Merge pull request #1 from jimkell/master

Numerous changes
Merge pull request #2 from jimkell/master

Added new Gurobi code - works
Added ReactionEquationUpdater
Added correct README back
Dist folder was missing
Many bugs in regarding reaction equations...

TextReactionsModelReader not constructing "used" map correctly.
TextReactionsModelReader creating used and...

name id maps correctly.
Adding metabolites by reaction editing...

works even with delete all unused metabolites
Rewriting methods to update equations, since...

old ones refuse to work. This will also make maintenance easier.
Items removed from maps for old equation...

Bug - sometimes add metabolite prompt shows 2x for same metabolite.
Suspicious metab. not deleting bug fixed...

Should not have been removed from MetabolitesNameIdMap since still
present in metabolites table
Fixed bug where id added to NameIdMap was...

2000, 2001, etc and not 0, 1, etc when adding new metabolites when
editing reactions in blank tables. Bug - formula bar updates twice.
After fix improperly spaced reactions, suspicious..

metabolites delete correctly by either context menu or delete all unused
metabolites.
Editing reaction equ'ns works except for "No" ...

button.
"No" button working for editing reaction equations

Bug - ReactionEquationMap not updating correctly.
Reaction equation editing bug where all...

SBMLReactionEquation objects in map were the same has been fixed by
copying the object before adding to map, due to original lists being
copies of the same list.
After editing reaction equ'n if not contains...

participating metabolite, is un-highlighted. Undo works for removing
added metabolites, but bugs when rows deleted. Redo not working.
Deleting row bug fixed for added metabolites...

when editing reactions. Undo and redo working except for bugs in
ReactionEquationMap, used metabolites, and participating metabolites
Undo/redo working for reaction equ'n, bug-

rows remain after added metabolites removed on undo, redo results in two
rows w/same id, one blank, one w/ correct value
Cleaned up code, Reaction Editor closes...

when selected row changed.