Class LineageSequence

  • All Implemented Interfaces:
    java.io.Serializable

    public class LineageSequence
    extends edu.msu.cme.rdp.readseq.readers.Sequence
    A ParsedRawSequence holds the data for a raw sequence.
    See Also:
    Serialized Form
    • Field Summary

      • Fields inherited from class edu.msu.cme.rdp.readseq.readers.Sequence

        desc, seqName, seqString
    • Constructor Summary

      Constructors 
      Constructor Description
      LineageSequence​(java.lang.String n, java.util.List<java.lang.String> al, java.lang.String seq)
      Creates new ParsedRawSequence.
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      java.util.List<java.lang.String> getAncestors()
      Returns the list of the ancestor taxa, with the highest ranked taxon first.
      java.lang.String getDesc()  
      edu.msu.cme.rdp.readseq.utils.orientation.GoodWordIterator getPartialSeqIteratorbyGoodBases​(int num_good_bases)  
      • Methods inherited from class edu.msu.cme.rdp.readseq.readers.Sequence

        getSeqName, getSeqString
      • Methods inherited from class java.lang.Object

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

      • LineageSequence

        public LineageSequence​(java.lang.String n,
                               java.util.List<java.lang.String> al,
                               java.lang.String seq)
        Creates new ParsedRawSequence.
    • Method Detail

      • getAncestors

        public java.util.List<java.lang.String> getAncestors()
        Returns the list of the ancestor taxa, with the highest ranked taxon first.
      • getDesc

        public java.lang.String getDesc()
        Overrides:
        getDesc in class edu.msu.cme.rdp.readseq.readers.Sequence
      • getPartialSeqIteratorbyGoodBases

        public edu.msu.cme.rdp.readseq.utils.orientation.GoodWordIterator getPartialSeqIteratorbyGoodBases​(int num_good_bases)
                                                                                                    throws java.io.IOException
        Throws:
        java.io.IOException