Class ClassifierSequence

  • All Implemented Interfaces:
    java.io.Serializable

    public class ClassifierSequence
    extends edu.msu.cme.rdp.readseq.readers.Sequence
    A Sequence containing the sequence information.
    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
      ClassifierSequence​(edu.msu.cme.rdp.readseq.readers.Sequence seq)
      Creates new ParsedSequence.
      ClassifierSequence​(java.lang.String seqName, java.lang.String desc, java.lang.String seqString)  
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      int getGoodWordCount()
      Returns the number of words with valid bases.
      ClassifierSequence getReversedSeq()
      Returns a Sequence object whose sequence string is the reverse complement of the current rRNA sequence string.
      int[] getWordIndexArr()  
      boolean isReverse()
      Returns true if the sequence string is a minus strand.
      protected void setSeqString​(java.lang.String s)
      Sets the sequence string.
      • Methods inherited from class edu.msu.cme.rdp.readseq.readers.Sequence

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

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

      • ClassifierSequence

        public ClassifierSequence​(edu.msu.cme.rdp.readseq.readers.Sequence seq)
                           throws java.io.IOException
        Creates new ParsedSequence.
        Throws:
        java.io.IOException
      • ClassifierSequence

        public ClassifierSequence​(java.lang.String seqName,
                                  java.lang.String desc,
                                  java.lang.String seqString)
                           throws java.io.IOException
        Throws:
        java.io.IOException
    • Method Detail

      • setSeqString

        protected void setSeqString​(java.lang.String s)
        Sets the sequence string.
      • getWordIndexArr

        public int[] getWordIndexArr()
      • isReverse

        public boolean isReverse()
        Returns true if the sequence string is a minus strand.
      • getReversedSeq

        public ClassifierSequence getReversedSeq()
                                          throws java.io.IOException
        Returns a Sequence object whose sequence string is the reverse complement of the current rRNA sequence string.
        Throws:
        java.io.IOException
      • getGoodWordCount

        public int getGoodWordCount()
        Returns the number of words with valid bases.