Many updates for PCR and cloning, including bugfixes, feature preserv…

…ation, and selecting insert from opened files

src/cloning.rs

@@ -1,7 +1,7 @@
 use crate::{
     gui::navigation::{Page, PageSeq},
     primer::make_cloning_primers,
-    sequence::{Feature, FeatureDirection, FeatureType, Seq},
+    sequence::{seq_to_str, Feature, FeatureDirection, FeatureType, Nucleotide, Seq},
     util::RangeIncl,
     Selection, State,
 };
@@ -17,6 +17,38 @@ pub struct CloningInsertData {
     pub seq_input: String,
 }
 
+/// Given a set of freatures and the sequence their ranges map to, set up our
+/// insert sequences.
+pub fn setup_insert_seqs(state: &mut State, features: Vec<Feature>, seq: Seq) {
+    // todo: Unecessary cloning if loading from file.
+    state.ui.cloning_insert.features_loaded = features;
+    state.ui.cloning_insert.seq_loaded = seq;
+
+    // Choose the initial insert as the CDS or gene with the largest len.
+    let mut best = None;
+    let mut best_len = 0;
+    for (i, feature) in state.ui.cloning_insert.features_loaded.iter().enumerate() {
+        let len = feature.len(state.generic[state.active].seq.len());
+        if (feature.feature_type == FeatureType::CodingRegion
+            || feature.feature_type == FeatureType::Gene)
+            && len > best_len
+        {
+            best_len = len;
+            best = Some(i);
+        }
+    }
+
+    if let Some(feat_i) = best {
+        let feature = &state.ui.cloning_insert.features_loaded[feat_i];
+
+        if let Some(seq_this_ft) = feature.range.index_seq(&state.ui.cloning_insert.seq_loaded) {
+            state.ui.cloning_insert.feature_selected = best;
+            state.ui.cloning_insert.seq_insert = seq_this_ft.to_owned();
+            state.ui.cloning_insert.seq_input = seq_to_str(&seq_this_ft);
+        }
+    }
+}
+
 /// Create a new tab containing of the cloning product.
 pub fn make_product_tab(state: &mut State) {
     // Note: This segment is almost a duplicate of `State::add_tab`, but retaining the generic data.
@@ -28,7 +60,6 @@ pub fn make_product_tab(state: &mut State) {
     state.portions.push(Default::default());
 
     state.active = state.generic.len() - 1;
-    // state.add_tab();
 
     // Make sure to create cloning primers before performing the insert, or the result will be wrong.
     make_cloning_primers(state);
@@ -46,8 +77,8 @@ pub fn make_product_tab(state: &mut State) {
     // todo: Use the already existing data instead.
     state.generic[state.active].features.push(Feature {
         range: RangeIncl::new(
-            state.cloning_insert_loc + 1,
-            state.cloning_insert_loc + state.ui.cloning_insert.seq_insert.len(),
+            state.cloning_insert_loc,
+            state.cloning_insert_loc + state.ui.cloning_insert.seq_insert.len() - 1,
         ),
         label,
         feature_type: FeatureType::CodingRegion,

src/gui/cloning.rs

@@ -6,10 +6,10 @@ use eframe::{
 };
 
 use crate::{
-    cloning::{make_product_tab, CloningInsertData},
+    cloning::{make_product_tab, setup_insert_seqs, CloningInsertData},
     file_io::save::load_import,
-    gui::{COL_SPACING, ROW_SPACING},
-    sequence::{seq_from_str, seq_to_str, FeatureType},
+    gui::{navigation::DEFAULT_TAB_NAME, COL_SPACING, ROW_SPACING},
+    sequence::{seq_from_str, seq_to_str},
     State,
 };
 
@@ -59,6 +59,65 @@ fn insert_selector(data: &mut CloningInsertData, ui: &mut Ui) {
     }
 }
 
+fn insert_file_section(state: &mut State, ui: &mut Ui) {
+    ui.horizontal(|ui| {
+        ui.label("Choose insert from:");
+
+        // Add buttons for each opened tab
+        for gen in &mut state.generic {
+            let name = &gen.metadata.plasmid_name;
+            let btn_name = if name.len() > 20 {
+                format!("{}...", &name[..20].to_string())
+            } else if name.is_empty() {
+                DEFAULT_TAB_NAME.to_owned()
+            } else {
+                name.to_owned()
+            };
+
+            if ui
+                // todo: Consider something like the actual tab name system, that uses file name,
+                // todo or a default A/R
+                .button(btn_name)
+                .on_hover_text("Select an insert from this sequence")
+                .clicked()
+            {
+                // This setup, including the break and variables, prevents borrow errors.
+                let g = gen.features.clone();
+                let s = gen.seq.clone();
+                setup_insert_seqs(state, g, s);
+                break;
+            }
+        }
+
+        ui.add_space(COL_SPACING);
+        if ui
+            .button("Pick insert from file")
+            .on_hover_text(
+                "Choose a GenBank, PlasCAD, SnapGene, or FASTA file to \
+        select an insert from. FASTA files require manual index selection.",
+            )
+            .clicked()
+        {
+            state.ui.file_dialogs.cloning_load.select_file();
+        }
+
+        ui.add_space(COL_SPACING);
+
+        state.ui.file_dialogs.cloning_load.update(ui.ctx());
+
+        if let Some(path) = state.ui.file_dialogs.cloning_load.take_selected() {
+            if let Some(state_loaded) = load_import(&path) {
+                // todo: Is there a way to do this without cloning?
+                setup_insert_seqs(
+                    state,
+                    state_loaded.generic.features.clone(),
+                    state_loaded.generic.seq.clone(),
+                );
+            }
+        }
+    });
+}
+
 pub fn seq_editor_slic(state: &mut State, ui: &mut Ui) {
     ui.heading("SLIC and FastCloning");
 
@@ -89,54 +148,6 @@ pub fn seq_editor_slic(state: &mut State, ui: &mut Ui) {
 
         ui.add_space(COL_SPACING);
 
-        if ui
-            .button("Pick insert from file")
-            .on_hover_text(
-                "Choose a GenBank, PlasCAD, SnapGene, or FASTA file to \
-        select an insert from. FASTA files require manual index selection.",
-            )
-            .clicked()
-        {
-            state.ui.file_dialogs.cloning_load.select_file();
-        }
-
-        ui.add_space(COL_SPACING);
-
-        state.ui.file_dialogs.cloning_load.update(ui.ctx());
-
-        if let Some(path) = state.ui.file_dialogs.cloning_load.take_selected() {
-            if let Some(state_loaded) = load_import(&path) {
-                state.ui.cloning_insert.features_loaded = state_loaded.generic.features;
-                state.ui.cloning_insert.seq_loaded = state_loaded.generic.seq;
-
-                // Choose the initial insert as the CDS or gene with the largest len.
-                let mut best = None;
-                let mut best_len = 0;
-                for (i, feature) in state.ui.cloning_insert.features_loaded.iter().enumerate() {
-                    let len = feature.len(state.generic[state.active].seq.len());
-                    if (feature.feature_type == FeatureType::CodingRegion
-                        || feature.feature_type == FeatureType::Gene)
-                        && len > best_len
-                    {
-                        best_len = len;
-                        best = Some(i);
-                    }
-                }
-
-                if let Some(feat_i) = best {
-                    let feature = &state.ui.cloning_insert.features_loaded[feat_i];
-
-                    if let Some(seq_this_ft) =
-                        feature.range.index_seq(&state.ui.cloning_insert.seq_loaded)
-                    {
-                        state.ui.cloning_insert.feature_selected = best;
-                        state.ui.cloning_insert.seq_insert = seq_this_ft.to_owned();
-                        state.ui.cloning_insert.seq_input = seq_to_str(&seq_this_ft);
-                    }
-                }
-            }
-        }
-
         if state.ui.cloning_insert.seq_insert.len() > 6 {
             if ui
                 .button(RichText::new("Clone").color(Color32::GOLD))
@@ -151,10 +162,12 @@ pub fn seq_editor_slic(state: &mut State, ui: &mut Ui) {
     });
 
     ui.add_space(ROW_SPACING);
-    insert_selector(&mut state.ui.cloning_insert, ui);
+    insert_file_section(state, ui);
 
     ui.add_space(ROW_SPACING);
+    insert_selector(&mut state.ui.cloning_insert, ui);
 
+    ui.add_space(ROW_SPACING);
     ui.horizontal(|ui| {
         ui.heading("Insert:");
         ui.label(&format!(

src/gui/navigation.rs

@@ -6,12 +6,12 @@ use bincode::{Decode, Encode};
 use eframe::egui::{Color32, RichText, Ui};
 
 use crate::{
-    gui::{set_window_title, COL_SPACING},
+    gui::{set_window_title, COL_SPACING, ROW_SPACING},
     State,
 };
 
 pub const NAV_BUTTON_COLOR: Color32 = Color32::from_rgb(0, 00, 110);
-const DEFAULT_TAB_NAME: &str = "New plasmid";
+pub const DEFAULT_TAB_NAME: &str = "New plasmid";
 
 #[derive(Clone, Copy, PartialEq, Encode, Decode)]
 pub enum Page {
@@ -113,6 +113,21 @@ pub fn tab_selector(state: &mut State, ui: &mut Ui) {
 
             ui.add_space(COL_SPACING / 2.);
         }
+
+        // todo: Right-align?
+        ui.add_space(2. * ROW_SPACING);
+
+        if ui
+            .button(
+                RichText::new("Close active tab")
+                    .color(Color32::WHITE)
+                    .background_color(Color32::DARK_RED),
+            )
+            .on_hover_text("Shortcut: Middle click the tab to close it.")
+            .clicked
+        {
+            tab_removed = Some(state.active)
+        };
     });
 
     if let Some(i) = tab_removed {

src/gui/pcr.rs

@@ -152,7 +152,7 @@ fn pcr_sim(state: &mut State, ui: &mut Ui) {
                             .to_vec() // todo unwrap is dicey.
                     };
 
-                    make_amplicon_tab(state, product_seq, fwd_primer, rev_primer);
+                    make_amplicon_tab(state, product_seq, range_combined, fwd_primer, rev_primer);
                 }
             } else {
                 ui.label("There must be exactly one match for each primer");

src/pcr.rs

@@ -3,8 +3,10 @@
 use bincode::{Decode, Encode};
 
 use crate::{
+    gui::navigation::{Page, PageSeq},
     primer::Primer,
     sequence::{Nucleotide, Seq},
+    util::RangeIncl,
     PcrUi, State,
 };
 
@@ -86,31 +88,40 @@ impl PcrParams {
 pub fn make_amplicon_tab(
     state: &mut State,
     product_seq: Seq,
+    range: RangeIncl,
     fwd_primer: Primer,
     rev_primer: Primer,
 ) {
+    let mut product_features = Vec::new();
+    for feature in &state.generic[state.active].features {
+        // todo: Handle circle wraps etc.
+        if range.start < feature.range.start && range.end > feature.range.end {
+            let mut product_feature = feature.clone();
+            // Find the indexes in the new product sequence.
+            product_feature.range.start -= range.start - 1;
+            product_feature.range.end -= range.start - 1;
+
+            product_features.push(product_feature);
+        }
+    }
+
     state.add_tab();
 
     // if let Some(seq) = range_combined.index_seq(&state.generic.seq) {
     state.generic[state.active].seq = product_seq;
-    let product_features = Vec::new();
 
     // Include the primers used for PCR, and features that are included in the new segment.
     // note that the feature indexes will need to change.
 
-    // todo: Syntax.
     let product_primers = vec![fwd_primer, rev_primer];
 
-    // for feature in &state.generic[state.active].features {
-    // todo: Implement.
-    // }
-
     state.generic[state.active].features = product_features;
     state.generic[state.active].primers = product_primers;
     state.generic[state.active].metadata.plasmid_name = "PCR amplicon".to_owned();
 
     state.sync_seq_related(None);
     // state.sync_primer_metrics();
 
-    // save_new_product("PCR product", state, ui);
+    state.ui.page = Page::Sequence;
+    state.ui.page_seq = PageSeq::View;
 }