jigcell.xpp
Class SBMLToXPPTranslator

java.lang.Object
  jigcell.xpp.SBMLToXPPTranslator

Direct Known Subclasses:

XPPLauncher

public class SBMLToXPPTranslator
extends java.lang.Object

Translates an SBML model to ODEs. This code is licensed under the DARPA BioCOMP Open Source License. See LICENSE for more details.

Author:

Nicholas Allen, Ranjit Randhawa, Marc Vass

Field Summary

private static java.util.regex.Pattern	checkIfExpression
private static java.util.regex.Pattern	checkNumber
private static java.util.regex.Pattern	cleanName
private java.util.Set	compartmentIDs
private java.util.List	differentialIDs
private jigcell.sbml2.jep.JEP	expressionParser
private static java.util.regex.Pattern	getBvarsFromFunction
private static java.util.regex.Pattern	getMassActionParams
private static java.util.regex.Pattern	getMichaelieMentenParams
private static java.util.regex.Pattern	getSpeciesFromFunction
private static java.util.regex.Pattern	getStochMassActionParams
private static java.util.regex.Pattern	getStochMichaelieMentenParams
private java.util.Set	hasNoDifferentialEquationSet
private java.util.Map	idToOriginalValue
private java.util.Map	idToXPPID
private int	maximumIdentifierLength
private jigcell.sbml2.Model	model
private java.util.List	nonDifferentialIDs
private java.lang.String	odeData
private static boolean	orderAlphbeticalSettingsList
private java.util.Set	parameterIDs
private static java.util.regex.Pattern	removeSpaces
private java.util.Set	speciesIDs
private java.util.Map	speciesIDToCompartment
private java.util.Map	speciesIDToEquation
private java.util.Map	speciesToCompartmentMap
private java.util.Set	speciesWithInitialAmountIDs
private jigcell.sbml2.math.SymbolTable	symbolTable
private java.io.File	targetFile
private java.util.Set	usedFunctionNames
private java.util.Map	variableToEquationMap
private static int	XPP_LINELENGTH

Constructor Summary

SBMLToXPPTranslator(jigcell.simulation.Simulator simulator, jigcell.sbml2.Model model, java.io.File targetFile, int maximumIdentifierLength)
Creates a new translator for SBML files.

Method Summary

private void	applyVelocityTerm(java.lang.String velocity, boolean positive, jigcell.sbml2.SpeciesReference reference) Adds a single velocity term to an equation.
private static java.lang.String	breakEquation(java.lang.String text) Breaks an equation along '+', '-', '*', '/', ',', or ' ' in order to fit on an XPP line.
private void	buildSymbolTable(jigcell.sbml2.Model model) Adds the name and id of all tracked SBML elements in a model to a symbol table.
private static void	buildSymbolTablePump(jigcell.sbml2.math.SymbolTable table, java.util.Collection collection) Takes SBML elements from a collection and adds their name and id to a symbol table.
private void	calculateAllEquationsInternal()
void	calculateEquationsFromReactions()
protected java.util.List	computeSelectionList(java.util.List returnData) Computes the list of species to return from simulation.
private void	computeVelocities() Computes the velocity terms that make up the species equations.
private java.lang.String	convertCapabilitiesToXPP(jigcell.simulation.Capabilities capabilities) Constructs a simulator setting string that can be passed to XPP.
private java.lang.String	convertIDToXPPID(java.lang.String id, int unique) Converts an SBML id to an XPP id.
protected java.lang.String	convertMathToInfix(java.lang.String math, boolean rateLaw)
private java.lang.String	fixFunctionNames(java.lang.String text) Replaces function calls that use different builtin names between SBML and XPP.
private java.lang.String	fixIDs(java.lang.String text) Replaces ids that differ between SBML and XPP.
static void	generateODEFromModelBuilder(jigcell.sbml2.Model model, java.io.File odeFile, boolean sortAlphabetically) Converts an SBML file to an ODE file from the ModelBuilder
private java.lang.String	generateVelocityFromMath(java.lang.String math) Generates the XPP velocity from a MathML string.
java.util.List	getAvailableSelections() A List[String] of tokens for each measurable element in the model.
java.lang.String	getConcentration(jigcell.sbml2.Species species)
java.lang.String	getEquation(java.lang.String math, java.lang.String equation)
double	getOriginalValue(java.lang.String id) The current value of a modifiable element in the model.
protected java.lang.String	getProgramDirectory() The location where XPP is installed.
java.util.List	getSettableNames() The name or id of every settable quantity.
static void	main(java.lang.String[] args) Converts an SBML file to an ODE file.
java.lang.String	printParseTreeMassAction(jigcell.sbml2.math.Node curr)
java.lang.String	printParseTreeMichaelisMenten(jigcell.sbml2.math.Node curr)
java.lang.String	printParseTreeStochMassAction(jigcell.sbml2.math.Node curr, java.lang.String equation)
java.lang.String	printParseTreeStochMichaelisMenten(jigcell.sbml2.math.Node curr)
private void	registerIDs() Identifies all of the SBML ids used in a model and constructs acceptable XPP ids for each.
private static java.lang.String	replaceFunctionName(java.lang.String text, java.lang.String oldName, java.lang.String newName) Replaces a function call with a function of another name.
protected java.lang.String	replaceIdWithName(java.lang.String equation)
double	setValue(jigcell.simulation.Simulator simulator, java.lang.String id, double value) Sets the value of a modifiable element in the model.
jigcell.compare.IDataElement	simulate(jigcell.simulation.Simulator simulator) Performs a simulation using the current model and settings.
protected jigcell.compare.IDataElement	simulate(jigcell.simulation.Simulator simulator, java.io.File targetFile, java.io.File outputFile) Performs a simulation using the current model and settings.
private java.lang.String	translate() Writes the model as an ODE file.
private void	translateCompartments(java.io.Writer writer) Writes equations for compartments controlled by rules to an ODE file.
private void	translateFunctions(java.io.Writer writer) Writes the function definitions in the model to an ODE file.
private void	translateGlobals(java.io.Writer writer) Writes the events in the model to an ODE file.
private void	translateParameters(java.io.Writer writer) Writes parameters that have been converted to equations in the model to an ODE file.
private void	translateSpecies(java.io.Writer writer) Writes the species defined by equations in the model to an ODE file.
private void	translateVariables(java.io.Writer writer) Writes the variables defined by rules in the model to an ODE file.
private void	writeSettingsAndValues(jigcell.simulation.Simulator simulator) Writes the parameter and initial condition settings to the ODE file.

Methods inherited from class java.lang.Object

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

Field Detail

XPP_LINELENGTH

private static final int XPP_LINELENGTH

See Also:

Constant Field Values

getSpeciesFromFunction

private static final java.util.regex.Pattern getSpeciesFromFunction

getMassActionParams

private static final java.util.regex.Pattern getMassActionParams

getStochMassActionParams

private static final java.util.regex.Pattern getStochMassActionParams

getMichaelieMentenParams

private static final java.util.regex.Pattern getMichaelieMentenParams

getStochMichaelieMentenParams

private static final java.util.regex.Pattern getStochMichaelieMentenParams

getBvarsFromFunction

private static final java.util.regex.Pattern getBvarsFromFunction

checkIfExpression

private static final java.util.regex.Pattern checkIfExpression

checkNumber

private static final java.util.regex.Pattern checkNumber

cleanName

private static final java.util.regex.Pattern cleanName

removeSpaces

private static final java.util.regex.Pattern removeSpaces

orderAlphbeticalSettingsList

private static boolean orderAlphbeticalSettingsList

maximumIdentifierLength

private final int maximumIdentifierLength

targetFile

private java.io.File targetFile

differentialIDs

private java.util.List differentialIDs

nonDifferentialIDs

private java.util.List nonDifferentialIDs

idToOriginalValue

private java.util.Map idToOriginalValue

idToXPPID

private java.util.Map idToXPPID

speciesIDToCompartment

private java.util.Map speciesIDToCompartment

speciesIDToEquation

private java.util.Map speciesIDToEquation

model

private jigcell.sbml2.Model model

compartmentIDs

private java.util.Set compartmentIDs

parameterIDs

private java.util.Set parameterIDs

speciesIDs

private java.util.Set speciesIDs

speciesWithInitialAmountIDs

private java.util.Set speciesWithInitialAmountIDs

usedFunctionNames

private java.util.Set usedFunctionNames

odeData

private final java.lang.String odeData

symbolTable

private jigcell.sbml2.math.SymbolTable symbolTable

expressionParser

private jigcell.sbml2.jep.JEP expressionParser

variableToEquationMap

private java.util.Map variableToEquationMap

speciesToCompartmentMap

private java.util.Map speciesToCompartmentMap

hasNoDifferentialEquationSet

private java.util.Set hasNoDifferentialEquationSet

Constructor Detail

SBMLToXPPTranslator

public SBMLToXPPTranslator(jigcell.simulation.Simulator simulator,
                           jigcell.sbml2.Model model,
                           java.io.File targetFile,
                           int maximumIdentifierLength)
                    throws java.lang.Exception

Creates a new translator for SBML files.

Parameters:

simulator - Simulator

targetFile - File to use for the ODEs. If this is null a temporary file is created.

model - SBML model

maximumIdentifierLength - Longest permitted length for an identifier

Throws:

java.lang.Exception

Method Detail

main

public static void main(java.lang.String[] args)
                 throws java.lang.Exception

Converts an SBML file to an ODE file.

Parameters:

args - Name of SBML and ODE files

Throws:

java.lang.Exception

breakEquation

private static java.lang.String breakEquation(java.lang.String text)

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

buildSymbolTablePump

private static void buildSymbolTablePump(jigcell.sbml2.math.SymbolTable table,
                                         java.util.Collection collection)
                                  throws java.lang.Exception

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

Throws:

java.lang.Exception

replaceFunctionName

private static java.lang.String replaceFunctionName(java.lang.String text,
                                                    java.lang.String oldName,
                                                    java.lang.String newName)

Replaces a function call with a function of another name.

getAvailableSelections

public java.util.List getAvailableSelections()

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

getSettableNames

public java.util.List getSettableNames()

The name or id of every settable quantity.

getOriginalValue

public double getOriginalValue(java.lang.String id)

The current value of a modifiable element in the model.

Parameters:

id - SBML id

setValue

public double setValue(jigcell.simulation.Simulator simulator,
                       java.lang.String id,
                       double value)

Sets the value of a modifiable element in the model.

Parameters:

id - SBML id

value - New element value

simulate

public jigcell.compare.IDataElement simulate(jigcell.simulation.Simulator simulator)
                                      throws java.lang.Exception

Performs a simulation using the current model and settings.

Parameters:

simulator - Simulator

Throws:

java.lang.Exception

computeSelectionList

protected java.util.List computeSelectionList(java.util.List returnData)

Computes the list of species to return from simulation.

Parameters:

returnData - List[String] of columns to return when simulating

simulate

protected jigcell.compare.IDataElement simulate(jigcell.simulation.Simulator simulator,
                                                java.io.File targetFile,
                                                java.io.File outputFile)
                                         throws java.lang.Exception

Performs a simulation using the current model and settings.

Parameters:

simulator - Simulator

targetFile - ODE file

outputFile - File that will contain the simulator output

Throws:

java.lang.Exception

applyVelocityTerm

private void applyVelocityTerm(java.lang.String velocity,
                               boolean positive,
                               jigcell.sbml2.SpeciesReference reference)
                        throws java.lang.Exception

Adds a single velocity term to an equation.

Throws:

java.lang.Exception

buildSymbolTable

private void buildSymbolTable(jigcell.sbml2.Model model)
                       throws java.lang.Exception

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

Throws:

java.lang.Exception

computeVelocities

private void computeVelocities()
                        throws java.lang.Exception

Computes the velocity terms that make up the species equations.

Throws:

java.lang.Exception

convertCapabilitiesToXPP

private java.lang.String convertCapabilitiesToXPP(jigcell.simulation.Capabilities capabilities)

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

Parameters:

capabilities - Simulator capabilities

convertIDToXPPID

private java.lang.String convertIDToXPPID(java.lang.String id,
                                          int unique)

Converts an SBML id to an XPP id. The conversion should avoid ids differing only by case but currently does not, bug #285.

fixFunctionNames

private java.lang.String fixFunctionNames(java.lang.String text)

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

fixIDs

private java.lang.String fixIDs(java.lang.String text)

Replaces ids that differ between SBML and XPP.

generateVelocityFromMath

private java.lang.String generateVelocityFromMath(java.lang.String math)
                                           throws java.lang.Exception

Generates the XPP velocity from a MathML string.

Throws:

java.lang.Exception

getProgramDirectory

protected java.lang.String getProgramDirectory()
                                        throws java.lang.Exception

The location where XPP is installed.

Throws:

java.lang.Exception

registerIDs

private void registerIDs()
                  throws java.lang.Exception

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

Throws:

java.lang.Exception

translate

private java.lang.String translate()
                            throws java.lang.Exception

Writes the model as an ODE file.

Throws:

java.lang.Exception

translateCompartments

private void translateCompartments(java.io.Writer writer)
                            throws java.lang.Exception

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

Throws:

java.lang.Exception

translateFunctions

private void translateFunctions(java.io.Writer writer)
                         throws java.lang.Exception

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

Throws:

java.lang.Exception

translateGlobals

private void translateGlobals(java.io.Writer writer)
                       throws java.lang.Exception

Writes the events in the model to an ODE file.

Throws:

java.lang.Exception

translateParameters

private void translateParameters(java.io.Writer writer)
                          throws java.lang.Exception

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

Throws:

java.lang.Exception

translateSpecies

private void translateSpecies(java.io.Writer writer)
                       throws java.lang.Exception

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

Throws:

java.lang.Exception

translateVariables

private void translateVariables(java.io.Writer writer)
                         throws java.lang.Exception

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

Throws:

java.lang.Exception

writeSettingsAndValues

private void writeSettingsAndValues(jigcell.simulation.Simulator simulator)
                             throws java.io.IOException

Writes the parameter and initial condition settings to the ODE file. This should be called again if those values are later changed.

Parameters:

simulator - Simulator

Throws:

java.io.IOException

generateODEFromModelBuilder

public static void generateODEFromModelBuilder(jigcell.sbml2.Model model,
                                               java.io.File odeFile,
                                               boolean sortAlphabetically)
                                        throws java.lang.Exception

Converts an SBML file to an ODE file from the ModelBuilder

Parameters:

odeFile - ODE File to save to

model - SBML model

Throws:

java.lang.Exception

calculateAllEquationsInternal

private void calculateAllEquationsInternal()

getConcentration

public java.lang.String getConcentration(jigcell.sbml2.Species species)

calculateEquationsFromReactions

public void calculateEquationsFromReactions()

convertMathToInfix

protected java.lang.String convertMathToInfix(java.lang.String math,
                                              boolean rateLaw)

getEquation

public java.lang.String getEquation(java.lang.String math,
                                    java.lang.String equation)

printParseTreeMassAction

public java.lang.String printParseTreeMassAction(jigcell.sbml2.math.Node curr)

printParseTreeStochMassAction

public java.lang.String printParseTreeStochMassAction(jigcell.sbml2.math.Node curr,
                                                      java.lang.String equation)

printParseTreeMichaelisMenten

public java.lang.String printParseTreeMichaelisMenten(jigcell.sbml2.math.Node curr)

printParseTreeStochMichaelisMenten

public java.lang.String printParseTreeStochMichaelisMenten(jigcell.sbml2.math.Node curr)

replaceIdWithName

protected java.lang.String replaceIdWithName(java.lang.String equation)