Package org.biojava.bio.dp.twohead
Class PairwiseDP
java.lang.Object
org.biojava.bio.dp.DP
org.biojava.bio.dp.twohead.PairwiseDP
- All Implemented Interfaces:
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:
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Nested Class Summary
Nested classes/interfaces inherited from class org.biojava.bio.dp.DP
DP.ReverseIterator
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptiondouble
backward
(SymbolList[] seqs, ScoreType scoreType) backwardMatrix
(SymbolList[] seqs, DPMatrix d, ScoreType scoreType) backwardMatrix
(SymbolList[] seqs, ScoreType scoreType) double
forward
(SymbolList[] seqs, ScoreType scoreType) forwardMatrix
(SymbolList[] seqs, DPMatrix d, ScoreType scoreType) forwardMatrix
(SymbolList[] seqs, ScoreType scoreType) void
update()
viterbi
(SymbolList[] seqs, ScoreType scoreType) 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, scoreWeightMatrix, setModel, stateList, unlockModel
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Constructor Details
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PairwiseDP
public PairwiseDP(MarkovModel mm, CellCalculatorFactoryMaker ccfm) throws IllegalSymbolException, IllegalTransitionException, BioException
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Method Details
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update
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backward
public double backward(SymbolList[] seqs, ScoreType scoreType) throws IllegalSymbolException, IllegalAlphabetException, IllegalTransitionException - Specified by:
backward
in classDP
- Throws:
IllegalSymbolException
IllegalAlphabetException
IllegalTransitionException
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backwardMatrix
public DPMatrix backwardMatrix(SymbolList[] seqs, ScoreType scoreType) throws IllegalSymbolException, IllegalAlphabetException, IllegalTransitionException - Specified by:
backwardMatrix
in classDP
- Throws:
IllegalSymbolException
IllegalAlphabetException
IllegalTransitionException
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backwardMatrix
public DPMatrix backwardMatrix(SymbolList[] seqs, DPMatrix d, ScoreType scoreType) throws IllegalSymbolException, IllegalAlphabetException, IllegalTransitionException - Specified by:
backwardMatrix
in classDP
- Throws:
IllegalSymbolException
IllegalAlphabetException
IllegalTransitionException
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forward
public double forward(SymbolList[] seqs, ScoreType scoreType) throws IllegalSymbolException, IllegalAlphabetException, IllegalTransitionException - Specified by:
forward
in classDP
- Throws:
IllegalSymbolException
IllegalAlphabetException
IllegalTransitionException
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forwardMatrix
public DPMatrix forwardMatrix(SymbolList[] seqs, ScoreType scoreType) throws IllegalSymbolException, IllegalAlphabetException, IllegalTransitionException - Specified by:
forwardMatrix
in classDP
- Throws:
IllegalSymbolException
IllegalAlphabetException
IllegalTransitionException
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forwardMatrix
public DPMatrix forwardMatrix(SymbolList[] seqs, DPMatrix d, ScoreType scoreType) throws IllegalSymbolException, IllegalAlphabetException, IllegalTransitionException - Specified by:
forwardMatrix
in classDP
- Throws:
IllegalSymbolException
IllegalAlphabetException
IllegalTransitionException
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viterbi
public StatePath viterbi(SymbolList[] seqs, ScoreType scoreType) throws IllegalSymbolException, IllegalAlphabetException, IllegalTransitionException - Specified by:
viterbi
in classDP
- Throws:
IllegalSymbolException
IllegalAlphabetException
IllegalTransitionException
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