Package org.snpeff.interval

Class Exon

java.lang.Object
org.snpeff.interval.Interval
org.snpeff.interval.Marker
org.snpeff.interval.MarkerSeq
org.snpeff.interval.Exon
All Implemented Interfaces:
Serializable, Cloneable, Comparable<Interval>, MarkerWithFrame, TxtSerializable
public class Exon extends MarkerSeq implements MarkerWithFrame
Interval for an exon
Author:
pcingola
See Also:

  • Field Details

    • ToStringVersion

      public static int ToStringVersion

  • Constructor Details

    • Exon

      public Exon()

    • Exon

      public Exon(Transcript parent, int start, int end, boolean strandMinus, String id, int rank)

  • Method Details

    • add

      public void add(SpliceSite ss)
      Add a splice site to the collection

    • apply

      public Exon apply(Variant variant)
      Apply variant to exon WARNING: There might be conditions which change the exon type (e.g. an intron is deleted). Nevertheless ExonSpliceType is not updated since it reflects the exon type before a sequence change.
      Overrides:
      apply in class MarkerSeq
      Returns:
      The marker result after applying variant

    • cloneShallow

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

    • createSpliceSiteRegionEnd

      public SpliceSiteRegion createSpliceSiteRegionEnd(int size)
      Create splice site regions

    • createSpliceSiteRegionStart

      public SpliceSiteRegion createSpliceSiteRegionStart(int size)
      Create splice site regions

    • frameCorrection

      public boolean frameCorrection(int frameCorrection)
      Correct exons according to frame information Shift the start position one base

    • getAaIdxEnd

      public int getAaIdxEnd()

    • getAaIdxStart

      public int getAaIdxStart()

    • getFrame

      public int getFrame()
      Specified by:
      getFrame in interface MarkerWithFrame

    • getRank

      public int getRank()

    • getSpliceSites

      public ArrayList<SpliceSite> getSpliceSites()

    • getSpliceType

      public Exon.ExonSpliceType getSpliceType()

    • isAdjustIfParentDoesNotInclude

      protected boolean isAdjustIfParentDoesNotInclude(Marker parent)
      Description copied from class: Marker
      Adjust parent if it does not include child?
      Overrides:
      isAdjustIfParentDoesNotInclude in class Marker

    • query

      public Markers query(Marker marker)
      Query all genomic regions that intersect 'marker'
      Overrides:
      query in class Marker

    • reset

      public void reset()

    • sanityCheck

      public ErrorWarningType sanityCheck(Variant variant)
      Check that the base in the exon corresponds with the one in the SNP

    • serializeParse

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

    • serializeSave

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

    • setAaIdx

      public void setAaIdx(int aaIdxStart, int aaIdxEnd)

    • setFrame

      public void setFrame(int frame)
      Frame can be {-1, 0, 1, 2}, where '-1' means unknown
      Specified by:
      setFrame in interface MarkerWithFrame

    • setRank

      public void setRank(int rank)

    • toString

      public String toString()
      Overrides:
      toString in class MarkerSeq

    • variantEffect

      public boolean variantEffect(Variant variant, VariantEffects variantEffects)
      Note: This only adds spliceSites effects, for detailed codon changes effects we use 'CodonChange' class
      Overrides:
      variantEffect in class Marker