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java.lang.ObjectJava.problem.Problem
public class Problem
Store and manage a problem
Constructor Summary | |
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Problem()
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Method Summary | |
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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 |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Constructor Detail |
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public Problem()
Method Detail |
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public void read(java.io.File file, int debug)
file
- to be readdebug
- debug levelpublic java.lang.String toString()
toString
in class java.lang.Object
public int getNumberOfExperiments()
public int getNumberOfReactionTypes()
public int getNumberOfVariables()
public int getNumberOfDependentVariables()
public int getNumberOfRanges()
public Experiment getExperiment(int i)
i
- the index
public ReactionType getReactionType(int i)
i
- the index
public java.util.Vector<ReactionType> getReactionTypes()
public java.util.Vector<Variable> getVariables()
public ReactionType getReactionType(java.lang.String nameOfType)
nameOfType
- the name
public Variable getVariable(int i)
i
- the index
public Range getRange(int i)
i
- the index
public VariableSet getVariableSet(int i)
i
- the index
public int getMaxpts()
public int getSEED()
public double getSmoothingParameter()
public int getRAND1()
public int getRAND2()
public java.lang.String getName()
public java.lang.String getType()
public boolean isSSystem()
public ErrorFunction getErrorFunction()
public int get_maxpts()
public int get_maxv()
public int get_maxk()
public int getMAX_PARAMETERS_PER_ODE()
public int getMaxNumberOfSamplesPerVariable()
public double[][] getAlpha()
public double[][] getBeta()
public double[][][] getG()
public double[][][] getH()
public boolean[][] getGnonzero()
public boolean[][] getHnonzero()
public void adaptSSystem()
public void printSSystem()
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