com.mockturtlesolutions.snifflib.mcmctools.database

Class ProposalDistributionDOM

java.lang.Object

com.mockturtlesolutions.snifflib.reposconfig.database.AbstractRepositoryStorage

com.mockturtlesolutions.snifflib.reposconfig.database.RepositoryStorageDOM

com.mockturtlesolutions.snifflib.mcmctools.database.ProposalDistributionDOM

All Implemented Interfaces:

ProposalDistributionStorage, DOMStorable, RepositoryStorage, RepositoryStorageTransfer

Direct Known Subclasses:

GaussianProposalDOM

public class ProposalDistributionDOM
extends RepositoryStorageDOM
implements ProposalDistributionStorage

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
ProposalDistributionDOM()

Method Summary

Methods

Modifier and Type	Method and Description
java.lang.Class	getDefaultGraphicalEditorClass()
java.lang.Class	getDOMStorageClass() Returns a DOM storage variant of this storage instance.
RepositoryElement	getMixingParametersRepositoryElement()
ParameterSetStorage	getMixingParameterStorage() Returns the repository storage for the mixing parameters of this proposal distribution.
RepositoryElement	getNewParametersRepositoryElement()
RepositoryElement	getOldParametersRepositoryElement()
java.lang.String	getRootElementName()
java.lang.Class	getStorageTransferAgentClass() This method should be overridden by subclasses wanting to extend the transfer method.
void	setMixingParametersRepositoryElement(RepositoryElement elem)
void	setNewLikelihood(DblMatrixStorage likestorage, ParameterSetStorage oldstorage, ParameterSetStorage proposalstorage)
void	setNewParametersRepositoryElement(RepositoryElement elem)
void	setNewProposal(ParameterSetStorage oldstorage, ParameterSetStorage proposalstorage) Old is given as the new should be generated from the old in a Markov process.
void	setOldParametersRepositoryElement(RepositoryElement elem)
protected void	specifyStorage(org.w3c.dom.Document doc, org.w3c.dom.Element root)

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.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

ProposalDistributionDOM

public ProposalDistributionDOM()

Method Detail

getDefaultGraphicalEditorClass

public java.lang.Class getDefaultGraphicalEditorClass()

Specified by:

getDefaultGraphicalEditorClass in interface RepositoryStorage

Overrides:

getDefaultGraphicalEditorClass in class RepositoryStorageDOM

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 AbstractRepositoryStorage

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 RepositoryStorageDOM

getRootElementName

public java.lang.String getRootElementName()

Overrides:

getRootElementName in class RepositoryStorageDOM

specifyStorage

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

Overrides:

specifyStorage in class RepositoryStorageDOM

getMixingParameterStorage

public ParameterSetStorage getMixingParameterStorage()

Returns the repository storage for the mixing parameters of this proposal distribution. This is a convenience method which establishes its own connection to the repository internally. As a result, this method may be less efficient than using a previously esatablished connection or a connection pool.

Specified by:

getMixingParameterStorage in interface ProposalDistributionStorage

getMixingParametersRepositoryElement

public RepositoryElement getMixingParametersRepositoryElement()

Specified by:

getMixingParametersRepositoryElement in interface ProposalDistributionStorage

setMixingParametersRepositoryElement

public void setMixingParametersRepositoryElement(RepositoryElement elem)

Specified by:

setMixingParametersRepositoryElement in interface ProposalDistributionStorage

getNewParametersRepositoryElement

public RepositoryElement getNewParametersRepositoryElement()

Specified by:

getNewParametersRepositoryElement in interface ProposalDistributionStorage

setNewParametersRepositoryElement

public void setNewParametersRepositoryElement(RepositoryElement elem)

Specified by:

setNewParametersRepositoryElement in interface ProposalDistributionStorage

getOldParametersRepositoryElement

public RepositoryElement getOldParametersRepositoryElement()

Specified by:

getOldParametersRepositoryElement in interface ProposalDistributionStorage

setOldParametersRepositoryElement

public void setOldParametersRepositoryElement(RepositoryElement elem)

Specified by:

setOldParametersRepositoryElement in interface ProposalDistributionStorage

setNewProposal

public void setNewProposal(ParameterSetStorage oldstorage,
                  ParameterSetStorage proposalstorage)

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

setNewLikelihood

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

Specified by:

setNewLikelihood in interface ProposalDistributionStorage