Class ChromosomeSequence

    • Method Detail

      • setChromosomeNumber

        public void setChromosomeNumber​(int chromosomeNumber)
        chromosomeNumber - the chromosomeNumber to set
      • getGeneSequences

        public LinkedHashMap<String,​GeneSequencegetGeneSequences()
        Get the list of genes that have been added to the ChromosomeSequence where accession.toString is the key. The list retains the order the genes are added
      • addGene

        public GeneSequence addGene​(AccessionID accession,
                                    int bioBegin,
                                    int bioEnd,
                                    Strand strand)
        Add a gene to the chromosome sequence using bioIndexing starts at 1 instead of 0. The GeneSequence that is returned will have a reference to parent chromosome sequence which actually contains the sequence data. Strand is important for positive and negative direction where negative strand means we need reverse complement. If negative strand then bioBegin will be greater than bioEnd
        accession -
        bioBegin -
        bioEnd -
        strand -
        A GeneSequence
      • getGene

        public GeneSequence getGene​(String accession)
        Get the gene based on accession. Will return null if not found
        accession -