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
- See Also:
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Nested Class Summary
Nested ClassesModifier and TypeClassDescription(package private) class
(package private) class
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
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Field Summary
FieldsModifier and TypeFieldDescription(package private) NmrMolecule
(package private) NMRTableCellRenderer
(package private) double
(package private) String[][]
(package private) String[][]
(package private) FrameDeltaDisplay
(package private) double
(package private) String[]
(package private) boolean
(package private) boolean
(package private) boolean
(package private) int
(package private) NMR_JmolPanel
private JButton
(package private) JButton
(package private) double
(package private) int[]
(package private) double
private ListSelectionModel
(package private) JButton
(package private) boolean
(package private) JTable
private NoeTable.NoeTableModel
(package private) double
(package private) double
(package private) int[]
(package private) double
(package private) double
(package private) NMR_Viewer
(package private) double
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
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
activate()
void
addMol()
void
allocateExpNoes
(int numAtoms) void
allocateLabelArray
(int numAtoms) private void
(package private) int
TODO This assumes we have the same structure in each model.protected void
(package private) boolean
checkNoe
(int i) void
close()
(package private) JComponent
(package private) JComponent
(package private) JComponent
double
get the correlation time in secondsdouble
get the cutoff distancegetExpDist
(int i, int j) getExpNoe
(int i, int j) boolean
int[]
getMeasurementCountPlusIndices
(int row) double
get the mixing timedouble
gets the NMR frequencydouble
int[]
boolean
getNoesy()
double
double
int
protected int
getViewerRow
(int i) double
void
setCorrelationTime
(double t) set the correlation time to be used in the NOE calculationvoid
setCutoff
(double c) sets the cutoff distance beyond which atom interactions are not consideredvoid
setExpDist
(String value, int i, int j) void
void
setFrameDeltaDisplay
(FrameDeltaDisplay frameDeltaDisplay) void
setLabelArray
(String[] labelArray) void
setlrefSingle
(boolean l) void
setMixingTime
(double t) sets the mixing time for the NOE experimentvoid
setmolCDKuptodate
(boolean value) void
setNMRfreq
(double f) set the NMR frequency for the NOE simulationvoid
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
(package private) void
void
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
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Field Details
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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
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noeSelection
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selectedNoeRow
int[] selectedNoeRow -
noedeleteButton
JButton noedeleteButton -
noedeleteAllButton
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noesetRefButton
JButton noesetRefButton -
expOrDistButton
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noeNPrefValue
double noeNPrefValue -
noeNPrefIndices
int[] noeNPrefIndices -
noeExprefValue
double noeExprefValue -
lrefSingle
boolean lrefSingle -
noeParameterSelectionPanel
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noeColourSelectionPanel
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Constructor Details
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NoeTable
Constructor- Parameters:
nmrPanel
- the NMRViewer in which the animation will take place (?)parentFrame
- the parent frame
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Method Details
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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 ??
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addMol
public void addMol() -
setmolCDKuptodate
public void setmolCDKuptodate(boolean value) -
allocateLabelArray
public void allocateLabelArray(int numAtoms) -
allocateExpNoes
public void allocateExpNoes(int numAtoms) -
getExpNoe
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getExpDist
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setExpNoe
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setExpDist
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setLabelArray
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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.
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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
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setNMRfreq
public void setNMRfreq(double f) set the NMR frequency for the NOE simulation- Parameters:
f
- the frequency in MHz
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setCutoff
public void setCutoff(double c) sets the cutoff distance beyond which atom interactions are not considered- Parameters:
c
- the cutoff distance in Angstroms
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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
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getMixingTime
public double getMixingTime()get the mixing time- Returns:
- the mixing time in seconds
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getNMRfreq
public double getNMRfreq()gets the NMR frequency- Returns:
- the NMR frequency in MHz
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getCutoff
public double getCutoff()get the cutoff distance- Returns:
- the cutoff in Angstroms
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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
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getlexpNoes
public boolean getlexpNoes()
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