Package org.snpeff.interval

Class NextProt

java.lang.Object
org.snpeff.interval.Interval
org.snpeff.interval.Marker
org.snpeff.interval.NextProt
All Implemented Interfaces:
Serializable, Cloneable, Comparable<Interval>, TxtSerializable
public class NextProt extends Marker
NextProt annotation marker
Author:
pcingola
See Also:

  • Constructor Details

    • NextProt

      public NextProt()

    • NextProt

      public NextProt(Transcript transcript, int start, int end, String id)

    • NextProt

      public NextProt(Transcript transcript, int start, int end, String id, String name)

  • Method Details

    • cloneShallow

      public NextProt cloneShallow()
      Description copied from class: Marker
      Perform a shallow clone
      Overrides:
      cloneShallow in class Marker

    • getName

      public String getName()

    • getTranscriptId

      public String getTranscriptId()

    • isDeferredAnalysis

      public boolean isDeferredAnalysis()
      Deferred analysis markers must be analyzed after 'standard' ones because their impact depends on other results For instance, a NextProt marker's impact would be different if the variant is synonymous or non-synonymous
      Overrides:
      isDeferredAnalysis in class Marker

    • isHighlyConservedAaSequence

      public boolean isHighlyConservedAaSequence()

    • setHighlyConservedAaSequence

      public void setHighlyConservedAaSequence(boolean highlyConservedAaSequence)

    • serializeParse

      public void serializeParse(MarkerSerializer markerSerializer)
      Description copied from class: Marker
      Parse a line from a serialized file
      Specified by:
      serializeParse in interface TxtSerializable
      Overrides:
      serializeParse in class Marker

    • serializeSave

      public String serializeSave(MarkerSerializer markerSerializer)
      Description copied from class: Marker
      Create a string to serialize to a file
      Specified by:
      serializeSave in interface TxtSerializable
      Overrides:
      serializeSave 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