com.mockturtlesolutions.snifflib.mcmctools.database

Class GaussianProposalXML

java.lang.Object

com.mockturtlesolutions.snifflib.reposconfig.database.AbstractRepositoryStorage

com.mockturtlesolutions.snifflib.reposconfig.database.RepositoryStorageXML

com.mockturtlesolutions.snifflib.mcmctools.database.ProposalDistributionXML

com.mockturtlesolutions.snifflib.mcmctools.database.GaussianProposalXML

All Implemented Interfaces:

GaussianProposalStorage, ProposalDistributionStorage, DOMStorable, RepositoryStorage, RepositoryStorageTransfer

public class GaussianProposalXML
extends ProposalDistributionXML
implements GaussianProposalStorage

Field Summary

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

nickname, reposListeners, transferAgent

Constructor Summary

Constructors

Constructor and Description
GaussianProposalXML(RepositoryConnectivity conn, java.lang.String repos)

Method Summary

Methods

Modifier and Type	Method and Description
java.util.Vector	getAllLogNormal()
java.lang.Class	getDefaultGraphicalEditorClass()
java.lang.Class	getDOMStorageClass() Returns a DOM storage variant of this storage instance.
java.lang.Class	getStorageTransferAgentClass() This method should be overridden by subclasses wanting to extend the transfer method.
java.lang.String	isLogNormal(java.lang.String pname) 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) This default implementation doesn't do anything other than copy old parameter set to the new parameter set.
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.ProposalDistributionXML

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

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

copyStorage, getComment, getCreatedBy, getCreatedOn, getDOM, getEnabled, getNickname, getStorage, getXMLDirectory, getXMLFilename, setComment, setCreatedBy, setCreatedOn, setEnabled, setNickname, transferStorage, writeXML

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

addRepositoryListener, afterCopyStorage, afterTransferStorage, beforeCopyStorage, beforeTransferStorage, copyStorageCommands, getStorageCalculationsAgentClass, removeRepositoryListener, show, 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

GaussianProposalXML

public GaussianProposalXML(RepositoryConnectivity conn,
                   java.lang.String repos)

Method Detail

getDefaultGraphicalEditorClass

public java.lang.Class getDefaultGraphicalEditorClass()

Specified by:

getDefaultGraphicalEditorClass in interface RepositoryStorage

Overrides:

getDefaultGraphicalEditorClass in class ProposalDistributionXML

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 ProposalDistributionXML

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 ProposalDistributionXML

setLogNormal

public void setLogNormal(java.lang.String pname)

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

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

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

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

isLogNormal

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

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: ProposalDistributionXML

This default implementation doesn't do anything other than copy old parameter set to the new parameter set.

Specified by:

setNewProposal in interface ProposalDistributionStorage

Overrides:

setNewProposal in class ProposalDistributionXML

setNewLikelihood

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

Specified by:

setNewLikelihood in interface ProposalDistributionStorage

Overrides:

setNewLikelihood in class ProposalDistributionXML