org.biopax.paxtools.impl.level3
Class BioSourceImpl

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.BioSourceImpl

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, BioPAXElement, BioSource, Level3Element, Named, UtilityClass, XReferrable

@Entity
@Indexed
public class BioSourceImpl
extends NamedImpl
implements BioSource

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from interface org.biopax.paxtools.model.BioPAXElement

BioPAXElement.Key

Field Summary

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

SEARCH_FIELD_AVAILABILITY, SEARCH_FIELD_COMMENT, SEARCH_FIELD_EC_NUMBER, SEARCH_FIELD_KEYWORD, SEARCH_FIELD_NAME, SEARCH_FIELD_SEQUENCE, SEARCH_FIELD_TERM, SEARCH_FIELD_XREF_DB, SEARCH_FIELD_XREF_ID, SEARCH_INDEX_NAME

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

UNKNOWN_DOUBLE, UNKNOWN_FLOAT, UNKNOWN_INT

Constructor Summary

BioSourceImpl()

Method Summary

int	equivalenceCode() If two elements are equivalent, then their equivalence code should be the same.
CellVocabulary	getCellType() A cell type, e.g.
java.lang.Class<? extends BioSource>	getModelInterface() This method returns the actual model interface that a class implements.
TissueVocabulary	getTissue() An external controlled vocabulary of tissue types.
protected boolean	semanticallyEquivalent(BioPAXElement element)
void	setCellType(CellVocabulary celltype) A cell type, e.g.
void	setTissue(TissueVocabulary tissue) An external controlled vocabulary of tissue types.
java.lang.String	toString()

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

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

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

addXref, getXref, hasCommonUnificationXref, removeXref, setXref

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

addComment, getComment, removeComment, setComment

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

getAnnotations, getProxyId, getRDFId, getVersion, isEquivalent, setProxyId, setRDFId, setVersion

Methods inherited from class java.lang.Object

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

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

addName, getDisplayName, getName, getStandardName, removeName, setDisplayName, 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

getAnnotations, getRDFId, isEquivalent

Constructor Detail

BioSourceImpl

public BioSourceImpl()

Method Detail

getModelInterface

public java.lang.Class<? extends BioSource> 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 XReferrableImpl

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 XReferrableImpl

Returns:

an integer that is same across all equivalent entities.

getCellType

public CellVocabulary getCellType()

Description copied from interface: BioSource

A cell type, e.g. 'HeLa'. This should reference a term in a controlled vocabulary of cell types. Best practice is to refer to OBOCell Ontology.

Specified by:

getCellType in interface BioSource

Returns:

cell type if this biosource is a cell line or a specific tissue. Null otherwise.

setCellType

public void setCellType(CellVocabulary celltype)

Description copied from interface: BioSource

A cell type, e.g. 'HeLa'. This should reference a term in a controlled vocabulary of cell types. Best practice is to refer to OBOCell Ontology.

Specified by:

setCellType in interface BioSource

Parameters:

celltype - if this biosource is a cell line or a specific tissue. Null for n/a.

getTissue

public TissueVocabulary getTissue()

Description copied from interface: BioSource

An external controlled vocabulary of tissue types. A reference to the BRENDA

Specified by:

getTissue in interface BioSource

Returns:

An external controlled vocabulary of tissue types.

setTissue

public void setTissue(TissueVocabulary tissue)

Description copied from interface: BioSource

An external controlled vocabulary of tissue types. A reference to the BRENDA

Specified by:

setTissue in interface BioSource

Parameters:

tissue - An external controlled vocabulary of tissue types.

toString

public java.lang.String toString()

Overrides:

toString in class BioPAXElementImpl