Package ubic.gemma.persistence.service.association.coexpression

Class CoexpressionValueObject

  • All Implemented Interfaces:
    Serializable, Comparable<CoexpressionValueObject>
    public class CoexpressionValueObject
extends Object
implements Comparable<CoexpressionValueObject>, Serializable
    Lightweight/convenient object for manipulating coexpression for a pair of genes. Importantly, this does not necessarily reflect the coexpression data in the database: it may have been filtered in accordance to the query settings in terms of the data sets searched and the maximum number of results. Note that hashCode and equals do not use the ID of the coexpression; they only use the genes (ignoring which is query vs. found) and the sign, since those are in effect unique in the system.
    Author:
    Paul
    See Also:
    Serialized Form

    • Constructor Detail

      • CoexpressionValueObject

        public CoexpressionValueObject()

      • CoexpressionValueObject

        public CoexpressionValueObject​(Gene2GeneCoexpression g2g)
        Construct a value object. The "tested-in" component is not filled in, it must be done later.
        Parameters:
        g2g - g2g

      • CoexpressionValueObject

        protected CoexpressionValueObject​(Long queryGeneId,
                                  Long coexGeneId,
                                  Boolean positiveCorrelation,
                                  Integer support,
                                  Long supportDetailsId,
                                  Set<Long> supportingDatasets)

      • CoexpressionValueObject

        protected CoexpressionValueObject​(Long coexGeneId,
                                  String coexGeneSymbol,
                                  boolean positiveCorrelation,
                                  Long queryGeneId,
                                  String queryGeneSymbol,
                                  Integer support,
                                  Long supportDetailsId,
                                  Collection<Long> supportingDatasets,
                                  Collection<Long> testedInDatasets)

      • CoexpressionValueObject

        protected CoexpressionValueObject​(Long coexGeneId,
                                  String coexGeneSymbol,
                                  boolean positiveCorrelation,
                                  Long queryGeneId,
                                  String queryGeneSymbol,
                                  Integer support,
                                  Long supportDetailsId,
                                  Set<Long> supportingDatasets,
                                  Set<Long> testedInDatasets)

    • Method Detail

      • getCoexGeneId

        public Long getCoexGeneId()

      • getCoexGeneSymbol

        public String getCoexGeneSymbol()

      • setCoexGeneSymbol

        public void setCoexGeneSymbol​(String coexGeneSymbol)

      • getMaxResults

        public int getMaxResults()

      • getNumDatasetsSupporting

        public Integer getNumDatasetsSupporting()
        Returns:
        number of data sets this link was found in

      • getNumDatasetsTestedIn

        public Integer getNumDatasetsTestedIn()
        Returns:
        number of data sets this link was tested in, of -1 if the information was not retrieved or if the value is zero (which is basically an error).

      • getQueryGeneId

        public Long getQueryGeneId()

      • getQueryGeneSymbol

        public String getQueryGeneSymbol()

      • setQueryGeneSymbol

        public void setQueryGeneSymbol​(String queryGeneSymbol)

      • getQueryStringency

        public int getQueryStringency()

      • getSupportDetailsId

        public Long getSupportDetailsId()

      • getSupportingDatasets

        public Set<Long> getSupportingDatasets()
        Returns:
        the IDs of the supporting data sets; or an empty collection if the information was not retrieved

      • getTestedInDatasets

        public Set<Long> getTestedInDatasets()

      • hashCode

        public int hashCode()
        Overrides:
        hashCode in class Object

      • isEeConstraint

        public boolean isEeConstraint()

      • isFromCache

        public boolean isFromCache()

      • setFromCache

        public void setFromCache​(boolean fromCache)

      • isInterQueryLink

        public boolean isInterQueryLink()

      • setInterQueryLink

        public void setInterQueryLink​(boolean interQueryLink)

      • isPositiveCorrelation

        public boolean isPositiveCorrelation()