Sonia change log
NOTE (2004-09-15): THIS DOCUMENT IS RATHER OUT OF DATE 

2/5/03
Attempting to deal with the acursed java PR rendering error caused by being pased large or NaN coords

changed LayoutUtils.rescale to deal with slices with no nodes

-added option to dotNetParser to treat times as integers, rather than intervals, meaning that the end time has 0.9999999999 added to it.  

- fixed transitioning off the end of stack problem (and related PR exception)

- Layout slices always have default coords of 0

2/6/03


- fixed problem reading in edges from dotNetParser.  

2/12   
  - messed with PI to try to add min radius funtion to break stacking
  

  
 2/14  added ability to handle negitve tie values (change them to positive and draw line as dashed)
 
 3/3/03
 
 LOTS OF CHANGES
 
 - Added "dotSonParser" for reading a sonia file format, is "column based" for easy translation from spreadsheets
   Also includes support for differnt shapes colors, sizes, of nodes.
   
 - Beefed up some internals so that rescaling, etc works better, 
 
 - Minor fixes to layouts
 
 - modified graphics code, should be speed improvement.  
 
 - rearranged, and some unused options in the "apply layout" dialog
 
 - added option in GraphisSettings to scale node size and to show node ID instead of label
 
 4/21/03
  - started some javaDoc, fixed rngSeed,
  - added ability to pass in rngSeed from command line

before:
updated screen redraw code to deal with apple's java 1.4.1 graphics/gui problems

play, step setup on separate threads, and display locking


code commenting

implemented more of .son functions


3/24/04:
 fixed mysterious error in netutils.reverse so that it worked again.  
 fixed window cosmetics for useability

3/25/04:
 added parameter to KK to control target epsilon decrease rate
 added default curve on cooling schedule for FR 

4/26/04
	added "updateDisplay" command in the soniaMovieMaker so that it would export correctly (under java1.3.1).  (otherwise it just uses the old screen).

6/?/04
	added ability to use non-numeric ids in .son files by using "AlphaID" instead of "NodeId"
lots of javadocing

6/19/04 
    added fields in graphics settings for setting layout window width and height, and set methods in the layout engine

8/25/04
  fixed time number formating in movie stats
  threaded movie output so it can be killed when something goes wrong

9/14
apply layout now defaults to the max/min times
added "phase plot" function to show network data as time series, along with slice settings.  Can be called from either the layout window or the layout settings dialog

9/15
program asks before quiting
ability to navigate by clicking the phase plot
stress plot updates as you changes slices
slices record errors
option to stop applying multiple on errors
errors indicated in red on phase plot
render settings on phase plot






Bugs:
QT export under mac java 1.4.1
shadows messing w/ screen readraw