MCMCRunDOM (Snifflib API)

java.lang.Object
- com.mockturtlesolutions.snifflib.reposconfig.database.AbstractRepositoryStorage
- - com.mockturtlesolutions.snifflib.reposconfig.database.RepositoryStorageDOM
  - - com.mockturtlesolutions.snifflib.mcmctools.database.MCMCRunDOM

All Implemented Interfaces:

MCMCRunStorage, DOMStorable, RepositoryStorage, RepositoryStorageTransfer
```
public class MCMCRunDOM
extends RepositoryStorageDOM
implements MCMCRunStorage
```

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

MCMCRunDOM()

Constructors
Constructor and Description
`MCMCRunDOM()`

Method Summary

Methods
Modifier and Type	Method and Description
`void`	`addDelegateState(java.lang.String state)` Add a delegate state.
`void`	`addParameterBlock()`
`void`	`addParameterBlockParameter(int index, java.lang.String pname)`
`void`	`advanceMCMCRunState()`
`protected void`	`clearALIKE()`
`protected void`	`clearAPRIOR()`
`protected void`	`clearAPROP()`
`protected void`	`clearBLIKE()`
`protected void`	`clearBPRIOR()`
`protected void`	`clearBPROP()`
`protected void`	`clearCandidateObjectSet()`
`protected void`	`clearCandidateParameterSet()`
`protected void`	`clearDelegates()`
`protected void`	`clearObjectTrace()`
`protected void`	`clearParameterBlocks()`
`protected void`	`clearParameterTrace()`
`protected void`	`clearParent()`
`protected void`	`clearPreviousObjectSet()`
`protected void`	`clearPreviousParameterSet()`
`protected void`	`clearProposalDistribution()`
`protected void`	`clearReferenceParameterSet()`
`protected void`	`clearSampler()`
`java.lang.String`	`getAcceptCount()`
`RepositoryElement`	`getALIKERepositoryElement()`
`RepositoryElement`	`getAPRIORRepositoryElement()`
`RepositoryElement`	`getAPROPRepositoryElement()`
`RepositoryElement`	`getBLIKERepositoryElement()`
`RepositoryElement`	`getBPRIORRepositoryElement()`
`RepositoryElement`	`getBPROPRepositoryElement()`
`RepositoryElement`	`getCandidateObjectRepositoryElement()`
`RepositoryElement`	`getCandidateParameterRepositoryElement()`
`ParameterSetStorage`	`getCandidateParameterStorage()` Returns the repository storage for the candidate parameters of this run.
`java.lang.String`	`getCurrentAlpha()`
`java.lang.String`	`getCurrentIterationNumber()`
`java.lang.String`	`getCurrentLinkCount()` Link count is used to name the parameter storages of the trace for example.
`java.lang.String`	`getCurrentParameterBlockCycleNumber()`
`java.lang.String`	`getCurrentParameterBlockIndex()`
`java.lang.Class`	`getDefaultGraphicalEditorClass()`
`java.util.Vector`	`getDelegateStates()`
`protected org.w3c.dom.Element`	`getDelegateStatesRoot()`
`java.lang.Class`	`getDOMStorageClass()` Returns a DOM storage variant of this storage instance.
`java.lang.String`	`getIsPriorFlat()`
`java.lang.String`	`getIsProposalSymmetric()`
`java.lang.String`	`getIsStateLocked()`
`java.lang.String`	`getIsStillRunning()`
`java.lang.String`	`getMaximumIterationNumber()`
`java.lang.String`	`getMCMCRunIdentifier()`
`java.lang.String`	`getMCMCRunState()`
`RepositoryElement`	`getMCMCSamplerRepositoryElement()`
`ParameterSetStorage`	`getMixingParameterStorage()` Returns the repository storage for the mixing parameters of this run's proposal distribution.
`java.lang.String`	`getObjectTraceCapacity()`
`RepositoryElement`	`getObjectTraceRepositoryElement()`
`protected org.w3c.dom.Element`	`getParameterBlock(int index)`
`int`	`getParameterBlockCount()`
`java.lang.String`	`getParameterBlockName(int index)`
`java.lang.String`	`getParameterBlockNumberOfCycles(int index)`
`java.util.Vector`	`getParameterBlockParameters(int index)`
`protected org.w3c.dom.Element`	`getParameterBlockRoot()`
`java.lang.String`	`getParameterTraceCapacity()`
`RepositoryElement`	`getParameterTraceRepositoryElement()`
`RepositoryElement`	`getParentMCMCRepositoryElement()`
`RepositoryElement`	`getPreviousObjectRepositoryElement()`
`RepositoryElement`	`getPreviousParameterRepositoryElement()`
`ParameterSetStorage`	`getPreviousParameterStorage()` Returns the repository storage for the previous parameters of this run.
`protected java.lang.String`	`getProcessingInstructionRef()`
`RepositoryElement`	`getProposalDistributionRepositoryElement()`
`ProposalDistributionStorage`	`getProposalDistributionStorage()` Returns the repository storage for the proposal distribution of this run.
`java.lang.String`	`getRecordObjectTrace()`
`java.lang.String`	`getRecordParameterTrace()`
`RepositoryElement`	`getReferenceParameterRepositoryElement()`
`ParameterSetStorage`	`getReferenceParameterStorage()` Returns the repository storage for the reference parameters of this run.
`java.lang.String`	`getRejectCount()`
`double`	`getRejectFraction()`
`java.lang.String`	`getRootElementName()`
`java.lang.String`	`getShouldHalt()`
`java.lang.String`	`getShouldRollBack()` Returns boolean indication of whether a roll back of the most recent iteration or proposal should occur.
`java.lang.Class`	`getStorageTransferAgentClass()` This method should be overridden by subclasses wanting to extend the transfer method.
`java.lang.String`	`hasDelegateState(java.lang.String state)`
`void`	`holdParameterFixed(java.lang.String pname)` Removes the named parameter from every parameter block.
`void`	`initialize()` Return the run to an initial state removing history of any previous evaluations.
`void`	`insertParameterBlock(int index)`
`void`	`removeDelegateState(java.lang.String state)`
`void`	`removeParameterBlock(int index)`
`void`	`removeParameterBlockParameter(int index, java.lang.String pname)`
`void`	`restartUsingParametersFrom(DblParamSet params)` Restarts the chain with a new candidate parameter set copied from the values in the given DblParamSet.
`void`	`restartUsingParametersFrom(ParameterSetStorage stor)` Restarts the chain with a new candidate parameter set copied from the values in the given parameter storage.
`void`	`setAcceptCount(java.lang.String v)`
`void`	`setALIKERepositoryElement(RepositoryElement elem)`
`void`	`setAPRIORRepositoryElement(RepositoryElement elem)`
`void`	`setAPROPRepositoryElement(RepositoryElement elem)`
`void`	`setBLIKERepositoryElement(RepositoryElement elem)`
`void`	`setBPRIORRepositoryElement(RepositoryElement elem)`
`void`	`setBPROPRepositoryElement(RepositoryElement elem)`
`void`	`setCandidateObjectRepositoryElement(RepositoryElement elem)`
`void`	`setCandidateParameterRepositoryElement(RepositoryElement elem)`
`void`	`setCurrentAlpha(java.lang.String prob)`
`void`	`setCurrentIterationNumber(java.lang.String v)`
`void`	`setCurrentLinkCount(java.lang.String v)`
`void`	`setCurrentParameterBlockCycleNumber(java.lang.String x)`
`void`	`setCurrentParameterBlockIndex(java.lang.String x)`
`void`	`setIsPriorFlat(java.lang.String bool)`
`void`	`setIsProposalSymmetric(java.lang.String bool)`
`void`	`setIsStateLocked(java.lang.String boole)`
`void`	`setIsStillRunning(java.lang.String boole)`
`void`	`setMaximumIterationNumber(java.lang.String v)`
`void`	`setMCMCRunIdentifier(java.lang.String s)`
`void`	`setMCMCRunState(java.lang.String state)`
`void`	`setMCMCSamplerRepositoryElement(RepositoryElement elem)`
`void`	`setObjectTraceCapacity(java.lang.String siz)`
`void`	`setObjectTraceRepositoryElement(RepositoryElement elem)`
`void`	`setParameterBlockName(int index, java.lang.String name)`
`void`	`setParameterBlockNumberOfCycles(int index, java.lang.String num)`
`void`	`setParameterTraceCapacity(java.lang.String siz)`
`void`	`setParameterTraceRepositoryElement(RepositoryElement elem)`
`void`	`setParentMCMCRepositoryElement(RepositoryElement elem)`
`void`	`setPreviousObjectRepositoryElement(RepositoryElement elem)`
`void`	`setPreviousParameterRepositoryElement(RepositoryElement elem)`
`void`	`setProposalDistributionRepositoryElement(RepositoryElement elem)`
`void`	`setRecordObjectTrace(java.lang.String bool)`
`void`	`setRecordParameterTrace(java.lang.String bool)`
`void`	`setReferenceParameterRepositoryElement(RepositoryElement elem)`
`void`	`setReferenceParametersFrom(DblParamSet P)`
`void`	`setReferenceParametersFrom(ParameterSetStorage P)`
`void`	`setRejectCount(java.lang.String v)`
`void`	`setShouldHalt(java.lang.String boole)`
`void`	`setShouldRollBack(java.lang.String bool)` Sets boolean indication of whether a roll back of the most recent iteration or proposal should occur.
`protected void`	`specifyStorage(org.w3c.dom.Document doc, org.w3c.dom.Element root)`
`void`	`start()` Attempts to start run.
`void`	`stop()` Attempts to stop run.

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
  - MCMCRunDOM
```
public MCMCRunDOM()
```
- Method Detail
  - getProcessingInstructionRef
```
protected java.lang.String getProcessingInstructionRef()
```
  - initialize
```
public void initialize()
```
    Return the run to an initial state removing history of any previous evaluations. The parameters are initialized to the reference parameter set.
    
    Specified by:
    
    initialize in interface MCMCRunStorage
  - setReferenceParametersFrom
```
public void setReferenceParametersFrom(ParameterSetStorage P)
```
    Specified by:
    
    setReferenceParametersFrom in interface MCMCRunStorage
  - getShouldRollBack
```
public java.lang.String getShouldRollBack()
```
    Returns boolean indication of whether a roll back of the most recent iteration or proposal should occur.
    
    Specified by:
    
    getShouldRollBack in interface MCMCRunStorage
  - setShouldRollBack
```
public void setShouldRollBack(java.lang.String bool)
```
    Sets boolean indication of whether a roll back of the most recent iteration or proposal should occur.
    
    Specified by:
    
    setShouldRollBack in interface MCMCRunStorage
  - setReferenceParametersFrom
```
public void setReferenceParametersFrom(DblParamSet P)
```
    Specified by:
    
    setReferenceParametersFrom in interface MCMCRunStorage
  - 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
  - clearDelegates
```
protected void clearDelegates()
```
  - clearParent
```
protected void clearParent()
```
  - clearSampler
```
protected void clearSampler()
```
  - clearProposalDistribution
```
protected void clearProposalDistribution()
```
  - clearCandidateParameterSet
```
protected void clearCandidateParameterSet()
```
  - clearPreviousParameterSet
```
protected void clearPreviousParameterSet()
```
  - clearReferenceParameterSet
```
protected void clearReferenceParameterSet()
```
  - clearCandidateObjectSet
```
protected void clearCandidateObjectSet()
```
  - clearPreviousObjectSet
```
protected void clearPreviousObjectSet()
```
  - clearParameterTrace
```
protected void clearParameterTrace()
```
  - clearObjectTrace
```
protected void clearObjectTrace()
```
  - clearALIKE
```
protected void clearALIKE()
```
  - clearBLIKE
```
protected void clearBLIKE()
```
  - clearAPRIOR
```
protected void clearAPRIOR()
```
  - clearBPRIOR
```
protected void clearBPRIOR()
```
  - clearAPROP
```
protected void clearAPROP()
```
  - clearBPROP
```
protected void clearBPROP()
```
  - clearParameterBlocks
```
protected void clearParameterBlocks()
```
  - specifyStorage
```
protected void specifyStorage(org.w3c.dom.Document doc,
                  org.w3c.dom.Element root)
```
    Overrides:
    
    specifyStorage in class RepositoryStorageDOM
  - getPreviousParameterStorage
```
public ParameterSetStorage getPreviousParameterStorage()
```
    Returns the repository storage for the previous parameters of this run. 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 established connection or a connection pool.
    
    Specified by:
    
    getPreviousParameterStorage in interface MCMCRunStorage
  - getCandidateParameterStorage
```
public ParameterSetStorage getCandidateParameterStorage()
```
    Returns the repository storage for the candidate parameters of this run. 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 established connection or a connection pool.
    
    Specified by:
    
    getCandidateParameterStorage in interface MCMCRunStorage
  - getReferenceParameterStorage
```
public ParameterSetStorage getReferenceParameterStorage()
```
    Returns the repository storage for the reference parameters of this run. 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 established connection or a connection pool.
    
    Specified by:
    
    getReferenceParameterStorage in interface MCMCRunStorage
  - getMixingParameterStorage
```
public ParameterSetStorage getMixingParameterStorage()
```
    Returns the repository storage for the mixing parameters of this run's proposal distribution. This is a convenience method which establishes its own connection to the proposal repository internally. As a result, this method may be less efficient than using a previously established connection or a connection pool.
    
    Specified by:
    
    getMixingParameterStorage in interface MCMCRunStorage
  - getProposalDistributionStorage
```
public ProposalDistributionStorage getProposalDistributionStorage()
```
    Returns the repository storage for the proposal distribution of this run. This is a convenience method which establishes its own connection to the proposal repository internally. As a result, this method may be less efficient than using a previously established connection or a connection pool.
    
    Specified by:
    
    getProposalDistributionStorage in interface MCMCRunStorage
  - hasDelegateState
```
public java.lang.String hasDelegateState(java.lang.String state)
```
    Specified by:
    
    hasDelegateState in interface MCMCRunStorage
  - addDelegateState
```
public void addDelegateState(java.lang.String state)
```
    Add a delegate state. This method has no effect if the state is already delegated.
    
    Specified by:
    
    addDelegateState in interface MCMCRunStorage
  - removeDelegateState
```
public void removeDelegateState(java.lang.String state)
```
    Specified by:
    
    removeDelegateState in interface MCMCRunStorage
  - getDelegateStates
```
public java.util.Vector getDelegateStates()
```
    Specified by:
    
    getDelegateStates in interface MCMCRunStorage
  - getDelegateStatesRoot
```
protected org.w3c.dom.Element getDelegateStatesRoot()
```
  - getCandidateParameterRepositoryElement
```
public RepositoryElement getCandidateParameterRepositoryElement()
```
    Specified by:
    
    getCandidateParameterRepositoryElement in interface MCMCRunStorage
  - setCandidateParameterRepositoryElement
```
public void setCandidateParameterRepositoryElement(RepositoryElement elem)
```
    Specified by:
    
    setCandidateParameterRepositoryElement in interface MCMCRunStorage
  - getCandidateObjectRepositoryElement
```
public RepositoryElement getCandidateObjectRepositoryElement()
```
    Specified by:
    
    getCandidateObjectRepositoryElement in interface MCMCRunStorage
  - getRejectFraction
```
public double getRejectFraction()
```
    Specified by:
    
    getRejectFraction in interface MCMCRunStorage
  - stop
```
public void stop()
```
    Attempts to stop run.
    
    Specified by:
    
    stop in interface MCMCRunStorage
  - start
```
public void start()
```
    Attempts to start run.
    
    Specified by:
    
    start in interface MCMCRunStorage
  - restartUsingParametersFrom
```
public void restartUsingParametersFrom(ParameterSetStorage stor)
```
    Restarts the chain with a new candidate parameter set copied from the values in the given parameter storage.
    
    Specified by:
    
    restartUsingParametersFrom in interface MCMCRunStorage
  - restartUsingParametersFrom
```
public void restartUsingParametersFrom(DblParamSet params)
```
    Restarts the chain with a new candidate parameter set copied from the values in the given DblParamSet.
    
    Specified by:
    
    restartUsingParametersFrom in interface MCMCRunStorage
  - setCandidateObjectRepositoryElement
```
public void setCandidateObjectRepositoryElement(RepositoryElement elem)
```
    Specified by:
    
    setCandidateObjectRepositoryElement in interface MCMCRunStorage
  - getPreviousParameterRepositoryElement
```
public RepositoryElement getPreviousParameterRepositoryElement()
```
    Specified by:
    
    getPreviousParameterRepositoryElement in interface MCMCRunStorage
  - setPreviousParameterRepositoryElement
```
public void setPreviousParameterRepositoryElement(RepositoryElement elem)
```
    Specified by:
    
    setPreviousParameterRepositoryElement in interface MCMCRunStorage
  - getReferenceParameterRepositoryElement
```
public RepositoryElement getReferenceParameterRepositoryElement()
```
    Specified by:
    
    getReferenceParameterRepositoryElement in interface MCMCRunStorage
  - setReferenceParameterRepositoryElement
```
public void setReferenceParameterRepositoryElement(RepositoryElement elem)
```
    Specified by:
    
    setReferenceParameterRepositoryElement in interface MCMCRunStorage
  - getPreviousObjectRepositoryElement
```
public RepositoryElement getPreviousObjectRepositoryElement()
```
    Specified by:
    
    getPreviousObjectRepositoryElement in interface MCMCRunStorage
  - setPreviousObjectRepositoryElement
```
public void setPreviousObjectRepositoryElement(RepositoryElement elem)
```
    Specified by:
    
    setPreviousObjectRepositoryElement in interface MCMCRunStorage
  - getParameterBlockRoot
```
protected org.w3c.dom.Element getParameterBlockRoot()
```
  - getParameterBlock
```
protected org.w3c.dom.Element getParameterBlock(int index)
```
  - getMCMCRunState
```
public java.lang.String getMCMCRunState()
```
    Specified by:
    
    getMCMCRunState in interface MCMCRunStorage
  - setMCMCRunState
```
public void setMCMCRunState(java.lang.String state)
```
    Specified by:
    
    setMCMCRunState in interface MCMCRunStorage
  - advanceMCMCRunState
```
public void advanceMCMCRunState()
```
    Specified by:
    
    advanceMCMCRunState in interface MCMCRunStorage
  - setMCMCRunIdentifier
```
public void setMCMCRunIdentifier(java.lang.String s)
```
    Specified by:
    
    setMCMCRunIdentifier in interface MCMCRunStorage
  - getMCMCRunIdentifier
```
public java.lang.String getMCMCRunIdentifier()
```
    Specified by:
    
    getMCMCRunIdentifier in interface MCMCRunStorage
  - getIsStateLocked
```
public java.lang.String getIsStateLocked()
```
    Specified by:
    
    getIsStateLocked in interface MCMCRunStorage
  - setIsStateLocked
```
public void setIsStateLocked(java.lang.String boole)
```
    Specified by:
    
    setIsStateLocked in interface MCMCRunStorage
  - getIsStillRunning
```
public java.lang.String getIsStillRunning()
```
    Specified by:
    
    getIsStillRunning in interface MCMCRunStorage
  - setIsStillRunning
```
public void setIsStillRunning(java.lang.String boole)
```
    Specified by:
    
    setIsStillRunning in interface MCMCRunStorage
  - getShouldHalt
```
public java.lang.String getShouldHalt()
```
    Specified by:
    
    getShouldHalt in interface MCMCRunStorage
  - setShouldHalt
```
public void setShouldHalt(java.lang.String boole)
```
    Specified by:
    
    setShouldHalt in interface MCMCRunStorage
  - getCurrentIterationNumber
```
public java.lang.String getCurrentIterationNumber()
```
    Specified by:
    
    getCurrentIterationNumber in interface MCMCRunStorage
  - setCurrentIterationNumber
```
public void setCurrentIterationNumber(java.lang.String v)
```
    Specified by:
    
    setCurrentIterationNumber in interface MCMCRunStorage
  - getCurrentLinkCount
```
public java.lang.String getCurrentLinkCount()
```
    Description copied from interface: MCMCRunStorage
    
    Link count is used to name the parameter storages of the trace for example.
    
    Specified by:
    
    getCurrentLinkCount in interface MCMCRunStorage
  - setCurrentLinkCount
```
public void setCurrentLinkCount(java.lang.String v)
```
    Specified by:
    
    setCurrentLinkCount in interface MCMCRunStorage
  - setCurrentParameterBlockCycleNumber
```
public void setCurrentParameterBlockCycleNumber(java.lang.String x)
```
    Specified by:
    
    setCurrentParameterBlockCycleNumber in interface MCMCRunStorage
  - getCurrentParameterBlockCycleNumber
```
public java.lang.String getCurrentParameterBlockCycleNumber()
```
    Specified by:
    
    getCurrentParameterBlockCycleNumber in interface MCMCRunStorage
  - getCurrentAlpha
```
public java.lang.String getCurrentAlpha()
```
    Specified by:
    
    getCurrentAlpha in interface MCMCRunStorage
  - setCurrentAlpha
```
public void setCurrentAlpha(java.lang.String prob)
```
    Specified by:
    
    setCurrentAlpha in interface MCMCRunStorage
  - getMaximumIterationNumber
```
public java.lang.String getMaximumIterationNumber()
```
    Specified by:
    
    getMaximumIterationNumber in interface MCMCRunStorage
  - setMaximumIterationNumber
```
public void setMaximumIterationNumber(java.lang.String v)
```
    Specified by:
    
    setMaximumIterationNumber in interface MCMCRunStorage
  - getRejectCount
```
public java.lang.String getRejectCount()
```
    Specified by:
    
    getRejectCount in interface MCMCRunStorage
  - setRejectCount
```
public void setRejectCount(java.lang.String v)
```
    Specified by:
    
    setRejectCount in interface MCMCRunStorage
  - getAcceptCount
```
public java.lang.String getAcceptCount()
```
    Specified by:
    
    getAcceptCount in interface MCMCRunStorage
  - setAcceptCount
```
public void setAcceptCount(java.lang.String v)
```
    Specified by:
    
    setAcceptCount in interface MCMCRunStorage
  - setIsPriorFlat
```
public void setIsPriorFlat(java.lang.String bool)
```
    Specified by:
    
    setIsPriorFlat in interface MCMCRunStorage
  - getIsPriorFlat
```
public java.lang.String getIsPriorFlat()
```
    Specified by:
    
    getIsPriorFlat in interface MCMCRunStorage
  - setIsProposalSymmetric
```
public void setIsProposalSymmetric(java.lang.String bool)
```
    Specified by:
    
    setIsProposalSymmetric in interface MCMCRunStorage
  - getIsProposalSymmetric
```
public java.lang.String getIsProposalSymmetric()
```
    Specified by:
    
    getIsProposalSymmetric in interface MCMCRunStorage
  - getCurrentParameterBlockIndex
```
public java.lang.String getCurrentParameterBlockIndex()
```
    Specified by:
    
    getCurrentParameterBlockIndex in interface MCMCRunStorage
  - setCurrentParameterBlockIndex
```
public void setCurrentParameterBlockIndex(java.lang.String x)
```
    Specified by:
    
    setCurrentParameterBlockIndex in interface MCMCRunStorage
  - addParameterBlock
```
public void addParameterBlock()
```
    Specified by:
    
    addParameterBlock in interface MCMCRunStorage
  - getParameterBlockCount
```
public int getParameterBlockCount()
```
    Specified by:
    
    getParameterBlockCount in interface MCMCRunStorage
  - insertParameterBlock
```
public void insertParameterBlock(int index)
```
    Specified by:
    
    insertParameterBlock in interface MCMCRunStorage
  - removeParameterBlock
```
public void removeParameterBlock(int index)
```
    Specified by:
    
    removeParameterBlock in interface MCMCRunStorage
  - setParameterBlockName
```
public void setParameterBlockName(int index,
                         java.lang.String name)
```
    Specified by:
    
    setParameterBlockName in interface MCMCRunStorage
  - getParameterBlockName
```
public java.lang.String getParameterBlockName(int index)
```
    Specified by:
    
    getParameterBlockName in interface MCMCRunStorage
  - getParameterBlockNumberOfCycles
```
public java.lang.String getParameterBlockNumberOfCycles(int index)
```
    Specified by:
    
    getParameterBlockNumberOfCycles in interface MCMCRunStorage
  - getParameterBlockParameters
```
public java.util.Vector getParameterBlockParameters(int index)
```
    Specified by:
    
    getParameterBlockParameters in interface MCMCRunStorage
  - addParameterBlockParameter
```
public void addParameterBlockParameter(int index,
                              java.lang.String pname)
```
    Specified by:
    
    addParameterBlockParameter in interface MCMCRunStorage
  - removeParameterBlockParameter
```
public void removeParameterBlockParameter(int index,
                                 java.lang.String pname)
```
    Specified by:
    
    removeParameterBlockParameter in interface MCMCRunStorage
  - holdParameterFixed
```
public void holdParameterFixed(java.lang.String pname)
```
    Removes the named parameter from every parameter block. This has the effect of holding the parameter fixed at its current value. If no parameter blocks are currently associated with the run then a single block is first created containing all parameters and then the fixed parameters are removed.
    
    Specified by:
    
    holdParameterFixed in interface MCMCRunStorage
  - setParameterBlockNumberOfCycles
```
public void setParameterBlockNumberOfCycles(int index,
                                   java.lang.String num)
```
    Specified by:
    
    setParameterBlockNumberOfCycles in interface MCMCRunStorage
  - setMCMCSamplerRepositoryElement
```
public void setMCMCSamplerRepositoryElement(RepositoryElement elem)
```
    Specified by:
    
    setMCMCSamplerRepositoryElement in interface MCMCRunStorage
  - getMCMCSamplerRepositoryElement
```
public RepositoryElement getMCMCSamplerRepositoryElement()
```
    Specified by:
    
    getMCMCSamplerRepositoryElement in interface MCMCRunStorage
  - getAPROPRepositoryElement
```
public RepositoryElement getAPROPRepositoryElement()
```
    Specified by:
    
    getAPROPRepositoryElement in interface MCMCRunStorage
  - getBPROPRepositoryElement
```
public RepositoryElement getBPROPRepositoryElement()
```
    Specified by:
    
    getBPROPRepositoryElement in interface MCMCRunStorage
  - getAPRIORRepositoryElement
```
public RepositoryElement getAPRIORRepositoryElement()
```
    Specified by:
    
    getAPRIORRepositoryElement in interface MCMCRunStorage
  - getBPRIORRepositoryElement
```
public RepositoryElement getBPRIORRepositoryElement()
```
    Specified by:
    
    getBPRIORRepositoryElement in interface MCMCRunStorage
  - getALIKERepositoryElement
```
public RepositoryElement getALIKERepositoryElement()
```
    Specified by:
    
    getALIKERepositoryElement in interface MCMCRunStorage
  - getBLIKERepositoryElement
```
public RepositoryElement getBLIKERepositoryElement()
```
    Specified by:
    
    getBLIKERepositoryElement in interface MCMCRunStorage
  - setAPROPRepositoryElement
```
public void setAPROPRepositoryElement(RepositoryElement elem)
```
    Specified by:
    
    setAPROPRepositoryElement in interface MCMCRunStorage
  - setBPROPRepositoryElement
```
public void setBPROPRepositoryElement(RepositoryElement elem)
```
    Specified by:
    
    setBPROPRepositoryElement in interface MCMCRunStorage
  - setAPRIORRepositoryElement
```
public void setAPRIORRepositoryElement(RepositoryElement elem)
```
    Specified by:
    
    setAPRIORRepositoryElement in interface MCMCRunStorage
  - setBPRIORRepositoryElement
```
public void setBPRIORRepositoryElement(RepositoryElement elem)
```
    Specified by:
    
    setBPRIORRepositoryElement in interface MCMCRunStorage
  - setALIKERepositoryElement
```
public void setALIKERepositoryElement(RepositoryElement elem)
```
    Specified by:
    
    setALIKERepositoryElement in interface MCMCRunStorage
  - setBLIKERepositoryElement
```
public void setBLIKERepositoryElement(RepositoryElement elem)
```
    Specified by:
    
    setBLIKERepositoryElement in interface MCMCRunStorage
  - setProposalDistributionRepositoryElement
```
public void setProposalDistributionRepositoryElement(RepositoryElement elem)
```
    Specified by:
    
    setProposalDistributionRepositoryElement in interface MCMCRunStorage
  - getObjectTraceRepositoryElement
```
public RepositoryElement getObjectTraceRepositoryElement()
```
    Specified by:
    
    getObjectTraceRepositoryElement in interface MCMCRunStorage
  - getParameterTraceRepositoryElement
```
public RepositoryElement getParameterTraceRepositoryElement()
```
    Specified by:
    
    getParameterTraceRepositoryElement in interface MCMCRunStorage
  - setObjectTraceRepositoryElement
```
public void setObjectTraceRepositoryElement(RepositoryElement elem)
```
    Specified by:
    
    setObjectTraceRepositoryElement in interface MCMCRunStorage
  - setParameterTraceRepositoryElement
```
public void setParameterTraceRepositoryElement(RepositoryElement elem)
```
    Specified by:
    
    setParameterTraceRepositoryElement in interface MCMCRunStorage
  - setParentMCMCRepositoryElement
```
public void setParentMCMCRepositoryElement(RepositoryElement elem)
```
    Specified by:
    
    setParentMCMCRepositoryElement in interface MCMCRunStorage
  - getParentMCMCRepositoryElement
```
public RepositoryElement getParentMCMCRepositoryElement()
```
    Specified by:
    
    getParentMCMCRepositoryElement in interface MCMCRunStorage
  - getProposalDistributionRepositoryElement
```
public RepositoryElement getProposalDistributionRepositoryElement()
```
    Specified by:
    
    getProposalDistributionRepositoryElement in interface MCMCRunStorage
  - setParameterTraceCapacity
```
public void setParameterTraceCapacity(java.lang.String siz)
```
  - getParameterTraceCapacity
```
public java.lang.String getParameterTraceCapacity()
```
  - setObjectTraceCapacity
```
public void setObjectTraceCapacity(java.lang.String siz)
```
  - getObjectTraceCapacity
```
public java.lang.String getObjectTraceCapacity()
```
  - setRecordParameterTrace
```
public void setRecordParameterTrace(java.lang.String bool)
```
    Specified by:
    
    setRecordParameterTrace in interface MCMCRunStorage
  - getRecordParameterTrace
```
public java.lang.String getRecordParameterTrace()
```
    Specified by:
    
    getRecordParameterTrace in interface MCMCRunStorage
  - setRecordObjectTrace
```
public void setRecordObjectTrace(java.lang.String bool)
```
    Specified by:
    
    setRecordObjectTrace in interface MCMCRunStorage
  - getRecordObjectTrace
```
public java.lang.String getRecordObjectTrace()
```
    Specified by:
    
    getRecordObjectTrace in interface MCMCRunStorage

Class MCMCRunDOM

Field Summary

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

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

Constructor Summary

Method Summary

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

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

Methods inherited from class java.lang.Object

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

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

Constructor Detail

MCMCRunDOM

Method Detail

getProcessingInstructionRef

initialize

setReferenceParametersFrom

getShouldRollBack

setShouldRollBack

setReferenceParametersFrom

getDefaultGraphicalEditorClass

getStorageTransferAgentClass

getDOMStorageClass

getRootElementName

clearDelegates

clearParent

clearSampler

clearProposalDistribution

clearCandidateParameterSet

clearPreviousParameterSet

clearReferenceParameterSet

clearCandidateObjectSet

clearPreviousObjectSet

clearParameterTrace

clearObjectTrace

clearALIKE

clearBLIKE

clearAPRIOR

clearBPRIOR

clearAPROP

clearBPROP

clearParameterBlocks

specifyStorage

getPreviousParameterStorage

getCandidateParameterStorage

getReferenceParameterStorage

getMixingParameterStorage

getProposalDistributionStorage

hasDelegateState

addDelegateState

removeDelegateState

getDelegateStates

getDelegateStatesRoot

getCandidateParameterRepositoryElement

setCandidateParameterRepositoryElement

getCandidateObjectRepositoryElement

getRejectFraction

stop

start

restartUsingParametersFrom

restartUsingParametersFrom

setCandidateObjectRepositoryElement

getPreviousParameterRepositoryElement

setPreviousParameterRepositoryElement

getReferenceParameterRepositoryElement

setReferenceParameterRepositoryElement

getPreviousObjectRepositoryElement

setPreviousObjectRepositoryElement

getParameterBlockRoot

getParameterBlock

getMCMCRunState

setMCMCRunState

advanceMCMCRunState

setMCMCRunIdentifier

getMCMCRunIdentifier

getIsStateLocked

setIsStateLocked

getIsStillRunning

setIsStillRunning

getShouldHalt