Package htsjdk.tribble
Class AbstractFeatureCodec<FEATURE_TYPE extends Feature,SOURCE>
- java.lang.Object
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- htsjdk.tribble.AbstractFeatureCodec<FEATURE_TYPE,SOURCE>
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- All Implemented Interfaces:
FeatureCodec<FEATURE_TYPE,SOURCE>
- Direct Known Subclasses:
AsciiFeatureCodec
public abstract class AbstractFeatureCodec<FEATURE_TYPE extends Feature,SOURCE> extends Object implements FeatureCodec<FEATURE_TYPE,SOURCE>
Simple basic class providing much of the basic functionality of codecs Every concrete subclass must implementFeatureCodec.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 thatonly one codec is allowed to identify itself as being able to decode any given file.
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Constructor Summary
Constructors Modifier Constructor Description protected
AbstractFeatureCodec(Class<FEATURE_TYPE> myClass)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description Feature
decodeLoc(SOURCE source)
Decode a line to obtain just its FeatureLoc for indexing -- contig, start, and stop.Class<FEATURE_TYPE>
getFeatureType()
This function returns the object the codec generates.-
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Methods inherited from interface htsjdk.tribble.FeatureCodec
canDecode, close, decode, getPathToDataFile, getTabixFormat, isDone, makeIndexableSourceFromStream, makeSourceFromStream, readHeader
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Constructor Detail
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AbstractFeatureCodec
protected AbstractFeatureCodec(Class<FEATURE_TYPE> myClass)
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Method Detail
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decodeLoc
public Feature decodeLoc(SOURCE source) throws IOException
Description copied from interface:FeatureCodec
Decode a line to obtain just its FeatureLoc for indexing -- contig, start, and stop.- Specified by:
decodeLoc
in interfaceFeatureCodec<FEATURE_TYPE extends Feature,SOURCE>
- Parameters:
source
- the input stream from which to decode the next record- Returns:
- Return the FeatureLoc encoded by the line, or null if the line does not represent a feature (e.g. is a comment)
- Throws:
IOException
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getFeatureType
public Class<FEATURE_TYPE> getFeatureType()
Description copied from interface:FeatureCodec
This 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
- Specified by:
getFeatureType
in interfaceFeatureCodec<FEATURE_TYPE extends Feature,SOURCE>
- Returns:
- the feature type this codec generates.
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