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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)

Public Attributes

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

Protected Member Functions

FeatureGui * makeGui ()

Detailed Description

The chromatogram data for the read.

Definition at line 147 of file featuredata.h.

Constructor & Destructor Documentation

ChromatData::ChromatData (   )  [inline]
 

Definition at line 150 of file featuredata.h.

00150                 : FeatureData(), cagt_vec(4)
00151   {}

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

Definition at line 311 of file featuredata.cpp.

00311                                                                               :
00312   FeatureData( readRecno, startPos, endPos ), cagt_vec(4)
00313 {}

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

Definition at line 154 of file featuredata.h.

00155   {}

Member Function Documentation

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

Implements FeatureData.

Definition at line 168 of file featuredata.h.

00168 { return new ChromatGui(this); }

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 346 of file featuredata.cpp.

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

00347 {
00348     FeatureData::readAttributes(attr);
00349     //Order is c, a, g, t
00350     if ( attr.value("c_vector") != "" ) {
00351       QString str = attr.value("c_vector");
00352       cagt_vec[0].readString(str);
00353 
00354     }
00355     if ( attr.value("a_vector") != "" ) {
00356       QString str = attr.value("a_vector");
00357       cagt_vec[1].readString(str);
00358 
00359     }
00360     if ( attr.value("g_vector") != "" ) {
00361       QString str = attr.value("g_vector");
00362       cagt_vec[2].readString(str);
00363 
00364     }
00365     if ( attr.value("t_vector") != "" ) {
00366       QString str = attr.value("t_vector");
00367       cagt_vec[3].readString(str);
00368 
00369     }
00370     if ( attr.value("phd") != "" ) {
00371       QString str = attr.value("phd");
00372       phd_vec.readString(str);
00373 
00374     }
00375     if ( attr.value("gap") != "" ) {
00376       QString str = attr.value("gap");
00377       gap_vec.readString(str);
00378 
00379     }
00380     
00381 }

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 FeatureData.

Definition at line 341 of file featuredata.cpp.

References FeatureData::readDom().

00342 {
00343     FeatureData::readDom( elem );
00344     //     tVector.readDom( elem );
00345 }

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 315 of file featuredata.cpp.

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

00316 {
00317   FeatureData::readStream( str );
00318   for( size_t i = 0; i < 4; i++ ) {
00319     str>>cagt_vec[i];
00320   }
00321   str>>phd_vec;
00322   str>>gap_vec;
00323 }

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 153 of file featuredata.h.

00153 { return std::string("ChromatData"); }

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 FeatureData.

Definition at line 335 of file featuredata.cpp.

References FeatureData::writeDom().

00336 {
00337     FeatureData::writeDom( elem );
00338     elem.setAttribute("cc", "11" );
00339 }

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 325 of file featuredata.cpp.

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

00326 {
00327   FeatureData::writeStream( str );
00328   for( size_t i = 0; i < 4; i++ ) {
00329     str<<cagt_vec[i];
00330   }
00331   str<<phd_vec;
00332   str<<gap_vec;
00333 }

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

Reimplemented from FeatureData.

Definition at line 382 of file featuredata.cpp.

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

00383 {
00384   FeatureData::writeXml(stream);
00385   if ( cagt_vec[0].stlVector().size() > 0 ) {
00386     stream<<" c_vector=\"";
00387     for( size_t i = 0; i < cagt_vec[0].stlVector().size(); i++ ) {
00388       stream<<' '<<cagt_vec[0].stlVector()[i];
00389     }
00390     stream<<"\"";
00391   }
00392   if ( cagt_vec[1].stlVector().size() > 0 ) {
00393     stream<<" a_vector=\"";
00394     for( size_t i = 0; i < cagt_vec[1].stlVector().size(); i++ ) {
00395       stream<<' '<<cagt_vec[1].stlVector()[i];
00396     }
00397     stream<<"\"";
00398   }
00399   if ( cagt_vec[2].stlVector().size() > 0 ) {
00400     stream<<" g_vector=\"";
00401     for( size_t i = 0; i < cagt_vec[2].stlVector().size(); i++ ) {
00402       stream<<' '<<cagt_vec[2].stlVector()[i];
00403     }
00404     stream<<"\"";
00405   }
00406   if ( cagt_vec[3].stlVector().size() > 0 ) {
00407     stream<<" t_vector=\"";
00408     for( size_t i = 0; i < cagt_vec[3].stlVector().size(); i++ ) {
00409       stream<<' '<<cagt_vec[3].stlVector()[i];
00410     }
00411     stream<<"\"";
00412   }
00413   if ( phd_vec.stlVector().size() > 0 ) {
00414     stream<<" phd=\"";
00415     for( size_t i = 0; i < phd_vec.stlVector().size(); i++ ) {
00416       stream<<' '<<phd_vec.stlVector()[i];
00417     }
00418     stream<<"\"";
00419   }
00420   if ( gap_vec.stlVector().size() > 0 ) {
00421     stream<<" gap=\"";
00422     for( size_t i = 0; i < gap_vec.stlVector().size(); i++ ) {
00423       stream<<' '<<gap_vec.stlVector()[i];
00424     }
00425     stream<<"\"";
00426   }
00427   
00428   stream<<"/>\n";
00429 }

Member Data Documentation

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

Definition at line 163 of file featuredata.h.

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

TrapperVector<Q_UINT32> ChromatData::gap_vec
 

Definition at line 165 of file featuredata.h.

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

TrapperVector<Q_UINT32> ChromatData::phd_vec
 

Definition at line 164 of file featuredata.h.

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

The documentation for this class was generated from the following files:
Generated on Fri Mar 17 17:44:57 2006 for trapper by  doxygen 1.4.4