Class Intron

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

public class Intron extends Marker
Intron
Author:
pcingola
See Also:
  • Constructor Details

    • Intron

      public Intron()
    • Intron

      public Intron(Transcript parent, int start, int end, boolean strandMinus, String id, Exon exonBefore, Exon exonAfter)
  • Method Details

    • add

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

      public Intron apply(Variant variant)
      Description copied from class: Marker
      Apply a variant to a marker.

      Calculate a the result of a marker, such that newMarker = marker.apply( variant ) variant = Diff( newMarker , marker ) // Differences in sequence

      Note: This method may return: - The same marker (this) when genetic coordinates remain unchanged - 'null' if the whole marker is removed by the variant (e.g. a deletion spanning the whole marker)

      For these reasons, the method should never be invoked directly. This is why the method is 'private' and 'final'

      Overrides:
      apply in class Marker
      Returns:
      The marker result after applying variant
    • cloneShallow

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

      public SpliceSiteAcceptor createSpliceSiteAcceptor(int maxSpliceSiteSize)
      Create a splice site acceptor of 'size' length Acceptor site: 3' end of the intron
    • createSpliceSiteDonor

      public SpliceSiteDonor createSpliceSiteDonor(int maxSpliceSiteSize)
      Create a splice site donor of 'maxSize' length Donor site: 5' end of the intron
    • createSpliceSiteRegionEnd

      public SpliceSiteRegion createSpliceSiteRegionEnd(int sizeMin, int sizeMax)
      Create splice site region
    • createSpliceSiteRegionStart

      public SpliceSiteRegion createSpliceSiteRegionStart(int sizeMin, int sizeMax)
      Create splice site region
    • getExonAfter

      public Exon getExonAfter()
    • getExonBefore

      public Exon getExonBefore()
    • getRank

      public int getRank()
    • getSpliceSites

      public ArrayList<SpliceSite> getSpliceSites()
    • getSpliceType

      public String getSpliceType()
    • query

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

      public void reset()
    • 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)
      Create a string to serialize to a file
      Specified by:
      serializeSave in interface TxtSerializable
      Overrides:
      serializeSave in class Marker
    • setRank

      public void setRank(int rank)
    • variantEffect

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