Package de.julielab.jules.ae.genemapping.genemodel

Class GeneSet

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      boolean equals​(java.lang.Object obj)  
      cc.mallet.types.FeatureVector getFeatureVector()  
      cc.mallet.types.Instance getInstance()  
      java.lang.String getRepresentationText()
      Returns the text of any gene mention in this set or null, if the set is empty.
      java.util.List<SynHit> getSetId()
      The set ID represent the gene ID that all elements in the set belong to
      GeneMention.SpecificType getSpecificType()  
      double getSpecificTypeConfidence()  
      int hashCode()  
      boolean isPlural()  
      void setFeatureVector​(cc.mallet.types.FeatureVector featureVector)  
      void setInstance​(cc.mallet.types.Instance instance)  
      void setPlural​(boolean isPlural)  
      void setSetId​(java.util.List<SynHit> setId)  
      void setSpecificType​(GeneMention.SpecificType specificType)  
      void setSpecificTypeConfidence​(double specificTypeConfidence)  

      • Methods inherited from class java.util.HashSet

        add, clear, clone, contains, isEmpty, iterator, remove, size, spliterator

      • Methods inherited from class java.util.AbstractSet

        removeAll

      • Methods inherited from class java.util.AbstractCollection

        addAll, containsAll, retainAll, toArray, toArray, toString

      • Methods inherited from class java.lang.Object

        finalize, getClass, notify, notifyAll, wait, wait, wait

      • Methods inherited from interface java.util.Collection

        parallelStream, removeIf, stream, toArray

      • Methods inherited from interface java.lang.Iterable

        forEach

      • Methods inherited from interface java.util.Set

        addAll, containsAll, removeAll, retainAll, toArray, toArray

    • Constructor Detail

      • GeneSet

        public GeneSet​(java.util.HashSet<GeneMention> genes,
               java.util.List<SynHit> setId)

      • GeneSet

        public GeneSet()

    • Method Detail

      • getInstance

        public cc.mallet.types.Instance getInstance()

      • setInstance

        public void setInstance​(cc.mallet.types.Instance instance)

      • getSetId

        public java.util.List<SynHit> getSetId()
        The set ID represent the gene ID that all elements in the set belong to
        Returns:
        The ID of the elements in this set.

      • setSetId

        public void setSetId​(java.util.List<SynHit> setId)

      • hashCode

        public int hashCode()
        Specified by:
        hashCode in interface java.util.Collection<GeneMention>
        Specified by:
        hashCode in interface java.util.Set<GeneMention>
        Overrides:
        hashCode in class java.util.AbstractSet<GeneMention>

      • equals

        public boolean equals​(java.lang.Object obj)
        Specified by:
        equals in interface java.util.Collection<GeneMention>
        Specified by:
        equals in interface java.util.Set<GeneMention>
        Overrides:
        equals in class java.util.AbstractSet<GeneMention>

      • getRepresentationText

        public java.lang.String getRepresentationText()
        Returns the text of any gene mention in this set or null, if the set is empty.
        Returns:
        Any gene mention text of this set.

      • getFeatureVector

        public cc.mallet.types.FeatureVector getFeatureVector()

      • setFeatureVector

        public void setFeatureVector​(cc.mallet.types.FeatureVector featureVector)

      • isPlural

        public boolean isPlural()

      • setPlural

        public void setPlural​(boolean isPlural)

      • getSpecificTypeConfidence

        public double getSpecificTypeConfidence()

      • setSpecificTypeConfidence

        public void setSpecificTypeConfidence​(double specificTypeConfidence)