htsjdk.beta.io.bundle

Class Bundle

java.lang.Object

htsjdk.beta.io.bundle.Bundle

All Implemented Interfaces:

java.io.Serializable, java.lang.Iterable<BundleResource>

Direct Known Subclasses:

ReadsBundle

public class Bundle
extends java.lang.Object
implements java.lang.Iterable<BundleResource>, java.io.Serializable

An immutable collection of related resources (a primary resource, such as "reads", "variants", "features", or "reference"), plus zero or more related companion resources ("index", "dictionary", "MD5", etc.).

Each resource in a Bundle is represented by a BundleResource, which in turn describes a binding mechanism for that resource (such as an IOPath in the case of a URI, Path or file name; or an input or output stream), and a "content type" string that is unique within that Bundle. Any string can be used as a content type. Predefined content type strings are defined in BundleResourceType.

A Bundle must have one resource that is designated as the "primary" resource, specified by a content type string. A resource with "primary content type" is is guaranteed to be present in the Bundle.

Since each resource in a Bundle has a content type that is unique within that Bundle, a Bundle can not be used to represent a list of similar items where each item is equivalent to each other item (i.e., a list of shards, where each shard in the list is equivalent to each other shard). Rather Bundles are used to represent related resources where each resource has a unique character or role relative to the other resources (i.e., a "reads" resource and a corresponding "index" resource).

Bundles that contain only serializable (IOPathResource) resources may be serialized to, and deserialized from JSON.

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
Bundle(java.lang.String primaryContentType, java.util.Collection<BundleResource> resources) Create a new bundle from an existing resource collection.

Method Summary

Modifier and Type	Method and Description
boolean	equals(java.lang.Object o)
java.util.Optional<BundleResource>	get(java.lang.String targetContentType) Get the BundleResource for the provided targetContentType string.
BundleResource	getOrThrow(java.lang.String requiredContentType) Get the BundleResource for the provided targetContentType string, or throw if no such resource exists.
java.lang.String	getPrimaryContentType() Get the primary content type for this bundle.
BundleResource	getPrimaryResource() Get the primary BundleResource for this bundle.
java.util.Collection<BundleResource>	getResources() Get the collection of resources from this Bundle.
int	hashCode()
java.util.Iterator<BundleResource>	iterator() Get an iterator of BundleResources for this bundle.
java.lang.String	toString()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Constructor Detail

Bundle

public Bundle(java.lang.String primaryContentType,
              java.util.Collection<BundleResource> resources)

Create a new bundle from an existing resource collection.

Parameters:

primaryContentType - the content type of the primary resource in this bundle. may not be null. a resource with this content type must be included in resources

resources - resources to include in this bundle, may not be null or empty

Method Detail

get

public java.util.Optional<BundleResource> get(java.lang.String targetContentType)

Get the BundleResource for the provided targetContentType string.

Parameters:

targetContentType - the content type to be retrieved from the bundle

Returns:

an Optional that contains the targetContent type

getOrThrow

public BundleResource getOrThrow(java.lang.String requiredContentType)

Get the BundleResource for the provided targetContentType string, or throw if no such resource exists.

Parameters:

requiredContentType - the content type to be retrieved from the bundle

Returns:

a BundleResource of type targetContentType

Throws:

java.lang.IllegalArgumentException - if the targetContentType resource isn't present in the bundle

getPrimaryContentType

public java.lang.String getPrimaryContentType()

Get the primary content type for this bundle.

Returns:

the primary content type for this bundle

getPrimaryResource

public BundleResource getPrimaryResource()

Get the primary BundleResource for this bundle.

Returns:

the primary BundleResource for this bundle.

getResources

public java.util.Collection<BundleResource> getResources()

Get the collection of resources from this Bundle.

iterator

public java.util.Iterator<BundleResource> iterator()

Get an iterator of BundleResources for this bundle.

Specified by:

iterator in interface java.lang.Iterable<BundleResource>

Returns:

iterator of BundleResources for this bundle.

equals

public boolean equals(java.lang.Object o)

Overrides:

equals in class java.lang.Object

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object