% testing for my old version of selection -- for the consulted files, I only commented out :-['source/hypothesisSelection_domainSpecific.pl'].

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Load in build-in libraries
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

:-use_module(library(lists)).
:-use_module(library(terms)).
:-use_module(library(ordsets)).
:-use_module(library(rbtrees)).
:-use_module(library(random)).
:-use_module(library(apply_macros)).


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%  mc-TopLog
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
:-['source/settings.pl'].

:-['source/genEIs_T.pl']. %_multiE
:-['source/topTheory_varConnection.pl'].

%:-['source/genTmE.pl'].
%:-['source/crossProduct_allEx.pl'].

:-['source/nonGroundHBuilder.pl'].

:-['source/covering.pl'].
%:-['source/covering_syngenta_1.pl']. % used before
%:-['source/multiECovering.pl'].

%:-['source/countingChoosing_temp.pl']. %countingChoosing_onlyCounting
%:-['source/allEITs_BayesianCounting.pl'].
%:-['source/bayes_syngenta.pl'].
%:-['source/countTheory.pl']. %
:-['source/insertTheories/decomposed_intoCla_outputed.pl']. 
%:-['source/insertTheories/decomposed_positionID.pl']. %decomposed_intoCla.pl
%:-['source/likelihood_posterial.pl'].

%:-['source/score/scoreCla_GE_BOTHTimeMutant_constrainted.pl']. %
%:-['source/score/scoreCla_GE_Time_Mutant_constrainted.pl'].  %scoreCla_GE %shared_NoLength %scoreTheory_GE_multivariate
%:-['source/score/shared_NoLength.pl'].
%:-['source/score/scoreTheory_GE_multivariate.pl'].

:-['source/cross_validation.pl']. % _temp
:-['source/exProcess.pl'].
:-['source/utilities.pl'].
:-['source/programTransform.pl']. % this one haven't been 


:-['source/cross_product_thretholdPruning.pl'].
:-['source/hypothesisSelection_preprocssing.pl'].
%:-['source/hypothesisSelection_domainSpecific.pl'].
%:-['source/treeConstruction/hypothesisSelection.pl'].

:-['source/treeConstruction/coverageNonSorted_fluxRecord.pl']. % coverageSorted_fluxRecord %_beamSearch
%:-['source/treeConstruction/differentDescriptionLength/hypothesisSelection_groupingChoosing_keepPreSelection_FluxPassing.pl']. 	%hypothesisSelection_noEIs_combineCheck	
%hypothesisSelection_groupingChoosing_noRecordForCombineAndCompeting
:-['source/treeConstruction/differentDescriptionLength/hypothesisSelection_group_ScoreBased.pl']. %hypothesisSelection_groupingChoosing_keepPreSelection_FluxPassing_beamSearch_EIsubsetIgnored %hypothesisSelection_groupingChoosing_keepPreSelection_FluxPassing_beamSearch_fewRecord
%:-['source/treeConstruction/differentDescriptionLength/hypothesisSelection_groupingChoosing_keepPreSelection_FluxPassing_beamSearch_fewRecord.pl'].

%:-['source/treeConstruction/draw.pl']. 
:-['source/claIndex.pl']. 


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%  Data 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% !!!!! remember to change the retract in 'covering.pl'
%:-['artificialData/bioNetwork/inoue/ex'].
%:-['artificialData/bioNetwork/metalog/hyEx'].
%:-['artificialData/bioNetwork/ecRule/ecClass1Ex'].
%:-['artificialData/animal/ex'].
%:-['artificialData/grammar/grammar'].
%:-['artificialData/bioNetwork/reactionReconstruction/ex'].
%:-['artificialData/odd_even/ex'].
%:-['artificialData/tomato/tomato_learningData/ex'].
%:-['artificialData/metalog/hyEx'].
:-['artificialData/tomato/tomato_data.pl']. 
%:-['artificialData/tomato/archive/11_30/tomato_data.pl']. 
%:-['artificialData/cancer/cancer_data.pl']. 
%:-['artificialData/hexose/hexose_data.pl']. 
%:-['artificialData/rsToy/candidateH0.pl'].
%:-['artificialData/toy_example.pl'].

%:-['artificialData/familyTree/family.pl']. 
%:-['artificialData/eventCalculus/data.pl']. 



:- ['close_world_assumption/cwa.pl'].
:- ['claID_mapping'].
:- ['finalH.pl'].

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Output Version Information
mcTopLog_version(1).
mcTopLog_manual('http://www.doc.ic.ac.uk/~dl308/MC-Toplog/user_manual.html').

versionInfo:-
	nl, nl,
	write('MC-TopLog Version '), 
	mcTopLog_version(Version), write(Version), nl,
	mcTopLog_manual(Man),
	write('Manual: '),
	write(Man), nl, nl.

% arguments to contain test.pl
:- 	yap_flag(argv,[InputFile1,InputFile2]),
  	consult(InputFile2),

	finalH(FinalH_EITIs,FinalH_ClaIDVersion),maplist(claID_mapping,FinalHI,FinalH_ClaIDVersion),tInterpreter(FinalHI,FinalH),
	addT(FinalH,Ref),
	%listing,
	test_examples(TestEIs),
	test(TestEIs,Result),
	removeT(Ref),
	write(Result), write(' ').