org.sigpath.task.navigator
Class TExportBase

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

Direct Known Subclasses:

TExportChangeLog, TExportComplex, TExportConcentrationMeasurement, TExportEnzymaticReaction, TExportKinetic, TExportKineticCustom, TExportLiteratureReference, TExportLiteratureReferences, TExportModel, TExportModifiedChemical, TExportNamedChemical, TExportNamedChemicalInteraction, TExportOrganism, TExportPathway, TExportPendingList, TExportProtein, TExportReaction, TExportSmallMolecule, TExportUserComment

public class TExportBase
extends BaseTask

Navigator Base Class for Exporting SigPath datamodel objects to SigPathSubmission. TODO: More methods may be added to BaseTask class.

Field Summary

protected List	idRefActions
protected SigpathSubmission	root

Fields inherited from class org.sigpath.task.util.BaseTask

SEPARATOR

Constructor Summary

TExportBase(NavigatorEntityManager entityManager, SigpathSubmission root, HashMap spidsToTempIDs, List idRefActions)

Method Summary

protected Change_log	addChangeLog(SigPathEntity spe) Adds Change Log Information to XML Document.
protected Reviews	addReviews(SigPathEntity spe) Adds Review Information to XML Document.
protected void	addStandalone(Model spModel) adds a standalone model to the submission (assumes the submission is standalone)
protected String	clearEmptyField(String description)
Molecule[]	componentsToMolecules(SigPathEntity entity) Converts the components of a complex into XLM molecules.
protected InteractionRef	createInteractionReference(Interaction interaction) Return an XML interaction-ref element.
Molecule	createMolecule(Chemical sp_chem, HashMap spidsToTempIDs, SigpathSubmission root) Creates a Castor molecule object given a SigPath chemical.
protected String	getACDB(Chemical chemical) Returns a valid ACDB for a Chemical object.
CustomKinetic	getCustomKinetic(Kinetic kinetic) Gets the kinetic custom when the parameter is of class (KineticCustom).
protected NavigatorEntityManager	getEntityManager()
protected EnzymaticParameters	getEnzymaticReactionParameters(EnzymaticReaction spEnzymaticReaction)
protected Enzyme	getEnzyme(EnzymaticReaction jdoInstance)
protected Formula	getFormula(KineticCustom kinetic)
protected HashMap	getIdMap() Gets HashMap.
protected KineticBindings	getKineticBindings(KineticInteraction kInt)
protected KineticRef	getKineticRef(KineticInteraction reaction) here the distinction between
NamedChemicalRef[]	getNamedChemicalRef(NamedChemicalInteraction jdoInstance)
protected ParametersBindingsDeclaration	getParametersBindingsDeclaration(KineticCustom kinetic)
protected PreviousVersion	getPreviousVersion(Model spModel)
Left	getReactionLeftSide(Collection left)
Modifiers	getReactionMidleSide(Collection modifiers)
protected Parameters	getReactionParameters(Reaction reaction)
Right	getReactionRightSide(Collection right)
protected SpeciesBindingsDeclaration	getSpeciesBindingsDeclaration(KineticCustom kinetic)
boolean	isStandaloneOutput() Deprecated. Use TExportStandaloneModel instead
protected void	postProcessConcentrationMeasurement(ConcentrationMeasurement spCM, Concentration_measurement cm)
protected void	postProcessEnzymaticReaction(EnzymaticReaction enzymaticReaction, EnzymaticReaction castorInstance)
protected void	postProcessModel(Model spModel, Model model)
protected void	postProcessPendingList(PendingList jdoInstance, Pending_list castorInstance)
protected void	postProcessReaction(Reaction jdoInstance, Reaction castorInstance)
protected void	processChemicals(Collection molecs, StringBuffer text) get short names for chemicals and builds a reaction's description while doing this
protected void	setExcludedReactions(Model spModel, Model model)
static boolean	setSpid(Chemical sp_chem, Molecule mol) Sets a spid attribute on the molecule only if the chemical does not refers to background information, and if no idref is provided for the molecule.
void	setStandaloneOutput(boolean standaloneOutput) Deprecated. Use TExportStandaloneModel instead

Methods inherited from class org.sigpath.task.util.BaseTask

addInContactWiths, getCompartment, getCreatedBy, getExcludedReactions, getModelCompartments, getMoleculeConcentration, getTargetUnit, localConcentrationToLocation, setOutsides, setUniqueIdsForCompartments

Methods inherited from class java.lang.Object

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

Field Detail

root

protected SigpathSubmission root

idRefActions

protected List idRefActions

Constructor Detail

TExportBase

public TExportBase(NavigatorEntityManager entityManager,
                   SigpathSubmission root,
                   HashMap spidsToTempIDs,
                   List idRefActions)

Method Detail

createInteractionReference

protected InteractionRef createInteractionReference(Interaction interaction)

Return an XML interaction-ref element.

Parameters:

interaction - The interaction the reference will point to.

Returns:

InteractionRef

getIdMap

protected HashMap getIdMap()

Gets HashMap.

Returns:

Hashmap of SPIDs to TempIDs

isStandaloneOutput

public boolean isStandaloneOutput()

Deprecated. Use TExportStandaloneModel instead

Should this model be exported standalone?

Returns:

True if the model should be exported so that it can be reimported in a fresh database.

setStandaloneOutput

public void setStandaloneOutput(boolean standaloneOutput)

Deprecated. Use TExportStandaloneModel instead

Decide if the output should be standalone. Standalone outputs will contain all the information needed to reconstruct a model in a fresh database. In practice, when standalone output is set to true, the XML output will include molecules even if they are background information. The model will also include reactions and nzymatic reactions that it references. Standalone outputs are useful to generate standalone XML submissions for models. This comes handy when building regression tests for model export.

Parameters:

standaloneOutput - true to generate standalone output. false (default) otherwise.

addChangeLog

protected Change_log addChangeLog(SigPathEntity spe)

Adds Change Log Information to XML Document.

addReviews

protected Reviews addReviews(SigPathEntity spe)

Adds Review Information to XML Document.

addStandalone

protected void addStandalone(Model spModel)

adds a standalone model to the submission (assumes the submission is standalone)

Parameters:

spModel -

clearEmptyField

protected String clearEmptyField(String description)

componentsToMolecules

public Molecule[] componentsToMolecules(SigPathEntity entity)

Converts the components of a complex into XLM molecules.

Parameters:

entity -

Returns:

org.sigpath.bioimport.reaction2.Molecule[]

createMolecule

public Molecule createMolecule(Chemical sp_chem,
                               HashMap spidsToTempIDs,
                               SigpathSubmission root)

Creates a Castor molecule object given a SigPath chemical. If the chemical has already been added to the submission then the molecule is created with an idRef to that castor chemical. If the chemical has not already been added and it is a complex or a modified chemical, then the Castor complex or modified chemical is created and the molecule has an idRef to that castor component. If the chemical has not already been added, and it is not a complex or a modified chemical then the molecule is created with the accession code/database pair and organism. SigPath tries to optimize which accession code/database pair to use, so that the pair identifies a single chemical in the current database. The current strategy is to look for accession codes from SwissProt, find the first one which uniquely identifies a chemical in the current database and return it. If no accession code for SwissProt is available, then the first accession code found is used.

Parameters:

sp_chem - Sigpath Chemical

spidsToTempIDs - HashMap that maps spids to idRefs

root - SigpathSubmission root

Returns:

org.sigpath.bioimport.reaction2.Molecule Castor molecule

setSpid

public static boolean setSpid(Chemical sp_chem,
                              Molecule mol)

Sets a spid attribute on the molecule only if the chemical does not refers to background information, and if no idref is provided for the molecule.

Parameters:

sp_chem - Chemical (source)

mol - molecule (destination).

Returns:

True if the spid attribute was set, false otherwise.

getCustomKinetic

public CustomKinetic getCustomKinetic(Kinetic kinetic)

Gets the kinetic custom when the parameter is of class (KineticCustom). The method uses the TExportKineticCustom export class

Parameters:

kinetic -

Returns:

CustomKinetic

getEnzymaticReactionParameters

protected EnzymaticParameters getEnzymaticReactionParameters(EnzymaticReaction spEnzymaticReaction)

getEnzyme

protected Enzyme getEnzyme(EnzymaticReaction jdoInstance)

getFormula

protected Formula getFormula(KineticCustom kinetic)
                      throws SigPathDatabaseException

Throws:

SigPathDatabaseException

getKineticBindings

protected KineticBindings getKineticBindings(KineticInteraction kInt)
                                      throws SigPathDatabaseException

Throws:

SigPathDatabaseException

getKineticRef

protected KineticRef getKineticRef(KineticInteraction reaction)

here the distinction between

Parameters:

reaction -

Returns:

KineticRef

getNamedChemicalRef

public NamedChemicalRef[] getNamedChemicalRef(NamedChemicalInteraction jdoInstance)

getParametersBindingsDeclaration

protected ParametersBindingsDeclaration getParametersBindingsDeclaration(KineticCustom kinetic)

getReactionLeftSide

public Left getReactionLeftSide(Collection left)

getReactionMidleSide

public Modifiers getReactionMidleSide(Collection modifiers)

getReactionParameters

protected Parameters getReactionParameters(Reaction reaction)

getReactionRightSide

public Right getReactionRightSide(Collection right)

getSpeciesBindingsDeclaration

protected SpeciesBindingsDeclaration getSpeciesBindingsDeclaration(KineticCustom kinetic)
                                                            throws SigPathDatabaseException

Throws:

SigPathDatabaseException

postProcessConcentrationMeasurement

protected void postProcessConcentrationMeasurement(ConcentrationMeasurement spCM,
                                                   Concentration_measurement cm)

getACDB

protected String getACDB(Chemical chemical)

Returns a valid ACDB for a Chemical object. Preference is given to the SWISSPROT database

Parameters:

chemical - The chemical to get the ACDB for

Returns:

A valid ACDB or null if none could be found

postProcessEnzymaticReaction

protected void postProcessEnzymaticReaction(EnzymaticReaction enzymaticReaction,
                                            EnzymaticReaction castorInstance)

postProcessReaction

protected void postProcessReaction(Reaction jdoInstance,
                                   Reaction castorInstance)

processChemicals

protected void processChemicals(Collection molecs,
                                StringBuffer text)
                         throws SigPathDatabaseException

get short names for chemicals and builds a reaction's description while doing this

Parameters:

molecs -

text -

Throws:

SigPathDatabaseException

getPreviousVersion

protected PreviousVersion getPreviousVersion(Model spModel)

setExcludedReactions

protected void setExcludedReactions(Model spModel,
                                    Model model)

postProcessModel

protected void postProcessModel(Model spModel,
                                Model model)

postProcessPendingList

protected void postProcessPendingList(PendingList jdoInstance,
                                      Pending_list castorInstance)

getEntityManager

protected NavigatorEntityManager getEntityManager()