org.biopax.paxtools.model.level3
Interface Evidence

All Superinterfaces:

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

All Known Implementing Classes:

EvidenceImpl

public interface Evidence
extends UtilityClass, XReferrable

Definition: The support for a particular assertion, such as the existence of an interaction or pathway.

Usage: At least one of confidence, evidenceCode, or experimentalForm must be instantiated when creating an evidence instance. XREF may reference a publication describing the experimental evidence using a publicationXref or may store a description of the experiment in an experimental description database using a unificationXref (if the referenced experiment is the same) or relationshipXref (if it is not identical, but similar in some way e.g. similar in protocol). Evidence is meant to provide more information than just an xref to the source paper.

Examples: A description of a molecular binding assay that was used to detect a protein-protein interaction.

Nested Class Summary

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

BioPAXElement.Key

Field Summary

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

UNKNOWN_DOUBLE, UNKNOWN_FLOAT, UNKNOWN_INT

Method Summary

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.
java.util.Set<Score>	getConfidence() Confidence in the containing instance.
java.util.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'.
java.util.Set<ExperimentalForm>	getExperimentalForm() Contents of this set should not be modified.
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.

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, getModelInterface, getRDFId, isEquivalent

Method Detail

getConfidence

java.util.Set<Score> getConfidence()

Confidence in the containing instance. Usually a statistical measure.

Returns:

a set of scores representing confidence

addConfidence

void addConfidence(Score confidence)

Confidence in the containing instance. Usually a statistical measure.

Parameters:

confidence - a new confidence measure to add

removeConfidence

void removeConfidence(Score confidence)

Confidence in the containing instance. Usually a statistical measure.

Parameters:

confidence - a confidence measure to be removed.

getEvidenceCode

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

Returns:

a set of evidence codes for this evidence type.

addEvidenceCode

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'.

Parameters:

evidenceCode - a new evidence code for this evidence.

removeEvidenceCode

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'.

Parameters:

evidenceCode - to be removed

getExperimentalForm

java.util.Set<ExperimentalForm> getExperimentalForm()

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

Returns:

The experimental forms associated with an evidence instance.

addExperimentalForm

void addExperimentalForm(ExperimentalForm experimentalForm)

Adds an experimental form.

Parameters:

experimentalForm - associated with an evidence instance.

removeExperimentalForm

void removeExperimentalForm(ExperimentalForm experimentalForm)

Removes an experimental form.

Parameters:

experimentalForm - associated with an evidence instance.