org.sigpath.bioimport.reaction2
Class Molecule

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

All Implemented Interfaces:

Serializable

public class Molecule
extends Object
implements Serializable

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)

Version:

$Revision$ $Date$

See Also:

Serialized Form

Constructor Summary

Molecule()

Method Summary

void	addLocation(int index, Location vLocation) Method addLocation
void	addLocation(Location vLocation) Method addLocation
void	clearLocation() Method clearLocation
void	deleteIsBuffered() Method deleteIsBuffered
void	deleteIsModelWillProvide() Method deleteIsModelWillProvide
void	deleteIsProduct() Method deleteIsProduct
void	deleteIsSubstrate() Method deleteIsSubstrate
Enumeration	enumerateLocation() Method enumerateLocation
String	getAc() Returns the value of field 'ac'.
String	getComments() Returns the value of field 'comments'.
String	getDescription() Returns the value of field 'description'.
Object	getIdref() Returns the value of field 'idref'.
String	getInteraction_site() Returns the value of field 'interaction_site'.
boolean	getIsBuffered() Returns the value of field 'isBuffered'.
boolean	getIsModelWillProvide() Returns the value of field 'isModelWillProvide'.
boolean	getIsProduct() Returns the value of field 'isProduct'.
boolean	getIsSubstrate() Returns the value of field 'isSubstrate'.
Location[]	getLocation() Method getLocation
Location	getLocation(int index) Method getLocation
int	getLocationCount() Method getLocationCount
String	getName() Returns the value of field 'name'.
String	getOrganism() Returns the value of field 'organism'.
String	getSpid() Returns the value of field 'spid'.
boolean	hasIsBuffered() Method hasIsBuffered
boolean	hasIsModelWillProvide() Method hasIsModelWillProvide
boolean	hasIsProduct() Method hasIsProduct
boolean	hasIsSubstrate() Method hasIsSubstrate
boolean	isValid() Method isValid
void	marshal(ContentHandler handler) Method marshal
void	marshal(Writer out) Method marshal
boolean	removeLocation(Location vLocation) Method removeLocation
void	setAc(String ac) Sets the value of field 'ac'.
void	setComments(String comments) Sets the value of field 'comments'.
void	setDescription(String description) Sets the value of field 'description'.
void	setIdref(Object idref) Sets the value of field 'idref'.
void	setInteraction_site(String interaction_site) Sets the value of field 'interaction_site'.
void	setIsBuffered(boolean isBuffered) Sets the value of field 'isBuffered'.
void	setIsModelWillProvide(boolean isModelWillProvide) Sets the value of field 'isModelWillProvide'.
void	setIsProduct(boolean isProduct) Sets the value of field 'isProduct'.
void	setIsSubstrate(boolean isSubstrate) Sets the value of field 'isSubstrate'.
void	setLocation(int index, Location vLocation) Method setLocation
void	setLocation(Location[] locationArray) Method setLocation
void	setName(String name) Sets the value of field 'name'.
void	setOrganism(String organism) Sets the value of field 'organism'.
void	setSpid(String spid) Sets the value of field 'spid'.
static Molecule	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

Molecule

public Molecule()

Method Detail

addLocation

public void addLocation(Location vLocation)
                 throws IndexOutOfBoundsException

Method addLocation

Parameters:

vLocation -

Throws:

IndexOutOfBoundsException

addLocation

public void addLocation(int index,
                        Location vLocation)
                 throws IndexOutOfBoundsException

Method addLocation

Parameters:

index -

vLocation -

Throws:

IndexOutOfBoundsException

clearLocation

public void clearLocation()

Method clearLocation

deleteIsBuffered

public void deleteIsBuffered()

Method deleteIsBuffered

deleteIsModelWillProvide

public void deleteIsModelWillProvide()

Method deleteIsModelWillProvide

deleteIsProduct

public void deleteIsProduct()

Method deleteIsProduct

deleteIsSubstrate

public void deleteIsSubstrate()

Method deleteIsSubstrate

enumerateLocation

public Enumeration enumerateLocation()

Method enumerateLocation

Returns:

Enumeration

getAc

public String getAc()

Returns the value of field 'ac'. The field 'ac' has the following description: Accession code of the molecule to be matched.

Returns:

String

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

getIdref

public Object getIdref()

Returns the value of field 'idref'. The field 'idref' has the following description: Reference to an identifier defined in this file (with the id attribute). When provided, the molecule will match the molecule that has the id attribute equals to idref.

Returns:

Object

getInteraction_site

public String getInteraction_site()

Returns the value of field 'interaction_site'. The field 'interaction_site' has the following description: Annotates the site at which two molecules interact

Returns:

String

getIsBuffered

public boolean getIsBuffered()

Returns the value of field 'isBuffered'.

Returns:

boolean

getIsModelWillProvide

public boolean getIsModelWillProvide()

Returns the value of field 'isModelWillProvide'.

Returns:

boolean

getIsProduct

public boolean getIsProduct()

Returns the value of field 'isProduct'. The field 'isProduct' has the following description: When true, indicates that this molecule is a product of the enclosing enzymatic reaction.

Returns:

boolean

getIsSubstrate

public boolean getIsSubstrate()

Returns the value of field 'isSubstrate'. The field 'isSubstrate' has the following description: When true, indicates that this molecule is a substrate of the enclosing enzymatic reaction.

Returns:

boolean

getLocation

public Location getLocation(int index)
                     throws IndexOutOfBoundsException

Method getLocation

Parameters:

index -

Returns:

Location

Throws:

IndexOutOfBoundsException

getLocation

public Location[] getLocation()

Method getLocation

Returns:

Location

getLocationCount

public int getLocationCount()

Method getLocationCount

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

getOrganism

public String getOrganism()

Returns the value of field 'organism'. The field 'organism' has the following description: Organism of the molecule to be matched. This is useful to further define the molecule matched by accession code when the match is still ambiguous.

Returns:

String

getSpid

public String getSpid()

Returns the value of field 'spid'.

Returns:

String

hasIsBuffered

public boolean hasIsBuffered()

Method hasIsBuffered

Returns:

boolean

hasIsModelWillProvide

public boolean hasIsModelWillProvide()

Method hasIsModelWillProvide

Returns:

boolean

hasIsProduct

public boolean hasIsProduct()

Method hasIsProduct

Returns:

boolean

hasIsSubstrate

public boolean hasIsSubstrate()

Method hasIsSubstrate

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

removeLocation

public boolean removeLocation(Location vLocation)

Method removeLocation

Parameters:

vLocation -

Returns:

boolean

setAc

public void setAc(String ac)

Sets the value of field 'ac'. The field 'ac' has the following description: Accession code of the molecule to be matched.

Parameters:

ac - the value of field 'ac'.

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'.

setIdref

public void setIdref(Object idref)

Sets the value of field 'idref'. The field 'idref' has the following description: Reference to an identifier defined in this file (with the id attribute). When provided, the molecule will match the molecule that has the id attribute equals to idref.

Parameters:

idref - the value of field 'idref'.

setInteraction_site

public void setInteraction_site(String interaction_site)

Sets the value of field 'interaction_site'. The field 'interaction_site' has the following description: Annotates the site at which two molecules interact

Parameters:

interaction_site - the value of field 'interaction_site'

setIsBuffered

public void setIsBuffered(boolean isBuffered)

Sets the value of field 'isBuffered'.

Parameters:

isBuffered - the value of field 'isBuffered'.

setIsModelWillProvide

public void setIsModelWillProvide(boolean isModelWillProvide)

Sets the value of field 'isModelWillProvide'.

Parameters:

isModelWillProvide - the value of field 'isModelWillProvide'.

setIsProduct

public void setIsProduct(boolean isProduct)

Sets the value of field 'isProduct'. The field 'isProduct' has the following description: When true, indicates that this molecule is a product of the enclosing enzymatic reaction.

Parameters:

isProduct - the value of field 'isProduct'.

setIsSubstrate

public void setIsSubstrate(boolean isSubstrate)

Sets the value of field 'isSubstrate'. The field 'isSubstrate' has the following description: When true, indicates that this molecule is a substrate of the enclosing enzymatic reaction.

Parameters:

isSubstrate - the value of field 'isSubstrate'.

setLocation

public void setLocation(int index,
                        Location vLocation)
                 throws IndexOutOfBoundsException

Method setLocation

Parameters:

index -

vLocation -

Throws:

IndexOutOfBoundsException

setLocation

public void setLocation(Location[] locationArray)

Method setLocation

Parameters:

locationArray -

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'.

setOrganism

public void setOrganism(String organism)

Sets the value of field 'organism'. The field 'organism' has the following description: Organism of the molecule to be matched. This is useful to further define the molecule matched by accession code when the match is still ambiguous.

Parameters:

organism - the value of field 'organism'.

setSpid

public void setSpid(String spid)

Sets the value of field 'spid'.

Parameters:

spid - the value of field 'spid'.

unmarshal

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

Method unmarshal

Parameters:

reader -

Returns:

Molecule

Throws:

MarshalException

ValidationException

validate

public void validate()
              throws ValidationException

Method validate

Throws:

ValidationException