htsjdk.beta.plugin

Enum HtsContentType

java.lang.Object

java.lang.Enum<HtsContentType>

htsjdk.beta.plugin.HtsContentType

All Implemented Interfaces:

java.io.Serializable, java.lang.Comparable<HtsContentType>

public enum HtsContentType
extends java.lang.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 the common interfaces that are defined for each type are:

• For HAPLOID_REFERENCE codecs, see the htsjdk.beta.plugin.hapref package
• For ALIGNED_READS codecs, see the htsjdk.beta.plugin.reads package
• For VARIANT_CONTEXTS codecs, see the htsjdk.beta.plugin.variants package
• For FEATURES codecs, see the htsjdk.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).

Enum Constant Summary

Enum Constants

Enum Constant and Description
ALIGNED_READS Aligned reads content type (see ReadsFormats for related formats)
FEATURES Features content type (see htsjdk.beta.plugin.features for related formats)
HAPLOID_REFERENCE Haploid reference content type (see HaploidReferenceFormats for related formats)
VARIANT_CONTEXTS Haploid reference content type (see VariantsFormats for related formats)

Method Summary

Modifier and Type	Method and Description
static HtsContentType	valueOf(java.lang.String name) Returns the enum constant of this type with the specified name.
static HtsContentType[]	values() Returns an array containing the constants of this enum type, in the order they are declared.

Methods inherited from class java.lang.Enum

clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Enum Constant Detail

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 htsjdk.beta.plugin.features for related formats)

Method Detail

values

public static HtsContentType[] values()

Returns an array containing the constants of this enum type, in the order they are declared. This method may be used to iterate over the constants as follows:

for (HtsContentType c : HtsContentType.values())
    System.out.println(c);

Returns:

an array containing the constants of this enum type, in the order they are declared

valueOf

public static HtsContentType valueOf(java.lang.String name)

Returns the enum constant of this type with the specified name. The string must match exactly an identifier used to declare an enum constant in this type. (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:

java.lang.IllegalArgumentException - if this enum type has no constant with the specified name

java.lang.NullPointerException - if the argument is null