JSME_release_notes.txt

JSME-2017-02-26
	- improved URL for searching InChI Key (google verbatim search)
	- bug fix: popup menu positions when the GUI is scaled
	- bug fix: getMolecularAreaScale() generated an infinite loop
	- bug fix: no error were reported when the V3000 parser fails
	- bug fix: setAtomMolecularAreaFontSize() was not working
	- bug fix: set or unset antialising did not update the drawings
	- improved template example page

JSME-2017-02-20
	- bug fix: chiral flag was not saved in the undo state
	- bug fix: ChemicalFormatDetector trimmed MOL first line if it is empty
	- improved template example page

JSME-2017-02-08
	- bug fix: SDF buffer navigation messages were not shown
	- HOME and END keys can be used to navigate the SDF buffer in addition to page up and page down keys

JSME-2017-02-06
	- bug fix: structure change event recorded after setting the chiral flag
	- bug fix: NEW button shown as disabled after structure change
	- new feature: when NEW button is on, the pasted or dropped structure is added to the molecular drawing area

JSME-2017-01-22
	- bug fix:  in depict mode, DnD arrow size does not vary with zoom level
	- DnD arrow in depict mode is smaller
	- new event types for reading  SMILES, SMIRKS, RXN, JME string
	- new event field: origin (GUI, INIT, DROP, or API)
	- new API method:readGenericMolecularInput()
	- import MOL in V3000 format accepted (extended stereo collections are ignored)
	- exported SVG contains an embedded MOL in V3000 format, this SVG can be pasted/imported back in JSME
	- bug fix: depict mode automatic scaling and resizing
	- bug fix: zooming in and out for reactions
	- new internal class: ChemicalFormatDetector
	- JME internal code cleanup

JSME-2016-12-06
	- new API methods: getMolecularAreaScale(), setMolecularAreaScale(), getMenuScale(), setMenuScale()
	- depict mode: structure can be moved around
	- multiple button after setting R option : GUI bug fixed
	
JSME-2016-11-13
	- improved documentation (options useoclidcode, toggle, InchiResult)
	- Search InChIKey can be customized by using a custom base URL or a custom callback function
	- Search InChIKey menu entry renamed
	- Inchi export disabled for IE < 9
	
JSME-2016-11-05
	- option parser code rewrite
	- bug fix Export SVG for IE < 9

JSME-2016-11-01
	- Export SVG for molecules using the OpenChemLib SVG depictor

JSME-2016-10-30
	- bug fix: parsing of chemical input for IE
	- bug fix: stereo cumulenes smiles generation
	- bug fix: EZ stereo bond in rings enabled (smiles generation)
	- Export InChI, InChiKey and auxinfo
	- Search google with InChiKey

JSME-2016-10-19
	- bug fix: getMolecularAreaGraphicsString
	- bug fix: slow down of FireFox SVG display

JSME-2016-10-17
	- bug fix: Cursor does not become a text edit cursor over SVG text
	- the right border uses a separate graphics, which fixes several bugs
	- bug fix: readMolfile sends JS event after repaint() of the applet

JSME-2016-10-09
	- useOclIDCode new option: preliminary implementation

JSME-2016-10-06
	- delete hydrogens popup  menu entry
	- bug fix: removehs fixed
	- bug fix: infinite loop when setAfterStructureModifiedCallback uses getMolecularAreaGraphicsString()

JSME-2016-10-02
	- clipboard window improved for long lines text

JSME-2016-09-25
	- display sp carbon in cumulene bond

JSME-2016-09-18
	- bug fix: H+, H-
	- undo shows empty state
	- depict bug fix
	- internal change for event reporting
	
JSME-2016-09-11
	- bug fix: cumulene and autoez option
	- getMolecularAreaGraphicsString function refreshes the drawing before yielding the SVG. Also, it does not show the touched atom or bond.

JSME-2016-09-05
	- small bug fixesm reading mutipart mol
	- readMolfile sends JS event after repaint() of the applet

JSME-2016-09-04
	- small bug fixes

JSME-2016-08-21
	- R number can be changed by selecting the R atom and typing a number on the keyboard
	- the */- button allows changing charge of metals with only two major oxidation states
	- X atom charge parsing bug fix for Ca2+
	- New keyboard shortcut for changing atomic charge '+' (works only for the Java applet)
	
JSME-2016-08-01
	- bug fix add new part was not working correctly if the pasted structure is multipart
    - autoez bug fix , autoez is on by default
    
JSME-2016-06-19
	- new options: showdraganddropsymbolindepictmode and noshowdraganddropsymbolindepictmode
	- new options: addnewpart and noaddnewpart
	- bug fix add new part was not supported for JME string input
	- split and merge new behavior
	- mutipart option is on by default

JSME-2016-05-16
	- bug fix: depict was not scaled anymore
	- MDL chiral flag reading was generating an exception if no digit character were present
	- New JSME initialization: <param name="smiles" value="c1ncncn1">


JSME-2016-04-27
	- disable SVG text selection with global CSS
	- Bug fix: bond addition with keyboard on selected atom
	- atom mapping option in the context popup menu is shown only in reaction or number or autonumber mode

JSME-2016-04-19
	- atom mapping option in the context popup menu is shown only in reaction mode
	- bug fix
	- Setting the chiral flag shows a message in the info area

JSME-2016-04-17
   - dialog box to set atom map available with the context menu
   - autonumbering of atom maps of a molecule using the context menu
   - read and write chiral flag for both V2000 and V3000
   - set MDL chiral flag with the context menu
   - in multipart, activate closest fragment by a mouse click
   - in multipart, move the fragment that is the closest to the mouse pointer coordinates 
   - in multipart paste, keep the original coordinates of the fragments
   - mouse wheel for zooming in and out (does not work correctly for reactions)
   - allow zooming option (zoom, nozoom)
   - openchemlib for SMILES input
   - SMIRKS input using openchemlib for SMILES input
   - use openchemlib option
   - highlight in red molecule to be deleted
   - highlight in blue molecule to be copied (in reaction mode)
   - various bug fixes
   - refactoring of bond code

JSME-2016-02-16
    - Bug fix for multipart copy
    - Reaction copy and  structure delete highlight (still buggy)
    - NCI website demo: example: http->https

    
JSME-2016-02-01
    - Bug fix for multipart and reaction (delete, add , undo stack)


JSME-2015-12-06
    - Bug fix bond rubberbanding

JSME-2015-11-22
    - Refactoring of JME code: bond creation bug fix
    
JSME-2015-11-15
    - Refactoring of JME code
    
JSME-2015-11-04
    - Tool chain bug fix
    - Applet resizes automatically when the browser window resizes
    
JSME-2015-11-01
    - Empty mol return a valid MOL with 0 atoms and bonds
    - After importing a reaction with atom mapping, the numbering atom tool will use the largest atom map + 1
    - Refactoring of JME code

JSME-2015-10-04:
   - Bug fix: clicking on NEW and 123 does not generate structure change events
   - Disable logging of null events
   - Changing atom type using the keyboard while the cursor is over an atom does not change the atom type menu selection
   - Using the ring keyboard shortcuts while the cursor is over an atom or a bond does not change the menu
   
JSME-2015-06-25
   - depictAction bug fix
    
JSME-2015-06-20
   - new generic callback
   - atom clicked and bond clicked callback

JSME-2015-06-14
    - New button for I/O
    - Updated smaller icon for drag and drop
JSME-2015-05-28
    - fixed broken links in doc.html
JSME-2015-05-14
    - bug fix: read JSME string with more than 10 marked atoms
    - replaced the star by a circle
    - jsa,css bug fix

JSME-2015-05-07
    - depict mode:leave 16 px for the DnD icon to avoid overlap
JSME 2015-05-03
    - bug fix: autonumber was not working anymore after array optimization (123)
    - remove linker name (e.g xsiframe) from the name of the distribution
    - Microsoft Edge compatibility test performed: Window clipboard is not supported anymore
JSME 2015-03-19
    - Fixed many bugs in the depict mode in order to allow to switch back and forth between depict and edit mode 
    - new methods isDepictMode(), addMouseOutHandler()
JSME 2015-03-01
    - Enable touch events on a ChromeBook
    - JavaScript Bootstrap library compatibility fix (computation of character height)
    - R4 to R9 smiles generation fix
JSME 2015-02-25
    - R4 to R9

JSME 2015-02-09
    - bug fix for SMILES generation of pyrrole [nH], H was missing
JSME 2015-01-28
    - Ctr V shortcut fixed
JSME 2015-01-22
   - file out browse button
   - V3000 export

- bug fix: missing event record for closing a bond on an atom
JSME 2014-12-24
    - bug fix: missing event record for paste
JSME 2014-12-20
    - reenable older event callback
JSME 2014-12-07
    - missing event record for more keyboard events, improve undo/redo record event
JSME 2014-12-04
    - missing event record for set atom type with keyboard

JSME_2014-11-19:
   - BUG: copy SDF of a multipart: invalid ISO
   - array JavaScript optimization
   - Record an event during add chain for each bond

JSME_2014-10-16
   - template bug fix
JSME_2014-10-13
   - Bug fix: JSME in a hidden DIV would not be visible
JSME_2014-09-21
   - Drag and Drop enabled on IE6 to IE9 (does not work with files)
   - Template 1st implementation
   - Missing new lines in doc.html

JSME_2014-08-26
   - incorrect atom mapping read from RXN when numbering option is set - fixed
   - export SMIRKS with "a" did not works with atom mapping - fixed

JSME_2014-07-14
    - Paste behavior changed: if current status is multipart or reaction, then the new structure will be added and will be the selected structure
    - new linker (xsiframe) for CDT testing

JSME_2014-06-28
    - Paste behavior changed: if current status is multipart or reaction, then the new structure will be added
    - remove H bug fix
    - bug fix: structure underneath the menu region: highlight must dissapear
JSME_2014-05-20
    - new resize method
JSME_2014-03-30
    - bond marking allowed
    - bug fix: paste of a multipart structure with isotopic atom
JSME_2014-03-12
    - setAction, depictaction
JSME_2014-02-20
    - Font size can be changed with setAtomMolecularAreaFontSize
JSME_2014-02-03
    - bug fix: date in exported MOL
    - new callback setAfterStructureModifiedCallback
JSME_2014-01-27
     - isotopic atoms implementation
     - star marker: the MOL generation now set the atom map for each marked atom

JSME_2014-01-05
     - smaller initial download size by about 25 %
     - scaling picture: further improved for very small depiction
     - high precision 2D coordinates

JSME_2013-11-06
     - removehsc new 
     - scaling picture: improved for very small depiction

JSME_2013-10-27:
     - initialization error will not open an alert but write a message to the console instead
     
JSME_2013-10-13:
     - small refactoring inside the JME code
     - bug fix in doc.html

JSME_2013-10-09:
     - callback function setNotifyStructuralChangeJSfunction does not need the nocanonize function anymore
JSME_2013-10-03:
     - bug fix:D&D icon disappears after resizing JSME
     - bug fix: resizing JSME, avoid multiple SVG/VML generation after each resize
     - improved setNotifyAtomHighLightChangeJSfunction
     - two more example pages about JSME resize
     - depict mode takes the callback function notifyAtomHighLightJSfunction
     - after clearing the canvas, the undo stack is not deleted anymore
     
JSME_2013-09-29:
     - bug fix in index.html
     
JSME_2013-09-28:
     - More simple installation examples
     - index.html file
     - improved doc.html file
     - star option documented
     

JSME_2013-09-19:
    - New methods: addClickHandler(), addMouseOverHandler()

JSME_2013-09-17:
    - New methods:  getOffsetSize(), getOffsetWidth(), getOffsetHeight(), setWidth(), setHeight(),  isVisible(), setVisible()
    - improved javadoc API
    
JSME_2013-09-15:
    - new utility function: Utils.runAfterBrowserEventLoopReturns
    - setSize() method
    - call back function argument for replaceAllAppletsByJSME
    - JME: cache font and font metrics for the drawing area useful for many depictions
    - scaling picture bug fix: the 2px padding around the atom labels was not scaled

JSME_2013-09-08:
    - Easy migration JME->JSME
    - new documentation file: doc.html - still incomplete
    - new option: paste/nopaste to disable pasting MOL into the applet
    - query mode disabled by default
    - aromaticity SMARTS query bug fix

JSME_2013-08-04:
    -xbutton, noxbutton options work
    
JSME_2013-06-29:
    - For IE11, the clipboard management had to be adapted because of the unconventional user agent in IE11 (=Firefox)
    - Android and iPad do not show the drag out button because dragging out does not work on these systems
    - bug fix: undo & redo was not working for atom atom mapping
    - Note: the number of GWT permutations has increased to 30


JSME_2013-06-09:
    - atom move atom button is optional (turned off by default)
    - improved JSME_chemical_resolver_demo.html page


JSME_2013-05-30:
    - move atom button
    - java application exits when its window is closed, no more END button
    - new simpler HTML demo page
    
JSME_2013-05-01:
    - bug fix: IE has no console unless the debugger window is open
    - deleting explicit hydrogens when importing a structure from chemical resolver (demo page)

JSME_2013-04-09:
    - Custom paste menu and custom paste operation
    - non GPL licensed image for the drag and drop icon
    - local antialias for VML
    - line width for the molecular area
    - JavaDoc of the API
    - clear function added 

JSME_2013-04-01:
    - bug fix in JSObject

JSME_2013-03-30 :
    - Drag out of MOL/RXN and drop onto another applet or on to a file system window to save the file
    - DnD demo page
    - No more alert window if the function jsmeOnLoad is not defined - instead provides a message to the console
    - clear SDF stack as well when clicking on the clear icon
    - stereo bond cancel bug fix (bug shows up visible with undo/redo)
    - interactive atom marking demo page
    - multiple instances of the editor in the same HTML page work
    
JSME_2013-03-24 :
    - Drag and drop of files onto the applet

JSME_2013-03-21 :
    - undo bug fix
    - showInfo function


JSME_2013-03-19 :
    - antialias is on by default for SVG and off for VML
    - new help page
    - first public release

JSME_2013-03-18 :
    - spiro button
    - triple bond in menu is improved - looks better with browser with poor antialias


JSME_2013-03-16 :
    - rename JavaScriptApplet to JSApplet to avoid trademark problems with JavaScript
    - disable molecule scaling for IOS
    - removes blue marking about atoms and bonds after click enabled unless touch device


JSME_2013-03-14 :
    - increased touch radius for atoms and bonds - much better usability on iPad

JSME_2013-03-13 : not for redistribution
    - first DIV shield - still bugs
    - rubber banding box was not saved in the undo stack - fixed

JSME_2013-03-12 : not for redistribution
    - Rollback of all the Smiles changes, no more example of NotifyStructuralChangeJSfunction provided
    - improved rotation&scaling on iPad. Scaling is still buggy
JSME_2013-03-11 : not for redistribution
    - Smiles generation changes the atom ordering of the atoms in the editor, which is a problem for the NotifyStructuralChangeJSfunction. Fixed.
JSME_2013-03-10 : not for redistribution
    - Scaling of the molecule implemented for touch devices - still buggy. Problem with rotation, does not work on Android
    - NotifyStructuralChangeJSfunction - problem with smiles generation
JSME_2013-03-07
    - Marked atoms are not displayed anymore with a blue square after touch/mouse up
    - Touch device: rotation bug fixed (random jump move at the end of the rotation)
    - bug fix for CSS distribution
JSME_2013-03-04
    - Touch device: rotation works on iPad


JSME_2013-03-03
    - Touch device: touch and hold will show the copy&paste popup menu
    - Touch device: mouse events of drawing area were replaced by touch events in order to have a faster response on the iPad
    - Touch device: structure can be moved. It is smooth on a iPad 4, slow on a Samsung Note
    - Touch device: bond angle can be changed, multichain works
    - CSS pollution: all global CSS definitions were removed from all the included CSS files from GWT and gwt-mosaic
    - CSS global protection: better protection against global CSS definitions from the host page
    
    
    
Known bug: scaling and bond length rubber banding