Package htsjdk.samtools.util

Class DiskBackedQueue<E>

  • All Implemented Interfaces:
    Iterable<E>, Collection<E>, Queue<E>
    public class DiskBackedQueue<E>
extends Object
implements Queue<E>
    A single-ended FIFO queue. Writes elements to temporary files when the queue gets too big. External references to elements in this queue are NOT guaranteed to be valid, due to the disk write/read

    NB: The queue becomes read-only after the first time that an on-disk record is "next up" to be read (i.e. has been loaded into headRecord). Max size is therefore non-deterministic. This avoids issues arising from conflicts between the input and output streams. This could perhaps be avoided by creating a version of BAMRecordCodec that operates on RandomAccessFiles or channels.

    Created by bradt on 4/28/14.

    • Method Detail

      • newInstance

        public static <T> DiskBackedQueue<T> newInstance​(SortingCollection.Codec<T> codec,
                                                 int maxRecordsInRam,
                                                 List<File> tmpDir)
        Syntactic sugar around the ctor, to save some typing of type parameters
        Parameters:
        codec - For writing records to file and reading them back into RAM
        maxRecordsInRam - how many records to accumulate in memory before spilling to disk
        tmpDir - Where to write files of records that will not fit in RAM

      • newInstanceFromPaths

        public static <T> DiskBackedQueue<T> newInstanceFromPaths​(SortingCollection.Codec<T> codec,
                                                          int maxRecordsInRam,
                                                          List<Path> tmpDir)
        Syntactic sugar around the ctor, to save some typing of type parameters
        Parameters:
        codec - For writing records to file and reading them back into RAM
        maxRecordsInRam - how many records to accumulate in memory before spilling to disk
        tmpDir - Where to write files of records that will not fit in RAM

      • canAdd

        public boolean canAdd()

      • getNumRecordsOnDisk

        public int getNumRecordsOnDisk()

      • headRecordIsFromDisk

        public boolean headRecordIsFromDisk()

      • add

        public boolean add​(E record)
            throws IllegalStateException
        Add the record to the tail of the queue, spilling to disk if necessary Must check that (canAdd() == true) before calling this method
        Specified by:
        add in interface Collection<E>
        Specified by:
        add in interface Queue<E>
        Parameters:
        record - The record to be added to the queue
        Returns:
        true (if add successful)
        Throws:
        IllegalStateException - if the queue cannot be added to

      • offer

        public boolean offer​(E e)
        Specified by:
        offer in interface Queue<E>

      • remove

        public E remove()
        Specified by:
        remove in interface Queue<E>

      • poll

        public E poll()
        Specified by:
        poll in interface Queue<E>

      • element

        public E element()
        Specified by:
        element in interface Queue<E>

      • peek

        public E peek()
        Specified by:
        peek in interface Queue<E>

      • size

        public int size()
        Return the total number of elements in the queue, both in memory and on disk
        Specified by:
        size in interface Collection<E>

      • addAll

        public boolean addAll​(Collection<? extends E> c)
        Add all elements from collection c to this DiskBackedQueue Must check that (canAdd() == true) before calling this method
        Specified by:
        addAll in interface Collection<E>
        Parameters:
        c - the collection of elements to add
        Returns:
        true if this collection changed as a result of the call
        Throws:
        IllegalStateException - if the queue cannot be added to

      • finalize

        protected void finalize()
                 throws Throwable
        Clean up disk resources in case clear() has not been explicitly called (as would be preferable) Closes the input and output streams associated with this DiskBackedQueue and deletes the temporary file
        Overrides:
        finalize in class Object
        Throws:
        Throwable

      • contains

        public boolean contains​(Object o)
        Not supported. It is not possible to check for the presence of a particular element, as some elements may have been written to disk
        Specified by:
        contains in interface Collection<E>
        Throws:
        UnsupportedOperationException