SRAIndexedSequenceFile (htsjdk 2.14.3 API)

java.lang.Object
- htsjdk.samtools.sra.SRAIndexedSequenceFile

All Implemented Interfaces:

ReferenceSequenceFile, Closeable, AutoCloseable
```
public class SRAIndexedSequenceFile
extends Object
implements ReferenceSequenceFile
```
Allows reading Reference data from SRA

Field Summary

Fields
Modifier and Type Field Description

protected SAMSequenceDictionary sequenceDictionary

Fields
Modifier and Type	Field	Description
`protected SAMSequenceDictionary`	`sequenceDictionary`

Constructor Summary

Constructors
Constructor Description

SRAIndexedSequenceFile(SRAAccession acc)

Constructors
Constructor	Description
`SRAIndexedSequenceFile(SRAAccession acc)`

Method Summary

All Methods Instance Methods Concrete 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()`
`protected SAMSequenceDictionary`	`loadSequenceDictionary()`
`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.

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

Methods inherited from interface htsjdk.samtools.reference.ReferenceSequenceFile
toString

- Field Detail
  - sequenceDictionary
```
protected SAMSequenceDictionary sequenceDictionary
```
- Constructor Detail
  - SRAIndexedSequenceFile
```
public SRAIndexedSequenceFile(SRAAccession acc)
```
    Parameters:
    
    acc - accession
- Method Detail
  - getSequenceDictionary
```
public SAMSequenceDictionary getSequenceDictionary()
```
    Description copied from interface: ReferenceSequenceFile
    
    Must return a sequence dictionary with at least the following fields completed for each sequence: name, length.
    
    Specified by:
    
    getSequenceDictionary in interface ReferenceSequenceFile
    
    Returns:
    
    a list of sequence records representing the sequences in this reference file
  - nextSequence
```
public ReferenceSequence nextSequence()
```
    Description copied from interface: ReferenceSequenceFile
    
    Retrieves the next whole sequences from the file.
    
    Specified by:
    
    nextSequence in interface ReferenceSequenceFile
    
    Returns:
    
    a ReferenceSequence or null if at the end of the file
  - reset
```
public void reset()
```
    Description copied from interface: ReferenceSequenceFile
    
    Resets the ReferenceSequenceFile so that the next call to nextSequence() will return the first sequence in the file.
    
    Specified by:
    
    reset in interface ReferenceSequenceFile
  - isIndexed
```
public boolean isIndexed()
```
    Specified by:
    
    isIndexed in interface ReferenceSequenceFile
    
    Returns:
    
    true if getSequence and getSubsequenceAt methods are allowed.
  - getSequence
```
public ReferenceSequence getSequence(String contig)
```
    Description copied from interface: ReferenceSequenceFile
    
    Retrieves the complete sequence described by this contig.
    
    Specified by:
    
    getSequence in interface ReferenceSequenceFile
    
    Parameters:
    
    contig - contig whose data should be returned.
    
    Returns:
    
    The full sequence associated with this contig.
  - getSubsequenceAt
```
public ReferenceSequence getSubsequenceAt(String contig,
                                          long start,
                                          long stop)
```
    Description copied from interface: ReferenceSequenceFile
    
    Gets the subsequence of the contig in the range [start,stop]
    
    Specified by:
    
    getSubsequenceAt in interface ReferenceSequenceFile
    
    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.
  - close
```
public void close()
           throws IOException
```
    Specified by:
    
    close in interface AutoCloseable
    
    Specified by:
    
    close in interface Closeable
    
    Specified by:
    
    close in interface ReferenceSequenceFile
    
    Throws:
    
    IOException
  - loadSequenceDictionary
```
protected SAMSequenceDictionary loadSequenceDictionary()
                                                throws ngs.ErrorMsg
```
    Throws:
    
    ngs.ErrorMsg

Class SRAIndexedSequenceFile

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface htsjdk.samtools.reference.ReferenceSequenceFile

Field Detail

sequenceDictionary

Constructor Detail

SRAIndexedSequenceFile

Method Detail

getSequenceDictionary

nextSequence

reset

isIndexed

getSequence

getSubsequenceAt

close

loadSequenceDictionary