Package htsjdk.beta.codecs.hapref.fasta

Class FASTACodecV1_0

java.lang.Object

htsjdk.beta.codecs.hapref.fasta.FASTACodecV1_0

All Implemented Interfaces:

HaploidReferenceCodec, HtsCodec<HaploidReferenceDecoderOptions,HaploidReferenceEncoderOptions>, Upgradeable

public class FASTACodecV1_0
extends Object
implements HaploidReferenceCodec

The v1.0 FASTA codec.

Field Summary

Fields

Modifier and Type	Field	Description
static final HtsVersion	VERSION_1

Constructor Summary

Constructors

Constructor	Description
FASTACodecV1_0()

Method Summary

Modifier and Type	Method	Description
boolean	canDecodeSignature(SignatureStream signatureStream, String sourceName)	Determine if the codec can decode an input stream by inspecting a signature embedded within the stream.
boolean	canDecodeURI(IOPath ioPath)	Determine if the URI for ioPath (obtained via IOPath.getURI()) conforms to the expected URI format this codec's file format.
HaploidReferenceDecoder	getDecoder(Bundle inputBundle, HaploidReferenceDecoderOptions options)	Get an HtsDecoder to decode the provided inputs.
HaploidReferenceEncoder	getEncoder(Bundle outputBundle, HaploidReferenceEncoderOptions options)	Get an HtsEncoder to encode to the provided outputs.
String	getFileFormat()	Get the name of the file format supported by this codec.
int	getSignatureLength()	Get the number of bytes in the format and version signature used by the file format supported by this codec.
HtsVersion	getVersion()	Get the version of the file format returned by HtsCodec.getFileFormat() that is supported by this codec.
boolean	runVersionUpgrade(HtsVersion sourceCodecVersion, HtsVersion targetCodecVersion)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface htsjdk.beta.plugin.hapref.HaploidReferenceCodec

getContentType

Methods inherited from interface htsjdk.beta.plugin.HtsCodec

getDisplayName, getSignatureProbeLength, ownsURI

Field Details

VERSION_1

public static final HtsVersion VERSION_1

Constructor Details

FASTACodecV1_0

public FASTACodecV1_0()

Method Details

getVersion

public HtsVersion getVersion()

Description copied from interface: HtsCodec

Get the version of the file format returned by HtsCodec.getFileFormat() that is supported by this codec.

Specified by:

getVersion in interface HtsCodec<HaploidReferenceDecoderOptions,HaploidReferenceEncoderOptions>

Returns:

the file format version (HtsVersion) supported by this codec

getFileFormat

public String getFileFormat()

Description copied from interface: HtsCodec

Get the name of the file format supported by this codec. The format name defines the underlying format handled by this codec, and also corresponds to the format of the primary bundle resource that is required when decoding or encoding (see BundleResourceType and BundleResource.getFileFormat()).

Specified by:

getFileFormat in interface HtsCodec<HaploidReferenceDecoderOptions,HaploidReferenceEncoderOptions>

Returns:

the name of the underlying file format handled by this codec

getSignatureLength

public int getSignatureLength()

Description copied from interface: HtsCodec

Get the number of bytes in the format and version signature used by the file format supported by this codec.

Specified by:

getSignatureLength in interface HtsCodec<HaploidReferenceDecoderOptions,HaploidReferenceEncoderOptions>

Returns:

if the file format supported by this codecs is not remote, and is accessible via a local file or stream, the size of the unique signature/version for this file format. otherwise 0.

Note: Codecs that are custom URI handlers (those that return true for HtsCodec.ownsURI(htsjdk.io.IOPath)), should always return 0 from this method. Since this method is used during codec resolution, implementations should avoid calling methods that may throw exceptions.

canDecodeSignature

public boolean canDecodeSignature(SignatureStream signatureStream,
 String sourceName)

Description copied from interface: HtsCodec

Determine if the codec can decode an input stream by inspecting a signature embedded within the stream.

The probingInputStream stream will contain only a fragment of the actual input stream, taken from the start of the stream, the size of which will be the lesser of:

1. the number of bytes returned by HtsCodec.getSignatureProbeLength()
2. the entire input stream, for streams that are smaller than HtsCodec.getSignatureProbeLength()

Codecs that handle custom URIs that reference remote resources (those that return true for HtsCodec.ownsURI(htsjdk.io.IOPath)) should generally not inspect the stream, and should return false from this method, since the method will never be called with any resource for which HtsCodec.ownsURI(htsjdk.io.IOPath) returned true. Since this method is used during codec resolution, implementations should avoid calling methods that may throw exceptions.

Specified by:

canDecodeSignature in interface HtsCodec<HaploidReferenceDecoderOptions,HaploidReferenceEncoderOptions>

Parameters:

signatureStream - the stream to be inspect for the resource's embedded signature and version

sourceName - a display name describing the source of the input stream, for use in error messages

Returns:

true if this codec recognizes the stream by it's signature, and can provide a decoder to decode the stream, otherwise false

canDecodeURI

public boolean canDecodeURI(IOPath ioPath)

Description copied from interface: HtsCodec

Determine if the URI for ioPath (obtained via IOPath.getURI()) conforms to the expected URI format this codec's file format.

Most implementations only look at the file extension (see IOPath.hasExtension(java.lang.String)). For codecs that implement formats that use specific, well known file extensions, the codec should reject inputs that do not conform to any of the accepted extensions. If the format does not use a specific extension, or if the codec cannot determine if it can decode the underlying resource without inspecting the underlying stream, it is safe to return true, after which the framework will subsequently call this codec's HtsCodec.canDecodeSignature(SignatureStream, String) method, at which time the codec can inspect the actual underlying stream via the SignatureStream.

Implementations should generally not inspect the URI's protocol scheme unless the file format supported by the codec requires the use a specific protocol scheme. For codecs that do own a specific scheme or URI format, the return values for HtsCodec.ownsURI(IOPath) and HtsCodec.canDecodeURI(IOPath) must always be the same (both true or both false) for a given IOPath. For codecs that do not use a custom URI (and rely on NIO access), @link #ownsURI(IOPath)} should always return false, with only the value returned from HtsCodec.canDecodeURI(IOPath) varying based on features such as file extension probes.

It is never safe to attempt to directly inspect the underlying stream for ioPath in this method. If the stream needs to be inspected, it should be done using the signature stream when the HtsCodec.canDecodeSignature(SignatureStream, String) method is called.

For custom URI handlers (see HtsCodec.ownsURI(IOPath), codecs should avoid making remote calls to determine the suitability of the input resource; the return value for this method should be based only on the format of the URI that is presented. Since this method is used during codec resolution, implementations should avoid calling methods that may throw exceptions.

Specified by:

canDecodeURI in interface HtsCodec<HaploidReferenceDecoderOptions,HaploidReferenceEncoderOptions>

Parameters:

ioPath - to be decoded

Returns:

true if the codec can provide a decoder to provide this URI

getDecoder

public HaploidReferenceDecoder getDecoder(Bundle inputBundle,
 HaploidReferenceDecoderOptions options)

Description copied from interface: HtsCodec

Get an HtsDecoder to decode the provided inputs. The input bundle must contain resources of the type required by this codec. To find a codec appropriate for decoding a given resource, use an HtsCodecResolver obtained from an HtsCodecRegistry.

The framework will never call thi* method unless either HtsCodec.ownsURI(IOPath), or HtsCodec.canDecodeURI(IOPath) and HtsCodec.canDecodeSignature(SignatureStream, String) (IOPath)} return true for inputBundle.

Specified by:

getDecoder in interface HtsCodec<HaploidReferenceDecoderOptions,HaploidReferenceEncoderOptions>

Parameters:

inputBundle - input to be decoded. To get a decoder for use with index queries that use HtsQuery methods, the bundle must contain an index resource.

options - options for the decoder to use

Returns:

an HtsDecoder that can decode the provided inputs

getEncoder

public HaploidReferenceEncoder getEncoder(Bundle outputBundle,
 HaploidReferenceEncoderOptions options)

Description copied from interface: HtsCodec

Get an HtsEncoder to encode to the provided outputs. The output bundle must contain resources of the type required by this codec. To find a codec appropriate for encoding a given resource, use an HtsCodecResolver obtained from an HtsCodecRegistry.

The framework will never call this method unless either HtsCodec.ownsURI(IOPath), or HtsCodec.canDecodeURI(IOPath) returned true for outputBundle.

Specified by:

getEncoder in interface HtsCodec<HaploidReferenceDecoderOptions,HaploidReferenceEncoderOptions>

Parameters:

outputBundle - target output for the encoder

options - encoder options to use

Returns:

an HtsEncoder suitable for writing to the provided outputs

runVersionUpgrade

public boolean runVersionUpgrade(HtsVersion sourceCodecVersion,
 HtsVersion targetCodecVersion)

Specified by:

runVersionUpgrade in interface Upgradeable