edu.msu.cme.rdp.classifier.readseqwrapper
Class ParsedSequence

java.lang.Object
  edu.msu.cme.rdp.classifier.readseqwrapper.ParsedSequence

All Implemented Interfaces:

Sequence

public class ParsedSequence
extends java.lang.Object
implements Sequence

A Sequence containing the sequence information.

Field Summary

private static int[]	charIntegerLookup
private static char[]	complementLookup
private java.lang.String	docText
private java.lang.Integer	goodWordCount
private static int[]	intComplementLookup
private static int	MAX_ASCII
private java.lang.String	name
private boolean	reverse
private java.lang.String	seqString
private java.lang.String	title

Fields inherited from interface edu.msu.cme.rdp.classifier.readseqwrapper.Sequence

MASK, RNA_BASES, WORDSIZE

Constructor Summary

ParsedSequence(java.lang.String name, java.lang.String seq)
Creates new ParsedSequence.

ParsedSequence(java.lang.String name, java.lang.String title, java.lang.String doc, java.lang.String seq)
Creates new ParsedSequence.

Method Summary

int[]	createWordIndexArr() Fetches every overlapping word from the sequence string, changes each word to integer format and saves in an array.
java.lang.String	getDocumentText() Returns the whole documentation in text.
int	getGoodWordCount() Returns the number of words with valid bases.
java.lang.String	getName() Returns the name of the sequence record.
Sequence	getReversedSeq() Returns a Sequence object whose sequence string is the reverse complement of the current rRNA sequence string.
static java.lang.String	getReversedSeqString(java.lang.String seqString) Returns the reverse complement string of the given rRNA sequence string .
static int[]	getReversedWord(int[] word) Returns the reverse complement of the word in an integer array format.
java.lang.String	getSeqString() Returns the sequence string.
java.lang.String	getTitle() Returns the title of the documentation of the sequcence record.
static int	getWordIndex(int[] word) Returns an integer representation of a single word.
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 java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

name

private java.lang.String name

title

private java.lang.String title

seqString

private java.lang.String seqString

docText

private java.lang.String docText

reverse

private boolean reverse

goodWordCount

private java.lang.Integer goodWordCount

MAX_ASCII

private static final int MAX_ASCII

See Also:

Constant Field Values

complementLookup

private static char[] complementLookup

charIntegerLookup

private static int[] charIntegerLookup

intComplementLookup

private static int[] intComplementLookup

Constructor Detail

ParsedSequence

public ParsedSequence(java.lang.String name,
                      java.lang.String seq)

Creates new ParsedSequence.

ParsedSequence

public ParsedSequence(java.lang.String name,
                      java.lang.String title,
                      java.lang.String doc,
                      java.lang.String seq)

Creates new ParsedSequence.

Method Detail

setSeqString

protected void setSeqString(java.lang.String s)

Sets the sequence string.

getName

public java.lang.String getName()

Returns the name of the sequence record.

Specified by:

getName in interface Sequence

getSeqString

public java.lang.String getSeqString()

Returns the sequence string.

Specified by:

getSeqString in interface Sequence

getTitle

public java.lang.String getTitle()

Returns the title of the documentation of the sequcence record.

Specified by:

getTitle in interface Sequence

getDocumentText

public java.lang.String getDocumentText()

Returns the whole documentation in text.

isReverse

public boolean isReverse()

Returns true if the sequence string is a minus strand.

Specified by:

isReverse in interface Sequence

getReversedSeq

public Sequence getReversedSeq()

Returns a Sequence object whose sequence string is the reverse complement of the current rRNA sequence string.

Specified by:

getReversedSeq in interface Sequence

getReversedSeqString

public static java.lang.String getReversedSeqString(java.lang.String seqString)

Returns the reverse complement string of the given rRNA sequence string .

getReversedWord

public static int[] getReversedWord(int[] word)

Returns the reverse complement of the word in an integer array format.

getWordIndex

public static int getWordIndex(int[] word)

Returns an integer representation of a single word.

createWordIndexArr

public int[] createWordIndexArr()

Fetches every overlapping word from the sequence string, changes each word to integer format and saves in an array.

Specified by:

createWordIndexArr in interface Sequence

getGoodWordCount

public int getGoodWordCount()

Returns the number of words with valid bases.

Specified by:

getGoodWordCount in interface Sequence