java.lang.Object
- pal.substmodel.GeneralREVRateMatrix

All Implemented Interfaces:

java.io.Serializable, NeoRateMatrix
```
public class GeneralREVRateMatrix
extends java.lang.Object
implements NeoRateMatrix
```
A general rate matrix class for REV style rate matrices (GTR but for all data types) Includes the ability for arbitarily constraints
Author:
Matthew Goode
- 11 May 2004 - Created file - will add parameter decoding and reporting later...
See Also:

Serialized Form

Constructor Summary

Constructors
Constructor	Description
`GeneralREVRateMatrix(int dimension)`	The general constructor for a fully specified REV model
`GeneralREVRateMatrix(int dimension, double[] specifiedDefaultParameters)`	The general constructor for a fully specified REV model
`GeneralREVRateMatrix(int dimension, int[] constraints)`	The general constructor Constraint ordering example, for nucleotide data `-> + A C G T A * 0 1 2 C * * 3 4 G * * * 5 T * * * *` if constraints were {0,1,1,0,0,1} then would be constrained so a-c = c-g = c-t and a-g = a-t = g-t (and there would be only one parameter)
`GeneralREVRateMatrix(int dimension, int[] constraints, double[] specifiedDefaultParameters)`	The general constructor Constraint ordering example, for nucleotide data `-> + A C G T A * 0 1 2 C * * 3 4 G * * * 5 T * * * *` if constraints were {0,1,1,0,0,1} then would be constrained so a-c = c-g = c-t and a-g = a-t = g-t (and there would be only one parameter)
`GeneralREVRateMatrix(int dimension, int[] constraints, double[] specifiedDefaultParameters, int fixedConstraintValue)`	The general constructor Constraint ordering example, for nucleotide data `-> + A C G T A * 0 1 2 C * * 3 4 G * * * 5 T * * * *` if constraints were {0,1,1,0,0,1} then would be constrained so a-c = c-g = c-t and a-g = a-t = g-t (and there would be only one parameter)

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`static GeneralREVRateMatrix`	`createGTR()`	Create a rate matrix equivalent to the GTR model
`static GeneralREVRateMatrix`	`createGTR(double[] defaultParameters)`	Create a rate matrix equivalent to the GTR model
`static GeneralREVRateMatrix`	`createGTR(double a, double b, double c, double d, double e)`	Create a rate matrix equivalent to the GTR model Parameters laid out * `-> + A C G T A * a b c C * * d e G * * * 1 T * * * *`
`static GeneralREVRateMatrix`	`createHKY()`	Create a rate matrix equivalent to the HKY model, the one parameter will be kappa
`static GeneralREVRateMatrix`	`createHKY(double defaultKappa)`	Create a rate matrix equivalent to the HKY model, the one parameter will be kappa
`void`	`createRelativeRates(double[][] rateStore, double[] rateParameters, int startIndex)`	Create the relative rates array
`void`	`getDefaultRateParameters(double[] store, int startIndex)`
`int`	`getDimension()`
`int`	`getNumberOfRateParameters()`
`double`	`getRateParameterLowerBound(int parameter)`
`double`	`getRateParameterUpperBound(int parameter)`
`java.lang.String`	`getUniqueName()`
`boolean`	`isDataTypeCompatible(DataType dt)`	Check the compatibility of a data type to be used with the rate matrix
`boolean`	`isReversible()`	Is the relative rate matrix described by this rate matrix meant to represent a reversible process? If true only the upper part of the rate matrix needs to be filled in (eg in matrix[i][j], for all where j > i );

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

- Constructor Detail
  - GeneralREVRateMatrix
```
public GeneralREVRateMatrix(int dimension)
```
    The general constructor for a fully specified REV model
    
    Parameters:
    
    dimension - the dimension of the data type
  - GeneralREVRateMatrix
```
public GeneralREVRateMatrix(int dimension,
                            double[] specifiedDefaultParameters)
```
    The general constructor for a fully specified REV model
    
    Parameters:
    
    dimension - the dimension of the data type
    
    specifiedDefaultParameters - the defaultParameters (potentially used as the starting parameters by a SubstitutionModel)
  - GeneralREVRateMatrix
```
public GeneralREVRateMatrix(int dimension,
                            int[] constraints)
```
    The general constructor
    Constraint ordering example, for nucleotide data -> + A C G T A * 0 1 2 C * * 3 4 G * * * 5 T * * * * if constraints were {0,1,1,0,0,1} then would be constrained so a-c = c-g = c-t and a-g = a-t = g-t (and there would be only one parameter)
    
    Parameters:
    
    dimension - the dimension of the data type
    
    constraints - the contraints, organised such that if constraints[i]==constraints[j] then transitions i and j will always be the same. The constraints are ordered like usual.
  - GeneralREVRateMatrix
```
public GeneralREVRateMatrix(int dimension,
                            int[] constraints,
                            double[] specifiedDefaultParameters)
```
    The general constructor
    Constraint ordering example, for nucleotide data -> + A C G T A * 0 1 2 C * * 3 4 G * * * 5 T * * * * if constraints were {0,1,1,0,0,1} then would be constrained so a-c = c-g = c-t and a-g = a-t = g-t (and there would be only one parameter)
    
    Parameters:
    
    dimension - the dimension of the data type
    
    constraints - the contraints, organised such that if constraints[i]==constraints[j] then transitions i and j will always be the same. The constraints are ordered like usual. The last constrained item is fixed at 1.
    
    specifiedDefaultParameters - the defaultParameters (potentially used as the starting parameters by a SubstitutionModel)
  - GeneralREVRateMatrix
```
public GeneralREVRateMatrix(int dimension,
                            int[] constraints,
                            double[] specifiedDefaultParameters,
                            int fixedConstraintValue)
```
    The general constructor
    Constraint ordering example, for nucleotide data -> + A C G T A * 0 1 2 C * * 3 4 G * * * 5 T * * * * if constraints were {0,1,1,0,0,1} then would be constrained so a-c = c-g = c-t and a-g = a-t = g-t (and there would be only one parameter)
    
    Parameters:
    
    dimension - the dimension of the data type
    
    constraints - the contraints, organised such that if constraints[i]==constraints[j] then transitions i and j will always be the same. The constraints are ordered like usual.
    
    specifiedDefaultParameters - the defaultParameters (potentially used as the starting parameters by a SubstitutionModel)
    
    fixedConstraintValue - the value of the constraint (in the constraints array) of the fixed constraint (that is, for which all related parts of the rate matrix are set to 1)
- Method Detail
  - getUniqueName
```
public java.lang.String getUniqueName()
```
    Specified by:
    
    getUniqueName in interface NeoRateMatrix
    
    Returns:
    
    a short unique human-readable identifier for this rate matrix.
  - isReversible
```
public boolean isReversible()
```
    Description copied from interface: NeoRateMatrix
    
    Is the relative rate matrix described by this rate matrix meant to represent a reversible process? If true only the upper part of the rate matrix needs to be filled in (eg in matrix[i][j], for all where j > i );
    
    Specified by:
    
    isReversible in interface NeoRateMatrix
    
    Returns:
    
    true
  - getDimension
```
public int getDimension()
```
    Specified by:
    
    getDimension in interface NeoRateMatrix
    
    Returns:
    
    the dimension of this rate matrix. (as for construction)
  - isDataTypeCompatible
```
public boolean isDataTypeCompatible(DataType dt)
```
    Check the compatibility of a data type to be used with the rate matrix
    
    Specified by:
    
    isDataTypeCompatible in interface NeoRateMatrix
    
    Parameters:
    
    dt - the data type to test
    
    Returns:
    
    true if data type state count is equal to dimension
  - createRelativeRates
```
public void createRelativeRates(double[][] rateStore,
                                double[] rateParameters,
                                int startIndex)
```
    Description copied from interface: NeoRateMatrix
    
    Create the relative rates array
    
    Specified by:
    
    createRelativeRates in interface NeoRateMatrix
    
    Parameters:
    
    rateStore - The place where the relative rates are stored (should be assumed to be large enough - based on dimension)
    
    rateParameters - The parameters to be used to construct the rate store
    
    startIndex - The index into the rateParameters to start reading parameters
  - getNumberOfRateParameters
```
public int getNumberOfRateParameters()
```
    Specified by:
    
    getNumberOfRateParameters in interface NeoRateMatrix
  - getRateParameterLowerBound
```
public double getRateParameterLowerBound(int parameter)
```
    Specified by:
    
    getRateParameterLowerBound in interface NeoRateMatrix
  - getRateParameterUpperBound
```
public double getRateParameterUpperBound(int parameter)
```
    Specified by:
    
    getRateParameterUpperBound in interface NeoRateMatrix
  - getDefaultRateParameters
```
public void getDefaultRateParameters(double[] store,
                                     int startIndex)
```
    Specified by:
    
    getDefaultRateParameters in interface NeoRateMatrix
  - createGTR
```
public static final GeneralREVRateMatrix createGTR()
```
    Create a rate matrix equivalent to the GTR model
    
    Returns:
    
    appropriate rate matrix
  - createGTR
```
public static final GeneralREVRateMatrix createGTR(double[] defaultParameters)
```
    Create a rate matrix equivalent to the GTR model
    
    Parameters:
    
    defaultParameters - the default parameters of the model
    
    Returns:
    
    appropriate rate matrix
  - createGTR
```
public static final GeneralREVRateMatrix createGTR(double a,
                                                   double b,
                                                   double c,
                                                   double d,
                                                   double e)
```
    Create a rate matrix equivalent to the GTR model Parameters laid out * -> + A C G T A * a b c C * * d e G * * * 1 T * * * *
    
    Parameters:
    
    a - the default a parameter of the model
    
    b - the default a parameter of the model
    
    c - the default a parameter of the model
    
    d - the default a parameter of the model
    
    e - the default a parameter of the model
    
    Returns:
    
    appropriate rate matrix
  - createHKY
```
public static final GeneralREVRateMatrix createHKY()
```
    Create a rate matrix equivalent to the HKY model, the one parameter will be kappa
    
    Returns:
    
    appropriate rate matrix
  - createHKY
```
public static final GeneralREVRateMatrix createHKY(double defaultKappa)
```
    Create a rate matrix equivalent to the HKY model, the one parameter will be kappa
    
    Parameters:
    
    defaultKappa - the default kappa value
    
    Returns:
    
    appropriate rate matrix

Class GeneralREVRateMatrix

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

GeneralREVRateMatrix

GeneralREVRateMatrix

GeneralREVRateMatrix

GeneralREVRateMatrix

GeneralREVRateMatrix

Method Detail

getUniqueName

isReversible

getDimension

isDataTypeCompatible

createRelativeRates

getNumberOfRateParameters

getRateParameterLowerBound

getRateParameterUpperBound

getDefaultRateParameters

createGTR

createGTR

createGTR

createHKY

createHKY