Models

Class RateCategory

java.lang.Object

Models.RateCategory

All Implemented Interfaces:

java.io.Serializable

public class RateCategory
extends java.lang.Object
implements java.io.Serializable

Represents a rate category of a phylogenetic model.

Version:

2.0

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	RateCategory.FrequencyType Enumeration of the different ways of defining the root frequency
static class	RateCategory.RateException Exception thrown if there is a problem within a RateClass

Constructor Summary

Constructors

Constructor and Description
RateCategory(java.lang.String[][] rates, RateCategory.FrequencyType freqType, java.util.HashMap<java.lang.String,java.lang.Integer> map) Constructor for when the root distribution is defined as the stationary or quasi-stationary distribution.
RateCategory(java.lang.String[][] rates, java.lang.String[] freq, java.util.Map<java.lang.String,java.lang.Integer> map) Constructor for when the root distribution is defined.

Method Summary

Methods

Modifier and Type	Method and Description
static RateCategory	fromFile(java.io.File mfile) Creates an instance from the information in a file.
java.util.Map<java.lang.String,java.lang.Integer>	getArrayMap() Gets the map that maps state to position in matrix Called this as getMap() is kept for comptability
double[]	getFreq() Gets the root frequencies
java.util.Map<java.lang.String,java.lang.Integer>	getMap() Gets the map that maps state to position in matrix
java.lang.String	getName() Get the name of the rate category
int	getNumberStates() Gets the number of states in the rate class
SquareMatrix	getP(double length) Gets the P-matrix for a given length
Root	getRoot() Get a root object that can be used to calculate the total likelihood from the root node likelihoods or provide the frequencies of the various states at the root
SquareMatrix	getScaledMatrix() Gets the scaled rate matrix
double	getTotalRate() Gets the total rate of the rate class.
RateCategory	multiplyBy(java.lang.String mult) Returns a new RateCategory where every position in the rate matrix is multiplied by a given value
void	setName(java.lang.String name) Sets the name of the rate category.
void	setParameters(Parameters p) Updates the parameters in the RateCategory and recalculates matrices / frequencies if necessary.
java.lang.String	toString()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

RateCategory

public RateCategory(java.lang.String[][] rates,
            RateCategory.FrequencyType freqType,
            java.util.HashMap<java.lang.String,java.lang.Integer> map)
             throws RateCategory.RateException

Constructor for when the root distribution is defined as the stationary or quasi-stationary distribution.

Parameters:

rates - Array representing the rate matrix

freqType - How the root frequency is calculated

map - Map from State to position in matrix (0-index). For example map would contain A -> 0 if state A was in the first position (column and row of the matrix.

Throws:

RateCategory.RateException - If the rate matrix is not square

RateCategory

public RateCategory(java.lang.String[][] rates,
            java.lang.String[] freq,
            java.util.Map<java.lang.String,java.lang.Integer> map)
             throws RateCategory.RateException

Constructor for when the root distribution is defined. In this instance variables can be used in the rate matrix that represent the calculated frequency for a state. These variables are named _StateName, for example if there is a state A, the parameter _A can be used to represent the frquency of A.

Parameters:

rates - Array representing the rate matrix

freq - Root frequency.

map - Map from State to position in matrix (0-index) or root frequency. For example map would contain A -> 0 if state A was in the first position (column and row) of the matrix and in the first position of the root frequency array.

Throws:

RateCategory.RateException - If the rate matrix is not square or the frequency array is not the same length as the rate matrix.

Method Detail

setParameters

public void setParameters(Parameters p)
                   throws RateCategory.RateException,
                          Parameters.ParameterException

Updates the parameters in the RateCategory and recalculates matrices / frequencies if necessary.

Parameters:

p - The new parameters

Throws:

RateCategory.RateException - If the parameters passed does not include all the parameters in the model.

Parameters.ParameterException - If a parameter that needs to be set for this rate category has not been passed

getTotalRate

public double getTotalRate()

Gets the total rate of the rate class.

Returns:

The total rate

getFreq

public double[] getFreq()

Gets the root frequencies

Returns:

An array containing the root frequencies. Order is that given by the map returned by getMap() and which was passed to the constuctor.

getRoot

public Root getRoot()

Get a root object that can be used to calculate the total likelihood from the root node likelihoods or provide the frequencies of the various states at the root

Returns:

A root object

getNumberStates

public int getNumberStates()

Gets the number of states in the rate class

Returns:

The number of states

getArrayMap

public java.util.Map<java.lang.String,java.lang.Integer> getArrayMap()

Gets the map that maps state to position in matrix Called this as getMap() is kept for comptability

Returns:

Map from state to position in matrix

getMap

public java.util.Map<java.lang.String,java.lang.Integer> getMap()

Gets the map that maps state to position in matrix

Returns:

Map from state to position in matrix

multiplyBy

public RateCategory multiplyBy(java.lang.String mult)
                        throws RateCategory.RateException

Returns a new RateCategory where every position in the rate matrix is multiplied by a given value

Parameters:

mult - Value to be multiplied (as a string as it will be evaluated as a equation)

Returns:

The new RateClass

Throws:

RateCategory.RateException - If the equation to multiply the rates by is invalid.

getP

public SquareMatrix getP(double length)
                  throws RateCategory.RateException

Gets the P-matrix for a given length

Parameters:

length - The length

Returns:

The probability matrix. Order is that given by the map returned by getMap() and which was passed to the constructor.

Throws:

RateCategory.RateException - Thrown if the matrix cannot be calculated.

getScaledMatrix

public SquareMatrix getScaledMatrix()

Gets the scaled rate matrix

Returns:

The scaled rate matrix

setName

public void setName(java.lang.String name)

Sets the name of the rate category. Used so there is something meaningful to return to the user'

Parameters:

name - The rate category's name

getName

public java.lang.String getName()

Get the name of the rate category

Returns:

The rate category's name.

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

fromFile

public static RateCategory fromFile(java.io.File mfile)
                             throws InputException,
                                    RateCategory.RateException

Creates an instance from the information in a file. See MathsParse for a description of the format of the equations that can be in the rate matrix and root distribution. File format is as follows:

• First line contains the number of states the RateCategory has
• Second line is blank
• Third line is a list of states in the order they appear in the rate matrix, tab-separated
• Forth line is blank
• Fifth and subsequent lines contain the rate matrix, one row per line. Columns in a row are separated by tabs. Each entry can be an equation.
• The rate matrix is followed by a blank line
• Finally thee is a line giving the base frequencies. Three different values are allowed:
  1. Model frequencies - This line contains an equation for the frequency of each state, in the same order as the rate matrix and tab-separated
  2. Stationary distribution - Line contains just "**S" (without the quotes)
  3. Quasi-stationary distribution - Line contains just "**Q" (without the quotes)

Parameters:

mfile - The input file

Returns:

An instance of this class

Throws:

InputException - If there is a problem with the input file

RateCategory.RateException - If the RateCategory can not be created