biouml.standard.type
Class SpecieReference

java.lang.Object
  com.beanexplorer.beans.Option
      ru.biosoft.access.MutableDataElementSupport
          biouml.standard.type.BaseSupport
              biouml.standard.type.GenericEntity
                  biouml.standard.type.SpecieReference

All Implemented Interfaces:

Base, DataElement, FormulaDelegate, MutableDataElement, Relation, SerializableAsText, Type

public class SpecieReference

extends GenericEntity

implements Relation, FormulaDelegate, SerializableAsText

SpecieReference specifies role of molecule involved in the Reaction.

Pendung:

is it property names clear and correct?

Field Summary

static java.lang.String	ACTION_CATALYST
static java.lang.String	ACTION_INHIBITOR
static java.lang.String	ACTION_SWITCH_OFF
static java.lang.String	ACTION_SWITCH_ON
protected static org.apache.log4j.Category	log
static java.lang.String	MODIFIER
protected java.lang.String	modifierAction Specifies the modifier action.
static java.lang.String	OTHER
static java.lang.String	PRODUCT
static java.lang.String	REACTANT
protected java.lang.String	specie Complete name of specie relative the module.
protected java.lang.String	stoichiometry Specifies the involved molecule stoichiometry.

Fields inherited from class biouml.standard.type.GenericEntity

comment

Fields inherited from class biouml.standard.type.BaseSupport

title, type

Fields inherited from class ru.biosoft.access.MutableDataElementSupport

name

Fields inherited from class com.beanexplorer.beans.Option

notificationEnabled, propagationEnabled

Fields inherited from interface biouml.standard.type.Relation

PARTICIPATION_DIRECT, PARTICIPATION_INDIRECT, PARTICIPATION_UNKNOWN

Fields inherited from interface biouml.standard.type.Type

CONSTANT, DATABASE_INFO, DIAGRAM_INFO, MATH, MATH_EQUATION, MATH_EVENT, MATH_FUNCTION, MATH_STATE, MATH_TRANSITION, TYPE_CELL, TYPE_CHEMICAL_ROLE, TYPE_COMPARTMENT, TYPE_CONCEPT, TYPE_DIAGRAM_REFERENCE, TYPE_FUNCTION, TYPE_GENE, TYPE_MOLECULE, TYPE_NOTE, TYPE_NOTE_LINK, TYPE_PROCESS, TYPE_PROTEIN, TYPE_REACTION, TYPE_RELATION, TYPE_RNA, TYPE_SEMANTIC_RELATION, TYPE_STATE, TYPE_SUBSTANCE, TYPE_UNKNOWN

Constructor Summary

SpecieReference(DataCollection origin, java.lang.String name)

SpecieReference(DataCollection origin, java.lang.String name, java.lang.String role)

SpecieReference(java.lang.String descr)

Method Summary

SpecieReference	clone(DataCollection origin, java.lang.String name)
java.lang.String	getAsText()
java.lang.String	getFormula()
java.lang.String	getModifierAction()
java.lang.String	getParticipation()
java.lang.String	getRole()
java.lang.String	getSpecie()
java.lang.String	getStoichiometry()
java.lang.String	getType()
boolean	isReactantOrProduct() Used in BeanInfo to disable editing of modifierAction property for reactant or product specie.
void	setModifierAction(java.lang.String modifierAction)
void	setParticipation(java.lang.String participation)
void	setRole(java.lang.String role)
void	setSpecie(java.lang.String specie)
void	setStoichiometry(java.lang.String stoichiometry)

Methods inherited from class biouml.standard.type.GenericEntity

getComment, getDate, setComment, setDate

Methods inherited from class biouml.standard.type.BaseSupport

getTitle, setTitle

Methods inherited from class ru.biosoft.access.MutableDataElementSupport

getName, getOrigin, toString

Methods inherited from class com.beanexplorer.beans.Option

addPropertyChangeListener, copyListenersTo, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getParent, isNotificationEnabled, isPropagationEnabled, removePropertyChangeListener, setNotificationEnabled, setParent, setPropagationEnabled

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface biouml.standard.type.Base

getTitle

Methods inherited from interface ru.biosoft.access.DataElement

getName, getOrigin

Methods inherited from interface biouml.model.dynamics.FormulaDelegate

addPropertyChangeListener, removePropertyChangeListener

Methods inherited from interface ru.biosoft.access.MutableDataElement

addPropertyChangeListener, removePropertyChangeListener

Field Detail

log

protected static org.apache.log4j.Category log

specie

protected java.lang.String specie

Complete name of specie relative the module.

REACTANT

public static final java.lang.String REACTANT

See Also:

Constant Field Values

PRODUCT

public static final java.lang.String PRODUCT

See Also:

Constant Field Values

MODIFIER

public static final java.lang.String MODIFIER

See Also:

Constant Field Values

OTHER

public static final java.lang.String OTHER

See Also:

Constant Field Values

stoichiometry

protected java.lang.String stoichiometry

Specifies the involved molecule stoichiometry.

ACTION_CATALYST

public static final java.lang.String ACTION_CATALYST

See Also:

Constant Field Values

ACTION_INHIBITOR

public static final java.lang.String ACTION_INHIBITOR

See Also:

Constant Field Values

ACTION_SWITCH_ON

public static final java.lang.String ACTION_SWITCH_ON

See Also:

Constant Field Values

ACTION_SWITCH_OFF

public static final java.lang.String ACTION_SWITCH_OFF

See Also:

Constant Field Values

modifierAction

protected java.lang.String modifierAction

Specifies the modifier action. This value is needed only if role is MODIFIER, othervise it should be empty.

Constructor Detail

SpecieReference

public SpecieReference(DataCollection origin,
                       java.lang.String name)

SpecieReference

public SpecieReference(DataCollection origin,
                       java.lang.String name,
                       java.lang.String role)

SpecieReference

public SpecieReference(java.lang.String descr)

Method Detail

getAsText

public java.lang.String getAsText()

Specified by:

getAsText in interface SerializableAsText

clone

public SpecieReference clone(DataCollection origin,
                             java.lang.String name)

getType

public java.lang.String getType()

Specified by:

getType in interface Base

Overrides:

getType in class BaseSupport

getSpecie

public java.lang.String getSpecie()

setSpecie

public void setSpecie(java.lang.String specie)

getRole

public java.lang.String getRole()

setRole

public void setRole(java.lang.String role)

isReactantOrProduct

public boolean isReactantOrProduct()

Used in BeanInfo to disable editing of modifierAction property for reactant or product specie.

getStoichiometry

public java.lang.String getStoichiometry()

setStoichiometry

public void setStoichiometry(java.lang.String stoichiometry)

getModifierAction

public java.lang.String getModifierAction()

setModifierAction

public void setModifierAction(java.lang.String modifierAction)

getParticipation

public java.lang.String getParticipation()

Specified by:

getParticipation in interface Relation

setParticipation

public void setParticipation(java.lang.String participation)

getFormula

public java.lang.String getFormula()

Specified by:

getFormula in interface FormulaDelegate