Class Upstream

All Implemented Interfaces:
Serializable, Cloneable, Comparable<Interval>, TxtSerializable

public class Upstream extends Marker
Interval for a gene, as well as some other information: exons, utrs, cds, etc.
Author:
pcingola
See Also:
  • Constructor Details

    • Upstream

      public Upstream()
    • Upstream

      public Upstream(Transcript parent, int start, int end, boolean strandMinus, String id)
  • Method Details

    • distanceToTr

      public int distanceToTr(Variant variant)
      Distance to transcript
    • isShowWarningIfParentDoesNotInclude

      protected boolean isShowWarningIfParentDoesNotInclude()
      Upstream sites are no included in transcript (by definition).
      Overrides:
      isShowWarningIfParentDoesNotInclude in class Marker
    • variantEffect

      public boolean variantEffect(Variant variant, VariantEffects variantEffects)
      Description copied from class: Marker
      Calculate the effect of this variant
      Overrides:
      variantEffect in class Marker