A B C D E F G I M O P R S T U V W

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.

A B C D E F G I M O P R S T U V W