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A
Acceptation
- Class in
PIANOS.generator
Generates calculations needed when generating the Fortarn module "main".
Acceptation()
- Constructor for class PIANOS.generator.
Acceptation
addAffected(Variable)
- Method in class PIANOS.datastructures.
Variable
Adds a new Variable at the end of the list of Variables that this Variable affects.
addDependence(Variable)
- Method in class PIANOS.datastructures.
Variable
Adds a new Variable at the end of the list of Variables that this Variables depends on.
addVariable(Variable)
- Method in class PIANOS.datastructures.
Entity
B
BetaDistribution
- Class in
PIANOS.datastructures
BetaDistribution()
- Constructor for class PIANOS.datastructures.
BetaDistribution
BinomialDistribution
- Class in
PIANOS.datastructures
BinomialDistribution()
- Constructor for class PIANOS.datastructures.
BinomialDistribution
C
ComputationalModel
- Class in
PIANOS.datastructures
ComputationalModel(int, int, int, int, String, LinkedList<Variable>, LinkedList<Entity>, HashMap<String, Entity>, HashMap<String, Variable>, String, String, String, String)
- Constructor for class PIANOS.datastructures.
ComputationalModel
ComputationalModelParser
- Class in
PIANOS.io
The PIANOS parser Reads input files with readModel and returns the corresponding model.
ContinuousUniformDistribution
- Class in
PIANOS.datastructures
ContinuousUniformDistribution()
- Constructor for class PIANOS.datastructures.
ContinuousUniformDistribution
D
Definitions
- Class in
PIANOS.generator
This class is used to generate the Fortran module "definitions".
Definitions()
- Constructor for class PIANOS.generator.
Definitions
DiscreteUniformDistribution
- Class in
PIANOS.datastructures
DiscreteUniformDistribution()
- Constructor for class PIANOS.datastructures.
DiscreteUniformDistribution
Distribution
- Class in
PIANOS.datastructures
Distribution(int)
- Constructor for class PIANOS.datastructures.
Distribution
DistributionFactory
- Class in
PIANOS.datastructures
DistributionFactory(String)
- Constructor for class PIANOS.datastructures.
DistributionFactory
E
Entity
- Class in
PIANOS.datastructures
Entity()
- Constructor for class PIANOS.datastructures.
Entity
EntityNotFoundException
- Exception in
PIANOS.exceptions
EntityNotFoundException(String)
- Constructor for exception PIANOS.exceptions.
EntityNotFoundException
Equation
- Class in
PIANOS.datastructures
Equation(String[], Variable[])
- Constructor for class PIANOS.datastructures.
Equation
F
FortranMain
- Class in
PIANOS.generator
FortranMain()
- Constructor for class PIANOS.generator.
FortranMain
FortranWriter
- Class in
PIANOS.io
FortranWriter, a class that receives lines of Fortran code, multilines and indents them correctly and writes them to a file.
FortranWriter(String)
- Constructor for class PIANOS.io.
FortranWriter
Creates a new
FortranWriter
.
G
generateAcceptationCode(Variable, String)
- Static method in class PIANOS.generator.
Acceptation
Generates code that decides whether the new value is accepted and makes the necessary changes: updates the value of the current parameter and all functional parameters depending on it.
generateAcceptationFormula(Variable)
- Static method in class PIANOS.generator.
Acceptation
Generates code that calculates the acceptance probability for the current parameter.
generateDefinitions(ComputationalModel)
- Static method in class PIANOS.generator.
Definitions
Generates and writes the Fortran module definitions.f90.
generateInput(String, ComputationalModel)
- Static method in class PIANOS.generator.
Input
Generates and writes the Fortran module input.f90.
generateIntroduction()
- Static method in class PIANOS.
Generator
generateMain(String, ComputationalModel)
- Static method in class PIANOS.generator.
FortranMain
generateNewValueCode(Variable)
- Static method in class PIANOS.generator.
Acceptation
Generates code that fetches a proposed new value for a parameter from its buffer or if the buffer is empty, calls the subroutine "generate".
generateNewValuesFunctionalCode(Variable)
- Static method in class PIANOS.generator.
Acceptation
Generates code that calculates new values for all the functional parameters depending on the current parameter.
generateOutput(String, ComputationalModel)
- Static method in class PIANOS.generator.
Output
Generates and writes the Fortran module output.f90.
generateProposal(ComputationalModel)
- Static method in class PIANOS.generator.
Proposal
Generates and writes the Fortran module proposal.f90.
Generator
- Class in
PIANOS
The PIANOS main class.
Generator()
- Constructor for class PIANOS.
Generator
getAffectsList()
- Method in class PIANOS.datastructures.
Variable
getAlgorithm()
- Method in class PIANOS.datastructures.
Variable
getBurnIn()
- Method in class PIANOS.datastructures.
ComputationalModel
getColumn()
- Method in class PIANOS.datastructures.
Variable
getDataFile()
- Method in class PIANOS.datastructures.
Entity
getDependsList()
- Method in class PIANOS.datastructures.
Variable
getDistribution(String)
- Method in class PIANOS.datastructures.
DistributionFactory
getDistribution()
- Method in class PIANOS.datastructures.
Variable
getEntity()
- Method in class PIANOS.datastructures.
Variable
getEntityList()
- Method in class PIANOS.datastructures.
ComputationalModel
getEntityMapper()
- Method in class PIANOS.datastructures.
ComputationalModel
getEquation()
- Method in class PIANOS.datastructures.
Equation
getEquation()
- Method in class PIANOS.datastructures.
Variable
getFreqCode(String[])
- Method in class PIANOS.datastructures.
BetaDistribution
getFreqCode(String[])
- Method in class PIANOS.datastructures.
BinomialDistribution
getFreqCode(String[])
- Method in class PIANOS.datastructures.
ContinuousUniformDistribution
getFreqCode(String[])
- Method in class PIANOS.datastructures.
DiscreteUniformDistribution
getFreqCode(String[])
- Method in class PIANOS.datastructures.
Distribution
getFreqCode(String[])
- Method in class PIANOS.datastructures.
PoissonDistribution
getFreqCode(String[])
- Method in class PIANOS.datastructures.
UserDefinedDistribution
getGenCode(String[])
- Method in class PIANOS.datastructures.
BetaDistribution
getGenCode(String[])
- Method in class PIANOS.datastructures.
BinomialDistribution
getGenCode(String[])
- Method in class PIANOS.datastructures.
ContinuousUniformDistribution
getGenCode(String[])
- Method in class PIANOS.datastructures.
DiscreteUniformDistribution
getGenCode(String[])
- Method in class PIANOS.datastructures.
Distribution
getGenCode(String[])
- Method in class PIANOS.datastructures.
PoissonDistribution
getGenCode(String[])
- Method in class PIANOS.datastructures.
UserDefinedDistribution
getInitialValueFile()
- Method in class PIANOS.datastructures.
ComputationalModel
getInitialValueFileName()
- Method in class PIANOS.datastructures.
ComputationalModel
getIntroduction()
- Method in class PIANOS.datastructures.
BetaDistribution
getIntroduction()
- Method in class PIANOS.datastructures.
BinomialDistribution
getIntroduction()
- Method in class PIANOS.datastructures.
ContinuousUniformDistribution
getIntroduction()
- Method in class PIANOS.datastructures.
DiscreteUniformDistribution
getIntroduction()
- Method in class PIANOS.datastructures.
Distribution
getIntroduction()
- Method in class PIANOS.datastructures.
PoissonDistribution
getIntroduction()
- Method in class PIANOS.datastructures.
UserDefinedDistribution
getIterations()
- Method in class PIANOS.datastructures.
ComputationalModel
getLastValuesFileName()
- Method in class PIANOS.datastructures.
ComputationalModel
getLineLength()
- Method in class PIANOS.datastructures.
Entity
getMissingValueCount()
- Method in class PIANOS.datastructures.
Variable
getModelFile()
- Method in class PIANOS.datastructures.
ComputationalModel
getModelFileName()
- Method in class PIANOS.datastructures.
ComputationalModel
getName()
- Method in class PIANOS.datastructures.
Entity
getName()
- Method in class PIANOS.datastructures.
Variable
getNeighbourCount()
- Method in class PIANOS.datastructures.
ComputationalModel
getNumberOfParameters()
- Method in class PIANOS.datastructures.
Distribution
getOutputFile()
- Method in class PIANOS.datastructures.
ComputationalModel
getOutputFileName()
- Method in class PIANOS.datastructures.
ComputationalModel
getParameter(int)
- Method in class PIANOS.datastructures.
Distribution
getParameters()
- Method in class PIANOS.datastructures.
Equation
getParameterString(int)
- Method in class PIANOS.datastructures.
Distribution
getProposal()
- Method in class PIANOS.datastructures.
Variable
getSize()
- Method in class PIANOS.datastructures.
Entity
getSpatialMatrixFile()
- Method in class PIANOS.datastructures.
Entity
getStrategy()
- Method in class PIANOS.datastructures.
Variable
getSummaryFile()
- Method in class PIANOS.datastructures.
ComputationalModel
getSummaryFileName()
- Method in class PIANOS.datastructures.
ComputationalModel
getThinning()
- Method in class PIANOS.datastructures.
ComputationalModel
getTopologicalVariableList()
- Method in class PIANOS.datastructures.
ComputationalModel
getUpdates()
- Method in class PIANOS.datastructures.
Variable
getUpdateStrategy()
- Method in class PIANOS.datastructures.
ComputationalModel
getVariableList()
- Method in class PIANOS.datastructures.
ComputationalModel
getVariableList()
- Method in class PIANOS.datastructures.
Entity
getVariableMapper()
- Method in class PIANOS.datastructures.
ComputationalModel
getXCoordinate()
- Method in class PIANOS.datastructures.
Entity
getYCoordinate()
- Method in class PIANOS.datastructures.
Entity
I
IllegalParametersException
- Exception in
PIANOS.exceptions
IllegalParametersException(String)
- Constructor for exception PIANOS.exceptions.
IllegalParametersException
incrementMissingValues()
- Method in class PIANOS.datastructures.
Variable
Adds one to the number of missing values.
Input
- Class in
PIANOS.generator
This class is used to generate the Fortran module "input".
Input()
- Constructor for class PIANOS.generator.
Input
integerfmt
- Static variable in class PIANOS.generator.
Output
InvalidModelException
- Exception in
PIANOS.exceptions
InvalidModelException(String)
- Constructor for exception PIANOS.exceptions.
InvalidModelException
InvalidProposalException
- Exception in
PIANOS.exceptions
InvalidProposalException(String)
- Constructor for exception PIANOS.exceptions.
InvalidProposalException
isData()
- Method in class PIANOS.datastructures.
Variable
isFunctional()
- Method in class PIANOS.datastructures.
Variable
isInteger(int)
- Method in class PIANOS.datastructures.
Distribution
isInteger()
- Method in class PIANOS.datastructures.
Variable
isMatrix()
- Method in class PIANOS.datastructures.
Entity
isOk()
- Method in class PIANOS.datastructures.
Variable
Runs this Variable through a health check.
isPrinted()
- Method in class PIANOS.datastructures.
Variable
isSpatial()
- Method in class PIANOS.datastructures.
Entity
isSpatial()
- Method in class PIANOS.datastructures.
Variable
M
main(String[])
- Static method in class PIANOS.
Generator
The PIANOS command-line interface.
MissingDistributionException
- Exception in
PIANOS.exceptions
MissingDistributionException(String)
- Constructor for exception PIANOS.exceptions.
MissingDistributionException
MissingFunctionException
- Exception in
PIANOS.exceptions
MissingFunctionException(String)
- Constructor for exception PIANOS.exceptions.
MissingFunctionException
modelTestOnly(String, String, DistributionFactory)
- Static method in class PIANOS.io.
ComputationalModelParser
O
Output
- Class in
PIANOS.generator
This class is used to generate the Fortran module "output".
Output()
- Constructor for class PIANOS.generator.
Output
P
parseVariable(File, boolean, String, HashMap<String, Variable>, DistributionFactory)
- Static method in class PIANOS.io.
ComputationalModelParser
Reads a variable definition line and returns a representation of the variable, public for testing purposes.
PIANOS
- package PIANOS
PIANOS.datastructures
- package PIANOS.datastructures
PIANOS.exceptions
- package PIANOS.exceptions
PIANOS.generator
- package PIANOS.generator
PIANOS.io
- package PIANOS.io
PoissonDistribution
- Class in
PIANOS.datastructures
PoissonDistribution()
- Constructor for class PIANOS.datastructures.
PoissonDistribution
Proposal
- Class in
PIANOS.generator
This class is used to generate the Fortran module "proposal".
Proposal()
- Constructor for class PIANOS.generator.
Proposal
R
readModel(String, String, String, String, String, String, DistributionFactory)
- Static method in class PIANOS.io.
ComputationalModelParser
The main interface for the Parser.
realfmt
- Static variable in class PIANOS.generator.
Output
S
setAlgorithm(String)
- Method in class PIANOS.datastructures.
Variable
(currently not implemented) This will set the update algorithm for this Variable.
setColumn(int)
- Method in class PIANOS.datastructures.
Variable
Sets the data column number for the Variable (See getColumn())
setData(boolean)
- Method in class PIANOS.datastructures.
Variable
setDataFile(String)
- Method in class PIANOS.datastructures.
Entity
setDistribution(Distribution)
- Method in class PIANOS.datastructures.
Variable
setEntity(Entity)
- Method in class PIANOS.datastructures.
Variable
setEquation(Equation)
- Method in class PIANOS.datastructures.
Variable
setFunctional(boolean)
- Method in class PIANOS.datastructures.
Variable
setLastValuesFileName(String)
- Method in class PIANOS.datastructures.
ComputationalModel
setLineLength(int)
- Method in class PIANOS.datastructures.
Entity
setMatrix(boolean)
- Method in class PIANOS.datastructures.
Entity
setModel(ComputationalModel)
- Static method in class PIANOS.
Generator
setName(String)
- Method in class PIANOS.datastructures.
Entity
setName(String)
- Method in class PIANOS.datastructures.
Variable
setParameter(int, int)
- Method in class PIANOS.datastructures.
Distribution
setParameter(int, double)
- Method in class PIANOS.datastructures.
Distribution
setParameter(int, Variable)
- Method in class PIANOS.datastructures.
Distribution
setParameters(Variable[])
- Method in class PIANOS.datastructures.
Equation
setParameters(Variable)
- Method in class PIANOS.datastructures.
Equation
setParameterString(int, String)
- Method in class PIANOS.datastructures.
Distribution
setPrinted()
- Method in class PIANOS.datastructures.
Variable
Sets that this Variable should be printed.
setProposal(Distribution)
- Method in class PIANOS.datastructures.
Variable
Sets the proposal Distribution for this variable (see the manual)
setSize(int)
- Method in class PIANOS.datastructures.
Entity
setSpatial(boolean)
- Method in class PIANOS.datastructures.
Variable
setSpatialMatrixFile(String)
- Method in class PIANOS.datastructures.
Entity
setStrategy(String)
- Method in class PIANOS.datastructures.
Variable
Sets the update strategy for this variable {sequential, random}
setTopologicalList(ArrayList<Variable>)
- Static method in class PIANOS.generator.
Acceptation
Sets the topological variable list that is used when calculating the correct new-value-generation order for functional parameters.
setType(boolean)
- Method in class PIANOS.datastructures.
Variable
setUpdates(int)
- Method in class PIANOS.datastructures.
Variable
Sets the number of updates this variable should have before end of simulation.
setXCoordinate(Entity)
- Method in class PIANOS.datastructures.
Entity
setYCoordinate(Entity)
- Method in class PIANOS.datastructures.
Entity
spatAffectedMap
- Static variable in class PIANOS.io.
ComputationalModelParser
Public for testing purposes, do not modify.
SyntaxException
- Exception in
PIANOS.exceptions
SyntaxException(String)
- Constructor for exception PIANOS.exceptions.
SyntaxException
T
testNoInitialValues(String, String, String, String, String, DistributionFactory)
- Static method in class PIANOS.io.
ComputationalModelParser
toBeChecked
- Static variable in class PIANOS.io.
ComputationalModelParser
Public for testing purposes, do not modify.
toString()
- Method in class PIANOS.datastructures.
ComputationalModel
toString()
- Method in class PIANOS.datastructures.
Distribution
toString()
- Method in class PIANOS.datastructures.
Entity
toString()
- Method in class PIANOS.datastructures.
Equation
toString()
- Method in class PIANOS.datastructures.
UserDefinedDistribution
toString()
- Method in class PIANOS.datastructures.
Variable
Prints a limited amount of information about this Variable similar to a model file variable definition line.
U
UserDefinedDistribution
- Class in
PIANOS.datastructures
UserDefinedDistribution(DistributionSkeleton)
- Constructor for class PIANOS.datastructures.
UserDefinedDistribution
V
Variable
- Class in
PIANOS.datastructures
A representation for a stochastic or functional variable/parameter in a statistical PIANOS model.
Variable()
- Constructor for class PIANOS.datastructures.
Variable
Constructs a new Variable from scratch, ready to take in field values.
W
write(ArrayList<String>)
- Method in class PIANOS.io.
FortranWriter
Writes lines of Fortran source code into the file.
write(String[])
- Method in class PIANOS.io.
FortranWriter
Writes lines of Fortran source code into the file.
writeProgram(String, String, String, String, String, String, String, String)
- Static method in class PIANOS.
Generator
The PIANOS main interface.
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