org.sigpath.task.model
Class TSBMLModelExport

java.lang.Object
  org.sigpath.task.DBTask
      org.sigpath.task.model.TExportModel
          org.sigpath.task.model.TSBMLModelExport

All Implemented Interfaces:

Task

public class TSBMLModelExport
extends TExportModel

This class enables creating an SBML model, constituted currently only by instances of SBMLcompartments, SBMLspecies and SBMLreactions (from elementary and enzymatic reactions). Then uses an instance of SBMLWriter to create the SBML output, or a JSimWriter instance to make a JSim output

Field Summary

protected static int	ACCROSS_TWO_COMPARTMENTS
protected String	comments
protected static int	K1
protected static int	K2
protected static int	K3
protected static int	KB
protected static int	KBKP
protected static int	KF
protected static int	KM
protected static int	KP
protected Model	model
protected String	modelSpid
protected Vector	sbmlCompartments
protected Vector	sbmlReactions
protected Vector	sbmlSpecies
protected StringBuffer	sbOut
protected Unit	targetUnit target unit for concentrations.
protected static int	VMAX
protected static int	WITHIN_A_COMPARTMENT
protected ExportWriter	writer

Fields inherited from class org.sigpath.task.DBTask

dbManager, embeddedTask, entityManager, errors, ftsm, progressListener, sigpathFactory, unitManager, userManager, xdebug

Constructor Summary

TSBMLModelExport(String spid, ExportWriter writer)

Method Summary

protected void	_execute() Goes trough the process of reading compartment, molecules, reactions, enzimatic reaction, converting all these into sbml-like objects, including splitting enzimatic reactions into 2 elementary reactions, and spatializing reaction
protected boolean	aSingleCompartmentInvoved(Vector sbmlspecies) checks if the reactions occurs within a single compartment
void	convertParameterValuesToTargetUnit(Vector sbmlEntities) converts all parameters of instances of SbmlEntity class found in the parameter Vector
ComplexImpl	createComplexMickaelis(SPDBManager dbm, EnzymaticReaction enzymaticReaction, HashMap cm) Creates a Comple representing the Michaelis complex
void	enzymaticReactionTreatment(SPDBManager dbm, Vector molecules, Vector rs, Vector eReactions, Set exReactions) for each EnzymaticReaction of the model : splits it into two elementary reactions, add them to a rs vector, and create the corresponding mikaelis complexe.
String	getOutFile()
Vector	getSbmlSpecies(Chemical chemical) gets all the SBMLSpecies in the sbmlSpecies set corresponding to a given Chemical.
protected boolean	isThereAnIsolatedSpecieAmongThese(Vector sbmlspecies) Check for isolated species.
void	setHideDate(boolean hideDate) Instruct the model export to output the date or not.
void	setHideDiagramCoordinates(boolean hideDiagramCoordinates) Instruct the model export to output the diagram coordinates or not.
void	setIncludeDiagramLayout(boolean includeDiagramLayout)
void	setModelSpid(String spid)
protected boolean	twoContiguousCompartments(Vector sbmlspecies) used to test if a SBMLreaction is consistent in a spatial point of view.

Methods inherited from class org.sigpath.task.DBTask

close, delete, execute, getDbManager, getErrors, isEmbeddedTask, isTaskThrewException, reindex, resolve, setDbManager, setEmbeddedTask, setEmbeddedTask, setObtainTransactionsFrom, setProgressListener, setTaskThrewException

Methods inherited from class java.lang.Object

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

Field Detail

KF

protected static final int KF

See Also:

Constant Field Values

KB

protected static final int KB

See Also:

Constant Field Values

KM

protected static final int KM

See Also:

Constant Field Values

VMAX

protected static final int VMAX

See Also:

Constant Field Values

KP

protected static final int KP

See Also:

Constant Field Values

KBKP

protected static final int KBKP

See Also:

Constant Field Values

K1

protected static final int K1

See Also:

Constant Field Values

K2

protected static final int K2

See Also:

Constant Field Values

K3

protected static final int K3

See Also:

Constant Field Values

WITHIN_A_COMPARTMENT

protected static final int WITHIN_A_COMPARTMENT

See Also:

Constant Field Values

ACCROSS_TWO_COMPARTMENTS

protected static final int ACCROSS_TWO_COMPARTMENTS

See Also:

Constant Field Values

targetUnit

protected Unit targetUnit

target unit for concentrations.

sbmlSpecies

protected Vector sbmlSpecies

sbmlCompartments

protected Vector sbmlCompartments

sbmlReactions

protected Vector sbmlReactions

sbOut

protected StringBuffer sbOut

comments

protected String comments

modelSpid

protected String modelSpid

model

protected Model model

writer

protected ExportWriter writer

Constructor Detail

TSBMLModelExport

public TSBMLModelExport(String spid,
                        ExportWriter writer)

Method Detail

setHideDate

public void setHideDate(boolean hideDate)

Instruct the model export to output the date or not. Defautl is to output the date. Setting hideDate to True is useful for junit tests that compare the expected result of the export to an export done at a latter date.

Specified by:

setHideDate in class TExportModel

Parameters:

hideDate - When true, the date will not be included in the model output.

setHideDiagramCoordinates

public void setHideDiagramCoordinates(boolean hideDiagramCoordinates)

Description copied from class: TExportModel

Instruct the model export to output the diagram coordinates or not. Default is to output the diagram coordinates. Setting hideDiagramCoordinates to True is useful for junit tests that compare the expected result of the export to an export done at a later time and on different plaforms. YFiles seem to create different layouts on hyperthreaded machines.

Specified by:

setHideDiagramCoordinates in class TExportModel

Parameters:

hideDiagramCoordinates - When true, the date will not be included in the model output.

getOutFile

public String getOutFile()

Specified by:

getOutFile in class TExportModel

setModelSpid

public void setModelSpid(String spid)

Specified by:

setModelSpid in class TExportModel

_execute

protected void _execute()
                 throws SigPathDatabaseException

Goes trough the process of reading compartment, molecules, reactions, enzimatic reaction, converting all these into sbml-like objects, including splitting enzimatic reactions into 2 elementary reactions, and spatializing reaction

Specified by:

_execute in class DBTask

Throws:

SigPathDatabaseException

isThereAnIsolatedSpecieAmongThese

protected boolean isThereAnIsolatedSpecieAmongThese(Vector sbmlspecies)

Check for isolated species. ********* Maybe not usefull anymore********************************************* checks if among a set of SBMLSpecies, one is isolated, i.e. in a compartment wich is not in contact with any of the compartments where the other species involved in the reaction are found this method may also be done building the symetrical matrix of contacts between species which may be required for large "species" vectors, since more optimal I guess

Parameters:

sbmlspecies -

Returns:

boolean

twoContiguousCompartments

protected boolean twoContiguousCompartments(Vector sbmlspecies)

used to test if a SBMLreaction is consistent in a spatial point of view. Consistent means : takes place in a single compartment, or only involves two adjacent compartments

Parameters:

sbmlspecies -

Returns:

returns the number of compartments referenced by a Vector of species

aSingleCompartmentInvoved

protected boolean aSingleCompartmentInvoved(Vector sbmlspecies)

checks if the reactions occurs within a single compartment

Parameters:

sbmlspecies -

Returns:

enzymaticReactionTreatment

public void enzymaticReactionTreatment(SPDBManager dbm,
                                       Vector molecules,
                                       Vector rs,
                                       Vector eReactions,
                                       Set exReactions)
                                throws SigPathDatabaseException

for each EnzymaticReaction of the model : splits it into two elementary reactions, add them to a rs vector, and create the corresponding mikaelis complexe. Mikaelis complexes are also if needed added to the database splits at the same time the Excluded reactions to make two excluded ones Scyto -> Pnuc gives Ecyto+Scyto->EScyto and EScyto->Pnuc+Enuc

Parameters:

dbm -

molecules -

rs - Vector of Reaction

Throws:

SigPathDatabaseException

createComplexMickaelis

public ComplexImpl createComplexMickaelis(SPDBManager dbm,
                                          EnzymaticReaction enzymaticReaction,
                                          HashMap cm)

Creates a Comple representing the Michaelis complex

Parameters:

dbm -

enzymaticReaction -

cm - HashMap with all the already created michaelis complex complexes

Returns:

getSbmlSpecies

public Vector getSbmlSpecies(Chemical chemical)

gets all the SBMLSpecies in the sbmlSpecies set corresponding to a given Chemical.

Parameters:

chemical -

Returns:

Vector of SBMLSpecies

convertParameterValuesToTargetUnit

public void convertParameterValuesToTargetUnit(Vector sbmlEntities)
                                        throws SigPathDatabaseException

converts all parameters of instances of SbmlEntity class found in the parameter Vector

Parameters:

sbmlEntities -

Throws:

SigPathDatabaseException

setIncludeDiagramLayout

public void setIncludeDiagramLayout(boolean includeDiagramLayout)