Individual Class Reference

#include <Individual.h>

List of all members.

Public Member Functions
	Individual ()
	Individual (const std::string &id)
	Individual (const std::string &id, int rowIndex, int tableIndex)
	Individual (const std::string &id, const std::string &motherId, const std::string &fatherId, const std::string &gender)
	Individual (const std::string &id, const std::string &motherId, const std::string &fatherId, const std::string &gender, int rowIndex, int tableIndex)
void	setOrdinaryFounder (bool value)
void	setOriginalFounder (bool value)
void	setExternalConnection (bool value)
void	setIsUnconnected (bool value)
void	setIsConsanguinous (bool value)
void	setMother (Individual *mother)
void	setFather (Individual *father)
void	setAdoptedComplement (Individual *adoptedComplement)
void	setDOB (Date *dob)
void	setAffectionStatus (Affected *affected)
void	setProbandStatus (Proband *proband)
void	setDeceasedStatus (LivingDead *deceased)
void	setVirtualIndividual (bool value)
void	setMotherId (std::string motherId)
void	setFatherId (std::string fatherId)
void	setTwin (std::string marker, Twin::TWIN_TYPE type)
void	setGender (std::string gender)
void	setSampled (Sampled *sampled)
void	setConsultandStatus (Consultand *consultand)
void	setCarrierStatus (Carrier *carrier)
void	setRelationshipEndedStatus (RelationshipEnded *relationshipEnded)
void	setInfertilityStatus (Infertility *infertility)
void	setSterilityStatus (Sterility *sterility)
void	setBirthOrder (unsigned birthOrder)
void	setLeftWidth (unsigned leftWidth)
void	setRightWidth (unsigned rightWidth)
void	setTotalWidth (unsigned totalWidth)
void	setX (double x)
void	setY (double y)
void	setLeftSideOfLoop (unsigned loopNumber)
void	setRightSideOfLoop (unsigned loopNumber)
void	setLeftSideOfExternalConnection (unsigned connectionNumber)
void	setRightSideOfExternalConnection (unsigned connectionNumber)
void	setHasBeenDrawn ()
void	setVisited (bool value)
void	setLeftSpouseConnector (bool value)
String	getId (void)
String	getMotherId (void)
String	getFatherId (void)
Gender	getGender (void)
Date *	getDOB (void)
bool	isOrdinaryFounder (void)
bool	isOriginalFounder (void)
bool	isVirtual (void)
bool	hasExternalConnection (void)
bool	hasBeenVisited (void)
bool	hasBeenDrawn (void)
bool	isConsanguinous (void)
bool	isAffected (void)
bool	isSampled (void)
bool	isProband (void)
bool	isConsultand (void)
bool	isCarrier (void)
bool	relationshipHasEnded (void)
bool	isInfertile (void)
bool	isSterile (void)
bool	isDeceased (void)
RelationshipEnded::TYPE	getRelationshipEndedType (void) const
Infertility::TYPE	getInfertilityType (void) const
Sterility::TYPE	getSterilityType (void) const
std::string	getInfertilityLabel (void) const
std::string	getSterilityLabel (void) const
unsigned	getBirthOrder (void)
unsigned	getRowIndex (void)
Individual *	getFather (void)
Individual *	getMother (void)
Individual *	getAdoptedComplement (void)
Individual *	getFirstSpouse (void)
Twin	getTwinMarker (void)
unsigned	getNumberOfSpouses (void)
unsigned	getNumberOfChildren (void)
unsigned	getNumberOfDescentTrees (void)
unsigned	getNumberOfNuclearFamilies (void)
NuclearFamily *	getNuclearFamily (unsigned index)
std::set< unsigned >	getDescentTrees (void)
unsigned	getLeftWidth (void)
unsigned	getRightWidth (void)
unsigned	getTotalWidth (void)
double	getX (void)
double	getY (void)
unsigned	getLeftSideOfLoop (void)
unsigned	getRightSideOfLoop (void)
unsigned	getLeftSideOfExternalConnection (void)
unsigned	getRightSideOfExternalConnection (void)
unsigned	getLeftFlag (bool consanguinousLoop)
unsigned	getRightFlag (bool consanguinousLoop)
bool	getLeftSpouseConnector (void)
std::vector< std::string >	getChildrenIds (Individual *spouse)
const std::set< Individual *, compareIndividual > *const	getSpouses (void) const
const std::set< Individual *, compareIndividual > *const	getChildren (void) const
void	getChildrenWithSpouse (Individual *spouse, std::vector< Individual * > &children)
void	getChildrenSortedByExternalConnections (Individual *spouse, std::vector< Individual * > &children)
void	setPedigreeDataTable (const DataTable *pedigreeTable)
Data *	getData (const std::string label)
void	sortSpouses (bool externalFlag=false)
void	addSpouse (Individual *spouse)
void	addChild (Individual *child)
void	addDescentTree (unsigned descentTreeId)
void	addNuclearFamily (NuclearFamily *nuclearFamily)
void	setChildrenIdsSortedByExternalConnections (std::string parentPair, std::vector< Individual * > children)
void	displayChildren ()
void	displaySpouses ()
void	displayNuclearFamilies ()
void	display ()
bool	isIndividualIndicatingNoOffspring (void)
bool	isIndividualIndicatingNonFertility (void)
bool	isIndividualIndicatingTerminatedPregnancy (void)
bool	isIndividualAdoptedIn (void)
bool	isIndividualAdoptedOut (void)
bool	isSpecial (void)
const DataTable *	getDataTable (void) const
int	getVisitCount ()
void	resetVisitCount ()
void	incrementVisitCount ()
Static Public Member Functions
static std::string	getRandomId ()
static void	groupIndividualsBasedOn (bool consanguinousLoop, const std::vector< Individual * > &individuals, std::deque< Individual * > &initial, std::deque< Individual * > &left, std::deque< Individual * > &right, bool unique=false)
static std::vector< Individual * >	sortIndividualsBasedOnDataField (const std::string &name, const std::vector< Individual * > &individuals, bool dobSortOrder)
static void	setSampledColumnPresent ()
static bool	getSampledColumnPresent ()
Private Member Functions
void	_init (void)
void	_checkForSpecialIndividualTypes (void)
void	_rearrangeMultipleSpouses (std::deque< Individual * > &initial, std::deque< Individual * > &left, std::deque< Individual * > &right, std::deque< Individual * > &result)
Private Attributes
String	_id
String	_motherId
String	_fatherId
Gender	_gender
Date *	_dob
Date *	_dod
Affected *	_affected
LivingDead *	_deceased
Proband *	_proband
Consultand *	_consultand
Carrier *	_carrier
RelationshipEnded *	_relationshipEnded
Sterility *	_sterility
Infertility *	_infertility
Twin	_twinMarker
Sampled *	_sampled
Individual *	_father
Individual *	_mother
Individual *	_adoptedComplement
bool	_isVirtual
bool	_isUnconnected
bool	_isConsanguinous
bool	_hasExternalConnection
unsigned	_birthOrder
bool	_isOriginalFounder
bool	_isOrdinaryFounder
unsigned	_leftWidth
unsigned	_rightWidth
unsigned	_totalWidth
double	_x
double	_y
bool	_hasBeenVisited
int	_visitCount
bool	_hasBeenDrawn
unsigned	_leftSideOfLoop
unsigned	_rightSideOfLoop
unsigned	_leftSideOfExternalConnection
unsigned	_rightSideOfExternalConnection
bool	_leftSpouseConnector
std::set< Individual *, compareIndividual >	_spouses
std::set< Individual *, compareIndividual >	_children
std::map< std::string, std::vector< Individual * > >	_childrenIdsSortedByExternalConnections
std::set< unsigned >	_descentTrees
std::vector< NuclearFamily * >	_nuclearFamilies
int	_rowIndex
int	_tableIndex
const DataTable *	_pedigreeTable
bool	_individualIndicatingNoOffspring
bool	_individualIndicatingNonFertility
bool	_individualIndicatingTerminatedPregnancy
bool	_individualAdoptedOut
bool	_individualAdoptedIn
bool	_isSpecial
Static Private Attributes
static bool	_sampledColumnPresent = false
Classes
struct	compareData
struct	compareIndividual

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Constructor & Destructor Documentation

Individual::Individual (   )

Individual::Individual (  const std::string &  id  )

Individual::Individual (  const std::string &  id, int  rowIndex, int  tableIndex )

Individual::Individual (  const std::string &  id, const std::string &  motherId, const std::string &  fatherId, const std::string &  gender )

Individual::Individual (  const std::string &  id, const std::string &  motherId, const std::string &  fatherId, const std::string &  gender, int  rowIndex, int  tableIndex )

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Member Function Documentation

void Individual::_checkForSpecialIndividualTypes (  void   )  [private]

void Individual::_init (  void   )  [inline, private]

void Individual::_rearrangeMultipleSpouses (  std::deque< Individual * > &  initial, std::deque< Individual * > &  left, std::deque< Individual * > &  right, std::deque< Individual * > &  result )  [private]

void Individual::addChild (  Individual *  child  )  [inline]

void Individual::addDescentTree (  unsigned  descentTreeId  )  [inline]

void Individual::addNuclearFamily (  NuclearFamily *  nuclearFamily  )  [inline]

void Individual::addSpouse (  Individual *  spouse  )

void Individual::display (   )

void Individual::displayChildren (   )

void Individual::displayNuclearFamilies (   )

void Individual::displaySpouses (   )

Individual* Individual::getAdoptedComplement (  void   )  [inline]

unsigned Individual::getBirthOrder (  void   )  [inline]

const std::set< Individual *, Individual::compareIndividual > *const Individual::getChildren (  void   )  const

std::vector< std::string > Individual::getChildrenIds (  Individual *  spouse  )

getChildrenIds: with a given spouse

void Individual::getChildrenSortedByExternalConnections (  Individual *  spouse, std::vector< Individual * > &  children )

void Individual::getChildrenWithSpouse (  Individual *  spouse, std::vector< Individual * > &  children )

Data* Individual::getData (  const std::string  label  )  [inline]

const DataTable* Individual::getDataTable (  void   )  const [inline]

std::set<unsigned> Individual::getDescentTrees (  void   )  [inline]

Date* Individual::getDOB (  void   )  [inline]

Individual* Individual::getFather (  void   )  [inline]

String Individual::getFatherId (  void   )  [inline]

Individual * Individual::getFirstSpouse (  void   )

getFirstSpouse: Used in cases with missing mother or father id in the input pedigree data table.

Gender Individual::getGender (  void   )  [inline]

String Individual::getId (  void   )  [inline]

std::string Individual::getInfertilityLabel (  void   )  const [inline]

Infertility::TYPE Individual::getInfertilityType (  void   )  const [inline]

unsigned Individual::getLeftFlag (  bool  consanguinousLoop  )

getLeftFlag: Get the consanguinity or external left flag

unsigned Individual::getLeftSideOfExternalConnection (  void   )  [inline]

unsigned Individual::getLeftSideOfLoop (  void   )  [inline]

bool Individual::getLeftSpouseConnector (  void   )  [inline]

unsigned Individual::getLeftWidth (  void   )  [inline]

Individual* Individual::getMother (  void   )  [inline]

String Individual::getMotherId (  void   )  [inline]

NuclearFamily * Individual::getNuclearFamily (  unsigned  index  )

unsigned Individual::getNumberOfChildren (  void   )  [inline]

unsigned Individual::getNumberOfDescentTrees (  void   )  [inline]

unsigned Individual::getNumberOfNuclearFamilies (  void   )  [inline]

unsigned Individual::getNumberOfSpouses (  void   )  [inline]

std::string Individual::getRandomId (   )  [static]

getRandomId: Generates a random id for virtual Individuals.

RelationshipEnded::TYPE Individual::getRelationshipEndedType (  void   )  const [inline]

unsigned Individual::getRightFlag (  bool  consanguinousLoop  )

getRightFlag: Get the consanguinity or external right flag

unsigned Individual::getRightSideOfExternalConnection (  void   )  [inline]

unsigned Individual::getRightSideOfLoop (  void   )  [inline]

unsigned Individual::getRightWidth (  void   )  [inline]

unsigned Individual::getRowIndex (  void   )  [inline]

bool Individual::getSampledColumnPresent (   )  [static]

const std::set< Individual *, Individual::compareIndividual > *const Individual::getSpouses (  void   )  const

std::string Individual::getSterilityLabel (  void   )  const [inline]

Sterility::TYPE Individual::getSterilityType (  void   )  const [inline]

unsigned Individual::getTotalWidth (  void   )  [inline]

Twin Individual::getTwinMarker (  void   )  [inline]

int Individual::getVisitCount (   )  [inline]

double Individual::getX (  void   )  [inline]

double Individual::getY (  void   )  [inline]

void Individual::groupIndividualsBasedOn (  bool  consanguinousLoop, const std::vector< Individual * > &  individuals, std::deque< Individual * > &  initial, std::deque< Individual * > &  left, std::deque< Individual * > &  right, bool  unique = false )  [static]

groupIndividualsBasedOn: Splits individuals into three queues left, right and initial based on the consanguinous/external flags. Individuals with left flag set are pushed onto the left queue in increasing order of the left flags. Individuals with right flag set are pushed onto the right queue in descending order of the right flags.

bool Individual::hasBeenDrawn (  void   )  [inline]

bool Individual::hasBeenVisited (  void   )  [inline]

bool Individual::hasExternalConnection (  void   )  [inline]

void Individual::incrementVisitCount (   )  [inline]

bool Individual::isAffected (  void   )  [inline]

bool Individual::isCarrier (  void   )  [inline]

bool Individual::isConsanguinous (  void   )  [inline]

bool Individual::isConsultand (  void   )  [inline]

bool Individual::isDeceased (  void   )  [inline]

bool Individual::isIndividualAdoptedIn (  void   )  [inline]

bool Individual::isIndividualAdoptedOut (  void   )  [inline]

bool Individual::isIndividualIndicatingNonFertility (  void   )  [inline]

bool Individual::isIndividualIndicatingNoOffspring (  void   )  [inline]

bool Individual::isIndividualIndicatingTerminatedPregnancy (  void   )  [inline]

bool Individual::isInfertile (  void   )  [inline]

bool Individual::isOrdinaryFounder (  void   )  [inline]

bool Individual::isOriginalFounder (  void   )  [inline]

bool Individual::isProband (  void   )  [inline]

bool Individual::isSampled (  void   )  [inline]

bool Individual::isSpecial (  void   )  [inline]

bool Individual::isSterile (  void   )  [inline]

bool Individual::isVirtual (  void   )  [inline]

bool Individual::relationshipHasEnded (  void   )  [inline]

void Individual::resetVisitCount (   )  [inline]

void Individual::setAdoptedComplement (  Individual *  adoptedComplement  )  [inline]

void Individual::setAffectionStatus (  Affected *  affected  )  [inline]

void Individual::setBirthOrder (  unsigned  birthOrder  )  [inline]

void Individual::setCarrierStatus (  Carrier *  carrier  )  [inline]

void Individual::setChildrenIdsSortedByExternalConnections (  std::string  parentPair, std::vector< Individual * >  children )

void Individual::setConsultandStatus (  Consultand *  consultand  )  [inline]

void Individual::setDeceasedStatus (  LivingDead *  deceased  )  [inline]

void Individual::setDOB (  Date *  dob  )  [inline]

void Individual::setExternalConnection (  bool  value  )  [inline]

void Individual::setFather (  Individual *  father  )  [inline]

void Individual::setFatherId (  std::string  fatherId  )  [inline]

void Individual::setGender (  std::string  gender  )  [inline]

void Individual::setHasBeenDrawn (   )  [inline]

void Individual::setInfertilityStatus (  Infertility *  infertility  )  [inline]

void Individual::setIsConsanguinous (  bool  value  )  [inline]

void Individual::setIsUnconnected (  bool  value  )  [inline]

void Individual::setLeftSideOfExternalConnection (  unsigned  connectionNumber  )  [inline]

void Individual::setLeftSideOfLoop (  unsigned  loopNumber  )  [inline]

void Individual::setLeftSpouseConnector (  bool  value  )  [inline]

void Individual::setLeftWidth (  unsigned  leftWidth  )  [inline]

void Individual::setMother (  Individual *  mother  )  [inline]

void Individual::setMotherId (  std::string  motherId  )  [inline]

void Individual::setOrdinaryFounder (  bool  value  )  [inline]

void Individual::setOriginalFounder (  bool  value  )  [inline]

void Individual::setPedigreeDataTable (  const DataTable *  pedigreeTable  )  [inline]

void Individual::setProbandStatus (  Proband *  proband  )  [inline]

void Individual::setRelationshipEndedStatus (  RelationshipEnded *  relationshipEnded  )  [inline]

void Individual::setRightSideOfExternalConnection (  unsigned  connectionNumber  )  [inline]

void Individual::setRightSideOfLoop (  unsigned  loopNumber  )  [inline]

void Individual::setRightWidth (  unsigned  rightWidth  )  [inline]

void Individual::setSampled (  Sampled *  sampled  )  [inline]

void Individual::setSampledColumnPresent (   )  [static]

void Individual::setSterilityStatus (  Sterility *  sterility  )  [inline]

void Individual::setTotalWidth (  unsigned  totalWidth  )  [inline]

void Individual::setTwin (  std::string  marker, Twin::TWIN_TYPE  type )  [inline]

void Individual::setVirtualIndividual (  bool  value  )  [inline]

void Individual::setVisited (  bool  value  )  [inline]

void Individual::setX (  double  x  )  [inline]

void Individual::setY (  double  y  )  [inline]

std::vector< Individual * > Individual::sortIndividualsBasedOnDataField (  const std::string &  name, const std::vector< Individual * > &  individuals, bool  dobSortOrder )  [static]

void Individual::sortSpouses (  bool  externalFlag = false  )

sortSpouses: If the descent tree has consanguinity/external connections find the optimal ordering of the spouses.

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Member Data Documentation

Individual* Individual::_adoptedComplement [private]

Affected* Individual::_affected [private]

unsigned Individual::_birthOrder [private]

Carrier* Individual::_carrier [private]

std::set<Individual *,compareIndividual> Individual::_children [private]

std::map<std::string, std::vector<Individual*> > Individual::_childrenIdsSortedByExternalConnections [private]

Consultand* Individual::_consultand [private]

LivingDead* Individual::_deceased [private]

std::set<unsigned> Individual::_descentTrees [private]

Date* Individual::_dob [private]

Date* Individual::_dod [private]

Individual* Individual::_father [private]

String Individual::_fatherId [private]

Gender Individual::_gender [private]

bool Individual::_hasBeenDrawn [private]

bool Individual::_hasBeenVisited [private]

bool Individual::_hasExternalConnection [private]

String Individual::_id [private]

bool Individual::_individualAdoptedIn [private]

bool Individual::_individualAdoptedOut [private]

bool Individual::_individualIndicatingNonFertility [private]

bool Individual::_individualIndicatingNoOffspring [private]

bool Individual::_individualIndicatingTerminatedPregnancy [private]

Infertility* Individual::_infertility [private]

bool Individual::_isConsanguinous [private]

bool Individual::_isOrdinaryFounder [private]

bool Individual::_isOriginalFounder [private]

bool Individual::_isSpecial [private]

bool Individual::_isUnconnected [private]

bool Individual::_isVirtual [private]

unsigned Individual::_leftSideOfExternalConnection [private]

unsigned Individual::_leftSideOfLoop [private]

bool Individual::_leftSpouseConnector [private]

unsigned Individual::_leftWidth [private]

Individual* Individual::_mother [private]

String Individual::_motherId [private]

std::vector<NuclearFamily*> Individual::_nuclearFamilies [private]

const DataTable* Individual::_pedigreeTable [private]

Proband* Individual::_proband [private]

RelationshipEnded* Individual::_relationshipEnded [private]

unsigned Individual::_rightSideOfExternalConnection [private]

unsigned Individual::_rightSideOfLoop [private]

unsigned Individual::_rightWidth [private]

int Individual::_rowIndex [private]

Sampled* Individual::_sampled [private]

bool Individual::_sampledColumnPresent = false [static, private]

std::set<Individual *,compareIndividual> Individual::_spouses [private]

Sterility* Individual::_sterility [private]

int Individual::_tableIndex [private]

unsigned Individual::_totalWidth [private]

Twin Individual::_twinMarker [private]

int Individual::_visitCount [private]

double Individual::_x [private]

double Individual::_y [private]

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The documentation for this class was generated from the following files:

• Individual.h
• Individual.cpp

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