org.sigpath.bioimport.reaction2
Class Complex

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

All Implemented Interfaces:

Serializable

public class Complex
extends Object
implements Serializable

element used to define a complex in SigPath

Version:

$Revision$ $Date$

See Also:

Serialized Form

Constructor Summary

Complex()

Method Summary

void	addMolecule(int index, Molecule vMolecule) Method addMolecule
void	addMolecule(Molecule vMolecule) Method addMolecule
void	clearMolecule() Method clearMolecule
void	deleteFullyDefined() Method deleteFullyDefined
Enumeration	enumerateMolecule() Method enumerateMolecule
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'.
boolean	getFullyDefined() Returns the value of field 'fullyDefined'.
String	getId() Returns the value of field 'id'.
InternalLinks	getInternalLinks() Returns the value of field 'internalLinks'.
Molecule[]	getMolecule() Method getMolecule
Molecule	getMolecule(int index) Method getMolecule
int	getMoleculeCount() Method getMoleculeCount
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	hasFullyDefined() Method hasFullyDefined
boolean	isValid() Method isValid
void	marshal(ContentHandler handler) Method marshal
void	marshal(Writer out) Method marshal
boolean	removeMolecule(Molecule vMolecule) Method removeMolecule
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	setFullyDefined(boolean fullyDefined) Sets the value of field 'fullyDefined'.
void	setId(String id) Sets the value of field 'id'.
void	setInternalLinks(InternalLinks internalLinks) Sets the value of field 'internalLinks'.
void	setMolecule(int index, Molecule vMolecule) Method setMolecule
void	setMolecule(Molecule[] moleculeArray) Method setMolecule
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 Complex	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

Complex

public Complex()

Method Detail

addMolecule

public void addMolecule(Molecule vMolecule)
                 throws IndexOutOfBoundsException

Method addMolecule

Parameters:

vMolecule -

Throws:

IndexOutOfBoundsException

addMolecule

public void addMolecule(int index,
                        Molecule vMolecule)
                 throws IndexOutOfBoundsException

Method addMolecule

Parameters:

index -

vMolecule -

Throws:

IndexOutOfBoundsException

clearMolecule

public void clearMolecule()

Method clearMolecule

deleteFullyDefined

public void deleteFullyDefined()

Method deleteFullyDefined

enumerateMolecule

public Enumeration enumerateMolecule()

Method enumerateMolecule

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

getFullyDefined

public boolean getFullyDefined()

Returns the value of field 'fullyDefined'. The field 'fullyDefined' has the following description: Used to annotate the fully-defined value of the complex. If the fully-defined value is true, the complex is believed to be complete. If the fully-defined value is false, the list of chemicals that form the complex is known to be incomplete. Other molecules that are not explicitly listed here may participate in this complex.

Returns:

boolean

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(int index)
                     throws IndexOutOfBoundsException

Method getMolecule

Parameters:

index -

Returns:

Molecule

Throws:

IndexOutOfBoundsException

getMolecule

public Molecule[] getMolecule()

Method getMolecule

Returns:

Molecule

getMoleculeCount

public int getMoleculeCount()

Method getMoleculeCount

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

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

hasFullyDefined

public boolean hasFullyDefined()

Method hasFullyDefined

Returns:

boolean

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

removeMolecule

public boolean removeMolecule(Molecule vMolecule)

Method removeMolecule

Parameters:

vMolecule -

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'.

setFullyDefined

public void setFullyDefined(boolean fullyDefined)

Sets the value of field 'fullyDefined'. The field 'fullyDefined' has the following description: Used to annotate the fully-defined value of the complex. If the fully-defined value is true, the complex is believed to be complete. If the fully-defined value is false, the list of chemicals that form the complex is known to be incomplete. Other molecules that are not explicitly listed here may participate in this complex.

Parameters:

fullyDefined - the value of field 'fullyDefined'.

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(int index,
                        Molecule vMolecule)
                 throws IndexOutOfBoundsException

Method setMolecule

Parameters:

index -

vMolecule -

Throws:

IndexOutOfBoundsException

setMolecule

public void setMolecule(Molecule[] moleculeArray)

Method setMolecule

Parameters:

moleculeArray -

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'.

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 Complex unmarshal(Reader reader)
                         throws MarshalException,
                                ValidationException

Method unmarshal

Parameters:

reader -

Returns:

Complex

Throws:

MarshalException

ValidationException

validate

public void validate()
              throws ValidationException

Method validate

Throws:

ValidationException