statalign.model.ext.plugins.structalign
Class AlignmentMove

java.lang.Object
  statalign.mcmc.McmcMove
      statalign.model.ext.plugins.structalign.AlignmentMove

public class AlignmentMove
extends McmcMove

Field Summary

static double	MAX_WINDOW_MULTIPLIER
static double	MIN_WINDOW_MULTIPLIER
double	minAcceptance
StructAlignMoveParams	moveParams

Fields inherited from class statalign.mcmc.McmcMove

acceptAllDuringFirstHalfBurnin, acceptanceCount, autoTune, lastMoveAccepted, lowCounts, maxAcceptance, maxProposalWidthControlVariable, moveProposed, name, proposalCount, proposalWidthControlVariable, spanMultiplier

Constructor Summary

AlignmentMove(StructAlign s, java.lang.String n)

Method Summary

void	afterFirstHalfBurnin()
void	afterMove(java.lang.Object externalState)
void	copyState(java.lang.Object externalState)
double	logPriorDensity(java.lang.Object externalState)
double	proposal(java.lang.Object externalState)
void	restoreState(java.lang.Object externalState)
void	updateLikelihood(java.lang.Object externalState)

Methods inherited from class statalign.mcmc.McmcMove

acceptanceRate, getOwner, getParam, getTime, isParamChangeAccepted, move

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

moveParams

public StructAlignMoveParams moveParams

minAcceptance

public double minAcceptance

MIN_WINDOW_MULTIPLIER

public static final double MIN_WINDOW_MULTIPLIER

See Also:

Constant Field Values

MAX_WINDOW_MULTIPLIER

public static final double MAX_WINDOW_MULTIPLIER

See Also:

Constant Field Values

Constructor Detail

AlignmentMove

public AlignmentMove(StructAlign s,
                     java.lang.String n)

Method Detail

copyState

public void copyState(java.lang.Object externalState)

Specified by:

copyState in class McmcMove

proposal

public double proposal(java.lang.Object externalState)

Specified by:

proposal in class McmcMove

logPriorDensity

public double logPriorDensity(java.lang.Object externalState)

Specified by:

logPriorDensity in class McmcMove

updateLikelihood

public void updateLikelihood(java.lang.Object externalState)

Specified by:

updateLikelihood in class McmcMove

restoreState

public void restoreState(java.lang.Object externalState)

Specified by:

restoreState in class McmcMove

afterMove

public void afterMove(java.lang.Object externalState)

Overrides:

afterMove in class McmcMove

afterFirstHalfBurnin

public void afterFirstHalfBurnin()

Overrides:

afterFirstHalfBurnin in class McmcMove