Class ChromosomeSequence

    • Constructor Detail

      • ChromosomeSequence

        public ChromosomeSequence()
        Empty constructor used by tools that need a proper Bean that allows the actual sequence data to be set after construction. Not recommended
      • ChromosomeSequence

        public ChromosomeSequence​(SequenceReader<NucleotideCompound> proxyLoader)
        Fairly important constructor given the size of a ChromsomeSequence where the ProxySequenceReader could load from disk via RandomAccessFile so that the sequence doesn't need to be kept in memory. Could also be a NCBI proxy to load sequence data as needed from remote web server.
        Parameters:
        proxyLoader -
    • Method Detail

      • getChromosomeNumber

        public int getChromosomeNumber()
        Returns:
        the chromosomeNumber
      • setChromosomeNumber

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

        public java.util.LinkedHashMap<java.lang.String,​GeneSequence> getGeneSequences()
        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
        Returns:
      • removeGeneSequence

        public GeneSequence removeGeneSequence​(java.lang.String accession)
        Parameters:
        accession -
        Returns:
      • 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
        Parameters:
        accession -
        begin -
        end -
        strand -
        Returns:
      • getGene

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