org.biojava.bio.dp
Class DP
java.lang.Object
|
+--org.biojava.bio.dp.DP
- Direct Known Subclasses:
- PairwiseDP
- public abstract class DP
- extends java.lang.Object
Method Summary |
abstract double |
backward(SymbolList[] resList)
|
abstract DPMatrix |
backwardMatrix(SymbolList[] resList)
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abstract DPMatrix |
backwardMatrix(SymbolList[] resList,
DPMatrix matrix)
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static int[][] |
backwardTransitions(MarkovModel model,
State[] states)
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static double[][] |
backwardTransitionScores(MarkovModel model,
State[] states,
int[][] transitions)
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static MarkovModel |
flatView(MarkovModel model)
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abstract double |
forward(SymbolList[] resList)
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abstract DPMatrix |
forwardMatrix(SymbolList[] resList)
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abstract DPMatrix |
forwardMatrix(SymbolList[] resList,
DPMatrix matrix)
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DPMatrix |
forwardsBackwards(SymbolList[] resList)
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static int[][] |
forwardTransitions(MarkovModel model,
State[] states)
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static double[][] |
forwardTransitionScores(MarkovModel model,
State[] states,
int[][] transitions)
|
StatePath |
generate(int length)
Generates an alignment from a model. |
int[][] |
getBackwardTransitions()
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double[][] |
getBackwardTransitionScores()
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int |
getDotStatesIndex()
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int[][] |
getForwardTransitions()
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double[][] |
getForwardTransitionScores()
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MarkovModel |
getModel()
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State[] |
getStates()
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void |
lockModel()
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static double |
scoreWeightMatrix(WeightMatrix matrix,
SymbolList symList,
int start)
Scores the SymbolList from symbol start to symbol (start+columns) with a
weight matrix. |
static State[] |
stateList(MarkovModel mm)
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void |
unlockModel()
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void |
updateTransitions()
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abstract StatePath |
viterbi(SymbolList[] resList)
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Methods inherited from class java.lang.Object |
clone,
equals,
finalize,
getClass,
hashCode,
notify,
notifyAll,
toString,
wait,
wait,
wait |
DP
public DP(MarkovModel model)
throws IllegalSymbolException,
IllegalTransitionException,
BioException
scoreWeightMatrix
public static double scoreWeightMatrix(WeightMatrix matrix,
SymbolList symList,
int start)
throws IllegalSymbolException
- Scores the SymbolList from symbol start to symbol (start+columns) with a
weight matrix.
- Parameters:
matrix
- the weight matrix used to evaluate the sequencessymList
- the SymbolList to assessstart
- the index of the first symbol in the window to evaluate- Returns:
- the log probability or likelyhood of this weight matrix
having generated symbols start to (start + columns) of symList
flatView
public static MarkovModel flatView(MarkovModel model)
throws IllegalAlphabetException,
IllegalSymbolException
stateList
public static State[] stateList(MarkovModel mm)
throws IllegalSymbolException,
IllegalTransitionException,
BioException
forwardTransitions
public static int[][] forwardTransitions(MarkovModel model,
State[] states)
throws IllegalSymbolException
forwardTransitionScores
public static double[][] forwardTransitionScores(MarkovModel model,
State[] states,
int[][] transitions)
throws IllegalSymbolException
backwardTransitions
public static int[][] backwardTransitions(MarkovModel model,
State[] states)
throws IllegalSymbolException
backwardTransitionScores
public static double[][] backwardTransitionScores(MarkovModel model,
State[] states,
int[][] transitions)
throws IllegalSymbolException
getDotStatesIndex
public int getDotStatesIndex()
getModel
public MarkovModel getModel()
getStates
public State[] getStates()
getForwardTransitions
public int[][] getForwardTransitions()
getForwardTransitionScores
public double[][] getForwardTransitionScores()
getBackwardTransitions
public int[][] getBackwardTransitions()
getBackwardTransitionScores
public double[][] getBackwardTransitionScores()
lockModel
public void lockModel()
unlockModel
public void unlockModel()
updateTransitions
public void updateTransitions()
forward
public abstract double forward(SymbolList[] resList)
throws IllegalSymbolException,
IllegalAlphabetException,
IllegalTransitionException
backward
public abstract double backward(SymbolList[] resList)
throws IllegalSymbolException,
IllegalAlphabetException,
IllegalTransitionException
forwardMatrix
public abstract DPMatrix forwardMatrix(SymbolList[] resList)
throws IllegalSymbolException,
IllegalAlphabetException,
IllegalTransitionException
backwardMatrix
public abstract DPMatrix backwardMatrix(SymbolList[] resList)
throws IllegalSymbolException,
IllegalAlphabetException,
IllegalTransitionException
forwardMatrix
public abstract DPMatrix forwardMatrix(SymbolList[] resList,
DPMatrix matrix)
throws java.lang.IllegalArgumentException,
IllegalSymbolException,
IllegalAlphabetException,
IllegalTransitionException
backwardMatrix
public abstract DPMatrix backwardMatrix(SymbolList[] resList,
DPMatrix matrix)
throws java.lang.IllegalArgumentException,
IllegalSymbolException,
IllegalAlphabetException,
IllegalTransitionException
viterbi
public abstract StatePath viterbi(SymbolList[] resList)
throws IllegalSymbolException,
java.lang.IllegalArgumentException,
IllegalAlphabetException,
IllegalTransitionException
forwardsBackwards
public DPMatrix forwardsBackwards(SymbolList[] resList)
throws BioException
generate
public StatePath generate(int length)
throws IllegalSymbolException,
BioException
- Generates an alignment from a model.
If the length is set to -1 then the model length will be sampled
using the model's transition to the end state. If the length is
fixed using length, then the transitions to the end state are implicitly
invoked.
- Parameters:
length
- the length of the sequence to generate- Returns:
- a StatePath generated at random