org.biojava.bio.dp.onehead

Interface DPCursor

All Known Implementing Classes:

SmallCursor

public interface DPCursor

Encapsulates the dynamic programmming matrix, and the context within algorithms work. The cursor should put DP.MAGICAL_SYMBOL symbols at either end of the sequence.

Author:

Matthew Pocock

Method Summary

Methods

Modifier and Type	Method and 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.

Method Detail

symList

SymbolList symList()

The symbol list being looped over.

length

int length()

The length of the sequence.

The matrix may allocate length+1 columns.

currentCol

double[] currentCol()

The current column of the matrix.

lastCol

double[] lastCol()

The previous column.

currentRes

Symbol currentRes()

The current symbol.

lastRes

Symbol lastRes()

The previous symbol.

canAdvance

boolean canAdvance()

Can we advance?

advance

void advance()

Advance.