org.sigpath.bioimport.reaction2
Class EnzymaticReaction

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

All Implemented Interfaces:

Serializable

public class EnzymaticReaction
extends Object
implements Serializable

element used to encapsulate data defining an enzymatic reaction in SigPath

Version:

$Revision$ $Date$

See Also:

Serialized Form

Constructor Summary

EnzymaticReaction()

Method Summary

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'.
EnzymaticParameters	getEnzymaticParameters() Returns the value of field 'enzymaticParameters'.
Enzyme	getEnzyme() Returns the value of field 'enzyme'.
String	getId() Returns the value of field 'id'.
KineticBindings	getKineticBindings() Returns the value of field 'kineticBindings'.
KineticRef	getKineticRef() Returns the value of field 'kineticRef'.
String	getName() Returns the value of field 'name'.
Publications	getPublications() Returns the value of field 'publications'.
Reaction	getReaction() Returns the value of field 'reaction'.
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	setComments(String comments) Sets the value of field 'comments'.
void	setDescription(String description) Sets the value of field 'description'.
void	setEnzymaticParameters(EnzymaticParameters enzymaticParameters) Sets the value of field 'enzymaticParameters'.
void	setEnzyme(Enzyme enzyme) Sets the value of field 'enzyme'.
void	setId(String id) Sets the value of field 'id'.
void	setKineticBindings(KineticBindings kineticBindings) Sets the value of field 'kineticBindings'.
void	setKineticRef(KineticRef kineticRef) Sets the value of field 'kineticRef'.
void	setName(String name) Sets the value of field 'name'.
void	setPublications(Publications publications) Sets the value of field 'publications'.
void	setReaction(Reaction reaction) Sets the value of field 'reaction'.
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 EnzymaticReaction	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

EnzymaticReaction

public EnzymaticReaction()

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

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

getEnzymaticParameters

public EnzymaticParameters getEnzymaticParameters()

Returns the value of field 'enzymaticParameters'. The field 'enzymaticParameters' has the following description: Groups the parameters of an enzymatic reaction in SigPath

Returns:

EnzymaticParameters

getEnzyme

public Enzyme getEnzyme()

Returns the value of field 'enzyme'. The field 'enzyme' has the following description: Identifies the enzyme for an enzymatic reaction

Returns:

Enzyme

getId

public String getId()

Returns the value of field 'id'.

Returns:

String

getKineticBindings

public KineticBindings getKineticBindings()

Returns the value of field 'kineticBindings'. The field 'kineticBindings' has the following description: name to constant/chemical elements

Returns:

KineticBindings

getKineticRef

public KineticRef getKineticRef()

Returns the value of field 'kineticRef'. The field 'kineticRef' has the following description: there are two way to define a kinetic, either indicating a class which realizes a specified kinetic, either indication a kinetic declaration, also part of the submission

Returns:

KineticRef

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

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

getReaction

public Reaction getReaction()

Returns the value of field 'reaction'. The field 'reaction' has the following description: element used to encapsulate data defining a reaction in SigPath

Returns:

Reaction

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'.

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'.

setEnzymaticParameters

public void setEnzymaticParameters(EnzymaticParameters enzymaticParameters)

Sets the value of field 'enzymaticParameters'. The field 'enzymaticParameters' has the following description: Groups the parameters of an enzymatic reaction in SigPath

Parameters:

enzymaticParameters - the value of field 'enzymaticParameters'.

setEnzyme

public void setEnzyme(Enzyme enzyme)

Sets the value of field 'enzyme'. The field 'enzyme' has the following description: Identifies the enzyme for an enzymatic reaction

Parameters:

enzyme - the value of field 'enzyme'.

setId

public void setId(String id)

Sets the value of field 'id'.

Parameters:

id - the value of field 'id'.

setKineticBindings

public void setKineticBindings(KineticBindings kineticBindings)

Sets the value of field 'kineticBindings'. The field 'kineticBindings' has the following description: name to constant/chemical elements

Parameters:

kineticBindings - the value of field 'kineticBindings'.

setKineticRef

public void setKineticRef(KineticRef kineticRef)

Sets the value of field 'kineticRef'. The field 'kineticRef' has the following description: there are two way to define a kinetic, either indicating a class which realizes a specified kinetic, either indication a kinetic declaration, also part of the submission

Parameters:

kineticRef - the value of field 'kineticRef'.

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'.

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'.

setReaction

public void setReaction(Reaction reaction)

Sets the value of field 'reaction'. The field 'reaction' has the following description: element used to encapsulate data defining a reaction in SigPath

Parameters:

reaction - the value of field 'reaction'.

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 EnzymaticReaction unmarshal(Reader reader)
                                   throws MarshalException,
                                          ValidationException

Method unmarshal

Parameters:

reader -

Returns:

EnzymaticReaction

Throws:

MarshalException

ValidationException

validate

public void validate()
              throws ValidationException

Method validate

Throws:

ValidationException