Uses of Interface
pal.misc.ExternalParameterListener
Packages that use ExternalParameterListener
Package
Description
Classes that don't fit elsewhere ;^)
Classes describing substitution models, i.e.
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Uses of ExternalParameterListener in pal.misc
Methods in pal.misc that return ExternalParameterListenerModifier and TypeMethodDescriptionstatic final ExternalParameterListener
PalEventMulticaster.add
(ExternalParameterListener old, ExternalParameterListener toAdd) For managing ExternalParamterListeners Usage: ExternalParamterListener current = null; ...static final ExternalParameterListener
PalEventMulticaster.remove
(ExternalParameterListener old, ExternalParameterListener toRemove) For managing ExternalParamterListeners Usage: ExternalParamterListener current = null; ...Methods in pal.misc with parameters of type ExternalParameterListenerModifier and TypeMethodDescriptionstatic final ExternalParameterListener
PalEventMulticaster.add
(ExternalParameterListener old, ExternalParameterListener toAdd) For managing ExternalParamterListeners Usage: ExternalParamterListener current = null; ...static final ExternalParameterListener
PalEventMulticaster.remove
(ExternalParameterListener old, ExternalParameterListener toRemove) For managing ExternalParamterListeners Usage: ExternalParamterListener current = null; ... -
Uses of ExternalParameterListener in pal.substmodel
Classes in pal.substmodel that implement ExternalParameterListenerModifier and TypeClassDescriptionclass
abstract base class for all rate matricesclass
base class of rate matrices for amino acidsclass
BLOSUM62 model of amino acid evolutionclass
base class for nucleotide rate matricesclass
CPREV model of amino acid evolution (J.Adachi et al.class
Dayhoff model for amino acid evolution Dayhoff, M.O., Schwartz, R.M., Orcutt, B.C.class
Felsenstein 1981 model of nucleotide evolutionclass
Felsenstein 1984 (PHYLIP) model of nucleotide evolutionclass
GTR (general time reversible) model of nucleotide evolution Lanave, C., G.class
Hasegawa-Kishino-Yano model of nucleotide evolution Hasegawa, M., H.class
JTT model of amino acid evolution Jones, D.class
MTREV24 model of amino acid evolutionclass
base class for nucleotide rate matricesclass
Tamura-Nei model of nucleotide evolution Tamura, K.class
implements the most general reversible rate matrix for two-state dataclass
VT (variable time matrix) model of amino acid evolution Modeling Amino Acid Replacement Mueller, T.class
WAG model of amino acid evolution (S.class
Yang's model of codon evolution More advanced codon Substitution Models (of Neilson and Yang) are now included (the M1, and M2 models).