Package edu.msu.cme.rdp.classifier.utils
Class ClassifierSequence
java.lang.Object
edu.msu.cme.rdp.readseq.readers.Sequence
edu.msu.cme.rdp.classifier.utils.ClassifierSequence
- All Implemented Interfaces:
Serializable
public class ClassifierSequence
extends edu.msu.cme.rdp.readseq.readers.Sequence
A Sequence containing the sequence information.
- See Also:
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Field Summary
Fields inherited from class edu.msu.cme.rdp.readseq.readers.Sequence
desc, seqName, seqString
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Constructor Summary
ConstructorsConstructorDescriptionClassifierSequence
(edu.msu.cme.rdp.readseq.readers.Sequence seq) Creates new ParsedSequence.ClassifierSequence
(String seqName, String desc, String seqString) -
Method Summary
Modifier and TypeMethodDescriptionint
Returns the number of words with valid bases.Returns a Sequence object whose sequence string is the reverse complement of the current rRNA sequence string.int[]
boolean
Returns true if the sequence string is a minus strand.protected void
Sets the sequence string.Methods inherited from class edu.msu.cme.rdp.readseq.readers.Sequence
getDesc, getSeqName, getSeqString
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Constructor Details
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ClassifierSequence
Creates new ParsedSequence.- Throws:
IOException
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ClassifierSequence
- Throws:
IOException
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Method Details
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setSeqString
Sets the sequence string. -
getWordIndexArr
public int[] getWordIndexArr() -
isReverse
public boolean isReverse()Returns true if the sequence string is a minus strand. -
getReversedSeq
Returns a Sequence object whose sequence string is the reverse complement of the current rRNA sequence string.- Throws:
IOException
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getGoodWordCount
public int getGoodWordCount()Returns the number of words with valid bases.
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