public class ClassifierSequence
extends edu.msu.cme.rdp.readseq.readers.Sequence
Constructor and Description |
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ClassifierSequence(edu.msu.cme.rdp.readseq.readers.Sequence seq)
Creates new ParsedSequence.
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ClassifierSequence(java.lang.String seqName,
java.lang.String desc,
java.lang.String seqString) |
Modifier and Type | Method and Description |
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int |
getGoodWordCount()
Returns the number of words with valid bases.
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ClassifierSequence |
getReversedSeq()
Returns a Sequence object whose sequence string is the reverse complement
of the current rRNA sequence string.
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int[] |
getWordIndexArr() |
boolean |
isReverse()
Returns true if the sequence string is a minus strand.
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protected void |
setSeqString(java.lang.String s)
Sets the sequence string.
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public ClassifierSequence(edu.msu.cme.rdp.readseq.readers.Sequence seq) throws java.io.IOException
java.io.IOException
public ClassifierSequence(java.lang.String seqName, java.lang.String desc, java.lang.String seqString) throws java.io.IOException
java.io.IOException
protected void setSeqString(java.lang.String s)
public int[] getWordIndexArr()
public boolean isReverse()
public ClassifierSequence getReversedSeq() throws java.io.IOException
java.io.IOException
public int getGoodWordCount()