org.sigpath.task.util
Class BaseTask

java.lang.Object
  org.sigpath.task.util.BaseTask

Direct Known Subclasses:

TExportBase

public class BaseTask
extends Object

BaseTask contains common methods shared by SigPath and Navigator TExport classes.

Field Summary

protected static String

SEPARATOR

Constructor Summary

BaseTask()

Method Summary

void	addInContactWiths(Model spModel, Model model) set contacts between compartments in the XML model.
Compartment	getCompartment(Model model, String compartmentName) Find the compartment by its name
String	getCreatedBy(PendingList jdoInstance)
ExcludedReactions	getExcludedReactions(Model spModel)
ModelCompartments	getModelCompartments(Model spModel)
MoleculeConcentration	getMoleculeConcentration(Molecule spMol)
TargetUnit	getTargetUnit(Model spModel)
Location	localConcentrationToLocation(LocalConcentration localConcentration, Model model)
void	setOutsides(Model spModel, Model model) set the outside compartments for each compartment in the xml model.
void	setUniqueIdsForCompartments(Model model)

Methods inherited from class java.lang.Object

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

Field Detail

SEPARATOR

protected static final String SEPARATOR

See Also:

Constant Field Values

Constructor Detail

BaseTask

public BaseTask()

Method Detail

getModelCompartments

public ModelCompartments getModelCompartments(Model spModel)

getTargetUnit

public TargetUnit getTargetUnit(Model spModel)

getCompartment

public Compartment getCompartment(Model model,
                                  String compartmentName)

Find the compartment by its name

Parameters:

model -

compartmentName -

Returns:

Compartment

getExcludedReactions

public ExcludedReactions getExcludedReactions(Model spModel)

addInContactWiths

public void addInContactWiths(Model spModel,
                              Model model)

set contacts between compartments in the XML model. nb: do not add contacts with itself (included in the datamodel Model)

Parameters:

spModel -

model -

setOutsides

public void setOutsides(Model spModel,
                        Model model)

set the outside compartments for each compartment in the xml model.

Parameters:

spModel -

model -

getMoleculeConcentration

public MoleculeConcentration getMoleculeConcentration(Molecule spMol)

localConcentrationToLocation

public Location localConcentrationToLocation(LocalConcentration localConcentration,
                                             Model model)

setUniqueIdsForCompartments

public void setUniqueIdsForCompartments(Model model)

getCreatedBy

public String getCreatedBy(PendingList jdoInstance)