public class MCMCRunDOM extends RepositoryStorageDOM implements MCMCRunStorage
document, dostylesheets, storageRoot, templateDOM
nickname, reposListeners, transferAgent
Constructor and Description |
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MCMCRunDOM() |
Modifier and Type | Method and Description |
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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.
|
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
addRepositoryListener, afterCopyStorage, afterTransferStorage, beforeCopyStorage, beforeTransferStorage, copyStorage, copyStorageCommands, getStorageCalculationsAgentClass, removeRepositoryListener, transferStorage, transferStorageCommands
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
addRepositoryListener, getComment, getCreatedBy, getCreatedOn, getEnabled, getNickname, removeRepositoryListener, setComment, setCreatedBy, setCreatedOn, setEnabled, setNickname
afterCopyStorage, afterTransferStorage, beforeCopyStorage, beforeTransferStorage, copyStorage, copyStorageCommands, transferStorage, transferStorageCommands
protected java.lang.String getProcessingInstructionRef()
public void initialize()
initialize
in interface MCMCRunStorage
public void setReferenceParametersFrom(ParameterSetStorage P)
setReferenceParametersFrom
in interface MCMCRunStorage
public java.lang.String getShouldRollBack()
getShouldRollBack
in interface MCMCRunStorage
public void setShouldRollBack(java.lang.String bool)
setShouldRollBack
in interface MCMCRunStorage
public void setReferenceParametersFrom(DblParamSet P)
setReferenceParametersFrom
in interface MCMCRunStorage
public java.lang.Class getDefaultGraphicalEditorClass()
getDefaultGraphicalEditorClass
in interface RepositoryStorage
getDefaultGraphicalEditorClass
in class RepositoryStorageDOM
public java.lang.Class getStorageTransferAgentClass()
AbstractRepositoryStorage
getStorageTransferAgentClass
in class AbstractRepositoryStorage
public java.lang.Class getDOMStorageClass()
AbstractRepositoryStorage
getDOMStorageClass
in interface DOMStorable
getDOMStorageClass
in class RepositoryStorageDOM
public java.lang.String getRootElementName()
getRootElementName
in class RepositoryStorageDOM
protected void clearDelegates()
protected void clearParent()
protected void clearSampler()
protected void clearProposalDistribution()
protected void clearCandidateParameterSet()
protected void clearPreviousParameterSet()
protected void clearReferenceParameterSet()
protected void clearCandidateObjectSet()
protected void clearPreviousObjectSet()
protected void clearParameterTrace()
protected void clearObjectTrace()
protected void clearALIKE()
protected void clearBLIKE()
protected void clearAPRIOR()
protected void clearBPRIOR()
protected void clearAPROP()
protected void clearBPROP()
protected void clearParameterBlocks()
protected void specifyStorage(org.w3c.dom.Document doc, org.w3c.dom.Element root)
specifyStorage
in class RepositoryStorageDOM
public ParameterSetStorage getPreviousParameterStorage()
getPreviousParameterStorage
in interface MCMCRunStorage
public ParameterSetStorage getCandidateParameterStorage()
getCandidateParameterStorage
in interface MCMCRunStorage
public ParameterSetStorage getReferenceParameterStorage()
getReferenceParameterStorage
in interface MCMCRunStorage
public ParameterSetStorage getMixingParameterStorage()
getMixingParameterStorage
in interface MCMCRunStorage
public ProposalDistributionStorage getProposalDistributionStorage()
getProposalDistributionStorage
in interface MCMCRunStorage
public java.lang.String hasDelegateState(java.lang.String state)
hasDelegateState
in interface MCMCRunStorage
public void addDelegateState(java.lang.String state)
addDelegateState
in interface MCMCRunStorage
public void removeDelegateState(java.lang.String state)
removeDelegateState
in interface MCMCRunStorage
public java.util.Vector getDelegateStates()
getDelegateStates
in interface MCMCRunStorage
protected org.w3c.dom.Element getDelegateStatesRoot()
public RepositoryElement getCandidateParameterRepositoryElement()
getCandidateParameterRepositoryElement
in interface MCMCRunStorage
public void setCandidateParameterRepositoryElement(RepositoryElement elem)
setCandidateParameterRepositoryElement
in interface MCMCRunStorage
public RepositoryElement getCandidateObjectRepositoryElement()
getCandidateObjectRepositoryElement
in interface MCMCRunStorage
public double getRejectFraction()
getRejectFraction
in interface MCMCRunStorage
public void stop()
stop
in interface MCMCRunStorage
public void start()
start
in interface MCMCRunStorage
public void restartUsingParametersFrom(ParameterSetStorage stor)
restartUsingParametersFrom
in interface MCMCRunStorage
public void restartUsingParametersFrom(DblParamSet params)
restartUsingParametersFrom
in interface MCMCRunStorage
public void setCandidateObjectRepositoryElement(RepositoryElement elem)
setCandidateObjectRepositoryElement
in interface MCMCRunStorage
public RepositoryElement getPreviousParameterRepositoryElement()
getPreviousParameterRepositoryElement
in interface MCMCRunStorage
public void setPreviousParameterRepositoryElement(RepositoryElement elem)
setPreviousParameterRepositoryElement
in interface MCMCRunStorage
public RepositoryElement getReferenceParameterRepositoryElement()
getReferenceParameterRepositoryElement
in interface MCMCRunStorage
public void setReferenceParameterRepositoryElement(RepositoryElement elem)
setReferenceParameterRepositoryElement
in interface MCMCRunStorage
public RepositoryElement getPreviousObjectRepositoryElement()
getPreviousObjectRepositoryElement
in interface MCMCRunStorage
public void setPreviousObjectRepositoryElement(RepositoryElement elem)
setPreviousObjectRepositoryElement
in interface MCMCRunStorage
protected org.w3c.dom.Element getParameterBlockRoot()
protected org.w3c.dom.Element getParameterBlock(int index)
public java.lang.String getMCMCRunState()
getMCMCRunState
in interface MCMCRunStorage
public void setMCMCRunState(java.lang.String state)
setMCMCRunState
in interface MCMCRunStorage
public void advanceMCMCRunState()
advanceMCMCRunState
in interface MCMCRunStorage
public void setMCMCRunIdentifier(java.lang.String s)
setMCMCRunIdentifier
in interface MCMCRunStorage
public java.lang.String getMCMCRunIdentifier()
getMCMCRunIdentifier
in interface MCMCRunStorage
public java.lang.String getIsStateLocked()
getIsStateLocked
in interface MCMCRunStorage
public void setIsStateLocked(java.lang.String boole)
setIsStateLocked
in interface MCMCRunStorage
public java.lang.String getIsStillRunning()
getIsStillRunning
in interface MCMCRunStorage
public void setIsStillRunning(java.lang.String boole)
setIsStillRunning
in interface MCMCRunStorage
public java.lang.String getShouldHalt()
getShouldHalt
in interface MCMCRunStorage
public void setShouldHalt(java.lang.String boole)
setShouldHalt
in interface MCMCRunStorage
public java.lang.String getCurrentIterationNumber()
getCurrentIterationNumber
in interface MCMCRunStorage
public void setCurrentIterationNumber(java.lang.String v)
setCurrentIterationNumber
in interface MCMCRunStorage
public java.lang.String getCurrentLinkCount()
MCMCRunStorage
getCurrentLinkCount
in interface MCMCRunStorage
public void setCurrentLinkCount(java.lang.String v)
setCurrentLinkCount
in interface MCMCRunStorage
public void setCurrentParameterBlockCycleNumber(java.lang.String x)
setCurrentParameterBlockCycleNumber
in interface MCMCRunStorage
public java.lang.String getCurrentParameterBlockCycleNumber()
getCurrentParameterBlockCycleNumber
in interface MCMCRunStorage
public java.lang.String getCurrentAlpha()
getCurrentAlpha
in interface MCMCRunStorage
public void setCurrentAlpha(java.lang.String prob)
setCurrentAlpha
in interface MCMCRunStorage
public java.lang.String getMaximumIterationNumber()
getMaximumIterationNumber
in interface MCMCRunStorage
public void setMaximumIterationNumber(java.lang.String v)
setMaximumIterationNumber
in interface MCMCRunStorage
public java.lang.String getRejectCount()
getRejectCount
in interface MCMCRunStorage
public void setRejectCount(java.lang.String v)
setRejectCount
in interface MCMCRunStorage
public java.lang.String getAcceptCount()
getAcceptCount
in interface MCMCRunStorage
public void setAcceptCount(java.lang.String v)
setAcceptCount
in interface MCMCRunStorage
public void setIsPriorFlat(java.lang.String bool)
setIsPriorFlat
in interface MCMCRunStorage
public java.lang.String getIsPriorFlat()
getIsPriorFlat
in interface MCMCRunStorage
public void setIsProposalSymmetric(java.lang.String bool)
setIsProposalSymmetric
in interface MCMCRunStorage
public java.lang.String getIsProposalSymmetric()
getIsProposalSymmetric
in interface MCMCRunStorage
public java.lang.String getCurrentParameterBlockIndex()
getCurrentParameterBlockIndex
in interface MCMCRunStorage
public void setCurrentParameterBlockIndex(java.lang.String x)
setCurrentParameterBlockIndex
in interface MCMCRunStorage
public void addParameterBlock()
addParameterBlock
in interface MCMCRunStorage
public int getParameterBlockCount()
getParameterBlockCount
in interface MCMCRunStorage
public void insertParameterBlock(int index)
insertParameterBlock
in interface MCMCRunStorage
public void removeParameterBlock(int index)
removeParameterBlock
in interface MCMCRunStorage
public void setParameterBlockName(int index, java.lang.String name)
setParameterBlockName
in interface MCMCRunStorage
public java.lang.String getParameterBlockName(int index)
getParameterBlockName
in interface MCMCRunStorage
public java.lang.String getParameterBlockNumberOfCycles(int index)
getParameterBlockNumberOfCycles
in interface MCMCRunStorage
public java.util.Vector getParameterBlockParameters(int index)
getParameterBlockParameters
in interface MCMCRunStorage
public void addParameterBlockParameter(int index, java.lang.String pname)
addParameterBlockParameter
in interface MCMCRunStorage
public void removeParameterBlockParameter(int index, java.lang.String pname)
removeParameterBlockParameter
in interface MCMCRunStorage
public void holdParameterFixed(java.lang.String pname)
holdParameterFixed
in interface MCMCRunStorage
public void setParameterBlockNumberOfCycles(int index, java.lang.String num)
setParameterBlockNumberOfCycles
in interface MCMCRunStorage
public void setMCMCSamplerRepositoryElement(RepositoryElement elem)
setMCMCSamplerRepositoryElement
in interface MCMCRunStorage
public RepositoryElement getMCMCSamplerRepositoryElement()
getMCMCSamplerRepositoryElement
in interface MCMCRunStorage
public RepositoryElement getAPROPRepositoryElement()
getAPROPRepositoryElement
in interface MCMCRunStorage
public RepositoryElement getBPROPRepositoryElement()
getBPROPRepositoryElement
in interface MCMCRunStorage
public RepositoryElement getAPRIORRepositoryElement()
getAPRIORRepositoryElement
in interface MCMCRunStorage
public RepositoryElement getBPRIORRepositoryElement()
getBPRIORRepositoryElement
in interface MCMCRunStorage
public RepositoryElement getALIKERepositoryElement()
getALIKERepositoryElement
in interface MCMCRunStorage
public RepositoryElement getBLIKERepositoryElement()
getBLIKERepositoryElement
in interface MCMCRunStorage
public void setAPROPRepositoryElement(RepositoryElement elem)
setAPROPRepositoryElement
in interface MCMCRunStorage
public void setBPROPRepositoryElement(RepositoryElement elem)
setBPROPRepositoryElement
in interface MCMCRunStorage
public void setAPRIORRepositoryElement(RepositoryElement elem)
setAPRIORRepositoryElement
in interface MCMCRunStorage
public void setBPRIORRepositoryElement(RepositoryElement elem)
setBPRIORRepositoryElement
in interface MCMCRunStorage
public void setALIKERepositoryElement(RepositoryElement elem)
setALIKERepositoryElement
in interface MCMCRunStorage
public void setBLIKERepositoryElement(RepositoryElement elem)
setBLIKERepositoryElement
in interface MCMCRunStorage
public void setProposalDistributionRepositoryElement(RepositoryElement elem)
setProposalDistributionRepositoryElement
in interface MCMCRunStorage
public RepositoryElement getObjectTraceRepositoryElement()
getObjectTraceRepositoryElement
in interface MCMCRunStorage
public RepositoryElement getParameterTraceRepositoryElement()
getParameterTraceRepositoryElement
in interface MCMCRunStorage
public void setObjectTraceRepositoryElement(RepositoryElement elem)
setObjectTraceRepositoryElement
in interface MCMCRunStorage
public void setParameterTraceRepositoryElement(RepositoryElement elem)
setParameterTraceRepositoryElement
in interface MCMCRunStorage
public void setParentMCMCRepositoryElement(RepositoryElement elem)
setParentMCMCRepositoryElement
in interface MCMCRunStorage
public RepositoryElement getParentMCMCRepositoryElement()
getParentMCMCRepositoryElement
in interface MCMCRunStorage
public RepositoryElement getProposalDistributionRepositoryElement()
getProposalDistributionRepositoryElement
in interface MCMCRunStorage
public void setParameterTraceCapacity(java.lang.String siz)
public java.lang.String getParameterTraceCapacity()
public void setObjectTraceCapacity(java.lang.String siz)
public java.lang.String getObjectTraceCapacity()
public void setRecordParameterTrace(java.lang.String bool)
setRecordParameterTrace
in interface MCMCRunStorage
public java.lang.String getRecordParameterTrace()
getRecordParameterTrace
in interface MCMCRunStorage
public void setRecordObjectTrace(java.lang.String bool)
setRecordObjectTrace
in interface MCMCRunStorage
public java.lang.String getRecordObjectTrace()
getRecordObjectTrace
in interface MCMCRunStorage
Copyright © 2011, 2013. Daniel P. Dougherty