Class BinList

  • All Implemented Interfaces:
    Iterable<Bin>

    public class BinList
    extends Object
    implements Iterable<Bin>
    Provides a list of all bins which could exist in the BAM file. Allows the user to iterate over all bins, selecting ones of interest for later inspection.
    • Constructor Detail

      • BinList

        protected BinList​(int referenceSequence,
                          BitSet bins)
        Create a new BinList over sequenceCount sequences, consisting of the given bins.
        Parameters:
        referenceSequence - Reference sequence to which these bins are relevant.
        bins - The given bins to include.
    • Method Detail

      • iterator

        public Iterator<Bin> iterator()
        Gets an iterator over all selected bins.
        Specified by:
        iterator in interface Iterable<Bin>
        Returns:
        An iterator over all selected bins.
      • getReferenceSequence

        protected int getReferenceSequence()
        Get the reference sequence to which this bin belongs.
        Returns:
        Integer representing the reference sequence.
      • getBins

        protected BitSet getBins()
        Retrieves the bins stored in this list.
        Returns:
        A bitset where a bin is present in the list if the bit is true.