DataTable< T > Class Template Reference

A class to aggregate structured data in an array. More...

#include <datatable.h>

Collaboration diagram for DataTable< T >:

Public Member Functions
	DataTable ()
	Default constructor. More...
	DataTable (unsigned int nbgroups, unsigned int nbclasses, unsigned int **classSizes)
	Constructor. More...
	~DataTable ()
void	allocate (unsigned int nbgroups, unsigned int nbclasses, unsigned int **classSizes)
	Creates a table of size given by the sum of all classes passed by the 'classSizes' matrix. More...
void	update (unsigned int nbgroups, unsigned int nbclasses, unsigned int **classSizes)
	Updates the group and classe sizes and re-allocates the table according to its new length. More...
void	free ()
	Deallocates all the allocated tables. More...
unsigned int	length ()
	Returns the length of the table (total number of elements present). More...
T *	getTable ()
	Accessor to the table array. More...
T *	getGroup (unsigned int group)
	Accessor to a group array. More...
T *	getClassWithinGroup (unsigned int group, unsigned int Class)
	Accessor to a class array whithin a group. More...
T	get (unsigned int group, unsigned int Class, unsigned int elmnt)
	Returns value stored of the element 'elmnt' of the class 'Class' in the group 'group'. More...
void	set (unsigned int group, unsigned int Class, unsigned int elmnt, T val)
	Sets the element 'elmnt' of the class 'Class' in the group 'group' to the value 'val'. More...
void	increment (unsigned int group, unsigned int Class, unsigned int elmnt)
	Increments 'elmnt' of the class 'Class' in the group 'group' by one. More...
void	plus (unsigned int group, unsigned int Class, unsigned int elmnt, T val)
	Adds 'val' to 'elmnt' in the class 'Class' in the group 'group'. More...
void	minus (unsigned int group, unsigned int Class, unsigned int elmnt, T val)
	Substracts 'val' from 'elmnt' in the class 'Class' in the group 'group'. More...
void	multiply (unsigned int group, unsigned int Class, unsigned int elmnt, T val)
	Multiplies 'elmnt' of the class 'Class' in the group 'group' by 'val'. More...
void	divide (unsigned int group, unsigned int Class, unsigned int elmnt, T val)
	Subdivide 'elmnt' of the class 'Class' in the group 'group' by 'val'. More...
void	init (T val)
	Sets all elements of the table to value 'val'. More...
unsigned int	getNumGroups ()
unsigned int	getNumClasses ()
unsigned int	size (unsigned int i, unsigned int j)
void	show_up ()

Private Member Functions
void	store_sizes (unsigned int nbgroups, unsigned int nbclasses, unsigned int **classSizes)
bool	sizeChange (unsigned int nbgroups, unsigned int nbclasses, unsigned int **classSizes)

Private Attributes
unsigned int	_length
	length of the table More...
unsigned int	_groups
	number of groups in the table More...
unsigned int	_classes
	number of classes within each group More...
unsigned int **	_cumulClassSizes
	Stores the indexes of each class of each group present in the table. More...
unsigned int *	_cumulGroupSizes
	Stores the indexes of each group present in the table. More...
unsigned int **	_sizes
T *	_table

Detailed Description

template<class T>
class DataTable< T >

A class to aggregate structured data in an array.

The information is subdivided into groups (e.g., patch) themselves structured in classes (e.g., age or sex classes).

Constructor & Destructor Documentation

DataTable() [1/2]

template<class T >

DataTable< T >::DataTable ( )

inline

Default constructor.

: _length(0), _groups(0), _classes(0), _cumulClassSizes(0), _cumulGroupSizes(0), _sizes(0), _table(0) { }

DataTable() [2/2]

template<class T >

DataTable< T >::DataTable ( unsigned int  nbgroups, unsigned int  nbclasses, unsigned int **  classSizes  )

inline

Constructor.

Parameters

nbgroups	the number of rows in the table, typically the number of patches
nbclasses	an array of the sizes of each row, i.e. the Patch sizes
classSizes	a matrix of the sizes of each class within each group

                                                                                      :
  _length(0), _groups(0), _classes(0), _cumulClassSizes(0), _cumulGroupSizes(0), _table(0) 
  {     allocate(nbgroups, nbclasses, classSizes); }

References DataTable< T >::allocate().

~DataTable()

template<class T >

DataTable< T >::~DataTable ( )

inline

{free();}

References DataTable< T >::free().

Member Function Documentation

allocate()

template<class T >

void DataTable< T >::allocate ( unsigned int  nbgroups, unsigned int  nbclasses, unsigned int **  classSizes  )

inline

Creates a table of size given by the sum of all classes passed by the 'classSizes' matrix.

Parameters

nbgroups	the number of rows in the table, typically the number of patches
nbclasses	the number of classes within a group, e.g. the age-classes
classSizes	a matrix (nbgroups X nbclasses) of the sizes of each class within each group

                                                                                                  { 
    //#ifdef _DEBUG_
    //    message("DataTable::allocate:\n");
    //#endif
 
    free();
    
    store_sizes(nbgroups, nbclasses, classSizes);
    
    _groups = nbgroups;
    _classes = nbclasses;
    _length = 0;
    
    _cumulClassSizes = new unsigned int*[_groups];
 
    for(unsigned int i = 0; i < _groups; i++){
      _cumulClassSizes[i] = new unsigned int [_classes];
      _cumulClassSizes[i][0] = 0;
      for(unsigned int j = 1; j < _classes; ++j)
        _cumulClassSizes[i][j] = _cumulClassSizes[i][j-1] + classSizes[i][j-1];
    }
    
    _cumulGroupSizes = new unsigned int[_groups];
    
    _cumulGroupSizes[0] = 0; 
    for(unsigned int i = 1; i < _groups; i++){
      _cumulGroupSizes[i] = _cumulGroupSizes[i-1];
      for(unsigned int j = 0; j < _classes; ++j) {
        _cumulGroupSizes[i] += classSizes[(i-1)][j];//total size of the previous group
        _length += classSizes[i][j];//aggregate to compute total length
      }
    }
    //add the sizes of first group classes to have the total length of the table
    for(unsigned int j = 0; j < _classes; ++j)
      _length += classSizes[0][j];
    
    _table = new T[_length];
    //#ifdef _DEBUG_
//        cout<<"DataTable::allocate:_table="<<_table<<endl;
    //#endif
  }

References DataTable< T >::_classes, DataTable< T >::_cumulClassSizes, DataTable< T >::_cumulGroupSizes, DataTable< T >::_groups, DataTable< T >::_length, DataTable< T >::_table, DataTable< T >::free(), and DataTable< T >::store_sizes().

Referenced by TTNeutralGenesSH::allocateTables(), DataTable< T >::DataTable(), and DataTable< T >::update().

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divide()

template<class T >

void DataTable< T >::divide ( unsigned int  group, unsigned int  Class, unsigned int  elmnt, T  val  )

inline

Subdivide 'elmnt' of the class 'Class' in the group 'group' by 'val'.

                                                                                         {
    _table[ _cumulGroupSizes[group] + _cumulClassSizes[group][Class] + elmnt ] /= val;
  }

References DataTable< T >::_cumulClassSizes, DataTable< T >::_cumulGroupSizes, and DataTable< T >::_table.

Referenced by TTNeutralGenesSH::setHeterozygosity().

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free()

template<class T >

void DataTable< T >::free ( )

inline

Deallocates all the allocated tables.

                {
//    cout << "\ncalling DataTable::free()\n";
//    cout <<  "    pointer state: table="<<_table<<" cumulGroupSizes="<<_cumulGroupSizes
//         <<"\n    cumulClassSizes="<<_cumulClassSizes<<" sizes="<<_sizes
//        <<endl;
 
    if(_table != NULL) delete [] _table;
    
    if(_cumulGroupSizes != NULL) delete [] _cumulGroupSizes;
//    cout << "    delete _cumulClassSizes\n";
    if(_cumulClassSizes != NULL){
      for(unsigned int i = 0; i < _groups; ++i) {
//        cout << "     "<<i<<":"<<_cumulClassSizes[i]<<endl;
        delete [] _cumulClassSizes[i];}
      delete [] _cumulClassSizes;
    }
//    cout << "    delete _sizes\n";
    if(_sizes != NULL){
      for(unsigned int i = 0; i < _groups; ++i) delete [] _sizes[i];
      delete [] _sizes;
    }
    
    _table = NULL;
    _cumulGroupSizes = NULL;
    _cumulClassSizes = NULL;
    _sizes = NULL;
    _length = 0;
//    cout << "DataTable::free() done\n";
}

References DataTable< T >::_cumulClassSizes, DataTable< T >::_cumulGroupSizes, DataTable< T >::_groups, DataTable< T >::_length, DataTable< T >::_sizes, and DataTable< T >::_table.

Referenced by DataTable< T >::allocate(), and DataTable< T >::~DataTable().

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get()

template<class T >

T DataTable< T >::get ( unsigned int  group, unsigned int  Class, unsigned int  elmnt  )

inline

Returns value stored of the element 'elmnt' of the class 'Class' in the group 'group'.

                                                                             {
    return _table[ _cumulGroupSizes[group] + _cumulClassSizes[group][Class] + elmnt ];
  } 

References DataTable< T >::_cumulClassSizes, DataTable< T >::_cumulGroupSizes, and DataTable< T >::_table.

Referenced by TTNeutralGenesSH::getHeterozygosity(), TTNeutralGenesSH::setAlleleTables(), TTNeutralGenesSH::setFst_li(), TTNeutralGenesSH::setFstatWeirCockerham(), TTNeutralGenesSH::setFstatWeirCockerham_MS(), TTNeutralGenesSH::setFstMatrix(), TTNeutralGenesSH::setHs(), TTNeutralGenesSH::setHs2(), TTNeutralGenesSH::setLociDivCounter(), TTNeutralGenesSH::setNeiGeneticDistance(), and TTNeutralGenesFH::write_varcompWC().

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getClassWithinGroup()

template<class T >

T* DataTable< T >::getClassWithinGroup ( unsigned int  group, unsigned int  Class  )

inline

Accessor to a class array whithin a group.

                                                                         {
    return &_table[ _cumulGroupSizes[group] + _cumulClassSizes[group][Class] ];}

References DataTable< T >::_cumulClassSizes, DataTable< T >::_cumulGroupSizes, and DataTable< T >::_table.

Referenced by TTQuantiSH::getSkewPerPatch(), and TTQuantiSH::setStats().

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getGroup()

template<class T >

T* DataTable< T >::getGroup ( unsigned int  group )

inline

Accessor to a group array.

{return &_table[ _cumulGroupSizes[group] ];}

References DataTable< T >::_cumulGroupSizes, and DataTable< T >::_table.

Referenced by TTQuantiSH::setStats().

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getNumClasses()

template<class T >

unsigned int DataTable< T >::getNumClasses ( )

inline

{return _classes;}

References DataTable< T >::_classes.

getNumGroups()

template<class T >

unsigned int DataTable< T >::getNumGroups ( )

inline

{return _groups;}

References DataTable< T >::_groups.

Referenced by TTNeutralGenesSH::getHeterozygosity(), TTNeutralGenesSH::setAlleleTables(), and TTNeutralGenesSH::setFstat().

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getTable()

template<class T >

T* DataTable< T >::getTable ( )

inline

Accessor to the table array.

{return _table;}

References DataTable< T >::_table.

increment()

template<class T >

void DataTable< T >::increment ( unsigned int  group, unsigned int  Class, unsigned int  elmnt  )

inline

Increments 'elmnt' of the class 'Class' in the group 'group' by one.

                                                                                     {
    ++_table[ _cumulGroupSizes[group] + _cumulClassSizes[group][Class] + elmnt ];
  }

References DataTable< T >::_cumulClassSizes, DataTable< T >::_cumulGroupSizes, and DataTable< T >::_table.

Referenced by TTNeutralGenesSH::setAlleleTables().

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init()

template<class T >

void DataTable< T >::init ( T  val )

inline

Sets all elements of the table to value 'val'.

{for(unsigned int i = 0; i < _length; ++i) _table[i] = val;} 

References DataTable< T >::_length, and DataTable< T >::_table.

Referenced by TTNeutralGenesSH::setAlleleTables(), and TTNeutralGenesSH::setHeteroTable().

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length()

template<class T >

unsigned int DataTable< T >::length ( )

inline

Returns the length of the table (total number of elements present).

{return _length;}

References DataTable< T >::_length.

minus()

template<class T >

void DataTable< T >::minus ( unsigned int  group, unsigned int  Class, unsigned int  elmnt, T  val  )

inline

Substracts 'val' from 'elmnt' in the class 'Class' in the group 'group'.

                                                                                        {
    _table[ _cumulGroupSizes[group] + _cumulClassSizes[group][Class] + elmnt ] -= val;
  }

References DataTable< T >::_cumulClassSizes, DataTable< T >::_cumulGroupSizes, and DataTable< T >::_table.

multiply()

template<class T >

void DataTable< T >::multiply ( unsigned int  group, unsigned int  Class, unsigned int  elmnt, T  val  )

inline

Multiplies 'elmnt' of the class 'Class' in the group 'group' by 'val'.

                                                                                           {
    _table[ _cumulGroupSizes[group] + _cumulClassSizes[group][Class] + elmnt ] *= val;
  }

References DataTable< T >::_cumulClassSizes, DataTable< T >::_cumulGroupSizes, and DataTable< T >::_table.

plus()

template<class T >

void DataTable< T >::plus ( unsigned int  group, unsigned int  Class, unsigned int  elmnt, T  val  )

inline

Adds 'val' to 'elmnt' in the class 'Class' in the group 'group'.

                                                                                       {
    _table[ _cumulGroupSizes[group] + _cumulClassSizes[group][Class] + elmnt ] += val;
  }

References DataTable< T >::_cumulClassSizes, DataTable< T >::_cumulGroupSizes, and DataTable< T >::_table.

Referenced by TTNeutralGenesSH::setHeteroTable().

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set()

template<class T >

void DataTable< T >::set ( unsigned int  group, unsigned int  Class, unsigned int  elmnt, T  val  )

inline

Sets the element 'elmnt' of the class 'Class' in the group 'group' to the value 'val'.

                                                                                      {
    _table[ _cumulGroupSizes[group] + _cumulClassSizes[group][Class] + elmnt ] = val;
  }

References DataTable< T >::_cumulClassSizes, DataTable< T >::_cumulGroupSizes, and DataTable< T >::_table.

Referenced by TTNeutralGenesSH::setAlleleTables(), and store_quanti_trait_values().

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show_up()

template<class T >

void DataTable< T >::show_up ( )

inline

  {
    message("DataTable: got %i groups of %i classes; total length is %i.\n", _groups, _classes, _length);
  }

References DataTable< T >::_classes, DataTable< T >::_groups, DataTable< T >::_length, and message().

size()

template<class T >

unsigned int DataTable< T >::size ( unsigned int  i, unsigned int  j  )

inline

{return _sizes[i][j];}

References DataTable< T >::_sizes.

Referenced by TTQuantiSH::getSkewPerPatch(), and TTQuantiSH::setDataTables().

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sizeChange()

template<class T >

bool DataTable< T >::sizeChange ( unsigned int  nbgroups, unsigned int  nbclasses, unsigned int **  classSizes  )

inlineprivate

                                                                                             {
    bool status = 0;
    if( nbgroups != _groups || nbclasses != _classes ) return true;
    else {
      for (unsigned int i = 0; i < _groups; i++)
        for (unsigned int j = 0; j < _classes; j++)
          status |= _sizes[i][j] != classSizes[i][j];
    }
    return status;
  }

References DataTable< T >::_classes, DataTable< T >::_groups, and DataTable< T >::_sizes.

Referenced by DataTable< T >::update().

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store_sizes()

template<class T >

void DataTable< T >::store_sizes ( unsigned int  nbgroups, unsigned int  nbclasses, unsigned int **  classSizes  )

inlineprivate

                                                                                              {
    
    if (_sizes != NULL) {
      for(unsigned int i = 0; i < nbgroups; ++i) delete [] _sizes[i];
      delete [] _sizes;
    }
    
    _sizes = new unsigned int * [nbgroups];
    
    for(unsigned int i = 0; i < nbgroups; ++i) {
      _sizes[i] = new unsigned int [nbclasses];
      for(unsigned int j = 0; j < nbclasses; ++j)
        _sizes[i][j] = classSizes[i][j];
    }
  }

References DataTable< T >::_sizes.

Referenced by DataTable< T >::allocate(), and DataTable< T >::update().

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update()

template<class T >

void DataTable< T >::update ( unsigned int  nbgroups, unsigned int  nbclasses, unsigned int **  classSizes  )

inline

Updates the group and classe sizes and re-allocates the table according to its new length.

Parameters

nbgroups	the number of rows in the table, typically the number of patches
nbclasses	the number of classes within a group, e.g. the age-class sizes
classSizes	a matrix of the sizes of each class within each group

                                                                                               {
    //#ifdef _DEBUG_
    //    message("DataTable::update:\n");
    //#endif
    if( nbgroups != _groups || nbclasses != _classes )
      
      allocate(nbgroups, nbclasses, classSizes); //free() is called in allocate
    
    else if ( sizeChange(nbgroups, nbclasses, classSizes) ) {
      
      store_sizes(nbgroups, nbclasses, classSizes);
      
      for(unsigned int i = 0; i < _groups; i++){
        for(unsigned int j = 1; j < _classes; ++j)
          _cumulClassSizes[i][j] = _cumulClassSizes[i][j-1] + classSizes[i][j-1];
      }
      _length = 0;
      _cumulGroupSizes[0] = 0; 
      for(unsigned int i = 1; i < _groups; i++){
        _cumulGroupSizes[i] = _cumulGroupSizes[i-1];
        for(unsigned int j = 0; j < _classes; ++j) {
          _cumulGroupSizes[i] += classSizes[(i-1)][j];
          _length += classSizes[i][j];
        }
      }
      
      for(unsigned int j = 0; j < _classes; ++j)
        _length += classSizes[0][j];
      
      if(_table != NULL) delete [] _table;
      
      _table = new T[_length];
    }
  }

References DataTable< T >::_classes, DataTable< T >::_cumulClassSizes, DataTable< T >::_cumulGroupSizes, DataTable< T >::_groups, DataTable< T >::_length, DataTable< T >::_table, DataTable< T >::allocate(), DataTable< T >::sizeChange(), and DataTable< T >::store_sizes().

Referenced by TTQuantiSH::setDataTables(), and TTNeutralGenesSH::setHeteroTable().

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Member Data Documentation

_classes

template<class T >

unsigned int DataTable< T >::_classes

private

number of classes within each group

Referenced by DataTable< T >::allocate(), DataTable< T >::getNumClasses(), DataTable< T >::show_up(), DataTable< T >::sizeChange(), and DataTable< T >::update().

_cumulClassSizes

template<class T >

unsigned int** DataTable< T >::_cumulClassSizes

private

Stores the indexes of each class of each group present in the table.

the aggregated sizes of each classe within each group given by: size(class i!=0) = sum of size( (class 0) to (class i-1) ) and size(class i=0) = 0. This is repeated for each group.

Referenced by DataTable< T >::allocate(), DataTable< T >::divide(), DataTable< T >::free(), DataTable< T >::get(), DataTable< T >::getClassWithinGroup(), DataTable< T >::increment(), DataTable< T >::minus(), DataTable< T >::multiply(), DataTable< T >::plus(), DataTable< T >::set(), and DataTable< T >::update().

_cumulGroupSizes

template<class T >

unsigned int* DataTable< T >::_cumulGroupSizes

private

Stores the indexes of each group present in the table.

the aggregated sizes of each group with size(group i=0) = 0 and size(group i!=0) = sum of size( (group 0) to (group i-1)) where the group sizes are the sum of the classe sizes of the groups.

Referenced by DataTable< T >::allocate(), DataTable< T >::divide(), DataTable< T >::free(), DataTable< T >::get(), DataTable< T >::getClassWithinGroup(), DataTable< T >::getGroup(), DataTable< T >::increment(), DataTable< T >::minus(), DataTable< T >::multiply(), DataTable< T >::plus(), DataTable< T >::set(), and DataTable< T >::update().

_groups

template<class T >

unsigned int DataTable< T >::_groups

private

number of groups in the table

Referenced by DataTable< T >::allocate(), DataTable< T >::free(), DataTable< T >::getNumGroups(), DataTable< T >::show_up(), DataTable< T >::sizeChange(), and DataTable< T >::update().

_length

template<class T >

unsigned int DataTable< T >::_length

private

length of the table

Referenced by DataTable< T >::allocate(), DataTable< T >::free(), DataTable< T >::init(), DataTable< T >::length(), DataTable< T >::show_up(), and DataTable< T >::update().

_sizes

template<class T >

unsigned int** DataTable< T >::_sizes

private

Referenced by DataTable< T >::free(), DataTable< T >::size(), DataTable< T >::sizeChange(), and DataTable< T >::store_sizes().

_table

template<class T >

T* DataTable< T >::_table

private

Referenced by DataTable< T >::allocate(), DataTable< T >::divide(), DataTable< T >::free(), DataTable< T >::get(), DataTable< T >::getClassWithinGroup(), DataTable< T >::getGroup(), DataTable< T >::getTable(), DataTable< T >::increment(), DataTable< T >::init(), DataTable< T >::minus(), DataTable< T >::multiply(), DataTable< T >::plus(), DataTable< T >::set(), and DataTable< T >::update().

---

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

• datatable.h