Class JMView

java.lang.Object
  java.awt.Component
      java.awt.Container
          java.awt.Panel
              java.applet.Applet
                  javax.swing.JApplet
                      JMView

All Implemented Interfaces:

javax.accessibility.Accessible, java.awt.image.ImageObserver, java.awt.MenuContainer, javax.swing.RootPaneContainer, java.lang.Runnable, java.io.Serializable

public class JMView

extends javax.swing.JApplet

implements java.lang.Runnable

Swing version of the MarvinView Applet.

Since:

2.0

Version:

3.3, 12/23/2003

Author:

Peter Csizmadia

See Also:

ViewPanel, Serialized Form

Nested Class Summary

Nested classes inherited from class javax.swing.JApplet

javax.swing.JApplet.AccessibleJApplet

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 javax.swing.JApplet

accessibleContext, rootPane, rootPaneCheckingEnabled

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

JMView()

Method Summary

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.
int	getAtomCount(int i) Get number of atoms in the specified molecule cell.
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.
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	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	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 the 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.
void	setM(int n, java.lang.String s, java.lang.String opts) Starts loading a molecule into the nth cell.
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	start() Starts the applet.
void	stop() Stops the applet.

Methods inherited from class javax.swing.JApplet

addImpl, createRootPane, getAccessibleContext, getContentPane, getGlassPane, getJMenuBar, getLayeredPane, getRootPane, isRootPaneCheckingEnabled, paramString, remove, setContentPane, setGlassPane, setJMenuBar, setLayeredPane, setLayout, setRootPane, setRootPaneCheckingEnabled, update

Methods inherited from class java.applet.Applet

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, 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, preferredSize, print, printComponents, processContainerEvent, processEvent, remove, removeAll, removeContainerListener, removeNotify, setFocusCycleRoot, setFocusTraversalKeys, setFocusTraversalPolicy, setFont, transferFocusBackward, 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, 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, setVisible, 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

JMView

public JMView()

Method Detail

init

public void init()

Initializes the applet.

start

public void start()

Starts the applet.

run

public void run()

Runs the thread that handles JavaScript calls.

Specified by:

run in interface java.lang.Runnable

stop

public void stop()

Stops the applet.

destroy

public void destroy()

Dispose all the frames.

getAppletInfo

public java.lang.String getAppletInfo()

Returns a string containing the version and the author.

Returns:

the information

animate

public void animate(java.lang.String arg)

Starts or stops animation. Animation can be an XYZ movie for multframe XYZ files, or simple 3D rotation in other cases. The argument of this method is in the same format as the "animate" applet parameter. Use "all" to start, "off" to stop animating all molecules. To animate only some of the molecules in in a table, use a comma separated list of indices (0...n-1). To stop animating them, use a comma separated list of negative integers (minus cell index minus one = -1...-n). Examples:

 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
 

Parameters:

arg - "off", "all" or a comma separated list of integers

Since:

3.0, 12/26/2002

getM

public java.lang.String getM(int n,
                             java.lang.String fmt)

Gets the nth molecule in a text format. For a simple viewer with only one molecule, n must be zero. Nonzero n should only be used if the viewer is a molecule table. The format descriptor string can also contain export options. Format and options are separated by a colon, multiple options can be separated by commas. See the text formats and their options on the File Formats in Marvin page. Examples:

 s1 = mview.getM(0, "mol");
 s2 = mview.getM(0, "smiles:a-H"); // aromatize and remove Hydrogens
 

Parameters:

n - molecule cell number

fmt - the format descriptor string

Returns:

string containing the molecule in a molecule file format

setM

public void setM(int n,
                 java.lang.String s)

Starts loading a molecule into the nth cell.

Parameters:

n - molecule cell number (0 for simple viewer)

s - molecule file contents, URL, or (Unix) filename

setM

public void setM(int n,
                 java.lang.String s,
                 java.lang.String opts)

Starts loading a molecule into the nth cell. The file format and/or import options can be specified if the second argument is in one of the following forms: "options", "format:", or "format:options".

Parameters:

n - molecule cell number (0 for simple viewer)

s - molecule file contents, URL, or (Unix) filename

opts - options or null

Since:

3.3

getL

public java.lang.String getL(int i)

Gets a label.

Parameters:

i - the label index

Returns:

the label

setL

public void setL(int i,
                 java.lang.String s)

Sets a label.

Parameters:

i - the label index

s - the label

getC

public boolean getC(int i)

Gets the state of a checkbox.

Parameters:

i - the checkbox index

Returns:

true if checked, false if unchecked

setC

public void setC(int i,
                 boolean s)

Sets the state of a checkbox.

Parameters:

i - the checkbox index

s - true to check, false to uncheck

setActionB

public void setActionB(int i,
                       java.lang.String s)

Sets the action string (URL or JavaScript expression) of a button.

Parameters:

i - the button number

s - action string

setActionC

public void setActionC(int i,
                       boolean c,
                       java.lang.String s)

Sets one of the two action strings (JavaScript expressions) of a checkbox.

Parameters:

i - the button number

c - checked (true) or unchecked (false) state

s - action string

getT

public java.lang.String getT(int i)

Gets the value of a text field.

Parameters:

i - the text field index

Returns:

the text

setT

public void setT(int i,
                 java.lang.String s)

Gets the value of a text field.

Parameters:

i - the text field index

s - the text

getCellCount

public int getCellCount()

Gets the number of cells in the table.

Returns:

the number of cells, or 1 if the viewer is not a table

Since:

2.1.1

getSelectedIndex

public int getSelectedIndex()

Gets the index of the molecule that is selected by the user.

Returns:

the cell index or -1 if no molecule is selected

Since:

2.1

setSelectedIndex

public void setSelectedIndex(int i)

Selects a molecule.

Parameters:

i - the cell index or -1 to unselect

Since:

2.2

getAtomCount

public int getAtomCount(int i)

Get number of atoms in the specified molecule cell.

Parameters:

i - molecule cell index

Returns:

the number of atoms, or 0 if there is no such cell

Since:

2.6

selectAllAtoms

public boolean selectAllAtoms(int i,
                              boolean v)

Select or unselect all atoms in the specified molecule.

Parameters:

i - molecule cell index

v - select (true) or unselect (false)

Returns:

true if the operation was succesful, false if there is no such molecule

Since:

2.6

selectAtom

public boolean selectAtom(int i,
                          int atom,
                          boolean v)

Select or unselect an atom in the specified molecule.

Parameters:

i - molecule cell index

atom - atom index

v - select (true) or unselect (false)

Returns:

true if the operation was succesful, false if there is no such molecule or atom

Since:

2.6

isSelected

public boolean isSelected(int i,
                          int atom)

Is the specified atom selected?

Parameters:

i - molecule cell index

atom - atom index

Returns:

true if selected, false if not

Since:

2.6

isAtomSetVisible

public boolean isAtomSetVisible(int id)

Is the specified atom set visible?

Parameters:

id - atom set identifier (0, ..., 63)

Returns:

true if the set is visible, false if not

Since:

3.3

setAtomSetVisible

public void setAtomSetVisible(int id,
                              boolean v)

Set the visibility of the specified atom set.

Parameters:

id - atom set identifier (0, ..., 63)

v - visibility

Since:

3.3

setAtomSetColor

public void setAtomSetColor(int i,
                            int rgb)

Sets the color of an atom set.

Parameters:

i - atom set identifier (0, ..., 63)

rgb - 24-bit RGB color value

Since:

3.3

setAtomSetSeq

public boolean setAtomSetSeq(int i,
                             int atom,
                             int id)

Sets the set sequence number of the atom.

Parameters:

i - molecule cell index

atom - atom index

id - a number between 0 and 63. 0 is the default set. It contains all atoms that are not in another set.

Returns:

true if the operation was succesful, false if there is no such molecule or atom

Since:

3.3

setBondSetColor

public void setBondSetColor(int i,
                            int rgb)

Sets the color of a bond set.

Parameters:

i - bond set identifier (1, ..., 31)

rgb - 24-bit RGB color value

Since:

3.3

setBondSetSeq

public boolean setBondSetSeq(int i,
                             int j1,
                             int j2,
                             int id)

Sets the set sequence number of a bond.

Parameters:

i - molecule cell index

j1 - first atom index

j2 - second atom index

id - a number between 0 and 31

Returns:

true if the operation was succesful, false if there is no such molecule or bond

Since:

3.3

setBondSetSeqAll

public boolean setBondSetSeqAll(int i,
                                int id)

Sets the set sequence number for each bond.

Parameters:

i - molecule cell index

id - a number between 0 and 31

Returns:

true if the operation was succesful, false if there is no such molecule or bond

Since:

3.3

isSetVisible

public boolean isSetVisible(int id)

Deprecated. as of Marvin 3.3, replaced by isAtomSetVisible

Parameters:

id - atom set identifier (0, ..., 63)

Returns:

true if the set is visible, false if not

setSetVisible

public void setSetVisible(int id,
                          boolean v)

Deprecated. as of Marvin 3.3, replaced by setAtomSetVisible

Parameters:

id - atom set identifier (0, ..., 63)

v - visibility

setSetColor

public void setSetColor(int i,
                        int rgb)

Deprecated. as of Marvin 3.3, replaced by setAtomSetColor

Parameters:

i - atom set identifier (0, ..., 63)

rgb - 24-bit RGB color value

setSetSeq

public boolean setSetSeq(int i,
                         int atom,
                         int id)

Deprecated. as of Marvin 3.3, replaced by setAtomSetSeq

Parameters:

i - molecule cell index

atom - atom index

id - a number between 0 and 63

Returns:

true if the operation was succesful, false if there is no such molecule or atom

Since:

2.9.3

getTabScale

public double getTabScale(int i)

Gets the magnification for a molecule cell. The scale that would be used in non-window mode is returned even if the cell is its window.

Parameters:

i - molecule cell index

Returns:

the magnification, or -1 if it still cannot be determined

Since:

2.9.2

getBestTabScale

public double getBestTabScale(int i)

Gets the best scale value for a molecule cell.

Parameters:

i - the cell index

Returns:

the best scaling factor

Since:

2.9.2

getBestTabScale

public double getBestTabScale()

Gets the smallest best scale value in the molecule table.

Returns:

the best scaling factor

Since:

2.9.2