org.sigpath.bioimport.reaction2
Class Kinetic

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

All Implemented Interfaces:

Serializable

public class Kinetic
extends Object
implements Serializable

This element declares a new type of kinetic. Two ways to define kinetic types are currently supported: (1) Reference kinetics can be implemented in a Java class and referenced by class name. (2) Custom kinetics that can be expressed with rate laws and described directly in the XML file. If defined in the XML file, the kinetic declaration must contain formulae, species and constant bindings declarations.

Version:

$Revision$ $Date$

See Also:

Serialized Form

Constructor Summary

Kinetic()

Method Summary

Change_log	getChange_log() Returns the value of field 'change_log'.
CustomKinetic	getCustomKinetic() Returns the value of field 'customKinetic'.
String	getDescription() Returns the value of field 'description'.
String	getId() Returns the value of field 'id'.
KineticTypeType	getKineticType() Returns the value of field 'kineticType'.
String	getName() Returns the value of field 'name'.
Publications	getPublications() Returns the value of field 'publications'.
Reviews	getReviews() Returns the value of field 'reviews'.
String	getSpid() Returns the value of field 'spid'.
UserComments	getUserComments() Returns the value of field 'userComments'.
boolean	isValid() Method isValid
void	marshal(ContentHandler handler) Method marshal
void	marshal(Writer out) Method marshal
void	setChange_log(Change_log change_log) Sets the value of field 'change_log'.
void	setCustomKinetic(CustomKinetic customKinetic) Sets the value of field 'customKinetic'.
void	setDescription(String description) Sets the value of field 'description'.
void	setId(String id) Sets the value of field 'id'.
void	setKineticType(KineticTypeType kineticType) Sets the value of field 'kineticType'.
void	setName(String name) Sets the value of field 'name'.
void	setPublications(Publications publications) Sets the value of field 'publications'.
void	setReviews(Reviews reviews) Sets the value of field 'reviews'.
void	setSpid(String spid) Sets the value of field 'spid'.
void	setUserComments(UserComments userComments) Sets the value of field 'userComments'.
static Kinetic	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

Kinetic

public Kinetic()

Method Detail

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

getCustomKinetic

public CustomKinetic getCustomKinetic()

Returns the value of field 'customKinetic'.

Returns:

CustomKinetic

getDescription

public String getDescription()

Returns the value of field 'description'.

Returns:

String

getId

public String getId()

Returns the value of field 'id'.

Returns:

String

getKineticType

public KineticTypeType getKineticType()

Returns the value of field 'kineticType'. The field 'kineticType' has the following description: Type of this kinetic. One of: org.sigpath.datamodel.KineticMassAction, org.sigpath.datamodel.KineticMichaelisMenten, or org.sigpath.datamodel.KineticCustom.".

Returns:

KineticTypeType

getName

public String getName()

Returns the value of field 'name'.

Returns:

String

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

getReviews

public Reviews getReviews()

Returns the value of field 'reviews'. The field 'reviews' has the following description: Used to annotate SigPath reviews

Returns:

Reviews

getSpid

public String getSpid()

Returns the value of field 'spid'.

Returns:

String

getUserComments

public UserComments getUserComments()

Returns the value of field 'userComments'. The field 'userComments' has the following description: Groups user-comment

Returns:

UserComments

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

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'.

setCustomKinetic

public void setCustomKinetic(CustomKinetic customKinetic)

Sets the value of field 'customKinetic'.

Parameters:

customKinetic - the value of field 'customKinetic'.

setDescription

public void setDescription(String description)

Sets the value of field 'description'.

Parameters:

description - the value of field 'description'.

setId

public void setId(String id)

Sets the value of field 'id'.

Parameters:

id - the value of field 'id'.

setKineticType

public void setKineticType(KineticTypeType kineticType)

Sets the value of field 'kineticType'. The field 'kineticType' has the following description: Type of this kinetic. One of: org.sigpath.datamodel.KineticMassAction, org.sigpath.datamodel.KineticMichaelisMenten, or org.sigpath.datamodel.KineticCustom.".

Parameters:

kineticType - the value of field 'kineticType'.

setName

public void setName(String name)

Sets the value of field 'name'.

Parameters:

name - the value of field 'name'.

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'.

setReviews

public void setReviews(Reviews reviews)

Sets the value of field 'reviews'. The field 'reviews' has the following description: Used to annotate SigPath reviews

Parameters:

reviews - the value of field 'reviews'.

setSpid

public void setSpid(String spid)

Sets the value of field 'spid'.

Parameters:

spid - the value of field 'spid'.

setUserComments

public void setUserComments(UserComments userComments)

Sets the value of field 'userComments'. The field 'userComments' has the following description: Groups user-comment

Parameters:

userComments - the value of field 'userComments'.

unmarshal

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

Method unmarshal

Parameters:

reader -

Returns:

Kinetic

Throws:

MarshalException

ValidationException

validate

public void validate()
              throws ValidationException

Method validate

Throws:

ValidationException