All Superinterfaces:

AutoCloseable, Closeable

All Known Implementing Classes:

BlockCompressedIndexedFastaSequenceFile, FastaSequenceFile, IndexedFastaSequenceFile, SRAIndexedSequenceFile
```
public interface ReferenceSequenceFile
extends Closeable
```
An interface for working with files of reference sequences regardless of the file format being used.

Method Summary

All Methods Instance Methods Abstract Methods
Modifier and Type	Method	Description
`void`	`close()`
`ReferenceSequence`	`getSequence(String contig)`	Retrieves the complete sequence described by this contig.
`SAMSequenceDictionary`	`getSequenceDictionary()`	Must return a sequence dictionary with at least the following fields completed for each sequence: name, length.
`ReferenceSequence`	`getSubsequenceAt(String contig, long start, long stop)`	Gets the subsequence of the contig in the range [start,stop]
`boolean`	`isIndexed()`
`ReferenceSequence`	`nextSequence()`	Retrieves the next whole sequences from the file.
`void`	`reset()`	Resets the ReferenceSequenceFile so that the next call to nextSequence() will return the first sequence in the file.
`String`	`toString()`

- Method Detail
  - getSequenceDictionary
```
SAMSequenceDictionary getSequenceDictionary()
```
    Must return a sequence dictionary with at least the following fields completed for each sequence: name, length.
    
    Returns:
    
    a list of sequence records representing the sequences in this reference file
  - nextSequence
```
ReferenceSequence nextSequence()
```
    Retrieves the next whole sequences from the file.
    
    Returns:
    
    a ReferenceSequence or null if at the end of the file
  - reset
```
void reset()
```
    Resets the ReferenceSequenceFile so that the next call to nextSequence() will return the first sequence in the file.
  - isIndexed
```
boolean isIndexed()
```
    Returns:
    
    true if getSequence and getSubsequenceAt methods are allowed.
  - getSequence
```
ReferenceSequence getSequence(String contig)
```
    Retrieves the complete sequence described by this contig.
    
    Parameters:
    
    contig - contig whose data should be returned.
    
    Returns:
    
    The full sequence associated with this contig.
    
    Throws:
    
    UnsupportedOperationException - if !sIndexed.
  - getSubsequenceAt
```
ReferenceSequence getSubsequenceAt(String contig,
                                   long start,
                                   long stop)
```
    Gets the subsequence of the contig in the range [start,stop]
    
    Parameters:
    
    contig - Contig whose subsequence to retrieve.
    
    start - inclusive, 1-based start of region.
    
    stop - inclusive, 1-based stop of region.
    
    Returns:
    
    The partial reference sequence associated with this range.
    
    Throws:
    
    UnsupportedOperationException - if !sIndexed.
  - toString
```
String toString()
```
    Overrides:
    
    toString in class Object
    
    Returns:
    
    Reference name, file name, or something other human-readable representation.
  - close
```
void close()
    throws IOException
```
    Specified by:
    
    close in interface AutoCloseable
    
    Specified by:
    
    close in interface Closeable
    
    Throws:
    
    IOException

Interface ReferenceSequenceFile

Method Summary

Method Detail

getSequenceDictionary

nextSequence

reset

isIndexed

getSequence

getSubsequenceAt

toString

close