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.

Constructor Summary

Constructors
Constructor	Description
`FastaSequenceFile(File file, boolean truncateNamesAtWhitespace)`	Constructs a FastaSequenceFile that reads from the specified file.
`FastaSequenceFile(String source, SeekableStream seekableStream, SAMSequenceDictionary dictionary, boolean truncateNamesAtWhitespace)`	Constructs a FastaSequenceFile that reads from the specified stream (which must not be compressed, i.e.
`FastaSequenceFile(Path path, boolean truncateNamesAtWhitespace)`	Constructs a FastaSequenceFile that reads from the specified file.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method	Description
`void`	`close()`	It's good to call this to free up memory.
`protected SAMSequenceDictionary`	`findAndLoadSequenceDictionary(Path fasta)`	Attempts to find and load the sequence dictionary if present.
`protected static File`	`findSequenceDictionary(File file)`	Deprecated. use findSequenceDictionary(Path) instead.
`protected static Path`	`findSequenceDictionary(Path fastaPath)`	Attempts to locate the sequence dictionary file adjacent to the reference fasta file.
`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.
`protected String`	`getSource()`	Returns the named source of the reference file.
`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, or the source if no path was specified.

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

- 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.
  - FastaSequenceFile
```
public FastaSequenceFile(String source,
                         SeekableStream seekableStream,
                         SAMSequenceDictionary dictionary,
                         boolean truncateNamesAtWhitespace)
```
    Constructs a FastaSequenceFile that reads from the specified stream (which must not be compressed, i.e. the caller is responsible for decompressing the stream).
- 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.
  - findAndLoadSequenceDictionary
```
protected SAMSequenceDictionary findAndLoadSequenceDictionary(Path fasta)
```
    Attempts to find and load the sequence dictionary if present.
  - findSequenceDictionary
```
@Deprecated
protected static File findSequenceDictionary(File file)
```
    Deprecated.
    use findSequenceDictionary(Path) instead.
  - findSequenceDictionary
```
protected static Path findSequenceDictionary(Path fastaPath)
```
    Attempts to locate the sequence dictionary file adjacent to the reference fasta file.
  - getPath
```
protected Path getPath()
```
    Returns the path to the reference file.
  - getSource
```
protected String getSource()
```
    Returns the named source of 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, or the source if no path was specified.
    
    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

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

FastaSequenceFile

FastaSequenceFile

FastaSequenceFile

Method Detail

close

nextSequence

reset

findAndLoadSequenceDictionary

findSequenceDictionary

findSequenceDictionary

getPath

getSource

getSequenceDictionary

getAbsolutePath

toString

isIndexed

getSequence

getSubsequenceAt