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## calhoun.analysis.crf.features.supporting.phylogenetic
Class NucleotideSubstitutionModel

    java.lang.Object
      calhoun.analysis.crf.features.supporting.phylogenetic.NucleotideSubstitutionModel

All Implemented Interfaces:
  java.io.Serializable

Direct Known Subclasses:
  HKY85Model, Kimura80Model

    public abstract class NucleotideSubstitutionModel

extends java.lang.Object
implements java.io.Serializable

See Also:
  Serialized Form

Constructor Summary
`NucleotideSubstitutionModel()`

Method Summary
`abstract java.lang.String` | `getEvolutionaryModelName()`
`abstract double[]` | `getParameters()`
`cern.colt.matrix.DoubleMatrix2D` | `getRateMatrix()`
`abstract void` | `setParameters(double[] parms)`
`abstract void` | `summarize()`
`cern.colt.matrix.DoubleMatrix2D` | `transitionMatrix(double t)`

Methods inherited from class java.lang.Object
`equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait`

Constructor Detail

### NucleotideSubstitutionModel

    public NucleotideSubstitutionModel()

Method Detail

### getEvolutionaryModelName

    public abstract java.lang.String getEvolutionaryModelName()

### getParameters

    public abstract double[] getParameters()

### setParameters

    public abstract void setParameters(double[] parms)

### getRateMatrix

    public cern.colt.matrix.DoubleMatrix2D getRateMatrix()

### transitionMatrix

    public cern.colt.matrix.DoubleMatrix2D transitionMatrix(double t)

### summarize

    public abstract void summarize()

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