Package ubic.gemma.model.association

Class BioSequence2GeneProduct

java.lang.Object
ubic.gemma.model.common.AbstractIdentifiable
ubic.gemma.model.association.BioSequence2GeneProduct
All Implemented Interfaces:
Identifiable
Direct Known Subclasses:
AnnotationAssociation, BlatAssociation, ReferenceAssociation
public abstract class BioSequence2GeneProduct extends AbstractIdentifiable
An association between a BioSequence and a Gene Product. This class is abstract and is variously subclassed with BlatAssociation in order to capture the scores and other parameters that document why we think there is a connection between a given sequence and a gene product.

  • Constructor Details

    • BioSequence2GeneProduct

      public BioSequence2GeneProduct()

  • Method Details

    • getBioSequence

      public BioSequence getBioSequence()

    • setBioSequence

      public void setBioSequence(BioSequence bioSequence)

    • getGeneProduct

      public GeneProduct getGeneProduct()
      Returns:
      A collection of GeneProducts that this BioSequence2GeneProduct corresponds to. A BioSequence can align to one or more GeneProducts.

    • setGeneProduct

      public void setGeneProduct(GeneProduct geneProduct)

    • getOverlap

      public Integer getOverlap()
      Returns:
      Degree to which the sequence overlaps with the gene product. This is often the overlap of a DNA sequence with the exons encoding the mRNA for the GeneProduct, but could have other interpretations

    • setOverlap

      public void setOverlap(Integer overlap)

    • getScore

      public Double getScore()
      Returns:
      The score for the association between the biosequence and the gene product. This could be a BLAT similarity or other score.

    • setScore

      public void setScore(Double score)

    • getSourceAnalysis

      public Analysis getSourceAnalysis()

    • setSourceAnalysis

      public void setSourceAnalysis(Analysis sourceAnalysis)

    • getSpecificity

      public Double getSpecificity()
      Returns:
      A measure of how specific this association is compared to others that were obtained in the same analysis. This can be misleading if the same sequence was analyzed multiple times with different algorithms, databases, or parameters. High values are "better" but the exactly interpretation is implementation-specific.

    • setSpecificity

      public void setSpecificity(Double specificity)

    • getThreePrimeDistance

      public Long getThreePrimeDistance()
      Returns:
      The distance from the 3' end where this BioSequence aligns with respect to the Gene Product. This is often the location of the alignment with respect to an mRNA 3' end.

    • setThreePrimeDistance

      public void setThreePrimeDistance(Long threePrimeDistance)

    • getThreePrimeDistanceMeasurementMethod

      public ThreePrimeDistanceMethod getThreePrimeDistanceMeasurementMethod()
      Returns:
      Specifies the method used to measure the distance from the threePrimeEnd.

    • setThreePrimeDistanceMeasurementMethod

      public void setThreePrimeDistanceMeasurementMethod(ThreePrimeDistanceMethod threePrimeDistanceMeasurementMethod)