pal.substmodel
Class AminoAcidModel

java.lang.Object
  |
  +--pal.substmodel.AbstractRateMatrix
        |
        +--pal.substmodel.AminoAcidModel
All Implemented Interfaces:
java.lang.Cloneable, NamedParameterized, Parameterized, RateMatrix, Report, java.io.Serializable
Direct Known Subclasses:
BLOSUM62, CPREV, Dayhoff, JTT, MTREV24, VT, WAG

public abstract class AminoAcidModel
extends AbstractRateMatrix
implements RateMatrix

base class of rate matrices for amino acids

See Also:
Serialized Form

Fields inherited from class pal.substmodel.AbstractRateMatrix
dataType, dimension, format, frequency, rate
 
Constructor Summary
protected AminoAcidModel(double[] f)
           
 
Method Summary
 double getDefaultValue(int n)
          get default value of parameter
static AminoAcidModel getInstance(int modelID, double[] freq)
          Create amino acid model according to model type
 double getLowerLimit(int n)
          get lower parameter limit
 int getNumParameters()
          get number of parameters
 double getParameter(int n)
          get model parameter
 java.lang.String getParameterName(int i)
           
static int getSuitableModelID(double[] freq)
          get numerical code of amino acid model that would probably be suitable for a given sequence data set
 double getUpperLimit(int n)
          get upper parameter limit
protected  void printFrequencies(java.io.PrintWriter out)
           
abstract  void report(java.io.PrintWriter out)
          print human readable report (e.g., on parameters and associated model)
 void setParameter(double param, int n)
          set model parameter
 void setParameterSE(double paramSE, int n)
          set standard errors for model parameter
 
Methods inherited from class pal.substmodel.AbstractRateMatrix
addPalObjectListener, clone, fireParametersChangedEvent, fireParametersChangedEvent, fromQToR, getDataType, getDimension, getEquilibriumFrequencies, getEquilibriumFrequency, getModelID, getRelativeRates, getTransitionProbabilities, getTransitionProbability, getTypeID, removePalObjectListener, setDistance, setFrequencies, updateMatrixExp
 
Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 
Methods inherited from interface pal.substmodel.RateMatrix
addPalObjectListener, clone, getDataType, getDimension, getEquilibriumFrequencies, getEquilibriumFrequency, getModelID, getRelativeRates, getTransitionProbabilities, getTransitionProbability, getTypeID, getUniqueName, removePalObjectListener, setDistance
 

Constructor Detail

AminoAcidModel

protected AminoAcidModel(double[] f)
Method Detail

getInstance

public static AminoAcidModel getInstance(int modelID,
                                         double[] freq)
Create amino acid model according to model type
Parameters:
modelID - model code
freq - model frequencies
Returns:
amino acid rate matrix

getSuitableModelID

public static int getSuitableModelID(double[] freq)
get numerical code of amino acid model that would probably be suitable for a given sequence data set
Parameters:
freq - amino acid frequencies of the data set
Returns:
numerical code of suitable AminoAcidModel

report

public abstract void report(java.io.PrintWriter out)
Description copied from interface: Report
print human readable report (e.g., on parameters and associated model)
Specified by:
report in interface Report
Following copied from interface: pal.misc.Report
Parameters:
out - output stream

getNumParameters

public int getNumParameters()
Description copied from interface: Parameterized
get number of parameters
Specified by:
getNumParameters in interface Parameterized
Following copied from interface: pal.misc.Parameterized
Returns:
number of parameters

setParameter

public void setParameter(double param,
                         int n)
Description copied from interface: Parameterized
set model parameter
Specified by:
setParameter in interface Parameterized
Following copied from interface: pal.misc.Parameterized
Parameters:
param - parameter value
n - parameter number

getParameter

public double getParameter(int n)
Description copied from interface: Parameterized
get model parameter
Specified by:
getParameter in interface Parameterized
Following copied from interface: pal.misc.Parameterized
Parameters:
n - parameter number
Returns:
parameter value

setParameterSE

public void setParameterSE(double paramSE,
                           int n)
Description copied from interface: Parameterized
set standard errors for model parameter
Specified by:
setParameterSE in interface Parameterized
Following copied from interface: pal.misc.Parameterized
Parameters:
paramSE - standard error of parameter value
n - parameter number

getLowerLimit

public double getLowerLimit(int n)
Description copied from interface: Parameterized
get lower parameter limit
Specified by:
getLowerLimit in interface Parameterized
Following copied from interface: pal.misc.Parameterized
Parameters:
n - parameter number
Returns:
lower bound

getUpperLimit

public double getUpperLimit(int n)
Description copied from interface: Parameterized
get upper parameter limit
Specified by:
getUpperLimit in interface Parameterized
Following copied from interface: pal.misc.Parameterized
Parameters:
n - parameter number
Returns:
upper bound

getDefaultValue

public double getDefaultValue(int n)
Description copied from interface: Parameterized
get default value of parameter
Specified by:
getDefaultValue in interface Parameterized
Following copied from interface: pal.misc.Parameterized
Parameters:
n - parameter number
Returns:
default value

getParameterName

public java.lang.String getParameterName(int i)
Specified by:
getParameterName in interface NamedParameterized
Following copied from interface: pal.misc.NamedParameterized
Returns:
a short identifier for this parameter type. Should be the same for all instances of a given class!

printFrequencies

protected void printFrequencies(java.io.PrintWriter out)
Overrides:
printFrequencies in class AbstractRateMatrix