Package org.biojava.bio.dp.onehead

Class SmallCursor

java.lang.Object

org.biojava.bio.dp.onehead.SmallCursor

All Implemented Interfaces:

DPCursor

public class SmallCursor
extends Object

Constant-memory implementation of single-head DP cursor.

Author:

Matthew Pocock

Constructor Summary

Constructors

Constructor	Description
SmallCursor(State[] states, SymbolList symList, Iterator symIterator)

Method Summary

Modifier and Type	Method	Description
void	advance()	Advance.
boolean	canAdvance()	Can we advance?
double[]	currentCol()	The current column of the matrix.
Symbol	currentRes()	The current symbol.
double[]	lastCol()	The previous column.
Symbol	lastRes()	The previous symbol.
int	length()	The length of the sequence.
SymbolList	symList()	The symbol list being looped over.

Methods inherited from class java.lang.Object

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

Constructor Detail

SmallCursor

public SmallCursor(State[] states,
                   SymbolList symList,
                   Iterator symIterator)

Method Detail

symList

public SymbolList symList()

Description copied from interface: DPCursor

The symbol list being looped over.

length

public int length()

Description copied from interface: DPCursor

The length of the sequence.

The matrix may allocate length+1 columns.

currentCol

public double[] currentCol()

Description copied from interface: DPCursor

The current column of the matrix.

lastCol

public double[] lastCol()

Description copied from interface: DPCursor

The previous column.

advance

public void advance()

Description copied from interface: DPCursor

Advance.

Specified by:

advance in interface DPCursor

currentRes

public Symbol currentRes()

Description copied from interface: DPCursor

The current symbol.

Specified by:

currentRes in interface DPCursor

lastRes

public Symbol lastRes()

Description copied from interface: DPCursor

The previous symbol.

Specified by:

lastRes in interface DPCursor

canAdvance

public boolean canAdvance()

Description copied from interface: DPCursor

Can we advance?

Specified by:

canAdvance in interface DPCursor