Package htsjdk.tribble.IntervalList
Class IntervalListCodec
- java.lang.Object
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- htsjdk.tribble.AbstractFeatureCodec<T,LineIterator>
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- htsjdk.tribble.AsciiFeatureCodec<Interval>
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- htsjdk.tribble.IntervalList.IntervalListCodec
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- All Implemented Interfaces:
FeatureCodec<Interval,LineIterator>
public class IntervalListCodec extends AsciiFeatureCodec<Interval>
A tribble codec for IntervalLists. Also contains the parsing code for the non-tribble parsing of IntervalLists
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Constructor Summary
Constructors Constructor Description IntervalListCodec()
IntervalListCodec(SAMSequenceDictionary dict)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description boolean
canDecode(String s)
This function returns true iff the File potentialInput can be parsed by this codec.Interval
decode(String line)
Object
readActualHeader(LineIterator lineIterator)
Read and return the header, or null if there is no header.-
Methods inherited from class htsjdk.tribble.AsciiFeatureCodec
close, decode, isDone, makeIndexableSourceFromStream, makeSourceFromStream, readHeader
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Methods inherited from class htsjdk.tribble.AbstractFeatureCodec
decodeLoc, getFeatureType
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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
getPathToDataFile, getTabixFormat
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Constructor Detail
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IntervalListCodec
public IntervalListCodec()
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IntervalListCodec
public IntervalListCodec(SAMSequenceDictionary dict)
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Method Detail
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decode
public Interval decode(String line)
- Specified by:
decode
in classAsciiFeatureCodec<Interval>
- See Also:
AsciiFeatureCodec.decode(htsjdk.tribble.readers.LineIterator)
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readActualHeader
public Object readActualHeader(LineIterator lineIterator)
Description copied from class:AsciiFeatureCodec
Read and return the header, or null if there is no header.- Specified by:
readActualHeader
in classAsciiFeatureCodec<Interval>
- Returns:
- the actual header data in the file, or null if none is available
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canDecode
public boolean canDecode(String s)
Description copied from interface:FeatureCodec
This function returns true iff the File potentialInput can be parsed by this codec. Note that checking the file's extension is a perfectly acceptable implementation of this method and file contents only rarely need to be checked.
There is an assumption that there's never a situation where two different Codecs return true for the same file. If this occurs, the recommendation would be to error out.
Note this function must never throw an error. All errors should be trapped and false returned.- Parameters:
s
- the file to test for parsability with this codec- Returns:
- true if potentialInput can be parsed, false otherwise
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