improvements and fixes

rsprocess/src/element.rs

@@ -20,6 +20,7 @@ impl PrintableWithTranslator for IdType {
     }
 }
 
+
 // -----------------------------------------------------------------------------
 
 #[derive(
@@ -108,3 +109,15 @@ impl From<(&IdType, &IdState)> for PositiveType {
         }
     }
 }
+
+impl From<PositiveType> for IdType {
+    fn from(value: PositiveType) -> Self {
+        value.id
+    }
+}
+
+impl From<&PositiveType> for IdType {
+    fn from(value: &PositiveType) -> Self {
+        value.id
+    }
+}

rsprocess/src/environment.rs

@@ -430,7 +430,7 @@ impl<'a> IntoIterator for &'a Environment {
 
 impl<const N: usize> From<[(IdType, Process); N]> for Environment {
     fn from(arr: [(IdType, Process); N]) -> Self {
-        Environment {
+        Self {
             definitions: BTreeMap::from(arr),
         }
     }
@@ -438,7 +438,7 @@ impl<const N: usize> From<[(IdType, Process); N]> for Environment {
 
 impl From<&[(IdType, Process)]> for Environment {
     fn from(arr: &[(IdType, Process)]) -> Self {
-        Environment {
+        Self {
             definitions: BTreeMap::from_iter(arr.to_vec()),
         }
     }
@@ -446,7 +446,7 @@ impl From<&[(IdType, Process)]> for Environment {
 
 impl From<Vec<(IdType, Process)>> for Environment {
     fn from(arr: Vec<(IdType, Process)>) -> Self {
-        Environment {
+        Self {
             definitions: BTreeMap::from_iter(arr),
         }
     }
@@ -812,3 +812,28 @@ impl From<Environment> for PositiveEnvironment {
         (&value).into()
     }
 }
+
+
+impl<const N: usize> From<[(IdType, PositiveProcess); N]> for PositiveEnvironment {
+    fn from(arr: [(IdType, PositiveProcess); N]) -> Self {
+        Self {
+            definitions: BTreeMap::from(arr),
+        }
+    }
+}
+
+impl From<&[(IdType, PositiveProcess)]> for PositiveEnvironment {
+    fn from(arr: &[(IdType, PositiveProcess)]) -> Self {
+        Self {
+            definitions: BTreeMap::from_iter(arr.to_vec()),
+        }
+    }
+}
+
+impl From<Vec<(IdType, PositiveProcess)>> for PositiveEnvironment {
+    fn from(arr: Vec<(IdType, PositiveProcess)>) -> Self {
+        Self {
+            definitions: BTreeMap::from_iter(arr),
+        }
+    }
+}

rsprocess/src/label.rs

@@ -16,11 +16,28 @@ where
         + Ord
         + Hash
         + PrintableWithTranslator,
-    for<'a> Self: Deserialize<'a>,
 {
     type Set: BasicSet;
 
     fn get_context(&self) -> (&Self::Set, &Self::Set, &Self::Set);
+
+    fn available_entities(&self) -> &Self::Set;
+    fn context(&self) -> &Self::Set;
+    fn t(&self) -> &Self::Set;
+    fn reactants(&self) -> &Self::Set;
+    fn reactants_absent(&self) -> &Self::Set;
+    fn inhibitors(&self) -> &Self::Set;
+    fn inhibitors_present(&self) -> &Self::Set;
+    fn products(&self) -> &Self::Set;
+
+    fn set_available_entities(&mut self, set: Self::Set);
+    fn set_context(&mut self, set: Self::Set);
+    fn set_t(&mut self, set: Self::Set);
+    fn set_reactants(&mut self, set: Self::Set);
+    fn set_reactants_absent(&mut self, set: Self::Set);
+    fn set_inhibitors(&mut self, set: Self::Set);
+    fn set_inhibitors_present(&mut self, set: Self::Set);
+    fn set_products(&mut self, set: Self::Set);
 }
 
 // -----------------------------------------------------------------------------
@@ -45,6 +62,57 @@ impl BasicLabel for Label {
     fn get_context(&self) -> (&Set, &Set, &Set) {
         (&self.available_entities, &self.context, &self.t)
     }
+
+    fn available_entities(&self) -> &Self::Set {
+        &self.available_entities
+    }
+    fn context(&self) -> &Self::Set {
+        &self.context
+    }
+    fn t(&self) -> &Self::Set {
+        &self.t
+    }
+    fn reactants(&self) -> &Self::Set {
+        &self.reactants
+    }
+    fn reactants_absent(&self) -> &Self::Set {
+        &self.reactants_absent
+    }
+    fn inhibitors(&self) -> &Self::Set {
+        &self.inhibitors
+    }
+    fn inhibitors_present(&self) -> &Self::Set {
+        &self.inhibitors_present
+    }
+    fn products(&self) -> &Self::Set {
+        &self.products
+    }
+
+
+    fn set_available_entities(&mut self, set: Self::Set) {
+        self.available_entities = set;
+    }
+    fn set_context(&mut self, set: Self::Set) {
+        self.context = set;
+    }
+    fn set_t(&mut self, set: Self::Set) {
+        self.t = set;
+    }
+    fn set_reactants(&mut self, set: Self::Set) {
+        self.reactants = set;
+    }
+    fn set_reactants_absent(&mut self, set: Self::Set) {
+        self.reactants_absent = set;
+    }
+    fn set_inhibitors(&mut self, set: Self::Set) {
+        self.inhibitors = set;
+    }
+    fn set_inhibitors_present(&mut self, set: Self::Set) {
+        self.inhibitors_present = set;
+    }
+    fn set_products(&mut self, set: Self::Set) {
+        self.products = set;
+    }
 }
 
 impl Label {
@@ -171,6 +239,57 @@ impl BasicLabel for PositiveLabel {
     fn get_context(&self) -> (&PositiveSet, &PositiveSet, &PositiveSet) {
         (&self.available_entities, &self.context, &self.t)
     }
+
+    fn available_entities(&self) -> &Self::Set {
+        &self.available_entities
+    }
+    fn context(&self) -> &Self::Set {
+        &self.context
+    }
+    fn t(&self) -> &Self::Set {
+        &self.t
+    }
+    fn reactants(&self) -> &Self::Set {
+        &self.reactants
+    }
+    fn reactants_absent(&self) -> &Self::Set {
+        &self.reactants_absent
+    }
+    fn inhibitors(&self) -> &Self::Set {
+        &self.inhibitors
+    }
+    fn inhibitors_present(&self) -> &Self::Set {
+        &self.inhibitors_present
+    }
+    fn products(&self) -> &Self::Set {
+        &self.products
+    }
+
+
+    fn set_available_entities(&mut self, set: Self::Set) {
+        self.available_entities = set;
+    }
+    fn set_context(&mut self, set: Self::Set) {
+        self.context = set;
+    }
+    fn set_t(&mut self, set: Self::Set) {
+        self.t = set;
+    }
+    fn set_reactants(&mut self, set: Self::Set) {
+        self.reactants = set;
+    }
+    fn set_reactants_absent(&mut self, set: Self::Set) {
+        self.reactants_absent = set;
+    }
+    fn set_inhibitors(&mut self, set: Self::Set) {
+        self.inhibitors = set;
+    }
+    fn set_inhibitors_present(&mut self, set: Self::Set) {
+        self.inhibitors_present = set;
+    }
+    fn set_products(&mut self, set: Self::Set) {
+        self.products = set;
+    }
 }
 
 impl PartialEq for PositiveLabel {

rsprocess/src/reaction.rs

@@ -226,9 +226,7 @@ impl Reaction {
 
 // -----------------------------------------------------------------------------
 
-#[derive(
+#[derive(Clone, Debug, Default, Serialize, Deserialize, PartialEq, Eq, Hash)]
-    Clone, Debug, Default, Serialize, Deserialize, PartialEq, Eq, Hash,
-)]
 pub struct PositiveReaction {
     pub reactants: PositiveSet,
     pub products:  PositiveSet,
@@ -308,3 +306,61 @@ impl PositiveReaction {
         Some(self.reactants.intersection(&other.reactants))
     }
 }
+
+// -----------------------------------------------------------------------------
+// Convert from list of reactions to list of positive reactions
+
+impl Reaction {
+    pub fn into_positive_reactions(reactions: &[Self]) -> Vec<PositiveReaction> {
+        let mut res = vec![];
+        let old_reactions = &reactions;
+
+        let all_products = Reaction::all_products(old_reactions);
+        for el in all_products {
+            let p =
+                Reaction::all_reactions_with_product(old_reactions, &el);
+            let mut tmp = vec![];
+            for r in p.iter() {
+                tmp.push(PositiveReaction::create(
+                    r.reactants.clone(),
+                    r.inhibitors.clone(),
+                    Set::from([el]),
+                ))
+            }
+            tmp.sort_by(|r1, r2| r1.reactants.cmp(&r2.reactants));
+
+            // remove reactions with only one element of opposite state
+            // as intersection (same product ```el```)
+            let mut pos = tmp.len() - 1;
+            while pos > 0 {
+                if let Some(intersection) =
+                    tmp[pos].differ_only_one_element(&tmp[pos - 1])
+                {
+                    tmp[pos - 1].reactants = intersection;
+                    tmp.remove(pos);
+                }
+                pos -= 1;
+            }
+
+            res.extend(tmp);
+            let prohib_set = Set::prohibiting_set(
+                &p.iter().map(|p| p.reactants.clone()).collect::<Vec<_>>(),
+                &p.iter().map(|p| p.inhibitors.clone()).collect::<Vec<_>>(),
+            )
+                .unwrap(); // since we have in input a valid system
+            for s in prohib_set {
+                res.push(PositiveReaction {
+                    reactants: s,
+                    products:  PositiveSet::from([(el, IdState::Negative)]),
+                })
+            }
+        }
+        res
+    }
+}
+
+impl PositiveReaction {
+    pub fn from_reactions(reactions: &[Reaction]) -> Vec<Self> {
+        Reaction::into_positive_reactions(reactions)
+    }
+}

rsprocess/src/set.rs

@@ -33,6 +33,7 @@ where
     fn len(&self) -> usize;
     fn is_empty(&self) -> bool;
     fn contains(&self, el: &Self::Element) -> bool;
+    fn add(&mut self, el: Self::Element);
 }
 
 pub trait ExtensionsSet {
@@ -140,6 +141,10 @@ impl BasicSet for Set {
     fn contains(&self, el: &Self::Element) -> bool {
         self.identifiers.contains(el)
     }
+
+    fn add(&mut self, el: Self::Element) {
+        self.identifiers.insert(el);
+    }
 }
 
 impl PartialEq for Set {
@@ -488,6 +493,10 @@ impl BasicSet for PositiveSet {
             false
         }
     }
+
+    fn add(&mut self, el: Self::Element) {
+        self.identifiers.insert(el.id, el.state);
+    }
 }
 
 impl PrintableWithTranslator for PositiveSet {

rsprocess/src/system.rs

@@ -703,6 +703,17 @@ impl System {
             products_elements: Rc::new(RefCell::new(None)),
         }
     }
+
+    pub fn overwrite_context_elements(&mut self, new_context_elements: Set) {
+        self.context_elements = Rc::new(RefCell::new(Some(new_context_elements)));
+    }
+
+    pub fn overwrite_product_elements(&mut self, new_product_elements: Set) {
+        // since context_elements depend on product elements we make sure that
+        // its computed to ensure consistent behaviour
+        self.context_elements();
+        self.products_elements = Rc::new(RefCell::new(Some(new_product_elements)));
+    }
 }
 
 // -----------------------------------------------------------------------------
@@ -1028,54 +1039,8 @@ impl From<System> for PositiveSystem {
         let new_available_entities =
             positive_entities.union(&negative_entities);
 
+        let new_reactions = Rc::new(PositiveReaction::from_reactions(value.reactions()));
         let new_context = value.context_process.into();
-        let new_reactions = {
-            let mut res = vec![];
-            let old_reactions = &value.reaction_rules;
-
-            let all_products = Reaction::all_products(old_reactions);
-            for el in all_products {
-                let p =
-                    Reaction::all_reactions_with_product(old_reactions, &el);
-                let mut tmp = vec![];
-                for r in p.iter() {
-                    tmp.push(PositiveReaction::create(
-                        r.reactants.clone(),
-                        r.inhibitors.clone(),
-                        Set::from([el]),
-                    ))
-                }
-                tmp.sort_by(|r1, r2| r1.reactants.cmp(&r2.reactants));
-
-                // remove reactions with only one element of opposite state
-                // as intersection (same product ```el```)
-                let mut pos = tmp.len() - 1;
-                while pos > 0 {
-                    if let Some(intersection) =
-                        tmp[pos].differ_only_one_element(&tmp[pos - 1])
-                    {
-                        tmp[pos - 1].reactants = intersection;
-                        tmp.remove(pos);
-                    }
-                    pos -= 1;
-                }
-
-                res.extend(tmp);
-                let prohib_set = Set::prohibiting_set(
-                    &p.iter().map(|p| p.reactants.clone()).collect::<Vec<_>>(),
-                    &p.iter().map(|p| p.inhibitors.clone()).collect::<Vec<_>>(),
-                )
-                .unwrap(); // since we have in input a valid system
-                for s in prohib_set {
-                    res.push(PositiveReaction {
-                        reactants: s,
-                        products:  PositiveSet::from([(el, IdState::Negative)]),
-                    })
-                }
-            }
-
-            Rc::new(res)
-        };
 
         Self::from(new_env, new_available_entities, new_context, new_reactions)
     }
@@ -1105,4 +1070,15 @@ impl PositiveSystem {
             .map(|el| (*el.0, IdState::Negative))
             .collect::<PositiveSet>()
     }
+
+    pub fn overwrite_context_elements(&mut self, new_context_elements: PositiveSet) {
+        self.context_elements = Rc::new(RefCell::new(Some(new_context_elements)));
+    }
+
+    pub fn overwrite_product_elements(&mut self, new_product_elements: PositiveSet) {
+        // since context_elements depend on product elements we make sure that
+        // its computed to ensure consistent behaviour
+        self.context_elements();
+        self.products_elements = Rc::new(RefCell::new(Some(new_product_elements)));
+    }
 }