minimization
Class MCMC

java.lang.Object
  java.lang.Thread
      minimization.MCMC

All Implemented Interfaces:

java.lang.Runnable

public class MCMC
extends java.lang.Thread

Nested Class Summary

Nested classes/interfaces inherited from class java.lang.Thread

java.lang.Thread.State, java.lang.Thread.UncaughtExceptionHandler

Field Summary

static int	MCMC
static int	SIMULATED_ANNEALING

Fields inherited from class java.lang.Thread

MAX_PRIORITY, MIN_PRIORITY, NORM_PRIORITY

Constructor Summary

MCMC(Kernel k, boolean[][] icFit, boolean[] vOffsFit, int steps, int type)

Method Summary

double	getAcceptanceRatio()
int[][]	getAccRatio()
int[][]	getAccRatioV()
int	getAllTrials()
double[]	getBest()
Kernel	getBestChainE()
double[]	getBestVoffs()
java.lang.Object[]	getBetas()
KernelList	getChain()
KernelList	getChainCopy()
double	getCurChi()
double[]	getCurrent()
double[]	getCurrentAverage_vOffs()
double[]	getCurrentAverage()
Kernel	getCurrentChainE()
double[]	getCurrentPercentile(double perc)
int	getCurrentSteps()
double[]	getCurrentTrial()
double[]	getCurrentVar_vOffs()
double[]	getCurrentVar()
double	getMinChi()
double	getSATemperature()
boolean	isReady()
void	run()
void	setAllowParSpace(AllowParSpace parSpace)
void	setAverageType(int at)
void	setBeta_Mu(double[] bm, double[] bmv)
void	setContraints(double[] min, double[] max, double[] vmin, double[] vmax)
void	setDiscard(int t)
void	setFitWithTransits(boolean fwT)
void	seticFit(boolean[][] icF)
void	setInitialConditions(double[][] iC)
void	setIntMethod(int method)
void	setLocalMin(boolean lm)
void	setLog(boolean[] logarr)
void	setProgressListener(ProgressListener pl)
void	setRestartEvery(int re)
void	setSaveEvery(int se)
void	setSimulatedAnnealingPars(double T0, double alpha, double DP, double DM)
void	setSteps(int st)
void	setTargetRate(double targetRate)

Methods inherited from class java.lang.Thread

activeCount, checkAccess, clone, countStackFrames, currentThread, destroy, dumpStack, enumerate, getAllStackTraces, getContextClassLoader, getDefaultUncaughtExceptionHandler, getId, getName, getPriority, getStackTrace, getState, getThreadGroup, getUncaughtExceptionHandler, holdsLock, interrupt, interrupted, isAlive, isDaemon, isInterrupted, join, join, join, resume, setContextClassLoader, setDaemon, setDefaultUncaughtExceptionHandler, setName, setPriority, setUncaughtExceptionHandler, sleep, sleep, start, stop, stop, suspend, toString, yield

Methods inherited from class java.lang.Object

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

Field Detail

SIMULATED_ANNEALING

public static final int SIMULATED_ANNEALING

See Also:

Constant Field Values

MCMC

public static final int MCMC

See Also:

Constant Field Values

Constructor Detail

MCMC

public MCMC(Kernel k,
            boolean[][] icFit,
            boolean[] vOffsFit,
            int steps,
            int type)

Method Detail

setLog

public void setLog(boolean[] logarr)

setSimulatedAnnealingPars

public void setSimulatedAnnealingPars(double T0,
                                      double alpha,
                                      double DP,
                                      double DM)

setInitialConditions

public void setInitialConditions(double[][] iC)

seticFit

public void seticFit(boolean[][] icF)

setFitWithTransits

public void setFitWithTransits(boolean fwT)

setSteps

public void setSteps(int st)

setBeta_Mu

public void setBeta_Mu(double[] bm,
                       double[] bmv)

setTargetRate

public void setTargetRate(double targetRate)

setIntMethod

public void setIntMethod(int method)

setRestartEvery

public void setRestartEvery(int re)

setContraints

public void setContraints(double[] min,
                          double[] max,
                          double[] vmin,
                          double[] vmax)

getChain

public KernelList getChain()

getChainCopy

public KernelList getChainCopy()

getCurrentChainE

public Kernel getCurrentChainE()

getCurrentTrial

public double[] getCurrentTrial()

getCurrent

public double[] getCurrent()

getAcceptanceRatio

public double getAcceptanceRatio()

getMinChi

public double getMinChi()

getCurChi

public double getCurChi()

getBest

public double[] getBest()

getBetas

public java.lang.Object[] getBetas()

getBestVoffs

public double[] getBestVoffs()

getBestChainE

public Kernel getBestChainE()

getCurrentSteps

public int getCurrentSteps()

getSATemperature

public double getSATemperature()

getAccRatio

public int[][] getAccRatio()

getAccRatioV

public int[][] getAccRatioV()

setSaveEvery

public void setSaveEvery(int se)

setAllowParSpace

public void setAllowParSpace(AllowParSpace parSpace)

getAllTrials

public int getAllTrials()

isReady

public boolean isReady()

setDiscard

public void setDiscard(int t)

setLocalMin

public void setLocalMin(boolean lm)

setAverageType

public void setAverageType(int at)

getCurrentAverage

public double[] getCurrentAverage()

getCurrentAverage_vOffs

public double[] getCurrentAverage_vOffs()

getCurrentVar

public double[] getCurrentVar()

getCurrentPercentile

public double[] getCurrentPercentile(double perc)

getCurrentVar_vOffs

public double[] getCurrentVar_vOffs()

setProgressListener

public void setProgressListener(ProgressListener pl)

run

public void run()

Specified by:

run in interface java.lang.Runnable

Overrides:

run in class java.lang.Thread