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matvec::RecombinationSet Class Reference

#include <gnodesetderived.h>

Inheritance diagram for matvec::RecombinationSet:

matvec::GNodeSet List of all members.

Detailed Description

This is the "Recombination set" class.

RecombinationSet class is used when we peel across pedigree and loci jointly.

Definition at line 259 of file gnodesetderived.h.

Public Methods

double getValue (void)
 ~RecombinationSet (void)
bool incr (void)
void reset (void)
void attachMeToMyGnodes (void)
void display (void)
virtual double getTargetValue (void)
virtual double getOldValue (void)

Public Attributes

double r
unsigned connectFlag
unsigned numberOfCuts

Static Public Attributes

GeneticDist * prior
unsigned currentLocus

Constructor & Destructor Documentation

matvec::RecombinationSet::~RecombinationSet (  void    )  [inline]
 

Definition at line 291 of file gnodesetderived.h. 

00291 {;}

Member Function Documentation

void matvec::GNodeSet::attachMeToMyGnodes (  void    )  [inherited]
 

Referenced by matvec::Population::initAlleleNodeList(), matvec::Population::initGenotypeNodeList(), and matvec::Population::initJointAlleleNodeList().

void matvec::GNodeSet::display (  void    )  [inherited]
 

virtual double matvec::GNodeSet::getOldValue (  void    )  [inline, virtual, inherited]
 

Reimplemented in matvec::CutSet.

Definition at line 125 of file gnodestuff.h. 

00125                                     {
00126       throw exception("GNodeSet::getOldValue(void): call for virtual function");
00127     };

virtual double matvec::GNodeSet::getTargetValue (  void    )  [inline, virtual, inherited]
 

Reimplemented in matvec::TransitionSet.

Definition at line 122 of file gnodestuff.h. 

00122                                        {
00123       throw exception("GNodeSet::getTargetValue(void): call for virtual function");
00124     };

double matvec::RecombinationSet::getValue (  void    )  [inline, virtual]
 

Reimplemented from matvec::GNodeSet.

Definition at line 262 of file gnodesetderived.h.

References r. 

00262                          {
00263       RecombinationSet::iterator it;
00264       it = begin();
00265       //cout << "Size of recombination set is = " << size() << endl;
00266       //cout << "Elements of recombination set are: ";
00267       //for(it=begin();it!=end();it++){
00268       //cout << (*it)->id << " " << (*it)->getState() << " ";
00269       //}
00270       //cout << endl;
00271       it = begin();
00272       if(size()==1){
00273         return 0.5;
00274       }
00275       else if(size()==2){
00276         unsigned segOne = (*it)->getState();
00277         it++;
00278         unsigned segTwo = (*it)->getState();
00279         if(segOne==segTwo){
00280           return 1-r;
00281         }
00282         else{
00283           return r;
00284         }
00285       }
00286       else{
00287         cerr << "Trouble: I have found more than two GNodes in a RecombinationSet" << endl;
00288         exit(1);
00289       }
00290     }

bool matvec::GNodeSet::incr (  void    )  [inherited]
 

Referenced by matvec::CutSet::operator *=(), matvec::CutSet::operator+=(), and matvec::CutSet::operator=().

void matvec::GNodeSet::reset (  void    )  [inherited]
 

Referenced by matvec::CutSet::operator *=(), matvec::CutSet::operator+=(), and matvec::CutSet::operator=().

Member Data Documentation

unsigned matvec::GNodeSet::connectFlag [inherited]
 

Definition at line 111 of file gnodestuff.h.

Referenced by matvec::CutSet::replaceMeWith().

unsigned matvec::GNodeSet::currentLocus [static, inherited]
 

Definition at line 43 of file gnodestuff.cpp.

Referenced by matvec::GenoFounderSet::getValue(), matvec::AlleleFounderSet::getValue(), and matvec::CutSet::replaceMeWith().

unsigned matvec::GNodeSet::numberOfCuts [inherited]
 

Definition at line 112 of file gnodestuff.h.

Referenced by matvec::CutSet::replaceMeWith().

GeneticDist * matvec::GNodeSet::prior [static, inherited]
 

Definition at line 42 of file gnodestuff.cpp.

Referenced by matvec::RAlleleFounderSet::getValue(), matvec::GenoFounderSet::getValue(), matvec::AlleleFounderSet::getValue(), and matvec::CutSet::replaceMeWith().

double matvec::RecombinationSet::r
 

Definition at line 261 of file gnodesetderived.h.

Referenced by getValue(), and matvec::Population::initJointAlleleNodeList().

The documentation for this class was generated from the following file:
Generated on Thu Jun 16 17:14:47 2005 for Matvec by doxygen1.2.16