TMatrix Class Reference

A class to handle matrix in params, coerces matrix into a vector of same total size. More...

#include <tmatrix.h>

Collaboration diagram for TMatrix:

Public Member Functions
	TMatrix ()
	TMatrix (const TMatrix &mat)
	copy constructor. More...
	TMatrix (unsigned int rows, unsigned int cols)
	Creates an array of doubles of size = rows*cols. More...
	~TMatrix ()
void	copy (const TMatrix &mat)
	Copy a matrix. More...
void	copy_recycle (const TMatrix &mat)
	Copy elements of 'mat', recycling elements of 'mat' if its size is smaller than current matrix. More...
void	set (unsigned int i, unsigned int j, double val)
	Sets element at row i and column j to value val. More...
void	set_row (unsigned int i, double val)
	Sets all elements at row i to value val. More...
void	set_row (unsigned int i, vector< double > vec)
	Sets elements at row i to values stored in vector vec. More...
void	set_col (unsigned int i, double val)
	Sets element at column i to value val. More...
void	set_col (unsigned int i, vector< double > vec)
	Sets element at column i to values stored in vector vec. More...
void	assign (double val)
	Assigns a value to all element of the matrix. More...
void	reset (unsigned int rows, unsigned int cols)
	Re-allocate the existing matrix with assigned rows and cols dimensions and all elements to 0. More...
void	reset (unsigned int rows, unsigned int cols, double value)
	Reset the existing matrix to the new dimensions and copies the value to all elements. More...
void	reset (unsigned int rows, unsigned int cols, const double *array)
	Reset the existing matrix to the new dimensions and copies the array, which has to be of the same total length. More...
void	reset ()
	Reset members to zero state. More...
double	get (unsigned int i, unsigned int j) const
	Accessor to element at row i and column j. More...
double *	get () const
	Accessor to the whole array. More...
double *	getValArray () const
unsigned int	get_dims (unsigned int *dims) const
	Accessor to the matrix dimensions. More...
unsigned int	getNbRows () const
	Gives the number of rows. More...
unsigned int	nrows () const
unsigned int	getNbCols () const
	Gives the number of columns. More...
unsigned int	ncols () const
unsigned int	length () const
	Returns the number of elements in the matrix. More...
void	getColumnView (unsigned int col, unsigned int n, double *array)
	Gives access to a column of the matrix. More...
void	getRowView (unsigned int row, unsigned int n, double *array)
	Gives access to a row of the matrix. More...
void	plus (unsigned int i, unsigned int j, double value)
	Adds a value to an element of the matrix. More...
void	matrix_increment (double value)
	Adds a value to all elements in a matrix. More...
void	sweep_plus (double value)
	Adds a value to all elements in a matrix. More...
void	minus (unsigned int i, unsigned int j, double value)
	Substracts a value from an element of the matrix. More...
void	sweep_minus (double value)
	Substracts a value to all elements in a matrix. More...
void	multi (unsigned int i, unsigned int j, double value)
	Multiply an element of the matrix by a value. More...
void	sweep_multiply (double value)
	multiply each element by a value. More...
void	divide (unsigned int i, unsigned int j, double value)
	Divide an element of the matrix by a value. More...
void	sweep_divide (double value)
	Divide all elements of the matrix by a value. More...
void	transpose ()
	Transpose the matrix, swaps columns for rows. More...
double	colSum (unsigned int col)
	Sum all elements in a column. More...
double	rowSum (unsigned int row)
	Sum all elements in a row. More...
void	show_up ()
string	to_string ()
	Writes the matrix into a string in Nemo's matrix input format. More...

Private Attributes
unsigned int	_rows
unsigned int	_cols
unsigned int	_length
double *	_val

Detailed Description

A class to handle matrix in params, coerces matrix into a vector of same total size.

Constructor & Destructor Documentation

TMatrix() [1/3]

TMatrix::TMatrix ( )

inline

: _rows(0), _cols(0), _length(0), _val(0) { }

TMatrix() [2/3]

TMatrix::TMatrix ( const TMatrix &  mat )

inline

copy constructor.

                                : _rows(0), _cols(0), _length(0), _val(0)
  {
    copy(mat);
  } 

TMatrix() [3/3]

TMatrix::TMatrix ( unsigned int  rows, unsigned int  cols  )

inline

Creates an array of doubles of size = rows*cols.

                                                   : _rows(0), _cols(0), _length(0), _val(0)
  {
    _length = rows*cols;
    _val = new double [_length];
    _rows = rows; _cols = cols;
  }

~TMatrix()

TMatrix::~TMatrix ( )

inline

{if(_val != NULL) delete [] _val;}

Member Function Documentation

assign()

void TMatrix::assign ( double  val )

inline

Assigns a value to all element of the matrix.

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

Referenced by LCE_Patch_Extinction::set_matrix_param(), LCE_Selection_base::set_param_rate_of_change(), LCE_Selection_base::set_sel_model(), LCE_Selection_base::set_std_rate_of_change(), TTNeutralGenesSH::setAlleleTables(), LCE_Disperse_base::setBasicLatticeMatrix(), TProtoQuanti::setDominanceParameters(), TTNeutralGenesSH::setFstMatrix(), LCE_Disperse_base::setIndentityDispMatrix(), TProtoQuanti::setMutationCorrelation(), TProtoQuanti::setMutationModel_no_pleio(), TTNeutralGenesSH::setNeiGeneticDistance(), LCE_Selection_base::setSelectionMatrix(), LCE_Selection_base::setSelectionOffset(), and LCE_Disperse_base::setSteppingStone1DMatrix().

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colSum()

double TMatrix::colSum ( unsigned int  col )

inline

Sum all elements in a column.

  {
    assert(col < _cols); //has to be [0, _cols-1]
    double sum = 0;
    for (unsigned int i = 0; i < _rows; ++i) {
      sum += _val[i*_cols + col];
    }
    return sum;
  }

Referenced by TProtoQuanti::get_trait_mutation_variance().

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copy()

void TMatrix::copy ( const TMatrix &  mat )

inline

Copy a matrix.

  {
    _rows = mat._rows;
    _cols = mat._cols;
    _length = _rows*_cols;
    if(_val) delete [] _val;
    _val = new double [_length];
    memcpy(_val,mat._val,_length*sizeof(double));
  }

References _cols, _rows, and _val.

Referenced by LCE_PhenotypeExpression::execute(), TTNOhtaStats::FHwrite(), TTQOhtaStats::FHwrite(), TProtoQuanti::setEpistasisParameters(), LCE_Breed_Wolbachia::setParameters(), Metapop::setPatchSizes(), and TProtoQuanti::TProtoQuanti().

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copy_recycle()

void TMatrix::copy_recycle ( const TMatrix &  mat )

inline

Copy elements of 'mat', recycling elements of 'mat' if its size is smaller than current matrix.

Will only copy as many elements as necessary given _rows and _cols of current matrix.

  {
    if(_rows == mat._rows && _cols == mat._cols)
      copy(mat);
    else if(_val == NULL || _length == 0)
      error("TMatrix::copy_recycle::matrix must be allocated before call\n");
    else {
      for(unsigned int i = 0; i < _rows; ++i)
         for(unsigned int j = 0; j < _cols; ++j)
           set(i, j, mat._val[ (i%mat._rows)*mat._cols + (j%mat._cols) ]); //mat.get( i%nrow, j%ncol )); _val[i*_cols + j]
    }
  }

References _cols, _rows, _val, and error().

Referenced by LCE_Selection_base::set_sel_model(), TProtoQuanti::setDominanceParameters(), TProtoQuanti::setEpistasisParameters(), TProtoQuanti::setMutationCorrelation(), TProtoQuanti::setMutationSigmaFromQuantiMutationVariance_no_pleio(), LCE_Breed_Disperse::setParameters(), TProtoBDMI::setParameters(), LCE_FileServicesNotifier::setSamplingParameters(), and LCE_Selection_base::setSelectionOffset().

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divide()

void TMatrix::divide ( unsigned int  i, unsigned int  j, double  value  )

inline

Divide an element of the matrix by a value.

  {
    if( i*j < _length)
      _val[i*_cols + j] /= value;
    else
      error("TMatrix::divide overflow!\n");
  }

References error().

Referenced by TTNeutralGenesSH::setAlleleTables().

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get() [1/2]

double* TMatrix::get ( ) const

inline

Accessor to the whole array.

{return _val;}

get() [2/2]

double TMatrix::get ( unsigned int  i, unsigned int  j  ) const

inline

Accessor to element at row i and column j.

                                                    {
    if( !((i+1)*(j+1) > _length) )
      return _val[i*_cols + j];
    else
      fatal("TMatrix::get overflow!\n"); 
    return 0;
  }

References fatal().

Referenced by Metapop::buildPatchArray(), LCE_Selection_base::changeLocalOptima(), LCE_PhenotypeExpression::check_g_index_matrix(), LCE_Disperse_base::checkBackwardDispersalMatrix(), LCE_Disperse_base::checkForwardDispersalMatrix(), LCE_Patch_Extinction::do_remove(), LCE_Patch_Extinction::execute(), LCE_PhenotypeExpression::execute(), LCE_QuantiModifier::execute(), LCE_Breed_Disperse::exponentialGrowth(), TTNOhtaStats::FHwrite(), TTQFreqExtractor::FHwrite(), TTQOhtaStats::FHwrite(), TProtoQuanti::get_diallele_value(), TProtoQuanti::get_dominance(), LCE_PhenotypeExpression::get_env_cue_no_noise(), LCE_PhenotypeExpression::get_env_cue_noise(), TTQuanti_continuous_full_pleio_epistasis::get_epistatic_genotype(), TTQuanti_diallelic_full_pleio_epistasis::get_epistatic_genotype(), TTQuanti_continuous_no_pleio_epistasis::get_epistatic_genotype(), TTQuanti_diallelic_no_pleio_epistasis::get_epistatic_genotype(), TTQuanti_diallelic_bitstring_no_pleio_epistasis::get_epistatic_genotype(), TTQuanti_diallelic_bitstring_full_pleio_epistasis::get_epistatic_genotype(), LCE_Patch_Extinction::get_harvest_size(), TProtoQuanti::get_init_value(), TProtoQuanti::get_init_variance(), TProtoQuanti::get_trait_mutation_variance(), TTNeutralGenesSH::getCoa(), LCE_Breed_base::getFecundity(), LCE_Selection_base::getFitnessMultivariateDisruptive(), LCE_Selection_base::getFitnessMultivariateGaussian(), LCE_Selection_base::getFitnessMultivariateGaussian_VE(), LCE_Selection_base::getFitnessTruncation(), LCE_Selection_base::getFitnessUnivariateDisruptive(), LCE_Selection_base::getFitnessUnivariateGaussian(), LCE_Selection_base::getFitnessUnivariateGaussian_VE(), LCE_Selection_base::getFitnessUnivariateLinear(), LCE_Selection_base::getFitnessUnivariateQuadratic(), TTNeutralGenesSH::getFst_ij(), TProtoBDMI::getGenoFitnessDiplo(), TProtoBDMI::getGenoFitnessHaplo(), TTNeutralGenesSH::getGlobalAlleleFreq(), LCE_Breed_base::getMeanFecundity(), TProtoQuanti::getMutationEffectBivariateDiallelic(), TProtoQuanti::getMutationEffectBivariateGaussian(), TProtoQuanti::getMutationEffectBivariateGaussianLocSpec(), TProtoQuanti::getMutationEffectUnivariateGaussian(), TProtoQuanti::getMutationEffectUnivariateGaussianLocSpec(), TTNeutralGenesSH::getNeiGeneticDistance(), Metapop::getPatchCapacity(), FileServices::getSampledPop(), TTQuantiSH::getVaNoDominance(), TTQuantiSH::getVaWithDominance(), TTDispersal::init_sequence(), LCE_Breed_Wolbachia::inoculate_wolbachia(), LCE_Breed_Disperse::logisticGrowth(), TProtoQuanti::mutate_diallelic_pleio(), TProtoQuanti::mutate_diallelic_var_pleio(), LCE_Breed_base::NonWrightFisherPopulation(), LCE_Breed_Quanti::NonWrightFisherPopulation(), LCE_Breed_Disperse::numFemOffspring_colonizers(), LCE_Breed_Disperse::numMalOffspring_random_colonizers(), LCE_Resize::removeDesignatedPatch(), TProtoQuanti::set_gsl_mutation_matrix_from_sigma(), FileHandler::set_OccMatrix(), LCE_Selection_base::set_param_rate_of_change(), LCE_PhenotypeExpression::set_phenot_g1_evol(), LCE_PhenotypeExpression::set_phenot_g1_g2_evol(), LCE_PhenotypeExpression::set_phenot_g2_evol(), LCE_PhenotypeExpression::set_phenot_no_evol(), LCE_Selection_base::set_sel_model(), LCE_Selection_base::set_std_rate_of_change(), LCE_Disperse_base::setBasicLatticeMatrix(), TProtoQuanti::setContinuousMutationModel_full_pleio(), TProtoQuanti::setContinuousMutationModel_var_pleio(), TProtoQuanti::setDiallelicMutationModel(), TProtoQuanti::setDominanceParameters(), TProtoDeletMutations_bitstring::setEffectsFromInput(), LCE_Breed_base::setFecundity(), TTNeutralGenesSH::setFst_li(), TTNeutralGenesSH::setFstatWeirCockerham(), TTNeutralGenesSH::setFstatWeirCockerham_MS(), TTNeutralGenesSH::setFstMatrix(), TTProtoWithMap::setGeneticMapParameters(), TProtoQuanti::setHeritabilityParams(), TTNeutralGenesSH::setHt(), TTNeutralGenesSH::setHt2(), LCE_PhenotypeExpression::setIndLiability(), LCE_PhenotypeExpression::setIndLiability_evolving(), LCE_PhenotypeExpression::setIndLiability_evolving_sigmoid(), LCE_PhenotypeExpression::setIndLiability_sigmoid(), LCE_Disperse_base::setLatticeAbsorbingMatrix(), LCE_Disperse_base::setLatticeReflectingMatrix(), LCE_Disperse_base::setLatticeTorrusMatrix(), TTNeutralGenesSH::setLociDivCounter(), TProtoQuanti::setMutationModel_no_pleio(), TProtoQuanti::setMutationModel_var_pleio(), TProtoQuanti::setMutationSigmaFromQuantiMutationVariance(), TProtoQuanti::setMutationSigmaFromQuantiMutationVariance_no_pleio(), TTProtoWithMap::setNumLociPerChromosome(), LCE_StatServiceNotifier::setOccurence(), LCE_Breed_Disperse::setParameters(), LCE_Resize::setParameters(), LCE_PhenotypeExpression::setParameters(), TProtoBDMI::setParameters(), Metapop::setPatchCapacities(), LCE_Init_BDMI::setPatchFreq(), LCE_Selection_base::setSelectionMatrix(), LCE_Selection_base::setSelectionOffset(), LCE_Selection_base::setSelectTraitMapping(), setSpatialMatrix(), LCE_Init_BDMI::setSpatialPattern(), TProtoQuanti::setTraitAndLocusTables_no_pleio(), TProtoBDMI::showGenoTable(), ParamsParser::sym_matrix(), transpose(), LCE_Resize::updatePatchCapacities(), Metapop::updatePatchState(), and TTNeutralGenesFH::write_varcompWC().

get_dims()

unsigned int TMatrix::get_dims ( unsigned int *  dims ) const

inline

Accessor to the matrix dimensions.

Parameters

dims	an array of at least 2 elements to store the row [0] and column [1] numbers. May be NULL.

Returns

the total size of the matrix

                                                   {
    if(dims != NULL) { dims[0] = _rows; dims[1] = _cols; }
    return _length;
  }

getColumnView()

void TMatrix::getColumnView ( unsigned int  col, unsigned int  n, double *  array  )

inline

Gives access to a column of the matrix.

Parameters

col	index of col to view
n	size of the storing array passed, must be equal to no. of rows
array	array where the column values will be stored

  {
    if(col > _cols-1) {
      error("TMatrix::getColumnView: not that many columns in matrix\n");
      return;
    }
    if(n != _rows) {
      error("TMatrix::getColumnView: array size not equal to number of rows in matrix\n");
      return;
    }
    for(unsigned int i = 0; i < _rows; ++i)
      array[i] = _val[i*_cols + col];
  }

References error().

getNbCols()

unsigned int TMatrix::getNbCols ( ) const

inline

Gives the number of columns.

{return _cols;}

Referenced by LCE_Resize::buildNewPatchArrayNoBackup(), LCE_Resize::buildNewPatchArrayWithBackup(), LCE_Disperse_base::checkBackwardDispersalMatrix(), LCE_Disperse_base::checkForwardDispersalMatrix(), LCE_Resize::execute(), TTNeutralGenesSH::getCoa(), TTNeutralGenesSH::getFst_ij(), TTNeutralGenesSH::getNeiGeneticDistance(), LCE_Resize::removeDesignatedPatch(), LCE_Patch_Extinction::set_matrix_param(), LCE_Selection_base::set_sel_model(), TProtoDeletMutations_bitstring::setEffectsFromInput(), TTProtoWithMap::setGeneticMapParameters(), TProtoQuanti::setMutationModel_var_pleio(), TTProtoWithMap::setNumLociPerChromosome(), LCE_Resize::setParameters(), LCE_Init_BDMI::setPatchFreq(), LCE_Selection_base::setSelectionMatrix(), setSpatialMatrix(), LCE_Init_BDMI::setSpatialPattern(), LCE_Resize::updateParameters(), and LCE_Resize::updatePatchCapacities().

getNbRows()

unsigned int TMatrix::getNbRows ( ) const

inline

Gives the number of rows.

{return _rows;}

Referenced by LCE_Disperse_base::checkBackwardDispersalMatrix(), LCE_Disperse_base::checkForwardDispersalMatrix(), TTDispersal::init_sequence(), LCE_Patch_Extinction::set_matrix_param(), LCE_Selection_base::set_sel_model(), TProtoDeletMutations_bitstring::setEffectsFromInput(), TTProtoWithMap::setGeneticMapParameters(), TProtoQuanti::setMutationModel_var_pleio(), TTProtoWithMap::setNumLociPerChromosome(), LCE_Init_BDMI::setPatchFreq(), LCE_Selection_base::setSelectionMatrix(), LCE_Selection_base::setSelectionOffset(), setSpatialMatrix(), and LCE_Init_BDMI::setSpatialPattern().

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getRowView()

void TMatrix::getRowView ( unsigned int  row, unsigned int  n, double *  array  )

inline

Gives access to a row of the matrix.

Parameters

row	index of row to view
n	size of the storing array passed, must be equal to no. of columns
array	array where the row values will be stored

  {
    if(row > _rows-1) {
      error("TMatrix::getRowView: not that many rows in matrix\n");
      return;
    }
    if(n != _cols) {
      error("TMatrix::getRowView: array size not equal to number of columns in matrix\n");
      return;
    }
    for(unsigned int i = 0, stride = row*_cols; i < _cols; ++i)
      array[i] = _val[stride + i];
  }

References error().

Referenced by LCE_QuantiInit::execute(), LCE_Init_BDMI::execute(), and LCE_NtrlInit::execute().

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getValArray()

double* TMatrix::getValArray ( ) const

inline

{return _val;}

Referenced by FileHandler::set_OccMatrix().

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length()

unsigned int TMatrix::length ( ) const

inline

Returns the number of elements in the matrix.

{return _length;}

Referenced by LCE_PhenotypeExpression::check_g_index_matrix(), TTQuanti_continuous_full_pleio_epistasis::get_epistatic_genotype(), TTQuanti_diallelic_full_pleio_epistasis::get_epistatic_genotype(), TTQuanti_continuous_no_pleio_epistasis::get_epistatic_genotype(), TTQuanti_diallelic_no_pleio_epistasis::get_epistatic_genotype(), TTQuanti_diallelic_bitstring_no_pleio_epistasis::get_epistatic_genotype(), TTQuanti_diallelic_bitstring_full_pleio_epistasis::get_epistatic_genotype(), FileServices::getSampledPop(), TProtoQuanti::setEpistasisParameters(), TTNeutralGenesSH::setFstMatrix(), TTNeutralGenesSH::setNeiGeneticDistance(), LCE_Breed_Disperse::setParameters(), LCE_PhenotypeExpression::setParameters(), and Metapop::setPatchCapacities().

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matrix_increment()

void TMatrix::matrix_increment ( double  value )

inline

Adds a value to all elements in a matrix.

  {
     for(unsigned int i = 0; i < _rows; ++i){
       for(unsigned int j = 0; j < _cols; ++j){
         plus(i,j,value);
       }
     }
  }

Referenced by LCE_FileServicesNotifier::setSamplingParameters().

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minus()

void TMatrix::minus ( unsigned int  i, unsigned int  j, double  value  )

inline

Substracts a value from an element of the matrix.

  {
    if( i*j < _length)
      _val[i*_cols + j] -= value;
    else
      error("TMatrix::minus overflow!\n");
  }

References error().

Referenced by LCE_PhenotypeExpression::check_g_index_matrix().

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multi()

void TMatrix::multi ( unsigned int  i, unsigned int  j, double  value  )

inline

Multiply an element of the matrix by a value.

  {
    if( i*j < _length)
      _val[i*_cols + j] *= value;
    else
      error("TMatrix::multi overflow!\n");
  }

References error().

Referenced by LCE_Selection_base::set_std_rate_of_change().

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ncols()

unsigned int TMatrix::ncols ( ) const

inline

{return _cols;}

Referenced by LCE_QuantiModifier::execute(), LCE_Breed_Quanti::execute(), FileServices::getSampledPop(), LCE_Breed_base::NonWrightFisherPopulation(), LCE_PhenotypeExpression::set_g_value_matrix(), FileHandler::set_OccMatrix(), LCE_Selection_base::set_param_rate_of_change(), LCE_Selection_base::set_sel_model(), LCE_Selection_base::set_std_rate_of_change(), TProtoQuanti::setContinuousMutationModel_full_pleio(), TProtoQuanti::setContinuousMutationModel_var_pleio(), TProtoQuanti::setDiallelicMutationModel(), TProtoQuanti::setDominanceParameters(), TProtoQuanti::setEpistasisParameters(), LCE_Breed_base::setFecundity(), TProtoQuanti::setHeritabilityParams(), TProtoQuanti::setInitialValuesParams(), TProtoQuanti::setMutationCorrelation(), TProtoQuanti::setMutationModel_no_pleio(), TProtoQuanti::setMutationModel_var_pleio(), TProtoQuanti::setMutationSigmaFromQuantiMutationVariance(), TProtoQuanti::setMutationSigmaFromQuantiMutationVariance_no_pleio(), LCE_StatServiceNotifier::setOccurence(), LCE_Breed_Disperse::setParameters(), TProtoBDMI::setParameters(), LCE_Init_BDMI::setParameters(), LCE_Breed_Wolbachia::setParameters(), LCE_FileServicesNotifier::setSamplingParameters(), LCE_Selection_base::setSelectionMatrix(), LCE_Selection_base::setSelectionOffset(), and LCE_Selection_base::setSelectTraitMapping().

nrows()

unsigned int TMatrix::nrows ( ) const

inline

{return _rows;}

Referenced by LCE_Selection_base::changeLocalOptima(), TTNOhtaStats::FHwrite(), TTQOhtaStats::FHwrite(), TProtoQuanti::get_trait_mutation_variance(), FileServices::getSampledPop(), LCE_PhenotypeExpression::set_g_value_matrix(), FileHandler::set_OccMatrix(), LCE_Selection_base::set_param_rate_of_change(), LCE_Selection_base::set_std_rate_of_change(), TProtoQuanti::setContinuousMutationModel_full_pleio(), TProtoQuanti::setContinuousMutationModel_no_pleio(), TProtoQuanti::setContinuousMutationModel_var_pleio(), TProtoQuanti::setDiallelicMutationModel(), TProtoQuanti::setDominanceParameters(), TProtoQuanti::setEpistasisParameters(), LCE_Breed_base::setFecundity(), TProtoQuanti::setHeritabilityParams(), TProtoQuanti::setInitialValuesParams(), TProtoQuanti::setMutationCorrelation(), TProtoQuanti::setMutationModel_no_pleio(), TProtoQuanti::setMutationModel_var_pleio(), TProtoQuanti::setMutationSigmaFromQuantiMutationVariance(), TProtoQuanti::setMutationSigmaFromQuantiMutationVariance_no_pleio(), LCE_StatServiceNotifier::setOccurence(), LCE_Breed_Disperse::setParameters(), LCE_QuantiModifier::setParameters(), TProtoBDMI::setParameters(), LCE_Init_BDMI::setParameters(), LCE_Breed_Wolbachia::setParameters(), LCE_FileServicesNotifier::setSamplingParameters(), and LCE_Selection_base::setSelectTraitMapping().

plus()

void TMatrix::plus ( unsigned int  i, unsigned int  j, double  value  )

inline

Adds a value to an element of the matrix.

  {
    if( i*j < _length)
      _val[i*_cols + j] += value;
    else
      error("TMatrix::plus overflow!\n");
  }

References error().

Referenced by LCE_Selection_base::changeLocalOptima(), LCE_PhenotypeExpression::execute(), TTNeutralGenesSH::setAlleleTables(), and LCE_Disperse_base::setLatticeAbsorbingMatrix().

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reset() [1/4]

void TMatrix::reset ( )

inline

Reset members to zero state.

  {
    _rows = 0; 
    _cols = 0; 
    _length = 0;
    if(_val != NULL) delete [] _val; 
    _val = NULL;
  }

reset() [2/4]

void TMatrix::reset ( unsigned int  rows, unsigned int  cols  )

inline

Re-allocate the existing matrix with assigned rows and cols dimensions and all elements to 0.

                                                    {
    _length = rows * cols;
    if(_length == 0) error("TMatrix::attempt to reset a matrix with size = 0!\n");
    if(_val != NULL) delete [] _val;
    _val = new double [_length];
    memset(_val, 0, _length*sizeof(double));
    _rows = rows; _cols = cols;
  }

References error().

Referenced by LCE_Disperse_base::allocateDispMatrix(), TTNeutralGenesSH::allocateTables(), Param::parse_matrix(), LCE_PhenotypeExpression::set_env_cue(), LCE_PhenotypeExpression::set_g_value_matrix(), TProtoQuanti::set_init_values(), LCE_Selection_base::set_local_optima(), LCE_Patch_Extinction::set_matrix_param(), FileHandler::set_OccMatrix(), LCE_Selection_base::set_param_rate_of_change(), LCE_Selection_base::set_sel_model(), LCE_Selection_base::set_std_rate_of_change(), TProtoQuanti::setContinuousMutationModel_full_pleio(), TProtoQuanti::setContinuousMutationModel_var_pleio(), TProtoQuanti::setDiallelicMutationModel(), TProtoQuanti::setDominanceParameters(), TProtoQuanti::setEpistasisParameters(), LCE_Breed_base::setFecundity(), TTNeutralGenesSH::setFstMatrix(), LCE_Disperse_base::setIndentityDispMatrix(), TProtoQuanti::setInitialValuesParams(), TProtoQuanti::setMutationCorrelation(), TProtoQuanti::setMutationModel_no_pleio(), TProtoQuanti::setMutationSigmaFromQuantiMutationVariance(), TProtoQuanti::setMutationSigmaFromQuantiMutationVariance_no_pleio(), TTNeutralGenesSH::setNeiGeneticDistance(), LCE_Breed_Disperse::setParameters(), LCE_PhenotypeExpression::setParameters(), LCE_QuantiModifier::setParameters(), LCE_FileServicesNotifier::setParameters(), TProtoBDMI::setParameters(), LCE_Init_BDMI::setParameters(), Metapop::setPatchCapacities(), LCE_FileServicesNotifier::setSamplingParameters(), LCE_Selection_base::setSelectionMatrix(), LCE_Selection_base::setSelectionOffset(), setSpatialMatrix(), and LCE_Resize::updateParameters().

reset() [3/4]

void TMatrix::reset ( unsigned int  rows, unsigned int  cols, const double *  array  )

inline

Reset the existing matrix to the new dimensions and copies the array, which has to be of the same total length.

                                                                         {
    reset(rows, cols);
    memcpy(_val, array, _length * sizeof(double));
  }  

reset() [4/4]

void TMatrix::reset ( unsigned int  rows, unsigned int  cols, double  value  )

inline

Reset the existing matrix to the new dimensions and copies the value to all elements.

                                                                  {
    reset(rows, cols);
    assign(value);
  }

rowSum()

double TMatrix::rowSum ( unsigned int  row )

inline

Sum all elements in a row.

  {
    assert(row < _rows); // has to be [0, _rows-1]
    double sum = 0;
    for (unsigned int i = 0; i < _cols; ++i) {
      sum += _val[row*_cols + i];
    }
    return sum;
  }

Referenced by LCE_Disperse_base::setLatticeReflectingMatrix(), and TProtoQuanti::setMutationModel_no_pleio().

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set()

void TMatrix::set ( unsigned int  i, unsigned int  j, double  val  )

inline

Sets element at row i and column j to value val.

                                                        {
    if( i*j < _length)
      _val[i*_cols + j] = val;
    else
      error("TMatrix::set overflow, i*j > length!\n");
  }

References error().

Referenced by LCE_Breed_Disperse::exponentialGrowth(), Param::parse_matrix(), LCE_Selection_base::set_param_rate_of_change(), LCE_Selection_base::set_std_rate_of_change(), LCE_Disperse_base::setBasicLatticeMatrix(), TProtoQuanti::setContinuousMutationModel_full_pleio(), TProtoQuanti::setContinuousMutationModel_var_pleio(), TProtoQuanti::setDiallelicMutationModel(), TProtoQuanti::setEpistasisParameters(), LCE_Breed_base::setFecundity(), TTNeutralGenesSH::setFstMatrix(), TProtoBDMI::setGenoFitnessValue(), LCE_Disperse_base::setIndentityDispMatrix(), LCE_Disperse_base::setIsland_MigrantPool_Matrix(), LCE_Disperse_base::setIsland_PropagulePool_Matrix(), LCE_Disperse_base::setLatticeAbsorbingMatrix(), LCE_Disperse_base::setLatticeReflectingMatrix(), LCE_Disperse_base::setLatticeTorrusMatrix(), TProtoQuanti::setMutationSigmaFromQuantiMutationVariance_no_pleio(), TTNeutralGenesSH::setNeiGeneticDistance(), LCE_PhenotypeExpression::setParameters(), TProtoBDMI::setParameters(), Metapop::setPatchCapacities(), LCE_Init_BDMI::setPatchFreq(), LCE_FileServicesNotifier::setSamplingParameters(), LCE_Selection_base::setSelectionMatrix(), setSpatialMatrix(), LCE_Init_BDMI::setSpatialPattern(), LCE_Disperse_base::setSteppingStone1DMatrix(), ParamsParser::sym_matrix(), and transpose().

set_col() [1/2]

void TMatrix::set_col ( unsigned int  i, double  val  )

inline

Sets element at column i to value val.

                                            {
    if( i < _cols)
      for(unsigned int j = 0; j < _rows; ++j)
        _val[j*_cols + i] = val;
    else
      error("TMatrix::set_col overflow, i > num cols!\n");
  }

References error().

Referenced by TProtoQuanti::setDiallelicMutationModel().

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set_col() [2/2]

void TMatrix::set_col ( unsigned int  i, vector< double >  vec  )

inline

Sets element at column i to values stored in vector vec.

                                                    {
 
    if(vec.size() < _rows)
      fatal("TMatrix::set_col copy from vector too small to fit\n");
 
    if( i < _cols)
      for(unsigned int j = 0; j < _rows; ++j)
        _val[j*_cols + i] = vec[j];
    else
      error("TMatrix::set_col overflow, i > num cols!\n");
  }

References error(), and fatal().

set_row() [1/2]

void TMatrix::set_row ( unsigned int  i, double  val  )

inline

Sets all elements at row i to value val.

                                            {
    if( i < _rows)
      for(unsigned int j = 0, stride = i*_cols; j < _cols; ++j)
        _val[stride + j] = val;
    else
      error("TMatrix::set_row overflow, i > num rows!\n");
  }

References error().

Referenced by TProtoQuanti::setMutationSigmaFromQuantiMutationVariance(), and LCE_Breed_Disperse::setParameters().

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set_row() [2/2]

void TMatrix::set_row ( unsigned int  i, vector< double >  vec  )

inline

Sets elements at row i to values stored in vector vec.

                                                    {
 
    if(vec.size() < _cols)
      fatal("TMatrix::set_row copy from vector too small to fit\n");
 
    if( i < _rows)
      for(unsigned int j = 0, stride = i*_cols; j < _cols; ++j)
        _val[stride + j] = vec[j];
    else
      error("TMatrix::set_row overflow, i > num rows!\n");
  }

References error(), and fatal().

show_up()

void TMatrix::show_up ( )

inline

  {
    message("TMatrix dimensions: \nrows = %i, columns = %i, length = %i\n",_rows,_cols, _length);
    for(unsigned int i = 0; i < _rows; i++) {
      for(unsigned int j = 0; j < _cols; j++)
        message("%.3f ",_val[i*_cols + j]);
      message("\n");
    }
  }

References message().

Referenced by TProtoQuanti::setContinuousMutationModel_full_pleio(), TProtoQuanti::setMutationSigmaFromQuantiMutationVariance(), TProtoQuanti::setMutationSigmaFromQuantiMutationVariance_no_pleio(), LCE_Disperse_base::setReducedDispMatrix(), and Metapop::show_up().

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sweep_divide()

void TMatrix::sweep_divide ( double  value )

inline

Divide all elements of the matrix by a value.

  {
    for(unsigned int i = 0; i < _rows; ++i){
      for(unsigned int j = 0; j < _cols; ++j){
        divide(i,j,value);
      }
    }
  }

sweep_minus()

void TMatrix::sweep_minus ( double  value )

inline

Substracts a value to all elements in a matrix.

  {
    for(unsigned int i = 0; i < _rows; ++i){
      for(unsigned int j = 0; j < _cols; ++j){
        minus(i,j,value);
      }
    }
  }

sweep_multiply()

void TMatrix::sweep_multiply ( double  value )

inline

multiply each element by a value.

  {
    for(unsigned int i = 0; i < _rows; ++i){
      for(unsigned int j = 0; j < _cols; ++j){
        multi(i,j,value);
      }
    }
  }

sweep_plus()

void TMatrix::sweep_plus ( double  value )

inline

Adds a value to all elements in a matrix.

  {
     for(unsigned int i = 0; i < _rows; ++i){
       for(unsigned int j = 0; j < _cols; ++j){
       plus(i,j,value);
       }
     }
  }

to_string()

string TMatrix::to_string ( )

inline

Writes the matrix into a string in Nemo's matrix input format.

  {
    ostringstream OUT;
    
    OUT << "{";
    for(unsigned int i = 0; i < _rows; i++) {
      OUT<<"{";
      for(unsigned int j = 0; j < _cols-1; j++) {
        OUT<<_val[i*_cols + j]<<",";
      }
      OUT<<_val[i*_cols + _cols-1]<<"}";
    }
    OUT << "}";
    
    return OUT.str();
  }

Referenced by LCE_Selection_base::set_std_rate_of_change(), and ParamsParser::sym_matrix().

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transpose()

void TMatrix::transpose ( )

inline

Transpose the matrix, swaps columns for rows.

  {
    TMatrix tmp(_cols, _rows);
    
    for(unsigned int i = 0; i < _rows; i++)
      for(unsigned int j = 0; j < _cols; j++)
        tmp.set(j, i, get(i, j));
    
    reset(_cols, _rows, tmp.get());
  }

References get(), and set().

Referenced by LCE_Disperse_base::setLatticeReflectingMatrix(), and LCE_Disperse_base::setSteppingStone1DMatrix().

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Member Data Documentation

_cols

unsigned int TMatrix::_cols

private

Referenced by copy(), and copy_recycle().

_length

unsigned int TMatrix::_length

private

_rows

unsigned int TMatrix::_rows

private

Referenced by copy(), and copy_recycle().

_val

double* TMatrix::_val

private

Referenced by copy(), and copy_recycle().

---

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

• tmatrix.h