ChromatData Class Reference

The chromatogram data for the read. More...

#include <featuredata.h>

Inheritance diagram for ChromatData:

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Collaboration diagram for ChromatData:

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List of all members.

Public Member Functions

 ChromatData ()
 ChromatData (db_recno_t readRecno, TR_DNA startPos, TR_DNA endPos)
std::string uniqueName ()
virtual ~ChromatData ()
void readStream (QDataStream &str)
void writeStream (QDataStream &str)
void writeDom (QDomElement &elem)
void readDom (QDomElement &elem)
void readAttributes (const QXmlAttributes &attr)
void writeXml (ostream &stream)
 ChromatData ()
 ChromatData (db_recno_t readRecno, TR_DNA startPos, TR_DNA endPos)
std::string uniqueName ()
virtual ~ChromatData ()
void readStream (QDataStream &str)
void writeStream (QDataStream &str)
void writeDom (QDomElement &elem)
void readDom (QDomElement &elem)
void readAttributes (const QXmlAttributes &attr)
void writeXml (ostream &stream)

Public Attributes

std::vector< TrapperVector<
Q_UINT32 > > 		cagt_vec
TrapperVector< Q_UINT32 > phd_vec
TrapperVector< Q_UINT32 > gap_vec
std::vector< TrapperVector<
Q_UINT32 > > 		cagt_vec
TrapperVector< Q_UINT32 > phd_vec
TrapperVector< Q_UINT32 > gap_vec

Protected Member Functions

FeatureGui * makeGui ()
FeatureGui * makeGui ()

Detailed Description

The chromatogram data for the read.

Definition at line 164 of file featuredata.h.

Constructor & Destructor Documentation

ChromatData::ChromatData (  )  [inline]

Definition at line 167 of file featuredata.h.

00167                 : SpatialFeatureData(), cagt_vec(4)
00168   {}

ChromatData::ChromatData ( db_recno_t  readRecno,
TR_DNA  startPos,
TR_DNA  endPos 
)

Definition at line 347 of file featuredata.cpp.

00347                                                                               :
00348   SpatialFeatureData( readRecno, startPos, endPos ), cagt_vec(4)
00349 {}

virtual ChromatData::~ChromatData (  )  [inline, virtual]

Definition at line 171 of file featuredata.h.

00172   {}

ChromatData::ChromatData (  )  [inline]

Definition at line 148 of file spatialfeaturedata.h.

00148                 : FeatureData(), cagt_vec(4)
00149   {}

ChromatData::ChromatData ( db_recno_t  readRecno,
TR_DNA  startPos,
TR_DNA  endPos 
)

virtual ChromatData::~ChromatData (  )  [inline, virtual]

Definition at line 152 of file spatialfeaturedata.h.

00153   {}

Member Function Documentation

std::string ChromatData::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 170 of file featuredata.h.

00170 { return std::string("ChromatData"); }

void ChromatData::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.

Reimplemented from FeatureData.

Definition at line 351 of file featuredata.cpp.

References cagt_vec, gap_vec, phd_vec, and SpatialFeatureData::readStream().

00352 {
00353   SpatialFeatureData::readStream( str );
00354   for( size_t i = 0; i < 4; i++ ) {
00355     str>>cagt_vec[i];
00356   }
00357   str>>phd_vec;
00358   str>>gap_vec;
00359 }

void ChromatData::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.

Reimplemented from FeatureData.

Definition at line 361 of file featuredata.cpp.

References cagt_vec, gap_vec, phd_vec, and SpatialFeatureData::writeStream().

00362 {
00363   SpatialFeatureData::writeStream( str );
00364   for( size_t i = 0; i < 4; i++ ) {
00365     str<<cagt_vec[i];
00366   }
00367   str<<phd_vec;
00368   str<<gap_vec;
00369 }

void ChromatData::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.

Definition at line 371 of file featuredata.cpp.

References QDomElement::setAttribute(), and GeneralData::writeDom().

00372 {
00373     SpatialFeatureData::writeDom( elem );
00374     elem.setAttribute("cc", "11" );
00375 }

void ChromatData::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.

Definition at line 377 of file featuredata.cpp.

References GeneralData::readDom().

00378 {
00379     SpatialFeatureData::readDom( elem );
00380     //     tVector.readDom( elem );
00381 }

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

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

Reimplemented from FeatureData.

Definition at line 382 of file featuredata.cpp.

References cagt_vec, gap_vec, phd_vec, SpatialFeatureData::readAttributes(), TrapperVector< T >::readString(), and QXmlAttributes::value().

Referenced by MacsimParser::endElement().

00383 {
00384     SpatialFeatureData::readAttributes(attr);
00385     //Order is c, a, g, t
00386     if ( attr.value("c_vector") != "" ) {
00387       QString str = attr.value("c_vector");
00388       cagt_vec[0].readString(str);
00389 
00390     }
00391     if ( attr.value("a_vector") != "" ) {
00392       QString str = attr.value("a_vector");
00393       cagt_vec[1].readString(str);
00394 
00395     }
00396     if ( attr.value("g_vector") != "" ) {
00397       QString str = attr.value("g_vector");
00398       cagt_vec[2].readString(str);
00399 
00400     }
00401     if ( attr.value("t_vector") != "" ) {
00402       QString str = attr.value("t_vector");
00403       cagt_vec[3].readString(str);
00404 
00405     }
00406     if ( attr.value("phd") != "" ) {
00407       QString str = attr.value("phd");
00408       phd_vec.readString(str);
00409 
00410     }
00411     if ( attr.value("gap") != "" ) {
00412       QString str = attr.value("gap");
00413       gap_vec.readString(str);
00414 
00415     }
00416     
00417 }

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

Reimplemented from FeatureData.

Definition at line 418 of file featuredata.cpp.

References cagt_vec, gap_vec, phd_vec, TrapperVector< T >::stlVector(), and SpatialFeatureData::writeXml().

00419 {
00420   SpatialFeatureData::writeXml(stream);
00421   if ( cagt_vec[0].stlVector().size() > 0 ) {
00422     stream<<" c_vector=\"";
00423     for( size_t i = 0; i < cagt_vec[0].stlVector().size(); i++ ) {
00424       stream<<' '<<cagt_vec[0].stlVector()[i];
00425     }
00426     stream<<"\"";
00427   }
00428   if ( cagt_vec[1].stlVector().size() > 0 ) {
00429     stream<<" a_vector=\"";
00430     for( size_t i = 0; i < cagt_vec[1].stlVector().size(); i++ ) {
00431       stream<<' '<<cagt_vec[1].stlVector()[i];
00432     }
00433     stream<<"\"";
00434   }
00435   if ( cagt_vec[2].stlVector().size() > 0 ) {
00436     stream<<" g_vector=\"";
00437     for( size_t i = 0; i < cagt_vec[2].stlVector().size(); i++ ) {
00438       stream<<' '<<cagt_vec[2].stlVector()[i];
00439     }
00440     stream<<"\"";
00441   }
00442   if ( cagt_vec[3].stlVector().size() > 0 ) {
00443     stream<<" t_vector=\"";
00444     for( size_t i = 0; i < cagt_vec[3].stlVector().size(); i++ ) {
00445       stream<<' '<<cagt_vec[3].stlVector()[i];
00446     }
00447     stream<<"\"";
00448   }
00449   if ( phd_vec.stlVector().size() > 0 ) {
00450     stream<<" phd=\"";
00451     for( size_t i = 0; i < phd_vec.stlVector().size(); i++ ) {
00452       stream<<' '<<phd_vec.stlVector()[i];
00453     }
00454     stream<<"\"";
00455   }
00456   if ( gap_vec.stlVector().size() > 0 ) {
00457     stream<<" gap=\"";
00458     for( size_t i = 0; i < gap_vec.stlVector().size(); i++ ) {
00459       stream<<' '<<gap_vec.stlVector()[i];
00460     }
00461     stream<<"\"";
00462   }
00463   
00464   stream<<"/>\n";
00465 }

FeatureGui* ChromatData::makeGui (  )  [inline, protected, virtual]

Implements FeatureData.

Definition at line 185 of file featuredata.h.

00185 { return new ChromatGui(this); }

std::string ChromatData::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 151 of file spatialfeaturedata.h.

00151 { return std::string("ChromatData"); }

void ChromatData::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.

Reimplemented from FeatureData.

void ChromatData::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.

Reimplemented from FeatureData.

void ChromatData::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.

void ChromatData::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.

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

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

Reimplemented from FeatureData.

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

Reimplemented from FeatureData.

FeatureGui* ChromatData::makeGui (  )  [inline, protected, virtual]

Implements FeatureData.

Definition at line 166 of file spatialfeaturedata.h.

00166 { return new ChromatGui(this); }

Member Data Documentation

std::vector<TrapperVector<Q_UINT32> > ChromatData::cagt_vec

Definition at line 180 of file featuredata.h.

Referenced by TrapperDoc::importChromat(), TrapperDoc::importPhd(), ChromatGui::paintMe(), readAttributes(), readStream(), writeStream(), and writeXml().

TrapperVector<Q_UINT32> ChromatData::phd_vec

Definition at line 181 of file featuredata.h.

Referenced by TrapperDoc::importPhd(), ChromatGui::paintMe(), readAttributes(), readStream(), writeStream(), and writeXml().

TrapperVector<Q_UINT32> ChromatData::gap_vec

Definition at line 182 of file featuredata.h.

Referenced by TrapperDoc::importPhd(), ChromatGui::paintMe(), readAttributes(), readStream(), writeStream(), and writeXml().

std::vector<TrapperVector<Q_UINT32> > ChromatData::cagt_vec

Definition at line 161 of file spatialfeaturedata.h.

TrapperVector<Q_UINT32> ChromatData::phd_vec

Definition at line 162 of file spatialfeaturedata.h.

TrapperVector<Q_UINT32> ChromatData::gap_vec

Definition at line 163 of file spatialfeaturedata.h.

The documentation for this class was generated from the following files:
Generated on Fri Jul 17 20:19:45 2009 for ngsview by  doxygen 1.5.1