DiskBackedQueue (htsjdk 2.8.1 API)

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 Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`boolean`	`add(E record)` Add the record to the tail of the queue, spilling to disk if necessary Must check that (canAdd() == true) before calling this method
`boolean`	`addAll(Collection<? extends E> c)` Add all elements from collection c to this DiskBackedQueue Must check that (canAdd() == true) before calling this method
`boolean`	`canAdd()`
`void`	`clear()`
`boolean`	`contains(Object o)` Not supported.
`boolean`	`containsAll(Collection<?> c)` Not supported.
`E`	`element()`
`protected void`	`finalize()` 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
`int`	`getNumRecordsOnDisk()`
`boolean`	`headRecordIsFromDisk()`
`boolean`	`isEmpty()`
`Iterator<E>`	`iterator()` Not supported at this time
`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
`boolean`	`offer(E e)`
`E`	`peek()`
`E`	`poll()`
`E`	`remove()`
`boolean`	`remove(Object o)` Not supported.
`boolean`	`removeAll(Collection<?> c)` Not supported.
`boolean`	`retainAll(Collection<?> c)` Not supported.
`int`	`size()` Return the total number of elements in the queue, both in memory and on disk
`Object[]`	`toArray()` Not supported at this time
`<T1> T1[]`	`toArray(T1[] a)` Not supported at this time

Methods inherited from class java.lang.Object
clone, equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface java.util.Collection
equals, hashCode, parallelStream, removeIf, spliterator, stream

Methods inherited from interface java.lang.Iterable
forEach

- 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
  - 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 Iterable<E>
    
    Specified by:
    
    iterator in interface Collection<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

Class DiskBackedQueue<E>

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface java.util.Collection

Methods inherited from interface java.lang.Iterable

Method Detail

newInstance

canAdd

getNumRecordsOnDisk

headRecordIsFromDisk

add

offer

remove

poll

element

peek

size

isEmpty

addAll

clear

finalize

remove

removeAll

retainAll

contains

containsAll

iterator

toArray

toArray