org.sigpath.bioimport.reaction2
Class SigpathSubmission

java.lang.Object
  org.sigpath.bioimport.reaction2.SigpathSubmission

All Implemented Interfaces:

Serializable

public class SigpathSubmission
extends Object
implements Serializable

Root element used to encapsulate data for SigPath Export or Import

Version:

$Revision$ $Date$

See Also:

Serialized Form

Constructor Summary

SigpathSubmission()

Method Summary

void	addEnzymaticReaction(EnzymaticReaction vEnzymaticReaction) Method addEnzymaticReaction
void	addEnzymaticReaction(int index, EnzymaticReaction vEnzymaticReaction) Method addEnzymaticReaction
void	addModel(int index, Model vModel) Method addModel
void	addModel(Model vModel) Method addModel
void	addPathway(int index, Pathway vPathway) Method addPathway
void	addPathway(Pathway vPathway) Method addPathway
void	addReaction(int index, Reaction vReaction) Method addReaction
void	addReaction(Reaction vReaction) Method addReaction
void	clearEnzymaticReaction() Method clearEnzymaticReaction
void	clearModel() Method clearModel
void	clearPathway() Method clearPathway
void	clearReaction() Method clearReaction
Enumeration	enumerateEnzymaticReaction() Method enumerateEnzymaticReaction
Enumeration	enumerateModel() Method enumerateModel
Enumeration	enumeratePathway() Method enumeratePathway
Enumeration	enumerateReaction() Method enumerateReaction
Components	getComponents() Returns the value of field 'components'.
Concentration_measurements	getConcentration_measurements() Returns the value of field 'concentration_measurements'.
EnzymaticReaction[]	getEnzymaticReaction() Method getEnzymaticReaction
EnzymaticReaction	getEnzymaticReaction(int index) Method getEnzymaticReaction
int	getEnzymaticReactionCount() Method getEnzymaticReactionCount
String	getExportBuildVersion() Returns the value of field 'exportBuildVersion'.
Date	getExportDateTime() Returns the value of field 'exportDateTime'.
Kinetics	getKinetics() Returns the value of field 'kinetics'.
Model[]	getModel() Method getModel
Model	getModel(int index) Method getModel
int	getModelCount() Method getModelCount
NamedChemicalInteractions	getNamedChemicalInteractions() Returns the value of field 'namedChemicalInteractions'.
NamedChemicals	getNamedChemicals() Returns the value of field 'namedChemicals'.
Pathway[]	getPathway() Method getPathway
Pathway	getPathway(int index) Method getPathway
int	getPathwayCount() Method getPathwayCount
Pending_reviews	getPending_reviews() Returns the value of field 'pending_reviews'.
Proteins	getProteins() Returns the value of field 'proteins'.
Reaction[]	getReaction() Method getReaction
Reaction	getReaction(int index) Method getReaction
int	getReactionCount() Method getReactionCount
SmallMolecules	getSmallMolecules() Returns the value of field 'smallMolecules'.
boolean	isValid() Method isValid
void	marshal(ContentHandler handler) Method marshal
void	marshal(Writer out) Method marshal
boolean	removeEnzymaticReaction(EnzymaticReaction vEnzymaticReaction) Method removeEnzymaticReaction
boolean	removeModel(Model vModel) Method removeModel
boolean	removePathway(Pathway vPathway) Method removePathway
boolean	removeReaction(Reaction vReaction) Method removeReaction
void	setComponents(Components components) Sets the value of field 'components'.
void	setConcentration_measurements(Concentration_measurements concentration_measurements) Sets the value of field 'concentration_measurements'.
void	setEnzymaticReaction(EnzymaticReaction[] enzymaticReactionArray) Method setEnzymaticReaction
void	setEnzymaticReaction(int index, EnzymaticReaction vEnzymaticReaction) Method setEnzymaticReaction
void	setExportBuildVersion(String exportBuildVersion) Sets the value of field 'exportBuildVersion'.
void	setExportDateTime(Date exportDateTime) Sets the value of field 'exportDateTime'.
void	setKinetics(Kinetics kinetics) Sets the value of field 'kinetics'.
void	setModel(int index, Model vModel) Method setModel
void	setModel(Model[] modelArray) Method setModel
void	setNamedChemicalInteractions(NamedChemicalInteractions namedChemicalInteractions) Sets the value of field 'namedChemicalInteractions'.
void	setNamedChemicals(NamedChemicals namedChemicals) Sets the value of field 'namedChemicals'.
void	setPathway(int index, Pathway vPathway) Method setPathway
void	setPathway(Pathway[] pathwayArray) Method setPathway
void	setPending_reviews(Pending_reviews pending_reviews) Sets the value of field 'pending_reviews'.
void	setProteins(Proteins proteins) Sets the value of field 'proteins'.
void	setReaction(int index, Reaction vReaction) Method setReaction
void	setReaction(Reaction[] reactionArray) Method setReaction
void	setSmallMolecules(SmallMolecules smallMolecules) Sets the value of field 'smallMolecules'.
static SigpathSubmission	unmarshal(Reader reader) Method unmarshal
void	validate() Method validate

Methods inherited from class java.lang.Object

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

Constructor Detail

SigpathSubmission

public SigpathSubmission()

Method Detail

addEnzymaticReaction

public void addEnzymaticReaction(EnzymaticReaction vEnzymaticReaction)
                          throws IndexOutOfBoundsException

Method addEnzymaticReaction

Parameters:

vEnzymaticReaction -

Throws:

IndexOutOfBoundsException

addEnzymaticReaction

public void addEnzymaticReaction(int index,
                                 EnzymaticReaction vEnzymaticReaction)
                          throws IndexOutOfBoundsException

Method addEnzymaticReaction

Parameters:

index -

vEnzymaticReaction -

Throws:

IndexOutOfBoundsException

addModel

public void addModel(Model vModel)
              throws IndexOutOfBoundsException

Method addModel

Parameters:

vModel -

Throws:

IndexOutOfBoundsException

addModel

public void addModel(int index,
                     Model vModel)
              throws IndexOutOfBoundsException

Method addModel

Parameters:

index -

vModel -

Throws:

IndexOutOfBoundsException

addPathway

public void addPathway(Pathway vPathway)
                throws IndexOutOfBoundsException

Method addPathway

Parameters:

vPathway -

Throws:

IndexOutOfBoundsException

addPathway

public void addPathway(int index,
                       Pathway vPathway)
                throws IndexOutOfBoundsException

Method addPathway

Parameters:

index -

vPathway -

Throws:

IndexOutOfBoundsException

addReaction

public void addReaction(Reaction vReaction)
                 throws IndexOutOfBoundsException

Method addReaction

Parameters:

vReaction -

Throws:

IndexOutOfBoundsException

addReaction

public void addReaction(int index,
                        Reaction vReaction)
                 throws IndexOutOfBoundsException

Method addReaction

Parameters:

index -

vReaction -

Throws:

IndexOutOfBoundsException

clearEnzymaticReaction

public void clearEnzymaticReaction()

Method clearEnzymaticReaction

clearModel

public void clearModel()

Method clearModel

clearPathway

public void clearPathway()

Method clearPathway

clearReaction

public void clearReaction()

Method clearReaction

enumerateEnzymaticReaction

public Enumeration enumerateEnzymaticReaction()

Method enumerateEnzymaticReaction

Returns:

Enumeration

enumerateModel

public Enumeration enumerateModel()

Method enumerateModel

Returns:

Enumeration

enumeratePathway

public Enumeration enumeratePathway()

Method enumeratePathway

Returns:

Enumeration

enumerateReaction

public Enumeration enumerateReaction()

Method enumerateReaction

Returns:

Enumeration

getComponents

public Components getComponents()

Returns the value of field 'components'. The field 'components' has the following description: Groups complex and modified chemical definitions in SigPath

Returns:

Components

getConcentration_measurements

public Concentration_measurements getConcentration_measurements()

Returns the value of field 'concentration_measurements'. The field 'concentration_measurements' has the following description: Groups concentration measurements in SigPath

Returns:

Concentration_measurements

getEnzymaticReaction

public EnzymaticReaction getEnzymaticReaction(int index)
                                       throws IndexOutOfBoundsException

Method getEnzymaticReaction

Parameters:

index -

Returns:

EnzymaticReaction

Throws:

IndexOutOfBoundsException

getEnzymaticReaction

public EnzymaticReaction[] getEnzymaticReaction()

Method getEnzymaticReaction

Returns:

EnzymaticReaction

getEnzymaticReactionCount

public int getEnzymaticReactionCount()

Method getEnzymaticReactionCount

Returns:

int

getExportBuildVersion

public String getExportBuildVersion()

Returns the value of field 'exportBuildVersion'. The field 'exportBuildVersion' has the following description: Optional field containing build version of the running sigpath, populated on xml export.

Returns:

String

getExportDateTime

public Date getExportDateTime()

Returns the value of field 'exportDateTime'. The field 'exportDateTime' has the following description: Optional field containing the date and time, populated on xml export.

Returns:

Date

getKinetics

public Kinetics getKinetics()

Returns the value of field 'kinetics'. The field 'kinetics' has the following description: group of kinetics declaration in SigPath

Returns:

Kinetics

getModel

public Model getModel(int index)
               throws IndexOutOfBoundsException

Method getModel

Parameters:

index -

Returns:

Model

Throws:

IndexOutOfBoundsException

getModel

public Model[] getModel()

Method getModel

Returns:

Model

getModelCount

public int getModelCount()

Method getModelCount

Returns:

int

getNamedChemicalInteractions

public NamedChemicalInteractions getNamedChemicalInteractions()

Returns the value of field 'namedChemicalInteractions'. The field 'namedChemicalInteractions' has the following description: Groups named-chemical-interaction definitions in SigPath

Returns:

NamedChemicalInteractions

getNamedChemicals

public NamedChemicals getNamedChemicals()

Returns the value of field 'namedChemicals'. The field 'namedChemicals' has the following description: Groups named-chemical definitions in SigPath

Returns:

NamedChemicals

getPathway

public Pathway getPathway(int index)
                   throws IndexOutOfBoundsException

Method getPathway

Parameters:

index -

Returns:

Pathway

Throws:

IndexOutOfBoundsException

getPathway

public Pathway[] getPathway()

Method getPathway

Returns:

Pathway

getPathwayCount

public int getPathwayCount()

Method getPathwayCount

Returns:

int

getPending_reviews

public Pending_reviews getPending_reviews()

Returns the value of field 'pending_reviews'. The field 'pending_reviews' has the following description: Groups pending reviews

Returns:

Pending_reviews

getProteins

public Proteins getProteins()

Returns the value of field 'proteins'. The field 'proteins' has the following description: Groups protein definitions in SigPath

Returns:

Proteins

getReaction

public Reaction getReaction(int index)
                     throws IndexOutOfBoundsException

Method getReaction

Parameters:

index -

Returns:

Reaction

Throws:

IndexOutOfBoundsException

getReaction

public Reaction[] getReaction()

Method getReaction

Returns:

Reaction

getReactionCount

public int getReactionCount()

Method getReactionCount

Returns:

int

getSmallMolecules

public SmallMolecules getSmallMolecules()

Returns the value of field 'smallMolecules'. The field 'smallMolecules' has the following description: Groups small molecule definitions in SigPath

Returns:

SmallMolecules

isValid

public boolean isValid()

Method isValid

Returns:

boolean

marshal

public void marshal(Writer out)
             throws MarshalException,
                    ValidationException

Method marshal

Parameters:

out -

Throws:

MarshalException

ValidationException

marshal

public void marshal(ContentHandler handler)
             throws IOException,
                    MarshalException,
                    ValidationException

Method marshal

Parameters:

handler -

Throws:

IOException

MarshalException

ValidationException

removeEnzymaticReaction

public boolean removeEnzymaticReaction(EnzymaticReaction vEnzymaticReaction)

Method removeEnzymaticReaction

Parameters:

vEnzymaticReaction -

Returns:

boolean

removeModel

public boolean removeModel(Model vModel)

Method removeModel

Parameters:

vModel -

Returns:

boolean

removePathway

public boolean removePathway(Pathway vPathway)

Method removePathway

Parameters:

vPathway -

Returns:

boolean

removeReaction

public boolean removeReaction(Reaction vReaction)

Method removeReaction

Parameters:

vReaction -

Returns:

boolean

setComponents

public void setComponents(Components components)

Sets the value of field 'components'. The field 'components' has the following description: Groups complex and modified chemical definitions in SigPath

Parameters:

components - the value of field 'components'.

setConcentration_measurements

public void setConcentration_measurements(Concentration_measurements concentration_measurements)

Sets the value of field 'concentration_measurements'. The field 'concentration_measurements' has the following description: Groups concentration measurements in SigPath

Parameters:

concentration_measurements - the value of field 'concentration_measurements'.

setEnzymaticReaction

public void setEnzymaticReaction(int index,
                                 EnzymaticReaction vEnzymaticReaction)
                          throws IndexOutOfBoundsException

Method setEnzymaticReaction

Parameters:

index -

vEnzymaticReaction -

Throws:

IndexOutOfBoundsException

setEnzymaticReaction

public void setEnzymaticReaction(EnzymaticReaction[] enzymaticReactionArray)

Method setEnzymaticReaction

Parameters:

enzymaticReactionArray -

setExportBuildVersion

public void setExportBuildVersion(String exportBuildVersion)

Sets the value of field 'exportBuildVersion'. The field 'exportBuildVersion' has the following description: Optional field containing build version of the running sigpath, populated on xml export.

Parameters:

exportBuildVersion - the value of field 'exportBuildVersion'.

setExportDateTime

public void setExportDateTime(Date exportDateTime)

Sets the value of field 'exportDateTime'. The field 'exportDateTime' has the following description: Optional field containing the date and time, populated on xml export.

Parameters:

exportDateTime - the value of field 'exportDateTime'.

setKinetics

public void setKinetics(Kinetics kinetics)

Sets the value of field 'kinetics'. The field 'kinetics' has the following description: group of kinetics declaration in SigPath

Parameters:

kinetics - the value of field 'kinetics'.

setModel

public void setModel(int index,
                     Model vModel)
              throws IndexOutOfBoundsException

Method setModel

Parameters:

index -

vModel -

Throws:

IndexOutOfBoundsException

setModel

public void setModel(Model[] modelArray)

Method setModel

Parameters:

modelArray -

setNamedChemicalInteractions

public void setNamedChemicalInteractions(NamedChemicalInteractions namedChemicalInteractions)

Sets the value of field 'namedChemicalInteractions'. The field 'namedChemicalInteractions' has the following description: Groups named-chemical-interaction definitions in SigPath

Parameters:

namedChemicalInteractions - the value of field 'namedChemicalInteractions'.

setNamedChemicals

public void setNamedChemicals(NamedChemicals namedChemicals)

Sets the value of field 'namedChemicals'. The field 'namedChemicals' has the following description: Groups named-chemical definitions in SigPath

Parameters:

namedChemicals - the value of field 'namedChemicals'.

setPathway

public void setPathway(int index,
                       Pathway vPathway)
                throws IndexOutOfBoundsException

Method setPathway

Parameters:

index -

vPathway -

Throws:

IndexOutOfBoundsException

setPathway

public void setPathway(Pathway[] pathwayArray)

Method setPathway

Parameters:

pathwayArray -

setPending_reviews

public void setPending_reviews(Pending_reviews pending_reviews)

Sets the value of field 'pending_reviews'. The field 'pending_reviews' has the following description: Groups pending reviews

Parameters:

pending_reviews - the value of field 'pending_reviews'.

setProteins

public void setProteins(Proteins proteins)

Sets the value of field 'proteins'. The field 'proteins' has the following description: Groups protein definitions in SigPath

Parameters:

proteins - the value of field 'proteins'.

setReaction

public void setReaction(int index,
                        Reaction vReaction)
                 throws IndexOutOfBoundsException

Method setReaction

Parameters:

index -

vReaction -

Throws:

IndexOutOfBoundsException

setReaction

public void setReaction(Reaction[] reactionArray)

Method setReaction

Parameters:

reactionArray -

setSmallMolecules

public void setSmallMolecules(SmallMolecules smallMolecules)

Sets the value of field 'smallMolecules'. The field 'smallMolecules' has the following description: Groups small molecule definitions in SigPath

Parameters:

smallMolecules - the value of field 'smallMolecules'.

unmarshal

public static SigpathSubmission unmarshal(Reader reader)
                                   throws MarshalException,
                                          ValidationException

Method unmarshal

Parameters:

reader -

Returns:

SigpathSubmission

Throws:

MarshalException

ValidationException

validate

public void validate()
              throws ValidationException

Method validate

Throws:

ValidationException