biouml.plugins.simulation
Class SimulationEngine

java.lang.Object
  com.beanexplorer.beans.Option
      biouml.plugins.simulation.SimulationEngine

Direct Known Subclasses:

JavaSimulationEngine, MatlabSimulationEngine

public abstract class SimulationEngine

extends com.beanexplorer.beans.Option

General class for simulation engine. It defines common contract (properties and methods) for any simulation engine.

Nested Class Summary

static class

SimulationEngine.VariableType

Field Summary

protected double	absTolerance
protected java.util.ResourceBundle	childResources Resource bundle containing necessary String data.
protected java.lang.String	currentIndent
static double	DEFAULT_ABSOLUTE_TOLERANCE
static double	DEFAULT_RELATIVE_TOLERANCE
protected Diagram	diagram
protected static java.lang.String	endl
protected java.util.List	equationList List of all equations.
protected java.util.Map	equationMap Stores list of equations for used diagram variable.
protected EModel	executableModel
protected boolean	hasConstVariables Indicates whether model has boundary variables that should be treated as constants.
protected org.apache.log4j.Category	log
protected java.util.Map	macros maps "variable name" -> "scalar equation, calculating this variable"
protected int	modelType Type of the model: STATIC, ODE, etc.
boolean	needToShowPlot
protected java.lang.String	outputDir Output directory where the code will be generated.
protected static java.util.ResourceBundle	parentResources Common description is located in biouml.plugins.simulation.resources.MessagesBundle.
protected double	relTolerance
protected java.util.ResourceBundle	resources Resource bundle containing necessary String data.
protected java.lang.String	solverName
static java.lang.String	srcDir
protected int	status Math processing status.
protected java.lang.String	tab
protected java.lang.String	tab2
protected java.lang.String	tab3
protected java.lang.String	tab4
protected java.util.List	usedVariableList List of all variables however used in model.
protected MathWriter	writer

Fields inherited from class com.beanexplorer.beans.Option

notificationEnabled, propagationEnabled

Constructor Summary

SimulationEngine()

Method Summary

void	clearContext()
boolean	containsDelays() Returns true if the differential equations contain delays when derivatives computing.
void	error(java.lang.String message)
void	error(java.lang.String messageBundleKey, java.lang.String[] params)
void	error(java.lang.String messageBundleKey, java.lang.String[] params, java.lang.Throwable t)
void	fillSimulationResult(SimulationResult result)
protected SimulationEngine.VariableType	findVariable(java.lang.String name)
abstract java.io.File[]	generateModel()
abstract java.lang.String	generateVariableCodeName(int n)
double	getAbsTolerance()
double	getCompletionTime()
Diagram	getDiagram()
EModel	getExecutableModel()
abstract Formatter	getFormatter() Returns formatter corresponding for given engine.
double	getInitialTime()
boolean	getNeedToShowPlot()
java.lang.String	getOutputDir()
java.lang.String	getQualifiedName(java.lang.String name, DiagramElement de) Resolves brief varibale name to fully qualified variable name.
double	getRelTolerance()
java.util.ResourceBundle	getResourceBundle()
java.lang.String	getResourceString(java.lang.String key) Returns string from the resource bundle for the specified key.
protected Equation[]	getScalarEquations()
java.lang.String	getSolverName()
double	getTimeIncrement()
protected void	init() Initilaze internal structures for model generation: 1) map: variable - List(equations) 2) variables type. 3) status, errors
protected void	initAlgebraic(DiagramElement de)
protected void	initMath(DiagramElement de) Initialize variable types and equations map.
protected void	initResources(java.lang.String resourceBundleName, java.lang.Class c) Initialize resources necessary to retrieve localized strings.
protected boolean	isSignificantVariable(java.lang.String type)
java.lang.String	normalize(java.lang.String name) Normalize name to be valid simulation script name.
protected void	parseAssignments(Assignment[] assignments, Role role)
protected void	parseEquation(DiagramElement de)
protected void	processMath(Node node, Role role) Substitutes BioUML variable names with variable names used in simulation script.
protected void	processVarNode(AstVarNode node, Role role)
void	setAbsTolerance(double absTolerance)
void	setCompletionTime(double completionTime)
void	setDiagram(Diagram diagram)
void	setInitialTime(double initialTime)
void	setNeedToShowPlot(boolean value)
void	setOutputDir(java.lang.String outputDir)
void	setRelTolerance(double relTolerance)
void	setSolverName(java.lang.String solverName)
void	setTimeIncrement(double timeIncrement)
abstract java.lang.String	simulate(java.io.File[] files)
void	warn(java.lang.String messageBundleKey, java.lang.String[] params)
void	writeAssignment(java.lang.String variable, java.lang.String expression, Role role)
protected void	writeAssignmentImpl(java.lang.String variable, java.lang.String expression, Role role, boolean declare)
abstract void	writeComment(java.lang.String comment)
void	writeFile(java.lang.String source, java.lang.String outDir, java.lang.String outFile, boolean rewrite) Utility method to write needed source files from the specified source to the specified directory.
protected void	writeFunctionDeclarations()
protected void	writeInitialStateEntering()
protected void	writeMath(java.lang.String math, Role role)
protected void	writeRateEquation(java.util.List list)
protected void	writeRules()
protected void	writeRulesImpl(boolean acceptInternal) Write rules that are equations with type TYPE_SCALAR.
protected void	writeScalarRule(Equation equation, boolean acceptInternal)
protected void	writeSignificantRules()
protected void	writeTransition(State currentState, Transition transition)

Methods inherited from class com.beanexplorer.beans.Option

addPropertyChangeListener, copyListenersTo, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getParent, isNotificationEnabled, isPropagationEnabled, removePropertyChangeListener, setNotificationEnabled, setParent, setPropagationEnabled

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

endl

protected static java.lang.String endl

currentIndent

protected java.lang.String currentIndent

tab

protected java.lang.String tab

tab2

protected java.lang.String tab2

tab3

protected java.lang.String tab3

tab4

protected java.lang.String tab4

DEFAULT_RELATIVE_TOLERANCE

public static final double DEFAULT_RELATIVE_TOLERANCE

See Also:

Constant Field Values

DEFAULT_ABSOLUTE_TOLERANCE

public static final double DEFAULT_ABSOLUTE_TOLERANCE

See Also:

Constant Field Values

srcDir

public static final java.lang.String srcDir

See Also:

Constant Field Values

log

protected org.apache.log4j.Category log

equationMap

protected java.util.Map equationMap

Stores list of equations for used diagram variable.

equationList

protected java.util.List equationList

List of all equations.

usedVariableList

protected java.util.List usedVariableList

List of all variables however used in model.

hasConstVariables

protected boolean hasConstVariables

Indicates whether model has boundary variables that should be treated as constants.

macros

protected java.util.Map macros

maps "variable name" -> "scalar equation, calculating this variable"

modelType

protected int modelType

Type of the model: STATIC, ODE, etc.

status

protected int status

Math processing status.

See Also:

ru.biosoft.math.model.Parser.

writer

protected MathWriter writer

diagram

protected Diagram diagram

executableModel

protected EModel executableModel

outputDir

protected java.lang.String outputDir

Output directory where the code will be generated.

solverName

protected java.lang.String solverName

absTolerance

protected double absTolerance

relTolerance

protected double relTolerance

needToShowPlot

public boolean needToShowPlot

resources

protected java.util.ResourceBundle resources

Resource bundle containing necessary String data. This resource bundle contains join of childResources with parentResources.

childResources

protected java.util.ResourceBundle childResources

Resource bundle containing necessary String data.

parentResources

protected static java.util.ResourceBundle parentResources

Common description is located in biouml.plugins.simulation.resources.MessagesBundle. This bundle is used as parent bundle for resources.

Constructor Detail

SimulationEngine

public SimulationEngine()

Method Detail

generateVariableCodeName

public abstract java.lang.String generateVariableCodeName(int n)

generateModel

public abstract java.io.File[] generateModel()
                                      throws java.lang.Exception

Throws:

java.lang.Exception

simulate

public abstract java.lang.String simulate(java.io.File[] files)
                                   throws java.lang.Exception

Throws:

java.lang.Exception

clearContext

public void clearContext()
                  throws java.lang.Exception

Throws:

java.lang.Exception

getFormatter

public abstract Formatter getFormatter()

Returns formatter corresponding for given engine.

containsDelays

public boolean containsDelays()

Returns true if the differential equations contain delays when derivatives computing.

getDiagram

public Diagram getDiagram()

setDiagram

public void setDiagram(Diagram diagram)

getExecutableModel

public EModel getExecutableModel()

getOutputDir

public java.lang.String getOutputDir()

setOutputDir

public void setOutputDir(java.lang.String outputDir)

getSolverName

public java.lang.String getSolverName()

setSolverName

public void setSolverName(java.lang.String solverName)

getInitialTime

public double getInitialTime()

setInitialTime

public void setInitialTime(double initialTime)

getCompletionTime

public double getCompletionTime()

setCompletionTime

public void setCompletionTime(double completionTime)

getTimeIncrement

public double getTimeIncrement()

setTimeIncrement

public void setTimeIncrement(double timeIncrement)

getAbsTolerance

public double getAbsTolerance()

setAbsTolerance

public void setAbsTolerance(double absTolerance)

getRelTolerance

public double getRelTolerance()

setRelTolerance

public void setRelTolerance(double relTolerance)

setNeedToShowPlot

public void setNeedToShowPlot(boolean value)

getNeedToShowPlot

public boolean getNeedToShowPlot()

getResourceBundle

public java.util.ResourceBundle getResourceBundle()

getResourceString

public java.lang.String getResourceString(java.lang.String key)

Returns string from the resource bundle for the specified key. If the sting is absent the key string is returned instead and the message is printed in log4j.Category.

initResources

protected void initResources(java.lang.String resourceBundleName,
                             java.lang.Class c)

Initialize resources necessary to retrieve localized strings.

error

public void error(java.lang.String message)

error

public void error(java.lang.String messageBundleKey,
                  java.lang.String[] params)

error

public void error(java.lang.String messageBundleKey,
                  java.lang.String[] params,
                  java.lang.Throwable t)

warn

public void warn(java.lang.String messageBundleKey,
                 java.lang.String[] params)

findVariable

protected SimulationEngine.VariableType findVariable(java.lang.String name)

getQualifiedName

public java.lang.String getQualifiedName(java.lang.String name,
                                         DiagramElement de)

Resolves brief varibale name to fully qualified variable name. Generates error if variable can not be resolved.

See Also:

EModel.getQualifiedName(java.lang.String, biouml.model.DiagramElement)

normalize

public java.lang.String normalize(java.lang.String name)

Normalize name to be valid simulation script name.

init

protected void init()
             throws java.lang.Exception

Initilaze internal structures for model generation: 1) map: variable - List(equations) 2) variables type. 3) status, errors

Throws:

java.lang.Exception

initMath

protected void initMath(DiagramElement de)

Initialize variable types and equations map.

initAlgebraic

protected void initAlgebraic(DiagramElement de)

parseEquation

protected void parseEquation(DiagramElement de)

parseAssignments

protected void parseAssignments(Assignment[] assignments,
                                Role role)

writeMath

protected void writeMath(java.lang.String math,
                         Role role)
                  throws java.lang.Exception

Throws:

java.lang.Exception

writeAssignmentImpl

protected void writeAssignmentImpl(java.lang.String variable,
                                   java.lang.String expression,
                                   Role role,
                                   boolean declare)

writeAssignment

public void writeAssignment(java.lang.String variable,
                            java.lang.String expression,
                            Role role)

writeComment

public abstract void writeComment(java.lang.String comment)

writeInitialStateEntering

protected void writeInitialStateEntering()

writeScalarRule

protected void writeScalarRule(Equation equation,
                               boolean acceptInternal)

writeRules

protected void writeRules()

writeSignificantRules

protected void writeSignificantRules()

writeRulesImpl

protected void writeRulesImpl(boolean acceptInternal)

Write rules that are equations with type TYPE_SCALAR.

writeRateEquation

protected void writeRateEquation(java.util.List list)

writeTransition

protected void writeTransition(State currentState,
                               Transition transition)

getScalarEquations

protected Equation[] getScalarEquations()

processMath

protected void processMath(Node node,
                           Role role)

Substitutes BioUML variable names with variable names used in simulation script.

processVarNode

protected void processVarNode(AstVarNode node,
                              Role role)

writeFunctionDeclarations

protected void writeFunctionDeclarations()

fillSimulationResult

public void fillSimulationResult(SimulationResult result)
                          throws java.lang.Exception

Throws:

java.lang.Exception

isSignificantVariable

protected boolean isSignificantVariable(java.lang.String type)

writeFile

public void writeFile(java.lang.String source,
                      java.lang.String outDir,
                      java.lang.String outFile,
                      boolean rewrite)
               throws java.lang.Exception

Utility method to write needed source files from the specified source to the specified directory.

Throws:

java.lang.Exception