edu.msu.cme.rdp.classifier.readseqwrapper
Interface Sequence

All Known Implementing Classes:

ParsedSequence

public interface Sequence

An abstract class, providing an interface for accessing a sequence.

Field Summary

static int	MASK The mask for converting a string to integer
static int	RNA_BASES The number of rna bases (ATGC).
static int	WORDSIZE The size of a word.

Method Summary

int[]	createWordIndexArr() Fetches every overlapping word from the sequence string, changes each word to integer format and saves in an array.
int	getGoodWordCount() Returns the number of words without invalid base(s).
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 sequence string.
java.lang.String	getSeqString() Returns the sequence string of the sequence record.
java.lang.String	getTitle() Returns the title of the sequence record.
boolean	isReverse() Returns true if the sequence string is a minus strand.

Field Detail

RNA_BASES

static final int RNA_BASES

The number of rna bases (ATGC). Initially set to 4.

See Also:

Constant Field Values

WORDSIZE

static final int WORDSIZE

The size of a word. Initially set to 8.

See Also:

Constant Field Values

MASK

static final int MASK

The mask for converting a string to integer

See Also:

Constant Field Values

Method Detail

getName

java.lang.String getName()

Returns the name of the sequence record.

getTitle

java.lang.String getTitle()

Returns the title of the sequence record.

getSeqString

java.lang.String getSeqString()

Returns the sequence string of the sequence record.

getReversedSeq

Sequence getReversedSeq()

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

createWordIndexArr

int[] createWordIndexArr()

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

getGoodWordCount

int getGoodWordCount()

Returns the number of words without invalid base(s).

isReverse

boolean isReverse()

Returns true if the sequence string is a minus strand.