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Lifeware
biocham
Commits
20c18df4
Commit
20c18df4
authored
Oct 19, 2015
by
Thierry Martinez
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parent
c117f67e
Changes
6
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6 changed files
with
48 additions
and
13 deletions
+48
-13
doc.pl
doc.pl
+7
-5
graph_editor.pl
graph_editor.pl
+21
-0
install-macos.sh
install-macos.sh
+1
-1
numerical_simulation.pl
numerical_simulation.pl
+7
-3
ode.pl
ode.pl
+10
-1
plot.pl
plot.pl
+2
-3
No files found.
doc.pl
View file @
20c18df4
...
...
@@ -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
).
...
...
@@ -835,6 +835,10 @@ write_command(begin, enumerate, Doc) :-
nb_setval
(
opened_li
,
false
),
write
(
Doc
,
'<ol>'
).
write_command
(
begin
,
example
,
Doc
)
:-
!,
write
(
Doc
,
'</div><div class="example"><div><strong>Example.</strong> '
).
write_command
(
item
,
Argument
,
Doc
)
:-
!,
close_opened_li
(
Doc
),
...
...
@@ -852,11 +856,9 @@ write_command(end, enumerate, Doc) :-
close_opened_li
(
Doc
),
write
(
Doc
,
'</ol>'
).
write_command
(
example
,
Argument
,
Doc
)
:-
write_command
(
end
,
example
,
Doc
)
:-
!,
write
(
Doc
,
'</div><div><strong>Example.</strong> '
),
atom_chars
(
Argument
,
ArgumentChars
),
write_doc_chars
(
ArgumentChars
,
Doc
).
write
(
Doc
,
'</div></div><div>'
).
write_command
(
Command
,
_Argument
,
_Doc
)
:-
throw
(
error
(
unknown_command
(
Command
))).
...
...
graph_editor.pl
0 → 100644
View file @
20c18df4
:-
module
(
graph_editor
,
[
new_graph
/
0
,
delete_graph
/
1
,
set_graph_name
/
1
,
list_graphs
/
0
,
select_graph
/
1
,
dot
/
0
,
export_dot
/
1
,
add_vertex
/
1
,
delete_vertex
/
1
,
add_attribute
/
2
,
delete_attribute
/
2
,
add_edge
/
1
,
delete_edge
/
1
,
list_edges
/
2
]
).
:-
devdoc
(
''
).
install-macos.sh
View file @
20c18df4
#!/bin/sh
brew
install
swi-prolog gsl libsbml
brew
install
swi-prolog gsl libsbml
gnuplot
numerical_simulation.pl
View file @
20c18df4
...
...
@@ -9,14 +9,18 @@
numerical_simulation
:-
biocham_command
,
doc
(
'performs a numerical simulation up to 20s.'
),
doc
(
'
performs a numerical simulation up to 20s.
\\begin{example}
'
),
biocham_silent
(
clear_model
),
biocham
(
a
=>
b
),
biocham
(
present
(
a
)),
biocham
(
list_reactions
),
biocham
(
list_ODE
),
biocham
(
numerical_simulation
),
biocham
(
plot
),
doc
(
'
\\end{example}
'
),
numerical_simulation
(
20
).
...
...
ode.pl
View file @
20c18df4
...
...
@@ -12,7 +12,16 @@ list_ODE :-
biocham_command
,
doc
(
'
returns the set of ordinary differential equations
and initial concentrations (one line per molecule).'
),
and initial concentrations (one line per molecule).
\\begin{example}
'
),
biocham_silent
(
clear_model
),
biocham
(
a
=>
b
),
biocham
(
present
(
a
)),
biocham
(
list_ODE
),
doc
(
'
\\end{example}
'
),
compute_ode
,
print_ode
.
...
...
plot.pl
View file @
20c18df4
...
...
@@ -4,7 +4,7 @@
plot
/
0
,
set_plot_driver
/
1
,
gnu_plot
/
0
,
plot_png
/
0
,
gnu_
plot_png
/
0
,
export_plot
/
1
,
export_plot_to_png
/
1
]
...
...
@@ -13,7 +13,6 @@
plot
:-
biocham_command
,
doc
(
'plots the current trace.'
),
doc
(
'\\example'
),
get_plot_driver
(
Driver
),
Driver
.
...
...
@@ -31,7 +30,7 @@ gnu_plot :-
execute_plot
([
'-persist'
,
'plot.plot'
]).
plot_png
:-
gnu_
plot_png
:-
count
(
plot_png
,
Index
),
format
(
atom
(
Filename
),
'plot~d.png'
,
[
Index
]),
export_plot_to_png
(
Filename
),
...
...
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