SortingLongCollection (htsjdk 2.14.3 API)

java.lang.Object
- htsjdk.samtools.util.SortingLongCollection

```
public class SortingLongCollection
extends Object
```
Accumulate a list of longs that can then be sorted in natural order and iterated over. If there are more values accumulated than a specified maximum, values are spilled to disk.
Note that because this class returns primitive longs rather than Longs, it does not conform to any of the Collection iteration interfaces. Use as follows:
1. ctor 2. call add() as many times as desired. 3. call doneAddingStartIteration(). 4. call hasNext() and next() until exhausted or had enough. 5. optionally call cleanup() to free space in temporary directory as soon as possible.
If there are few enough values so that they all can be kept in RAM, then the array is sorted and iterated over trivially.
If there are more values that can fit in RAM, then values are sorted and written to a temp file when the max number to be stored in RAM is reached. Multiple temp files are then merged during iteration via PriorityQueue.
c.f. SortingCollection for more details.

Field Summary

Fields
Modifier and Type Field Description

static int MAX_ITEMS_IN_RAM

static int SIZEOF

Fields
Modifier and Type	Field	Description
`static int`	`MAX_ITEMS_IN_RAM`
`static int`	`SIZEOF`

Constructor Summary

Constructors
Constructor	Description
`SortingLongCollection(int maxValuesInRam, File... tmpDir)`	Prepare to accumulate values to be sorted
`SortingLongCollection(int maxValuesInRam, Path... tmpDir)`	Prepare to accumulate values to be sorted

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`add(long value)`	Add a value to the collection.
`void`	`cleanup()`	Delete any temporary files.
`void`	`doneAddingStartIteration()`	This method must be called after done adding, and before calling hasNext() or next().
`boolean`	`hasNext()`	Call only after doneAddingStartIteration() has been called.
`long`	`next()`	Call only if hasNext() == true.

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

- Field Detail
  - SIZEOF
```
public static final int SIZEOF
```
    See Also:
    
    Constant Field Values
  - MAX_ITEMS_IN_RAM
```
public static final int MAX_ITEMS_IN_RAM
```
- Constructor Detail
  - SortingLongCollection
```
public SortingLongCollection(int maxValuesInRam,
                             File... tmpDir)
```
    Prepare to accumulate values to be sorted
    
    Parameters:
    
    maxValuesInRam - how many values to accumulate before spilling to disk
    
    tmpDir - Where to write files of values that will not fit in RAM
  - SortingLongCollection
```
public SortingLongCollection(int maxValuesInRam,
                             Path... tmpDir)
```
    Prepare to accumulate values to be sorted
    
    Parameters:
    
    maxValuesInRam - how many values to accumulate before spilling to disk
    
    tmpDir - Where to write files of values that will not fit in RAM
- Method Detail
  - add
```
public void add(long value)
```
    Add a value to the collection.
    
    Parameters:
    
    value -
  - doneAddingStartIteration
```
public void doneAddingStartIteration()
```
    This method must be called after done adding, and before calling hasNext() or next().
  - cleanup
```
public void cleanup()
```
    Delete any temporary files. After this method is called, no other method calls should be made on this object.
  - hasNext
```
public boolean hasNext()
```
    Call only after doneAddingStartIteration() has been called.
    
    Returns:
    
    true if there is another value to be gotten.
  - next
```
public long next()
```
    Call only if hasNext() == true.
    
    Returns:
    
    next value from collection, in natural sort order.

Class SortingLongCollection

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

SIZEOF

MAX_ITEMS_IN_RAM

Constructor Detail

SortingLongCollection

SortingLongCollection

Method Detail

add

doneAddingStartIteration

cleanup

hasNext

next