org.textensor.stochdiff.numeric.chem

Class ReactionTable

java.lang.Object

org.textensor.stochdiff.numeric.chem.ReactionTable

public class ReactionTable
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field and Description
(package private) double[]	diffusionConstants
(package private) int	nreaction
int	nspecie
(package private) int[][]	productIndices
(package private) Matrix	productionMatrix
(package private) int[][]	productStochiometry
(package private) double[]	rates
(package private) int[][]	reactantIndices
(package private) int[][]	reactantStochiometry
(package private) java.lang.String[]	speciesIDs

Constructor Summary

Constructors

Constructor and Description
ReactionTable(int nr, int ns)

Method Summary

Methods

Modifier and Type	Method and Description
double[]	getDiffusionConstants()
Matrix	getIncrementRateMatrix(Column mconc)
int	getNReaction()
int	getNSpecies()
int[][]	getProductIndices()
Column	getProductionColumn(Column mconc)
Matrix	getProductionMatrix()
int[][]	getProductStochiometry()
Column	getRateColumn(Column mconc)
double[]	getRates()
int[][]	getReactantIndices()
int[][]	getReactantStochiometry()
java.lang.String[]	getSpecieIDs()
int	getSpecieIndex(java.lang.String specieID)
java.lang.String[]	getSpeciesIDs()
void	print()
void	setCatalyzedReactionData(int ireact, int na, int nb, int icat, int[][] aidx, int[][] bidx, double rate)
void	setDiffusionConstants(double[] d)
void	setReactionData(int ireact, int[][] aidx, int[][] bidx, double rate)
void	setSpeciesIDs(java.lang.String[] sa)
Column	stepResiduals(Column vc, Column vdc, double dt)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

nreaction

int nreaction

nspecie

public int nspecie

speciesIDs

java.lang.String[] speciesIDs

diffusionConstants

double[] diffusionConstants

reactantIndices

int[][] reactantIndices

productIndices

int[][] productIndices

reactantStochiometry

int[][] reactantStochiometry

productStochiometry

int[][] productStochiometry

rates

double[] rates

productionMatrix

Matrix productionMatrix

Constructor Detail

ReactionTable

public ReactionTable(int nr,
             int ns)

Method Detail

getSpecieIDs

public java.lang.String[] getSpecieIDs()

print

public void print()

setReactionData

public void setReactionData(int ireact,
                   int[][] aidx,
                   int[][] bidx,
                   double rate)

setCatalyzedReactionData

public void setCatalyzedReactionData(int ireact,
                            int na,
                            int nb,
                            int icat,
                            int[][] aidx,
                            int[][] bidx,
                            double rate)

setSpeciesIDs

public void setSpeciesIDs(java.lang.String[] sa)

getSpeciesIDs

public java.lang.String[] getSpeciesIDs()

getNSpecies

public int getNSpecies()

setDiffusionConstants

public void setDiffusionConstants(double[] d)

getDiffusionConstants

public double[] getDiffusionConstants()

getRateColumn

public Column getRateColumn(Column mconc)

getProductionMatrix

public Matrix getProductionMatrix()

getProductionColumn

public Column getProductionColumn(Column mconc)

getIncrementRateMatrix

public Matrix getIncrementRateMatrix(Column mconc)

stepResiduals

public final Column stepResiduals(Column vc,
                   Column vdc,
                   double dt)

getNReaction

public int getNReaction()

getRates

public double[] getRates()

getReactantIndices

public int[][] getReactantIndices()

getProductIndices

public int[][] getProductIndices()

getReactantStochiometry

public int[][] getReactantStochiometry()

getProductStochiometry

public int[][] getProductStochiometry()

getSpecieIndex

public int getSpecieIndex(java.lang.String specieID)