(show note ruleRanks tval pnet pnet1)



(createDefSorts JSONB/sorts.json ALLOPS)


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


(savePNet pnet3 sos1subnet sos1subnet.json)

*** one dishnet
(mkNSaveDishNet RKB DishNets rasDish)

*** the allDish dishnet
(mkNSaveAllDish RKB DishNets)

*** a list of dishnets
(mkNSaveDishNets RKB DishNets rasDish tgfaDish)

(Dishes2Json RKB QQQ)

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

(reset control)
(reset wait4s)

**** restore maudes state
(graphics2d OK)
(iop_remote_actor OK)

**** getting info from Maude
**** showing bits
(show notes gval graph1)
(show note selections gval graph2)
(show entry gval graph1)
(show val gval graph1)

(show note usedLocNames qval occmap RKB)

**** also for gval gname >> tval tname <extra tags>

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

**** ask g2d evalute an expression
(g2dexe graphics2d (invoke java.lang.System.err "println" (getAttr (getAttr (fetch "RKB") "jkb") "componentInfoSpec")))


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

**** saving something
(save rasDish-net1.txt C entry tval pnet pnet1)
(save EgfDish.txt C entry gval graph5)

**** save all entries in eset.txt
(save eset.txt C eset)


*************** testing jkb

**** initialize viewer kb
(show notes qval RKB)
(createDefBasicJKB JSONB RKB LOCATIONOPS MODIFICATIONOPS PROTEINOPS CHEMICALOPS)


(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")))

(g2dexe graphics2d (apply initJKB "RKB"))

(g2dexe graphics2d (apply loadbasicjkb "RKB" "JSONB"))


*** needed while Maude is in control of nids
(g2dexe graphics2d  (apply fixNids "RKB"))

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

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

**** 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))))
