(show summary)
(show notes tval dish allDish) 
(show val tval dish allDish) 

*** the allDish dishnet
(mkNSaveAllDish RKB DishNets)

(Dishes2Json RKB QQQ)
(Dishes2Json RKB QQQ allDish)





*** what is going on
(show control)
(show requests)
(show wait4s)
(show log)
(show summary)

(reset control)
(reset wait4s)
(graphics2d OK)

**** coloring by location
(g2dexe graphics2d (apply colorLoc "graph2" "TnfR1C"))
(g2dexe graphics2d (apply colorLoc "graph2" "EgfRC"))
(g2dexe graphics2d (apply restoreColor "graph2"))

**** turn on IOP/g2d VERBOSITY
 (g2dexe graphics2d (supdate "g2d.util.ActorMsg" "VERBOSE" (boolean true)))
 (g2dexe graphics2d (supdate "g2d.Main" "DEBUG" (boolean true)))

**** turn off IOP/g2d VERBOSITY
 (g2dexe graphics2d (supdate "g2d.util.ActorMsg" "VERBOSE" (boolean false)))
 (g2dexe graphics2d (supdate "g2d.Main" "DEBUG" (boolean false)))

(g2dexe graphics2d (supdate "g2d.graph.Dot" "dotDebug" (boolean true)))

**** saving LoLa input  (by turning on loladebug)
(g2dexe graphics2d (seq (define lolaDebug (boolean true)) (invoke java.lang.System.err "println" (concat "lolaDebug = " lolaDebug))))

**** by turning off loladebug
(g2dexe graphics2d (seq (define lolaDebug (boolean false)) (invoke java.lang.System.err "println" (concat "lolaDebug = " lolaDebug))))


**** geting the exploration history  -- replace ? by the xpnet id
(show note history tval xnet xpnet?)

**** showing bits
(show notes gval graph1)
(show note selections gval graph2)
(show entry gval graph1)
(show val gval graph1)

**** saving a net and its graph 
**** the show is a check that you have the right net/graph ids
(show note source tval pnet pnet1)

(save eset.txt C eset)
(save log.txt C log)

**** save net of type <nettype> with id <pname> in <filename>
(save <filename> C entry tval <nettype> <pname>)

**** glycan debug
(g2dexe graphics2d  (apply setGlycanLabelsKB "RKB"))

(loadg2dlib graphics2d ../../PLALib/G2D/listGlycans.lsp)
(g2dexe graphics2d (apply exportGlycanIds "RKB"  "GlycanIds.txt"))
(g2dexe graphics2d (define badG (apply glycanIdCheck "RKB")))
(g2dexe graphics2d (invoke java.lang.System.err "println" (concat "badG " badG)))

(g2dexe graphics2d  (seq (define rkb (fetch "RKB") ) (invoke java.lang.System.err "println" rkb)))
(g2dexe graphics2d (seq (define jkb (getAttr rkb "jkb") ) (invoke java.lang.System.err "println" jkb)))
(g2dexe graphics2d (invoke java.lang.System.err "println" (getAttr jkb "componentInfoSpec")))
