org.biopax.paxtools.impl.level3

Class EvidenceImpl

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.EvidenceImpl

All Implemented Interfaces:

Serializable, Cloneable, BioPAXElement, Evidence, Level3Element, UtilityClass, XReferrable

@Entity
 @Indexed
public class EvidenceImpl
extends XReferrableImpl
implements Evidence

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
EvidenceImpl() Constructor.

Method Summary

Modifier and Type	Method and Description
void	addConfidence(Score confidence) Confidence in the containing instance.
void	addEvidenceCode(EvidenceCodeVocabulary evidenceCode) A pointer to a term in an external controlled vocabulary, such as the GO, PSI-MI or BioCyc evidence codes, that describes the nature of the support, such as 'traceable author statement' or 'yeast two-hybrid'.
void	addExperimentalForm(ExperimentalForm experimentalForm) Adds an experimental form.
Set<Score>	getConfidence() Confidence in the containing instance.
Set<EvidenceCodeVocabulary>	getEvidenceCode() A pointer to a term in an external controlled vocabulary, such as the GO, PSI-MI or BioCyc evidence codes, that describes the nature of the support, such as 'traceable author statement' or 'yeast two-hybrid'.
Set<ExperimentalForm>	getExperimentalForm() Contents of this set should not be modified.
Class<? extends Evidence>	getModelInterface() This method returns the actual model interface that a class implements.
void	removeConfidence(Score confidence) Confidence in the containing instance.
void	removeEvidenceCode(EvidenceCodeVocabulary evidenceCode) A pointer to a term in an external controlled vocabulary, such as the GO, PSI-MI or BioCyc evidence codes, that describes the nature of the support, such as 'traceable author statement' or 'yeast two-hybrid'.
void	removeExperimentalForm(ExperimentalForm experimentalForm) Removes an experimental form.
protected boolean	semanticallyEquivalent(BioPAXElement element) Answers whether two Evidence objects are semantically equivalent.
void	setConfidence(Set<Score> confidence) Confidence in the containing instance.
void	setEvidenceCode(Set<EvidenceCodeVocabulary> evidenceCode) A pointer to a term in an external controlled vocabulary, such as the GO, PSI-MI or BioCyc evidence codes, that describes the nature of the support, such as 'traceable author statement' or 'yeast two-hybrid'.
void	setExperimentalForm(Set<ExperimentalForm> experimentalForm)

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.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

Constructor Detail

EvidenceImpl

public EvidenceImpl()

Constructor.

Method Detail

getModelInterface

public Class<? extends Evidence> 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.

getConfidence

public Set<Score> getConfidence()

Confidence in the containing instance. Usually a statistical measure.

Specified by:

getConfidence in interface Evidence

Returns:

a set of scores representing confidence

setConfidence

public void setConfidence(Set<Score> confidence)

Confidence in the containing instance. Usually a statistical measure. WARNING: This method should only be used for batch operations and with care. For regular manipulation use add/remove instead.

Parameters:

confidence - a set of scores representing confidence

addConfidence

public void addConfidence(Score confidence)

Confidence in the containing instance. Usually a statistical measure.

Specified by:

addConfidence in interface Evidence

Parameters:

confidence - a new confidence measure to add

removeConfidence

public void removeConfidence(Score confidence)

Confidence in the containing instance. Usually a statistical measure.

Specified by:

removeConfidence in interface Evidence

Parameters:

confidence - a confidence measure to be removed.

getEvidenceCode

public Set<EvidenceCodeVocabulary> getEvidenceCode()

A pointer to a term in an external controlled vocabulary, such as the GO, PSI-MI or BioCyc evidence codes, that describes the nature of the support, such as 'traceable author statement' or 'yeast two-hybrid'.

Specified by:

getEvidenceCode in interface Evidence

Returns:

a set of evidence codes for this evidence type.

setEvidenceCode

public void setEvidenceCode(Set<EvidenceCodeVocabulary> evidenceCode)

A pointer to a term in an external controlled vocabulary, such as the GO, PSI-MI or BioCyc evidence codes, that describes the nature of the support, such as 'traceable author statement' or 'yeast two-hybrid'. WARNING: This method should only be used for batch operations and with care. For regular manipulation use add/remove instead.

Parameters:

evidenceCode - a new set of evidence codes for this evidence type.

addEvidenceCode

public void addEvidenceCode(EvidenceCodeVocabulary evidenceCode)

A pointer to a term in an external controlled vocabulary, such as the GO, PSI-MI or BioCyc evidence codes, that describes the nature of the support, such as 'traceable author statement' or 'yeast two-hybrid'.

Specified by:

addEvidenceCode in interface Evidence

Parameters:

evidenceCode - a new evidence code for this evidence.

removeEvidenceCode

public void removeEvidenceCode(EvidenceCodeVocabulary evidenceCode)

A pointer to a term in an external controlled vocabulary, such as the GO, PSI-MI or BioCyc evidence codes, that describes the nature of the support, such as 'traceable author statement' or 'yeast two-hybrid'.

Specified by:

removeEvidenceCode in interface Evidence

Parameters:

evidenceCode - to be removed

getExperimentalForm

public Set<ExperimentalForm> getExperimentalForm()

Description copied from interface: Evidence

Contents of this set should not be modified. Use add/remove methods instead.

Specified by:

getExperimentalForm in interface Evidence

Returns:

The experimental forms associated with an evidence instance.

setExperimentalForm

public void setExperimentalForm(Set<ExperimentalForm> experimentalForm)

addExperimentalForm

public void addExperimentalForm(ExperimentalForm experimentalForm)

Description copied from interface: Evidence

Adds an experimental form.

Specified by:

addExperimentalForm in interface Evidence

Parameters:

experimentalForm - associated with an evidence instance.

removeExperimentalForm

public void removeExperimentalForm(ExperimentalForm experimentalForm)

Description copied from interface: Evidence

Removes an experimental form.

Specified by:

removeExperimentalForm in interface Evidence

Parameters:

experimentalForm - associated with an evidence instance.

semanticallyEquivalent

protected boolean semanticallyEquivalent(BioPAXElement element)

Answers whether two Evidence objects are semantically equivalent. (Currently, it considers only member UnificationXrefs and EvidenceCodeVocabularies for comparison...) TODO: review; add comparing ExperimentalForm and Confidence values...

Overrides:

semanticallyEquivalent in class BioPAXElementImpl