Package htsjdk.beta.plugin

Enum Class HtsContentType

java.lang.Object
java.lang.Enum<HtsContentType>
htsjdk.beta.plugin.HtsContentType
All Implemented Interfaces:
Serializable, Comparable<HtsContentType>, Constable
public enum HtsContentType extends Enum<HtsContentType>
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 common interfaces that are defined for each type are:

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).

  • Enum Constant Details

    • HAPLOID_REFERENCE

      public static final HtsContentType HAPLOID_REFERENCE
      Haploid reference content type (see HaploidReferenceFormats for related formats)

    • ALIGNED_READS

      public static final HtsContentType ALIGNED_READS
      Aligned reads content type (see ReadsFormats for related formats)

    • VARIANT_CONTEXTS

      public static final HtsContentType VARIANT_CONTEXTS
      Haploid reference content type (see VariantsFormats for related formats)

    • FEATURES

      public static final HtsContentType FEATURES
      Features content type (see
      invalid reference 
      htsjdk.beta.plugin.features
      for related formats)

  • Method Details

    • values

      public static HtsContentType[] 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

      public static HtsContentType valueOf(String name)
      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 name
      NullPointerException - if the argument is null