Package org.openscience.jmol.app.janocchio

Class NoeTable

java.lang.Object

java.awt.Component

java.awt.Container

javax.swing.JComponent

javax.swing.JTabbedPane

org.openscience.jmol.app.janocchio.NoeTable

All Implemented Interfaces:

ImageObserver, MenuContainer, Serializable, Accessible, SwingConstants

public class NoeTable
extends JTabbedPane

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
(package private) class	NoeTable.NoeListWindowListener
(package private) class	NoeTable.NoeTableModel

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

JTabbedPane.AccessibleJTabbedPane, JTabbedPane.ModelListener

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

JComponent.AccessibleJComponent

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

Container.AccessibleAWTContainer

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

Component.AccessibleAWTComponent, Component.BaselineResizeBehavior, Component.BltBufferStrategy, Component.FlipBufferStrategy

Field Summary

Fields

Modifier and Type	Field	Description
(package private) NmrMolecule	calcProps
(package private) NMRTableCellRenderer	colorCellRenderer
(package private) double	cutoff
(package private) String[][]	expDists
(package private) String[][]	expNoes
(package private) JComboBox<String>	expOrDistButton
(package private) FrameDeltaDisplay	frameDeltaDisplay
(package private) double	freq
(package private) String[]	labelArray
(package private) boolean	lexpNoes
(package private) boolean	lrefSingle
(package private) boolean	molCDKuptodate
(package private) int	natomsPerModel
(package private) NMR_JmolPanel	nmrPanel
NoeColourSelectionPanel	noeColourSelectionPanel
private JButton	noedeleteAllButton
(package private) JButton	noedeleteButton
(package private) double	noeExprefValue
(package private) int[]	noeNPrefIndices
(package private) double	noeNPrefValue
NoeParameterSelectionPanel	noeParameterSelectionPanel
private ListSelectionModel	noeSelection
(package private) JButton	noesetRefButton
(package private) boolean	noesy
(package private) JTable	noeTable
private NoeTable.NoeTableModel	noeTableModel
(package private) double	redValue
(package private) double	rhoStar
(package private) int[]	selectedNoeRow
(package private) double	tau
(package private) double	tMix
(package private) NMR_Viewer	viewer
(package private) double	yellowValue

Fields inherited from class javax.swing.JTabbedPane

changeEvent, changeListener, model, SCROLL_TAB_LAYOUT, tabPlacement, WRAP_TAB_LAYOUT

Fields inherited from class javax.swing.JComponent

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

accessibleContext, 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

Fields inherited from interface javax.swing.SwingConstants

BOTTOM, CENTER, EAST, HORIZONTAL, LEADING, LEFT, NEXT, NORTH, NORTH_EAST, NORTH_WEST, PREVIOUS, RIGHT, SOUTH, SOUTH_EAST, SOUTH_WEST, TOP, TRAILING, VERTICAL, WEST

Constructor Summary

Constructors

Constructor	Description
NoeTable(NMR_JmolPanel nmrPanel, JFrame parentFrame)	Constructor

Method Summary

Modifier and Type	Method	Description
void	activate()
void	addMol()
void	allocateExpNoes(int numAtoms)
void	allocateLabelArray(int numAtoms)
private void	calcFrameDelta()
(package private) int	calcNatomsPerModel()	TODO This assumes we have the same structure in each model.
protected void	centerDialog()
(package private) boolean	checkNoe(int i)
void	close()
(package private) JComponent	constructDismissButtonPanel()
(package private) JComponent	constructNoeButtonPanel()
(package private) JComponent	constructNoeTable()
double	getCorrelationTime()	get the correlation time in seconds
double	getCutoff()	get the cutoff distance
String	getExpDist(int i, int j)
String	getExpNoe(int i, int j)
boolean	getlexpNoes()
int[]	getMeasurementCountPlusIndices(int row)
double	getMixingTime()	get the mixing time
double	getNMRfreq()	gets the NMR frequency
double	getNoeExprefValue()
int[]	getnoeNPrefIndices()
boolean	getNoesy()
double	getRedValue()
double	getRhoStar()
int	getRowCount()
protected int	getViewerRow(int i)
double	getYellowValue()
void	setCorrelationTime(double t)	set the correlation time to be used in the NOE calculation
void	setCutoff(double c)	sets the cutoff distance beyond which atom interactions are not considered
void	setExpDist(String value, int i, int j)
void	setExpNoe(String value, int i, int j)
void	setFrameDeltaDisplay(FrameDeltaDisplay frameDeltaDisplay)
void	setLabelArray(String[] labelArray)
void	setlrefSingle(boolean l)
void	setMixingTime(double t)	sets the mixing time for the NOE experiment
void	setmolCDKuptodate(boolean value)
void	setNMRfreq(double f)	set the NMR frequency for the NOE simulation
void	setNoeExprefValue(double value)
void	setNoeNPrefIndices(int[] noeNPrefIndices)
void	setNoesy(boolean b)
void	setRedValue(double value)
void	setRhoStar(double c)
void	setYellowValue(double value)
(package private) void	updateNoeTableData()
(package private) void	updateNoeTableStructure()
void	updateTables()

Methods inherited from class javax.swing.JTabbedPane

add, add, add, add, add, addChangeListener, addTab, addTab, addTab, createChangeListener, fireStateChanged, getAccessibleContext, getBackgroundAt, getBoundsAt, getChangeListeners, getComponentAt, getDisabledIconAt, getDisplayedMnemonicIndexAt, getForegroundAt, getIconAt, getMnemonicAt, getModel, getSelectedComponent, getSelectedIndex, getTabComponentAt, getTabCount, getTabLayoutPolicy, getTabPlacement, getTabRunCount, getTitleAt, getToolTipText, getToolTipTextAt, getUI, getUIClassID, indexAtLocation, indexOfComponent, indexOfTab, indexOfTab, indexOfTabComponent, insertTab, isEnabledAt, paramString, remove, remove, removeAll, removeChangeListener, removeTabAt, setBackgroundAt, setComponentAt, setDisabledIconAt, setDisplayedMnemonicIndexAt, setEnabledAt, setForegroundAt, setIconAt, setMnemonicAt, setModel, setSelectedComponent, setSelectedIndex, setTabComponentAt, setTabLayoutPolicy, setTabPlacement, setTitleAt, setToolTipTextAt, 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, getTopLevelAncestor, getTransferHandler, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, hide, 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

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, 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, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getToolkit, getTreeLock, gotFocus, handleEvent, hasFocus, 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, requestFocus, requestFocus, requestFocusInWindow, resize, resize, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setFocusable, setFocusTraversalKeysEnabled, setIgnoreRepaint, setLocale, setLocation, setLocation, setMixingCutoutShape, 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

nmrPanel

NMR_JmolPanel nmrPanel

viewer

NMR_Viewer viewer

labelArray

String[] labelArray

molCDKuptodate

boolean molCDKuptodate

natomsPerModel

int natomsPerModel

expNoes

String[][] expNoes

expDists

String[][] expDists

lexpNoes

boolean lexpNoes

calcProps

NmrMolecule calcProps

freq

double freq

tau

double tau

tMix

double tMix

cutoff

double cutoff

rhoStar

double rhoStar

noesy

boolean noesy

yellowValue

double yellowValue

redValue

double redValue

frameDeltaDisplay

FrameDeltaDisplay frameDeltaDisplay

colorCellRenderer

NMRTableCellRenderer colorCellRenderer

noeTable

JTable noeTable

noeTableModel

private NoeTable.NoeTableModel noeTableModel

noeSelection

private ListSelectionModel noeSelection

selectedNoeRow

int[] selectedNoeRow

noedeleteButton

JButton noedeleteButton

noedeleteAllButton

private JButton noedeleteAllButton

noesetRefButton

JButton noesetRefButton

expOrDistButton

JComboBox<String> expOrDistButton

noeNPrefValue

double noeNPrefValue

noeNPrefIndices

int[] noeNPrefIndices

noeExprefValue

double noeExprefValue

lrefSingle

boolean lrefSingle

noeParameterSelectionPanel

public NoeParameterSelectionPanel noeParameterSelectionPanel

noeColourSelectionPanel

public NoeColourSelectionPanel noeColourSelectionPanel

Constructor Detail

NoeTable

public NoeTable(NMR_JmolPanel nmrPanel,
                JFrame parentFrame)

Constructor

Parameters:

parentFrame - the parent frame

nmrPanel - the NMRViewer in which the animation will take place (?)

Method Detail

constructNoeTable

JComponent constructNoeTable()

constructNoeButtonPanel

JComponent constructNoeButtonPanel()

constructDismissButtonPanel

JComponent constructDismissButtonPanel()

centerDialog

protected void centerDialog()

close

public void close()

activate

public void activate()

updateNoeTableData

void updateNoeTableData()

updateNoeTableStructure

void updateNoeTableStructure()

getRowCount

public int getRowCount()

getMeasurementCountPlusIndices

public int[] getMeasurementCountPlusIndices(int row)

calcFrameDelta

private void calcFrameDelta()

updateTables

public void updateTables()

getViewerRow

protected int getViewerRow(int i)

checkNoe

boolean checkNoe(int i)

calcNatomsPerModel

int calcNatomsPerModel()

TODO This assumes we have the same structure in each model.

Returns:

average number of atoms per model ??

addMol

public void addMol()

setmolCDKuptodate

public void setmolCDKuptodate(boolean value)

allocateLabelArray

public void allocateLabelArray(int numAtoms)

allocateExpNoes

public void allocateExpNoes(int numAtoms)

getExpNoe

public String getExpNoe(int i,
                        int j)

getExpDist

public String getExpDist(int i,
                         int j)

setExpNoe

public void setExpNoe(String value,
                      int i,
                      int j)

setExpDist

public void setExpDist(String value,
                       int i,
                       int j)

setLabelArray

public void setLabelArray(String[] labelArray)

setCorrelationTime

public void setCorrelationTime(double t)

set the correlation time to be used in the NOE calculation

Parameters:

t - the correlation time in seconds. Typical value would be 80E-12.

setMixingTime

public void setMixingTime(double t)

sets the mixing time for the NOE experiment

Parameters:

t - the mixing time in seconds. Typically 0.5-1.5 seconds for small molecules

setNMRfreq

public void setNMRfreq(double f)

set the NMR frequency for the NOE simulation

Parameters:

f - the frequency in MHz

setCutoff

public void setCutoff(double c)

sets the cutoff distance beyond which atom interactions are not considered

Parameters:

c - the cutoff distance in Angstroms

setRhoStar

public void setRhoStar(double c)

setNoesy

public void setNoesy(boolean b)

setlrefSingle

public void setlrefSingle(boolean l)

getCorrelationTime

public double getCorrelationTime()

get the correlation time in seconds

Returns:

the correlation time in seconds

getMixingTime

public double getMixingTime()

get the mixing time

Returns:

the mixing time in seconds

getNMRfreq

public double getNMRfreq()

gets the NMR frequency

Returns:

the NMR frequency in MHz

getCutoff

public double getCutoff()

get the cutoff distance

Returns:

the cutoff in Angstroms

getRhoStar

public double getRhoStar()

getNoesy

public boolean getNoesy()

setRedValue

public void setRedValue(double value)

setYellowValue

public void setYellowValue(double value)

getRedValue

public double getRedValue()

getYellowValue

public double getYellowValue()

getnoeNPrefIndices

public int[] getnoeNPrefIndices()

setNoeNPrefIndices

public void setNoeNPrefIndices(int[] noeNPrefIndices)

getNoeExprefValue

public double getNoeExprefValue()

setNoeExprefValue

public void setNoeExprefValue(double value)

setFrameDeltaDisplay

public void setFrameDeltaDisplay(FrameDeltaDisplay frameDeltaDisplay)

getlexpNoes

public boolean getlexpNoes()