Package htsjdk.samtools.util
Interface SortingCollection.Codec<T>
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- All Superinterfaces:
Cloneable
- All Known Implementing Classes:
BAMRecordCodec
,IntervalCodec
,VCFRecordCodec
- Enclosing class:
- SortingCollection<T>
public static interface SortingCollection.Codec<T> extends Cloneable
Client must implement this class, which defines the way in which records are written to and read from file.
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description SortingCollection.Codec<T>
clone()
Must return a cloned copy of the codec that can be used independently of the original instance.T
decode()
Read the next record from the input stream and convert into a java object.void
encode(T val)
Write object to output streamvoid
setInputStream(InputStream is)
Where to read encoded input fromvoid
setOutputStream(OutputStream os)
Where to write encoded output
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Method Detail
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setOutputStream
void setOutputStream(OutputStream os)
Where to write encoded output
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setInputStream
void setInputStream(InputStream is)
Where to read encoded input from
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encode
void encode(T val)
Write object to output stream- Parameters:
val
- what to write
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decode
T decode()
Read the next record from the input stream and convert into a java object.- Returns:
- null if no more records. Should throw exception if EOF is encountered in the middle of a record.
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clone
SortingCollection.Codec<T> clone()
Must return a cloned copy of the codec that can be used independently of the original instance. This is required so that multiple codecs can exist simultaneously that each is reading a separate file.
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