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Commit e493dd5a authored by eliott suits's avatar eliott suits
Browse files

added examples

parent 94a3cf15
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% Exemples of the search reductions commands with the Circadian clock models
search_reduction('BIOMD0000000145.xml', 'BIOMD0000000117.xml').
% reduction without restriction finds a result
search_reduction_rest('BIOMD0000000145.xml', 'BIOMD0000000117.xml', ['IP3' -> 'z', 'Ca_ER' -> 'deleted']).
% with some specific restriction, doesn't
\ No newline at end of file
% Exemples of the search reductions commands with the Circadian clock models
search_reduction('BIOMD0000000022.xml', 'BIOMD0000000170.xml').
% reduction without merge restriction finds a result
search_reduction_merge('BIOMD0000000022.xml', 'BIOMD0000000170.xml').
% with merge restriction, doesn't
\ No newline at end of file
......@@ -3,9 +3,9 @@
[
% Public API
search_reduction/2,
search_reduction/3,
search_reduction_rest/3,
search_reduction_merge/2,
search_reduction_merge/3
search_reduction_merge_rest/3
]
).
......@@ -336,7 +336,7 @@ write_morph([X|Tail], G1, G2, I) :-
write_morph(Tail, G1, G2, I1).
run_glucose(Filename) :-
process_create('./modules/glucose/glucose-syrup/simp/glucose', ['-verb=0',Filename, '/tmp/out.sat'], [process(Id)]),
process_create('/usr/bin/glucose', ['-verb=0',Filename, '/tmp/out.sat'], [process(Id)]),
catch(call_with_time_limit(1800,wait(Id,_)), _, (process_kill(Id), write('\ntimed out 30min\n'))).
......@@ -429,22 +429,17 @@ constraints(G1, G2, [(Label1 -> Label2)|T], Stream) :-
search_reduction(FileName1, FileName2, 'labels') :-
biocham_command,
(get_graphs_infos(FileName1, FileName2, G1, G2),
once(search_sepi(G1, G2, Stream)),
once(label_constraints(G1, G2, Stream)),
close(Stream),
solve_sat(G1, G2)); write('no sepi found'), !.
search_reduction(FileName1, FileName2, Restriction_list) :-
search_reduction_rest(FileName1, FileName2, Restriction_list) :-
biocham_command,
(get_graphs_infos(FileName1, FileName2, G1, G2),
once(search_sepi(G1, G2, Stream)),
once(constraints(G1, G2, Restriction_list, Stream)),
close(Stream),
solve_sat(G1, G2)); write('no sepi found'), !.
search_reduction(_, _, _) :-
solve_sat(G1, G2); write('no sepi found')), !.
search_reduction_rest(_, _, _) :-
format('invalid option~n').
search_reduction(FileName1, FileName2) :-
biocham_command,
doc('checks whether there exists one model reduction from a first
......@@ -458,18 +453,19 @@ search_reduction_merge(FileName1, FileName2) :-
biocham_command,
doc('checks whether there exists one model reduction from a first
Biocham model to a second model,
and returns the first model reduction found, as a description of a morphisme from the first model to the second. The merge operation in the model reduction is restricted to two nodes, our a chain of nodes, sharing at least one neigbour.'),
and returns the first model reduction found, as a description of a morphisme from the first model to the second. The merge operation in the model reduction is restricted to two nodes, our a chain of nodes, sharing at least one neigbour. As in the search_reduction command a list of restriction can be added'),
(get_graphs_infos(FileName1, FileName2, G1, G2),
once(search_sepi_merge(G1, G2, Stream)), close(Stream),
solve_sat(G1, G2); write('no sepi found\n')), !.
search_reduction_merge(FileName1, FileName2, Restriction_list) :-
search_reduction_merge_rest(FileName1, FileName2, Restriction_list) :-
biocham_command,
(get_graphs_infos(FileName1, FileName2, G1, G2),
once(search_sepi_merge(G1, G2, Stream)),
once(constraints(G1, G2, Restriction_list, Stream)),
close(Stream),
solve_sat(G1, G2); write('no sepi found\n')), !.
search_reduction_merge(_, _, _) :-
search_reduction_merge_rest(_, _, _) :-
format('invalid option~n').
......
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