Uses of Class
org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix
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Packages that use BasicSymmetricalDistanceMatrix Package Description org.biojava.nbio.phylo org.forester.evoinference.distance -
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Uses of BasicSymmetricalDistanceMatrix in org.biojava.nbio.phylo
Methods in org.biojava.nbio.phylo that return BasicSymmetricalDistanceMatrix Modifier and Type Method Description static BasicSymmetricalDistanceMatrix
ForesterWrapper. cloneDM(BasicSymmetricalDistanceMatrix distM)
Helper function to clone a forester symmetrical DistanceMatrix.Methods in org.biojava.nbio.phylo with parameters of type BasicSymmetricalDistanceMatrix Modifier and Type Method Description static BasicSymmetricalDistanceMatrix
ForesterWrapper. cloneDM(BasicSymmetricalDistanceMatrix distM)
Helper function to clone a forester symmetrical DistanceMatrix.static Phylogeny
TreeConstructor. distanceTree(BasicSymmetricalDistanceMatrix distM, TreeConstructorType constructor)
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Uses of BasicSymmetricalDistanceMatrix in org.forester.evoinference.distance
Methods in org.forester.evoinference.distance that return BasicSymmetricalDistanceMatrix Modifier and Type Method Description static BasicSymmetricalDistanceMatrix
PairwiseDistanceCalculator. calcFractionalDissimilarities(Msa msa)
static BasicSymmetricalDistanceMatrix
PairwiseDistanceCalculator. calcKimuraDistances(Msa msa)
static BasicSymmetricalDistanceMatrix
PairwiseDistanceCalculator. calcKimuraDistances(Msa msa, double value_for_too_large_distance_for_kimura_formula)
static BasicSymmetricalDistanceMatrix
PairwiseDistanceCalculator. calcPoissonDistances(Msa msa)
Methods in org.forester.evoinference.distance with parameters of type BasicSymmetricalDistanceMatrix Modifier and Type Method Description Phylogeny
NeighborJoining. execute(BasicSymmetricalDistanceMatrix distance)
Phylogeny
NeighborJoiningF. execute(BasicSymmetricalDistanceMatrix distance)
Phylogeny
NeighborJoiningR. execute(BasicSymmetricalDistanceMatrix distance)
void
Sarray. initialize(BasicSymmetricalDistanceMatrix d)
void
Sset. initialize(BasicSymmetricalDistanceMatrix d)
Method parameters in org.forester.evoinference.distance with type arguments of type BasicSymmetricalDistanceMatrix Modifier and Type Method Description java.util.List<Phylogeny>
NeighborJoining. execute(java.util.List<BasicSymmetricalDistanceMatrix> distances_list)
java.util.List<Phylogeny>
NeighborJoiningF. execute(java.util.List<BasicSymmetricalDistanceMatrix> distances_list)
java.util.List<Phylogeny>
NeighborJoiningR. execute(java.util.List<BasicSymmetricalDistanceMatrix> distances_list)
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