org.sigpath.bioimport.reaction2
Class ModifiedChemical

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

All Implemented Interfaces:

Serializable

public class ModifiedChemical
extends Object
implements Serializable

Defines a modified chemical (for example the active isoform of a specified molecule) in SigPath.

Version:

$Revision$ $Date$

See Also:

Serialized Form

Constructor Summary

ModifiedChemical()

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'.
String	getId() Returns the value of field 'id'.
InternalLinks	getInternalLinks() Returns the value of field 'internalLinks'.
Molecule	getMolecule() Returns the value of field 'molecule'.
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'.
TypeType	getType() Returns the value of field 'type'.
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	setId(String id) Sets the value of field 'id'.
void	setInternalLinks(InternalLinks internalLinks) Sets the value of field 'internalLinks'.
void	setMolecule(Molecule molecule) Sets the value of field 'molecule'.
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	setType(TypeType type) Sets the value of field 'type'.
void	setUserComments(UserComments userComments) Sets the value of field 'userComments'.
static ModifiedChemical	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

ModifiedChemical

public ModifiedChemical()

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

getId

public String getId()

Returns the value of field 'id'.

Returns:

String

getInternalLinks

public InternalLinks getInternalLinks()

Returns the value of field 'internalLinks'. The field 'internalLinks' has the following description: Used to describe internal links within SigPath

Returns:

InternalLinks

getMolecule

public Molecule getMolecule()

Returns the value of field 'molecule'. The field 'molecule' has the following description: Identifies a molecule in SigPath (for example as part of a reaction or as part of a complex) by using at least one of three attributes: idref (unique identifier for new molecules; this attribute has the highest precedence), ac. (accession number; this attribute has the second highest precedence) or spid (unique SigPath identifier; this identifier has the lowest precedence)

Returns:

Molecule

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

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

getType

public TypeType getType()

Returns the value of field 'type'. The field 'type' has the following description: Specifies whether a modified chemical is a protein or a small molecule

Returns:

TypeType

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'.

setId

public void setId(String id)

Sets the value of field 'id'.

Parameters:

id - the value of field 'id'.

setInternalLinks

public void setInternalLinks(InternalLinks internalLinks)

Sets the value of field 'internalLinks'. The field 'internalLinks' has the following description: Used to describe internal links within SigPath

Parameters:

internalLinks - the value of field 'internalLinks'.

setMolecule

public void setMolecule(Molecule molecule)

Sets the value of field 'molecule'. The field 'molecule' has the following description: Identifies a molecule in SigPath (for example as part of a reaction or as part of a complex) by using at least one of three attributes: idref (unique identifier for new molecules; this attribute has the highest precedence), ac. (accession number; this attribute has the second highest precedence) or spid (unique SigPath identifier; this identifier has the lowest precedence)

Parameters:

molecule - the value of field 'molecule'.

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'.

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'.

setType

public void setType(TypeType type)

Sets the value of field 'type'. The field 'type' has the following description: Specifies whether a modified chemical is a protein or a small molecule

Parameters:

type - the value of field 'type'.

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 ModifiedChemical unmarshal(Reader reader)
                                  throws MarshalException,
                                         ValidationException

Method unmarshal

Parameters:

reader -

Returns:

ModifiedChemical

Throws:

MarshalException

ValidationException

validate

public void validate()
              throws ValidationException

Method validate

Throws:

ValidationException