Package ubic.gemma.model.association.coexpression

Class GeneCoexpressionNodeDegreeValueObject

java.lang.Object
ubic.gemma.model.association.coexpression.GeneCoexpressionNodeDegreeValueObject
All Implemented Interfaces:
Serializable
public class GeneCoexpressionNodeDegreeValueObject extends Object implements Serializable
Represents a GeneCoexpressionNodeDegree
Author:
Paul
See Also:

  • Constructor Details

    • GeneCoexpressionNodeDegreeValueObject

      public GeneCoexpressionNodeDegreeValueObject()

    • GeneCoexpressionNodeDegreeValueObject

      public GeneCoexpressionNodeDegreeValueObject(GeneCoexpressionNodeDegree entity)

  • Method Details

    • asDoubleArrayNegRanks

      public double[] asDoubleArrayNegRanks()

    • asDoubleArrayPosRanks

      public double[] asDoubleArrayPosRanks()

    • asIntArrayNeg

      public int[] asIntArrayNeg()
      Returns:
      counts at each level of support, starting from 0 (which will be 0), up to the maximum support.

    • asIntArrayPos

      public int[] asIntArrayPos()
      Returns:
      counts at each level of support, starting from 0 (which will be 0), up to the maximum support.

    • getGeneId

      public Long getGeneId()

    • getLinksWithExactSupport

      public Integer getLinksWithExactSupport(Integer support, boolean positive)
      Parameters:
      support - value
      positive - positive
      Returns:
      how many links have this much support (specifically).

    • getLinksWithMinimumSupport

      public Integer getLinksWithMinimumSupport(int i)
      Parameters:
      i - support
      Returns:
      total number of links (this is just the total of positive and negative; if some of those are with the same genes it's a double count, sorry)

    • getLinksWithMinimumSupport

      public Integer getLinksWithMinimumSupport(Integer support, boolean positive)
      Parameters:
      support - threshold
      positive - positive
      Returns:
      how many links have at least this much support (cumulative)

    • getMaxSupportNeg

      public int getMaxSupportNeg()

    • getMaxSupportPos

      public int getMaxSupportPos()
      Returns:
      the largest value for support for this gene

    • getRankAtMinimumSupport

      public Double getRankAtMinimumSupport(Integer support, boolean positive)

    • hashCode

      public int hashCode()
      Overrides:
      hashCode in class Object

    • equals

      public boolean equals(Object obj)
      Overrides:
      equals in class Object

    • toString

      public String toString()
      Overrides:
      toString in class Object

    • increment

      public void increment(Integer support, boolean positive)

    • total

      public int total()
      Equivalent to getLinksWithMinimumSupport( 0 )
      Returns:
      how many links this gene has in total, across all levels of support (positive and negative correlations combined)

    • clear

      public void clear()
      Used during recomputation only.

    • toEntity

      public GeneCoexpressionNodeDegree toEntity()