org.sigpath.bioimport.reaction2
Class Model

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

All Implemented Interfaces:

Serializable

public class Model
extends Object
implements Serializable

encapsulates data defining a model

Version:

$Revision$ $Date$

See Also:

Serialized Form

Constructor Summary

Model()

Method Summary

void	addModelConcentration(int index, ModelConcentration vModelConcentration) Method addModelConcentration
void	addModelConcentration(ModelConcentration vModelConcentration) Method addModelConcentration
void	addModelReaction(int index, ModelReaction vModelReaction) Method addModelReaction
void	addModelReaction(ModelReaction vModelReaction) Method addModelReaction
void	clearModelConcentration() Method clearModelConcentration
void	clearModelReaction() Method clearModelReaction
Enumeration	enumerateModelConcentration() Method enumerateModelConcentration
Enumeration	enumerateModelReaction() Method enumerateModelReaction
Change_log	getChange_log() Returns the value of field 'change_log'.
String	getComments() Returns the value of field 'comments'.
String	getDescription() Returns the value of field 'description'.
ExcludedReactions	getExcludedReactions() Returns the value of field 'excludedReactions'.
String	getId() Returns the value of field 'id'.
ModelCompartments	getModelCompartments() Returns the value of field 'modelCompartments'.
ModelConcentration[]	getModelConcentration() Method getModelConcentration
ModelConcentration	getModelConcentration(int index) Method getModelConcentration
int	getModelConcentrationCount() Method getModelConcentrationCount
ModelReaction[]	getModelReaction() Method getModelReaction
ModelReaction	getModelReaction(int index) Method getModelReaction
int	getModelReactionCount() Method getModelReactionCount
String	getName() Returns the value of field 'name'.
PreviousVersion	getPreviousVersion() Returns the value of field 'previousVersion'.
Publications	getPublications() Returns the value of field 'publications'.
String	getSpid() Returns the value of field 'spid'.
TargetUnit	getTargetUnit() Returns the value of field 'targetUnit'.
boolean	isValid() Method isValid
void	marshal(ContentHandler handler) Method marshal
void	marshal(Writer out) Method marshal
boolean	removeModelConcentration(ModelConcentration vModelConcentration) Method removeModelConcentration
boolean	removeModelReaction(ModelReaction vModelReaction) Method removeModelReaction
void	setChange_log(Change_log change_log) Sets the value of field 'change_log'.
void	setComments(String comments) Sets the value of field 'comments'.
void	setDescription(String description) Sets the value of field 'description'.
void	setExcludedReactions(ExcludedReactions excludedReactions) Sets the value of field 'excludedReactions'.
void	setId(String id) Sets the value of field 'id'.
void	setModelCompartments(ModelCompartments modelCompartments) Sets the value of field 'modelCompartments'.
void	setModelConcentration(int index, ModelConcentration vModelConcentration) Method setModelConcentration
void	setModelConcentration(ModelConcentration[] modelConcentrationArray) Method setModelConcentration
void	setModelReaction(int index, ModelReaction vModelReaction) Method setModelReaction
void	setModelReaction(ModelReaction[] modelReactionArray) Method setModelReaction
void	setName(String name) Sets the value of field 'name'.
void	setPreviousVersion(PreviousVersion previousVersion) Sets the value of field 'previousVersion'.
void	setPublications(Publications publications) Sets the value of field 'publications'.
void	setSpid(String spid) Sets the value of field 'spid'.
void	setTargetUnit(TargetUnit targetUnit) Sets the value of field 'targetUnit'.
static Model	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

Model

public Model()

Method Detail

addModelConcentration

public void addModelConcentration(ModelConcentration vModelConcentration)
                           throws IndexOutOfBoundsException

Method addModelConcentration

Parameters:

vModelConcentration -

Throws:

IndexOutOfBoundsException

addModelConcentration

public void addModelConcentration(int index,
                                  ModelConcentration vModelConcentration)
                           throws IndexOutOfBoundsException

Method addModelConcentration

Parameters:

index -

vModelConcentration -

Throws:

IndexOutOfBoundsException

addModelReaction

public void addModelReaction(ModelReaction vModelReaction)
                      throws IndexOutOfBoundsException

Method addModelReaction

Parameters:

vModelReaction -

Throws:

IndexOutOfBoundsException

addModelReaction

public void addModelReaction(int index,
                             ModelReaction vModelReaction)
                      throws IndexOutOfBoundsException

Method addModelReaction

Parameters:

index -

vModelReaction -

Throws:

IndexOutOfBoundsException

clearModelConcentration

public void clearModelConcentration()

Method clearModelConcentration

clearModelReaction

public void clearModelReaction()

Method clearModelReaction

enumerateModelConcentration

public Enumeration enumerateModelConcentration()

Method enumerateModelConcentration

Returns:

Enumeration

enumerateModelReaction

public Enumeration enumerateModelReaction()

Method enumerateModelReaction

Returns:

Enumeration

getChange_log

public Change_log getChange_log()

Returns the value of field 'change_log'. The field 'change_log' has the following description: Used to annotate change log information, including who submitted this record, when the record was submitted, and when the record was last modified.

Returns:

Change_log

getComments

public String getComments()

Returns the value of field 'comments'. The field 'comments' has the following description: Allows you to annotate SigPath submission components with comments

Returns:

String

getDescription

public String getDescription()

Returns the value of field 'description'. The field 'description' has the following description: Allows you to attach a description to a reaction, molecule, compartment, model or review

Returns:

String

getExcludedReactions

public ExcludedReactions getExcludedReactions()

Returns the value of field 'excludedReactions'.

Returns:

ExcludedReactions

getId

public String getId()

Returns the value of field 'id'.

Returns:

String

getModelCompartments

public ModelCompartments getModelCompartments()

Returns the value of field 'modelCompartments'. The field 'modelCompartments' has the following description: Groups compartments of a model

Returns:

ModelCompartments

getModelConcentration

public ModelConcentration getModelConcentration(int index)
                                         throws IndexOutOfBoundsException

Method getModelConcentration

Parameters:

index -

Returns:

ModelConcentration

Throws:

IndexOutOfBoundsException

getModelConcentration

public ModelConcentration[] getModelConcentration()

Method getModelConcentration

Returns:

ModelConcentration

getModelConcentrationCount

public int getModelConcentrationCount()

Method getModelConcentrationCount

Returns:

int

getModelReaction

public ModelReaction getModelReaction(int index)
                               throws IndexOutOfBoundsException

Method getModelReaction

Parameters:

index -

Returns:

ModelReaction

Throws:

IndexOutOfBoundsException

getModelReaction

public ModelReaction[] getModelReaction()

Method getModelReaction

Returns:

ModelReaction

getModelReactionCount

public int getModelReactionCount()

Method getModelReactionCount

Returns:

int

getName

public String getName()

Returns the value of field 'name'. The field 'name' has the following description: Allows you to name a molecule or a model -

Returns:

String

getPreviousVersion

public PreviousVersion getPreviousVersion()

Returns the value of field 'previousVersion'. The field 'previousVersion' has the following description: previous version of a sigpathEntity

Returns:

PreviousVersion

getPublications

public Publications getPublications()

Returns the value of field 'publications'. The field 'publications' has the following description: Annotates publications in relation to a reaction or molecule concentration

Returns:

Publications

getSpid

public String getSpid()

Returns the value of field 'spid'.

Returns:

String

getTargetUnit

public TargetUnit getTargetUnit()

Returns the value of field 'targetUnit'. The field 'targetUnit' has the following description: Selects the concentration units required for creating/submitting a model

Returns:

TargetUnit

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

removeModelConcentration

public boolean removeModelConcentration(ModelConcentration vModelConcentration)

Method removeModelConcentration

Parameters:

vModelConcentration -

Returns:

boolean

removeModelReaction

public boolean removeModelReaction(ModelReaction vModelReaction)

Method removeModelReaction

Parameters:

vModelReaction -

Returns:

boolean

setChange_log

public void setChange_log(Change_log change_log)

Sets the value of field 'change_log'. The field 'change_log' has the following description: Used to annotate change log information, including who submitted this record, when the record was submitted, and when the record was last modified.

Parameters:

change_log - the value of field 'change_log'.

setComments

public void setComments(String comments)

Sets the value of field 'comments'. The field 'comments' has the following description: Allows you to annotate SigPath submission components with comments

Parameters:

comments - the value of field 'comments'.

setDescription

public void setDescription(String description)

Sets the value of field 'description'. The field 'description' has the following description: Allows you to attach a description to a reaction, molecule, compartment, model or review

Parameters:

description - the value of field 'description'.

setExcludedReactions

public void setExcludedReactions(ExcludedReactions excludedReactions)

Sets the value of field 'excludedReactions'.

Parameters:

excludedReactions - the value of field 'excludedReactions'.

setId

public void setId(String id)

Sets the value of field 'id'.

Parameters:

id - the value of field 'id'.

setModelCompartments

public void setModelCompartments(ModelCompartments modelCompartments)

Sets the value of field 'modelCompartments'. The field 'modelCompartments' has the following description: Groups compartments of a model

Parameters:

modelCompartments - the value of field 'modelCompartments'.

setModelConcentration

public void setModelConcentration(int index,
                                  ModelConcentration vModelConcentration)
                           throws IndexOutOfBoundsException

Method setModelConcentration

Parameters:

index -

vModelConcentration -

Throws:

IndexOutOfBoundsException

setModelConcentration

public void setModelConcentration(ModelConcentration[] modelConcentrationArray)

Method setModelConcentration

Parameters:

modelConcentrationArray -

setModelReaction

public void setModelReaction(int index,
                             ModelReaction vModelReaction)
                      throws IndexOutOfBoundsException

Method setModelReaction

Parameters:

index -

vModelReaction -

Throws:

IndexOutOfBoundsException

setModelReaction

public void setModelReaction(ModelReaction[] modelReactionArray)

Method setModelReaction

Parameters:

modelReactionArray -

setName

public void setName(String name)

Sets the value of field 'name'. The field 'name' has the following description: Allows you to name a molecule or a model -

Parameters:

name - the value of field 'name'.

setPreviousVersion

public void setPreviousVersion(PreviousVersion previousVersion)

Sets the value of field 'previousVersion'. The field 'previousVersion' has the following description: previous version of a sigpathEntity

Parameters:

previousVersion - the value of field 'previousVersion'.

setPublications

public void setPublications(Publications publications)

Sets the value of field 'publications'. The field 'publications' has the following description: Annotates publications in relation to a reaction or molecule concentration

Parameters:

publications - the value of field 'publications'.

setSpid

public void setSpid(String spid)

Sets the value of field 'spid'.

Parameters:

spid - the value of field 'spid'.

setTargetUnit

public void setTargetUnit(TargetUnit targetUnit)

Sets the value of field 'targetUnit'. The field 'targetUnit' has the following description: Selects the concentration units required for creating/submitting a model

Parameters:

targetUnit - the value of field 'targetUnit'.

unmarshal

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

Method unmarshal

Parameters:

reader -

Returns:

Model

Throws:

MarshalException

ValidationException

validate

public void validate()
              throws ValidationException

Method validate

Throws:

ValidationException