Class JMView

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

All Implemented Interfaces:

java.awt.event.FocusListener, java.awt.event.MouseListener, java.awt.image.ImageObserver, java.awt.MenuContainer, java.beans.PropertyChangeListener, java.io.Serializable, java.util.EventListener, javax.accessibility.Accessible, javax.swing.RootPaneContainer

public class JMView
extends javax.swing.JApplet
implements java.awt.event.FocusListener, java.beans.PropertyChangeListener, java.awt.event.MouseListener

Swing version of the MarvinView Applet.

Since:

Marvin 2.0

Version:

5.1.6, 03/20/2009

Author:

Peter Csizmadia, Tamas Vertse, Nora Mate, Zsolt Mohacsi, Istvan Fajth

See Also:

Serialized Form

Nested Class Summary

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

javax.swing.JApplet.AccessibleJApplet

Nested classes/interfaces inherited from class java.applet.Applet

java.applet.Applet.AccessibleApplet

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

java.awt.Panel.AccessibleAWTPanel

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.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	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	evaluateChemicalTerms(java.lang.String expression, int n) Evaluates a Chemical Terms expression on the molecule in given cell, and returns the result in string format.
void	focusGained(java.awt.event.FocusEvent e)
void	focusLost(java.awt.event.FocusEvent e)
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.
double	getMolExactMass(int n) Gets the exact molecule weight.
java.lang.String	getMolFormula(int n) Gets the molecule formula.
double	getMolMass(int n) Gets the molecule weight.
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.
boolean	hasValenceError(int i) Determines if the molecule in the specified cell has a valence error on any of its atoms.
void	init() Initializes the applet.
boolean	isAtomSetVisible(int id) Is the specified atom set visible?
boolean	isChemicalTermsExpressionSyntaxError() Returns true, if the last Chemical Terms expression evaluated by the evaluateChemicalTerms(String, int) method is a syntactically not correct expression.
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	mouseClicked(java.awt.event.MouseEvent e)
void	mouseEntered(java.awt.event.MouseEvent e)
void	mouseExited(java.awt.event.MouseEvent e)
void	mousePressed(java.awt.event.MouseEvent e)
void	mouseReleased(java.awt.event.MouseEvent e)
void	propertyChange(java.beans.PropertyChangeEvent ev) Invoke propertyChange(prop) JavaScript method on applet's page.
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 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 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	setParentApplet(javax.swing.JApplet parent) Sets the parent applet object in which the JMView applet is embedded.
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, getComponentZOrder, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getInsets, getLayout, getListeners, getMaximumSize, getMinimumSize, getMousePosition, getPreferredSize, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paint, paintComponents, preferredSize, print, printComponents, processContainerEvent, processEvent, remove, removeAll, removeContainerListener, removeNotify, setComponentZOrder, setFocusCycleRoot, setFocusTraversalKeys, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, 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, firePropertyChange, firePropertyChange, firePropertyChange, 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, getMousePosition, 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, isMaximumSizeSet, isMinimumSizeSet, isOpaque, isPreferredSizeSet, 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, setMaximumSize, setMinimumSize, setName, setPreferredSize, 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.

Overrides:

init in class java.applet.Applet

propertyChange

public void propertyChange(java.beans.PropertyChangeEvent ev)

Invoke propertyChange(prop) JavaScript method on applet's page. Only for internal usage.

Specified by:

propertyChange in interface java.beans.PropertyChangeListener

Since:

Marvin 5.0 08/29/2007

mouseClicked

public void mouseClicked(java.awt.event.MouseEvent e)

Specified by:

mouseClicked in interface java.awt.event.MouseListener

mouseEntered

public void mouseEntered(java.awt.event.MouseEvent e)

Specified by:

mouseEntered in interface java.awt.event.MouseListener

mouseExited

public void mouseExited(java.awt.event.MouseEvent e)

Specified by:

mouseExited in interface java.awt.event.MouseListener

mousePressed

public void mousePressed(java.awt.event.MouseEvent e)

Specified by:

mousePressed in interface java.awt.event.MouseListener

mouseReleased

public void mouseReleased(java.awt.event.MouseEvent e)

Specified by:

mouseReleased in interface java.awt.event.MouseListener

start

public void start()

Starts the applet.

Overrides:

start in class java.applet.Applet

stop

public void stop()

Stops the applet.

Overrides:

stop in class java.applet.Applet

destroy

public void destroy()

Dispose all the frames.

Overrides:

destroy in class java.applet.Applet

getAppletInfo

public java.lang.String getAppletInfo()

Returns a string containing the version and the author.

Overrides:

getAppletInfo in class java.applet.Applet

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:

Marvin 3.0, 12/26/2002

isEmpty

public boolean isEmpty(int n)

Returns true if molecule cell is empty.

Parameters:

n - molecule cell number

Returns:

true if molecule cell is empty

Since:

Marvin 3.5.1

getM

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

Gets the nth molecule in a text format. Should be called after the nth molecule has been loaded. 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

getMProperty

public java.lang.String getMProperty(int n,
                                     java.lang.String key)

Gets an RDfile/SDfile property. Should be called after the nth molecule has been loaded. 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.

Parameters:

n - molecule cell number

key - the property key

Returns:

the value of the property, or null if the key is not found

Since:

Marvin 3.4.1

setMProperty

public void setMProperty(int n,
                         java.lang.String key,
                         java.lang.String value)

Sets an RDfile/SDfile property. Setting null value removes the property. Should be called after the nth molecule has been loaded. 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.

Parameters:

n - molecule cell number

key - the property name

value - the value or null

Since:

Marvin 3.4.1

getMPropertyCount

public int getMPropertyCount(int n)

Gets the number of RDfile/SDfile properties. Should be called after the nth molecule has been loaded. 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.

Parameters:

n - molecule cell number

Returns:

the number of RDfile/SDfile properties

Since:

Marvin 3.5

getMPropertyKey

public java.lang.String getMPropertyKey(int n,
                                        int i)

Gets an RDfile/SDfile property key. Should be called after the nth molecule has been loaded. 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.

Parameters:

n - molecule cell number

i - the property key index

Returns:

the the property key

Since:

Marvin 3.5

setAtomAlias

public void setAtomAlias(int n,
                         int i,
                         java.lang.String alias)

Sets atom alias. Should be called after the nth molecule has been loaded. 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.

Parameters:

n - molecule cell number

i - the atom index

alias - the alias

Since:

Marvin 3.5

getAtomAlias

public java.lang.String getAtomAlias(int n,
                                     int i)

Gets atom alias. Should be called after the nth molecule has been loaded. 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.

Parameters:

n - molecule cell number

i - the atom index

Returns:

the atom alias

Since:

Marvin 3.5

setAtomExtraLabel

public void setAtomExtraLabel(int n,
                              int i,
                              java.lang.String label)

Sets extra atom label. Should be called after the nth molecule has been loaded. 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.

Parameters:

n - molecule cell number

i - the atom index

label - the extra atom label

Since:

Marvin 3.5

getAtomExtraLabel

public java.lang.String getAtomExtraLabel(int n,
                                          int i)

Gets extra atom label. Should be called after the nth molecule has been loaded. 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.

Parameters:

n - molecule cell number

i - the atom index

Returns:

the extra atom label

Since:

Marvin 3.5

getMolMass

public double getMolMass(int n)

Gets the molecule weight. Should be called after the nth molecule has been loaded.

Parameters:

n - molecule cell number

Returns:

the molecule weight

Since:

Marvin 4.0.2

getMolExactMass

public double getMolExactMass(int n)

Gets the exact molecule weight. Should be called after the nth molecule has been loaded.

Parameters:

n - molecule cell number

Returns:

the exact molecule weight

Since:

Marvin 4.0.2

getMolFormula

public java.lang.String getMolFormula(int n)

Gets the molecule formula. Should be called after the nth molecule has been loaded.

Parameters:

n - molecule cell number

Returns:

the molecule formula

Since:

Marvin 4.0.2

evaluateChemicalTerms

public java.lang.String evaluateChemicalTerms(java.lang.String expression,
                                              int n)

Evaluates a Chemical Terms expression on the molecule in given cell, and returns the result in string format. Should be called after the n-th molecule has been loaded.

Examples:

 s1 = MView.evaluateChemicalTerms("atomCount()", 0);
 s2 = MView.evaluateChemicalTerms("logP() <= 5", 1);
 

See the Chemical Terms Language Reference and the Chemical Terms Reference Tables for more.

Parameters:

expression - the Chemical Terms expression

n - molecule cell number

Returns:

the result of the evaluation

Since:

Marvin 5.1

isChemicalTermsExpressionSyntaxError

public boolean isChemicalTermsExpressionSyntaxError()

Returns true, if the last Chemical Terms expression evaluated by the evaluateChemicalTerms(String, int) method is a syntactically not correct expression. Should be called after evaluateChemicalTerms(String, int).

Returns:

true, if the last evaluated Chemical Terms expression is syntactically not correct

Since:

Marvin 5.1.2

addMol

public void addMol(java.lang.String s)

Starts loading molecules in a separate thread. Sets molecules in empty cells. Experimental: for internal use only.

Parameters:

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

Since:

Marvin 3.4.1, 07/16/2004

addMol

public void addMol(java.lang.String s,
                   java.lang.String opts)

Starts loading molecules in a separate thread. Sets molecules in empty cells. Experimental: for internal use only. 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:

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

opts - options or null

Since:

Marvin 3.4.1, 07/16/2004

setMol

public void setMol(java.lang.String s)

Starts loading molecules in a separate thread. Sets molecules in consecutive cells starting from cell0.

Parameters:

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

Since:

Marvin 3.4.1, 07/08/2004

setMol

public void setMol(java.lang.String s,
                   java.lang.String opts)

Starts loading molecules in a separate thread. Sets molecules in consecutive cells starting from cell0. 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". See the text formats and their options on the File Formats in Marvin page.

Parameters:

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

opts - options or null

Since:

Marvin 3.4.1, 07/08/2004

setM

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

Starts loading a molecule into the nth cell in a separate thread.

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 in a separate thread. The file format and/or import options can be specified if the third argument is in one of the following forms: "options", "format:", or "format:options". See the text formats and their options on the File Formats in Marvin page.

Parameters:

n - molecule cell number (0 for simple viewer)

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

opts - options or null

Since:

Marvin 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:

Marvin 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:

Marvin 2.1

setSelectedIndex

public void setSelectedIndex(int i)

Selects a molecule.

Parameters:

i - the cell index or -1 to unselect

Since:

Marvin 2.2

getAtomCount

public int getAtomCount(int i)

Gets the 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:

Marvin 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:

Marvin 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:

Marvin 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:

Marvin 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:

Marvin 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:

Marvin 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:

Marvin 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:

Marvin 3.3

setBondSetColor

public void setBondSetColor(int i,
                            int rgb)

Sets the color of a bond set.

Parameters:

i - bond set identifier (1, ..., 63)

rgb - 24-bit RGB color value

Since:

Marvin 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:

Marvin 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:

Marvin 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 (1, ..., 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:

Marvin 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:

Marvin 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:

Marvin 2.9.2

getBestTabScale

public double getBestTabScale()

Gets the smallest best scale value in the molecule table.

Returns:

the best scaling factor

Since:

Marvin 2.9.2

hasValenceError

public boolean hasValenceError(int i)

Determines if the molecule in the specified cell has a valence error on any of its atoms.

Parameters:

i - the cell index

Returns:

true if there is an atom with valence error, false if there is no valence error or there is no molecule in the cell

Since:

Marvin 4.1.3 11/13/2006

focusGained

public void focusGained(java.awt.event.FocusEvent e)

Specified by:

focusGained in interface java.awt.event.FocusListener

focusLost

public void focusLost(java.awt.event.FocusEvent e)

Specified by:

focusLost in interface java.awt.event.FocusListener

setParentApplet

public void setParentApplet(javax.swing.JApplet parent)

Sets the parent applet object in which the JMView applet is embedded. The parent must be set if embedding the JMView applet into another applet, otherwise the parent has to be null. It defaults to null. If the applet is embeded into another applet, the followings have taken care of

• The parent has to be set before the init method called
• The applet and its contents will use the contentPane, and Menubar in the parent.
• The contents, and menus initialized, and painted while the applet init process.
• The functionalities, which are being used from javaScript has to be delegated to the parent applet
• The applet should be added to the parents contentPane

Parameters:

parent -

Since:

5.1.6 (Not included in 5.2.0)