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biocham
Commit 4292f8d4 authored by Thierry Martinez's avatar Thierry Martinez
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parents 58458c6d 20c18df4
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Showing with 499 additions and 244 deletions
Makefile
View file @ 4292f8d4
......@@ -10,8 +10,8 @@ biocham: $(MODULES) toc.org Makefile
@echo $(MODULES)
swipl -o biocham --goal=start --toplevel=toplevel -c $(MODULES)
biocham_debug: $(MODULES) toc.org Makefile
swipl -o biocham_debug --goal=initialize -c $(MODULES)
biocham_debug: $(MODULES) $(TEST_MODULES) toc.org Makefile
swipl -o biocham_debug --goal=initialize -c $(MODULES) $(TEST_MODULES)
tests: biocham_tests
./biocham_tests
......
aliases.pl
View file @ 4292f8d4
......@@ -29,7 +29,9 @@ add_equivalence_class_list(EquivalenceClassList) :-
true
;
list_to_equals(EquivalenceClassList, EquivalenceClass),
add_item(alias, EquivalenceClassList, alias(EquivalenceClass)),
add_item([
kind: alias, key: EquivalenceClassList, item: alias(EquivalenceClass)
]),
simplify_all_reactions
).
......@@ -81,7 +83,7 @@ canonical(Object, Canonical) :-
list_aliases :-
biocham_command,
doc('shows the values of all known aliases.'),
list_items([model: current_model, kind: alias]).
list_items([kind: alias]).
delete_alias(Object) :-
......
aliases.plt
View file @ 4292f8d4
......@@ -6,6 +6,6 @@ test('alias', [true(Reactions == [2 * a => c])]) :-
clear_model,
add_reaction(a + b => c),
command(alias(a = b)),
all_items([model: current_model, kind: reaction], Reactions).
all_items([kind: reaction], Reactions).
:- end_tests(aliases).
conservation_laws.pl
View file @ 4292f8d4
......@@ -31,7 +31,7 @@ add_conservation(Conservation) :-
a warning.'
),
solution_to_conservation(Conservation, C),
add_item(conservation, [], Conservation, Id),
add_item([kind: conservation, item: Conservation, id: Id]),
set_annotation(Id, conservation_list, C).
......
conservation_laws.plt
View file @ 4292f8d4
......@@ -7,14 +7,14 @@
test(
'add_conservation adds a conservation',
[
setup(models:clear_model),
cleanup(models:clear_model),
setup(clear_model),
cleanup(clear_model),
forall(member(Input, ['a-a' + 2*'a', 'b', 'a' + 'b'])),
true(Conservations == [Input])
]
) :-
command(add_conservation(Input)),
all_items([model: current_model, kind: conservation], Conservations).
all_items([kind: conservation], Conservations).
%%% FIXME should test that conservations are properly used for numerical
%%% integration
......@@ -23,31 +23,31 @@ test(
'delete_conservation deletes the correct conservation',
[
setup(set_some_conservations),
cleanup(models:clear_model),
cleanup(clear_model),
true(Conservations == ['a-a'+2*a,'c-c'+2*c])
]
) :-
command(delete_conservation(b-b + 2*b)),
all_items([model: current_model, kind: conservation], Conservations).
all_items([kind: conservation], Conservations).
test(
'delete_conservations deletes all conservations',
[
setup(set_some_conservations),
cleanup(models:clear_model),
cleanup(clear_model),
true(Conservations == [])
]
) :-
command(delete_conservations),
all_items([model: current_model, kind: conservation], Conservations).
all_items([kind: conservation], Conservations).
test(
'list_conservations lists all conservations',
[
setup(set_some_conservations),
cleanup(models:clear_model),
cleanup(clear_model),
true(Conservations ==
'[0] a-a+2*a\n[1] b-b+2*b\n[2] c-c+2*c\n')
]
......@@ -58,8 +58,8 @@ test(
test(
'check_conservations is ok with trivial P-invariants',
[
setup((models:clear_model, set_prolog_flag(verbose, silent))),
cleanup((models:clear_model, set_prolog_flag(verbose, normal)))
setup((clear_model, set_prolog_flag(verbose, silent))),
cleanup((clear_model, set_prolog_flag(verbose, normal)))
]
) :-
command(add_reaction(a => b)),
......@@ -71,8 +71,8 @@ test(
test(
'check_conservations is ok with kinetically conserved moieties',
[
setup((models:clear_model, set_prolog_flag(verbose, silent))),
cleanup((models:clear_model, set_prolog_flag(verbose, normal)))
setup((clear_model, set_prolog_flag(verbose, silent))),
cleanup((clear_model, set_prolog_flag(verbose, normal)))
]
) :-
command(add_reaction(k*[a] for a => b)),
......@@ -84,8 +84,8 @@ test(
test(
'check_conservations is unhappy with non-conserved moieties',
[
setup((models:clear_model, set_prolog_flag(verbose, silent))),
cleanup((models:clear_model, set_prolog_flag(verbose, normal))),
setup((clear_model, set_prolog_flag(verbose, silent))),
cleanup((clear_model, set_prolog_flag(verbose, normal))),
true(Warnings == 1)
]
) :-
......@@ -101,7 +101,7 @@ test(
set_some_conservations :-
models:clear_model,
clear_model,
command(add_conservation(a-a + 2*a)),
command(add_conservation(b-b + 2*b)),
command(add_conservation(c-c + 2*c)).
......
doc.pl
View file @ 4292f8d4
......@@ -36,7 +36,7 @@ biocham_silent(_).
generate_doc :-
set_plot_driver(plot_png),
set_plot_driver(gnu_plot_png),
set_counter(plot_png, 0),
generate_doc(doc),
generate_doc(devdoc).
......@@ -839,6 +839,10 @@ write_command(begin, enumerate, Stream) :-
nb_setval(opened_li, false),
write(Stream, '</div>\n<ol>\n').
write_command(begin, example, Stream) :-
!,
write(Stream, '</div><div class="example"><div><strong>Example.</strong> ').
write_command(item, Argument, Stream) :-
!,
close_opened_li(Stream),
......@@ -856,18 +860,17 @@ write_command(end, enumerate, Stream) :-
close_opened_li(Stream),
write(Stream, '</ol>\n<div>').
write_command(example, Argument, Stream) :-
write_command(end, example, Doc) :-
!,
write(Stream, '</div>\n<div><strong>Example.</strong> '),
write_doc(Stream, Argument).
write(Doc, '</div></div><div>').
write_command(section, Argument, Stream) :-
!,
nb_getval(current_counters, Counters),
length(Counnters, CounterCount),
length(Counters, CounterCount),
SectionLevel is CounterCount + 2,
format(Stream, '</div>\n<h~d>', [SectionLevel]),
write_doc(Stream, Argument)
write_doc(Stream, Argument),
format(Stream, '</h~d>\n<div>', [SectionLevel]).
write_command(Command, _Argument, _Stream) :-
......
graph_editor.pl 0 → 100644
View file @ 4292f8d4
:- module(
graph_editor,
[
new_graph/0,
delete_graph/1,
set_graph_name/1,
list_graphs/0,
select_graph/1,
draw_graph/0,
export_graph/1,
add_vertex/1,
delete_vertex/1,
add_attribute/2,
delete_attribute/2,
list_attributes/1,
edge/1,
add_edge/1,
delete_edge/1,
list_edges/0,
get_current_graph/1
]
).
:- devdoc('\\section{Commands}').
new_graph :-
biocham_command,
doc('Creates a new graph.'),
add_item([kind: graph, key: new_graph, id: Id]),
set_current_graph(Id).
delete_graph(Name) :-
biocham_command,
type(Name, name),
doc('Deletes a graph.'),
delete_items([kind: graph, key: Name]).
set_graph_name(Name) :-
biocham_command,
type(Name, name),
doc('Sets the name of the current graph.'),
get_current_graph(Id),
replace_item(Id, graph, Name, Name).
list_graphs :-
biocham_command,
doc('Lists the graph of the current model.'),
list_items([kind: graph]).
select_graph(Name) :-
biocham_command,
type(Name, name),
doc('Selects a graph'),
find_item([kind: graph, key: Name, id: Id]),
set_current_graph(Id).
draw_graph :-
biocham_command,
doc('').
export_graph(Argument) :-
biocham_command,
type(Argument, type),
doc('').
add_vertex(Name) :-
biocham_command,
type(Name, name),
doc('Adds a vertex to the current graph.'),
get_current_graph(GraphId),
add_item([parent: GraphId, kind: vertex, key: Name]).
delete_vertex(Name) :-
biocham_command,
type(Name, name),
doc('Removes a vertex from the current graph.'),
get_current_graph(GraphId),
delete_item([parent: GraphId, kind: vertex, key: Name]).
add_attribute(Name, Attribute) :-
biocham_command,
type(Name, name),
type(Attribute, name),
doc('Adds an attribute to a vertex.'),
find_vertex(Name, Id),
(
find_item([parent: Id, kind: attribute, key: Attribute])
->
true
;
add_item([parent: Id, kind: attribute, key: Attribute])
).
delete_attribute(Name, Attribute) :-
biocham_command,
type(Name, name),
type(Abbribute, name),
doc('Removes an attribute from a vertex.'),
find_vertex(Name, Id),
delete_item([parent: Id, kind: attribute, key: Attribute]).
list_attributes(Name) :-
biocham_command,
type(Name, name),
doc('List the attributes of a vertex.'),
find_vertex(Name, Id),
list_items([parent: Id, kind: attribute]).
:- grammar(edge).
edge(From -> To) :-
name(From),
name(To).
add_edge(Edge) :-
biocham_command,
type(Edge, edge),
doc('Adds an edge'),
Edge = (From -> To),
find_vertex(From, FromId),
find_vertex(To, ToId),
get_current_graph(GraphId),
add_item([parent: GraphId, kind: edge, key: Edge, id: Id]),
add_dependency(Id, FromId),
add_dependency(Id, ToId).
delete_edge(Edge) :-
biocham_command,
type(Edge, edge),
doc('Deletes an edge'),
get_current_graph(GraphId),
delete_item([parent: GraphId, kind: edge, key: Edge]).
list_edges :-
biocham_command,
doc('Lists the edges of the current graph'),
get_current_graph(GraphId),
list_items([parent: GraphId, kind: edge]).
:- devdoc('\\section{End of commands}').
find_vertex(Name, Id) :-
get_current_graph(GraphId),
find_item([parent: GraphId, kind: vertex, key: Name, id: Id]).
deselect_graph :-
\+ (
item([kind: Graph, id: Id]),
\+ (
(
delete_annotation(Id, selected)
->
true
;
true
)
)
).
set_current_graph(Id) :-
deselect_graph,
set_annotation(Id, selected, selected).
get_current_graph(Id) :-
(
item([kind: Graph, id: Id]),
get_annotation(Id, selected, selected)
->
true
;
throw(error(no_graph_selected))
).
initial_state.pl
View file @ 4292f8d4
......@@ -17,7 +17,7 @@
get_initial_state(Object, State) :-
(
item([model: current_model, kind: initial_state, key: Object, item: Item])
item([kind: initial_state, key: Object, item: Item])
->
(
Item = present(Object)
......@@ -59,7 +59,7 @@ list_initial_state :-
doc('
lists the objects which are present (including their initial concentration)
and absent from the initial state.'),
list_items([model: current_model, kind: initial_state]).
list_items([kind: initial_state]).
clear_initial_state :-
......@@ -67,12 +67,7 @@ clear_initial_state :-
doc('
makes undefined all objects possibly present or absent in the initial
state.'),
\+ (
item([model: current_model, kind: initial_state, id: Id]),
\+ (
delete_item(Id)
)
).
delete_items([kind: initial_state]).
present(ObjectSet) :-
......@@ -109,7 +104,7 @@ set_state(ObjectSet, Object, State) :-
member(Object, ObjectSet),
\+ (
undefined_object(Object),
add_item(initial_state, Object, State)
add_item([kind: initial_state, key: Object, item: State])
)
).
......@@ -130,7 +125,7 @@ undefined(ObjectSet) :-
undefined_object(Object) :-
(
item([model: current_model, kind: initial_state, key: Object, id: Id])
item([kind: initial_state, key: Object, id: Id])
->
delete_item(Id)
;
......@@ -169,4 +164,4 @@ make_absent_not_present :-
defined(Object) :-
once(item([model: current_model, kind: initial_state, key: Object])).
once(item([kind: initial_state, key: Object])).
initial_state.plt
View file @ 4292f8d4
......@@ -8,7 +8,7 @@ test(
) :-
clear_model,
command(present({ a, b })),
all_items([model: current_model, kind: initial_state], InitialState).
all_items([kind: initial_state], InitialState).
test(
'absent',
......@@ -16,7 +16,7 @@ test(
) :-
clear_model,
command(absent({ a, b })),
all_items([model: current_model, kind: initial_state], InitialState).
all_items([kind: initial_state], InitialState).
test(
'undefined',
......@@ -26,7 +26,7 @@ test(
command(present({ a, b, c })),
command(absent({ b, c, e })),
command(undefined({ c, d, e })),
all_items([model: current_model, kind: initial_state], InitialState).
all_items([kind: initial_state], InitialState).
test(
'make_absent_not_present',
......@@ -36,7 +36,7 @@ test(
add_reaction(a => b),
command(present(a)),
make_absent_not_present,
all_items([model: current_model, kind: initial_state], InitialState).
all_items([kind: initial_state], InitialState).
test(
'make_present_not_absent',
......@@ -46,6 +46,6 @@ test(
add_reaction(a => b),
command(absent(a)),
make_present_not_absent,
all_items([model: current_model, kind: initial_state], InitialState).
all_items([kind: initial_state], InitialState).
:- end_tests(initial_state).
install-macos.sh
View file @ 4292f8d4
#!/bin/sh
brew install swi-prolog gsl libsbml
brew install swi-prolog gsl libsbml gnuplot
macros.pl
View file @ 4292f8d4
......@@ -21,7 +21,7 @@ set_macro(MacroList) :-
replace_item(Id, macro, Macro, macro(Macro = Value))
),
error(unknown_item),
add_item(macro, Macro, macro(Macro = Value))
add_item([kind: macro, key: Macro, item: macro(Macro = Value)])
)
)
).
......@@ -31,9 +31,7 @@ show_macro(Macro) :-
biocham_command,
type(Macro, macro),
doc('shows the expression associated to the given macro.'),
find_item(
[model: current_model, kind: macro, key: Macro, item: macro(_ = Expression)]
),
find_item([kind: macro, key: Macro, item: macro(_ = Expression)]),
write(Expression),
nl.
......@@ -41,7 +39,7 @@ show_macro(Macro) :-
list_macros :-
biocham_command,
doc('lists all known macros.'),
list_items([model: current_model, kind: macro]).
list_items([kind: macro]).
delete_macro(MacroSet) :-
......@@ -51,7 +49,6 @@ delete_macro(MacroSet) :-
\+ (
member(Macro, MacroSet),
\+ (
find_item([model: current_model, kind: macro, key: Macro, id: Id]),
delete_item(Id)
delete_item([kind: macro, key: Macro])
)
).
macros.plt
View file @ 4292f8d4
......@@ -9,6 +9,6 @@ test(
clear_model,
command(set_macro(a = 1, b = 2)),
command(set_macro(b = 3)),
all_items([model: current_model, kind: macro], Macros).
all_items([kind: macro], Macros).
:- end_tests(macros).
models.pl
View file @ 4292f8d4
......@@ -2,20 +2,23 @@
models,
[
load/1,
add/1,
load_biocham/1,
add_biocham/1,
new_model/0,
clear_model/0,
get_model_name/1,
get_model_name/2,
set_model_name/1,
list_models/0,
list_current_models/0,
range/1,
ref/1,
select_model/1,
set_model_name/1,
delete/1,
get_model_name/1,
get_model_name/2,
current_models/1,
single_model/1,
add_item/2,
add_item/3,
add_item/4,
add_item/1,
replace_item/4,
set_annotation/3,
get_annotation/3,
......@@ -28,14 +31,12 @@
list_ids/1,
delete_item/1,
delete_items/1,
delete/1,
range/1
add_dependency/2
]
).
:- dynamic(fresh/0).
:- devdoc('\\section{Commands}').
load(InputFile) :-
......@@ -85,6 +86,113 @@ add_biocham(InputFile) :-
add_all('.bc', InputFile).
new_model :-
biocham_command,
doc('opens a new fresh model.'),
new_model(_Id).
clear_model :-
biocham_command,
doc('clears the current model.'),
current_models(CurrentModels),
\+ (
member(Id, CurrentModels),
\+ (
delete_item(Id)
)
).
list_models :-
biocham_command,
doc('lists all open models'),
list_items([parent: top, kind: model]).
list_current_models :-
biocham_command,
doc('lists current models'),
current_models(CurrentModels),
list_ids(CurrentModels).
:- grammar(range).
range(Integer0 - Integer1) :-
integer(Integer0),
integer(Integer1).
range(Integer) :-
integer(Integer).
:- grammar(ref).
ref(Range) :-
list(range, Range).
ref(Name) :-
name(Name).
select_model(RefSet) :-
biocham_command,
type(RefSet, {ref}),
doc('selects some models.'),
findall(
Id,
(
member(Ref, RefSet),
(
list(Ref)
->
ranges_ids(Ref, Ids),
member(Id, Ids)
;
find_item([parent: top, key: Ref, id: Id])
)
),
CurrentModels
),
set_current_models(CurrentModels).
set_model_name(Name) :-
biocham_command,
type(Name, name),
doc('changes the current model name.'),
single_model(Id),
replace_item(Id, model, Name, Name).
delete(Indexes) :-
biocham_command(*),
type(Indexes, '*'([range])),
doc('deletes the listed elements from the model.'),
indexes_ids(Indexes, Ids),
\+ (
member(Id, Ids),
\+ (
delete_item(Id)
)
).
:- dynamic(fresh/0).
get_model_name(Name) :-
single_model(Id),
get_model_name(Id, Name).
get_model_name(Id, Name) :-
find_item([parent: top, id: Id, item: Name]).
load_all(Suffix, InputFile) :-
findall(
Id,
......@@ -184,12 +292,6 @@ set_current_models(Models) :-
nb_setval(current_models, Models).
new_model :-
biocham_command,
doc('opens a new fresh model.'),
new_model(_Id).
new_model(Id) :-
(
fresh,
......@@ -197,87 +299,12 @@ new_model(Id) :-
->
true
;
create_item_id(Id),
add_item(top, model, new_model, new_model, Id),
add_item([parent: top, kind: model, key: new_model, id: Id]),
set_current_models([Id]),
assertz(fresh)
).
list_models :-
biocham_command,
doc('lists all open models'),
list_items([model: top, kind: model]).
list_current_models :-
biocham_command,
doc('lists current models'),
current_models(CurrentModels),
list_ids(CurrentModels).
:- grammar(ref).
ref(Range) :-
list(range, Range).
ref(Name) :-
name(Name).
select_model(RefSet) :-
biocham_command,
type(RefSet, {ref}),
doc('selects some models.'),
findall(
Id,
(
member(Ref, RefSet),
(
list(Ref)
->
ranges_ids(Ref, Ids),
member(Id, Ids)
;
find_item([model: top, key: Ref, id: Id])
)
),
CurrentModels
),
set_current_models(CurrentModels).
clear_model :-
biocham_command,
doc('clears the current model.'),
current_models(CurrentModels),
\+ (
member(Id, CurrentModels),