org.biopax.paxtools.impl.level3

Class SmallMoleculeReferenceImpl

java.lang.Object

org.biopax.paxtools.impl.BioPAXElementImpl

org.biopax.paxtools.impl.level3.L3ElementImpl

org.biopax.paxtools.impl.level3.XReferrableImpl

org.biopax.paxtools.impl.level3.NamedImpl

org.biopax.paxtools.impl.level3.EntityReferenceImpl

org.biopax.paxtools.impl.level3.SmallMoleculeReferenceImpl

All Implemented Interfaces:

Serializable, Cloneable, BioPAXElement, EntityReference, Level3Element, Named, Observable, SmallMoleculeReference, UtilityClass, XReferrable

@Entity
 @Indexed
public class SmallMoleculeReferenceImpl
extends EntityReferenceImpl
implements SmallMoleculeReference

See Also:

Serialized Form

Field Summary

Fields inherited from class org.biopax.paxtools.impl.BioPAXElementImpl

FIELD_AVAILABILITY, FIELD_COMMENT, FIELD_DATASOURCE, FIELD_ECNUMBER, FIELD_KEYWORD, FIELD_NAME, FIELD_ORGANISM, FIELD_PATHWAY, FIELD_SEQUENCE, FIELD_TERM, FIELD_XREFDB, FIELD_XREFID, FILTER_BY_DATASOURCE, FILTER_BY_ORGANISM

Fields inherited from interface org.biopax.paxtools.model.BioPAXElement

UNKNOWN_DOUBLE, UNKNOWN_FLOAT, UNKNOWN_INT

Constructor Summary

Constructors

Constructor and Description
SmallMoleculeReferenceImpl()

Method Summary

Modifier and Type	Method and Description
String	getChemicalFormula()
Class<? extends SmallMoleculeReference>	getModelInterface() This method returns the actual model interface that a class implements.
float	getMolecularWeight()
ChemicalStructure	getStructure()
protected boolean	semanticallyEquivalent(BioPAXElement element)
void	setChemicalFormula(String formula)
void	setMolecularWeight(float molecularWeight)
void	setStructure(ChemicalStructure structure)

Methods inherited from class org.biopax.paxtools.impl.level3.EntityReferenceImpl

addEntityFeature, addEntityReferenceType, addEvidence, addMemberEntityReference, getEntityFeature, getEntityReferenceOf, getEntityReferenceType, getEvidence, getMemberEntityReference, getMemberEntityReferenceOf, removeEntityFeature, removeEntityReferenceType, removeEvidence, removeMemberEntityReference, setEntityFeature, setEntityReferenceOf, setEntityReferenceType, setEvidence, setMemberEntity, setMemberEntityReference, setMemberEntityReferenceOf

Methods inherited from class org.biopax.paxtools.impl.level3.NamedImpl

addName, getDisplayName, getDisplayNameX, getName, getStandardName, getStandardNameX, removeName, setDisplayName, setDisplayNameX, setName, setStandardName, setStandardNameX

Methods inherited from class org.biopax.paxtools.impl.level3.XReferrableImpl

addXref, equivalenceCode, getXref, removeXref, setXref

Methods inherited from class org.biopax.paxtools.impl.level3.L3ElementImpl

addComment, getComment, getDatasources, getKeywords, getOrganisms, getParentPathways, removeComment, setComment

Methods inherited from class org.biopax.paxtools.impl.BioPAXElementImpl

equals, getAnnotations, getPk, getRDFId, hashCode, isEquivalent, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.biopax.paxtools.model.level3.EntityReference

addEntityFeature, addEntityReferenceType, addMemberEntityReference, getEntityFeature, getEntityReferenceOf, getEntityReferenceType, getMemberEntityReference, getMemberEntityReferenceOf, removeEntityFeature, removeEntityReferenceType, removeMemberEntityReference

Methods inherited from interface org.biopax.paxtools.model.level3.Named

addName, getDisplayName, getName, getStandardName, removeName, setDisplayName, setName, setStandardName

Methods inherited from interface org.biopax.paxtools.model.level3.XReferrable

addXref, getXref, removeXref

Methods inherited from interface org.biopax.paxtools.model.level3.Level3Element

addComment, getComment, removeComment

Methods inherited from interface org.biopax.paxtools.model.BioPAXElement

equivalenceCode, getAnnotations, getRDFId, isEquivalent

Methods inherited from interface org.biopax.paxtools.model.level3.Observable

addEvidence, getEvidence, removeEvidence

Constructor Detail

SmallMoleculeReferenceImpl

public SmallMoleculeReferenceImpl()

Method Detail

getModelInterface

public Class<? extends SmallMoleculeReference> getModelInterface()

Description copied from interface: BioPAXElement

This method returns the actual model interface that a class implements.

Specified by:

getModelInterface in interface BioPAXElement

Overrides:

getModelInterface in class EntityReferenceImpl

Returns:

an interface from org.biopax.paxtools.model package corresponding to a BioPAX class.

getChemicalFormula

@Field(name="keyword",
       store=YES,
       analyze=YES)
 @Boost(value=1.100000023841858f)
public String getChemicalFormula()

Specified by:

getChemicalFormula in interface SmallMoleculeReference

setChemicalFormula

public void setChemicalFormula(String formula)

Specified by:

setChemicalFormula in interface SmallMoleculeReference

getMolecularWeight

public float getMolecularWeight()

Specified by:

getMolecularWeight in interface SmallMoleculeReference

setMolecularWeight

public void setMolecularWeight(float molecularWeight)

Specified by:

setMolecularWeight in interface SmallMoleculeReference

getStructure

public ChemicalStructure getStructure()

Specified by:

getStructure in interface SmallMoleculeReference

setStructure

public void setStructure(ChemicalStructure structure)

Specified by:

setStructure in interface SmallMoleculeReference

semanticallyEquivalent

protected boolean semanticallyEquivalent(BioPAXElement element)

Overrides:

semanticallyEquivalent in class BioPAXElementImpl