Class SAMSequenceFile

  • All Implemented Interfaces:
    CounterSequenceFile, uk.ac.babraham.FastQC.Sequence.SequenceFile

    public class SAMSequenceFile
    extends Object
    implements CounterSequenceFile
    This class define a SequenceFile for SAM files.
    Since:
    2.0
    Author:
    Laurent Jourdren
    • Constructor Detail

      • SAMSequenceFile

        public SAMSequenceFile​(DataFile inFile)
                        throws IOException
        Public constructor.
        Parameters:
        inFile - SAM input file
        Throws:
        IOException - if an error occurs when opening the file
    • Method Detail

      • 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