org.biojava.bio.dp.twohead
Class PairwiseDP
java.lang.Object
org.biojava.bio.dp.DP
org.biojava.bio.dp.twohead.PairwiseDP
- All Implemented Interfaces:
- java.io.Serializable
- public class PairwiseDP
- extends DP
- implements java.io.Serializable
Algorithms for dynamic programming (alignments) between pairs
of SymbolLists.
Based on a single-head DP implementation by Matt Pocock.
- Author:
- Thomas Down, Matthew Pocock
- See Also:
- Serialized Form
Methods inherited from class org.biojava.bio.dp.DP |
backwardTransitions, backwardTransitionScores, flatView, forwardsBackwards, forwardTransitions, forwardTransitionScores, generate, getBackwardTransitions, getBackwardTransitionScores, getDotStatesIndex, getForwardTransitions, getForwardTransitionScores, getModel, getStates, lockModel, scoreWeightMatrix, stateList, unlockModel |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
PairwiseDP
public PairwiseDP(MarkovModel mm,
CellCalculatorFactoryMaker ccfm)
throws IllegalSymbolException,
IllegalTransitionException,
BioException
update
public void update()
- Overrides:
update
in class DP
backward
public double backward(SymbolList[] seqs,
ScoreType scoreType)
throws IllegalSymbolException,
IllegalAlphabetException,
IllegalTransitionException
- Specified by:
backward
in class DP
- Throws:
IllegalSymbolException
IllegalAlphabetException
IllegalTransitionException
backwardMatrix
public DPMatrix backwardMatrix(SymbolList[] seqs,
ScoreType scoreType)
throws IllegalSymbolException,
IllegalAlphabetException,
IllegalTransitionException
- Specified by:
backwardMatrix
in class DP
- Throws:
IllegalSymbolException
IllegalAlphabetException
IllegalTransitionException
backwardMatrix
public DPMatrix backwardMatrix(SymbolList[] seqs,
DPMatrix d,
ScoreType scoreType)
throws IllegalSymbolException,
IllegalAlphabetException,
IllegalTransitionException
- Specified by:
backwardMatrix
in class DP
- Throws:
IllegalSymbolException
IllegalAlphabetException
IllegalTransitionException
forward
public double forward(SymbolList[] seqs,
ScoreType scoreType)
throws IllegalSymbolException,
IllegalAlphabetException,
IllegalTransitionException
- Specified by:
forward
in class DP
- Throws:
IllegalSymbolException
IllegalAlphabetException
IllegalTransitionException
forwardMatrix
public DPMatrix forwardMatrix(SymbolList[] seqs,
ScoreType scoreType)
throws IllegalSymbolException,
IllegalAlphabetException,
IllegalTransitionException
- Specified by:
forwardMatrix
in class DP
- Throws:
IllegalSymbolException
IllegalAlphabetException
IllegalTransitionException
forwardMatrix
public DPMatrix forwardMatrix(SymbolList[] seqs,
DPMatrix d,
ScoreType scoreType)
throws IllegalSymbolException,
IllegalAlphabetException,
IllegalTransitionException
- Specified by:
forwardMatrix
in class DP
- Throws:
IllegalSymbolException
IllegalAlphabetException
IllegalTransitionException
viterbi
public StatePath viterbi(SymbolList[] seqs,
ScoreType scoreType)
throws IllegalSymbolException,
IllegalAlphabetException,
IllegalTransitionException
- Specified by:
viterbi
in class DP
- Throws:
IllegalSymbolException
IllegalAlphabetException
IllegalTransitionException