elvis/ReactionSystems
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Refactoring names of structures, removing useless functions

Browse Source
This commit is contained in:
elvis
2025-07-09 16:12:22 +02:00
parent 6b0a825210
commit 1b9c0ce44b
10 changed files with 90 additions and 120 deletions
Download Patch File Download Diff File Expand all files Collapse all files

8
src/examples.rs
View File

@ -188,8 +188,8 @@ pub fn limit_freq() -> std::io::Result<()> {
let (_, sets) = read_file(&mut translator, path, parser_experiment)?;
let res = match frequency::limit_frequency(&sets,
system.get_reaction_rules(),
system.get_available_entities()) {
&system.reaction_rules,
&system.available_entities) {
Some(e) => e,
None => {return Ok(());}
};
@ -216,8 +216,8 @@ pub fn fast_freq() -> std::io::Result<()> {
let (weights, sets) = read_file(&mut translator, path, parser_experiment)?;
let res = match frequency::fast_frequency(&sets,
system.get_reaction_rules(),
system.get_available_entities(),
&system.reaction_rules,
&system.available_entities,
&weights) {
Some(e) => e,
None => {return Ok(());}

2
src/rsprocess/classical.rs
View File

@ -16,7 +16,7 @@ pub fn compute_step<'a>(
reaction: &'a RSreaction
) -> Option<&'a RSset> {
if reaction.enabled(current_state) {
Some(reaction.products())
Some(&reaction.products)
} else {
None
}

8
src/rsprocess/graph.rs
View File

@ -86,7 +86,7 @@ impl GraphMapNodesTy {
format!("{}",
translator::RSsetDisplay::from(
&translator,
node.get_available_entities())
&node.available_entities)
)
)
},
@ -94,7 +94,7 @@ impl GraphMapNodesTy {
Box::new(
move |_, node: &RSsystem| {
let masked_entities =
node.get_available_entities()
node.available_entities
.intersection(&mask);
format!("{}",
translator::RSsetDisplay::from(
@ -110,7 +110,7 @@ impl GraphMapNodesTy {
format!("{}",
translator::RSprocessDisplay::from(
&translator,
node.get_context_process())
&node.context_process)
)
)
},
@ -373,7 +373,7 @@ pub fn default_node_formatter(
Box::new(
move |_g, n|
String::from(
match original_graph.node_weight(n.0).unwrap().get_context_process()
match original_graph.node_weight(n.0).unwrap().context_process
{
RSprocess::Nill =>
", fillcolor=white",

24
src/rsprocess/perpetual.rs
View File

@ -115,9 +115,9 @@ pub fn lollipops_decomposed(
// see lollipop
pub fn lollipops(system: RSsystem) -> Vec<(Vec<RSset>, Vec<RSset>)> {
lollipops_decomposed(
system.get_delta(),
system.get_reaction_rules(),
system.get_available_entities(),
&system.delta,
&system.reaction_rules,
&system.available_entities,
)
}
@ -125,12 +125,12 @@ pub fn lollipops(system: RSsystem) -> Vec<(Vec<RSset>, Vec<RSset>)> {
pub fn lollipops_only_loop(system: RSsystem) -> Vec<Vec<RSset>> {
// FIXME: i think we are only interested in "x", not all symbols that
// satisfy X = pre(Q, rec(X))
let filtered = system.get_delta().iter().filter_map(filter_delta);
let filtered = system.delta.iter().filter_map(filter_delta);
let find_loop_fn = |q| {
find_only_loop(
system.get_reaction_rules(),
system.get_available_entities().clone(),
&system.reaction_rules,
system.available_entities.clone(),
q,
)
};
@ -226,9 +226,9 @@ pub fn lollipops_named(
symb: IdType
) -> Option<(Vec<RSset>, Vec<RSset>)> {
lollipops_decomposed_named(
system.get_delta(),
system.get_reaction_rules(),
system.get_available_entities(),
&system.delta,
&system.reaction_rules,
&system.available_entities,
symb,
)
}
@ -239,15 +239,15 @@ pub fn lollipops_only_loop_named(
symb: IdType
) -> Option<Vec<RSset>> {
let filtered = system
.get_delta()
.delta
.iter()
.filter_map(|x| filter_delta_named(x, &symb))
.next();
let find_loop_fn = |q| {
find_only_loop(
system.get_reaction_rules(),
system.get_available_entities().clone(),
&system.reaction_rules,
system.available_entities.clone(),
q,
)
};

30
src/rsprocess/statistics.rs
View File

@ -13,17 +13,17 @@ pub fn of_RSsystem<'a>(translator: &'a Translator, system: &'a RSsystem) -> Stri
);
result.push_str(&format!(
"the initial state has {} entities:\n",
system.get_available_entities().len()
system.available_entities.len()
));
result.push_str(&format!(
"{}\n",
translator::RSsetDisplay::from(translator, system.get_available_entities())
translator::RSsetDisplay::from(translator, &system.available_entities)
));
let reactants = system
.get_reaction_rules()
.reaction_rules
.iter()
.fold(RSset::new(), |acc, new| acc.union(new.reactants()));
.fold(RSset::new(), |acc, new| acc.union(&new.reactants));
result.push_str(&format!(
"The reactants are {}:\n{}\n",
reactants.len(),
@ -31,9 +31,9 @@ pub fn of_RSsystem<'a>(translator: &'a Translator, system: &'a RSsystem) -> Stri
));
let inhibitors = system
.get_reaction_rules()
.reaction_rules
.iter()
.fold(RSset::new(), |acc, new| acc.union(new.inihibitors()));
.fold(RSset::new(), |acc, new| acc.union(&new.inihibitors));
result.push_str(&format!(
"The inhibitors are {}:\n{}\n",
inhibitors.len(),
@ -41,9 +41,9 @@ pub fn of_RSsystem<'a>(translator: &'a Translator, system: &'a RSsystem) -> Stri
));
let products = system
.get_reaction_rules()
.reaction_rules
.iter()
.fold(RSset::new(), |acc, new| acc.union(new.products()));
.fold(RSset::new(), |acc, new| acc.union(&new.products));
result.push_str(&format!(
"The products are {}:\n{}\n",
products.len(),
@ -57,14 +57,14 @@ pub fn of_RSsystem<'a>(translator: &'a Translator, system: &'a RSsystem) -> Stri
translator::RSsetDisplay::from(translator, &total)
));
let entities_env = system.get_delta().all_elements();
let entities_env = system.delta.all_elements();
result.push_str(&format!(
"The environment involves {} entities:\n{}\n",
entities_env.len(),
translator::RSsetDisplay::from(translator, &entities_env)
));
let entities_context = system.get_context_process().all_elements();
let entities_context = system.context_process.all_elements();
result.push_str(&format!(
"The context involves {} entities:\n{}\n",
entities_context.len(),
@ -74,7 +74,7 @@ pub fn of_RSsystem<'a>(translator: &'a Translator, system: &'a RSsystem) -> Stri
let entities_all = total
.union(&entities_env)
.union(&entities_context)
.union(system.get_available_entities());
.union(&system.available_entities);
result.push_str(&format!(
"The whole RS involves {} entities:\n{}\n",
@ -83,7 +83,7 @@ pub fn of_RSsystem<'a>(translator: &'a Translator, system: &'a RSsystem) -> Stri
));
let possible_e = products
.union(system.get_available_entities())
.union(&system.available_entities)
.union(&entities_context);
let missing_e = reactants.subtraction(&possible_e);
result.push_str(&format!(
@ -101,14 +101,14 @@ pub fn of_RSsystem<'a>(translator: &'a Translator, system: &'a RSsystem) -> Stri
result.push_str(&format!(
"There are {} reactions in total.\n",
system.get_reaction_rules().len()
system.reaction_rules.len()
));
let mut admissible_reactions = vec![];
let mut nonadmissible_reactions = vec![];
for reaction in system.get_reaction_rules().iter() {
if reaction.reactants().is_disjoint(&missing_e) {
for reaction in system.reaction_rules.iter() {
if reaction.reactants.is_disjoint(&missing_e) {
admissible_reactions.push(reaction);
} else {
nonadmissible_reactions.push(reaction);

84
src/rsprocess/structure.rs
View File

@ -10,7 +10,7 @@ use std::rc::Rc;
// -----------------------------------------------------------------------------
#[derive(Clone, Debug, PartialEq, Eq, PartialOrd, Ord, Hash)]
pub struct RSset {
identifiers: BTreeSet<IdType>,
pub identifiers: BTreeSet<IdType>,
}
impl<const N: usize> From<[IdType; N]> for RSset {
@ -89,10 +89,6 @@ impl RSset {
RSset { identifiers: res }
}
pub fn set(&self) -> &BTreeSet<IdType> {
&self.identifiers
}
pub fn iter(&self) -> std::collections::btree_set::Iter<'_, IdType> {
self.identifiers.iter()
}
@ -134,9 +130,9 @@ impl IntoIterator for RSset {
// -----------------------------------------------------------------------------
#[derive(Clone, Debug)]
pub struct RSreaction {
reactants: RSset,
inihibitors: RSset,
products: RSset,
pub reactants: RSset,
pub inihibitors: RSset,
pub products: RSset,
}
impl RSreaction {
@ -161,22 +157,6 @@ impl RSreaction {
self.reactants.is_subset(current_state)
&& self.inihibitors.is_disjoint(current_state)
}
pub fn products_clone(&self) -> RSset {
self.products.clone()
}
pub fn reactants(&self) -> &RSset {
&self.reactants
}
pub fn inihibitors(&self) -> &RSset {
&self.inihibitors
}
pub fn products(&self) -> &RSset {
&self.products
}
}
impl Default for RSreaction {
@ -434,10 +414,10 @@ impl From<Vec<(IdType, RSprocess)>> for RSenvironment {
// -----------------------------------------------------------------------------
#[derive(Clone, Debug)]
pub struct RSsystem {
delta: Rc<RSenvironment>,
available_entities: RSset,
context_process: RSprocess,
reaction_rules: Rc<Vec<RSreaction>>,
pub delta: Rc<RSenvironment>,
pub available_entities: RSset,
pub context_process: RSprocess,
pub reaction_rules: Rc<Vec<RSreaction>>,
}
impl RSsystem {
@ -463,24 +443,10 @@ impl RSsystem {
reaction_rules: Rc::clone(&reaction_rules),
}
}
pub fn get_delta(&self) -> &Rc<RSenvironment> {
&self.delta
}
pub fn get_available_entities(&self) -> &RSset {
&self.available_entities
}
pub fn get_context_process(&self) -> &RSprocess {
&self.context_process
}
pub fn get_reaction_rules(&self) -> &Rc<Vec<RSreaction>> {
&self.reaction_rules
}
}
/// Equality does not care about delta or reaction rules, only entities and
/// context is compared
impl PartialEq for RSsystem {
// we ignore delta and reaction rules
fn eq(&self, other: &RSsystem) -> bool {
@ -489,8 +455,12 @@ impl PartialEq for RSsystem {
}
}
/// Equality does not care about delta or reaction rules, only entities and
/// context is compared
impl Eq for RSsystem {}
/// Hash does not care about delta or reaction rules, only entities and
/// context is hashed
impl Hash for RSsystem {
// ignores delta and reaction rules
fn hash<H: std::hash::Hasher>(&self, state: &mut H) {
@ -513,11 +483,10 @@ pub struct RSlabel {
pub available_entities: RSset,
pub context: RSset,
pub t: RSset,
/// union of available_entities and context
pub reactants: RSset,
pub reactantsi: RSset, // reactants absent
pub reactants_absent: RSset,
pub inihibitors: RSset,
pub ireactants: RSset, // inhibitors present
pub inihibitors_present: RSset,
pub products: RSset,
}
@ -528,9 +497,9 @@ impl RSlabel {
context: RSset::new(),
t: RSset::new(),
reactants: RSset::new(),
reactantsi: RSset::new(),
reactants_absent: RSset::new(),
inihibitors: RSset::new(),
ireactants: RSset::new(),
inihibitors_present: RSset::new(),
products: RSset::new(),
}
}
@ -541,9 +510,9 @@ impl RSlabel {
context: RSset,
t: RSset,
reactants: RSset,
reactantsi: RSset,
reactants_absent: RSset,
inihibitors: RSset,
ireactants: RSset,
inihibitors_present: RSset,
products: RSset,
) -> Self {
RSlabel {
@ -551,19 +520,18 @@ impl RSlabel {
context,
t,
reactants,
reactantsi,
reactants_absent,
inihibitors,
ireactants,
inihibitors_present,
products,
}
}
pub fn get_context(&self) -> (RSset, RSset, RSset) {
// TODO remove clone?
pub fn get_context(&self) -> (&RSset, &RSset, &RSset) {
(
self.available_entities.clone(),
self.context.clone(),
self.t.clone(),
&self.available_entities,
&self.context,
&self.t,
)
}
}

22
src/rsprocess/support_structures.rs
View File

@ -13,7 +13,7 @@ impl<'a> TransitionsIterator<'a> {
pub fn from(
system: &'a RSsystem
) -> Result<TransitionsIterator<'a>, String> {
match unfold(system.get_delta(), system.get_context_process()) {
match unfold(&system.delta, &system.context_process) {
Ok(o) => Ok(TransitionsIterator {
choices_iterator: o.into_iter(),
system,
@ -28,9 +28,9 @@ impl<'a> Iterator for TransitionsIterator<'a> {
fn next(&mut self) -> Option<(RSlabel, RSsystem)> {
let (c, k) = self.choices_iterator.next()?;
let t = self.system.get_available_entities().union(c.as_ref());
let t = self.system.available_entities.union(c.as_ref());
let (reactants, reactantsi, inihibitors, ireactants, products) =
self.system.get_reaction_rules().iter().fold(
self.system.reaction_rules.iter().fold(
(
RSset::new(), // reactants
RSset::new(), // reactantsi
@ -41,18 +41,18 @@ impl<'a> Iterator for TransitionsIterator<'a> {
|acc, reaction| {
if reaction.enabled(&t) {
(
acc.0.union(reaction.reactants()),
acc.0.union(&reaction.reactants),
acc.1,
acc.2.union(reaction.inihibitors()),
acc.2.union(&reaction.inihibitors),
acc.3,
acc.4.union(reaction.products()),
acc.4.union(&reaction.products),
)
} else {
(
acc.0,
acc.1.union(&reaction.inihibitors().intersection(&t)),
acc.1.union(&reaction.inihibitors.intersection(&t)),
acc.2,
acc.3.union(&reaction.reactants().subtraction(&t)),
acc.3.union(&reaction.reactants.subtraction(&t)),
acc.4,
)
}
@ -60,7 +60,7 @@ impl<'a> Iterator for TransitionsIterator<'a> {
);
let label = RSlabel::from(
self.system.get_available_entities().clone(),
self.system.available_entities.clone(),
(*c).clone(),
t,
reactants,
@ -70,10 +70,10 @@ impl<'a> Iterator for TransitionsIterator<'a> {
products.clone(),
);
let new_system = RSsystem::from(
Rc::clone(self.system.get_delta()),
Rc::clone(&self.system.delta),
products,
(*k).clone(),
Rc::clone(self.system.get_reaction_rules()),
Rc::clone(&self.system.reaction_rules),
);
Some((label, new_system))
}

10
src/rsprocess/transitions.rs
View File

@ -115,7 +115,7 @@ pub fn target(
) -> Result<(i64, RSset), String> {
let current = one_transition(system)?;
if current.is_none() {
return Ok((0, system.get_available_entities().clone()));
return Ok((0, system.available_entities.clone()));
}
let mut n = 1;
let mut current = current.unwrap().1;
@ -123,7 +123,7 @@ pub fn target(
current = next;
n += 1;
}
Ok((n, current.get_available_entities().clone()))
Ok((n, current.available_entities.clone()))
}
// see oneRun, run, smartOneRunEK, smartRunEK
@ -145,11 +145,13 @@ pub fn run_separated(
return Ok(res);
}
let current = current.unwrap();
res.push(current.0.get_context());
let (available_entities, context, t) = current.0.get_context();
res.push((available_entities.clone(), context.clone(), t.clone()));
let mut current = current.1;
while let Some((label, next)) = one_transition(&current)? {
current = next;
res.push(label.get_context());
let (available_entities, context, t) = label.get_context();
res.push((available_entities.clone(), context.clone(), t.clone()));
}
Ok(res)
}

18
src/rsprocess/translator.rs
View File

@ -121,9 +121,9 @@ fn print_reaction(
write!(
f,
"(r: {}, i: {}, p: {})",
RSsetDisplay::from(translator, reaction.reactants()),
RSsetDisplay::from(translator, reaction.inihibitors()),
RSsetDisplay::from(translator, reaction.products())
RSsetDisplay::from(translator, &reaction.reactants),
RSsetDisplay::from(translator, &reaction.inihibitors),
RSsetDisplay::from(translator, &reaction.products)
)
}
@ -294,11 +294,11 @@ fn print_system(
write!(
f,
"[delta: {}, available_entities: {}, context_process: {}, reaction_rules: [",
RSenvironmentDisplay::from(translator, system.get_delta()),
RSsetDisplay::from(translator, system.get_available_entities()),
RSprocessDisplay::from(translator, system.get_context_process())
RSenvironmentDisplay::from(translator, &system.delta),
RSsetDisplay::from(translator, &system.available_entities),
RSprocessDisplay::from(translator, &system.context_process)
)?;
let mut it = system.get_reaction_rules().iter().peekable();
let mut it = system.reaction_rules.iter().peekable();
while let Some(el) = it.next() {
if it.peek().is_none() {
write!(f, "{}", RSreactionDisplay::from(translator, el))?;
@ -327,9 +327,9 @@ fn print_label(
RSsetDisplay::from(translator, &label.context),
RSsetDisplay::from(translator, &label.t),
RSsetDisplay::from(translator, &label.reactants),
RSsetDisplay::from(translator, &label.reactantsi),
RSsetDisplay::from(translator, &label.reactants_absent),
RSsetDisplay::from(translator, &label.inihibitors),
RSsetDisplay::from(translator, &label.ireactants),
RSsetDisplay::from(translator, &label.inihibitors_present),
RSsetDisplay::from(translator, &label.products),
)
}