DataTable Class Reference

#include <DataTable.h>

List of all members.

Public Types
enum	TableType {   PEDIGREE, GENETICMAP, DECOMPOSED, RESULTS,   ALLELEFREQUENCY, UNKNOWNTABLETYPE }
Public Member Functions
	DataTable (TableParser &parser)
	~DataTable ()
void	addColumn (DataColumn *column)
unsigned	getColumnOrdinal (const char *name) const
std::string	getColumnName (unsigned ordinal) const
unsigned	getNumberOfColumns (void) const
DataColumn *	getColumn (unsigned ordinal) const
DataColumn *	getColumn (const std::string &name) const
void	deleteFrontColumn ()
void	display ()
void	printInputTableAsTabDelimited (std::string filename) const
void	printPedigreeTableAsTabDelimited (std::string filename) const
const TableType	getTableType (void) const
std::string	getTableTypeAsString (void) const
const unsigned	getNumberOfRows (void) const
bool	columnExists (const std::string &name) const
void	toggleColumnsForPedigree (const std::vector< std::string > &columns)
unsigned	getNumberOfShowOnPedigreeColumns () const
Data *	getDataAtIndex (const std::string name, unsigned long index) const
Data *	getDataAtIndex (unsigned columnIndex, unsigned long index) const
int	getAffectedColumnIndex (void) const
int	getDeceasedColumnIndex (void) const
int	getDOBColumnIndex (void) const
int	getDZTwinColumnIndex (void) const
int	getMZTwinColumnIndex (void) const
int	getProbandColumnIndex (void) const
int	getSampledColumnIndex (void) const
int	getSuperscriptColumnIndex (void) const
int	getConsultandColumnIndex (void) const
int	getCarrierColumnIndex (void) const
int	getRelationshipEndedColumnIndex (void) const
int	getInfertilityColumnIndex (void) const
int	getSterilityColumnIndex (void) const
unsigned	getIconColumnCount (void) const
unsigned	getIconColumnIndex (unsigned nth) const
unsigned	getLabelColumnIndex (unsigned nth) const
const std::vector< unsigned > *	getIconColumnVector (void) const
const std::vector< unsigned > *	getLabelColumnVector (void) const
ColorSeriesStack *	getColorSeriesStack (void) const
ColorSeries *	getColorSeriesFromStack (unsigned nth) const
ColorSeries *	getBlackAndWhiteSeriesFromStack (unsigned nth) const
Static Public Attributes
static const int	COLUMN_IS_MISSING = -1
static FieldLabels	labels
Private Member Functions
void	_setDeclaredTypesFromParser (const std::vector< char > *pDeclaredTypes)
void	_determineTableType (const std::vector< std::string > *pTitles)
void	_classifyRemainingColumns (const std::vector< std::string > *pElements, const std::vector< std::string > *pTitles)
void	_setColorSeriesStack (void)
Private Attributes
TableType	_tabletype
FileTypeClassifier	_fileTypeClassifier
FileTypeClassifier::FILE_TYPE	_fileType
const char *	_fileTypeName
std::set< DataColumn *, ltstr >	_columnSet
std::vector< std::set< DataColumn *, ltstr >::iterator >	_columnVector
std::vector< DATATYPE >	_finalTypes
unsigned long	_rows
unsigned	_columns
std::vector< unsigned >	_iconColumns
std::vector< unsigned >	_labelColumns
ColorSeriesStack *	_colorSeriesStack
ColorSeriesStack *	_blackAndWhiteSeriesStack
int	_affectedColumnIndex
int	_deceasedColumnIndex
int	_dobColumnIndex
int	_dzTwinColumnIndex
int	_mzTwinColumnIndex
int	_probandColumnIndex
int	_sampledColumnIndex
int	_superscriptColumnIndex
int	_consultandColumnIndex
int	_carrierColumnIndex
int	_relationshipEndedColumnIndex
int	_infertilityColumnIndex
int	_sterilityColumnIndex
Classes
struct	ltstr

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Detailed Description

This class is used to store data tables that have been read in from files. The files are read from a Parser class, classified, and then have their columns classified.

This class is used as a container for all types of data tables encountered in Madeline. At the same time, some aspects of the class are specific to pedigree tables (the most common table type encountered in Madeline). Due to the way that the table classi- fication code works, we felt it was better --without being very expensive-- to add some pedigree-table-specific functionality directly into DataTable rather than have to break out separate subclasses for each table type.

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Member Enumeration Documentation

enum DataTable::TableType

Enumerator: PEDIGREE  GENETICMAP  DECOMPOSED  RESULTS  ALLELEFREQUENCY  UNKNOWNTABLETYPE

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Constructor & Destructor Documentation

DataTable::DataTable (  TableParser &  parser  )

DataTable::~DataTable (   )

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Member Function Documentation

void DataTable::_classifyRemainingColumns (  const std::vector< std::string > *  pElements, const std::vector< std::string > *  pTitles )  [private]

void DataTable::_determineTableType (  const std::vector< std::string > *  pTitles  )  [private]

_determineTableType: This method determines the type of the data table. This method also classifies the column types of known core columns

void DataTable::_setColorSeriesStack (  void   )  [private]

void DataTable::_setDeclaredTypesFromParser (  const std::vector< char > *  pDeclaredTypes  )  [private]

void DataTable::addColumn (  DataColumn *  column  )

bool DataTable::columnExists (  const std::string &  name  )  const

columnExists(): Check if a column exists in a data table by searching the table header.

void DataTable::deleteFrontColumn (   )

void DataTable::display (   )

int DataTable::getAffectedColumnIndex (  void   )  const [inline]

ColorSeries * DataTable::getBlackAndWhiteSeriesFromStack (  unsigned  nth  )  const

int DataTable::getCarrierColumnIndex (  void   )  const [inline]

ColorSeries * DataTable::getColorSeriesFromStack (  unsigned  nth  )  const

ColorSeriesStack * DataTable::getColorSeriesStack (  void   )  const

DataColumn * DataTable::getColumn (  const std::string &  name  )  const

getColumn(): Get a column by name.

DataColumn * DataTable::getColumn (  unsigned  ordinal  )  const

getColumn(): Get a column by index/ordinal.

std::string DataTable::getColumnName (  unsigned  ordinal  )  const

getColumnName(): Returns the name of the column at physical position 'ordinal'.

unsigned DataTable::getColumnOrdinal (  const char *  name  )  const

getColumnOrdinal(): Returns the columns physical position.

int DataTable::getConsultandColumnIndex (  void   )  const [inline]

Data * DataTable::getDataAtIndex (  unsigned  columnIndex, unsigned long  index )  const

Data * DataTable::getDataAtIndex (  const std::string  name, unsigned long  index )  const

int DataTable::getDeceasedColumnIndex (  void   )  const [inline]

int DataTable::getDOBColumnIndex (  void   )  const [inline]

int DataTable::getDZTwinColumnIndex (  void   )  const [inline]

unsigned DataTable::getIconColumnCount (  void   )  const

getIconColumnCount(): Get a count of number of data fields that will be displayed on the icon. By default all the fields that have 'Affected' as the prefix will be used to display on the icon.

unsigned DataTable::getIconColumnIndex (  unsigned  nth  )  const

const std::vector< unsigned > * DataTable::getIconColumnVector (  void   )  const

getIconColumnVector(): Return a pointer to the _iconColumns vector.

int DataTable::getInfertilityColumnIndex (  void   )  const [inline]

unsigned DataTable::getLabelColumnIndex (  unsigned  nth  )  const

const std::vector< unsigned > * DataTable::getLabelColumnVector (  void   )  const

getlabelColumnVector(): Return a pointer to the _labelColumns vector.

int DataTable::getMZTwinColumnIndex (  void   )  const [inline]

unsigned DataTable::getNumberOfColumns (  void   )  const

getNumberOfColumns(): Returns the number of columns in the table.

const unsigned DataTable::getNumberOfRows (  void   )  const [inline]

unsigned DataTable::getNumberOfShowOnPedigreeColumns (   )  const

getNumberOfShowOnPedigreeColumns(): Get number of data columns that will be displayed on the pedigree output.

int DataTable::getProbandColumnIndex (  void   )  const [inline]

int DataTable::getRelationshipEndedColumnIndex (  void   )  const [inline]

int DataTable::getSampledColumnIndex (  void   )  const [inline]

int DataTable::getSterilityColumnIndex (  void   )  const [inline]

int DataTable::getSuperscriptColumnIndex (  void   )  const [inline]

const TableType DataTable::getTableType (  void   )  const [inline]

std::string DataTable::getTableTypeAsString (  void   )  const

void DataTable::printInputTableAsTabDelimited (  std::string  filename  )  const

void DataTable::printPedigreeTableAsTabDelimited (  std::string  filename  )  const

void DataTable::toggleColumnsForPedigree (  const std::vector< std::string > &  columns  )

toggleColumnsForPedigree(): User can specify any number of columns to be displayed on the pedigree. Mark all such columns for output display, if they exist.

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Member Data Documentation

int DataTable::_affectedColumnIndex [private]

ColorSeriesStack* DataTable::_blackAndWhiteSeriesStack [private]

int DataTable::_carrierColumnIndex [private]

ColorSeriesStack* DataTable::_colorSeriesStack [private]

unsigned DataTable::_columns [private]

std::set<DataColumn *,ltstr> DataTable::_columnSet [private]

std::vector< std::set<DataColumn *,ltstr>::iterator > DataTable::_columnVector [private]

int DataTable::_consultandColumnIndex [private]

int DataTable::_deceasedColumnIndex [private]

int DataTable::_dobColumnIndex [private]

int DataTable::_dzTwinColumnIndex [private]

FileTypeClassifier::FILE_TYPE DataTable::_fileType [private]

FileTypeClassifier DataTable::_fileTypeClassifier [private]

const char* DataTable::_fileTypeName [private]

std::vector<DATATYPE> DataTable::_finalTypes [private]

std::vector<unsigned> DataTable::_iconColumns [private]

int DataTable::_infertilityColumnIndex [private]

std::vector<unsigned> DataTable::_labelColumns [private]

int DataTable::_mzTwinColumnIndex [private]

int DataTable::_probandColumnIndex [private]

int DataTable::_relationshipEndedColumnIndex [private]

unsigned long DataTable::_rows [private]

int DataTable::_sampledColumnIndex [private]

int DataTable::_sterilityColumnIndex [private]

int DataTable::_superscriptColumnIndex [private]

TableType DataTable::_tabletype [private]

const int DataTable::COLUMN_IS_MISSING = -1 [static]

FieldLabels DataTable::labels [static]

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

• DataTable.h
• DataTable.cpp

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