org.sigpath.bioimport.reaction2
Class NamedChemicalInteraction

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

All Implemented Interfaces:

Serializable

public class NamedChemicalInteraction
extends Object
implements Serializable

Annotates an interaction between two named-chemicals in SigPath. In situations when it is a target-source interaction, the source named-chemical should be listed first, followed by the target named-chemical.

Version:

$Revision$ $Date$

See Also:

Serialized Form

Constructor Summary

NamedChemicalInteraction()

Method Summary

void	addExternalReference(ExternalReference vExternalReference) Method addExternalReference
void	addExternalReference(int index, ExternalReference vExternalReference) Method addExternalReference
void	addNamedChemicalRef(int index, NamedChemicalRef vNamedChemicalRef) Method addNamedChemicalRef
void	addNamedChemicalRef(NamedChemicalRef vNamedChemicalRef) Method addNamedChemicalRef
void	clearExternalReference() Method clearExternalReference
void	clearNamedChemicalRef() Method clearNamedChemicalRef
Enumeration	enumerateExternalReference() Method enumerateExternalReference
Enumeration	enumerateNamedChemicalRef() Method enumerateNamedChemicalRef
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'.
ExternalReference[]	getExternalReference() Method getExternalReference
ExternalReference	getExternalReference(int index) Method getExternalReference
int	getExternalReferenceCount() Method getExternalReferenceCount
String	getId() Returns the value of field 'id'.
String	getName() Returns the value of field 'name'.
NamedChemicalRef[]	getNamedChemicalRef() Method getNamedChemicalRef
NamedChemicalRef	getNamedChemicalRef(int index) Method getNamedChemicalRef
int	getNamedChemicalRefCount() Method getNamedChemicalRefCount
Publications	getPublications() Returns the value of field 'publications'.
String	getSpid() Returns the value of field 'spid'.
String	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
boolean	removeExternalReference(ExternalReference vExternalReference) Method removeExternalReference
boolean	removeNamedChemicalRef(NamedChemicalRef vNamedChemicalRef) Method removeNamedChemicalRef
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	setExternalReference(ExternalReference[] externalReferenceArray) Method setExternalReference
void	setExternalReference(int index, ExternalReference vExternalReference) Method setExternalReference
void	setId(String id) Sets the value of field 'id'.
void	setName(String name) Sets the value of field 'name'.
void	setNamedChemicalRef(int index, NamedChemicalRef vNamedChemicalRef) Method setNamedChemicalRef
void	setNamedChemicalRef(NamedChemicalRef[] namedChemicalRefArray) Method setNamedChemicalRef
void	setPublications(Publications publications) Sets the value of field 'publications'.
void	setSpid(String spid) Sets the value of field 'spid'.
void	setType(String type) Sets the value of field 'type'.
void	setUserComments(UserComments userComments) Sets the value of field 'userComments'.
static NamedChemicalInteraction	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

NamedChemicalInteraction

public NamedChemicalInteraction()

Method Detail

addExternalReference

public void addExternalReference(ExternalReference vExternalReference)
                          throws IndexOutOfBoundsException

Method addExternalReference

Parameters:

vExternalReference -

Throws:

IndexOutOfBoundsException

addExternalReference

public void addExternalReference(int index,
                                 ExternalReference vExternalReference)
                          throws IndexOutOfBoundsException

Method addExternalReference

Parameters:

index -

vExternalReference -

Throws:

IndexOutOfBoundsException

addNamedChemicalRef

public void addNamedChemicalRef(NamedChemicalRef vNamedChemicalRef)
                         throws IndexOutOfBoundsException

Method addNamedChemicalRef

Parameters:

vNamedChemicalRef -

Throws:

IndexOutOfBoundsException

addNamedChemicalRef

public void addNamedChemicalRef(int index,
                                NamedChemicalRef vNamedChemicalRef)
                         throws IndexOutOfBoundsException

Method addNamedChemicalRef

Parameters:

index -

vNamedChemicalRef -

Throws:

IndexOutOfBoundsException

clearExternalReference

public void clearExternalReference()

Method clearExternalReference

clearNamedChemicalRef

public void clearNamedChemicalRef()

Method clearNamedChemicalRef

enumerateExternalReference

public Enumeration enumerateExternalReference()

Method enumerateExternalReference

Returns:

Enumeration

enumerateNamedChemicalRef

public Enumeration enumerateNamedChemicalRef()

Method enumerateNamedChemicalRef

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

getExternalReference

public ExternalReference getExternalReference(int index)
                                       throws IndexOutOfBoundsException

Method getExternalReference

Parameters:

index -

Returns:

ExternalReference

Throws:

IndexOutOfBoundsException

getExternalReference

public ExternalReference[] getExternalReference()

Method getExternalReference

Returns:

ExternalReference

getExternalReferenceCount

public int getExternalReferenceCount()

Method getExternalReferenceCount

Returns:

int

getId

public String getId()

Returns the value of field 'id'.

Returns:

String

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

getNamedChemicalRef

public NamedChemicalRef getNamedChemicalRef(int index)
                                     throws IndexOutOfBoundsException

Method getNamedChemicalRef

Parameters:

index -

Returns:

NamedChemicalRef

Throws:

IndexOutOfBoundsException

getNamedChemicalRef

public NamedChemicalRef[] getNamedChemicalRef()

Method getNamedChemicalRef

Returns:

NamedChemicalRef

getNamedChemicalRefCount

public int getNamedChemicalRefCount()

Method getNamedChemicalRefCount

Returns:

int

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

getType

public String getType()

Returns the value of field 'type'.

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

removeExternalReference

public boolean removeExternalReference(ExternalReference vExternalReference)

Method removeExternalReference

Parameters:

vExternalReference -

Returns:

boolean

removeNamedChemicalRef

public boolean removeNamedChemicalRef(NamedChemicalRef vNamedChemicalRef)

Method removeNamedChemicalRef

Parameters:

vNamedChemicalRef -

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'.

setExternalReference

public void setExternalReference(int index,
                                 ExternalReference vExternalReference)
                          throws IndexOutOfBoundsException

Method setExternalReference

Parameters:

index -

vExternalReference -

Throws:

IndexOutOfBoundsException

setExternalReference

public void setExternalReference(ExternalReference[] externalReferenceArray)

Method setExternalReference

Parameters:

externalReferenceArray -

setId

public void setId(String id)

Sets the value of field 'id'.

Parameters:

id - the value of field 'id'.

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'.

setNamedChemicalRef

public void setNamedChemicalRef(int index,
                                NamedChemicalRef vNamedChemicalRef)
                         throws IndexOutOfBoundsException

Method setNamedChemicalRef

Parameters:

index -

vNamedChemicalRef -

Throws:

IndexOutOfBoundsException

setNamedChemicalRef

public void setNamedChemicalRef(NamedChemicalRef[] namedChemicalRefArray)

Method setNamedChemicalRef

Parameters:

namedChemicalRefArray -

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'.

setType

public void setType(String type)

Sets the value of field 'type'.

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 NamedChemicalInteraction unmarshal(Reader reader)
                                          throws MarshalException,
                                                 ValidationException

Method unmarshal

Parameters:

reader -

Returns:

NamedChemicalInteraction

Throws:

MarshalException

ValidationException

validate

public void validate()
              throws ValidationException

Method validate

Throws:

ValidationException