Package 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
public class EvidenceImpl extends XReferrableImpl implements Evidence
See Also:

  • Constructor Details

    • EvidenceImpl

      public EvidenceImpl()
      Constructor.

  • Method Details

    • 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

    • 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.

    • 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.

    • 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; compare ExperimentalForm and Confidence values; or - simply always return false!
      Overrides:
      semanticallyEquivalent in class BioPAXElementImpl