Package fr.ens.biologie.genomique.eoulsan.modules.fastqc

Class FastqSequenceFile

java.lang.Object
fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastqSequenceFile
All Implemented Interfaces:
CounterSequenceFile, uk.ac.babraham.FastQC.Sequence.SequenceFile
public class FastqSequenceFile extends Object implements CounterSequenceFile
This class define a SequenceFile for FASTQ files.
Since:
2.0
Author:
Laurent Jourdren

  • Constructor Details

    • FastqSequenceFile

      public FastqSequenceFile(DataFile fastqFile) throws IOException
      Public constructor.
      Parameters:
      fastqFile - FASTQ input file
      Throws:
      IOException - if an error occurs when opening the file

  • Method Details

    • getFile

      public File getFile()
      Specified by:
      getFile in interface uk.ac.babraham.FastQC.Sequence.SequenceFile

    • getPercentComplete

      public int getPercentComplete()
      Specified by:
      getPercentComplete in interface uk.ac.babraham.FastQC.Sequence.SequenceFile

    • hasNext

      public boolean hasNext()
      Specified by:
      hasNext in interface uk.ac.babraham.FastQC.Sequence.SequenceFile

    • isColorspace

      public boolean isColorspace()
      Specified by:
      isColorspace in interface uk.ac.babraham.FastQC.Sequence.SequenceFile

    • name

      public String name()
      Specified by:
      name in interface uk.ac.babraham.FastQC.Sequence.SequenceFile

    • next

      public uk.ac.babraham.FastQC.Sequence.Sequence next() throws uk.ac.babraham.FastQC.Sequence.SequenceFormatException
      Specified by:
      next in interface uk.ac.babraham.FastQC.Sequence.SequenceFile
      Throws:
      uk.ac.babraham.FastQC.Sequence.SequenceFormatException

    • getCount

      public long getCount()
      Description copied from interface: CounterSequenceFile
      Get the count of the read entries.
      Specified by:
      getCount in interface CounterSequenceFile
      Returns:
      the count of the read entries