jigcell.xpp
Class SBMLToStochKitTranslator

java.lang.Object
  jigcell.xpp.SBMLToStochKitTranslator

Direct Known Subclasses:

EnsembleLauncher, StochKitLauncher

public class SBMLToStochKitTranslator
extends java.lang.Object

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. * Vector x = x1 in Propensity function * add parameter decalaration in events v1.7 * changed the order of species index to confirm with RunManager v1.8

Author:

wpy last edited: 7-26-2007

Nested Class Summary

private class

SBMLToStochKitTranslator.LocalRule

Field Summary

private java.lang.String	code
private java.io.File	cwd
static java.lang.String	DEFAULT_LOWER_BOUND
protected static java.lang.String	DEFAULT_MODEL_NAME
static java.lang.String	DEFAULT_NML_FILENAME
static java.lang.String	DEFAULT_UPPER_BOUND
private java.util.Hashtable	defaultInitialConditionsContents
static java.lang.String	EST_TASK
private static java.lang.String	EXTRACT_PARAMS
static java.lang.String	INDENT
private static int	MAX_CHARS_PER_LINE
private static int	MAX_EXP_NAME_LENGTH
private static int	MAX_ID_LENGTH
private jigcell.sbml2.Model	model
private SymbolTable	mySymbol
private int	numRuleVars
private int	numVars
static java.lang.String	PRE_RUN
(package private) java.util.Hashtable	reactionIndex
private java.util.ArrayList	ruleArray
private java.util.Hashtable	ruleHash
static java.lang.String	RUN_PE
static java.lang.String	SIM_TASK
(package private) java.util.Hashtable	speciesIndex
static java.lang.String	STATUS
private SymbolTable	symbolTable
(package private) java.io.File	targetFile
static java.lang.String	TRANSFORM_TASK
private static java.lang.String	usage Allow SBMLTranslator to be run independent from parent programs as a command line tool.
private static java.lang.String	VERSION_MESG

Constructor Summary

SBMLToStochKitTranslator(jigcell.sbml2.Model model)
Creates a SBMLTranslator instance ready to create C++ code for model.

SBMLToStochKitTranslator(java.io.Reader reader)
Creates a SBMLTranslator instance ready to create Fortran code from the SBML read from reader.

SBMLToStochKitTranslator(java.lang.String fileName)
Creates a SBMLTranslator instance ready to create Fortran code from the SBML file fileName.

Method Summary

private static java.lang.String	appendAndBreak_(java.lang.String s1, java.lang.String s2, boolean addIndent) Underlying method for appendAndBreak and appendAndBreakNoIndent.
private static java.lang.String	appendAndBreak(java.lang.String s1, java.lang.String s2) Returns s1 and s2 appended with line breaks added if the resulting string is longer than MAX_CHARS_PER_LINE characters.
private static java.lang.String	appendAndBreakNoIndent(java.lang.String s1, java.lang.String s2) Like appendAndBreak but no additional white space is added when the second line is created.
private static java.lang.String	breakAFortranString(int maxWidth, java.lang.String prefix, java.lang.String fortranString, java.lang.String suffix, java.lang.String indent) Builds a Fortran expression and adds breaks as necessary to keep the maximum line width below maxWidth.
private SymbolTable	buildSymbolTable(jigcell.sbml2.Model model) Creates a table of variable assignments to be inserted as Fortran code.
protected java.util.List	computeSelectionList(java.util.List returnData) Computes the list of species to return from simulation.
java.util.Map	estimatorStatus(java.lang.String modelName) Multithreaded callers of Biopack can call this method to get the status of the current running estimator.
java.util.Hashtable	extractParameters(java.lang.String f90Model, java.lang.String report) Extract the parameter values and names from f90Model and report and put them in a Hashtable.
java.util.List	getAvailableSelections() A List[String] of tokens for each measurable element in the model.
private static java.lang.String	getModelId(jigcell.sbml2.Model model)
private static java.lang.String	getModelName(jigcell.sbml2.Model model)
protected java.lang.String	getProgramDirectory() The location where StochKit is installed.
java.util.List	getSettableNames() The name or id of every settable quantity.
static void	main(java.lang.String[] args)
private static void	missingArgument(java.lang.String arg)
private static jigcell.sbml2.math.Node	multiplyByCompartments(java.lang.String id, jigcell.sbml2.math.Node node, java.util.Map compartmentMap, java.util.Map speciesMap) Take the math in node and search for all species multiplying each species by the volume of its compartment.
private static jigcell.sbml2.math.Node	multiplyTermsByCompartments(java.lang.String id, jigcell.sbml2.math.Node node, java.util.Map compartmentMap, java.util.Map speciesMap) Takes each term (separated by + and - signs) and calls multiplyByCompartments.
private void	ruleGenerateCode(java.util.Map compartmentMap, java.util.Map speciesMap)
void	setCWD(java.io.File cwd) Sets the directory which all sub processes will be started from.
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 void	translate() to translate the SBML into CPP, called by writeCppCode_
private void	writeCppCode_(java.io.PrintWriter out)
void	writeCppCode(java.io.PrintWriter out) Writes compilable Fortran code to out.

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_MODEL_NAME

protected static final java.lang.String DEFAULT_MODEL_NAME

See Also:

Constant Field Values

DEFAULT_LOWER_BOUND

public static final java.lang.String DEFAULT_LOWER_BOUND

See Also:

Constant Field Values

DEFAULT_NML_FILENAME

public static final java.lang.String DEFAULT_NML_FILENAME

See Also:

Constant Field Values

DEFAULT_UPPER_BOUND

public static final java.lang.String DEFAULT_UPPER_BOUND

See Also:

Constant Field Values

EST_TASK

public static final java.lang.String EST_TASK

See Also:

Constant Field Values

INDENT

public static final java.lang.String INDENT

See Also:

Constant Field Values

EXTRACT_PARAMS

private static final java.lang.String EXTRACT_PARAMS

See Also:

Constant Field Values

MAX_CHARS_PER_LINE

private static final int MAX_CHARS_PER_LINE

See Also:

Constant Field Values

MAX_EXP_NAME_LENGTH

private static final int MAX_EXP_NAME_LENGTH

See Also:

Constant Field Values

MAX_ID_LENGTH

private static final int MAX_ID_LENGTH

PRE_RUN

public static final java.lang.String PRE_RUN

See Also:

Constant Field Values

RUN_PE

public static final java.lang.String RUN_PE

See Also:

Constant Field Values

SIM_TASK

public static final java.lang.String SIM_TASK

See Also:

Constant Field Values

STATUS

public static final java.lang.String STATUS

See Also:

Constant Field Values

TRANSFORM_TASK

public static final java.lang.String TRANSFORM_TASK

See Also:

Constant Field Values

VERSION_MESG

private static final java.lang.String VERSION_MESG

See Also:

Constant Field Values

cwd

private java.io.File cwd

model

private jigcell.sbml2.Model model

symbolTable

private SymbolTable symbolTable

mySymbol

private SymbolTable mySymbol

speciesIndex

java.util.Hashtable speciesIndex

reactionIndex

java.util.Hashtable reactionIndex

defaultInitialConditionsContents

private java.util.Hashtable defaultInitialConditionsContents

numVars

private int numVars

ruleHash

private java.util.Hashtable ruleHash

ruleArray

private java.util.ArrayList ruleArray

numRuleVars

private int numRuleVars

code

private java.lang.String code

targetFile

java.io.File targetFile

usage

private static java.lang.String usage

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

Constructor Detail

SBMLToStochKitTranslator

public SBMLToStochKitTranslator(jigcell.sbml2.Model model)
                         throws java.lang.Exception

Creates a SBMLTranslator instance ready to create C++ code for model. Conforms to the Biopack API 1.0.

Parameters:

model - Create Fortran code for this Model.

Throws:

java.lang.Exception

SBMLToStochKitTranslator

public SBMLToStochKitTranslator(java.lang.String fileName)
                         throws java.lang.Exception

Creates a SBMLTranslator instance ready to create Fortran code from the SBML file fileName. Conforms to the Biopack API 1.0.

Parameters:

fileName - The SBML file containing the model for this SBMLTranslator instance.

Throws:

java.lang.Exception

SBMLToStochKitTranslator

public SBMLToStochKitTranslator(java.io.Reader reader)
                         throws java.lang.Exception

Creates a SBMLTranslator instance ready to create Fortran code from the SBML read from reader. Conforms to the Biopack API 1.0.

Parameters:

reader - A Reader that reads a stream of characters from some source where the characters are the SBML file text.

Throws:

java.lang.Exception

Method Detail

estimatorStatus

public java.util.Map estimatorStatus(java.lang.String modelName)
                              throws java.lang.Exception

Multithreaded callers of Biopack can call this method to get the status of the current running estimator. A Map is returned that contains keys that are strings representing names of attributes of the current running estimator. The values are objects representing the state.

Throws:

java.lang.Exception

extractParameters

public java.util.Hashtable extractParameters(java.lang.String f90Model,
                                             java.lang.String report)
                                      throws java.lang.Exception

Extract the parameter values and names from f90Model and report and put them in a Hashtable. The f90Model file contains the Fortran code written by writeFortranCode. The report file contains the output of ODRPACK. This routine reads the values from the parameter estimation done by ODRPACK and the names from the f90Model file. The names and values are paired up according to their order and stored in the returned Hashtable.

The equivalence statements in the f90Model file must be in the same order as the report file. The order should be the numerical order of the indexes of the MODEL_PARAMS array. Biopack generated f90 files will always have this order.

Throws:

java.lang.Exception

setCWD

public void setCWD(java.io.File cwd)

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

writeCppCode

public void writeCppCode(java.io.PrintWriter out)
                  throws java.lang.Exception

Writes compilable Fortran code to out. The code is enough to simulate the model represented by this SBMLTranslator instance. If the readComparatorFiles method was successfully called then the code is enough to do parameter estimation.

Throws:

java.lang.Exception

ruleGenerateCode

private void ruleGenerateCode(java.util.Map compartmentMap,
                              java.util.Map speciesMap)
                       throws java.lang.Exception

Throws:

java.lang.Exception

writeCppCode_

private void writeCppCode_(java.io.PrintWriter out)
                    throws java.lang.Exception

Throws:

java.lang.Exception

translate

private void translate()
                throws java.lang.Exception

to translate the SBML into CPP, called by writeCppCode_

Throws:

java.lang.Exception

appendAndBreak

private static java.lang.String appendAndBreak(java.lang.String s1,
                                               java.lang.String s2)

Returns s1 and s2 appended with line breaks added if the resulting string is longer than MAX_CHARS_PER_LINE characters. When a line break is added the indent is copied from the previous line. If the previous line is the only line the indent is expanded by 4 white spaces. An & is appended before the break to make the string a valid Fortran line continuation.

appendAndBreakNoIndent

private static java.lang.String appendAndBreakNoIndent(java.lang.String s1,
                                                       java.lang.String s2)

Like appendAndBreak but no additional white space is added when the second line is created. Normally the second line is indented 4 whitespaces more than the first. In this version the second and first line have the same indent.

appendAndBreak_

private static java.lang.String appendAndBreak_(java.lang.String s1,
                                                java.lang.String s2,
                                                boolean addIndent)

Underlying method for appendAndBreak and appendAndBreakNoIndent.

breakAFortranString

private static java.lang.String breakAFortranString(int maxWidth,
                                                    java.lang.String prefix,
                                                    java.lang.String fortranString,
                                                    java.lang.String suffix,
                                                    java.lang.String indent)
                                             throws java.lang.Exception

Builds a Fortran expression and adds breaks as necessary to keep the maximum line width below maxWidth. The resulting expression (without line breaks) looks like: prefix+'"'+fortranString+'"'+suffix. Breaks are inserted between prefix and suffix but not inside either. Breaks are inserted inside fortranString of the form "&\n"+indent+"&". prefix must be less than maxWidth. suffix must be equal to or less than maxWidth. fortranString must be smaller than the maximum permitted string in Fortran.

Throws:

java.lang.Exception

buildSymbolTable

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

Creates a table of variable assignments to be inserted as Fortran code. The table has the form: <name> <assignmentChar> <value> <delimeter> <name> <assignmentChar> <value> <delimeter> ... Line breaks are inserted before the line exceeds MAX_CHARS_PER_LINE and the columns are lined up on the assignementChar and delimeter with name and value left justified. An example table might look like:

     k1  = 3  ; k2  = 4
     k23 = 3.4; k5  = 6
     

The last delimeter on each line is ommited. All the name widths are the same (even if the name widths are from different columns). All the value widths are the same (even if the value widths are from different columns). The maximum field width is determined by the largest name and largest value. The table is indented by indent.

Throws:

java.lang.Exception

getModelId

private static java.lang.String getModelId(jigcell.sbml2.Model model)

getModelName

private static java.lang.String getModelName(jigcell.sbml2.Model model)

multiplyByCompartments

private static jigcell.sbml2.math.Node multiplyByCompartments(java.lang.String id,
                                                              jigcell.sbml2.math.Node node,
                                                              java.util.Map compartmentMap,
                                                              java.util.Map speciesMap)
                                                       throws java.lang.Exception

Take the math in node and search for all species multiplying each species by the volume of its compartment. Returns the new root node (maybe the same as the old root node). This requires that the "ci" tags in node are SBML ids. id is the target species (left hand side). Appearances of id in the RHS will not be multiplied by the compartment volume. Terms with species other than id will be divided by the compartment volume of id.

Throws:

java.lang.Exception

multiplyTermsByCompartments

private static jigcell.sbml2.math.Node multiplyTermsByCompartments(java.lang.String id,
                                                                   jigcell.sbml2.math.Node node,
                                                                   java.util.Map compartmentMap,
                                                                   java.util.Map speciesMap)
                                                            throws java.lang.Exception

Takes each term (separated by + and - signs) and calls multiplyByCompartments. Takes the root node and pushes it on the nodes stack. Then iterates until the node stack is empty by

1. pop the node stack
2. if operator string then
   1. pop children count children off of children stack into an array
   2. create new node
   3. pop children count off of children stack
   4. push result onto children stack
3. else if addition or subtraction node then
   1. push operator on node stack
   2. push children on node stack
   3. push children count (of parent node) on children stack.
   else if other node
   1. call multiplyByCompartments and push result on children stack.
   2. increment children count
4. children stack should have one element, return it as the new root node.

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

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.

getProgramDirectory

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

The location where StochKit is installed.

Throws:

java.lang.Exception

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

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 - SBML file

outputFile - File that will contain the simulator output

Throws:

java.lang.Exception

missingArgument

private static void missingArgument(java.lang.String arg)

main

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