com.mockturtlesolutions.snifflib.mcmctools.database

Class GaussianProposalDOM

java.lang.Object

com.mockturtlesolutions.snifflib.reposconfig.database.AbstractRepositoryStorage

com.mockturtlesolutions.snifflib.reposconfig.database.RepositoryStorageDOM

com.mockturtlesolutions.snifflib.mcmctools.database.ProposalDistributionDOM

com.mockturtlesolutions.snifflib.mcmctools.database.GaussianProposalDOM

All Implemented Interfaces:

GaussianProposalStorage, ProposalDistributionStorage, DOMStorable, RepositoryStorage, RepositoryStorageTransfer

public class GaussianProposalDOM
extends ProposalDistributionDOM
implements GaussianProposalStorage

Field Summary

Fields inherited from class com.mockturtlesolutions.snifflib.reposconfig.database.RepositoryStorageDOM

document, dostylesheets, storageRoot, templateDOM

Fields inherited from class com.mockturtlesolutions.snifflib.reposconfig.database.AbstractRepositoryStorage

nickname, reposListeners, transferAgent

Constructor Summary

Constructors

Constructor and Description
GaussianProposalDOM()

Method Summary

Methods

Modifier and Type	Method and Description
void	clearLogNormal()
protected void	clearMixingParameters()
protected void	clearNewParameters()
protected void	clearOldParameters()
java.util.Vector	getAllLogNormal()
java.lang.Class	getDefaultGraphicalEditorClass()
java.lang.Class	getDOMStorageClass() Returns a DOM storage variant of this storage instance.
protected org.w3c.dom.Element	getLogNormalRoot()
java.lang.String	getRootElementName()
java.lang.Class	getStorageTransferAgentClass() This method should be overridden by subclasses wanting to extend the transfer method.
java.lang.String	isLogNormal(java.lang.String param) Returns true if the given parameter is considered log-normal.
void	setAllLogNormal(java.util.Collection pnames) Sets up all parameters whose name appears as a String in the given Collection to be sampled from a Log-Normal distribution.
void	setLogNormal(java.lang.String pname) Sets up the given parameter to be sampled from a Log-Normal distribution.
void	setNewLikelihood(DblMatrixStorage likestorage, ParameterSetStorage oldstorage, ParameterSetStorage proposalstorage)
void	setNewProposal(ParameterSetStorage oldstorage, ParameterSetStorage proposalstorage) Old is given as the new should be generated from the old in a Markov process.
protected void	specifyStorage(org.w3c.dom.Document doc, org.w3c.dom.Element root)
void	unSetAllLogNormal(java.util.Collection pnames) Puts log normal setting back to default.
void	unSetLogNormal(java.lang.String pname) Puts all log normal settings back to default.

Methods inherited from class com.mockturtlesolutions.snifflib.mcmctools.database.ProposalDistributionDOM

getMixingParametersRepositoryElement, getMixingParameterStorage, getNewParametersRepositoryElement, getOldParametersRepositoryElement, setMixingParametersRepositoryElement, setNewParametersRepositoryElement, setOldParametersRepositoryElement

Methods inherited from class com.mockturtlesolutions.snifflib.reposconfig.database.RepositoryStorageDOM

createElementByName, getAttributeByElementName, getComment, getCommentElementName, getCreatedBy, getCreatedByAttributeName, getCreatedOn, getCreatedOnAttributeName, getDocument, getEnabled, getEnabledAttributeName, getNickname, getNicknameAttributeName, getStorage, getStorageRoot, getStylesheetRef, getTemplateDOM, getTextNodeByElementName, isValidXML, readXML, setComment, setCreatedBy, setCreatedOn, setEnabled, setNickname, setProcessingInstructions, setTextNodeByElementName, show, show, useStyleSheetInfo, usingStyleSheetInfo, writeTemplateXML, writeXML

Methods inherited from class com.mockturtlesolutions.snifflib.reposconfig.database.AbstractRepositoryStorage

addRepositoryListener, afterCopyStorage, afterTransferStorage, beforeCopyStorage, beforeTransferStorage, copyStorage, copyStorageCommands, getStorageCalculationsAgentClass, removeRepositoryListener, transferStorage, transferStorageCommands

Methods inherited from class java.lang.Object

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

Methods inherited from interface com.mockturtlesolutions.snifflib.mcmctools.database.ProposalDistributionStorage

getMixingParametersRepositoryElement, getMixingParameterStorage, getNewParametersRepositoryElement, getOldParametersRepositoryElement, setMixingParametersRepositoryElement, setNewParametersRepositoryElement, setOldParametersRepositoryElement

Methods inherited from interface com.mockturtlesolutions.snifflib.reposconfig.database.RepositoryStorage

addRepositoryListener, getComment, getCreatedBy, getCreatedOn, getEnabled, getNickname, removeRepositoryListener, setComment, setCreatedBy, setCreatedOn, setEnabled, setNickname

Methods inherited from interface com.mockturtlesolutions.snifflib.reposconfig.database.RepositoryStorageTransfer

afterCopyStorage, afterTransferStorage, beforeCopyStorage, beforeTransferStorage, copyStorage, copyStorageCommands, transferStorage, transferStorageCommands

Constructor Detail

GaussianProposalDOM

public GaussianProposalDOM()

Method Detail

getDefaultGraphicalEditorClass

public java.lang.Class getDefaultGraphicalEditorClass()

Specified by:

getDefaultGraphicalEditorClass in interface RepositoryStorage

Overrides:

getDefaultGraphicalEditorClass in class ProposalDistributionDOM

getStorageTransferAgentClass

public java.lang.Class getStorageTransferAgentClass()

Description copied from class: AbstractRepositoryStorage

This method should be overridden by subclasses wanting to extend the transfer method.

Overrides:

getStorageTransferAgentClass in class ProposalDistributionDOM

getDOMStorageClass

public java.lang.Class getDOMStorageClass()

Description copied from class: AbstractRepositoryStorage

Returns a DOM storage variant of this storage instance. DOM storage classes, because they are independent of any repository, are by definition transient and often used when transfering amond RepositoryStorage classes which may be more persistent (e.g. backed by an XML or an SQL repository).

Specified by:

getDOMStorageClass in interface DOMStorable

Overrides:

getDOMStorageClass in class ProposalDistributionDOM

getRootElementName

public java.lang.String getRootElementName()

Overrides:

getRootElementName in class ProposalDistributionDOM

specifyStorage

protected void specifyStorage(org.w3c.dom.Document doc,
                  org.w3c.dom.Element root)

Overrides:

specifyStorage in class ProposalDistributionDOM

getLogNormalRoot

protected org.w3c.dom.Element getLogNormalRoot()

clearMixingParameters

protected void clearMixingParameters()

clearNewParameters

protected void clearNewParameters()

clearOldParameters

protected void clearOldParameters()

clearLogNormal

public void clearLogNormal()

setAllLogNormal

public void setAllLogNormal(java.util.Collection pnames)

Description copied from interface: GaussianProposalStorage

Sets up all parameters whose name appears as a String in the given Collection to be sampled from a Log-Normal distribution. The mixing standard deviation is automatically overwritten to be 0.1.

Specified by:

setAllLogNormal in interface GaussianProposalStorage

setLogNormal

public void setLogNormal(java.lang.String pname)

Description copied from interface: GaussianProposalStorage

Sets up the given parameter to be sampled from a Log-Normal distribution. The mixing standard deviation is automatically overwritten to be 0.1.

Specified by:

setLogNormal in interface GaussianProposalStorage

unSetAllLogNormal

public void unSetAllLogNormal(java.util.Collection pnames)

Description copied from interface: GaussianProposalStorage

Puts log normal setting back to default.

Specified by:

unSetAllLogNormal in interface GaussianProposalStorage

unSetLogNormal

public void unSetLogNormal(java.lang.String pname)

Description copied from interface: GaussianProposalStorage

Puts all log normal settings back to default.

Specified by:

unSetLogNormal in interface GaussianProposalStorage

isLogNormal

public java.lang.String isLogNormal(java.lang.String param)

Description copied from interface: GaussianProposalStorage

Returns true if the given parameter is considered log-normal. This method should respond to the current setting of ReverseLogNormalSense

Specified by:

isLogNormal in interface GaussianProposalStorage

getAllLogNormal

public java.util.Vector getAllLogNormal()

Specified by:

getAllLogNormal in interface GaussianProposalStorage

setNewProposal

public void setNewProposal(ParameterSetStorage oldstorage,
                  ParameterSetStorage proposalstorage)

Description copied from class: ProposalDistributionDOM

Old is given as the new should be generated from the old in a Markov process. This default implementation doesn't do anything other than copy old parameter set to the new parameter set. Gaussian proposal for example would use the old to be the mean of the new in combination with some known mixing standard deviations.

Specified by:

setNewProposal in interface ProposalDistributionStorage

Overrides:

setNewProposal in class ProposalDistributionDOM

setNewLikelihood

public void setNewLikelihood(DblMatrixStorage likestorage,
                    ParameterSetStorage oldstorage,
                    ParameterSetStorage proposalstorage)

Specified by:

setNewLikelihood in interface ProposalDistributionStorage

Overrides:

setNewLikelihood in class ProposalDistributionDOM