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matvec::GenotypeNode Class Reference

#include <gnodederived.h>

Inheritance diagram for matvec::GenotypeNode:

matvec::GNode List of all members.

Detailed Description

This is the genotype node class.

GenotypeNode class has methods relevant to a genotype node

Definition at line 116 of file gnodederived.h.

Public Methods

 GenotypeNode (void)
unsigned getState (void)
unsigned getOldState (void)
unsigned getAcceptedMatState (void)
unsigned getAcceptedPatState (void)
unsigned getmState (void)
unsigned getpState (void)
unsigned getWeight (void)
void reset (int i)
void resetAndSwitch (int i)
bool incr ()
 the method used to increment the genotypeState of a GenotypeNode

 ~GenotypeNode (void)
float getCutsetMagnitude (void)
void updateMysets (void)
CutSet * makeNeighSet (void)
CutSet calcBCutSetForPrevGNode (CutSet *FCutSetPrevGNode)
CutSet calcMyBCutSet (void)
void peel (void)
void reComputeGNode ()
void reverseSampleGNode ()
void sampleGNode ()
void release (void)
bool isMyNeighbor (GNode *refGNode)
virtual unsigned getAcceptedAlleleState (void)
virtual unsigned getMyAlleleState (void)
virtual unsigned getMyAlleleOrigin (void)

Public Attributes

unsigned genotypeState
unsigned candidateGenotypeState
unsigned acceptedGenotypeState
SafeSTLVector< MaternalPaternalAlleles > genotypeVector
SafeSTLVector< unsigned > genotypeCount
SafeSTLVector< MaternalPaternalAlleles > acceptedGenotypeVector
bool sampled
unsigned weight
set< GNodeSet * > SetofGNsts
CutSet * generatedSet
CutSet * myOldGNodeProbs
unsigned peelorder
unsigned id
unsigned connectFlag
unsigned numberOfCuts
SafeSTLVector< int > sampledStateCount

Static Public Attributes

GNodeList * gNodeListPtr

Constructor & Destructor Documentation

matvec::GenotypeNode::GenotypeNode (  void    )  [inline]
 

Definition at line 119 of file gnodederived.h.

References acceptedGenotypeVector, genotypeVector, and SafeSTLVector< MaternalPaternalAlleles >::name. 

00119                             {
00120                   genotypeVector.name = "genotypeVector";
00121                   acceptedGenotypeVector.name = "acceptedGenotypeVector";
00122           }

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

Definition at line 157 of file gnodederived.h. 

00157 {;}

Member Function Documentation

CutSet matvec::GNode::calcBCutSetForPrevGNode (  CutSet *    FCutSetPrevGNode )  [inherited]
 

CutSet matvec::GNode::calcMyBCutSet (  void    )  [inherited]
 

virtual unsigned matvec::GNode::getAcceptedAlleleState (  void    )  [inline, virtual, inherited]
 

Reimplemented in matvec::AlleleStateNode.

Definition at line 68 of file gnodestuff.h. 

00068                                                  {
00069       throw exception("GNode::getAcceptedAlleleState(): called for virtual function");
00070     };

unsigned matvec::GenotypeNode::getAcceptedMatState (  void    )  [inline, virtual]
 

Reimplemented from matvec::GNode.

Definition at line 133 of file gnodederived.h.

References acceptedGenotypeState. 

00133                                                    {
00134                   return acceptedGenotypeVector[acceptedGenotypeState].maternal;
00135           };

unsigned matvec::GenotypeNode::getAcceptedPatState (  void    )  [inline, virtual]
 

Reimplemented from matvec::GNode.

Definition at line 136 of file gnodederived.h.

References acceptedGenotypeState. 

00136                                                    {
00137                   return acceptedGenotypeVector[acceptedGenotypeState].paternal;
00138           };

float matvec::GNode::getCutsetMagnitude (  void    )  [inherited]
 

unsigned matvec::GenotypeNode::getmState (  void    )  [inline, virtual]
 

Reimplemented from matvec::GNode.

Definition at line 139 of file gnodederived.h.

References genotypeState. 

00139                                          {
00140                   return genotypeVector[genotypeState].maternal;
00141           };

virtual unsigned matvec::GNode::getMyAlleleOrigin (  void    )  [inline, virtual, inherited]
 

Reimplemented in matvec::AlleleOriginNode.

Definition at line 74 of file gnodestuff.h. 

00074                                             {
00075       throw exception("GNode::getmState(): called for virtual function");
00076     };

virtual unsigned matvec::GNode::getMyAlleleState (  void    )  [inline, virtual, inherited]
 

Reimplemented in matvec::AlleleStateNode.

Definition at line 71 of file gnodestuff.h. 

00071                                            {
00072       throw exception("GNode::getmState(): called for virtual function");
00073     };

unsigned matvec::GenotypeNode::getOldState (  void    )  [inline, virtual]
 

Reimplemented from matvec::GNode.

Definition at line 130 of file gnodederived.h.

References acceptedGenotypeState. 

00130                                             {
00131                   return acceptedGenotypeState;
00132           };

unsigned matvec::GenotypeNode::getpState (  void    )  [inline, virtual]
 

Reimplemented from matvec::GNode.

Definition at line 142 of file gnodederived.h.

References genotypeState. 

00142                                          {
00143                   return genotypeVector[genotypeState].paternal;
00144           };

unsigned matvec::GenotypeNode::getState (  void    )  [inline, virtual]
 

Reimplemented from matvec::GNode.

Definition at line 127 of file gnodederived.h.

References genotypeState. 

00127                                          {
00128                   return genotypeState;
00129           };

unsigned matvec::GenotypeNode::getWeight (  void    )  [inline, virtual]
 

Reimplemented from matvec::GNode.

Definition at line 145 of file gnodederived.h. 

00145                                           {
00146                   return genotypeVector.size();
00147           };

bool matvec::GenotypeNode::incr (  void    )  [virtual]
 

the method used to increment the genotypeState of a GenotypeNode

Reimplemented from matvec::GNode.

Definition at line 335 of file gnodederived.cpp.

References genotypeState, and genotypeVector. 

00335                        {
00336   // Authors: L. Radu Totir and Rohan L. Fernando 
00337   // (based on the incr() of Bernt Guldbrantdsen)
00338   // (June, 2003) 
00339   // Contributors:
00340   genotypeState++;
00341   if (genotypeState==genotypeVector.size()){
00342     genotypeState=0;
00343     return 0;
00344   }
00345   else {
00346     return 1;
00347   }
00348 }

bool matvec::GNode::isMyNeighbor (  GNode *    refGNode )  [inherited]
 

CutSet* matvec::GNode::makeNeighSet (  void    )  [inherited]
 

void matvec::GNode::peel (  void    )  [inherited]
 

void matvec::GNode::reComputeGNode (    )  [inherited]
 

Referenced by matvec::GNodeList::peelCutAndCompute().

void matvec::GNode::release (  void    )  [inherited]
 

Referenced by matvec::GNode::~GNode().

void matvec::GenotypeNode::reset (  int    i )  [inline, virtual]
 

Reimplemented from matvec::GNode.

Definition at line 148 of file gnodederived.h.

References genotypeState. 

00148                            {
00149                   genotypeState = i;
00150           };

void matvec::GenotypeNode::resetAndSwitch (  int    i )  [inline, virtual]
 

Reimplemented from matvec::GNode.

Definition at line 151 of file gnodederived.h.

References acceptedGenotypeState, and genotypeState. 

00151                                     {
00152                   acceptedGenotypeState = genotypeState; 
00153                   acceptedGenotypeVector = genotypeVector;
00154                   genotypeState = i;
00155           };

void matvec::GNode::reverseSampleGNode (    )  [inherited]
 

void matvec::GNode::sampleGNode (    )  [inherited]
 

Referenced by matvec::GNodeList::peelCutAndSample(), and matvec::GNodeList::peelOrderCutAndSample().

void matvec::GNode::updateMysets (  void    )  [inherited]
 

Member Data Documentation

unsigned matvec::GenotypeNode::acceptedGenotypeState
 

Definition at line 118 of file gnodederived.h.

Referenced by getAcceptedMatState(), getAcceptedPatState(), getOldState(), and resetAndSwitch().

SafeSTLVector<MaternalPaternalAlleles> matvec::GenotypeNode::acceptedGenotypeVector
 

Definition at line 125 of file gnodederived.h.

Referenced by GenotypeNode().

unsigned matvec::GenotypeNode::candidateGenotypeState
 

Definition at line 118 of file gnodederived.h.

unsigned matvec::GNode::connectFlag [inherited]
 

Definition at line 48 of file gnodestuff.h.

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

CutSet* matvec::GNode::generatedSet [inherited]
 

Definition at line 44 of file gnodestuff.h.

SafeSTLVector<unsigned> matvec::GenotypeNode::genotypeCount
 

Definition at line 124 of file gnodederived.h.

unsigned matvec::GenotypeNode::genotypeState
 

Definition at line 118 of file gnodederived.h.

Referenced by getmState(), getpState(), getState(), incr(), reset(), and resetAndSwitch().

SafeSTLVector<MaternalPaternalAlleles> matvec::GenotypeNode::genotypeVector
 

Definition at line 123 of file gnodederived.h.

Referenced by GenotypeNode(), and incr().

GNodeList * matvec::GNode::gNodeListPtr [static, inherited]
 

Definition at line 41 of file gnodestuff.cpp.

unsigned matvec::GNode::id [inherited]
 

Definition at line 47 of file gnodestuff.h.

Referenced by matvec::GNodeList::calcDistancefrom(), matvec::GNodeList::findSampleGNode(), matvec::Population::initAlleleNodeList(), matvec::Population::initGenotypeNodeList(), matvec::Population::initJointAlleleNodeList(), matvec::GNodeList::peelCutAndCompute(), matvec::GNodeList::peelCutAndSample(), and matvec::GNodeList::peelOrderCutAndSample().

CutSet* matvec::GNode::myOldGNodeProbs [inherited]
 

Definition at line 45 of file gnodestuff.h.

unsigned matvec::GNode::numberOfCuts [inherited]
 

Definition at line 49 of file gnodestuff.h.

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

unsigned matvec::GNode::peelorder [inherited]
 

Definition at line 46 of file gnodestuff.h.

Referenced by matvec::GNodeList::fill(), and matvec::compareGNodesPeelId::operator()().

bool matvec::GNode::sampled [inherited]
 

Definition at line 41 of file gnodestuff.h.

Referenced by matvec::compareGNodesWeight::operator()().

SafeSTLVector<int> matvec::GNode::sampledStateCount [inherited]
 

Definition at line 61 of file gnodestuff.h.

set< GNodeSet*> matvec::GNode::SetofGNsts [inherited]
 

Definition at line 43 of file gnodestuff.h.

Referenced by matvec::GNodeList::calcDistancefrom(), and matvec::GNodeList::inputGNodeSets().

unsigned matvec::GNode::weight [inherited]
 

Definition at line 42 of file gnodestuff.h.

Referenced by matvec::GNodeList::fill().

The documentation for this class was generated from the following files:
Generated on Thu Jun 16 17:14:23 2005 for Matvec by doxygen1.2.16