Package htsjdk.beta.plugin
Enum Class HtsContentType
- All Implemented Interfaces:
Serializable
,Comparable<HtsContentType>
,Constable
The plugin framework defines a set of supported content types, each of which represents a type
of HTS data such as "aligned reads". Each content type has an associated set of interfaces that
are used with that type (for example, codecs with content type
ALIGNED_READS
expose a
set interfaces for reading and writing aligned reads data). The content types and the packages
containing the the common interfaces that are defined for each type are:
- For
HAPLOID_REFERENCE
codecs, see thehtsjdk.beta.plugin.hapref
package - For
ALIGNED_READS
codecs, see thehtsjdk.beta.plugin.reads
package - For
VARIANT_CONTEXTS
codecs, see thehtsjdk.beta.plugin.variants
package - For
FEATURES
codecs, see thehtsjdk.beta.plugin.features
package
There can be many codecs for a given content type, each representing a different version of an
underlying format (i.e, ReadsFormats.SAM
,
ReadsFormats.BAM
or ReadsFormats.CRAM
for ALIGNED_READS
) and or access mechanism or protocol (for example,
ReadsFormats.HTSGET_BAM
).
-
Nested Class Summary
Nested classes/interfaces inherited from class java.lang.Enum
Enum.EnumDesc<E extends Enum<E>>
-
Enum Constant Summary
Enum ConstantDescriptionAligned reads content type (seeReadsFormats
for related formats)Features content type (seehtsjdk.beta.plugin.features
for related formats)Haploid reference content type (seeHaploidReferenceFormats
for related formats)Haploid reference content type (seeVariantsFormats
for related formats) -
Method Summary
Modifier and TypeMethodDescriptionstatic HtsContentType
Returns the enum constant of this class with the specified name.static HtsContentType[]
values()
Returns an array containing the constants of this enum class, in the order they are declared.
-
Enum Constant Details
-
HAPLOID_REFERENCE
Haploid reference content type (seeHaploidReferenceFormats
for related formats) -
ALIGNED_READS
Aligned reads content type (seeReadsFormats
for related formats) -
VARIANT_CONTEXTS
Haploid reference content type (seeVariantsFormats
for related formats) -
FEATURES
Features content type (seehtsjdk.beta.plugin.features
for related formats)
-
-
Method Details
-
values
Returns an array containing the constants of this enum class, in the order they are declared.- Returns:
- an array containing the constants of this enum class, in the order they are declared
-
valueOf
Returns the enum constant of this class with the specified name. The string must match exactly an identifier used to declare an enum constant in this class. (Extraneous whitespace characters are not permitted.)- Parameters:
name
- the name of the enum constant to be returned.- Returns:
- the enum constant with the specified name
- Throws:
IllegalArgumentException
- if this enum class has no constant with the specified nameNullPointerException
- if the argument is null
-