org.biopax.paxtools.impl.level3

Class ChemicalStructureImpl

java.lang.Object

org.biopax.paxtools.impl.BioPAXElementImpl

org.biopax.paxtools.impl.level3.L3ElementImpl

org.biopax.paxtools.impl.level3.ChemicalStructureImpl

All Implemented Interfaces:

Serializable, Cloneable, BioPAXElement, ChemicalStructure, Level3Element, UtilityClass

@Entity
 @Indexed
public class ChemicalStructureImpl
extends L3ElementImpl
implements ChemicalStructure

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
ChemicalStructureImpl()

Method Summary

Modifier and Type	Method and Description
int	equivalenceCode() If two elements are equivalent, then their equivalence code should be the same.
Class<? extends ChemicalStructure>	getModelInterface() This method returns the actual model interface that a class implements.
String	getStructureData() This property holds a string defining chemical structure,in one of the three formats: CML, SMILES or InChI.
StructureFormatType	getStructureFormat() This property specifies which format is used to define chemical structure.
protected boolean	semanticallyEquivalent(BioPAXElement element)
void	setStructureData(String structureData) This property holds a string of data defining chemical structure,in one of the three formats: CML, SMILES or InChI.
void	setStructureFormat(StructureFormatType structureFormat) This property specifies which format is used to define chemical structure.

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.Level3Element

addComment, getComment, removeComment

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

getAnnotations, getRDFId, isEquivalent

Constructor Detail

ChemicalStructureImpl

public ChemicalStructureImpl()

Method Detail

getModelInterface

public Class<? extends ChemicalStructure> getModelInterface()

Description copied from interface: BioPAXElement

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

Specified by:

getModelInterface in interface BioPAXElement

Returns:

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

semanticallyEquivalent

protected boolean semanticallyEquivalent(BioPAXElement element)

Overrides:

semanticallyEquivalent in class BioPAXElementImpl

equivalenceCode

public int equivalenceCode()

Description copied from interface: BioPAXElement

If two elements are equivalent, then their equivalence code should be the same.

Specified by:

equivalenceCode in interface BioPAXElement

Overrides:

equivalenceCode in class BioPAXElementImpl

Returns:

an integer that is same across all equivalent entities.

getStructureData

@Field(name="keyword",
       analyze=YES)
public String getStructureData()

Description copied from interface: ChemicalStructure

This property holds a string defining chemical structure,in one of the three formats: CML, SMILES or InChI. If, for example,the CML format is used, then the value of this property is a string containing the XML encoding of the CML data.

Specified by:

getStructureData in interface ChemicalStructure

Returns:

a string defining chemical structure

setStructureData

public void setStructureData(String structureData)

Description copied from interface: ChemicalStructure

This property holds a string of data defining chemical structure,in one of the three formats: CML, SMILES or InChI. If, for example,the CML format is used, then the value of this property is a string containing the XML encoding of the CML data.

Specified by:

setStructureData in interface ChemicalStructure

Parameters:

structureData - a string defining chemical structure

getStructureFormat

@Field(name="keyword",
       analyze=YES)
public StructureFormatType getStructureFormat()

Description copied from interface: ChemicalStructure

This property specifies which format is used to define chemical structure.

Specified by:

getStructureFormat in interface ChemicalStructure

Returns:

format used to define chemical structure

setStructureFormat

public void setStructureFormat(StructureFormatType structureFormat)

Description copied from interface: ChemicalStructure

This property specifies which format is used to define chemical structure.

Specified by:

setStructureFormat in interface ChemicalStructure

Parameters:

structureFormat - format used to define chemical structure