chemaxon.marvin.applet
Class JMView

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

All Implemented Interfaces:

chemaxon.marvin.applet.JMViewIface, chemaxon.marvin.applet.MAppletIface, 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 AbstractMarvinApplet
implements chemaxon.marvin.applet.JMViewIface

Swing version of the MarvinView Applet.

Since:

Marvin 2.0

Version:

5.3, 11/08/2009

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.BaselineResizeBehavior, java.awt.Component.BltBufferStrategy, java.awt.Component.FlipBufferStrategy

Field Summary

Fields inherited from class chemaxon.marvin.applet.AbstractMarvinApplet

debug, panel

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.
protected void	createGUI()
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.
protected java.lang.String	evaluateChemicalTerms0(java.lang.String expression, chemaxon.struc.Molecule mol)
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.
protected chemaxon.marvin.view.swing.ViewPanel	getPanel()
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.
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?
void	mouseClicked(java.awt.event.MouseEvent e) Does nothing.
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	setSelectedIndex(int i) Selects a molecule.
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 chemaxon.marvin.applet.AbstractMarvinApplet

destroy, enqueueForPrivilegedProcessing, getAppletInBrowser, getAppletInfo, getCodeBase, getParameter, init, isChemicalTermsExpressionSyntaxError, mouseEntered, mouseExited, mousePressed, mouseReleased, propertyChange, setPanel, setParentApplet, validateMoleculeStr, validateMoleculeStr

Methods inherited from class javax.swing.JApplet

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

Methods inherited from class java.applet.Applet

getAppletContext, getAudioClip, getAudioClip, getDocumentBase, getImage, getImage, getLocale, 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, getBaseline, getBaselineResizeBehavior, getBounds, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusCycleRootAncestor, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getFontMetrics, getForeground, 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, 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

Methods inherited from interface chemaxon.marvin.applet.MAppletIface

isChemicalTermsExpressionSyntaxError, setParentApplet, validateMoleculeStr, validateMoleculeStr

Constructor Detail

JMView

public JMView()

Method Detail

createGUI

protected void createGUI()

Specified by:

createGUI in class AbstractMarvinApplet

getPanel

protected chemaxon.marvin.view.swing.ViewPanel getPanel()

Specified by:

getPanel in class AbstractMarvinApplet

mouseClicked

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

Does nothing. @param ev the event object

Specified by:

mouseClicked in interface java.awt.event.MouseListener

Overrides:

mouseClicked in class AbstractMarvinApplet

stop

public void stop()

Stops the applet.

Overrides:

stop in class AbstractMarvinApplet

start

public void start()

Description copied from class: AbstractMarvinApplet

Starts the applet.

Overrides:

start in class AbstractMarvinApplet

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
 

Specified by:

animate in interface chemaxon.marvin.applet.JMViewIface

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.

Specified by:

isEmpty in interface chemaxon.marvin.applet.JMViewIface

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
 

Specified by:

getM in interface chemaxon.marvin.applet.JMViewIface

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.

Specified by:

getMProperty in interface chemaxon.marvin.applet.JMViewIface

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.

Specified by:

setMProperty in interface chemaxon.marvin.applet.JMViewIface

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.

Specified by:

getMPropertyCount in interface chemaxon.marvin.applet.JMViewIface

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.

Specified by:

getMPropertyKey in interface chemaxon.marvin.applet.JMViewIface

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.

Specified by:

setAtomAlias in interface chemaxon.marvin.applet.JMViewIface

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.

Specified by:

getAtomAlias in interface chemaxon.marvin.applet.JMViewIface

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.

Specified by:

setAtomExtraLabel in interface chemaxon.marvin.applet.JMViewIface

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.

Specified by:

getAtomExtraLabel in interface chemaxon.marvin.applet.JMViewIface

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.

Specified by:

getMolMass in interface chemaxon.marvin.applet.JMViewIface

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.

Specified by:

getMolExactMass in interface chemaxon.marvin.applet.JMViewIface

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.

Specified by:

getMolFormula in interface chemaxon.marvin.applet.JMViewIface

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.

Specified by:

evaluateChemicalTerms in interface chemaxon.marvin.applet.JMViewIface

Parameters:

expression - the Chemical Terms expression

n - molecule cell number

Returns:

the result of the evaluation

Since:

Marvin 5.1

evaluateChemicalTerms0

protected java.lang.String evaluateChemicalTerms0(java.lang.String expression,
                                                  chemaxon.struc.Molecule mol)

Overrides:

evaluateChemicalTerms0 in class AbstractMarvinApplet

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.

Specified by:

addMol in interface chemaxon.marvin.applet.JMViewIface

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".

Specified by:

addMol in interface chemaxon.marvin.applet.JMViewIface

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.

Specified by:

setMol in interface chemaxon.marvin.applet.JMViewIface

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.

Specified by:

setMol in interface chemaxon.marvin.applet.JMViewIface

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.

Specified by:

setM in interface chemaxon.marvin.applet.JMViewIface

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.

Specified by:

setM in interface chemaxon.marvin.applet.JMViewIface

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.

Specified by:

getL in interface chemaxon.marvin.applet.JMViewIface

Parameters:

i - the label index

Returns:

the label

setL

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

Sets a label.

Specified by:

setL in interface chemaxon.marvin.applet.JMViewIface

Parameters:

i - the label index

s - the label

getC

public boolean getC(int i)

Gets the state of a checkbox.

Specified by:

getC in interface chemaxon.marvin.applet.JMViewIface

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.

Specified by:

setC in interface chemaxon.marvin.applet.JMViewIface

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.

Specified by:

setActionB in interface chemaxon.marvin.applet.JMViewIface

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.

Specified by:

setActionC in interface chemaxon.marvin.applet.JMViewIface

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.

Specified by:

getT in interface chemaxon.marvin.applet.JMViewIface

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.

Specified by:

setT in interface chemaxon.marvin.applet.JMViewIface

Parameters:

i - the text field index

s - the text

getCellCount

public int getCellCount()

Gets the number of cells in the table.

Specified by:

getCellCount in interface chemaxon.marvin.applet.JMViewIface

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.

Specified by:

getSelectedIndex in interface chemaxon.marvin.applet.JMViewIface

Returns:

the cell index or -1 if no molecule is selected

Since:

Marvin 2.1

setSelectedIndex

public void setSelectedIndex(int i)

Selects a molecule.

Specified by:

setSelectedIndex in interface chemaxon.marvin.applet.JMViewIface

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.

Specified by:

getAtomCount in interface chemaxon.marvin.applet.JMViewIface

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.

Specified by:

selectAllAtoms in interface chemaxon.marvin.applet.JMViewIface

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.

Specified by:

selectAtom in interface chemaxon.marvin.applet.JMViewIface

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?

Specified by:

isSelected in interface chemaxon.marvin.applet.JMViewIface

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?

Specified by:

isAtomSetVisible in interface chemaxon.marvin.applet.JMViewIface

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.

Specified by:

setAtomSetVisible in interface chemaxon.marvin.applet.JMViewIface

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.

Specified by:

setAtomSetColor in interface chemaxon.marvin.applet.JMViewIface

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.

Specified by:

setAtomSetSeq in interface chemaxon.marvin.applet.JMViewIface

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.

Specified by:

setBondSetColor in interface chemaxon.marvin.applet.JMViewIface

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.

Specified by:

setBondSetSeq in interface chemaxon.marvin.applet.JMViewIface

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.

Specified by:

setBondSetSeqAll in interface chemaxon.marvin.applet.JMViewIface

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

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.

Specified by:

getTabScale in interface chemaxon.marvin.applet.JMViewIface

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.

Specified by:

getBestTabScale in interface chemaxon.marvin.applet.JMViewIface

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.

Specified by:

getBestTabScale in interface chemaxon.marvin.applet.JMViewIface

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.

Specified by:

hasValenceError in interface chemaxon.marvin.applet.JMViewIface

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