Package edu.msu.cme.rdp.classifier.utils
Class ClassifierSequence
- java.lang.Object
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- edu.msu.cme.rdp.readseq.readers.Sequence
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- edu.msu.cme.rdp.classifier.utils.ClassifierSequence
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- 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
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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)
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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.
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Constructor Detail
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ClassifierSequence
public ClassifierSequence(edu.msu.cme.rdp.readseq.readers.Sequence seq) throws java.io.IOException
Creates new ParsedSequence.- Throws:
java.io.IOException
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ClassifierSequence
public ClassifierSequence(java.lang.String seqName, java.lang.String desc, java.lang.String seqString) throws java.io.IOException
- Throws:
java.io.IOException
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Method Detail
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setSeqString
protected void setSeqString(java.lang.String s)
Sets the sequence string.
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getWordIndexArr
public int[] getWordIndexArr()
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isReverse
public boolean isReverse()
Returns true if the sequence string is a minus strand.
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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
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getGoodWordCount
public int getGoodWordCount()
Returns the number of words with valid bases.
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