Package htsjdk.tribble.IntervalList

Class IntervalListCodec

java.lang.Object

htsjdk.tribble.AbstractFeatureCodec<T,LineIterator>

htsjdk.tribble.AsciiFeatureCodec<Interval>

htsjdk.tribble.IntervalList.IntervalListCodec

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

Constructor Summary

Constructors

Constructor	Description
IntervalListCodec()
IntervalListCodec(SAMSequenceDictionary dict)

Method Summary

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

Methods inherited from class htsjdk.tribble.AbstractFeatureCodec

decodeLoc, getFeatureType

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface htsjdk.tribble.FeatureCodec

getPathToDataFile, getTabixFormat

Constructor Details

IntervalListCodec

public IntervalListCodec()

IntervalListCodec

public IntervalListCodec(SAMSequenceDictionary dict)

Method Details

decode

public Interval decode(String line)

Specified by:

decode in class AsciiFeatureCodec<Interval>

See Also:

• AsciiFeatureCodec.decode(htsjdk.tribble.readers.LineIterator)

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 class AsciiFeatureCodec<Interval>

Returns:

the actual header data in the file, or null if none is available

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