full commit
fixed transparency with mesh objects
Fixed Substructures, First and next amino acid fragment, others.
fixed messaging between gadgets and data and with scene refresh
Combined AtomList and Substrucutre.
Updated Contour, moved gadget factory to abstract class.
fixed fragments, amino acid searching, refactored atomlist into
substructure,
Cleaned up warnings.
Simplified Bond Gadget Representation
Improved management of subpanel dialogs. still need to work on event
handling and addition of sub-sub panels (specifically MO list under new
MO dialog)
Moved file samples to resources/samples director
Updating missing files - SpatialDataSelector and Logger
Refactored Point3D and Vector3D to be mathematically consistent
Adjusted for some warnings.
Refactored GobPoly to use vertexList
Cleaned up problem list
Routed all exceptions through Logger class
added HUD support
Introduced generic  properties and accessors.  allows simple integration
into talbes.
added HUD - 2D text overlay for to display properties, titles and other
statistics.
Reformated files impacted by Point/Vector refactor
Local JNLP files work with refactored target directory
Cleaned up property accessor
Some documentation of utils
Setting up messaging for selections
rewrote events and logging for debugging purposes.
Embedded applet now works.