From 7852b58e211a1bb87568e6d0c3ad4a46a67b99f4 Mon Sep 17 00:00:00 2001
From: Simon Penel <simon.penel@univ-lyon1.fr>
Date: Wed, 15 May 2024 17:01:14 +0200
Subject: [PATCH] Adding gene_colors in Options

---
 Cargo.toml              |  2 +-
 examples/test_colors.rs | 45 +++++++++++++++++++++++++++++++++++++++++
 src/arena.rs            |  3 +++
 src/drawing.rs          | 10 ++++++++-
 4 files changed, 58 insertions(+), 2 deletions(-)
 create mode 100644 examples/test_colors.rs

diff --git a/Cargo.toml b/Cargo.toml
index 8c25d35..9c8bb06 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "light_phylogeny"
-version = "2.1.8"
+version = "2.1.9"
 authors = ["Simon Penel <simon.penel@univ-lyon1.fr>"]
 edition = "2018"
 description ="Methods and functions for phylogeny."
diff --git a/examples/test_colors.rs b/examples/test_colors.rs
new file mode 100644
index 0000000..c33a1fe
--- /dev/null
+++ b/examples/test_colors.rs
@@ -0,0 +1,45 @@
+// Display a reconciled tree form recPhyloXML format
+
+use light_phylogeny::{ArenaTree,Options,Config,read_recphyloxml_multi,recphyloxml_processing};
+
+fn main() {
+
+    let transfers = vec![];
+    let mut options: Options = Options::new();
+    let config: Config = Config::new();
+
+    options.free_living = true;
+    options.gene_internal = true;
+    options.species_internal = true;
+
+
+    let mut sp_tree: ArenaTree<String> = ArenaTree::default();
+    let mut gene_trees:std::vec::Vec<ArenaTree<String>> = Vec::new();
+    let mut global_roots: std::vec::Vec<usize> = Vec::new();
+    read_recphyloxml_multi("examples/free_living_reconciliated_quadruple.recphylo".to_string(),
+        &mut sp_tree, &mut gene_trees, &mut global_roots);
+    recphyloxml_processing(&mut sp_tree, &mut gene_trees, &mut options, &config, true,
+         &transfers, "test_colors1.svg".to_string());
+    println!("Please open output file 'test_colors1.svg' with your browser");
+
+
+    let transfers = vec![];
+    let mut options: Options = Options::new();
+    let config: Config = Config::new();
+
+    options.free_living = true;
+    options.gene_internal = true;
+    options.species_internal = true;
+    options.gene_colors.push("green".to_string());
+    options.gene_colors.push("pink".to_string());
+    options.gene_colors.push("#7A5050".to_string());
+
+    let mut sp_tree: ArenaTree<String> = ArenaTree::default();
+    let mut gene_trees:std::vec::Vec<ArenaTree<String>> = Vec::new();
+    let mut global_roots: std::vec::Vec<usize> = Vec::new();
+    read_recphyloxml_multi("examples/free_living_reconciliated_quadruple.recphylo".to_string(),
+        &mut sp_tree, &mut gene_trees, &mut global_roots);
+    recphyloxml_processing(&mut sp_tree, &mut gene_trees, &mut options, &config, true,
+         &transfers, "test_colors2.svg".to_string());
+    println!("Please open output file 'test_colors2.svg' with your browser");
+}
diff --git a/src/arena.rs b/src/arena.rs
index 5ab85a3..2b42f43 100644
--- a/src/arena.rs
+++ b/src/arena.rs
@@ -436,6 +436,8 @@ pub struct Options{
     /// place les duplication et les branchingout
     /// a mi distance de leur parent
     pub mid_dist: bool,
+    /// user-defined list of colors for genes
+    pub gene_colors: Vec<String>
 }
 impl Options {
     pub fn new() -> Self {
@@ -472,6 +474,7 @@ impl Options {
             trans_start:None,
             trans_end:None,
             mid_dist:false,
+            gene_colors: Vec::new(),
         }
     }
 }
diff --git a/src/drawing.rs b/src/drawing.rs
index abc71e1..156e8c3 100644
--- a/src/drawing.rs
+++ b/src/drawing.rs
@@ -536,11 +536,19 @@ pub fn draw_sptree_gntrees (
              4 => Color::Yellow,
              _ => Color::Monochrome, // Jamais
         };
-        let gene_color = RandomColor::new()
+        let mut gene_color = RandomColor::new()
             .hue(base_couleur)
             .luminosity(Luminosity::Bright) // Optional
             .alpha(1.0) // Optional
             .to_rgb_string(); //
+
+        
+        if options.gene_colors.len() > 0 {
+            let _idx_user_color = &idx_rcgen % options.gene_colors.len();
+            println!("DEBUG {:?} {}",options.gene_colors,_idx_user_color);
+            gene_color = options.gene_colors[_idx_user_color].clone();
+        }    
+
         // Style de la font pour le gene
         let added_style = " .gene_".to_owned() + &idx_rcgen.to_string()
              + " { font-size: " + &config.gene_police_size.to_string() + "px; fill:"