Merge pull request #19 from thenlevy/dev

v 0.3.1

CHANGELOG.md

@@ -1,6 +1,17 @@
 # Changelog
 
+
 <!-- next-header -->
+## 0.3.1
+
+- Improve flexibility of the cross-over suggestions interface. The parameters are in the "Eddition" tab
+- Update wgpu to 0.11
+- Files that do not have an `.ens` extensions won't be overiden when saving a design. This fixes a problem that caused
+ENSnano to overide cadnano files for example.
+- Selected/candidate nucleotide are now highlighted in the 2D view.
+- Fix a bug that would cause high CPU usage while ENSnano was in the background on MacOS
+
+
 ## 0.3.0
 - It is now possible to translate several helices at once.
 - It is now possible to change the color of several strands at once. Moreover, the red hilighting

Cargo.toml

@@ -3,7 +3,7 @@ members = [ "ensnano-design", "ensnano-interactor", "ensnano-organizer" ]
 
 [package]
 name = "ensnano"
-version = "0.3.0"
+version = "0.3.1"
 authors = ["thenlevy <nicolaspierrelevy@gmail.com>"]
 edition = "2018"
 license = "GPL-3.0-or-later"
@@ -12,11 +12,11 @@ resolver = "2"
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
 
 [dependencies]
-iced = { git = "https://github.com/hecrj/iced", rev = "099981c", features=["image"] }
-iced_wgpu = { git = "https://github.com/hecrj/iced", rev = "099981c", features = ["spirv"] }
-iced_graphics = { git = "https://github.com/hecrj/iced", rev = "099981c" }
-iced_winit = { git = "https://github.com/hecrj/iced", rev = "099981c" }
-iced_native = { git = "https://github.com/hecrj/iced", rev = "099981c" }
+iced = { git = "https://github.com/hecrj/iced", rev = "61c747b53589d98f477fea95f85d2ea5349666d3", features=["image"] }
+iced_wgpu = { git = "https://github.com/hecrj/iced", rev = "61c747b53589d98f477fea95f85d2ea5349666d3", features = ["spirv"] }
+iced_graphics = { git = "https://github.com/hecrj/iced", rev = "61c747b53589d98f477fea95f85d2ea5349666d3" }
+iced_winit = { git = "https://github.com/hecrj/iced", rev = "61c747b53589d98f477fea95f85d2ea5349666d3" }
+iced_native = { git = "https://github.com/hecrj/iced", rev = "61c747b53589d98f477fea95f85d2ea5349666d3" }
 ultraviolet = { git = "https://github.com/termhn/ultraviolet", rev = "b2fb29e" , features = ["bytemuck", "f64", "serde"] }
 bytemuck = "1.2.0"
 failure = "0.1.8"
@@ -40,7 +40,7 @@ ordered-float = "2.0"
 rfd = "0.4"
 material-icons = "0.1.0"
 ensnano_organizer = { path = "ensnano-organizer" }
-iced_aw = { git = "https://github.com/thenlevy/iced_aw", rev = "b566bdb" , features = ["tab_bar"]}
+iced_aw = { git = "https://github.com/thenlevy/iced_aw", rev = "4ee0a6ac70633" , features = ["tab_bar"]}
 num_enum = "0.5.1"
 cadnano-format = "0.1.0"
 open = "1"

ensnano-design/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "ensnano_design"
-version = "0.3.0"
+version = "0.3.1"
 authors = ["thenlevy <nicolaspierrelevy@gmail.com>"]
 edition = "2018"
 license = "GPL-3.0-or-later"

ensnano-design/src/lib.rs

@@ -423,6 +423,15 @@ impl Design {
     pub fn prepare_for_save(&mut self, saving_information: SavingInformation) {
         self.saved_camera = saving_information.camera;
     }
+
+    pub fn get_nucl_position(&self, nucl: Nucl) -> Option<Vec3> {
+        let helix = self.helices.get(&nucl.helix)?;
+        Some(helix.space_pos(
+            &self.parameters.unwrap_or_default(),
+            nucl.position,
+            nucl.forward,
+        ))
+    }
 }
 
 pub struct SavingInformation {

ensnano-interactor/Cargo.toml

@@ -29,6 +29,6 @@ num_enum = "0.5.1"
 open = "1"
 ensnano_design = { path = "../ensnano-design" }
 ensnano_organizer = { path = "../ensnano-organizer" }
-iced_wgpu = { git = "https://github.com/hecrj/iced", rev = "099981c" }
-iced_winit = { git = "https://github.com/hecrj/iced", rev = "099981c" }
+iced_wgpu = { git = "https://github.com/hecrj/iced", rev = "61c747b53589d98f477fea95f85d2ea5349666d3" }
+iced_winit = { git = "https://github.com/hecrj/iced", rev = "61c747b53589d98f477fea95f85d2ea5349666d3" }
 

ensnano-interactor/src/lib.rs

@@ -450,3 +450,49 @@ pub struct StrandBuildingStatus {
     pub prime5: Nucl,
     pub dragged_nucl: Nucl,
 }
+
+/// Parameters of strand suggestions
+#[derive(Clone, PartialEq, Eq, Debug)]
+pub struct SuggestionParameters {
+    pub include_scaffold: bool,
+    pub include_intra_strand: bool,
+    pub include_xover_ends: bool,
+    pub ignore_groups: bool,
+}
+
+impl Default for SuggestionParameters {
+    fn default() -> Self {
+        Self {
+            include_intra_strand: true,
+            include_scaffold: true,
+            include_xover_ends: false,
+            ignore_groups: false,
+        }
+    }
+}
+
+impl SuggestionParameters {
+    pub fn with_include_scaffod(&self, include_scaffold: bool) -> Self {
+        let mut ret = self.clone();
+        ret.include_scaffold = include_scaffold;
+        ret
+    }
+
+    pub fn with_intra_strand(&self, intra_strand: bool) -> Self {
+        let mut ret = self.clone();
+        ret.include_intra_strand = intra_strand;
+        ret
+    }
+
+    pub fn with_ignore_groups(&self, ignore_groups: bool) -> Self {
+        let mut ret = self.clone();
+        ret.ignore_groups = ignore_groups;
+        ret
+    }
+
+    pub fn with_xover_ends(&self, include_xover_ends: bool) -> Self {
+        let mut ret = self.clone();
+        ret.include_xover_ends = include_xover_ends;
+        ret
+    }
+}

ensnano-organizer/Cargo.toml

@@ -7,11 +7,11 @@ edition = "2018"
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
 
 [dependencies]
-iced = { git = "https://github.com/hecrj/iced", rev = "099981c", features=["image"] }
-iced_wgpu = { git = "https://github.com/hecrj/iced", rev = "099981c" }
-iced_graphics = { git = "https://github.com/hecrj/iced", rev = "099981c" }
-iced_winit = { git = "https://github.com/hecrj/iced", rev = "099981c" }
-iced_native = { git = "https://github.com/hecrj/iced", rev = "099981c" }
+iced = { git = "https://github.com/hecrj/iced", rev = "61c747b53589d98f477fea95f85d2ea5349666d3", features=["image"] }
+iced_wgpu = { git = "https://github.com/hecrj/iced", rev = "61c747b53589d98f477fea95f85d2ea5349666d3" }
+iced_graphics = { git = "https://github.com/hecrj/iced", rev = "61c747b53589d98f477fea95f85d2ea5349666d3" }
+iced_winit = { git = "https://github.com/hecrj/iced", rev = "61c747b53589d98f477fea95f85d2ea5349666d3" }
+iced_native = { git = "https://github.com/hecrj/iced", rev = "61c747b53589d98f477fea95f85d2ea5349666d3" }
 iced_aw = { git = "https://github.com/iced-rs/iced_aw", rev = "84ccfa8", features=["icons", "icon_text"] }
 serde = "1.0.116"
 serde_derive = "1.0.116"

ensnano-organizer/src/drag_drop_target.rs

@@ -1,6 +1,6 @@
 use iced::{Container, Element};
 use iced_native::{
-    event, layout, overlay, Align, Clipboard, Event, Hasher, Layout, Length, Point, Rectangle,
+    event, layout, overlay, Alignment, Clipboard, Event, Hasher, Layout, Length, Point, Rectangle,
     Widget,
 };
 use std::hash::Hash;
@@ -17,8 +17,8 @@ pub(super) struct DragDropTarget<'a, Message, K> {
     height: Length,
     max_width: u32,
     max_height: u32,
-    horizontal_alignment: Align,
-    vertical_alignment: Align,
+    horizontal_alignment: Alignment,
+    vertical_alignment: Alignment,
     content: Container<'a, Message>,
     identifier: Identifier<K>,
 }
@@ -35,8 +35,8 @@ impl<'a, Message, K> DragDropTarget<'a, Message, K> {
             height: Length::Shrink,
             max_width: u32::MAX,
             max_height: u32::MAX,
-            horizontal_alignment: Align::Start,
-            vertical_alignment: Align::Start,
+            horizontal_alignment: Alignment::Start,
+            vertical_alignment: Alignment::Start,
             content: Container::new(content).width(Length::Fill),
             identifier,
         }

ensnano-organizer/src/lib.rs

@@ -1550,7 +1550,7 @@ impl<E: OrganizerElement> GroupContent<E> {
 }
 
 fn icon(unicode: char) -> Text {
-    use iced::HorizontalAlignment;
+    use iced::alignment::Horizontal as HorizontalAlignment;
     Text::new(&unicode.to_string())
         .font(ICONS)
         .size(ICON_SIZE)

src/app_state.rs

@@ -37,7 +37,7 @@ use crate::apply_update;
 use crate::controller::SimulationRequest;
 use address_pointer::AddressPointer;
 use ensnano_design::Design;
-use ensnano_interactor::{DesignOperation, RigidBodyConstants};
+use ensnano_interactor::{DesignOperation, RigidBodyConstants, SuggestionParameters};
 use ensnano_organizer::GroupId;
 
 pub use design_interactor::controller::ErrOperation;
@@ -65,6 +65,13 @@ impl std::fmt::Debug for AppState {
     }
 }
 
+impl std::fmt::Pointer for AppState {
+    fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result {
+        let ptr = self.0.get_ptr();
+        std::fmt::Pointer::fmt(&ptr, f)
+    }
+}
+
 impl Default for AppState {
     fn default() -> Self {
         let ret = AppState(Default::default());
@@ -128,6 +135,12 @@ impl AppState {
         Self(AddressPointer::new(new_state))
     }
 
+    pub fn with_suggestion_parameters(&self, suggestion_parameters: SuggestionParameters) -> Self {
+        let mut new_state = (*self.0).clone();
+        new_state.suggestion_parameters = suggestion_parameters;
+        Self(AddressPointer::new(new_state))
+    }
+
     pub fn with_action_mode(&self, action_mode: ActionMode) -> Self {
         let mut new_state = (*self.0).clone();
         new_state.action_mode = action_mode;
@@ -200,9 +213,15 @@ impl AppState {
     }
 
     fn updated(self) -> Self {
+        let old_self = self.clone();
         let mut interactor = self.0.design.clone_inner();
-        interactor = interactor.with_updated_design_reader();
-        self.with_interactor(interactor)
+        interactor = interactor.with_updated_design_reader(&self.0.suggestion_parameters);
+        let new = self.with_interactor(interactor);
+        if old_self.design_was_modified(&new) {
+            new
+        } else {
+            old_self
+        }
     }
 
     fn with_interactor(self, interactor: DesignInteractor) -> Self {
@@ -313,6 +332,7 @@ impl AppState {
         *self = self.with_candidates(vec![]);
         *self = self.with_action_mode(source.0.action_mode.clone());
         *self = self.with_selection_mode(source.0.selection_mode.clone());
+        *self = self.with_suggestion_parameters(source.0.suggestion_parameters.clone());
     }
 
     pub(super) fn is_pasting(&self) -> PastingStatus {
@@ -448,6 +468,7 @@ struct AppState_ {
     widget_basis: WidgetBasis,
     strand_on_new_helix: Option<NewHelixStrand>,
     center_of_selection: Option<CenterOfSelection>,
+    suggestion_parameters: SuggestionParameters,
 }
 
 #[derive(Clone, Default)]

src/app_state/address_pointer.rs

@@ -66,6 +66,10 @@ impl<T: Default> AddressPointer<T> {
     pub fn show_address(&self) {
         println!("{:p}", Arc::as_ptr(&self.0))
     }
+
+    pub fn get_ptr(&self) -> *const T {
+        Arc::as_ptr(&self.0)
+    }
 }
 
 use std::ops::Deref;

src/app_state/design_interactor.rs

@@ -20,7 +20,7 @@ use super::AddressPointer;
 use ensnano_design::{group_attributes::GroupAttribute, Design, Parameters};
 use ensnano_interactor::{
     operation::Operation, DesignOperation, RigidBodyConstants, Selection, SimulationState,
-    StrandBuilder,
+    StrandBuilder, SuggestionParameters,
 };
 
 mod presenter;
@@ -200,12 +200,16 @@ impl DesignInteractor {
         ret
     }
 
-    pub(super) fn with_updated_design_reader(mut self) -> Self {
+    pub(super) fn with_updated_design_reader(
+        mut self,
+        suggestion_parameters: &SuggestionParameters,
+    ) -> Self {
         if cfg!(test) {
             print!("Old design: ");
             self.design.show_address();
         }
-        let (new_presenter, new_design) = update_presenter(&self.presenter, self.design.clone());
+        let (new_presenter, new_design) =
+            update_presenter(&self.presenter, self.design.clone(), suggestion_parameters);
         self.presenter = new_presenter;
         if cfg!(test) {
             print!("New design: ");
@@ -216,7 +220,7 @@ impl DesignInteractor {
             if !self.controller.get_simulation_state().is_runing() {
                 self.simulation_update = None;
             }
-            self.after_applying_simulation_update(update)
+            self.after_applying_simulation_update(update, suggestion_parameters)
         } else {
             self
         }
@@ -230,9 +234,17 @@ impl DesignInteractor {
         self
     }
 
-    fn after_applying_simulation_update(mut self, update: Arc<dyn SimulationUpdate>) -> Self {
-        let (new_presenter, new_design) =
-            apply_simulation_update(&self.presenter, self.design.clone(), update);
+    fn after_applying_simulation_update(
+        mut self,
+        update: Arc<dyn SimulationUpdate>,
+        suggestion_parameters: &SuggestionParameters,
+    ) -> Self {
+        let (new_presenter, new_design) = apply_simulation_update(
+            &self.presenter,
+            self.design.clone(),
+            update,
+            suggestion_parameters,
+        );
         self.presenter = new_presenter;
         self.design = new_design;
         self
@@ -425,7 +437,8 @@ mod tests {
     fn read_one_helix() {
         let path = one_helix_path();
         let interactor = DesignInteractor::new_with_path(&path).ok().unwrap();
-        let interactor = interactor.with_updated_design_reader();
+        let suggestion_parameters = Default::default();
+        let interactor = interactor.with_updated_design_reader(&suggestion_parameters);
         let reader = interactor.get_design_reader();
         assert_eq!(reader.get_all_visible_nucl_ids().len(), 24)
     }
@@ -817,7 +830,6 @@ mod tests {
 
     #[test]
     fn positioning_xovers_paste() {
-        use crate::flatscene::DesignReader;
         let mut app_state = pastable_design();
         let (n1, n2) = app_state.get_design_reader().get_xover_with_id(0).unwrap();
         app_state
@@ -851,7 +863,6 @@ mod tests {
 
     #[test]
     fn pasting_when_positioning_xovers() {
-        use crate::flatscene::DesignReader;
         let mut app_state = pastable_design();
         let (n1, n2) = app_state.get_design_reader().get_xover_with_id(0).unwrap();
         app_state
@@ -865,7 +876,6 @@ mod tests {
 
     #[test]
     fn duplicating_xovers() {
-        use crate::flatscene::DesignReader;
         let mut app_state = pastable_design();
         let (n1, n2) = app_state.get_design_reader().get_xover_with_id(0).unwrap();
         app_state
@@ -899,7 +909,6 @@ mod tests {
 
     #[test]
     fn duplicating_xovers_pasting_status() {
-        use crate::flatscene::DesignReader;
         let mut app_state = pastable_design();
         let (n1, n2) = app_state.get_design_reader().get_xover_with_id(0).unwrap();
         app_state

src/app_state/design_interactor/controller/clipboard.rs

@@ -315,7 +315,7 @@ impl Controller {
         let mut domains_vec = vec![domains_0];
         for n in 1..clipboard.templates.len() {
             let t = clipboard.templates.get(n);
-            println!("updated template {:?}", t);
+            log::info!("updated template {:?}", t);
             let domains = t.as_ref().and_then(|t| {
                 clipboard
                     .template_edges
@@ -760,9 +760,9 @@ impl Controller {
         let (edge, shift) = copy_edge;
         for (n1, n2) in xovers.iter() {
             let copy_1 = self.translate_nucl_by_edge(n1, &edge, shift, design, grid_manager);
-            println!("copy 1 {:?}", copy_1);
+            log::debug!("copy 1 {:?}", copy_1);
             let copy_2 = self.translate_nucl_by_edge(n2, &edge, shift, design, grid_manager);
-            println!("copy 2 {:?}", copy_2);
+            log::debug!("copy 2 {:?}", copy_2);
             if let Some((copy_1, copy_2)) = copy_1.zip(copy_2) {
                 if !design.is_true_xover_end(&copy_1) && !design.is_true_xover_end(&copy_2) {
                     // If general_cross_over returns an error we simply ignore this cross_over