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Packages that use WeightMatrix | |
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org.biojava.bio.dp | HMM and Dynamic Programming Algorithms. |
Uses of WeightMatrix in org.biojava.bio.dp |
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Classes in org.biojava.bio.dp that implement WeightMatrix | |
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class |
SimpleWeightMatrix
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Methods in org.biojava.bio.dp that return WeightMatrix | |
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static WeightMatrix |
XmlMarkovModel.readMatrix(Element root)
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Methods in org.biojava.bio.dp with parameters of type WeightMatrix | |
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static double |
DP.scoreWeightMatrix(WeightMatrix matrix,
SymbolList symList,
int start)
Scores the SymbolList from symbol start to symbol (start+columns) with a weight matrix. |
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. |
static void |
XmlMarkovModel.writeMatrix(WeightMatrix matrix,
PrintStream out)
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Constructors in org.biojava.bio.dp with parameters of type WeightMatrix | |
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WeightMatrixAnnotator(WeightMatrix wm,
double threshold)
Create a new annotator that uses PROBABILITY score type. |
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WeightMatrixAnnotator(WeightMatrix wm,
ScoreType scoreType,
double threshold)
Create a new annotator that uses a specific score type. |
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WeightMatrixAnnotator(WeightMatrix wm,
ScoreType scoreType,
double threshold,
String wmID)
Create a new annotator that uses the PROBABILITY score type and an ID for the weight matrix. |
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WMAsMM(WeightMatrix wm)
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