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Packages that use MarkovModel | |
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org.biojava.bio.dp | HMM and Dynamic Programming Algorithms. |
org.biojava.bio.dp.onehead | |
org.biojava.bio.dp.twohead | |
org.biojava.bio.program.hmmer | Tools for working with profile Hidden Markov Models from the HMMer package. |
Uses of MarkovModel in org.biojava.bio.dp |
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Classes in org.biojava.bio.dp that implement MarkovModel | |
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class |
ProfileHMM
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class |
SimpleMarkovModel
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class |
WMAsMM
Wraps a weight matrix up so that it appears to be a very simple HMM. |
Methods in org.biojava.bio.dp that return MarkovModel | |
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static MarkovModel |
DP.flatView(MarkovModel model)
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MarkovModel |
SimpleModelInState.getModel()
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MarkovModel |
ModelInState.getModel()
The model that is inside this state. |
MarkovModel |
DP.getModel()
|
MarkovModel |
DPMatrix.model()
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static MarkovModel |
XmlMarkovModel.readModel(org.w3c.dom.Element root)
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Methods in org.biojava.bio.dp with parameters of type MarkovModel | |
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static int[][] |
DP.backwardTransitions(MarkovModel model,
State[] states)
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static double[][] |
DP.backwardTransitionScores(MarkovModel model,
State[] states,
int[][] transitions,
ScoreType scoreType)
|
DP |
DPFactory.createDP(MarkovModel model)
|
DP |
DPFactory.DefaultFactory.createDP(MarkovModel model)
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static MarkovModel |
DP.flatView(MarkovModel model)
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static int[][] |
DP.forwardTransitions(MarkovModel model,
State[] states)
Returns a matrix for the specified States describing all valid Transitions between those States. |
static double[][] |
DP.forwardTransitionScores(MarkovModel model,
State[] states,
int[][] transitions,
ScoreType scoreType)
Compute the log(score) of all transitions between the specified States. |
void |
SimpleModelTrainer.registerModel(MarkovModel model)
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void |
ModelTrainer.registerModel(MarkovModel model)
Registers an HMM with this trainer. |
void |
DP.setModel(MarkovModel model)
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State[] |
DP.stateList(MarkovModel mm)
|
static void |
XmlMarkovModel.writeModel(MarkovModel model,
java.io.PrintStream out)
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Constructors in org.biojava.bio.dp with parameters of type MarkovModel | |
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DP(MarkovModel model)
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SimpleHMMTrainer(MarkovModel model)
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SimpleModelInState(MarkovModel model,
java.lang.String name)
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Uses of MarkovModel in org.biojava.bio.dp.onehead |
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Fields in org.biojava.bio.dp.onehead declared as MarkovModel | |
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protected MarkovModel |
SingleDPMatrix.model
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Methods in org.biojava.bio.dp.onehead that return MarkovModel | |
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MarkovModel |
SingleDPMatrix.model()
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Constructors in org.biojava.bio.dp.onehead with parameters of type MarkovModel | |
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SingleDP(MarkovModel model)
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Uses of MarkovModel in org.biojava.bio.dp.twohead |
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Methods in org.biojava.bio.dp.twohead that return MarkovModel | |
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MarkovModel |
PairDPMatrix.model()
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Methods in org.biojava.bio.dp.twohead with parameters of type MarkovModel | |
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static java.lang.String |
DPCompiler.makeName(java.lang.String prefix,
MarkovModel model)
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Constructors in org.biojava.bio.dp.twohead with parameters of type MarkovModel | |
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PairwiseDP(MarkovModel mm,
CellCalculatorFactoryMaker ccfm)
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Uses of MarkovModel in org.biojava.bio.program.hmmer |
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Classes in org.biojava.bio.program.hmmer that implement MarkovModel | |
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class |
FullHmmerProfileHMM
This is a class for representing the full HMMER generated Profile HMM (including loop states N and C terminal looping states). |
class |
HmmerProfileHMM
This is a class for representing HMMER generated Profile HMM. |
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