Package org.snpeff.interval

Class Gene

java.lang.Object
org.snpeff.interval.Interval
org.snpeff.interval.Marker
org.snpeff.interval.IntervalAndSubIntervals<Transcript>
org.snpeff.interval.Gene
All Implemented Interfaces:
Serializable, Cloneable, Comparable<Interval>, Iterable<Transcript>, TxtSerializable
public class Gene extends IntervalAndSubIntervals<Transcript> implements Serializable
Interval for a gene, as well as transcripts
Author:
pcingola
See Also:

  • Field Details

  • Constructor Details

    • Gene

      public Gene()

    • Gene

      public Gene(Marker parent, int start, int end, boolean strandMinus, String id, String geneName, BioType bioType)

  • Method Details

    • addPerGene

      public void addPerGene(Marker marker)
      Add a gene dependent marker

    • adjust

      public boolean adjust()
      Adjust start, end and strand values
      Returns:
      true if any adjustment was done

    • buildPerGene

      public void buildPerGene()
      Build gene dependent interval tree

    • canonical

      public Transcript canonical()
      Get canonical transcript Canonical transcripts are defined as the longest CDS of amongst the protein coding transcripts. If none of the transcripts is protein coding, then it is the longest cDNA.

    • circularClone

      public Gene circularClone()
      In a circular genome, a gene can have negative coordinates or crosses over chromosome end. These genes are mirrored to the opposite end of the chromosome so that they can be referenced by both circular coordinates.

    • cloneShallow

      public Gene cloneShallow()
      Description copied from class: Marker
      Perform a shallow clone
      Overrides:
      cloneShallow in class IntervalAndSubIntervals<Transcript>

    • cpgExonBias

      public double cpgExonBias()
      Calculate CpG bias: number of CpG / expected[CpG]

    • filterTranscriptSupportLevel

      public void filterTranscriptSupportLevel(TranscriptSupportLevel maxTsl)
      Filter transcripts by TSL

    • geneType

      public Gene.GeneType geneType()

    • getBioType

      public BioType getBioType()

    • getGeneName

      public String getGeneName()

    • isProteinCoding

      public boolean isProteinCoding()
      Is any of the transcripts protein coding?

    • isShowWarningIfParentDoesNotInclude

      protected boolean isShowWarningIfParentDoesNotInclude()
      Description copied from class: Marker
      Show an error if parent does not include child?
      Overrides:
      isShowWarningIfParentDoesNotInclude in class Marker

    • keepTranscripts

      public int keepTranscripts(Set<String> trIds)
      Remove all transcripts in trIds
      Returns:
      : Number of transcripts removed

    • keepTranscriptsProteinCoding

      public int keepTranscriptsProteinCoding()
      Keep only protein coding transcripts
      Returns:
      : Number of transcripts removed

    • markers

      public Markers markers()
      Description copied from class: IntervalAndSubIntervals
      A list of all markers in this transcript
      Overrides:
      markers in class IntervalAndSubIntervals<Transcript>

    • removeNonCanonical

      public void removeNonCanonical(String trId)
      Remove all non-canonical transcripts

    • removeUnverified

      public boolean removeUnverified()
      Remove unverified or corrected transcripts
      Returns:
      : True if ALL transcripts have been removed

    • serializeParse

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

    • serializeSave

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

    • setBioType

      public void setBioType(BioType bioType)

    • sizeof

      public int sizeof(String type)
      Size of a genetic region for a given gene

    • toString

      public String toString()
      Overrides:
      toString in class Marker

    • toString

      public String toString(boolean showTr)

    • variantEffect

      public boolean variantEffect(Variant variant, VariantEffects variantEffects)
      Get some details about the effect on this gene
      Overrides:
      variantEffect in class Marker

    • variantEffectGene

      protected void variantEffectGene(Variant variant, VariantEffects variantEffects)
      Add gene-specific annotations