Package org.biojava.bio.dp.twohead

Class DPInterpreter

java.lang.Object

org.biojava.bio.dp.twohead.DPInterpreter

All Implemented Interfaces:

Serializable, CellCalculatorFactory

public class DPInterpreter
extends Object
implements CellCalculatorFactory, Serializable

Author:

Matthew Pocock, Thomas Down

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	DPInterpreter.Maker

Constructor Summary

Constructors

Constructor	Description
DPInterpreter(DP dp)

Method Summary

Modifier and Type	Method	Description
CellCalculator	backwards(ScoreType scoreType)
CellCalculator	forwards(ScoreType scoreType)
CellCalculator	viterbi(ScoreType scoreType, BackPointer terminal)

Methods inherited from class java.lang.Object

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

Constructor Detail

DPInterpreter

public DPInterpreter(DP dp)

Method Detail

forwards

public CellCalculator forwards(ScoreType scoreType)
                        throws IllegalSymbolException,
                               IllegalAlphabetException,
                               IllegalTransitionException

Specified by:

forwards in interface CellCalculatorFactory

Throws:

IllegalSymbolException

IllegalAlphabetException

IllegalTransitionException

backwards

public CellCalculator backwards(ScoreType scoreType)
                         throws IllegalSymbolException,
                                IllegalAlphabetException,
                                IllegalTransitionException

Specified by:

backwards in interface CellCalculatorFactory

Throws:

IllegalSymbolException

IllegalAlphabetException

IllegalTransitionException

viterbi

public CellCalculator viterbi(ScoreType scoreType,
                              BackPointer terminal)
                       throws IllegalSymbolException,
                              IllegalAlphabetException,
                              IllegalTransitionException

Specified by:

viterbi in interface CellCalculatorFactory

Throws:

IllegalSymbolException

IllegalAlphabetException

IllegalTransitionException