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:

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 and 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

Modifier and Type	Method and 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.