Class LineageSequenceParser


  • public class LineageSequenceParser
    extends java.lang.Object
    A parser to parse a reader containing the raw sequences.
    • Field Summary

      Fields 
      Modifier and Type Field Description
      static java.lang.String delimiter  
    • Constructor Summary

      Constructors 
      Constructor Description
      LineageSequenceParser​(java.io.File inFile)
      Creates new RawSequenceParser to parse the input fasta file.
      LineageSequenceParser​(java.io.InputStream is)
      Creates new RawSequenceParser to parse the input fasta file.
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void close()
      Closes the reader.
      boolean hasNext()
      Returns true if there is a parsed sequence available.
      LineageSequence next()
      Returns the next parsed sequence.
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Constructor Detail

      • LineageSequenceParser

        public LineageSequenceParser​(java.io.File inFile)
                              throws java.io.IOException
        Creates new RawSequenceParser to parse the input fasta file.
        Throws:
        java.io.IOException
      • LineageSequenceParser

        public LineageSequenceParser​(java.io.InputStream is)
                              throws java.io.IOException
        Creates new RawSequenceParser to parse the input fasta file.
        Throws:
        java.io.IOException
    • Method Detail

      • close

        public void close()
                   throws java.io.IOException
        Closes the reader.
        Throws:
        java.io.IOException
      • hasNext

        public boolean hasNext()
                        throws java.io.IOException
        Returns true if there is a parsed sequence available.
        Throws:
        java.io.IOException
      • next

        public LineageSequence next()
                             throws java.util.NoSuchElementException,
                                    java.io.IOException
        Returns the next parsed sequence.
        Throws:
        java.util.NoSuchElementException
        java.io.IOException