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

All Implemented Interfaces:: SortingCollection.Codec<Interval>, Cloneable

public class IntervalCodec
extends Object
implements SortingCollection.Codec<Interval>

Constructor Summary

Constructors
Constructor Description

IntervalCodec(SAMSequenceDictionary dict)
Creates a new binary codec to read or write.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`IntervalCodec`	`clone()`	Must return a cloned copy of the codec that can be used independently of the original instance.
`Interval`	`decode()`	Reads an interval from the input stream.
`void`	`encode(Interval interval)`	Writes the interval to the output stream.
`void`	`setInputStream(InputStream is)`	Sets the input stream that records will be read from.
`void`	`setInputStream(InputStream is, String filename)`	Sets the input stream that records will be read from.
`void`	`setOutputStream(OutputStream os)`	Sets the output stream that records will be written to.
`void`	`setOutputStream(OutputStream os, String filename)`	Sets the output stream that records will be written to.

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

- Constructor Detail
  - IntervalCodec
```
public IntervalCodec(SAMSequenceDictionary dict)
```
    Creates a new binary codec to read or write.
    
    Parameters:
    
    dict - the sequence dictionary associated with the intervals.
- Method Detail
  - clone
```
public IntervalCodec clone()
```
    Description copied from interface: SortingCollection.Codec
    
    Must return a cloned copy of the codec that can be used independently of the original instance. This is required so that multiple codecs can exist simultaneously that each is reading a separate file.
    
    Specified by:
    
    clone in interface SortingCollection.Codec<Interval>
    
    Overrides:
    
    clone in class Object
  - setOutputStream
```
public void setOutputStream(OutputStream os)
```
    Sets the output stream that records will be written to.
    
    Specified by:
    
    setOutputStream in interface SortingCollection.Codec<Interval>
  - setOutputStream
```
public void setOutputStream(OutputStream os,
                            String filename)
```
    Sets the output stream that records will be written to.
  - setInputStream
```
public void setInputStream(InputStream is)
```
    Sets the input stream that records will be read from.
    
    Specified by:
    
    setInputStream in interface SortingCollection.Codec<Interval>
  - setInputStream
```
public void setInputStream(InputStream is,
                           String filename)
```
    Sets the input stream that records will be read from.
  - encode
```
public void encode(Interval interval)
```
    Writes the interval to the output stream.
    
    Specified by:
    
    encode in interface SortingCollection.Codec<Interval>
    
    Parameters:
    
    interval - the interval to write.
  - decode
```
public Interval decode()
```
    Reads an interval from the input stream.
    
    Specified by:
    
    decode in interface SortingCollection.Codec<Interval>
    
    Returns:
    
    null if no more intervals, otherwise the next interval.

Class IntervalCodec

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

IntervalCodec

Method Detail

clone

setOutputStream

setOutputStream

setInputStream

setInputStream

encode

decode