Package htsjdk.beta.io.bundle

Class Bundle

java.lang.Object
htsjdk.beta.io.bundle.Bundle
All Implemented Interfaces:
Serializable, Iterable<BundleResource>
Direct Known Subclasses:
ReadsBundle, VariantsBundle
public class Bundle extends Object implements Iterable<BundleResource>, Serializable
An immutable collection of related resources, including a (single, required) primary resource, such as "reads", "variants", "features", or "reference", plus zero or more related secondary 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 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. Note that the order of resources in a bundle is not significant, and is not guaranteed to be preserved.

See Also:

  • Constructor Details

    • Bundle

      public Bundle(String primaryContentType, 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 Details

    • get

      public Optional<BundleResource> get(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(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:
      IllegalArgumentException - if the targetContentType resource isn't present in the bundle

    • getPrimaryContentType

      public 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 Collection<BundleResource> getResources()
      Get the collection of resources from this Bundle.

    • iterator

      public Iterator<BundleResource> iterator()
      Get an iterator of BundleResources for this bundle.
      Specified by:
      iterator in interface Iterable<BundleResource>
      Returns:
      iterator of BundleResources for this bundle.

    • equals

      public boolean equals(Object o)
      Overrides:
      equals in class Object

    • hashCode

      public int hashCode()
      Overrides:
      hashCode in class Object

    • toString

      public String toString()
      Overrides:
      toString in class Object

    • equalsIgnoreOrder

      public static boolean equalsIgnoreOrder(Bundle bundle1, Bundle bundle2)