org.biojava.bio.dp
Class PairwiseDP
java.lang.Object
|
+--org.biojava.bio.dp.DP
|
+--org.biojava.bio.dp.PairwiseDP
- 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)
throws IllegalSymbolException,
IllegalTransitionException,
BioException
updateTransitions
public void updateTransitions()
- Overrides:
- updateTransitions in class DP
getEmission
protected double[] getEmission(java.util.List symList,
CrossProductAlphabet alpha)
throws IllegalSymbolException
backward
public double backward(SymbolList[] seqs)
throws IllegalSymbolException,
IllegalAlphabetException,
IllegalTransitionException
- Overrides:
- backward in class DP
backwardMatrix
public DPMatrix backwardMatrix(SymbolList[] seqs)
throws IllegalSymbolException,
IllegalAlphabetException,
IllegalTransitionException
- Overrides:
- backwardMatrix in class DP
backwardMatrix
public DPMatrix backwardMatrix(SymbolList[] seqs,
DPMatrix d)
throws IllegalSymbolException,
IllegalAlphabetException,
IllegalTransitionException
- Overrides:
- backwardMatrix in class DP
forward
public double forward(SymbolList[] seqs)
throws IllegalSymbolException,
IllegalAlphabetException,
IllegalTransitionException
- Overrides:
- forward in class DP
forwardMatrix
public DPMatrix forwardMatrix(SymbolList[] seqs)
throws IllegalSymbolException,
IllegalAlphabetException,
IllegalTransitionException
- Overrides:
- forwardMatrix in class DP
forwardMatrix
public DPMatrix forwardMatrix(SymbolList[] seqs,
DPMatrix d)
throws IllegalSymbolException,
IllegalAlphabetException,
IllegalTransitionException
- Overrides:
- forwardMatrix in class DP
viterbi
public StatePath viterbi(SymbolList[] seqs)
throws IllegalSymbolException,
IllegalAlphabetException,
IllegalTransitionException
- Overrides:
- viterbi in class DP