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

A

addSymbol(String) - Method in class jigcell.xpp.SymbolTable

Add id to the symbol table.

addSymbol(String, String) - Method in class jigcell.xpp.SymbolTable

Add a symbol with name and id.

addToMatrix(IEditableDataElement, IDataElement) - Static method in class jigcell.xpp.AsynchronousCultureRunner

matrix1 = matrix1 + matrix2

addToRow(IEditableDataElement, IDataElement) - Static method in class jigcell.xpp.AsynchronousCultureRunner

row1 = row1 + row2

appendAndBreak(String, String) - Static method in class jigcell.xpp.SBMLToStochKitTranslator

Returns s1 and s2 appended with line breaks added if the resulting string is longer than MAX_CHARS_PER_LINE characters.

appendAndBreak_(String, String, boolean) - Static method in class jigcell.xpp.SBMLToStochKitTranslator

Underlying method for appendAndBreak and appendAndBreakNoIndent.

appendAndBreakNoIndent(String, String) - Static method in class jigcell.xpp.SBMLToStochKitTranslator

Like appendAndBreak but no additional white space is added when the second line is created.

applySimulatorCapabilities(double, double, double, int) - Method in class jigcell.xpp.Oscill8Simulator

Combines the existing simulator capability settings and simulation parameters to determine the capabilities that will be used for this simulation.

applySimulatorCapabilities(double, double, double, int) - Method in class jigcell.xpp.XPPSimulator

Combines the existing simulator capability settings and simulation parameters to determine the capabilities that will be used for this simulation.

applyVelocityTerm(String, boolean, SpeciesReference) - Method in class jigcell.xpp.SBMLToXPPTranslator

Adds a single velocity term to an equation.

associative - Static variable in class jigcell.xpp.CPPExpression

AsynchronousCultureRunner - Class in jigcell.xpp

Computes the average concentration levels in an asynchronous culture.

AsynchronousCultureRunner() - Constructor for class jigcell.xpp.AsynchronousCultureRunner

B

breakAFortranString(int, String, String, String, String) - Static method in class jigcell.xpp.SBMLToStochKitTranslator

Builds a Fortran expression and adds breaks as necessary to keep the maximum line width below maxWidth.

breakEquation(String) - Static method in class jigcell.xpp.SBMLToXPPTranslator

Breaks an equation along '+', '-', '*', '/', ',', or ' ' in order to fit on an XPP line.

buildSymbolTable(Model) - Method in class jigcell.xpp.SBMLToStochKitTranslator

Creates a table of variable assignments to be inserted as Fortran code.

buildSymbolTable(Model) - Method in class jigcell.xpp.SBMLToXPPTranslator

Adds the name and id of all tracked SBML elements in a model to a symbol table.

buildSymbolTablePump(SymbolTable, Collection) - Static method in class jigcell.xpp.SBMLToXPPTranslator

Takes SBML elements from a collection and adds their name and id to a symbol table.

C

calculateAllEquationsInternal() - Method in class jigcell.xpp.SBMLToXPPTranslator

calculateEquationsFromReactions() - Method in class jigcell.xpp.SBMLToXPPTranslator

checkIfExpression - Static variable in class jigcell.xpp.SBMLToXPPTranslator

checkNumber - Static variable in class jigcell.xpp.SBMLToXPPTranslator

cleanName - Static variable in class jigcell.xpp.SBMLToXPPTranslator

code - Variable in class jigcell.xpp.SBMLToStochKitTranslator

compartmentIDs - Variable in class jigcell.xpp.SBMLToXPPTranslator

computeSelectionList(List) - Method in class jigcell.xpp.SBMLToStochKitTranslator

Computes the list of species to return from simulation.

computeSelectionList(List) - Method in class jigcell.xpp.SBMLToXPPTranslator

Computes the list of species to return from simulation.

computeVelocities() - Method in class jigcell.xpp.SBMLToXPPTranslator

Computes the velocity terms that make up the species equations.

convertCapabilitiesToXPP(Capabilities) - Method in class jigcell.xpp.SBMLToXPPTranslator

Constructs a simulator setting string that can be passed to XPP.

convertIDToXPPID(String, int) - Method in class jigcell.xpp.SBMLToXPPTranslator

Converts an SBML id to an XPP id.

convertMathToInfix(String, boolean) - Method in class jigcell.xpp.SBMLToXPPTranslator

CPPExpression - Class in jigcell.xpp

This code is licensed under the DARPA BioCOMP Open Source License.

CPPExpression(SymbolTable, SymbolTable, Node, int) - Constructor for class jigcell.xpp.CPPExpression

CPPExpression(SymbolTable, SymbolTable, Node) - Constructor for class jigcell.xpp.CPPExpression

CPPExpression(SymbolTable, SymbolTable, MathMLExpression) - Constructor for class jigcell.xpp.CPPExpression

CPPExpression(SymbolTable, MathMLExpression) - Constructor for class jigcell.xpp.CPPExpression

CPPExpression(SymbolTable, Node, int) - Constructor for class jigcell.xpp.CPPExpression

CPPExpression(SymbolTable, Node) - Constructor for class jigcell.xpp.CPPExpression

CPPExpression(MathMLExpression) - Constructor for class jigcell.xpp.CPPExpression

CPPExpression(Node) - Constructor for class jigcell.xpp.CPPExpression

CPPExpression(Node, int) - Constructor for class jigcell.xpp.CPPExpression

createDefaultCapabilities() - Static method in class jigcell.xpp.EnsembleSimulator

Default capabilities for this simulator.

createDefaultCapabilities() - Static method in class jigcell.xpp.Oscill8Simulator

Default capabilities for this simulator.

createDefaultCapabilities() - Static method in class jigcell.xpp.StochKitSimulator

Default capabilities for this simulator.

createDefaultCapabilities() - Static method in class jigcell.xpp.XPPSimulator

Default capabilities for this simulator.

cwd - Variable in class jigcell.xpp.SBMLToStochKitTranslator

D

DEBUG - Static variable in class jigcell.xpp.CPPExpression

DEFAULT_LOWER_BOUND - Static variable in class jigcell.xpp.SBMLToStochKitTranslator

DEFAULT_MODEL_NAME - Static variable in class jigcell.xpp.SBMLToStochKitTranslator

DEFAULT_NML_FILENAME - Static variable in class jigcell.xpp.SBMLToStochKitTranslator

DEFAULT_UPPER_BOUND - Static variable in class jigcell.xpp.SBMLToStochKitTranslator

defaultInitialConditionsContents - Variable in class jigcell.xpp.SBMLToStochKitTranslator

differentialIDs - Variable in class jigcell.xpp.SBMLToXPPTranslator

displayConcentration - Variable in class jigcell.xpp.EnsembleLauncher

displayConcentration - Variable in class jigcell.xpp.StochKitLauncher

DONT_LOOKUP_SYMBOLS - Static variable in class jigcell.xpp.CPPExpression

dumpSymbolTable(PrintWriter) - Method in class jigcell.xpp.SymbolTable

Write the symbol table to out.

dumpSymbolTable() - Method in class jigcell.xpp.SymbolTable

E

emptySymbolTable() - Method in class jigcell.xpp.SymbolTable

EnsembleLauncher - Class in jigcell.xpp

Runs StochKit on an SBML file multiple times to collect ensemble result.

EnsembleLauncher(Simulator, Model) - Constructor for class jigcell.xpp.EnsembleLauncher

Runs StochKit on an SBML file.

EnsembleLauncher(Simulator, Model, boolean, int) - Constructor for class jigcell.xpp.EnsembleLauncher

EnsembleSimulator - Class in jigcell.xpp

Makes the StochKit simulator available to the simulator API.

EnsembleSimulator() - Constructor for class jigcell.xpp.EnsembleSimulator

Creates a new simulator.

EnsembleSimulator(Capabilities) - Constructor for class jigcell.xpp.EnsembleSimulator

Creates a new simulator.

EST_TASK - Static variable in class jigcell.xpp.SBMLToStochKitTranslator

estimatorStatus(String) - Method in class jigcell.xpp.SBMLToStochKitTranslator

Multithreaded callers of Biopack can call this method to get the status of the current running estimator.

expression - Variable in class jigcell.xpp.CPPExpression

expressionParser - Variable in class jigcell.xpp.SBMLToXPPTranslator

EXTRACT_PARAMS - Static variable in class jigcell.xpp.SBMLToStochKitTranslator

extractParameters(String, String) - Method in class jigcell.xpp.SBMLToStochKitTranslator

Extract the parameter values and names from f90Model and report and put them in a Hashtable.

F

findAFortranName(String) - Method in class jigcell.xpp.SymbolTable

Takes a valid Fortran identifier name or string and finds a similar identifier name that is not already used in fortranNameCol.

fixFunctionNames(String) - Method in class jigcell.xpp.SBMLToXPPTranslator

Replaces function calls that use different builtin names between SBML and XPP.

fixIDs(String) - Method in class jigcell.xpp.SBMLToXPPTranslator

Replaces ids that differ between SBML and XPP.

forbiddenSymbols - Static variable in class jigcell.xpp.SymbolTable

formatReal(String) - Static method in class jigcell.xpp.CPPExpression

Takes a number in a string and ensures it ends in "_R8" and has a decimal place.

formatReal(double) - Static method in class jigcell.xpp.CPPExpression

FORTRAN_CHARACTER_STRING - Static variable in class jigcell.xpp.SymbolTable.Mode

The mode for Fortran character strings.

FORTRAN_IDENTIFIER - Static variable in class jigcell.xpp.SymbolTable.Mode

fortranNameCol - Variable in class jigcell.xpp.SymbolTable

fortranNameColRev - Variable in class jigcell.xpp.SymbolTable

G

generateODEFromModelBuilder(Model, File, boolean) - Static method in class jigcell.xpp.SBMLToXPPTranslator

Converts an SBML file to an ODE file from the ModelBuilder

generateVelocityFromMath(String) - Method in class jigcell.xpp.SBMLToXPPTranslator

Generates the XPP velocity from a MathML string.

genExpression(Node) - Method in class jigcell.xpp.CPPExpression

Convert a parse tree into Fortran 90 code.

getAvailableSelections() - Method in class jigcell.xpp.SBMLToStochKitTranslator

A List[String] of tokens for each measurable element in the model.

getAvailableSelections() - Method in class jigcell.xpp.SBMLToXPPTranslator

A List[String] of tokens for each measurable element in the model.

getBvarsFromFunction - Static variable in class jigcell.xpp.SBMLToXPPTranslator

getConcentration(Species) - Method in class jigcell.xpp.SBMLToXPPTranslator

getElapsedTime() - Static method in class jigcell.xpp.Stopwatch

returns elapsed time in milliseconds if the watch has never been started then return zero

getEquation(String, String) - Method in class jigcell.xpp.SBMLToXPPTranslator

getExpression() - Method in class jigcell.xpp.CPPExpression

getExpression(String, int) - Method in class jigcell.xpp.CPPExpression

getExpression(String, int, String) - Method in class jigcell.xpp.CPPExpression

getMassActionParams - Static variable in class jigcell.xpp.SBMLToXPPTranslator

getMichaelieMentenParams - Static variable in class jigcell.xpp.SBMLToXPPTranslator

getModelId(Model) - Static method in class jigcell.xpp.SBMLToStochKitTranslator

getModelName(Model) - Static method in class jigcell.xpp.SBMLToStochKitTranslator

getOrder(Node) - Method in class jigcell.xpp.CPPExpression

getOriginalValue(String) - Method in class jigcell.xpp.SBMLToXPPTranslator

The current value of a modifiable element in the model.

getProgramDirectory() - Method in class jigcell.xpp.Oscill8Launcher

The location where Oscill8 is installed.

getProgramDirectory() - Method in class jigcell.xpp.SBMLToStochKitTranslator

The location where StochKit is installed.

getProgramDirectory() - Method in class jigcell.xpp.SBMLToXPPTranslator

The location where XPP is installed.

getSelectableNamesInternal() - Method in class jigcell.xpp.EnsembleSimulator

getSelectableNamesInternal() - Method in class jigcell.xpp.StochKitSimulator

getSelectableNamesInternal() - Method in class jigcell.xpp.XPPSimulator

getSettableNames() - Method in class jigcell.xpp.SBMLToStochKitTranslator

The name or id of every settable quantity.

getSettableNames() - Method in class jigcell.xpp.SBMLToXPPTranslator

The name or id of every settable quantity.

getSpeciesFromFunction - Static variable in class jigcell.xpp.SBMLToXPPTranslator

getStochMassActionParams - Static variable in class jigcell.xpp.SBMLToXPPTranslator

getStochMichaelieMentenParams - Static variable in class jigcell.xpp.SBMLToXPPTranslator

getSymbol(String) - Method in class jigcell.xpp.CPPExpression

Follows the correct logic for this CPPExpression to get a symbol for name.

getValueInternal(String) - Method in class jigcell.xpp.XPPSimulator

getValueNamesInternal() - Method in class jigcell.xpp.EnsembleSimulator

getValueNamesInternal() - Method in class jigcell.xpp.StochKitSimulator

getValueNamesInternal() - Method in class jigcell.xpp.XPPSimulator

H

hasNoDifferentialEquationSet - Variable in class jigcell.xpp.SBMLToXPPTranslator

I

id - Variable in class jigcell.xpp.SBMLToStochKitTranslator.LocalRule

ID_END - Static variable in class jigcell.xpp.SymbolTable

ID_START - Static variable in class jigcell.xpp.SymbolTable

ID_WIDTH - Static variable in class jigcell.xpp.SymbolTable

idCol - Variable in class jigcell.xpp.SymbolTable

IDENTITY - Static variable in class jigcell.xpp.SymbolTable.Mode

idNameMap - Variable in class jigcell.xpp.SymbolTable

idToOriginalValue - Variable in class jigcell.xpp.SBMLToXPPTranslator

idToXPPID - Variable in class jigcell.xpp.SBMLToXPPTranslator

INDENT - Static variable in class jigcell.xpp.SBMLToStochKitTranslator

index - Variable in class jigcell.xpp.SBMLToStochKitTranslator.LocalRule

initMaps() - Method in class jigcell.xpp.CPPExpression

is - Variable in class jigcell.xpp.StreamGobbler

isAlgebraic - Variable in class jigcell.xpp.SBMLToStochKitTranslator.LocalRule

isRate - Variable in class jigcell.xpp.SBMLToStochKitTranslator.LocalRule

J

jigcell.xpp - package jigcell.xpp

L

loadSBMLInternal(Model) - Method in class jigcell.xpp.EnsembleSimulator

loadSBMLInternal(Model, boolean, int) - Method in class jigcell.xpp.EnsembleSimulator

loadSBMLInternal(Model) - Method in class jigcell.xpp.Oscill8Simulator

loadSBMLInternal(Model) - Method in class jigcell.xpp.StochKitSimulator

loadSBMLInternal(Model, boolean, int) - Method in class jigcell.xpp.StochKitSimulator

loadSBMLInternal(Model, boolean, int) - Method in class jigcell.xpp.XPPSimulator

loadSBMLInternal(Model) - Method in class jigcell.xpp.XPPSimulator

localSymbols - Variable in class jigcell.xpp.CPPExpression

LOOKUP_BY_ID - Static variable in class jigcell.xpp.CPPExpression

LOOKUP_BY_NAME - Static variable in class jigcell.xpp.CPPExpression

lookupFortranNameIndex(String) - Method in class jigcell.xpp.SymbolTable

Finds fname in fortranNameColRev.

lookupId(String) - Method in class jigcell.xpp.SymbolTable

Returns the id for the JigCell name.

lookupName(String) - Method in class jigcell.xpp.SymbolTable

Returns the JigCell name for id.

lookupSymbol(String) - Method in class jigcell.xpp.SymbolTable

Find the fortranName for name.

lookupSymbolById(String) - Method in class jigcell.xpp.SymbolTable

Returns the Fortran name for id.

lookupSymbolIndex(String, ArrayList) - Method in class jigcell.xpp.SymbolTable

Finds the index of name in the internal symbol table.

M

main(String[]) - Static method in class jigcell.xpp.AsynchronousCultureRunner

main(String[]) - Static method in class jigcell.xpp.SBMLToStochKitTranslator

main(String[]) - Static method in class jigcell.xpp.SBMLToXPPTranslator

Converts an SBML file to an ODE file.

makeFortranCharacterSafe_(String, int, boolean, char) - Static method in class jigcell.xpp.SymbolTable

Makes a string safe as a Fortran character string.

makeFortranIdSafe(String) - Method in class jigcell.xpp.SymbolTable

Convert a string to a Fortran safe identifier.

makeFortranIdSafe_(String, int) - Static method in class jigcell.xpp.SymbolTable

makeFortranSafe(String) - Method in class jigcell.xpp.SymbolTable

Returns a Fortran safe string according to mode

makeFortranSafe(String, SymbolTable.Mode) - Method in class jigcell.xpp.SymbolTable

Makes string Fortran safe according to mode.

makeFortranSafe(String, SymbolTable.Mode, int) - Method in class jigcell.xpp.SymbolTable

makeFortranSafe(String, SymbolTable.Mode, int, boolean, char) - Static method in class jigcell.xpp.SymbolTable

Makes string Fortran safe according to mode and maxLength.

map - Static variable in class jigcell.xpp.CPPExpression

math - Variable in class jigcell.xpp.SBMLToStochKitTranslator.LocalRule

mathTree - Variable in class jigcell.xpp.SBMLToStochKitTranslator.LocalRule

MAX_CHARS_PER_LINE - Static variable in class jigcell.xpp.SBMLToStochKitTranslator

MAX_EXP_NAME_LENGTH - Static variable in class jigcell.xpp.SBMLToStochKitTranslator

MAX_ID_LENGTH - Static variable in class jigcell.xpp.SBMLToStochKitTranslator

maximumIdentifierLength - Variable in class jigcell.xpp.SBMLToXPPTranslator

maxLength - Variable in class jigcell.xpp.SymbolTable

maxLength - Variable in class jigcell.xpp.SymbolTable.Mode

maxLength() - Method in class jigcell.xpp.SymbolTable.Mode

mergeExpression(ArrayList, String, int, String) - Static method in class jigcell.xpp.CPPExpression

Merges strings in expression and addes line breaks to maintain a width no greater than width.

missingArgument(String) - Static method in class jigcell.xpp.SBMLToStochKitTranslator

mode - Variable in class jigcell.xpp.CPPExpression

mode - Variable in class jigcell.xpp.SymbolTable

model - Variable in class jigcell.xpp.SBMLToStochKitTranslator

model - Variable in class jigcell.xpp.SBMLToXPPTranslator

modeString - Variable in class jigcell.xpp.CPPExpression

multiplyByCompartments(String, Node, Map, Map) - Static method in class jigcell.xpp.SBMLToStochKitTranslator

Take the math in node and search for all species multiplying each species by the volume of its compartment.

multiplyTermsByCompartments(String, Node, Map, Map) - Static method in class jigcell.xpp.SBMLToStochKitTranslator

Takes each term (separated by + and - signs) and calls multiplyByCompartments.

mySymbol - Variable in class jigcell.xpp.SBMLToStochKitTranslator

N

name - Variable in class jigcell.xpp.SBMLToStochKitTranslator.LocalRule

name - Variable in class jigcell.xpp.SymbolTable.Mode

nameCol - Variable in class jigcell.xpp.SymbolTable

nameColRev - Variable in class jigcell.xpp.SymbolTable

nonDifferentialIDs - Variable in class jigcell.xpp.SBMLToXPPTranslator

NORMAL - Static variable in class jigcell.xpp.CPPExpression

numRuleVars - Variable in class jigcell.xpp.SBMLToStochKitTranslator

numVars - Variable in class jigcell.xpp.SBMLToStochKitTranslator

O

odeData - Variable in class jigcell.xpp.SBMLToXPPTranslator

order - Static variable in class jigcell.xpp.CPPExpression

orderAlphbeticalSettingsList - Static variable in class jigcell.xpp.SBMLToXPPTranslator

Oscill8Launcher - Class in jigcell.xpp

Runs Oscill8 on an SBML file.

Oscill8Launcher(Simulator, Model) - Constructor for class jigcell.xpp.Oscill8Launcher

Runs Oscill8 on an SBML file.

Oscill8Simulator - Class in jigcell.xpp

Makes the Oscill8 simulator available to the simulator API.

Oscill8Simulator() - Constructor for class jigcell.xpp.Oscill8Simulator

Creates a new simulator.

P

padCharacter - Variable in class jigcell.xpp.SymbolTable

padToLength - Variable in class jigcell.xpp.SymbolTable

parameterIDs - Variable in class jigcell.xpp.SBMLToXPPTranslator

PRE_RUN - Static variable in class jigcell.xpp.SBMLToStochKitTranslator

printCSVAverageMatrix(PrintWriter, Iterator, IEditableDataElement, double) - Static method in class jigcell.xpp.AsynchronousCultureRunner

printParseTreeMassAction(Node) - Method in class jigcell.xpp.SBMLToXPPTranslator

printParseTreeMichaelisMenten(Node) - Method in class jigcell.xpp.SBMLToXPPTranslator

printParseTreeStochMassAction(Node, String) - Method in class jigcell.xpp.SBMLToXPPTranslator

printParseTreeStochMichaelisMenten(Node) - Method in class jigcell.xpp.SBMLToXPPTranslator

R

reactionIndex - Variable in class jigcell.xpp.SBMLToStochKitTranslator

readSimulationData(Simulator, Process, File) - Method in class jigcell.xpp.EnsembleLauncher

Reads simulation data that a running process will write to disk.

readSimulationData(Simulator, Process, File) - Method in class jigcell.xpp.StochKitLauncher

Reads simulation data that a running process will write to disk.

readSimulationData(Simulator, Process, File) - Method in class jigcell.xpp.XPPLauncher

Reads simulation data that a running process will write to disk.

registerIDs() - Method in class jigcell.xpp.SBMLToXPPTranslator

Identifies all of the SBML ids used in a model and constructs acceptable XPP ids for each.

removeSpaces - Static variable in class jigcell.xpp.SBMLToXPPTranslator

replaceFunctionName(String, String, String) - Static method in class jigcell.xpp.SBMLToXPPTranslator

Replaces a function call with a function of another name.

replaceIdWithName(String) - Method in class jigcell.xpp.SBMLToXPPTranslator

reset() - Static method in class jigcell.xpp.Stopwatch

reverseLookupId(String) - Method in class jigcell.xpp.SymbolTable

Returns the JigCell id for fortranName.

ruleArray - Variable in class jigcell.xpp.SBMLToStochKitTranslator

ruleGenerateCode(Map, Map) - Method in class jigcell.xpp.SBMLToStochKitTranslator

ruleHash - Variable in class jigcell.xpp.SBMLToStochKitTranslator

run() - Method in class jigcell.xpp.StreamGobbler

RUN_PE - Static variable in class jigcell.xpp.SBMLToStochKitTranslator

running - Static variable in class jigcell.xpp.Stopwatch

S

SBMLToStochKitTranslator - Class in jigcell.xpp

Translate SBML file produced from JigCell into C++ file as input of Stochkit feature history: supports algebaric rule, and assignment rule - mediate variable assignment (seems useless and causes error) * support for pow + support for function * support for safe name check + support for events * adjust rules * clean up the code * assign event number by calculating power in vivo v1.4 * make name c++ safe by edit SymbolTable.makeFortranSafe * special treatment for Vn, should be changed later v1.5 + execute stochkit + add "double t" to eventAction method v1.6 * LOG and SQRT to log and sqrt * eliminate NaN in parameter declaration.

SBMLToStochKitTranslator(Model) - Constructor for class jigcell.xpp.SBMLToStochKitTranslator

Creates a SBMLTranslator instance ready to create C++ code for model.

SBMLToStochKitTranslator(String) - Constructor for class jigcell.xpp.SBMLToStochKitTranslator

Creates a SBMLTranslator instance ready to create Fortran code from the SBML file fileName.

SBMLToStochKitTranslator(Reader) - Constructor for class jigcell.xpp.SBMLToStochKitTranslator

Creates a SBMLTranslator instance ready to create Fortran code from the SBML read from reader.

SBMLToStochKitTranslator.LocalRule - Class in jigcell.xpp

SBMLToStochKitTranslator.LocalRule() - Constructor for class jigcell.xpp.SBMLToStochKitTranslator.LocalRule

SBMLToXPPTranslator - Class in jigcell.xpp

Translates an SBML model to ODEs.

SBMLToXPPTranslator(Simulator, Model, File, int) - Constructor for class jigcell.xpp.SBMLToXPPTranslator

Creates a new translator for SBML files.

setCWD(File) - Method in class jigcell.xpp.SBMLToStochKitTranslator

Sets the directory which all sub processes will be started from.

setValue(Simulator, String, double) - Method in class jigcell.xpp.SBMLToXPPTranslator

Sets the value of a modifiable element in the model.

setValueInternal(String, double) - Method in class jigcell.xpp.XPPSimulator

SIM_TASK - Static variable in class jigcell.xpp.SBMLToStochKitTranslator

simulate(Simulator, File, File) - Method in class jigcell.xpp.EnsembleLauncher

Performs a simulation using the current model and settings.

simulate(Simulator, File, File) - Method in class jigcell.xpp.Oscill8Launcher

Performs a simulation using the current model and settings.

simulate(Simulator) - Method in class jigcell.xpp.SBMLToStochKitTranslator

Performs a simulation using the current model and settings.

simulate(Simulator, File, File) - Method in class jigcell.xpp.SBMLToStochKitTranslator

Performs a simulation using the current model and settings.

simulate(Simulator) - Method in class jigcell.xpp.SBMLToXPPTranslator

Performs a simulation using the current model and settings.

simulate(Simulator, File, File) - Method in class jigcell.xpp.SBMLToXPPTranslator

Performs a simulation using the current model and settings.

simulate(Simulator, File, File) - Method in class jigcell.xpp.StochKitLauncher

Performs a simulation using the current model and settings.

simulate(Simulator, File, File) - Method in class jigcell.xpp.XPPLauncher

Performs a simulation using the current model and settings.

simulateInternal(double, double, double, int) - Method in class jigcell.xpp.EnsembleSimulator

simulateInternal(double, double, double, int) - Method in class jigcell.xpp.StochKitSimulator

simulateInternal(double, double, double, int) - Method in class jigcell.xpp.XPPSimulator

speciesIDs - Variable in class jigcell.xpp.SBMLToXPPTranslator

speciesIDToCompartment - Variable in class jigcell.xpp.SBMLToXPPTranslator

speciesIDToEquation - Variable in class jigcell.xpp.SBMLToXPPTranslator

speciesIndex - Variable in class jigcell.xpp.SBMLToStochKitTranslator

speciesToCompartmentMap - Variable in class jigcell.xpp.SBMLToXPPTranslator

speciesWithInitialAmountIDs - Variable in class jigcell.xpp.SBMLToXPPTranslator

start() - Static method in class jigcell.xpp.Stopwatch

startTime - Static variable in class jigcell.xpp.Stopwatch

STATUS - Static variable in class jigcell.xpp.SBMLToStochKitTranslator

StochKitLauncher - Class in jigcell.xpp

Runs StochKit on an SBML file.

StochKitLauncher(Simulator, Model) - Constructor for class jigcell.xpp.StochKitLauncher

Runs StochKit on an SBML file.

StochKitLauncher(Simulator, Model, boolean, int) - Constructor for class jigcell.xpp.StochKitLauncher

StochKitSimulator - Class in jigcell.xpp

Makes the StochKit simulator available to the simulator API.

StochKitSimulator() - Constructor for class jigcell.xpp.StochKitSimulator

Creates a new simulator.

StochKitSimulator(Capabilities) - Constructor for class jigcell.xpp.StochKitSimulator

Creates a new simulator.

stop() - Static method in class jigcell.xpp.Stopwatch

stopTime - Static variable in class jigcell.xpp.Stopwatch

Stopwatch - Class in jigcell.xpp

A class to help benchmark code It simulates a real stop watch

Stopwatch() - Constructor for class jigcell.xpp.Stopwatch

StreamGobbler - Class in jigcell.xpp

StreamGobbler(InputStream, String) - Constructor for class jigcell.xpp.StreamGobbler

symbolTable - Variable in class jigcell.xpp.CPPExpression

symbolTable - Variable in class jigcell.xpp.SBMLToStochKitTranslator

symbolTable - Variable in class jigcell.xpp.SBMLToXPPTranslator

SymbolTable - Class in jigcell.xpp

Caution: This code has been modified by Pengyuan to be used for CPP code.

SymbolTable() - Constructor for class jigcell.xpp.SymbolTable

Create a new empty symbol table.

SymbolTable(int) - Constructor for class jigcell.xpp.SymbolTable

Create a new SymbolTable object with specified maximum ID length.

SymbolTable(SymbolTable.Mode) - Constructor for class jigcell.xpp.SymbolTable

Creates a new empty SymbolTable object with the specified mode.

SymbolTable(SymbolTable.Mode, int) - Constructor for class jigcell.xpp.SymbolTable

Creates a new empty SymbolTable with the specified mode and maximum id length.

SymbolTable(SymbolTable.Mode, int, boolean) - Constructor for class jigcell.xpp.SymbolTable

Creates a new empty SymbolTable with the specified mode and maximum id length and request to pad.

SymbolTable.Mode - Class in jigcell.xpp

These constants describe the type of symbol table.

SymbolTable.Mode(String, int) - Constructor for class jigcell.xpp.SymbolTable.Mode

T

targetFile - Variable in class jigcell.xpp.SBMLToStochKitTranslator

targetFile - Variable in class jigcell.xpp.SBMLToXPPTranslator

tic() - Static method in class jigcell.xpp.Stopwatch

Get elapsed time and restart stopwatch

toString() - Method in class jigcell.xpp.SymbolTable.Mode

TRANSFORM_TASK - Static variable in class jigcell.xpp.SBMLToStochKitTranslator

translate() - Method in class jigcell.xpp.SBMLToStochKitTranslator

to translate the SBML into CPP, called by writeCppCode_

translate() - Method in class jigcell.xpp.SBMLToXPPTranslator

Writes the model as an ODE file.

translateCompartments(Writer) - Method in class jigcell.xpp.SBMLToXPPTranslator

Writes equations for compartments controlled by rules to an ODE file.

translateFunctions(Writer) - Method in class jigcell.xpp.SBMLToXPPTranslator

Writes the function definitions in the model to an ODE file.

translateGlobals(Writer) - Method in class jigcell.xpp.SBMLToXPPTranslator

Writes the events in the model to an ODE file.

translateParameters(Writer) - Method in class jigcell.xpp.SBMLToXPPTranslator

Writes parameters that have been converted to equations in the model to an ODE file.

translateSpecies(Writer) - Method in class jigcell.xpp.SBMLToXPPTranslator

Writes the species defined by equations in the model to an ODE file.

translateVariables(Writer) - Method in class jigcell.xpp.SBMLToXPPTranslator

Writes the variables defined by rules in the model to an ODE file.

translator - Variable in class jigcell.xpp.EnsembleSimulator

StochKit simulator

translator - Variable in class jigcell.xpp.StochKitSimulator

StochKit simulator

translator - Variable in class jigcell.xpp.XPPSimulator

XPP simulator

type - Variable in class jigcell.xpp.StreamGobbler

U

usage - Static variable in class jigcell.xpp.SBMLToStochKitTranslator

Allow SBMLTranslator to be run independent from parent programs as a command line tool.

usedFunctionNames - Variable in class jigcell.xpp.SBMLToXPPTranslator

V

variableToEquationMap - Variable in class jigcell.xpp.SBMLToXPPTranslator

VERSION_MESG - Static variable in class jigcell.xpp.SBMLToStochKitTranslator

volumeColumn - Variable in class jigcell.xpp.EnsembleLauncher

volumeColumn - Variable in class jigcell.xpp.StochKitLauncher

W

wasAddedToRuleRhs - Variable in class jigcell.xpp.SBMLToStochKitTranslator.LocalRule

writeCppCode(PrintWriter) - Method in class jigcell.xpp.SBMLToStochKitTranslator

Writes compilable Fortran code to out.

writeCppCode_(PrintWriter) - Method in class jigcell.xpp.SBMLToStochKitTranslator

writeSettingsAndValues(Simulator) - Method in class jigcell.xpp.SBMLToXPPTranslator

Writes the parameter and initial condition settings to the ODE file.

X

XPP_LINELENGTH - Static variable in class jigcell.xpp.SBMLToXPPTranslator

XPPLauncher - Class in jigcell.xpp

Runs XPP on an SBML file.

XPPLauncher(Simulator, Model) - Constructor for class jigcell.xpp.XPPLauncher

Runs XPP on an SBML file.

XPPSimulator - Class in jigcell.xpp

Makes the XPP simulator available to the simulator API.

XPPSimulator() - Constructor for class jigcell.xpp.XPPSimulator

Creates a new simulator.

XPPSimulator(Capabilities) - Constructor for class jigcell.xpp.XPPSimulator

Creates a new simulator.

Z

zeroMatrix(int, int) - Static method in class jigcell.xpp.AsynchronousCultureRunner

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