## Uses of Interface
org.biojava.bio.dp.WeightMatrix

Packages that use WeightMatrix
org.biojava.bio.dp: HMM and Dynamic Programming Algorithms.

Uses of WeightMatrix in org.biojava.bio.dp

Classes in org.biojava.bio.dp that implement WeightMatrix
`class` `SimpleWeightMatrix`

Methods in org.biojava.bio.dp that return WeightMatrix
`static WeightMatrix` `XmlMarkovModel.readMatrix(Element root)`

Methods in org.biojava.bio.dp with parameters of type WeightMatrix
`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)`

Constructors in org.biojava.bio.dp with parameters of type WeightMatrix
`WeightMatrixAnnotator(WeightMatrix wm, double threshold)` Create a new annotator that uses PROBABILITY score type.
`WeightMatrixAnnotator(WeightMatrix wm, ScoreType scoreType, double threshold)` Create a new annotator that uses a specific score type.
`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.
`WMAsMM(WeightMatrix wm)`