com.mockturtlesolutions.snifflib.mcmctools.workbench

Class MCMCRunPanel

java.lang.Object

java.awt.Component

java.awt.Container

javax.swing.JComponent

javax.swing.JPanel

com.mockturtlesolutions.snifflib.mcmctools.workbench.MCMCRunPanel

All Implemented Interfaces:

MCMCRunStorage, DOMStorable, RepositoryStorage, RepositoryStorageTransfer, java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, javax.accessibility.Accessible

public class MCMCRunPanel
extends javax.swing.JPanel
implements MCMCRunStorage

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class javax.swing.JPanel

javax.swing.JPanel.AccessibleJPanel

Nested classes/interfaces inherited from class javax.swing.JComponent

javax.swing.JComponent.AccessibleJComponent

Nested classes/interfaces inherited from class java.awt.Container

java.awt.Container.AccessibleAWTContainer

Nested classes/interfaces inherited from class java.awt.Component

java.awt.Component.AccessibleAWTComponent, java.awt.Component.BaselineResizeBehavior, java.awt.Component.BltBufferStrategy, java.awt.Component.FlipBufferStrategy

Field Summary

Fields

Modifier and Type	Field and Description
protected MCMCConfig	Config
protected MCMCStorageConnectivity	Connection

Fields inherited from class javax.swing.JComponent

accessibleContext, listenerList, TOOL_TIP_TEXT_KEY, ui, UNDEFINED_CONDITION, WHEN_ANCESTOR_OF_FOCUSED_COMPONENT, WHEN_FOCUSED, WHEN_IN_FOCUSED_WINDOW

Fields inherited from class java.awt.Component

BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT

Fields inherited from interface java.awt.image.ImageObserver

ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH

Constructor Summary

Constructors

Constructor and Description
MCMCRunPanel()
MCMCRunPanel(MCMCStorage stor) Allows for the panel to associate with the given MCMCStorage.

Method Summary

Methods

Modifier and Type	Method and Description
void	addDelegateState(java.lang.String state)
void	addParameterBlock()
void	addParameterBlockParameter(int index, java.lang.String pname)
void	addRepositoryListener(RepositoryListener l)
void	advanceMCMCRunState()
void	afterCopyStorage()
void	afterTransferStorage()
void	beforeCopyStorage()
void	beforeTransferStorage()
void	copyStorage(RepositoryStorage x)
void	copyStorageCommands(RepositoryStorage x)
void	fireRepositoryChanged(RepositoryEvent ev)
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	getComment() Gets the descriptive comment for this Wedge inverse problem as a whole.
java.lang.String	getCreatedBy()
java.lang.String	getCreatedOn()
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()
java.lang.Class	getDOMStorageClass()
java.lang.String	getEnabled() Gets the state of the (possibly remote) storage.
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	getNickname() Gets the project name for this Wedge inverse problem.
RepositoryElement	getObjectTraceRepositoryElement()
int	getParameterBlockCount()
java.lang.String	getParameterBlockName(int index)
java.lang.String	getParameterBlockNumberOfCycles(int index)
java.util.Vector	getParameterBlockParameters(int index)
RepositoryElement	getParameterTraceRepositoryElement()
RepositoryElement	getParentMCMCRepositoryElement()
RepositoryElement	getPreviousObjectRepositoryElement()
RepositoryElement	getPreviousParameterRepositoryElement()
ParameterSetStorage	getPreviousParameterStorage() Returns the repository storage for the previous parameters of this run.
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	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()
java.lang.String	hasDelegateState(java.lang.String state)
void	holdParameterFixed(java.lang.String pname) Removes the named parameter from every parameter block.
void	initialize()
void	insertParameterBlock(int j)
void	removeDelegateState(java.lang.String state)
void	removeParameterBlock(int index)
void	removeParameterBlockParameter(int index, java.lang.String pname)
void	removeRepositoryListener(RepositoryListener l)
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	setComment(java.lang.String txt)
void	setCreatedBy(java.lang.String txt)
void	setCreatedOn(java.lang.String txt)
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	setDockedToParent(boolean x)
void	setEditable(boolean b) Toggles the editability of the MCMCRun panel.
void	setEnabled(java.lang.String n) Sets the enabled state of the (possibly remote) storage instance.
void	setIsPriorFlat(java.lang.String b)
void	setIsProposalSymmetric(java.lang.String b)
void	setIsStateLocked(java.lang.String boole)
void	setIsStillRunning(java.lang.String boole)
void	setMaximumIterationNumber(java.lang.String v)
void	setMCMCRunIdentifier(java.lang.String sampler) Sets a "unique" nickname modifier so that particualr storage instances are associated with this optimization stream.
void	setMCMCRunState(java.lang.String s)
void	setMCMCSamplerRepositoryElement(RepositoryElement elem)
void	setNickname(java.lang.String txt) Sets the project name for this Wedge inverse problem.
void	setObjectTraceRepositoryElement(RepositoryElement elem)
void	setParameterBlockName(int index, java.lang.String name)
void	setParameterBlockNumberOfCycles(int index, java.lang.String num)
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 siz)
void	setRecordParameterTrace(java.lang.String siz)
void	setReferenceParameterRepositoryElement(RepositoryElement elem)
void	setReferenceParametersFrom(DblParamSet P)
void	setReferenceParametersFrom(ParameterSetStorage P)
void	setRejectCount(java.lang.String v)
void	setRepository(java.lang.String repos)
void	setShouldHalt(java.lang.String boole)
void	setShouldRollBack(java.lang.String boole) Sets boolean indication of whether a roll back of the most recent iteration or proposal should occur.
void	start() Attempts to start run.
void	stop() Attempts to stop run.
void	transferStorage(RepositoryStorage that)
void	transferStorageCommands(RepositoryStorage X)

Methods inherited from class javax.swing.JPanel

getAccessibleContext, getUI, getUIClassID, paramString, setUI, updateUI

Methods inherited from class javax.swing.JComponent

addAncestorListener, addNotify, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, fireVetoableChange, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAncestorListeners, getAutoscrolls, getBaseline, getBaselineResizeBehavior, getBorder, getBounds, getClientProperty, getComponentGraphics, getComponentPopupMenu, getConditionForKeyStroke, getDebugGraphicsOptions, getDefaultLocale, getFontMetrics, getGraphics, getHeight, getInheritsPopupMenu, getInputMap, getInputMap, getInputVerifier, getInsets, getInsets, getListeners, getLocation, getMaximumSize, getMinimumSize, getNextFocusableComponent, getPopupLocation, getPreferredSize, getRegisteredKeyStrokes, getRootPane, getSize, getToolTipLocation, getToolTipText, getToolTipText, getTopLevelAncestor, getTransferHandler, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingForPrint, isPaintingOrigin, isPaintingTile, isRequestFocusEnabled, isValidateRoot, paint, paintBorder, paintChildren, paintComponent, paintImmediately, paintImmediately, print, printAll, printBorder, printChildren, printComponent, processComponentKeyEvent, processKeyBinding, processKeyEvent, processMouseEvent, processMouseMotionEvent, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeNotify, removeVetoableChangeListener, repaint, repaint, requestDefaultFocus, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resetKeyboardActions, reshape, revalidate, scrollRectToVisible, setActionMap, setAlignmentX, setAlignmentY, setAutoscrolls, setBackground, setBorder, setComponentPopupMenu, setDebugGraphicsOptions, setDefaultLocale, setDoubleBuffered, setEnabled, setFocusTraversalKeys, setFont, setForeground, setInheritsPopupMenu, setInputMap, setInputVerifier, setMaximumSize, setMinimumSize, setNextFocusableComponent, setOpaque, setPreferredSize, setRequestFocusEnabled, setToolTipText, setTransferHandler, setUI, setVerifyInputWhenFocusTarget, setVisible, unregisterKeyboardAction, update

Methods inherited from class java.awt.Container

add, add, add, add, add, addContainerListener, addImpl, addPropertyChangeListener, addPropertyChangeListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getLayout, getMousePosition, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, printComponents, processContainerEvent, processEvent, remove, remove, removeAll, removeContainerListener, setComponentZOrder, setFocusCycleRoot, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setLayout, transferFocusDownCycle, validate, validateTree

Methods inherited from class java.awt.Component

action, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, coalesceEvents, contains, createImage, createImage, createVolatileImage, createVolatileImage, disableEvents, dispatchEvent, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusCycleRootAncestor, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getForeground, getGraphicsConfiguration, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocale, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getToolkit, getTreeLock, gotFocus, handleEvent, hasFocus, hide, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isPreferredSizeSet, isShowing, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, postEvent, prepareImage, prepareImage, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, resize, resize, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setFocusable, setFocusTraversalKeysEnabled, setIgnoreRepaint, setLocale, setLocation, setLocation, setName, setSize, setSize, show, show, size, toString, transferFocus, transferFocusBackward, transferFocusUpCycle

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

Connection

protected MCMCStorageConnectivity Connection

Config

protected MCMCConfig Config

Constructor Detail

MCMCRunPanel

public MCMCRunPanel()

MCMCRunPanel

public MCMCRunPanel(MCMCStorage stor)

Allows for the panel to associate with the given MCMCStorage.

Method Detail

setDockedToParent

public void setDockedToParent(boolean x)

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

setRepository

public void setRepository(java.lang.String repos)

fireRepositoryChanged

public void fireRepositoryChanged(RepositoryEvent ev)

transferStorageCommands

public void transferStorageCommands(RepositoryStorage X)

Specified by:

transferStorageCommands in interface RepositoryStorageTransfer

getDOMStorageClass

public java.lang.Class getDOMStorageClass()

Specified by:

getDOMStorageClass in interface DOMStorable

getStorageTransferAgentClass

public java.lang.Class getStorageTransferAgentClass()

transferStorage

public void transferStorage(RepositoryStorage that)

Specified by:

transferStorage in interface RepositoryStorageTransfer

afterTransferStorage

public void afterTransferStorage()

Specified by:

afterTransferStorage in interface RepositoryStorageTransfer

beforeTransferStorage

public void beforeTransferStorage()

Specified by:

beforeTransferStorage in interface RepositoryStorageTransfer

beforeCopyStorage

public void beforeCopyStorage()

Specified by:

beforeCopyStorage in interface RepositoryStorageTransfer

afterCopyStorage

public void afterCopyStorage()

Specified by:

afterCopyStorage in interface RepositoryStorageTransfer

copyStorageCommands

public void copyStorageCommands(RepositoryStorage x)

Specified by:

copyStorageCommands in interface RepositoryStorageTransfer

copyStorage

public void copyStorage(RepositoryStorage x)

Specified by:

copyStorage in interface RepositoryStorageTransfer

addRepositoryListener

public void addRepositoryListener(RepositoryListener l)

Specified by:

addRepositoryListener in interface RepositoryStorage

removeRepositoryListener

public void removeRepositoryListener(RepositoryListener l)

Specified by:

removeRepositoryListener in interface RepositoryStorage

setEditable

public void setEditable(boolean b)

Toggles the editability of the MCMCRun panel.

setEnabled

public void setEnabled(java.lang.String n)

Description copied from interface: RepositoryStorage

Sets the enabled state of the (possibly remote) storage instance. Typically a storage is backed by static information stored in a database.

Specified by:

setEnabled in interface RepositoryStorage

getDefaultGraphicalEditorClass

public java.lang.Class getDefaultGraphicalEditorClass()

Specified by:

getDefaultGraphicalEditorClass in interface RepositoryStorage

getEnabled

public java.lang.String getEnabled()

Description copied from interface: RepositoryStorage

Gets the state of the (possibly remote) storage. For example, dis-enabled storages may be slated for deletion from some repostories. Typically a storage is backed by static information stored in a database.

Specified by:

getEnabled in interface RepositoryStorage

setComment

public void setComment(java.lang.String txt)

Specified by:

setComment in interface RepositoryStorage

getComment

public java.lang.String getComment()

Description copied from interface: RepositoryStorage

Gets the descriptive comment for this Wedge inverse problem as a whole.

Specified by:

getComment in interface RepositoryStorage

setCreatedOn

public void setCreatedOn(java.lang.String txt)

Specified by:

setCreatedOn in interface RepositoryStorage

getCreatedOn

public java.lang.String getCreatedOn()

Specified by:

getCreatedOn in interface RepositoryStorage

setCreatedBy

public void setCreatedBy(java.lang.String txt)

Specified by:

setCreatedBy in interface RepositoryStorage

getCreatedBy

public java.lang.String getCreatedBy()

Specified by:

getCreatedBy in interface RepositoryStorage

setNickname

public void setNickname(java.lang.String txt)

Description copied from interface: RepositoryStorage

Sets the project name for this Wedge inverse problem.

Specified by:

setNickname in interface RepositoryStorage

getNickname

public java.lang.String getNickname()

Description copied from interface: RepositoryStorage

Gets the project name for this Wedge inverse problem.

Specified by:

getNickname in interface RepositoryStorage

getMCMCRunState

public java.lang.String getMCMCRunState()

Specified by:

getMCMCRunState in interface MCMCRunStorage

setMCMCRunState

public void setMCMCRunState(java.lang.String s)

Specified by:

setMCMCRunState in interface MCMCRunStorage

advanceMCMCRunState

public void advanceMCMCRunState()

Specified by:

advanceMCMCRunState 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

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

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

initialize

public void initialize()

Specified by:

initialize in interface MCMCRunStorage

setMCMCRunIdentifier

public void setMCMCRunIdentifier(java.lang.String sampler)

Sets a "unique" nickname modifier so that particualr storage instances are associated with this optimization stream.

Specified by:

setMCMCRunIdentifier in interface MCMCRunStorage

getMCMCRunIdentifier

public java.lang.String getMCMCRunIdentifier()

Specified by:

getMCMCRunIdentifier 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

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

getShouldRollBack

public java.lang.String getShouldRollBack()

Description copied from interface: MCMCRunStorage

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 boole)

Description copied from interface: MCMCRunStorage

Sets boolean indication of whether a roll back of the most recent iteration or proposal should occur.

Specified by:

setShouldRollBack 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

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 b)

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 b)

Specified by:

setIsProposalSymmetric in interface MCMCRunStorage

getIsProposalSymmetric

public java.lang.String getIsProposalSymmetric()

Specified by:

getIsProposalSymmetric in interface MCMCRunStorage

holdParameterFixed

public void holdParameterFixed(java.lang.String pname)

Removes the named parameter from every parameter block.

Specified by:

holdParameterFixed 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

getParameterBlockCount

public int getParameterBlockCount()

Specified by:

getParameterBlockCount in interface MCMCRunStorage

addParameterBlock

public void addParameterBlock()

Specified by:

addParameterBlock in interface MCMCRunStorage

insertParameterBlock

public void insertParameterBlock(int j)

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

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

setPreviousParameterRepositoryElement

public void setPreviousParameterRepositoryElement(RepositoryElement elem)

Specified by:

setPreviousParameterRepositoryElement in interface MCMCRunStorage

getPreviousParameterRepositoryElement

public RepositoryElement getPreviousParameterRepositoryElement()

Specified by:

getPreviousParameterRepositoryElement in interface MCMCRunStorage

setReferenceParameterRepositoryElement

public void setReferenceParameterRepositoryElement(RepositoryElement elem)

Specified by:

setReferenceParameterRepositoryElement in interface MCMCRunStorage

getReferenceParameterRepositoryElement

public RepositoryElement getReferenceParameterRepositoryElement()

Specified by:

getReferenceParameterRepositoryElement in interface MCMCRunStorage

setPreviousObjectRepositoryElement

public void setPreviousObjectRepositoryElement(RepositoryElement elem)

Specified by:

setPreviousObjectRepositoryElement in interface MCMCRunStorage

getPreviousObjectRepositoryElement

public RepositoryElement getPreviousObjectRepositoryElement()

Specified by:

getPreviousObjectRepositoryElement in interface MCMCRunStorage

setReferenceParametersFrom

public void setReferenceParametersFrom(DblParamSet P)

Specified by:

setReferenceParametersFrom in interface MCMCRunStorage

setReferenceParametersFrom

public void setReferenceParametersFrom(ParameterSetStorage P)

Specified by:

setReferenceParametersFrom 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(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

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

setCandidateParameterRepositoryElement

public void setCandidateParameterRepositoryElement(RepositoryElement elem)

Specified by:

setCandidateParameterRepositoryElement in interface MCMCRunStorage

getCandidateParameterRepositoryElement

public RepositoryElement getCandidateParameterRepositoryElement()

Specified by:

getCandidateParameterRepositoryElement in interface MCMCRunStorage

setCandidateObjectRepositoryElement

public void setCandidateObjectRepositoryElement(RepositoryElement elem)

Specified by:

setCandidateObjectRepositoryElement in interface MCMCRunStorage

getCandidateObjectRepositoryElement

public RepositoryElement getCandidateObjectRepositoryElement()

Specified by:

getCandidateObjectRepositoryElement in interface MCMCRunStorage

getCurrentParameterBlockCycleNumber

public java.lang.String getCurrentParameterBlockCycleNumber()

Specified by:

getCurrentParameterBlockCycleNumber in interface MCMCRunStorage

setCurrentParameterBlockCycleNumber

public void setCurrentParameterBlockCycleNumber(java.lang.String x)

Specified by:

setCurrentParameterBlockCycleNumber 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

getParentMCMCRepositoryElement

public RepositoryElement getParentMCMCRepositoryElement()

Specified by:

getParentMCMCRepositoryElement in interface MCMCRunStorage

setParentMCMCRepositoryElement

public void setParentMCMCRepositoryElement(RepositoryElement elem)

Specified by:

setParentMCMCRepositoryElement in interface MCMCRunStorage

getParameterTraceRepositoryElement

public RepositoryElement getParameterTraceRepositoryElement()

Specified by:

getParameterTraceRepositoryElement in interface MCMCRunStorage

setParameterTraceRepositoryElement

public void setParameterTraceRepositoryElement(RepositoryElement elem)

Specified by:

setParameterTraceRepositoryElement in interface MCMCRunStorage

getObjectTraceRepositoryElement

public RepositoryElement getObjectTraceRepositoryElement()

Specified by:

getObjectTraceRepositoryElement in interface MCMCRunStorage

setObjectTraceRepositoryElement

public void setObjectTraceRepositoryElement(RepositoryElement elem)

Specified by:

setObjectTraceRepositoryElement in interface MCMCRunStorage

getProposalDistributionRepositoryElement

public RepositoryElement getProposalDistributionRepositoryElement()

Specified by:

getProposalDistributionRepositoryElement in interface MCMCRunStorage

setProposalDistributionRepositoryElement

public void setProposalDistributionRepositoryElement(RepositoryElement elem)

Specified by:

setProposalDistributionRepositoryElement in interface MCMCRunStorage

setRecordParameterTrace

public void setRecordParameterTrace(java.lang.String siz)

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 siz)

Specified by:

setRecordObjectTrace in interface MCMCRunStorage

getRecordObjectTrace

public java.lang.String getRecordObjectTrace()

Specified by:

getRecordObjectTrace in interface MCMCRunStorage

getDelegateStates

public java.util.Vector getDelegateStates()

Specified by:

getDelegateStates 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)

Specified by:

addDelegateState in interface MCMCRunStorage

removeDelegateState

public void removeDelegateState(java.lang.String state)

Specified by:

removeDelegateState in interface MCMCRunStorage