@Entity @Indexed public class EvidenceImpl extends XReferrableImpl implements Evidence
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
UNKNOWN_DOUBLE, UNKNOWN_FLOAT, UNKNOWN_INT
Constructor and Description |
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EvidenceImpl()
Constructor.
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Modifier and Type | Method and Description |
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void |
addConfidence(Score confidence)
Confidence in the containing instance.
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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'.
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void |
addExperimentalForm(ExperimentalForm experimentalForm)
Adds an experimental form.
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Set<Score> |
getConfidence()
Confidence in the containing instance.
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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'.
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Set<ExperimentalForm> |
getExperimentalForm()
Contents of this set should not be modified.
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Class<? extends Evidence> |
getModelInterface()
This method returns the actual model interface that a class implements.
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void |
removeConfidence(Score confidence)
Confidence in the containing instance.
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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'.
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void |
removeExperimentalForm(ExperimentalForm experimentalForm)
Removes an experimental form.
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protected boolean |
semanticallyEquivalent(BioPAXElement element)
Answers whether two Evidence objects are semantically equivalent.
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void |
setConfidence(Set<Score> confidence)
Confidence in the containing instance.
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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'.
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void |
setExperimentalForm(Set<ExperimentalForm> experimentalForm) |
addXref, equivalenceCode, getXref, removeXref, setXref
addComment, getComment, getDatasources, getKeywords, getOrganisms, getParentPathways, removeComment, setComment
equals, getAnnotations, getPk, getRDFId, hashCode, isEquivalent, toString
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
addXref, getXref, removeXref
addComment, getComment, removeComment
equivalenceCode, getAnnotations, getRDFId, isEquivalent
public EvidenceImpl()
public Class<? extends Evidence> getModelInterface()
BioPAXElement
getModelInterface
in interface BioPAXElement
org.biopax.paxtools.model
package
corresponding to a BioPAX class.public Set<Score> getConfidence()
getConfidence
in interface Evidence
public void setConfidence(Set<Score> confidence)
confidence
- a set of scores representing confidencepublic void addConfidence(Score confidence)
addConfidence
in interface Evidence
confidence
- a new confidence measure to addpublic void removeConfidence(Score confidence)
removeConfidence
in interface Evidence
confidence
- a confidence measure to be removed.public Set<EvidenceCodeVocabulary> getEvidenceCode()
getEvidenceCode
in interface Evidence
public void setEvidenceCode(Set<EvidenceCodeVocabulary> evidenceCode)
evidenceCode
- a new set of evidence codes for this evidence type.public void addEvidenceCode(EvidenceCodeVocabulary evidenceCode)
addEvidenceCode
in interface Evidence
evidenceCode
- a new evidence code for this evidence.public void removeEvidenceCode(EvidenceCodeVocabulary evidenceCode)
removeEvidenceCode
in interface Evidence
evidenceCode
- to be removedpublic Set<ExperimentalForm> getExperimentalForm()
Evidence
getExperimentalForm
in interface Evidence
public void setExperimentalForm(Set<ExperimentalForm> experimentalForm)
public void addExperimentalForm(ExperimentalForm experimentalForm)
Evidence
addExperimentalForm
in interface Evidence
experimentalForm
- associated with an evidence instance.public void removeExperimentalForm(ExperimentalForm experimentalForm)
Evidence
removeExperimentalForm
in interface Evidence
experimentalForm
- associated with an evidence instance.protected boolean semanticallyEquivalent(BioPAXElement element)
semanticallyEquivalent
in class BioPAXElementImpl
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