Uses of Interface
pal.math.LMSSolver

Packages that use LMSSolver
pal.math Classes for math stuff such as optimisation, numerical derivatives, matrix exponentials, random numbers, special function etc. 
pal.supgma   
 

Uses of LMSSolver in pal.math
 

Methods in pal.math that return LMSSolver
static LMSSolver LMSSolver.Utils.getSimpleSolver()
          Obtain a simple LMSSolver that uses the "traditional" method for LMS stuff (IE, using row reduction to find the inverse, with poor numerical accuracy)
 

Uses of LMSSolver in pal.supgma
 

Methods in pal.supgma with parameters of type LMSSolver
 Tree SUPGMABase.generateAlignmentBootstrappedSUPGMATree(AlgorithmCallback callback, ClusterTree.ClusteringMethod cm, SUPGMABase.PopulationParameters pp, int numberOfReplicates, LMSSolver solver)
           
 Tree SUPGMABase.PopulationParameters.generateSUPGMATree(AlgorithmCallback callback, ClusterTree.ClusteringMethod cm, DistanceMatrixGenerator replicateSource, int numberOfAlignmentBootstrapReplicates, LMSSolver solver)
           
 SUPGMABase.CISummary SUPGMABase.PopulationParameters.inferCI(AlgorithmCallback callback, int numberOfReplicates, SimulatedAlignment.Factory alignmentFactory, SubstitutionModel evolutionaryModel, LMSSolver solver)
           
 SUPGMABase.PopulationParameters SUPGMABase.process(AlgorithmCallback callback, LMSSolver solver)
           
 SUPGMABase.PopulationParameters SUPGMABase.process(DistanceMatrixAccess alternativeSource, AlgorithmCallback callback, LMSSolver solver)
           
 Tree[] SUPGMABase.PopulationParameters.simulateTrees(int numberOfTreesToSimulate, AlgorithmCallback callback, LMSSolver solver)
           
 Tree SUPGMABase.solve(AlgorithmCallback callback, ClusterTree.ClusteringMethod cm, LMSSolver solver)