com.mockturtlesolutions.snifflib.mcmctools.database

Class MCMCDOM

java.lang.Object

com.mockturtlesolutions.snifflib.reposconfig.database.AbstractRepositoryStorage

com.mockturtlesolutions.snifflib.reposconfig.database.RepositoryStorageDOM

com.mockturtlesolutions.snifflib.mcmctools.database.MCMCDOM

All Implemented Interfaces:

MCMCStorage, DOMStorable, RepositoryStorage, RepositoryStorageTransfer

public class MCMCDOM
extends RepositoryStorageDOM
implements MCMCStorage

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
MCMCDOM()

Method Summary

Methods

Modifier and Type	Method and Description
void	addMCMCRun(java.lang.String name) Adds the named run to the list of associated runs.
void	clearMCMCRuns()
java.lang.Class	getDefaultGraphicalEditorClass()
java.lang.Class	getDOMStorageClass() Returns a DOM storage variant of this storage instance.
StatisticalModelStorage	getLikelihoodStorage()
java.lang.String	getLikelihoodStorageConfigClass()
java.lang.String	getLikelihoodStorageNickname()
java.lang.String	getLikelihoodStorageRepositoryName()
java.util.Vector	getMCMCRunNames() Gets a list of names of runs associated with this MCMC configuration.
protected org.w3c.dom.Element	getMCMCRunsRoot()
java.lang.String	getPriorStorageConfigClass()
java.lang.String	getPriorStorageNickname()
java.lang.String	getPriorStorageRepositoryName()
RepositoryElement	getReferenceParameterSetRepositoryElement()
java.lang.String	getRootElementName()
java.lang.Class	getStorageTransferAgentClass() This method should be overridden by subclasses wanting to extend the transfer method.
void	removeMCMCRun(java.lang.String nameRun) Removes the named run from the list of associated runs.
void	setLikelihoodStorageConfigClass(java.lang.String cls)
void	setLikelihoodStorageNickname(java.lang.String cls)
void	setLikelihoodStorageRepositoryName(java.lang.String cls)
void	setPriorStorageConfigClass(java.lang.String cls)
void	setPriorStorageNickname(java.lang.String cls)
void	setPriorStorageRepositoryName(java.lang.String cls)
void	setReferenceParameterSetRepositoryElement(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

MCMCDOM

public MCMCDOM()

Method Detail

getDefaultGraphicalEditorClass

public java.lang.Class getDefaultGraphicalEditorClass()

Specified by:

getDefaultGraphicalEditorClass in interface RepositoryStorage

Overrides:

getDefaultGraphicalEditorClass 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

getMCMCRunsRoot

protected org.w3c.dom.Element getMCMCRunsRoot()

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

getReferenceParameterSetRepositoryElement

public RepositoryElement getReferenceParameterSetRepositoryElement()

Specified by:

getReferenceParameterSetRepositoryElement in interface MCMCStorage

setReferenceParameterSetRepositoryElement

public void setReferenceParameterSetRepositoryElement(RepositoryElement elem)

Specified by:

setReferenceParameterSetRepositoryElement in interface MCMCStorage

setLikelihoodStorageConfigClass

public void setLikelihoodStorageConfigClass(java.lang.String cls)

Specified by:

setLikelihoodStorageConfigClass in interface MCMCStorage

getLikelihoodStorageConfigClass

public java.lang.String getLikelihoodStorageConfigClass()

Specified by:

getLikelihoodStorageConfigClass in interface MCMCStorage

setLikelihoodStorageRepositoryName

public void setLikelihoodStorageRepositoryName(java.lang.String cls)

Specified by:

setLikelihoodStorageRepositoryName in interface MCMCStorage

getLikelihoodStorageRepositoryName

public java.lang.String getLikelihoodStorageRepositoryName()

Specified by:

getLikelihoodStorageRepositoryName in interface MCMCStorage

setLikelihoodStorageNickname

public void setLikelihoodStorageNickname(java.lang.String cls)

Specified by:

setLikelihoodStorageNickname in interface MCMCStorage

getLikelihoodStorageNickname

public java.lang.String getLikelihoodStorageNickname()

Specified by:

getLikelihoodStorageNickname in interface MCMCStorage

setPriorStorageConfigClass

public void setPriorStorageConfigClass(java.lang.String cls)

Specified by:

setPriorStorageConfigClass in interface MCMCStorage

getPriorStorageConfigClass

public java.lang.String getPriorStorageConfigClass()

Specified by:

getPriorStorageConfigClass in interface MCMCStorage

setPriorStorageRepositoryName

public void setPriorStorageRepositoryName(java.lang.String cls)

Specified by:

setPriorStorageRepositoryName in interface MCMCStorage

getPriorStorageRepositoryName

public java.lang.String getPriorStorageRepositoryName()

Specified by:

getPriorStorageRepositoryName in interface MCMCStorage

setPriorStorageNickname

public void setPriorStorageNickname(java.lang.String cls)

Specified by:

setPriorStorageNickname in interface MCMCStorage

getPriorStorageNickname

public java.lang.String getPriorStorageNickname()

Specified by:

getPriorStorageNickname in interface MCMCStorage

getLikelihoodStorage

public StatisticalModelStorage getLikelihoodStorage()

Specified by:

getLikelihoodStorage in interface MCMCStorage

addMCMCRun

public void addMCMCRun(java.lang.String name)

Adds the named run to the list of associated runs.

Specified by:

addMCMCRun in interface MCMCStorage

removeMCMCRun

public void removeMCMCRun(java.lang.String nameRun)

Removes the named run from the list of associated runs.

Specified by:

removeMCMCRun in interface MCMCStorage

clearMCMCRuns

public void clearMCMCRuns()

Specified by:

clearMCMCRuns in interface MCMCStorage

getMCMCRunNames

public java.util.Vector getMCMCRunNames()

Gets a list of names of runs associated with this MCMC configuration.

Specified by:

getMCMCRunNames in interface MCMCStorage