ReferenceSequenceFileWalker (htsjdk 2.18.2 API)

java.lang.Object
- htsjdk.samtools.reference.ReferenceSequenceFileWalker

All Implemented Interfaces:

Closeable, AutoCloseable
```
public class ReferenceSequenceFileWalker
extends Object
implements Closeable
```
Manages a ReferenceSequenceFile. Loads the requested sequence, ensuring that access is in order, and confirming that sequence name and index agree.

Constructor Summary

Constructors
Constructor	Description
`ReferenceSequenceFileWalker(ReferenceSequenceFile referenceSequenceFile)`
`ReferenceSequenceFileWalker(File file)`
`ReferenceSequenceFileWalker(Path path)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`close()`
`ReferenceSequence`	`get(int sequenceIndex)`	Get reference sequence without validating name or length.
`ReferenceSequence`	`get(int sequenceIndex, String sequenceName, int length)`	Ensure that the requested sequence is loaded.
`SAMSequenceDictionary`	`getSequenceDictionary()`

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

- Constructor Detail
  - ReferenceSequenceFileWalker
```
public ReferenceSequenceFileWalker(ReferenceSequenceFile referenceSequenceFile)
```
  - ReferenceSequenceFileWalker
```
public ReferenceSequenceFileWalker(Path path)
```
  - ReferenceSequenceFileWalker
```
public ReferenceSequenceFileWalker(File file)
```
- Method Detail
  - get
```
public ReferenceSequence get(int sequenceIndex,
                             String sequenceName,
                             int length)
```
    Ensure that the requested sequence is loaded. Throws an exception if out-of-order request is made, or if there is a mismatch between the requested name and the name found in the ReferenceSequenceFile
  - get
```
public ReferenceSequence get(int sequenceIndex)
```
    Get reference sequence without validating name or length. This is OK if the entire sequence dictionary was validated before reading sequences.
  - getSequenceDictionary
```
public SAMSequenceDictionary getSequenceDictionary()
```
  - close
```
public void close()
           throws IOException
```
    Specified by:
    
    close in interface AutoCloseable
    
    Specified by:
    
    close in interface Closeable
    
    Throws:
    
    IOException