A C D E F G H I J L M O P R S T U V W X Y _

A

actionPerformed(ActionEvent) - Method in class Java.PlotExperiment
Update the graph
adaptEquationToParaest(String, ReactionType) - Static method in class Java.generateFortran.GenerateFortran
Adapt an equation to the Fortran parameter estimation routine
adaptEquationToSim(String, ReactionType) - Static method in class Java.generateFortran.GenerateFortran
Adapt an equation to the Fortran simulation routine
adaptEquationToSimSingle(String, ReactionType, int) - Static method in class Java.generateFortran.GenerateFortran
Adapt an equation to the Fortran routine for simulation of a single variable
adaptSSystem() - Method in class Java.problem.Problem
Adapt information of S-system to a reaction kinetic problem relevant if problem is based on an S-system
addInitialBound(InitialBound, Variable) - Method in class Java.problem.Experiment
Add initial bound
addLine(String, JComponent) - Method in class Java.gui.AlignedInputPanel
Add one line to the panel
addPossibleReaction(PossibleReaction) - Method in class Java.problem.Variable
Add possible reaction r to the model space of this variable
addReaction(Reaction) - Method in class Java.problem.Variable
Add reaction r to this variable
addSample(Sample) - Method in class Java.problem.Experiment
Add one sample
AlignedInputPanel - Class in Java.gui
Panel for two column dialogs: left: input description, right input fields
AlignedInputPanel() - Constructor for class Java.gui.AlignedInputPanel
 

C

calcSpline(double) - Method in class Java.gui.Pppack_smooth
Constructs the cubic smoothing spline to given data (x(),y()).
calcSpline(boolean, double) - Method in class Java.gui.Pppack_smooth
Constructs an interpolation/approximation function to given data (x(),y()).
calculate(Stack) - Method in class Java.parser.FunctionParser.Function
 
chol1d(double, double[][], double[], int, int, double[], double[]) - Static method in class Java.generateFortran.Pppack
 
clear() - Method in class Java.gui.GraphPanel
 
constructor(Object) - Static method in class Java.debug.Debug
Debug printout from constructor
constructor(Object, String) - Static method in class Java.debug.Debug
Debug printout from constructor
convertToPFN() - Method in class Java.parser.FunctionParser
 

D

d1f - Variable in class Java.gui.Pppack_smooth
 
d2f - Variable in class Java.gui.Pppack_smooth
 
d3f - Variable in class Java.gui.Pppack_smooth
 
Debug - Class in Java.debug
Debug printouts and error messages
Debug() - Constructor for class Java.debug.Debug
 
determineFunctionForToken(String) - Method in class Java.parser.FunctionParser
 
DumpPFN() - Method in class Java.parser.FunctionParser
 

E

emptyReactions() - Method in class Java.problem.Variable
Set list of reactions to the empty list
ERROR - Static variable in class Java.debug.Debug
Error messages on or off
error(Object, String) - Static method in class Java.debug.Debug
Error message and program termination
error(Object, String, String) - Static method in class Java.debug.Debug
Error message and program termination
ERROR_FORMEVAL - Static variable in class Java.parser.FunctionParser
 
ErrorFunction - Class in Java.problem
Description of the error function
ErrorFunction() - Constructor for class Java.problem.ErrorFunction
 
Experiment - Class in Java.problem
Description of an experiment
Experiment(int, int) - Constructor for class Java.problem.Experiment
Constricts an experiment
expr - Variable in class Java.parser.FunctionParser
 

F

f - Variable in class Java.gui.Pppack_smooth
Array of smoothed ordinates, corresponded to abscissae
fixExponent(double) - Static method in class Java.generateFortran.GenerateFortran
Java double to Fortran double, replace E by d, or add d0 at end
FunctionParser - Class in Java.parser
Class supporting parsing of equations
FunctionParser(String) - Constructor for class Java.parser.FunctionParser
 
FunctionParser.Function - Class in Java.parser
 
FunctionParser.Function() - Constructor for class Java.parser.FunctionParser.Function
 
FunctionParser.PFNField - Class in Java.parser
 
FunctionParser.PFNField() - Constructor for class Java.parser.FunctionParser.PFNField
 
FunctionParser.SBMLNode - Class in Java.parser
 
FunctionParser.SBMLNode() - Constructor for class Java.parser.FunctionParser.SBMLNode
 

G

generate(Problem, String, String) - Method in class Java.generateFortran.GenerateFortran
Generate Fortran files that are based on code skeletons in files
generate(String, Problem) - Static method in class Java.generateFortran.GenerateFortran_myReactions
Make reactions.f in directory for a certain problem
generate(String, Problem) - Static method in class Java.generateFortran.GenerateFortran_readProblem
Make readProblem.f in directory for a certain problem
generate(String, Problem) - Static method in class Java.generateFortran.GenerateFortran_spline
Make spline.f in directory for a certain problem
GenerateFortran - Class in Java.generateFortran
Generates the Fortan program
GenerateFortran(String, Problem) - Constructor for class Java.generateFortran.GenerateFortran
Generates the Fortan program in directory for a certain problem
GenerateFortran_myReactions - Class in Java.generateFortran
Generate reactions.f
GenerateFortran_myReactions() - Constructor for class Java.generateFortran.GenerateFortran_myReactions
 
GenerateFortran_readProblem - Class in Java.generateFortran
Generate readProblem.f
GenerateFortran_readProblem() - Constructor for class Java.generateFortran.GenerateFortran_readProblem
 
GenerateFortran_spline - Class in Java.generateFortran
Generate spline.f
GenerateFortran_spline() - Constructor for class Java.generateFortran.GenerateFortran_spline
 
GenerateProgram - Class in Java
Generate Fortran program to solve problem given as argv[0]
GenerateProgram() - Constructor for class Java.GenerateProgram
 
get(double) - Method in class Java.gui.Pppack_smooth
Calculates value of the function.
get(double, int) - Method in class Java.gui.Pppack_smooth
Calculates value of the function.
get_dfdk(int) - Method in class Java.problem.ReactionType
Get the partial derivative of the kinetic equation wrt parameter ipara
get_dfdX(int) - Method in class Java.problem.ReactionType
Get the partial derivative of the kinetic equation wrt variable ivar
get_maxk() - Method in class Java.problem.Problem
Get maximum number of parameters in a reaction type
get_maxpts() - Method in class Java.problem.Problem
Get maximum number of samples in the experiments
get_maxv() - Method in class Java.problem.Problem
Get maximum number of variables in a reaction type
getAlpha() - Method in class Java.problem.Problem
Get the alpha matrix, relevant if problem is based on an S-system
getArgs() - Method in class Java.parser.FunctionParser.Function
 
getBeta() - Method in class Java.problem.Problem
Get the beta matrix, relevant if problem is based on an S-system
getCoef(double[], double[], double[], int, double) - Static method in class Java.generateFortran.Pppack
 
getDouble(String, int) - Static method in class Java.misc.Misc
Reads a real number from a String in an input file on line line_no
getDoubleValue(double, double) - Method in class Java.gui.MyJSlider
Returns the slider's value.
getEquation() - Method in class Java.problem.ErrorFunction
Get the equation in string form
getEquation() - Method in class Java.problem.ReactionType
Get the kinetic equation
getErrorFunction() - Method in class Java.problem.Problem
Get error function
getExperiment(int) - Method in class Java.problem.Problem
Get experiment i
getf(int, int) - Method in class Java.gui.Pppack_smooth
Get value of variable f at position val for a certain derivative [0,1,2,3}.
getFuncNum(FunctionParser.Function) - Method in class Java.parser.FunctionParser
 
getG() - Method in class Java.problem.Problem
Get the g matrix, relevant if problem is based on an S-system
getGnonzero() - Method in class Java.problem.Problem
Get information of non-zero elements of the g matrix, relevant if problem is based on an S-system
getH() - Method in class Java.problem.Problem
Get the h matrix, relevant if problem is based on an S-system
getHnonzero() - Method in class Java.problem.Problem
Get information of non-zero elements of the h matrix, relevant if problem is based on an S-system
getId() - Method in class Java.problem.ReactionType
Get id of the reaction type
getId() - Method in class Java.problem.Variable
Get id of variable, numbered 0...N-1
getInitialGuess() - Method in class Java.problem.Range
Get initial guess, a value taken from the range
getInteger(String, int) - Static method in class Java.misc.Misc
returns index after underscore in string s if s ends with underscore, return -1
getIntegers(String, int) - Static method in class Java.misc.Misc
returns 2 integer indeces after underscore in string s
getLambda() - Method in class Java.problem.ErrorFunction
Get the lambda parameter
getLocalParameter(int) - Method in class Java.problem.Reaction
Get local parameter i
getLocalParameterName(int) - Method in class Java.problem.ReactionType
Get the name of local parameter i in the kinetic equation
getLocalRange(int) - Method in class Java.problem.PossibleReaction
Get the locally defined range i for this possible reaction
getLocalRange(int) - Method in class Java.problem.Reaction
Get local range i
getLocalVariable(int) - Method in class Java.problem.Reaction
Get local variable i
getLocalVariableName(int) - Method in class Java.problem.ReactionType
Get the name of local variable i in the kinetic equation
getLocalVariableSet(int) - Method in class Java.problem.PossibleReaction
Get the locally defined variable set i for this possible reaction
getLowerBound() - Method in class Java.problem.InitialBound
Get lower bound
getLowerBound() - Method in class Java.problem.Range
Get lower bound of the range
getLowerInitialBound(int) - Method in class Java.problem.Experiment
Get lower initial bound for variable i
getMAX_PARAMETERS_PER_ODE() - Method in class Java.problem.Problem
Get maximum number of parameters per ODE
getMaxNumberOfSamplesPerVariable() - Method in class Java.problem.Problem
Get maximum number of samples for one variable
getMaxpts() - Method in class Java.problem.Problem
Get maximum number of sampling points
getMaxTime() - Method in class Java.problem.Experiment
Get the max time point over all samples
getMaxValue() - Method in class Java.problem.Experiment
Get the max data value over all samples
getMaxValue(int) - Method in class Java.problem.Experiment
Get the max data value over all samples for variable i
getMember(int) - Method in class Java.problem.VariableSet
Get member variable i from the set of variables
getMinTime() - Method in class Java.problem.Experiment
Get the min time point over all samples
getMinValue() - Method in class Java.problem.Experiment
Get the min data value over all samples
getMinValue(int) - Method in class Java.problem.Experiment
Get the min data value over all samples for variable i
getName() - Method in class Java.parser.FunctionParser.Function
 
getName() - Method in class Java.problem.Problem
Get problem name
getName() - Method in class Java.problem.ReactionType
Get the name of the reaction type
getName() - Method in class Java.problem.Variable
Get name of variable
getName() - Method in class Java.solution.Solution
Get the name of the solution
getNextMorphem() - Method in class Java.parser.FunctionParser
 
getNumberOfDependentVariables() - Method in class Java.problem.Problem
Get the number of dependent variables
getNumberOfExperiments() - Method in class Java.problem.Problem
Get the number of experiments
getNumberOfLocalParameters() - Method in class Java.problem.Reaction
Get number of local parameters
getNumberOfLocalParameters() - Method in class Java.problem.ReactionType
Get the number of local parameters in the kinetic equation
getNumberOfLocalRanges() - Method in class Java.problem.PossibleReaction
Get the number of locally defined ranges for this possible reaction
getNumberOfLocalRanges() - Method in class Java.problem.Reaction
Get number of local ranges
getNumberOfLocalVariables() - Method in class Java.problem.Reaction
Get number of local variables
getNumberOfLocalVariables() - Method in class Java.problem.ReactionType
Get the number of local variables in the kinetic equation
getNumberOfLocalVariableSets() - Method in class Java.problem.PossibleReaction
Get the number of locally defined variable sets for this possible reaction
getNumberOfMembers() - Method in class Java.problem.VariableSet
Get the number of member variables
getNumberOfPossibleReactions() - Method in class Java.problem.Variable
Get number of possible reactions assigned to the model space of this variable
getNumberOfRanges() - Method in class Java.problem.Problem
Get the number of ranges
getNumberOfReactions() - Method in class Java.problem.Variable
Get number of reactions assigned to this variable
getNumberOfReactionTypes() - Method in class Java.problem.Problem
Get the number of reaction types
getNumberOfSamples() - Method in class Java.problem.Experiment
Get the number of samples
getNumberOfVariables() - Method in class Java.problem.Problem
Get the number of variables
getPossibleReaction(int) - Method in class Java.problem.Variable
Get possible reaction i assigned to the model space of this variable
getRAND1() - Method in class Java.problem.Problem
Get number of random starts in local parameter estimation
getRAND1() - Method in class Java.solution.Solution
Get the number of random starts in local parameter estimation
getRAND2() - Method in class Java.problem.Problem
Get number of random starts in global parameter estimation
getRAND2() - Method in class Java.solution.Solution
Get the number of random starts in global parameter estimation
getRange(int) - Method in class Java.problem.Problem
Get range i
getReaction(int) - Method in class Java.problem.Variable
Get reaction i assigned to this variable
getReactionType() - Method in class Java.problem.PossibleReaction
Get type of the reaction
getReactionType(int) - Method in class Java.problem.Problem
Get reaction type i
getReactionType(String) - Method in class Java.problem.Problem
Get reaction type named nameOfType
getReactionType() - Method in class Java.problem.Reaction
 
getReactionTypes() - Method in class Java.problem.Problem
Get all reaction types in a vector
getSample(int) - Method in class Java.problem.Experiment
Get sample i
getSBML() - Method in class Java.parser.FunctionParser.Function
 
getSBML() - Method in class Java.parser.FunctionParser
 
getSBML() - Method in class Java.problem.ReactionType
Get SBML representation of the reaction equation
getSdev(int) - Method in class Java.problem.Sample
Get standard deviation of the sample for variable i
getSdevArray(int) - Method in class Java.problem.Experiment
Get data standard deviations for variable i
getSEED() - Method in class Java.problem.Problem
Get random seed
getSEED() - Method in class Java.solution.Solution
Get random seed used to generate solution
getSmoothingParameter() - Method in class Java.problem.Problem
Get smoothing parameter
getSmoothingParameter() - Method in class Java.solution.Solution
Get the smoothing parameter used to process data in problem
getTime() - Method in class Java.problem.Sample
Get time-point of the sample
getTimeArray() - Method in class Java.problem.Experiment
Get time-points
getType() - Method in class Java.problem.ErrorFunction
Get the type
getType() - Method in class Java.problem.Problem
Get problem type
getType() - Method in class Java.problem.Variable
Get type of variable; dependent or inputVariable
getUpperBound() - Method in class Java.problem.InitialBound
Get upper bound
getUpperBound() - Method in class Java.problem.Range
Get upper bound of the range
getUpperInitialBound(int) - Method in class Java.problem.Experiment
Get upper initial bound for variable i
getValue(int) - Method in class Java.problem.Sample
Get value of the sample for variable i
getValueArray(int) - Method in class Java.problem.Experiment
Get data values for variable i
getVariable(int) - Method in class Java.problem.Problem
Get variable i
getVariables() - Method in class Java.problem.Problem
Get all variables in a vector
getVariableSet(int) - Method in class Java.problem.Problem
Get variable set i
GraphPanel - Class in Java.gui
The panel for the graph
GraphPanel(Problem, Experiment, JCheckBox[], Color[]) - Constructor for class Java.gui.GraphPanel
The plot

H

hasPerfectData() - Method in class Java.problem.Experiment
Indication if data is perfect

I

index - Static variable in class Java.parser.FunctionParser
 
InitialBound - Class in Java.problem
Description of an initial bound
InitialBound() - Constructor for class Java.problem.InitialBound
 
isDependent() - Method in class Java.problem.Variable
Check if type of variable is dependent
isInputVariable() - Method in class Java.problem.Variable
Check if type of variable is inputVariable
isSSystem() - Method in class Java.problem.Problem
Is the problem of S-system type
itemStateChanged(ItemEvent) - Method in class Java.PlotExperiment
Update checked variables in plot

J

Java - package Java
 
Java.debug - package Java.debug
 
Java.generateFortran - package Java.generateFortran
 
Java.gui - package Java.gui
 
Java.misc - package Java.misc
 
Java.parser - package Java.parser
 
Java.problem - package Java.problem
 
Java.solution - package Java.solution
 

L

lastElement - Variable in class Java.gui.Pppack_smooth
Number of data points
left - Variable in class Java.parser.FunctionParser.SBMLNode
 

M

main(String[]) - Static method in class Java.GenerateProgram
Generate Fortran program to solve problem given as argv[0]
main(String[]) - Static method in class Java.MakeSBML
Make SBML file of a solution model given as argv[0]
main(String[]) - Static method in class Java.parser.FunctionParser
 
main(String[]) - Static method in class Java.PlotExperiment
Plot experiment of a problem given as argv[0]
main(String[]) - Static method in class Java.VerifyProblem
Verify syntax of a problem given as argv[0] Print out debug information by adding a second argument "-d" to argv[1], e.g., java VerifyProblem problemFile -d
MakeSBML - Class in Java
Make SBML file of a solution model
MakeSBML() - Constructor for class Java.MakeSBML
 
MAX_WARNINGS - Static variable in class Java.debug.Debug
Max number of printed out warnings, default 5
Misc - Class in Java.misc
 
Misc() - Constructor for class Java.misc.Misc
 
MyJSlider - Class in Java.gui
Slider to set smoothing parameter in smoothing spline interpolation
MyJSlider(double, double, double) - Constructor for class Java.gui.MyJSlider
 

O

ON - Static variable in class Java.debug.Debug
Debug printouts on or off

P

paintComponent(Graphics) - Method in class Java.gui.GraphPanel
 
PFNExpr - Variable in class Java.parser.FunctionParser
 
PlotExperiment - Class in Java
Plot an experiment from a problem file
PlotExperiment(Problem, Experiment) - Constructor for class Java.PlotExperiment
Create panels and action handling
PossibleReaction - Class in Java.problem
Description of a possible reaction
PossibleReaction() - Constructor for class Java.problem.PossibleReaction
 
Pppack - Class in Java.generateFortran
The code in this class is a Java implementation of the program Pppack published in C.
Pppack() - Constructor for class Java.generateFortran.Pppack
 
Pppack_smooth - Class in Java.gui
Smoothing spline interpolation This class provides an interpolation/approximation facility to work with data.
Pppack_smooth(double[], double[], double[]) - Constructor for class Java.gui.Pppack_smooth
Constructs the spline class.
prettyPrint(BufferedWriter, String, int) - Static method in class Java.generateFortran.GenerateFortran
Pretty printout in Fortran program, no line number in column 1-6
prettyPrint(BufferedWriter, String, int, int) - Static method in class Java.generateFortran.GenerateFortran
Pretty printout in Fortran program
print(Object, String) - Static method in class Java.debug.Debug
Debug printout
print(Object, String, String) - Static method in class Java.debug.Debug
Debug printout
printExperimentDefinition(BufferedWriter, boolean, boolean, boolean) - Static method in class Java.generateFortran.GenerateFortran
Print definition for the experiments in Fortran program
printMaxDefinition(BufferedWriter, Problem) - Static method in class Java.generateFortran.GenerateFortran
Print max sizes of arrays in Fortran program
printModelDefinition(BufferedWriter, boolean) - Static method in class Java.generateFortran.GenerateFortran
Print model definition in Fortran program
printSSystem() - Method in class Java.problem.Problem
Print information of an S-system, relevant if problem is based on an S-system
printTempModelDefinition(BufferedWriter, boolean) - Static method in class Java.generateFortran.GenerateFortran
Print definition for temporary model variables in Fortran program
printTempModelDefinition2(BufferedWriter, boolean) - Static method in class Java.generateFortran.GenerateFortran
Print definition for second temporary model variables in Fortran program
Problem - Class in Java.problem
Store and manage a problem
Problem() - Constructor for class Java.problem.Problem
 

R

Range - Class in Java.problem
Description of a range with lower and upper bounds, and an initial guess
Range() - Constructor for class Java.problem.Range
 
Range(double, double) - Constructor for class Java.problem.Range
 
Range(double, double, double) - Constructor for class Java.problem.Range
 
Reaction - Class in Java.problem
Description of a reaction given in the model
If an initial model in a problem, then one range for each parameter stored in a Vector called localRanges
If a solution model, then one value for each parameter stored in a Vector called localParameters
Reaction() - Constructor for class Java.problem.Reaction
 
ReactionType - Class in Java.problem
Description of a reaction type:
ReactionType() - Constructor for class Java.problem.ReactionType
 
read(String[], BufferedReader, int, int) - Method in class Java.problem.ErrorFunction
Read error function from input file in form of a buffered reader
read(String[], BufferedReader, int, int) - Method in class Java.problem.Experiment
Read range from input file in form of a buffered reader
read(String[], BufferedReader, int, int, Vector<Variable>, Vector<Experiment>) - Method in class Java.problem.InitialBound
Read range from input file in form of a buffered reader
read(String[], BufferedReader, int, int, Vector<Variable>, Vector<ReactionType>, Vector<VariableSet>, Vector<Range>) - Method in class Java.problem.PossibleReaction
Read range from input file in form of a buffered reader
read(File, int) - Method in class Java.problem.Problem
Read the problem
read(String[], BufferedReader, int, int) - Method in class Java.problem.Range
Read range from input file in form of a buffered reader
read(String[], BufferedReader, int, int, Vector<Variable>, Vector<ReactionType>, Vector<Range>) - Method in class Java.problem.Reaction
Read reaction from input file in form of a buffered reader
read(String[], BufferedReader, int, int) - Method in class Java.problem.ReactionType
Read reaction type from input file in form of a buffered reader
read(String[], BufferedReader, int, int, Vector<Variable>, Vector<Experiment>) - Method in class Java.problem.Sample
Read sample from input file in form of a buffered reader
read(String[], BufferedReader, int, int) - Method in class Java.problem.Variable
Read variable from input file in form of a buffered reader
read(String[], BufferedReader, int, int, Vector<Variable>) - Method in class Java.problem.VariableSet
Read variable set form input file in form of a buffered reader
read(File, int) - Method in class Java.solution.Solution
Read the solution file
readDerivatives(int, int) - Method in class Java.problem.ReactionType
Read the derivatives from file REACTIONS.txt
rf - Variable in class Java.parser.FunctionParser.SBMLNode
 
right - Variable in class Java.parser.FunctionParser.SBMLNode
 
Round(double, int) - Static method in class Java.misc.Misc
Round to a double to Ndec decimals

S

Sample - Class in Java.problem
Description of a sample:
Vector of data-points (values) and standard deviations (sdevs) for each variable at time-point time.
Sample() - Constructor for class Java.problem.Sample
 
saveSBML(File, String, int) - Method in class Java.solution.Solution
save the solution model as SBML
set(double, double, double) - Method in class Java.gui.MyJSlider
Set the slider's min, max and value.
setAsGMAterm(int) - Method in class Java.problem.ReactionType
Set as a GMA term with gma variables, e.g., alpha*X1^g11*X2^g12*X3^g13 for gma=3.
SetAxesDialog - Class in Java.gui
Set up the dialog for the axes settings
SetAxesDialog() - Constructor for class Java.gui.SetAxesDialog
 
setCheckedVariables(JCheckBox[]) - Method in class Java.gui.GraphPanel
 
setLocalRange(int, Range) - Method in class Java.problem.PossibleReaction
Set the locally defined range i for this possible reaction
setLocalRange(int, Range) - Method in class Java.problem.Reaction
Set the local range for parameter i of this reaction
setLocalSmoothingParameter(double) - Method in class Java.gui.GraphPanel
 
setLocalVariable(int, Variable) - Method in class Java.problem.Reaction
Set the local variable i of this reaction
setLocalVariableSet(int, VariableSet) - Method in class Java.problem.PossibleReaction
Set the locally defined variable set i for this possible reaction
setMaxMin() - Method in class Java.gui.GraphPanel
 
setReactionType(ReactionType) - Method in class Java.problem.PossibleReaction
Set type of the reaction
setReactionType(ReactionType) - Method in class Java.problem.Reaction
Set the reaction type
setupq(double[], double[], double[], int, double[][], double[]) - Static method in class Java.generateFortran.Pppack
 
smooth(double[], double[], double[], int, double, double[][], double[][]) - Static method in class Java.generateFortran.Pppack
 
Solution - Class in Java.solution
Description of a solution to a problem
Solution(Problem) - Constructor for class Java.solution.Solution
To read a solution requires reactionsTypes and variables from the problem
split(String, int, int) - Static method in class Java.misc.Misc
Split an input String at spaces, return array of Strings.
stat(String, String) - Static method in class Java.debug.Debug
Debug printout from static environment
stat(String, String, String) - Static method in class Java.debug.Debug
Debug printout from static environment
staterror(String, String) - Static method in class Java.debug.Debug
Error message and program terminationca
staterror(String, String, String) - Static method in class Java.debug.Debug
Error message and program termination
statwarning(String, String) - Static method in class Java.debug.Debug
Warning message and program termination
statwarning(String, String, String) - Static method in class Java.debug.Debug
Warning message and program termination

T

TOK_CLOSE_BRACKET - Static variable in class Java.parser.FunctionParser.PFNField
 
TOK_NUMBER - Static variable in class Java.parser.FunctionParser.PFNField
 
TOK_OPEN_BRACKET - Static variable in class Java.parser.FunctionParser.PFNField
 
TOK_OPERATOR - Static variable in class Java.parser.FunctionParser.PFNField
 
TOK_PARAMETER - Static variable in class Java.parser.FunctionParser.PFNField
 
TOK_UNUSED - Static variable in class Java.parser.FunctionParser.PFNField
 
tokenExpr - Variable in class Java.parser.FunctionParser
 
tokenize() - Method in class Java.parser.FunctionParser
 
tokenStack - Variable in class Java.parser.FunctionParser
 
toString() - Method in class Java.parser.FunctionParser.SBMLNode
 
toString() - Method in class Java.problem.ErrorFunction
Get string representation
toString() - Method in class Java.problem.Experiment
 
toString() - Method in class Java.problem.InitialBound
Get string representation
toString() - Method in class Java.problem.PossibleReaction
Get string representation
toString() - Method in class Java.problem.Problem
String value of experiments, calling toString in Experiment
toString() - Method in class Java.problem.Range
Get string representation
toString() - Method in class Java.problem.Reaction
Get string representation
toString() - Method in class Java.problem.ReactionType
Get string representation
toString() - Method in class Java.problem.Sample
Get string representation
toString() - Method in class Java.problem.Variable
Get string representation
toString() - Method in class Java.problem.VariableSet
Get string representation
toString() - Method in class Java.solution.Solution
String value of solution

U

useNumericalDerivaties() - Method in class Java.problem.ReactionType
Monitor if analytical derivatives are defined.

V

Variable - Class in Java.problem
Description of a variable
Variable() - Constructor for class Java.problem.Variable
 
VariableSet - Class in Java.problem
Description of a variable set
VariableSet() - Constructor for class Java.problem.VariableSet
 
VariableSet(Variable) - Constructor for class Java.problem.VariableSet
Create variable set containing one variable
VariableSet(Vector<Variable>) - Constructor for class Java.problem.VariableSet
Create variable set containing a vector of variables
VerifyProblem - Class in Java
Verify syntax of a problem
VerifyProblem() - Constructor for class Java.VerifyProblem
 

W

WARNING - Static variable in class Java.debug.Debug
Warning messages on or off
warning(Object, String) - Static method in class Java.debug.Debug
Warning message and program termination
warning(Object, String, String) - Static method in class Java.debug.Debug
Warning message and program termination

X

x - Variable in class Java.gui.Pppack_smooth
Array of data abscissae, assumed to be strictly increasing

Y

y - Variable in class Java.gui.Pppack_smooth
Array of data ordinates, corresponded to abscissae

_

_doubleValue - Variable in class Java.parser.FunctionParser.PFNField
 
_error - Variable in class Java.parser.FunctionParser
 
_func - Variable in class Java.parser.FunctionParser.PFNField
 
_functions - Variable in class Java.parser.FunctionParser
Supported functions Here, order is significant.
_strValue - Variable in class Java.parser.FunctionParser.PFNField
 
_type - Variable in class Java.parser.FunctionParser.PFNField
 

A C D E F G H I J L M O P R S T U V W X Y _