Package htsjdk.samtools.util

Class DiskBackedQueue<E>

java.lang.Object
htsjdk.samtools.util.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 Details

    • 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>

    • isEmpty

      public boolean isEmpty()
      Specified by:
      isEmpty 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

    • clear

      public void clear()
      Specified by:
      clear in interface Collection<E>

    • 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

    • remove

      public boolean remove(Object o)
      Not supported. Cannot access particular elements, as some elements may have been written to disk
      Specified by:
      remove in interface Collection<E>
      Throws:
      UnsupportedOperationException

    • removeAll

      public boolean removeAll(Collection<?> c)
      Not supported. Cannot access particular elements, as some elements may have been written to disk
      Specified by:
      removeAll in interface Collection<E>
      Throws:
      UnsupportedOperationException

    • retainAll

      public boolean retainAll(Collection<?> c)
      Not supported. Cannot access particular elements, as some elements may have been written to disk
      Specified by:
      retainAll in interface Collection<E>
      Throws:
      UnsupportedOperationException

    • 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

    • containsAll

      public boolean containsAll(Collection<?> c)
      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:
      containsAll in interface Collection<E>
      Throws:
      UnsupportedOperationException

    • iterator

      public Iterator<E> iterator()
      Not supported at this time
      Specified by:
      iterator in interface Collection<E>
      Specified by:
      iterator in interface Iterable<E>
      Throws:
      UnsupportedOperationException

    • toArray

      public Object[] toArray()
      Not supported at this time
      Specified by:
      toArray in interface Collection<E>
      Throws:
      UnsupportedOperationException

    • toArray

      public <T1> T1[] toArray(T1[] a)
      Not supported at this time
      Specified by:
      toArray in interface Collection<E>
      Throws:
      UnsupportedOperationException