Java.problem
Class Problem

java.lang.Object
  extended by Java.problem.Problem

public class Problem
extends java.lang.Object

Store and manage a problem

Since:
1.0

Constructor Summary
Problem()
           
 
Method Summary
 void adaptSSystem()
          Adapt information of S-system to a reaction kinetic problem relevant if problem is based on an S-system
 int get_maxk()
          Get maximum number of parameters in a reaction type
 int get_maxpts()
          Get maximum number of samples in the experiments
 int get_maxv()
          Get maximum number of variables in a reaction type
 double[][] getAlpha()
          Get the alpha matrix, relevant if problem is based on an S-system
 double[][] getBeta()
          Get the beta matrix, relevant if problem is based on an S-system
 ErrorFunction getErrorFunction()
          Get error function
 Experiment getExperiment(int i)
          Get experiment i
 double[][][] getG()
          Get the g matrix, relevant if problem is based on an S-system
 boolean[][] getGnonzero()
          Get information of non-zero elements of the g matrix, relevant if problem is based on an S-system
 double[][][] getH()
          Get the h matrix, relevant if problem is based on an S-system
 boolean[][] getHnonzero()
          Get information of non-zero elements of the h matrix, relevant if problem is based on an S-system
 int getMAX_PARAMETERS_PER_ODE()
          Get maximum number of parameters per ODE
 int getMaxNumberOfSamplesPerVariable()
          Get maximum number of samples for one variable
 int getMaxpts()
          Get maximum number of sampling points
 java.lang.String getName()
          Get problem name
 int getNumberOfDependentVariables()
          Get the number of dependent variables
 int getNumberOfExperiments()
          Get the number of experiments
 int getNumberOfRanges()
          Get the number of ranges
 int getNumberOfReactionTypes()
          Get the number of reaction types
 int getNumberOfVariables()
          Get the number of variables
 int getRAND1()
          Get number of random starts in local parameter estimation
 int getRAND2()
          Get number of random starts in global parameter estimation
 Range getRange(int i)
          Get range i
 ReactionType getReactionType(int i)
          Get reaction type i
 ReactionType getReactionType(java.lang.String nameOfType)
          Get reaction type named nameOfType
 java.util.Vector<ReactionType> getReactionTypes()
          Get all reaction types in a vector
 int getSEED()
          Get random seed
 double getSmoothingParameter()
          Get smoothing parameter
 java.lang.String getType()
          Get problem type
 Variable getVariable(int i)
          Get variable i
 java.util.Vector<Variable> getVariables()
          Get all variables in a vector
 VariableSet getVariableSet(int i)
          Get variable set i
 boolean isSSystem()
          Is the problem of S-system type
 void printSSystem()
          Print information of an S-system, relevant if problem is based on an S-system
 void read(java.io.File file, int debug)
          Read the problem
 java.lang.String toString()
          String value of experiments, calling toString in Experiment
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Constructor Detail

Problem

public Problem()
Method Detail

read

public void read(java.io.File file,
                 int debug)
Read the problem

Parameters:
file - to be read
debug - debug level

toString

public java.lang.String toString()
String value of experiments, calling toString in Experiment

Overrides:
toString in class java.lang.Object
Returns:
the string value of the experiments

getNumberOfExperiments

public int getNumberOfExperiments()
Get the number of experiments

Returns:
the number

getNumberOfReactionTypes

public int getNumberOfReactionTypes()
Get the number of reaction types

Returns:
the number

getNumberOfVariables

public int getNumberOfVariables()
Get the number of variables

Returns:
the number

getNumberOfDependentVariables

public int getNumberOfDependentVariables()
Get the number of dependent variables

Returns:
the number

getNumberOfRanges

public int getNumberOfRanges()
Get the number of ranges

Returns:
the number

getExperiment

public Experiment getExperiment(int i)
Get experiment i

Parameters:
i - the index
Returns:
the experiment

getReactionType

public ReactionType getReactionType(int i)
Get reaction type i

Parameters:
i - the index
Returns:
the reaction type

getReactionTypes

public java.util.Vector<ReactionType> getReactionTypes()
Get all reaction types in a vector

Returns:
the reaction types

getVariables

public java.util.Vector<Variable> getVariables()
Get all variables in a vector

Returns:
the variables

getReactionType

public ReactionType getReactionType(java.lang.String nameOfType)
Get reaction type named nameOfType

Parameters:
nameOfType - the name
Returns:
the reaction type

getVariable

public Variable getVariable(int i)
Get variable i

Parameters:
i - the index
Returns:
the variable

getRange

public Range getRange(int i)
Get range i

Parameters:
i - the index
Returns:
the range

getVariableSet

public VariableSet getVariableSet(int i)
Get variable set i

Parameters:
i - the index
Returns:
the variable set

getMaxpts

public int getMaxpts()
Get maximum number of sampling points

Returns:
the number

getSEED

public int getSEED()
Get random seed

Returns:
the seed

getSmoothingParameter

public double getSmoothingParameter()
Get smoothing parameter

Returns:
the parameter

getRAND1

public int getRAND1()
Get number of random starts in local parameter estimation

Returns:
the number

getRAND2

public int getRAND2()
Get number of random starts in global parameter estimation

Returns:
the number

getName

public java.lang.String getName()
Get problem name

Returns:
the name

getType

public java.lang.String getType()
Get problem type

Returns:
the type

isSSystem

public boolean isSSystem()
Is the problem of S-system type

Returns:
true if it is an S-system, ow false

getErrorFunction

public ErrorFunction getErrorFunction()
Get error function

Returns:
the error function

get_maxpts

public int get_maxpts()
Get maximum number of samples in the experiments

Returns:
the number

get_maxv

public int get_maxv()
Get maximum number of variables in a reaction type

Returns:
the number

get_maxk

public int get_maxk()
Get maximum number of parameters in a reaction type

Returns:
the number

getMAX_PARAMETERS_PER_ODE

public int getMAX_PARAMETERS_PER_ODE()
Get maximum number of parameters per ODE

Returns:
the number

getMaxNumberOfSamplesPerVariable

public int getMaxNumberOfSamplesPerVariable()
Get maximum number of samples for one variable

Returns:
the number

getAlpha

public double[][] getAlpha()
Get the alpha matrix, relevant if problem is based on an S-system

Returns:
the matrix

getBeta

public double[][] getBeta()
Get the beta matrix, relevant if problem is based on an S-system

Returns:
the matrix

getG

public double[][][] getG()
Get the g matrix, relevant if problem is based on an S-system

Returns:
the matrix

getH

public double[][][] getH()
Get the h matrix, relevant if problem is based on an S-system

Returns:
the matrix

getGnonzero

public boolean[][] getGnonzero()
Get information of non-zero elements of the g matrix, relevant if problem is based on an S-system

Returns:
a boolean matrix, true if element is non-zero, ow false

getHnonzero

public boolean[][] getHnonzero()
Get information of non-zero elements of the h matrix, relevant if problem is based on an S-system

Returns:
a boolean matrix, true if element is non-zero, ow false

adaptSSystem

public void adaptSSystem()
Adapt information of S-system to a reaction kinetic problem relevant if problem is based on an S-system


printSSystem

public void printSSystem()
Print information of an S-system, relevant if problem is based on an S-system