export.client

Class JSME

java.lang.Object

export.client.JSME

public class JSME
extends java.lang.Object

Constructor Summary

Constructors

Constructor and Description
JSME(java.lang.String htmlId)
JSME(java.lang.String htmlId, JavaScriptObject parameterJso)
JSME(java.lang.String htmlId, java.lang.String width, java.lang.String height)
JSME(java.lang.String htmlId, java.lang.String width, java.lang.String height, JavaScriptObject parameterJso)

Method Summary

Modifier and Type	Method and Description
void	addClickHandler(JsClosureJsme jsEventHandler) Add a click handler to a JSME instance.
void	addMouseDownHandler(JsClosureJsme jsEventHandler) Add a mouse down handler to a JSME instance.
void	addMouseOutHandler(JsClosureJsme jsEventHandler) Add a mouse out handler to a JSME instance.
void	addMouseOverHandler(JsClosureJsme jsEventHandler) Add a mouse over handler to a JSME instance.
void	alert(java.lang.String message) Display an alert box with the look and feel of JSME
void	clear() Same effect as clicking on the clear icon: clear the molecular drawing area
void	deferredRepaint() Repaint the applet after the browser event loop returns.
java.lang.String[]	getAlldefinedCallBackNames() Return an array containing all possible callback names.
JsArrayString	getAllGraphicsString() Returns all graphics representations used in the applet, either a SVG or a VML string This is an advanced feature.
JavaScriptObject	getCallBack(java.lang.String callbackName) Generic callback
int	getCreationIndex() The JSME class keeps tract of the number of instance that have been created.
java.lang.String	getHelpURL()
double	getMenuScale()
boolean	getMolecularAreaAntiAlias() Return the antialias setting for the molecular drawing area
java.lang.String	getMolecularAreaGraphicsString() Returns the graphics representation used in the molecular area, either a SVG or a VML string This is an advanced feature.
float	getMolecularAreaLineWidth()
double	getMolecularAreaScale()
java.lang.String	getNotifyStructuralChangeJSfunction() Deprecated.
int	getOffsetHeight() Gets the object's offset height in pixels.
JsArrayInteger	getOffsetSize() Gets the object's offset width and height in pixels.
int	getOffsetWidth() Gets the object's offset width in pixels.
com.google.gwt.user.client.Element	getParentContainer() Return the parent DOM element that contains myself.
java.lang.String	getPasteLabel() See setPasteLabel(String)
java.lang.String	getPrePasteJSfunction()
java.lang.String	getWebSearchInchiKeyBaseUrl()
void	initializationError(java.lang.String message)
boolean	isDepictMode()
boolean	isVisible() Returns whether the given element is visible in a way consistent with setVisible(boolean).
java.lang.String	jmeFile()
java.lang.String	molFile(boolean isV3000)
java.lang.String	nonisomericSmiles()
void	options(java.lang.String options) options is a comma separated value list - same as original JME
boolean	read_MOL_SDF_RXN(java.lang.String s) Read a molecular structure encoded in MOL or SDF format, or a reaction encoded in RXN format.
void	readGenericMolecularInput(java.lang.String s)
void	readMolecule(java.lang.String s) Read a molecular structure encoded in JME format
void	readMolFile(java.lang.String s) Read a molecular structure encoded in MOL format, or a reaction encoded in RXN format
void	repaint() Redraw the whole applet if it is visible
static int	replaceAllAppletsByJSME() Scan the DOM for DIV's containing an attribute code="JME.class" and install a running JSME.
static int	replaceAllAppletsByJSME(JsClosure jsFunctionWithJsmeInstanceArg) Scan the DOM for DIV's containing an attribute code="JME.class" and install a running JSME.
void	reset()
void	resetAtomColors(int molIndex) Reset background colors
void	setAction(int action) select one of the menu action without having to click on the menu.
void	setAfterDepictEditToggleEventHandler(JsClosureJsme jsEventHandler)
void	setAfterPasteCallback(JavaScriptObject callbackFunction) Deprecated.
void	setAfterStructureModifiedCallback(JavaScriptObject callbackFunction) Deprecated.
void	setAntialias(boolean onOff) Set globally antialias
void	setAtomBackgroundColors(int molIndex, java.lang.String atomAndColorCSV)
void	setAtomMolecularAreaFontSize(float fs)
void	setAtomToHighLight(int molIndex, int atomIndex)
void	setBeforePasteCallback(JavaScriptObject callbackFunction) Deprecated.
void	setCallBack(java.lang.String callbackName, JavaScriptObject callbackFunction) Generic call back.
void	setHeight(java.lang.String width) Sets the object's height.
void	setHelpURL(java.lang.String url) set the url to display the JSME help page.
void	setMenuScale(double scale)
void	setMolecularAreaAntiAlias(boolean molecularAreaAntiAlias) Set antialias for the molecular drawing area
void	setMolecularAreaLineWidth(float molecularAreaLineWidth) Line width in pixel
void	setMolecularAreaScale(double scale)
void	setNotifyAtomHighLightChangeJSfunction(java.lang.String notifyAtomHighLightJSfunction) Deprecated.
void	setNotifyStructuralChangeJSfunction(java.lang.String notifyStructuralChangeJSfunction) Deprecated.
void	setPasteLabel(java.lang.String pasteLabel) Set the label of the context popup menu for pasting string, instead of using the default label.
void	setPrePasteJSfunction(java.lang.String prePasteJSfunction) Deprecated.
void	setSize(int width, int height) Sets the object's size.
void	setSize(int width, int height, boolean resizeParent) Sets the object's size.
void	setSize(java.lang.String width, java.lang.String height) Sets the object's size.
void	setSize(java.lang.String width, java.lang.String height, boolean resizeParent) Sets the object's size.
void	setSubstituent(java.lang.String s) Select the next FG to be used.
void	setTemplate(java.lang.String templateAsJmeMol, java.lang.String templateName) Provide a template, a molecular fragment with one marked atom, in JME format.
void	setVisible(boolean visible) Shows or hides the given element.
void	setWebSearchInchiKeyBaseUrl(java.lang.String webSearchInchiKeyBaseUrl) Set the base url for inchi key search.
void	setWidth(java.lang.String width) Sets the object's width.
void	showInfo(java.lang.String message) Display a message in the bottom bar.
java.lang.String	smiles()

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

JSME

public JSME(java.lang.String htmlId,
            java.lang.String width,
            java.lang.String height)

JSME

public JSME(java.lang.String htmlId)

JSME

public JSME(java.lang.String htmlId,
            java.lang.String width,
            java.lang.String height,
            JavaScriptObject parameterJso)

JSME

public JSME(java.lang.String htmlId,
            JavaScriptObject parameterJso)

Parameters:

htmlId -

parameterJso -

Method Detail

getAllGraphicsString

public JsArrayString getAllGraphicsString()

Returns all graphics representations used in the applet, either a SVG or a VML string This is an advanced feature.

Returns:

an array of strings that can be used in a DOM element innerHTML

getMolecularAreaGraphicsString

public java.lang.String getMolecularAreaGraphicsString()

Returns the graphics representation used in the molecular area, either a SVG or a VML string This is an advanced feature.

Returns:

a string that can be used in a DOM element innerHTML

getWebSearchInchiKeyBaseUrl

public java.lang.String getWebSearchInchiKeyBaseUrl()

Returns:

the web search InchiKey base Url See also see setWebSearchInchiKeyBaseUrl(String webSearchInchiKeyBaseUrl)

setWebSearchInchiKeyBaseUrl

public void setWebSearchInchiKeyBaseUrl(java.lang.String webSearchInchiKeyBaseUrl)

Set the base url for inchi key search. For instance: "http://www.google.com/search?q="

Parameters:

webSearchInchiKeyBaseUrl: - the web search InchiKey base Url to set Note: alternatively, one can replace the web search by a custom function call. See setCallBack(String,JavaScriptObject) To find the inchi key search callback name, see getAlldefinedCallBackNames() See also see getWebSearchInchiKeyBaseUrl()

getMolecularAreaScale

public double getMolecularAreaScale()

Returns:

the scale of the molecular area

setMolecularAreaScale

public void setMolecularAreaScale(double scale)

getMenuScale

public double getMenuScale()

setMenuScale

public void setMenuScale(double scale)

getCreationIndex

public int getCreationIndex()

The JSME class keeps tract of the number of instance that have been created. Each instance has a copy of its creation count, which can be used as a index. The first instance has an index equal to 0.

Returns:

the creation index.

getParentContainer

public com.google.gwt.user.client.Element getParentContainer()

Return the parent DOM element that contains myself. This is equivalent to using document.getElementById("id") where "id" is the id of the element that was used to create the JSME instance.

initializationError

public void initializationError(java.lang.String message)

setAntialias

public void setAntialias(boolean onOff)

Set globally antialias

Parameters:

onOff -

options

public void options(java.lang.String options)

options is a comma separated value list - same as original JME

Parameters:

options -

readMolecule

public void readMolecule(java.lang.String s)

Read a molecular structure encoded in JME format

Parameters:

s -

readMolFile

public void readMolFile(java.lang.String s)

Read a molecular structure encoded in MOL format, or a reaction encoded in RXN format

Parameters:

molecule -

read_MOL_SDF_RXN

public boolean read_MOL_SDF_RXN(java.lang.String s)

Read a molecular structure encoded in MOL or SDF format, or a reaction encoded in RXN format. If the input is a SDF with more than one structure, then all SDF entries will be stored in the internal SDF buffer. Return true if successful or false otherwise. TODO: fix bug with paste event - infinite recursion

Parameters:

s -

Returns:

success

readGenericMolecularInput

public void readGenericMolecularInput(java.lang.String s)

molFile

public java.lang.String molFile(boolean isV3000)

Parameters:

isV3000 -

Returns:

the MOL or the RXN

smiles

public java.lang.String smiles()

Returns:

the smiles

nonisomericSmiles

public java.lang.String nonisomericSmiles()

Returns:

non isomeric smiles

jmeFile

public java.lang.String jmeFile()

reset

public void reset()

clear

public void clear()

Same effect as clicking on the clear icon: clear the molecular drawing area

setTemplate

public void setTemplate(java.lang.String templateAsJmeMol,
                        java.lang.String templateName)

Provide a template, a molecular fragment with one marked atom, in JME format.

Parameters:

templateAsJmeMol -

templateName -

setSubstituent

public void setSubstituent(java.lang.String s)

Select the next FG to be used. Deprecated because of the FG popup menu.

Parameters:

s -

repaint

public void repaint()

Redraw the whole applet if it is visible

deferredRepaint

public void deferredRepaint()

Repaint the applet after the browser event loop returns. TODO: this is not an applet.repaint() but a rerendering of all graphics objects See also export.client.Utils.runAfterBrowserEventLoopReturns

getHelpURL

public java.lang.String getHelpURL()

Returns:

the url used to display JSME help page

setHelpURL

public void setHelpURL(java.lang.String url)

set the url to display the JSME help page. This method can be used to redefine the standard help page.

Parameters:

url -

alert

public void alert(java.lang.String message)

Display an alert box with the look and feel of JSME

Parameters:

message -

showInfo

public void showInfo(java.lang.String message)

Display a message in the bottom bar. Can be used to display e.g.the name or the MW of the compound in the editor.

Parameters:

message -

getNotifyStructuralChangeJSfunction

@Deprecated
public java.lang.String getNotifyStructuralChangeJSfunction()

Deprecated.

Returns:

the notifyStructuralChangeJSfunction

setNotifyStructuralChangeJSfunction

@Deprecated
public void setNotifyStructuralChangeJSfunction(java.lang.String notifyStructuralChangeJSfunction)

Deprecated.

Specify a JS function that will be called each time the molecular structure in the editor has been changed. This method is deprecated. Use the setAfterStructureModifiedCallback(JavaScriptObject) method instead.

Parameters:

notifyStructuralChangeJSfunction - the name of the JavaScript function This method is deprecated. Use setCallBack(String,JavaScriptObject) instead.

setAfterStructureModifiedCallback

@Deprecated
public void setAfterStructureModifiedCallback(JavaScriptObject callbackFunction)

Deprecated.

Specify a JS function that will be called each time the molecular structure in the editor has been changed. The argument of the function will be a JSMEevent object that contains the fields: src (the jsme instance), the action, the atom index, the bond index and molecule index. Not all events have been mapped to a JSMEevent yet - action is then null.

Parameters:

callbackFunction, - a Javascript function - not the name of the function This method is deprecated. Use setCallBack(String,JavaScriptObject) instead.

setCallBack

public void setCallBack(java.lang.String callbackName,
                        JavaScriptObject callbackFunction)

Generic call back. The callback function is a JavaScript function that receives an instance of JSMEevent. See getAlldefinedCallBackNames() for all predefined callback names.

Parameters:

callbackName -

callbackFunction -

getCallBack

public JavaScriptObject getCallBack(java.lang.String callbackName)

Generic callback

Parameters:

callbackName -

Returns:

the JavaScript function (can be null)

getAlldefinedCallBackNames

public java.lang.String[] getAlldefinedCallBackNames()

Return an array containing all possible callback names.

setAtomToHighLight

public void setAtomToHighLight(int molIndex,
                               int atomIndex)

setNotifyAtomHighLightChangeJSfunction

@Deprecated
public void setNotifyAtomHighLightChangeJSfunction(java.lang.String notifyAtomHighLightJSfunction)

Deprecated.

Specify a JS function that will be called each time the mouse pointer touches an atom. When the cursor leaves the atom, the atom index sent is 0. The argument is the name of a JavaScript function that receives two arguments: the molecule index and the atom index. To cancel, set the argument to null. Note valid atom indices are > 0. This method is deprecated. Use setCallBack(String,JavaScriptObject) instead.

Parameters:

notifyAtomHighLightJSfunction - must be a string

setAfterPasteCallback

@Deprecated
public void setAfterPasteCallback(JavaScriptObject callbackFunction)

Deprecated.

Specify a JavaScript function that will be called after a successful paste operation. Unlike the setNotify* methods that have a string as an argument, this method requires a function. Example: jsmeApplet.setAfterPasteCallBack(function(jsmeEvent, pasteContent) { console.log(jsmeEvent.src..smiles()); console.log(pasteContent); }); This method might be removed in the future . Not supported by the pure Java applet JME.

Parameters:

callbackFunction - with two arguments, the jsme instance and the content that was pasted. This method is deprecated. Use setCallBack(String,JavaScriptObject) instead.

setBeforePasteCallback

@Deprecated
public void setBeforePasteCallback(JavaScriptObject callbackFunction)

Deprecated.

Specify a JavaScript function that will be called before a paste operation. Unlike the setNotify* methods that have a string as an argument, this method requires a function. Example: jsmeApplet.setBeforePasteCallBack(function(jsmeEvent, pasteContent) { console.log(jsmeEvent.src.smiles()); console.log(pasteContent); }); Note that the paste operation into JSME is not performed. See the example shown in the file JSME_chemical_resolver_demo.html It is not supported by the pure Java applet JME.

Parameters:

callbackFunction - with two arguments, the jsme instance and the content that was pasted. This method is deprecated. Use setCallBack(String,JavaScriptObject) instead.

setAtomBackgroundColors

public void setAtomBackgroundColors(int molIndex,
                                    java.lang.String atomAndColorCSV)

Parameters:

molIndex -

atomAndColorCSV - : at,c,at,c,at,c, ... at: atom index; c: color index

resetAtomColors

public void resetAtomColors(int molIndex)

Reset background colors

Parameters:

molIndex -

getPrePasteJSfunction

public java.lang.String getPrePasteJSfunction()

Returns:

See Also:

setPrePasteJSfunction

setPrePasteJSfunction

@Deprecated
public void setPrePasteJSfunction(java.lang.String prePasteJSfunction)

Deprecated.

Set a JS function that will be called before the paste is performed. This function will receive one argument: a string that a represent a molecular structure. The return value of the function is a string. Purpose: convert a name or a SMILES or an InchI into a MOL.

Parameters:

prePasteJSfunction - This method is deprecated. Use setCallBack(String,JavaScriptObject) instead.

getPasteLabel

public java.lang.String getPasteLabel()

See setPasteLabel(String)

Returns:

the currently used label.

setPasteLabel

public void setPasteLabel(java.lang.String pasteLabel)

Set the label of the context popup menu for pasting string, instead of using the default label. Purpose: This function can be used in case the paste action is customized with a callback function. See setPrePasteJSfunction(String)

Parameters:

pasteLabel -

getMolecularAreaLineWidth

public float getMolecularAreaLineWidth()

Returns:

line width in pixel

setMolecularAreaLineWidth

public void setMolecularAreaLineWidth(float molecularAreaLineWidth)

Line width in pixel

Parameters:

molecularAreaLineWidth -

setAtomMolecularAreaFontSize

public void setAtomMolecularAreaFontSize(float fs)

getMolecularAreaAntiAlias

public boolean getMolecularAreaAntiAlias()

Return the antialias setting for the molecular drawing area

setMolecularAreaAntiAlias

public void setMolecularAreaAntiAlias(boolean molecularAreaAntiAlias)

Set antialias for the molecular drawing area

Parameters:

molecularAreaAntiAlias -

setSize

public void setSize(java.lang.String width,
                    java.lang.String height)

Sets the object's size. This size does not include decorations such as border, margin, and padding. Setting the height to "100%" does not work.

Parameters:

width - the applet's new width, in CSS units (e.g. "10px", "1em", "100%")

height - the applet's new height, in CSS units (e.g. "10px", "1em")

setSize

public void setSize(int width,
                    int height)

Sets the object's size. This size does not include decorations such as border, margin, and padding. Setting the height to "100%" does not work.

Parameters:

width - the applet's new width, in pixels

height - the applet's new height, in pixels

setSize

public void setSize(java.lang.String width,
                    java.lang.String height,
                    boolean resizeParent)

Sets the object's size. This size does not include decorations such as border, margin, and padding. Setting the height to "100%" does not work. if resizeParent is true, then the parent HTML container (e.g. a DIV) in which the applet resides will be resized as well

Parameters:

width - the applet's new width, in CSS units (e.g. "10px", "1em", "100%")

height - the applet's new height, in CSS units (e.g. "10px", "1em")

setSize

public void setSize(int width,
                    int height,
                    boolean resizeParent)

Sets the object's size. This size does not include decorations such as border, margin, and padding. Setting the height to "100%" does not work. if resizeParent is true, then the parent HTML container (e.g. a DIV) in which the applet resides will be resized as well

Parameters:

width - the object's new width, in pixels

height - the object's new height, in pixels

setWidth

public void setWidth(java.lang.String width)

Sets the object's width. This width does not include decorations such as border, margin, and padding.

Parameters:

width - the object's new width, in CSS units (e.g. "10px", "1em")

setHeight

public void setHeight(java.lang.String width)

Sets the object's height. This height does not include decorations such as border, margin, and padding.

Parameters:

height - the object's new height, in CSS units (e.g. "10px", "1em")

getOffsetSize

public JsArrayInteger getOffsetSize()

Gets the object's offset width and height in pixels. This is the total width (height) of the object, including decorations such as border and padding, but not margin.

Returns:

an array of size 2 containing the width and height

getOffsetWidth

public int getOffsetWidth()

Gets the object's offset width in pixels. This is the total width of the object, including decorations such as border and padding, but not margin.

getOffsetHeight

public int getOffsetHeight()

Gets the object's offset height in pixels. This is the total height of the object, including decorations such as border and padding, but not margin.

setVisible

public void setVisible(boolean visible)

Shows or hides the given element. Also updates the "aria-hidden" attribute.

Warning: implemented with a heuristic based on the "display" style: clears the "display" style to its default value if visible is true, else forces the style to "none". If the "display" style is set to "none" via CSS style sheets, the element remains invisible after a call to setVisible(true).

isVisible

public boolean isVisible()

Returns whether the given element is visible in a way consistent with setVisible(boolean).

Warning: implemented with a heuristic. The value returned takes into account only the "display" style, ignoring CSS and Aria roles, thus may not accurately reflect whether the element is actually visible in the browser.

replaceAllAppletsByJSME

public static int replaceAllAppletsByJSME()

Scan the DOM for DIV's containing an attribute code="JME.class" and install a running JSME.

Returns:

the number of JSME installed.

replaceAllAppletsByJSME

public static int replaceAllAppletsByJSME(JsClosure jsFunctionWithJsmeInstanceArg)

Scan the DOM for DIV's containing an attribute code="JME.class" and install a running JSME. Call the argument when done. See also getCreationIndex.

Parameters:

jsFunction: - a function defined in JavaScript such as : function(eachJsmeInstance){alert("JSME created. Creation index: "+ eachJsmeInstance.getCreationIndex() )};

Returns:

the number of new JSME installed.

addClickHandler

public void addClickHandler(JsClosureJsme jsEventHandler)

Add a click handler to a JSME instance. The argument is a JavaScript function with two arguments: - the JSME instance that received the click event. - the mouse event Example: document.JSME.addClickHandler(function(jsme, evt) { alert("My smiles is: " + jsme.smiles()); }); Purpose: intercept a click event on JSME in depict mode.

Parameters:

jsEventHandler: - a JavaScript function with two arguments.

addMouseDownHandler

public void addMouseDownHandler(JsClosureJsme jsEventHandler)

Add a mouse down handler to a JSME instance. The argument is a JavaScript function with two arguments: - the JSME instance that received the click event. - the mouse event Example: document.JSME.addMouseDownHandler(function(jsme, evt) { alert("My smiles is: " + jsme.smiles()); }); Purpose: intercept a click event on JSME in depict mode.

Parameters:

jsEventHandler: - a JavaScript function with two arguments.

addMouseOverHandler

public void addMouseOverHandler(JsClosureJsme jsEventHandler)

Add a mouse over handler to a JSME instance. The argument is a JavaScript function with two arguments: - the JSME instance that received the event. - the mouse event Example: document.JSME.addMouseOverHandler(function(jsme, evt) { console.log("My smiles is: " + jsme.smiles()); }); Purpose: intercept a mouse event on JSME in depict mode.

Parameters:

jsEventHandler: - a JavaScript function with two arguments.

addMouseOutHandler

public void addMouseOutHandler(JsClosureJsme jsEventHandler)

Add a mouse out handler to a JSME instance. The argument is a JavaScript function with two arguments: - the JSME instance that received the event. - the mouse event Example: document.JSME.addMouseOutHandler(function(jsme, evt) { console.log("My smiles is: " + jsme.smiles()); }); Purpose: intercept a mouse event on JSME in depict mode.

Parameters:

jsEventHandler: - a JavaScript function with two arguments.

setAfterDepictEditToggleEventHandler

public void setAfterDepictEditToggleEventHandler(JsClosureJsme jsEventHandler)

setAction

public void setAction(int action)

select one of the menu action without having to click on the menu. Purpose: enable some action in depict mode, e.g. the atom selection with the star option. Example : 105 is the code for ACTION_MARK. In theory, it is possible to program a new menu interface for JSME using all action codes.

Parameters:

action -

isDepictMode

public boolean isDepictMode()

Returns:

true if the editor is in depict mode