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

Packages that use WeightMatrix

Package	Description
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

Modifier and Type	Class and Description
class	SimpleWeightMatrix

Methods in org.biojava.bio.dp that return WeightMatrix

Modifier and Type	Method and Description
static WeightMatrix	XmlMarkovModel.readMatrix(Element root)

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

Modifier and Type	Method and Description
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

Constructor and Description
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)