Class Gene

    • Field Detail

      • CIRCULAR_GENE_ID

        public static final java.lang.String CIRCULAR_GENE_ID
        See Also:
        Constant Field Values
    • Constructor Detail

      • Gene

        public Gene()
      • Gene

        public Gene​(Marker parent,
                    int start,
                    int end,
                    boolean strandMinus,
                    java.lang.String id,
                    java.lang.String geneName,
                    BioType bioType)
    • Method Detail

      • 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.
      • cpgExonBias

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

        public void filterTranscriptSupportLevel​(TranscriptSupportLevel maxTsl)
        Filter transcripts by TSL
      • getBioType

        public BioType getBioType()
      • getGeneName

        public java.lang.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​(java.util.Set<java.lang.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
      • removeNonCanonical

        public void removeNonCanonical​(java.lang.String trId)
        Remove all non-canonical transcripts
      • removeUnverified

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

        public void setBioType​(BioType bioType)
      • sizeof

        public int sizeof​(java.lang.String type)
        Size of a genetic region for a given gene
      • toString

        public java.lang.String toString()
        Overrides:
        toString in class Marker
      • toString

        public java.lang.String toString​(boolean showTr)
      • variantEffectGene

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