maxScore(EI,EI-TIsMaxScore):- findall(Score,candidateH_score(EI,TI,EIList1,Score),Scores), % gather a list first, TI-Score max(Scores,-1000000,MaxScore), findall(TI2,candidateH_score(EI,TI2,EIList2,MaxScore),TIsMaxScore), write(EI), write(' maximum TI are '), write(TIsMaxScore),nl. trainANDcount(PosEIs,FinalTI):- tell('tomato_candidateH_constrainIncorporated1.pl'), %tell('grammar_candidateH.pl'), genAll(PosEIs,AllTs,TotalNum),%genAll_EIsigned(PosEIs,AllTs,TotalNum), write('%Total is '), write(TotalNum),nl, %print_list(AllTs),nl, told, consult('tomato_candidateH_constrainIncorporated1.pl'), %consult('grammar_candidateH.pl'), rb_new(Tree0), insertTheories(PosEIs,Tree0,Tree), % insertTheories(AllTs,Tree0,Tree) *** be careful about the function you are using rb_visit(Tree,Clas), write('/******************Cla Counted********************/'), print_list(Clas),nl,nl,nl, selectlist(claLengthCheck, Clas, NonOneClas0), print_list(NonOneClas0),nl, maplist(extractCla,NonOneClas0,NonOneClas), FinalTI=NonOneClas. extractCla(NonOneClas-EIList,NonOneClas). claLengthCheck([rs-{RID,enzymeLimiting,Change,Time}]-EIList):- length(EIList,K),K>1. /*consult('tomatoCountedResult.pl'), maplist(maxScore,PosEIs,EIsTIsMaxScore), write('*** Here is the input for cross product'), write(EIsTIsMaxScore), % nothing was left because of the constraint, crossProductlyCombine_and_check(EIsTIsMaxScore,[[]],FinalTIs), write(FinalTIs), print_list(FinalTIs), told, */ /* %tell('tomato_countingResult.txt'),rb_visit(Tree,Ts), print_list(Ts),nl, %maplist(scoreByCountingSharedExNum,Ts,ScoredHs0), % score Hs %sort(ScoredHs0,ScoredHs), %nl,write('--------New Round--------'),nl, %print_list(ScoredHs), %checklist(claDetail,ScoredHs), tell('tomatoDAG.pl'), forAll(candidateH0(EI_any,TI_any,T),assertOneHypothesizedTheory(T,Tree,start,EI_any-TI_any)), listing, told. */ scoreByCountingSharedExNum(RS-ExList,ExNum-RS-ExList):- length(ExList,ExNum). %1-100-([reaction_state-{100,'5426','1.5.3.11',activated,'RIN_L'}]-[365]) % agreed with GE? which pathway. claDetail(ScoredCla):- ScoredCla=Coverage-[rs-{ReactionID,LimitingType,HypothesizedState,Time}]-CoveredEIs, write(Coverage-[rs-{ReactionID,LimitingType,HypothesizedState,Time}]), checkItsGEData(ReactionID,HypothesizedState,Time,Score_GE), write(Score_GE), ((member_of(ReactionID,PathwayID,'IMPD'),concept_name(PathwayID,PathwayName,true))-> write('(Pathway '), write(PathwayName), write(') '); write(' No pathway annotated') ), nl. /* writeReaction(ReactionID), maplist(compountNameMaping,CoveredEIs,CoveredEINames), nl, write('Covered Metabolites '),writeq(CoveredEINames), nl,nl. */ checkItsGEData(ReactionID,HypothesizedState,Time,Score_GE):- catalyzed_by_ECclass(ReactionID,EC_Number),!, write(EC_Number), (concentration_enzClass(EC_Number,GEChange,Time)-> (propotional(HypothesizedState,GEChange)-> Score_GE=agreed;%write('Yes, agreed'),nl; % whatever up/down/no_change, as long as they agree with each other Score_GE=disagreed %,write('No, disagreed'),nl ); Score_GE=notMeasured ). checkItsGEData(ReactionID,HypothesizedState,Time,notAnnotated). /* claDetail(ScoredCla):- nl,write(ScoredCla), ScoredCla=Coverage-Score-([reaction_state-{Sign,ReactionID,EC,Change,Time}]-CoveredEIs), writeReaction(ReactionID), maplist(compountNameMaping,CoveredEIs,CoveredEINames), nl, write('Covered Metabolites '),writeq(CoveredEINames), nl,nl. */ compountNameMaping(EI,Name-Change):- ex0(EI,concentration(Name,Change,Time),1). %sort(Ts,Ts1),print_list(Ts1),nl, % this is just to check the result /* sort(PosEIs,PosEIs1), % the reason to sort it is to facilitate the subtract later %FinalTI=Ts. chooseH(PosEIs1,Ts,[],FinalTI), write('check here'),write(FinalTI), testPoint(1), print_list(FinalTI),nl. */ testPoint(1). chooseH([],_,FinalH,FinalH):- !. chooseH(UncoverExs,Hs,HSofar,FinalH):- maplist(scoreCountedT,Hs,ScoredHs0), % score Hs sort(ScoredHs0,ScoredHs), nl,write('--------New Round--------'),nl, print_list(ScoredHs), getLast(ScoredHs,RestHs,Coverage-Score-(Cla-ExList)), % check when you record portray_clause(Coverage-Score-(Cla-ExList)),nl, ExList=CoveredExs0, %extractCoveredEx(ExList,CoveredExs0), sort(CoveredExs0,CoveredExs), %ordered setsubstract ord_subtract(UncoverExs,CoveredExs,NewUncoverExs), testPoint(1),write(NewUncoverExs),nl, updataHcovergae(CoveredExs0,RestHs,NewRestHs), % remove covered chooseH(NewUncoverExs,NewRestHs,[Cla|HSofar],FinalH). getLast([LastEle],[],LastEle). getLast([Coverage-Score-T|List],[T|Rest],LastEle):- getLast(List,Rest,LastEle). extractCoveredEx(ExList,CoveredExs):- maplist(extractEI,ExList,CoveredExs). extractEI({EI,Length},EI). %updataHcovergae(CoveredExs0,RestHs,NewRestHs):- % maplist(updateEIList(CoveredExs0),RestHs,NewRestHs). updataHcovergae(CoveredExs,[],[]). updataHcovergae(CoveredExs,[Cla-LengthedEI|Hs],NewHs):- updataHcovergae(CoveredExs,Hs,HsSoFar), updateEIList(CoveredExs,Cla-LengthedEI,Cla-NewLengthedEI), (NewLengthedEI==[] -> NewHs=HsSoFar; NewHs=[Cla-NewLengthedEI|HsSoFar] ). updateEIList(CoveredExs,[enzyme_state-{Sign,EC_Number,Change}]-LengthedEI,[enzyme_state-{Sign,EC_Number,Change}]-NewLengthedEI):- removeCoveredEx(CoveredExs,LengthedEI,[],NewLengthedEI). /* removeCoveredEx(CoveredExs,[],Final,Final). removeCoveredEx(CoveredExs,[{EI,ExNum}|Rest],Sofar,Final):- member(EI,CoveredExs), !, removeCoveredEx(CoveredExs,Rest,Sofar,Final). removeCoveredEx(CoveredExs,[{EI,ExNum}|Rest],Sofar,Final):- removeCoveredEx(CoveredExs,Rest,[{EI,ExNum}|Sofar],Final). % I can't remember why this one is retained removeCoveredEx([],_,Final,Final):- !. removeCoveredEx(CoveredExs,[],Final,Final):- !. removeCoveredEx(CoveredExs,[{EI,ExNum}|Rest],Sofar,Final):- append(Pre,[EI|Post],CoveredExs), !, %member(EI,CoveredExs), removeCoveredEx(Post,Rest,Sofar,Final). removeCoveredEx(CoveredExs,[{EI,ExNum}|Rest],Sofar,Final):- removeCoveredEx(CoveredExs,Rest,[{EI,ExNum}|Sofar],Final). */ removeCoveredEx(CoveredExs,[],Final,Final). removeCoveredEx(CoveredExs,[EI|Rest],Sofar,Final):- member(EI,CoveredExs), !, removeCoveredEx(CoveredExs,Rest,Sofar,Final). removeCoveredEx(CoveredExs,[EI|Rest],Sofar,Final):- removeCoveredEx(CoveredExs,Rest,[EI|Sofar],Final).