|
||||||||||
PREV NEXT | FRAMES NO FRAMES |
Packages that use ScoreType | |
---|---|
org.biojava.bio.dp | HMM and Dynamic Programming Algorithms. |
org.biojava.bio.dp.onehead | |
org.biojava.bio.dp.twohead |
Uses of ScoreType in org.biojava.bio.dp |
---|
Classes in org.biojava.bio.dp that implement ScoreType | |
---|---|
static class |
ScoreType.NullModel
In this class, calculateScore returns the probability of a Symbol being emitted by the null model. |
static class |
ScoreType.Odds
In this class, calculateScore returns the odds ratio of a symbol being emitted. |
static class |
ScoreType.Probability
In this class, calculateScore returns the probability of a Symbol being emitted. |
Fields in org.biojava.bio.dp declared as ScoreType | |
---|---|
static ScoreType |
ScoreType.NULL_MODEL
|
static ScoreType |
ScoreType.ODDS
|
static ScoreType |
ScoreType.PROBABILITY
|
Methods in org.biojava.bio.dp with parameters of type ScoreType | |
---|---|
abstract double |
DP.backward(SymbolList[] symList,
ScoreType scoreType)
|
abstract DPMatrix |
DP.backwardMatrix(SymbolList[] symList,
DPMatrix matrix,
ScoreType scoreType)
|
abstract DPMatrix |
DP.backwardMatrix(SymbolList[] symList,
ScoreType scoreType)
|
static double[][] |
DP.backwardTransitionScores(MarkovModel model,
State[] states,
int[][] transitions,
ScoreType scoreType)
|
abstract double |
DP.forward(SymbolList[] symList,
ScoreType scoreType)
|
abstract DPMatrix |
DP.forwardMatrix(SymbolList[] symList,
DPMatrix matrix,
ScoreType scoreType)
|
abstract DPMatrix |
DP.forwardMatrix(SymbolList[] symList,
ScoreType scoreType)
|
DPMatrix |
DP.forwardsBackwards(SymbolList[] symList,
ScoreType scoreType)
|
static double[][] |
DP.forwardTransitionScores(MarkovModel model,
State[] states,
int[][] transitions,
ScoreType scoreType)
Compute the log(score) of all transitions between the specified States. |
double[][] |
DP.getBackwardTransitionScores(ScoreType scoreType)
|
double[][] |
DP.getForwardTransitionScores(ScoreType scoreType)
|
static double |
DP.scoreWeightMatrix(WeightMatrix matrix,
SymbolList symList,
ScoreType scoreType,
int start)
Scores the SymbolList from symbol start to symbol (start+columns) with a weight matrix using a particular ScoreType. |
protected double |
BaumWelchSampler.singleSequenceIteration(ModelTrainer trainer,
SymbolList symList,
ScoreType scoreType)
|
abstract StatePath |
DP.viterbi(SymbolList[] symList,
ScoreType scoreType)
|
Constructors in org.biojava.bio.dp with parameters of type ScoreType | |
---|---|
WeightMatrixAnnotator(WeightMatrix wm,
ScoreType scoreType,
double threshold)
Create a new annotator that uses a specific score type. |
|
WeightMatrixAnnotator(WeightMatrix wm,
ScoreType scoreType,
double threshold,
java.lang.String wmID)
Create a new annotator that uses the PROBABILITY score type and an ID for the weight matrix. |
Uses of ScoreType in org.biojava.bio.dp.onehead |
---|
Methods in org.biojava.bio.dp.onehead with parameters of type ScoreType | |
---|---|
protected void |
SingleDP.backward_initialize(DPCursor dpCursor,
ScoreType scoreType)
|
protected void |
SingleDP.backward_recurse(DPCursor dpCursor,
ScoreType scoreType)
|
protected double |
SingleDP.backward_termination(DPCursor dpCursor,
ScoreType scoreType)
|
protected double |
SingleDP.backward(DPCursor dpCursor,
ScoreType scoreType)
|
double |
SingleDP.backward(SymbolList[] seq,
ScoreType scoreType)
|
DPMatrix |
SingleDP.backwardMatrix(SymbolList[] seq,
DPMatrix matrix,
ScoreType scoreType)
|
DPMatrix |
SingleDP.backwardMatrix(SymbolList[] seq,
ScoreType scoreType)
|
protected void |
SingleDP.forward_initialize(DPCursor dpCursor,
ScoreType scoreType)
|
protected double |
SingleDP.forward(DPCursor dpCursor,
ScoreType scoreType)
|
double |
SingleDP.forward(SymbolList[] seq,
ScoreType scoreType)
|
DPMatrix |
SingleDP.forwardMatrix(SymbolList[] seq,
DPMatrix matrix,
ScoreType scoreType)
|
DPMatrix |
SingleDP.forwardMatrix(SymbolList[] seq,
ScoreType scoreType)
|
double[] |
SingleDP.getEmission(Symbol sym,
ScoreType scoreType)
This method is public for the benefit of training algorithms, and in the future we should look at a better way of exposing the emissions cache. |
StatePath |
SingleDP.viterbi(SymbolList[] symList,
ScoreType scoreType)
|
Uses of ScoreType in org.biojava.bio.dp.twohead |
---|
Constructors in org.biojava.bio.dp.twohead with parameters of type ScoreType | |
---|---|
EmissionCache(Alphabet alpha,
State[] states,
int dsi,
ScoreType scoreType)
|
|
||||||||||
PREV NEXT | FRAMES NO FRAMES |