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java.lang.Object java.awt.Component java.awt.Container java.awt.Panel java.applet.Applet MView
AWT version of the MarvinView Applet.
Nested Class Summary |
Nested classes inherited from class java.applet.Applet |
java.applet.Applet.AccessibleApplet |
Nested classes inherited from class java.awt.Panel |
java.awt.Panel.AccessibleAWTPanel |
Nested classes inherited from class java.awt.Container |
java.awt.Container.AccessibleAWTContainer |
Nested classes inherited from class java.awt.Component |
java.awt.Component.AccessibleAWTComponent, java.awt.Component.BltBufferStrategy, java.awt.Component.FlipBufferStrategy |
Field Summary |
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 | |
MView()
|
Method Summary | |
void |
addMol(java.lang.String s)
Starts loading molecules in a separate thread. |
void |
addMol(java.lang.String s,
java.lang.String opts)
Starts loading molecules in a separate thread. |
void |
animate(java.lang.String arg)
Starts or stops animation. |
void |
destroy()
Dispose all the frames. |
java.lang.String |
getAppletInfo()
Returns a string containing the version and the author. |
java.lang.String |
getAtomAlias(int n,
int i)
Gets atom alias. |
int |
getAtomCount(int i)
Gets the number of atoms in the specified molecule cell. |
java.lang.String |
getAtomExtraLabel(int n,
int i)
Gets extra atom label. |
double |
getBestTabScale()
Gets the smallest best scale value in the molecule table. |
double |
getBestTabScale(int i)
Gets the best scale value for a molecule cell. |
boolean |
getC(int i)
Gets the state of a checkbox. |
int |
getCellCount()
Gets the number of cells in the table. |
java.lang.String |
getL(int i)
Gets a label. |
java.lang.String |
getM(int n,
java.lang.String fmt)
Gets the nth molecule in a text format. |
java.lang.String |
getMProperty(int n,
java.lang.String key)
Gets an RDfile/SDfile property. |
int |
getMPropertyCount(int n)
Gets the number of RDfile/SDfile properties. |
java.lang.String |
getMPropertyKey(int n,
int i)
Gets an RDfile/SDfile property key. |
int |
getSelectedIndex()
Gets the index of the molecule that is selected by the user. |
java.lang.String |
getT(int i)
Gets the value of a text field. |
double |
getTabScale(int i)
Gets the magnification for a molecule cell. |
void |
init()
Initializes the applet. |
boolean |
isAtomSetVisible(int id)
Is the specified atom set visible? |
boolean |
isEmpty(int n)
Returns true if molecule cell is empty. |
boolean |
isSelected(int i,
int atom)
Is the specified atom selected? |
boolean |
isSetVisible(int id)
Deprecated. as of Marvin 3.3, replaced by isAtomSetVisible |
void |
run()
Runs the thread that handles JavaScript calls. |
boolean |
selectAllAtoms(int i,
boolean v)
Select or unselect all atoms in the specified molecule. |
boolean |
selectAtom(int i,
int atom,
boolean v)
Select or unselect an atom in the specified molecule. |
void |
setActionB(int i,
java.lang.String s)
Sets the action string (URL or JavaScript expression) of a button. |
void |
setActionC(int i,
boolean c,
java.lang.String s)
Sets one of the two action strings (JavaScript expressions) of a checkbox. |
void |
setAtomAlias(int n,
int i,
java.lang.String alias)
Sets atom alias. |
void |
setAtomExtraLabel(int n,
int i,
java.lang.String label)
Sets extra atom label. |
void |
setAtomSetColor(int i,
int rgb)
Sets the color of an atom set. |
boolean |
setAtomSetSeq(int i,
int atom,
int id)
Sets the set sequence number of a atom. |
void |
setAtomSetVisible(int id,
boolean v)
Set the visibility of the specified atom set. |
void |
setBondSetColor(int i,
int rgb)
Sets the color of a bond set. |
boolean |
setBondSetSeq(int i,
int j1,
int j2,
int id)
Sets the set sequence number of a bond. |
boolean |
setBondSetSeqAll(int i,
int id)
Sets the set sequence number for each bond. |
void |
setC(int i,
boolean s)
Sets the state of a checkbox. |
void |
setL(int i,
java.lang.String s)
Sets a label. |
void |
setM(int n,
java.lang.String s)
Starts loading a molecule into the nth cell in a separate thread. |
void |
setM(int n,
java.lang.String s,
java.lang.String opts)
Starts loading a molecule into the nth cell in a separate thread. |
void |
setMol(java.lang.String s)
Starts loading molecules in a separate thread. |
void |
setMol(java.lang.String s,
java.lang.String opts)
Starts loading molecules in a separate thread. |
void |
setMProperty(int n,
java.lang.String key,
java.lang.String value)
Sets an RDfile/SDfile property. |
void |
setSelectedIndex(int i)
Selects a molecule. |
void |
setSetColor(int i,
int rgb)
Deprecated. as of Marvin 3.3, replaced by setAtomSetColor |
boolean |
setSetSeq(int i,
int atom,
int id)
Deprecated. as of Marvin 3.3, replaced by setAtomSetSeq |
void |
setSetVisible(int id,
boolean v)
Deprecated. as of Marvin 3.3, replaced by setAtomSetVisible |
void |
setT(int i,
java.lang.String s)
Gets the value of a text field. |
void |
setVisible(boolean v)
Show or hide the applet. |
void |
start()
Starts the applet. |
void |
stop()
Stops the applet. |
Methods inherited from class java.applet.Applet |
getAccessibleContext, getAppletContext, getAudioClip, getAudioClip, getCodeBase, getDocumentBase, getImage, getImage, getLocale, getParameter, getParameterInfo, isActive, newAudioClip, play, play, resize, resize, setStub, showStatus |
Methods inherited from class java.awt.Panel |
addNotify |
Methods inherited from class java.awt.Container |
add, add, add, add, add, addContainerListener, addImpl, addPropertyChangeListener, addPropertyChangeListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getAlignmentX, getAlignmentY, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getInsets, getLayout, getListeners, getMaximumSize, getMinimumSize, getPreferredSize, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paint, paintComponents, paramString, preferredSize, print, printComponents, processContainerEvent, processEvent, remove, remove, removeAll, removeContainerListener, removeNotify, setFocusCycleRoot, setFocusTraversalKeys, setFocusTraversalPolicy, setFont, setLayout, transferFocusBackward, transferFocusDownCycle, update, 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, contains, createImage, createImage, createVolatileImage, createVolatileImage, disable, disableEvents, dispatchEvent, enable, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBounds, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusCycleRootAncestor, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getFontMetrics, getForeground, getGraphics, getGraphicsConfiguration, getHeight, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocation, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getSize, getToolkit, getTreeLock, getWidth, getX, getY, gotFocus, handleEvent, hasFocus, hide, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isDoubleBuffered, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isOpaque, isShowing, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, postEvent, prepareImage, prepareImage, printAll, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processKeyEvent, processMouseEvent, processMouseMotionEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, repaint, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, reshape, setBackground, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setEnabled, setFocusable, setFocusTraversalKeysEnabled, setForeground, setIgnoreRepaint, setLocale, setLocation, setLocation, setName, setSize, setSize, show, show, size, toString, transferFocus, transferFocusUpCycle |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Constructor Detail |
public MView()
Method Detail |
public void init()
public void start()
public void run()
run
in interface java.lang.Runnable
public void stop()
public void destroy()
public java.lang.String getAppletInfo()
public void animate(java.lang.String arg)
MView.animate("all"); // starts animating all molecules MView.animate("off"); // stops animating all molecules MView.animate("3"); // starts animation in cell 3 MView.animate("0,1,2"); // starts animation in cells 0, 1 and 2 MView.animate("-1,-2,-3"); // stops animation in cells 0, 1 and 2
arg
- "off", "all" or a
comma separated list of integerspublic boolean isEmpty(int n)
true
if molecule cell is empty.
n
- molecule cell number
true
if molecule cell is emptypublic java.lang.String getM(int n, java.lang.String fmt)
s1 = mview.getM(0, "mol"); s2 = mview.getM(0, "smiles:a-H"); // aromatize and remove Hydrogens
n
- molecule cell numberfmt
- the format descriptor string
public java.lang.String getMProperty(int n, java.lang.String key)
n
- molecule cell numberkey
- the property key
public void setMProperty(int n, java.lang.String key, java.lang.String value)
n
- molecule cell numberkey
- the property namevalue
- the value or nullpublic int getMPropertyCount(int n)
n
- molecule cell number
public java.lang.String getMPropertyKey(int n, int i)
n
- molecule cell numberi
- the property key index
public void setAtomAlias(int n, int i, java.lang.String alias)
n
- molecule cell numberi
- the atom indexalias
- the aliaspublic java.lang.String getAtomAlias(int n, int i)
n
- molecule cell numberi
- the atom index
public void setAtomExtraLabel(int n, int i, java.lang.String label)
n
- molecule cell numberi
- the atom indexlabel
- the extra atom labelpublic java.lang.String getAtomExtraLabel(int n, int i)
n
- molecule cell numberi
- the atom index
public void addMol(java.lang.String s)
s
- molecule file contents, URL, or (Unix) filenamepublic void addMol(java.lang.String s, java.lang.String opts)
s
- molecule file contents, URL, or (Unix) filenameopts
- options or nullpublic void setMol(java.lang.String s)
s
- molecule file contents, URL, or (Unix) filenamepublic void setMol(java.lang.String s, java.lang.String opts)
s
- molecule file contents, URL, or (Unix) filenameopts
- options or nullpublic void setM(int n, java.lang.String s)
n
- molecule cell number (0 for simple viewer)s
- molecule file contents, URL, or (Unix) filenamepublic void setM(int n, java.lang.String s, java.lang.String opts)
n
- molecule cell number (0 for simple viewer)s
- molecule file contents, URL, or (Unix) filenameopts
- options or nullpublic java.lang.String getL(int i)
i
- the label index
public void setL(int i, java.lang.String s)
i
- the label indexs
- the labelpublic boolean getC(int i)
i
- the checkbox index
public void setC(int i, boolean s)
i
- the checkbox indexs
- true to check, false to uncheckpublic void setActionB(int i, java.lang.String s)
i
- the button numbers
- action stringpublic void setActionC(int i, boolean c, java.lang.String s)
i
- the button numberc
- checked (true) or unchecked (false) states
- action stringpublic java.lang.String getT(int i)
i
- the text field index
public void setT(int i, java.lang.String s)
i
- the text field indexs
- the textpublic int getCellCount()
public int getSelectedIndex()
public void setSelectedIndex(int i)
i
- the cell index or -1 to unselectpublic int getAtomCount(int i)
i
- molecule cell index
public boolean selectAllAtoms(int i, boolean v)
i
- molecule cell indexv
- select (true) or unselect (false)
public boolean selectAtom(int i, int atom, boolean v)
i
- molecule cell indexatom
- atom indexv
- select (true) or unselect (false)
public boolean isSelected(int i, int atom)
i
- molecule cell indexatom
- atom index
public boolean isAtomSetVisible(int id)
id
- atom set identifier (0, ..., 63)
public void setAtomSetVisible(int id, boolean v)
id
- atom set identifier (0, ..., 63)v
- visibilitypublic void setAtomSetColor(int i, int rgb)
i
- atom set identifier (0, ..., 63)rgb
- 24-bit RGB color valuepublic boolean setAtomSetSeq(int i, int atom, int id)
i
- molecule cell indexatom
- atom indexid
- a number between 0 and 63
public void setBondSetColor(int i, int rgb)
i
- bond set identifier (1, ..., 63)rgb
- 24-bit RGB color valuepublic boolean setBondSetSeq(int i, int j1, int j2, int id)
i
- molecule cell indexj1
- first atom indexj2
- second atom indexid
- a number between 0 and 31
public boolean setBondSetSeqAll(int i, int id)
i
- molecule cell indexid
- a number between 0 and 31
public boolean isSetVisible(int id)
id
- atom set identifier (0, ..., 63)
public void setSetVisible(int id, boolean v)
id
- atom set identifier (0, ..., 63)v
- visibilitypublic void setSetColor(int i, int rgb)
i
- atom set identifier (0, ..., 63)rgb
- 24-bit RGB color valuepublic boolean setSetSeq(int i, int atom, int id)
i
- molecule cell indexatom
- atom indexid
- a number between 0 and 63
public double getTabScale(int i)
i
- molecule cell index
public double getBestTabScale(int i)
i
- the cell index
public double getBestTabScale()
public void setVisible(boolean v)
v
- true to show, false to hide
|
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