public abstract class AbstractFeatureCodec<FEATURE_TYPE extends Feature,SOURCE> extends java.lang.Object implements FeatureCodec<FEATURE_TYPE,SOURCE>
FeatureCodec.canDecode(String) to indicate whether it can decode the file.
Note that that method is the only way that the right codec for a file is identified and that | Modifier | Constructor and Description |
|---|---|
protected |
AbstractFeatureCodec(java.lang.Class<FEATURE_TYPE> myClass) |
| Modifier and Type | Method and Description |
|---|---|
Feature |
decodeLoc(SOURCE source)
Decode a line to obtain just its FeatureLoc for indexing -- contig, start, and stop.
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java.lang.Class<FEATURE_TYPE> |
getFeatureType()
This function returns the object the codec generates.
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, waitcanDecode, close, decode, getTabixFormat, isDone, makeIndexableSourceFromStream, makeSourceFromStream, readHeaderprotected AbstractFeatureCodec(java.lang.Class<FEATURE_TYPE> myClass)
public Feature decodeLoc(SOURCE source) throws java.io.IOException
FeatureCodecdecodeLoc in interface FeatureCodec<FEATURE_TYPE extends Feature,SOURCE>source - the input stream from which to decode the next recordjava.io.IOExceptionpublic java.lang.Class<FEATURE_TYPE> getFeatureType()
FeatureCodecThis function returns the object the codec generates. This is allowed to be Feature in the case where conditionally different types are generated. Be as specific as you can though.
This function is used by reflections based tools, so we can know the underlying type
getFeatureType in interface FeatureCodec<FEATURE_TYPE extends Feature,SOURCE>