp.

References FeatureData::StorageData::readRecno.

Referenced by getIndexMap().

00451 {
00452     memset(skey, 0, sizeof(Dbt));
00453     StorageData * data = ( StorageData * ) pdata->get_data();
00454     skey->set_data( ( u_int8_t * ) (& (data->readRecno)) );
00455     skey->set_size(sizeof( db_recno_t ));
00456     return(0);
00457 }

FeatureGui * FeatureData::gui (   ) 
 

Definition at line 39 of file featuredata.cpp.

References m_gui, and makeGui().

Referenced by TrapperView::paintFeatures().

00040 {
00041   
00042   if ( !m_gui )
00043     m_gui = makeGui();
00044   
00045   return m_gui;
00046 }

FeatureInfo * FeatureData::info (   ) 
 

Definition at line 48 of file featuredata.cpp.

References m_info, and makeInfo().

Referenced by TrapperView::getInfo().

00049 {
00050   
00051   if ( !m_info )
00052     m_info = makeInfo();
00053   
00054   return m_info;
00055 }

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

Implemented in DnpData, DnaStrData, ChromatData, and QualityData.

Referenced by gui().

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

Reimplemented in DnpData, DnaStrData, and QualityData.

Definition at line 57 of file featuredata.cpp.

Referenced by info().

00058 {
00059   
00060   return new FeatureInfo(this);
00061 }

void FeatureData::print_debug_info (   )  [virtual]
 

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

Reimplemented from GeneralData.

Definition at line 132 of file featuredata.cpp.

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

00133 {
00134   cerr<<"readRecno: "<<s.readRecno<<endl;
00135 }

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 DnpData, DnaStrData, ChromatData, and QualityData.

Definition at line 110 of file featuredata.cpp.

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

Referenced by ChromatData::readAttributes(), QualityData::readAttributes(), DnaStrData::readAttributes(), and DnpData::readAttributes().

00111 {
00112   
00113   if ( attr.value("startPos") != "" ) {
00114     QString startPosStr = attr.value("startPos");
00115     long startPosLong = startPosStr.toLong();
00116     // is long the same thing as Q_INT64 ?
00117     s.startPos = startPosLong;
00118   }
00119   if ( attr.value("endPos") != "" ) {  
00120     QString endPosStr = attr.value("endPos");
00121     ulong endPosLong = endPosStr.toLong();
00122     s.endPos = endPosLong;
00123   }
00124 }

void FeatureData::readDom (  QDomElement &  elem  )  [virtual]
 

Loads the state of this object from a dom tree. Or in other words reads in the values of the data members of this class from a dom tree underneath the QDomElement elem. This method is used for importing.

Reimplemented from GeneralData.

Reimplemented in DnpData, DnaStrData, ChromatData, and QualityData.

Definition at line 95 of file featuredata.cpp.

References FeatureData::StorageData::endPos, GeneralData::readDom(), FeatureData::StorageData::readRecno, s, and FeatureData::StorageData::startPos.

Referenced by ChromatData::readDom(), QualityData::readDom(), DnaStrData::readDom(), and DnpData::readDom().

00096 {
00097     GeneralData::readDom( elem );
00098     QString startPosStr = elem.attribute("startPos");
00099     long startPosLong = startPosStr.toLong();
00100     // is long the same thing as Q_INT64 ?
00101     s.startPos = startPosLong;
00102     QString endPosStr = elem.attribute("endPos");
00103     ulong endPosLong = endPosStr.toLong();
00104     s.endPos = endPosLong;
00105     QString readRecnoStr = elem.attribute("readRecno");
00106     ulong readRecnoLong = readRecnoStr.toLong();
00107     s.readRecno = static_cast< db_recno_t >( readRecnoLong );
00108 }

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 DnpData, DnaStrData, ChromatData, and QualityData.

Definition at line 88 of file featuredata.cpp.

References s.

Referenced by ChromatData::readStream(), QualityData::readStream(), DnaStrData::readStream(), and DnpData::readStream().

00089 {
00090     QIODevice * dev = stream.device();
00091     Q_ASSERT( dev );
00092     stream.readRawBytes( ( char * ) &s, sizeof ( StorageData ) );
00093 }

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

Definition at line 54 of file featuredata.h.

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

00054 { s.endPos = endPos; }

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

Definition at line 55 of file featuredata.h.

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

Referenced by MAl::commit_feat_to_db(), Destroyer::destroy(), TrapperView::getInfo(), TrapperDoc::importChromat(), TrapperDoc::importPhd(), TrapperView::paintFeatures(), MAl_Readonly::read_feat_from_db(), TrapperView::readSelected(), TrapperDoc::saveExport(), TrapperParser::startElement(), and TrapperView::writeSelected().

00055 {  s.readRecno = readRecno; }

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

Definition at line 53 of file featuredata.h.

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

00053 { s.startPos = startPos; }

TR_DNA FeatureData::startPos (   )  [inline]
 

Definition at line 51 of file featuredata.h.

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

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

00051 { return s.startPos; }

void FeatureData::writeDom (  QDomElement &  elem  )  [virtual]
 

Saves the state of this object to a dom tree. Or in other words writes out the internal data held in this class to a dom tree underneath the QDomElement elem. This method is used for exporting.

Reimplemented from GeneralData.

Reimplemented in DnpData, DnaStrData, ChromatData, and QualityData.

Definition at line 137 of file featuredata.cpp.

References FeatureData::StorageData::endPos, FeatureData::StorageData::readRecno, s, FeatureData::StorageData::startPos, and GeneralData::writeDom().

Referenced by ChromatData::writeDom(), QualityData::writeDom(), DnaStrData::writeDom(), and DnpData::writeDom().

00138 {
00139     GeneralData::writeDom( elem );
00140     Q_UINT32 readRecno = s.readRecno;
00141     QString startPosStr, endPosStr, readRecnoStr;
00142     startPosStr.setNum( ( Q_INT32 ) s.startPos );
00143     endPosStr.setNum( ( Q_INT32 ) s.endPos );
00144     readRecnoStr.setNum( readRecno );
00145     elem.setAttribute("startPos", startPosStr );
00146     elem.setAttribute("endPos", endPosStr);
00147     elem.setAttribute("readRecno", readRecnoStr);
00148 }

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 DnpData, DnaStrData, ChromatData, and QualityData.

Definition at line 76 of file featuredata.cpp.

References s.

Referenced by TrapperView::writeSelected(), ChromatData::writeStream(), QualityData::writeStream(), DnaStrData::writeStream(), and DnpData::writeStream().

00077 {
00078     QIODevice * dev = stream.device();
00079     Q_ASSERT( dev );
00080     if ( ! ( IO_WriteOnly & dev->mode() ) )
00081     {
00082         cerr << "data stream should be writeonly" << endl;
00083         exit(1);
00084     }
00085     stream.writeRawBytes( ( char * ) &s, sizeof ( StorageData ) );
00086 }

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

Reimplemented in DnpData, DnaStrData, ChromatData, and QualityData.

Definition at line 125 of file featuredata.cpp.

References FeatureData::StorageData::endPos, s, FeatureData::StorageData::startPos, and GeneralData::uniqueName().

Referenced by TrapperDoc::saveExport(), ChromatData::writeXml(), QualityData::writeXml(), DnaStrData::writeXml(), and DnpData::writeXml().

00126 {
00127   stream<<'<'<<uniqueName()<<' '
00128         <<"startPos=\""<<s.startPos<<"\" "
00129         <<"endPos=\""<<s.endPos<<"\"";
00130 }

Member Data Documentation

FeatureGui* FeatureData::m_gui [protected]
 

Definition at line 86 of file featuredata.h.

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

FeatureInfo* FeatureData::m_info [protected]
 

Definition at line 88 of file featuredata.h.

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

StorageData FeatureData::s [protected]
 

Definition at line 85 of file featuredata.h.

Referenced by endPos(), FeatureData(), print_debug_info(), readAttributes(), readDom(), readStream(), setEndPos(), setReadRecno(), setStartPos(), startPos(), writeDom(), writeStream(), and writeXml().

The documentation for this class was generated from the following files:
Generated on Fri Mar 17 17:44:58 2006 for trapper by  doxygen 1.4.4