Class SnpEffPredictorFactoryGff

    • Field Detail

    • Constructor Detail

      • SnpEffPredictorFactoryGff

        public SnpEffPredictorFactoryGff​(Config config)
    • Method Detail

      • addExon

        protected Exon addExon​(Transcript tr,
                               GffMarker gffMarker,
                               java.lang.String exonId)
        Create a new exon
      • addExons

        protected java.util.List<Exon> addExons​(GffMarker gffMarker)
        Create and add a new exon
      • addGene

        protected Gene addGene​(GffMarker gffMarker,
                               boolean findNextGeneId)
        Create and add a gene based on GffMarker
      • addInterval

        protected boolean addInterval​(GffMarker gffMarker)
        Add interval based on GffMarker data
        Returns:
        true if on success
      • addIntronConserved

        protected IntronConserved addIntronConserved​(GffMarker gffMarker)
        Add an intron conserved region
      • addUtr3

        protected java.util.List<Utr3prime> addUtr3​(GffMarker gffMarker)
        Create new UTR3primes
      • addUtr5

        protected java.util.List<Utr5prime> addUtr5​(GffMarker gffMarker)
        Create UTR5primes
      • findOrCreateExon

        protected Exon findOrCreateExon​(java.lang.String parentId,
                                        GffMarker gffMarker)
        Find an exon for a given parentId
      • findOrCreateGene

        protected Gene findOrCreateGene​(GffMarker gffMarker)
        Find or create a gene based on GffMarker
      • findOrCreateTranscript

        protected Transcript findOrCreateTranscript​(GffMarker gffMarker)
        Create and add a transcript based on GffMarker
      • parse

        protected boolean parse​(java.lang.String line)
        Parse a line
        Returns:
        true if a line was parsed
      • readExonSequencesGff

        protected void readExonSequencesGff​(java.lang.String gffFileName)
        Read chromosome sequence from GFF3 file and extract exons' sequences
      • readGff

        protected void readGff()
                        throws java.lang.Exception
        Read GFF file from the beginning looking for 'typeToRead' elements
        Throws:
        java.lang.Exception