Created by Francois Nedelec ( nedelec.embl-heidelberg.de )
       EMBL, European Molecular Biology Laboratory, Heidelberg, Germany
                           April-May 2002.


 WARNING: I make NO GARANTY of any kind, bla-bla-bla, use this your own risks...

 NOTE: The Java source is included in the jar distribution, and you can adapt
    it to your needs.  If you do any modifications which you think can be 
    usefull to other people, I'll be happy to see them. 

 ********   I need your feed-back to improve this program, Thanks !  *******

 
--------------------------  INTRODUCTION ------------------------------------

  JPLAY is the graphic side of the cytoskeletal simulation CYTOSIM.

  CYTOSIM produce a coordinate file <result.out> which contains several
    successive 'frames', each containing a snap-shot of the position of all
    the objects in the simulation, at regular time intervals.

  JPLAY opens a coordinate file, and produces a graphical output on the sreen.
    It allows you to zoom in/out (type + or -), to move around (type i j k m),
    to go to the next/previous frame (type < or >). Advancement is automatic
    if you press 'p'.

  JPLAY can be slow at reading big files, in that case be patient !
    not drawing the free complexes allow to go faster by skiping a part of
    the file (in Menu Motors, Selection, uncheck free).

  The gray scale-bar in top left corner represents a total of 5 micro-meters,
    the first micro-meter is graduated in tenths of micro-meter.

-----------------------------   MENUS   -------------------------------------

File Menu:

     Open:       Allow selection of the coordinate files.
                 by default, jplay tries to open "result.out" when started.

     Help:       Display this text

     Reset view: Re-center the image, reset the zooming

Set Menu:

     Currently disabled

Motors Menu:

     Selection:  Show/hide motor complexes according to their states:

        Free:    Complexes not bound to any filament.
        Bound:   Complexes bound to one and only one filament.
        Link:    Complexes bound to two filaments, making a link between them.

     Draw:       Select the drawing method:

        Head:    Draw a disc at the position of each motor.
                                      (change size with '8' and '9')
        Tail:    Draw a line between the position of the complex on the 
                 previous frame and the current position (free complex only).
        Stretch: Draw a colored rectangle between the two motor of a complex
                 bound twice (i.e. linking).

Tubes Menu:

     Selection:  Show/hide asters
        
        Aster1:  Select microtubules belonging to first aster.
        Aster2:  Select microtubules belonging to second aster.
	Color:   If selected, draw first aster white, and second one gray.

     Draw:       Select the drawing method:

        Lines:   Draw filaments as lines (change width with '2' and '3').
        Arrows:  Add arrows indicating the filament's polarity.
        Points:  Draw inflection points in the filaments.
                      (filaments are modeled as segmented lines)


-----------------------------   KEYBOARD   -----------------------------------

    The most important commands are also available through the keyboard:


Main keyboard commands:

     '>' or '.'        next frame
     '<' or ','        previous frame

     'p'               play movie forward
     'o'               play movie backward
                           for 'p' and 'o' typing several time reduce the
                           delay between frames 
                           (but file reading is usually limiting) 
     'l'               toggle automatic looping
     's'               stop movie

     '-' or '_'        zoom out
     '+' or '='        zoom in
 
     'i'               move up
     'j'               move left
     'k'               move right
     'm'               move down

     '8'               decrease motor disc size
     '9'               increase motor disc size

     '2'               decrease filament width
     '3'               increase filament width

     ' ' (space)       force screen redraw

Shortcuts:

     'q'               quit
     'z'               reset view and return to frame 1



----------------------------  CUSTOMIZATION ----------------------------------

You can change the colors of the displayed objects:
- edit the file <ColorServer.java> and recompile (in the jar bundle)