htsjdk.beta.plugin.registry.HtsCodecRegistry Maven / Gradle / Ivy
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package htsjdk.beta.plugin.registry;
import htsjdk.beta.plugin.HtsCodec;
import htsjdk.beta.plugin.hapref.HaploidReferenceCodec;
import htsjdk.beta.plugin.reads.ReadsCodec;
import htsjdk.beta.plugin.variants.VariantsCodec;
import htsjdk.beta.exception.HtsjdkPluginException;
import htsjdk.beta.exception.HtsjdkUnsupportedOperationException;
/**
* A registry for tracking {@link HtsCodec} instances.
*
* Registries are populated with {@link HtsCodec} objects that are either discovered
* and registered statically in the {@link HtsDefaultRegistry}, or manually registered in a private
* registry (see {@link HtsCodecRegistry#createPrivateRegistry()}) via the {@link #registerCodec(HtsCodec)}
* method.
*
* The global static {@link HtsDefaultRegistry} is immutable. A private, mutable registry for registering
* custom codecs can be created with {@link HtsCodecRegistry#createPrivateRegistry()}.
*/
public class HtsCodecRegistry {
private final HaploidReferenceResolver htsHaploidReferenceResolver = new HaploidReferenceResolver();
private final ReadsResolver htsReadsResolver = new ReadsResolver();
private final VariantsResolver htsVariantsResolver = new VariantsResolver();
/**
* Create a registry. Protected to prevent use outside of the registry package. To create
* a private registry from outside the registry package, use {@link #createPrivateRegistry}.
*/
protected HtsCodecRegistry() { }
/**
* Add a codec to the registry. If a codec that supports the same (format, version) (determined
* by {@link HtsCodec#getFileFormat()} and {@link HtsCodec#getVersion()} methods) is already
* registered, the new registry is updated to contain the new codec, and the previously registered
* codec is returned.
*
* @param codec the codec to be added
* @return a previously registered codec with the same (format, version), or null if no codec
* was previously registered
*/
public synchronized HtsCodec registerCodec(final HtsCodec codec) {
switch (codec.getContentType()) {
case HAPLOID_REFERENCE:
return htsHaploidReferenceResolver.registerCodec((HaploidReferenceCodec) codec);
case ALIGNED_READS:
return htsReadsResolver.registerCodec((ReadsCodec) codec);
case VARIANT_CONTEXTS:
return htsVariantsResolver.registerCodec((VariantsCodec) codec);
case FEATURES:
throw new HtsjdkUnsupportedOperationException("Features codec type not yet implemented");
default:
throw new HtsjdkPluginException(String.format("Unknown codec content type %s", codec.getContentType()));
}
}
/**
* Create a mutable registry for private use. The {@link HtsDefaultRegistry} is immutable, but
* a private registry can be populated with, and used to resolve against, custom codecs. A private registry
* is initially populated with all codecs that are registered in the {@link HtsDefaultRegistry}. Custom
* codecs can be then be installed into the private registry using
* {@link HtsCodecRegistry#registerCodec(HtsCodec)}.
*
* @return a mutable registry instance for private use
*/
public synchronized static HtsCodecRegistry createPrivateRegistry() {
final HtsCodecRegistry privateRegistry = new HtsCodecRegistry();
// propagate the codecs from the sourceRegistry to the new registry
HtsDefaultRegistry.htsDefaultCodecRegistry.getHaploidReferenceResolver().getCodecs()
.forEach(c -> privateRegistry.registerCodec(c));
HtsDefaultRegistry.htsDefaultCodecRegistry.getReadsResolver().getCodecs().
forEach(c -> privateRegistry.registerCodec(c));
HtsDefaultRegistry.htsDefaultCodecRegistry.getVariantsResolver().getCodecs()
.forEach(c -> privateRegistry.registerCodec(c));
return privateRegistry;
}
/**
* Get the {@link HaploidReferenceResolver} for this registry.
*
* @return the {@link HaploidReferenceResolver} for this registry
*/
public synchronized HaploidReferenceResolver getHaploidReferenceResolver() { return htsHaploidReferenceResolver; }
/**
* Get the {@link ReadsResolver} for this registry.
*
* @return the {@link ReadsResolver} for this registry
*/
public synchronized ReadsResolver getReadsResolver() { return htsReadsResolver; }
/**
* Get the {@link VariantsResolver} for this registry.
*
* @return the {@link VariantsResolver} for this registry
*/
public synchronized VariantsResolver getVariantsResolver() { return htsVariantsResolver; }
}