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public interface RateMatrix
abstract base class for all rate matrices
Nested Class Summary |
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Nested classes/interfaces inherited from interface pal.misc.Parameterized |
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Parameterized.Null, Parameterized.ParameterizedBase, Parameterized.ParameterizedUser, Parameterized.Utils |
Method Summary | |
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void |
addPalObjectListener(PalObjectListener pol)
Add a PalObjectListener to be notified of changes to the model. |
java.lang.Object |
clone()
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DataType |
getDataType()
Get the data type of this rate matrix |
int |
getDimension()
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double[] |
getEquilibriumFrequencies()
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double |
getEquilibriumFrequency(int i)
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int |
getModelID()
get numerical code describing the model type |
OrthogonalHints |
getOrthogonalHints()
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double[][] |
getRelativeRates()
Deprecated. try not to use. |
void |
getTransitionProbabilities(double[][] probabilityStore)
A utility method for speed, transfers trans prob information quickly into store |
double |
getTransitionProbability(int fromState,
int toState)
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int |
getTypeID()
get numerical code describing the data type |
java.lang.String |
getUniqueName()
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void |
removePalObjectListener(PalObjectListener pol)
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void |
scale(double scaleValue)
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void |
setDistance(double distance)
Sets the distance (such as time/branch length) used when calculating the probabilities. |
void |
setDistanceTranspose(double distance)
Sets the distance (such as time/branch length) used when calculating the probabilities. |
double |
setParametersNoScale(double[] parameters)
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Methods inherited from interface pal.misc.NamedParameterized |
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getParameterName |
Methods inherited from interface pal.misc.Parameterized |
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getDefaultValue, getLowerLimit, getNumParameters, getParameter, getUpperLimit, setParameter, setParameterSE |
Methods inherited from interface pal.misc.Report |
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report |
Method Detail |
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int getTypeID()
int getModelID()
java.lang.String getUniqueName()
int getDimension()
double[] getEquilibriumFrequencies()
double getEquilibriumFrequency(int i)
DataType getDataType()
double[][] getRelativeRates()
double getTransitionProbability(int fromState, int toState)
fromState
- The state from which we are startingtoState
- The resulting state
void getTransitionProbabilities(double[][] probabilityStore)
void setDistance(double distance)
void setDistanceTranspose(double distance)
void addPalObjectListener(PalObjectListener pol)
void removePalObjectListener(PalObjectListener pol)
OrthogonalHints getOrthogonalHints()
java.lang.Object clone()
double setParametersNoScale(double[] parameters)
void scale(double scaleValue)
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