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 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:

    • 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