FastaSequenceFile (htsjdk 2.8.1 API)

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

All Implemented Interfaces:

ReferenceSequenceFile, Closeable, AutoCloseable
```
public class FastaSequenceFile
extends Object
```
Implementation of ReferenceSequenceFile for reading from FASTA files.

Field Summary

Fields
Modifier and Type Field and Description

protected SAMSequenceDictionary sequenceDictionary

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

Constructor Summary

Constructors
Constructor and Description
`FastaSequenceFile(File file, boolean truncateNamesAtWhitespace)` Constructs a FastaSequenceFile that reads from the specified file.
`FastaSequenceFile(Path path, boolean truncateNamesAtWhitespace)` Constructs a FastaSequenceFile that reads from the specified file.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`close()` It's good to call this to free up memory.
`protected static File`	`findSequenceDictionary(File file)`
`protected static Path`	`findSequenceDictionary(Path path)`
`protected String`	`getAbsolutePath()` Returns the full path to the reference file.
`protected Path`	`getPath()` Returns the path to the reference file.
`ReferenceSequence`	`getSequence(String contig)` default implementation -- override if index is supported
`SAMSequenceDictionary`	`getSequenceDictionary()` Returns the list of sequence records associated with the reference sequence if found otherwise null.
`ReferenceSequence`	`getSubsequenceAt(String contig, long start, long stop)` default implementation -- override if index is supported
`boolean`	`isIndexed()` default implementation -- override if index is supported
`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()` Returns the full path to the reference file.

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

- Field Detail
  - sequenceDictionary
```
protected SAMSequenceDictionary sequenceDictionary
```
- Constructor Detail
  - FastaSequenceFile
```
public FastaSequenceFile(File file,
                         boolean truncateNamesAtWhitespace)
```
    Constructs a FastaSequenceFile that reads from the specified file.
  - FastaSequenceFile
```
public FastaSequenceFile(Path path,
                         boolean truncateNamesAtWhitespace)
```
    Constructs a FastaSequenceFile that reads from the specified file.
- Method Detail
  - close
```
public void close()
```
    It's good to call this to free up memory.
  - nextSequence
```
public ReferenceSequence nextSequence()
```
    Description copied from interface: ReferenceSequenceFile
    
    Retrieves the next whole sequences from the file.
    
    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.
  - findSequenceDictionary
```
protected static File findSequenceDictionary(File file)
```
  - findSequenceDictionary
```
protected static Path findSequenceDictionary(Path path)
```
  - getPath
```
protected Path getPath()
```
    Returns the path to the reference file.
  - getSequenceDictionary
```
public SAMSequenceDictionary getSequenceDictionary()
```
    Returns the list of sequence records associated with the reference sequence if found otherwise null.
    
    Specified by:
    
    getSequenceDictionary in interface ReferenceSequenceFile
    
    Returns:
    
    a list of sequence records representing the sequences in this reference file
  - getAbsolutePath
```
protected String getAbsolutePath()
```
    Returns the full path to the reference file.
  - toString
```
public String toString()
```
    Returns the full path to the reference file.
    
    Specified by:
    
    toString in interface ReferenceSequenceFile
    
    Overrides:
    
    toString in class Object
    
    Returns:
    
    Reference name, file name, or something other human-readable representation.
  - isIndexed
```
public boolean isIndexed()
```
    default implementation -- override if index is supported
    
    Specified by:
    
    isIndexed in interface ReferenceSequenceFile
    
    Returns:
    
    true if getSequence and getSubsequenceAt methods are allowed.
  - getSequence
```
public ReferenceSequence getSequence(String contig)
```
    default implementation -- override if index is supported
    
    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)
```
    default implementation -- override if index is supported
    
    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.

Class FastaSequenceFile

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

sequenceDictionary

Constructor Detail

FastaSequenceFile

FastaSequenceFile

Method Detail

close

nextSequence

reset

findSequenceDictionary

findSequenceDictionary

getPath

getSequenceDictionary

getAbsolutePath

toString

isIndexed

getSequence

getSubsequenceAt