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+ "windows_aarch64_msvc",
+ "windows_i686_gnu",
+ "windows_i686_gnullvm",
+ "windows_i686_msvc",
+ "windows_x86_64_gnu",
+ "windows_x86_64_gnullvm",
+ "windows_x86_64_msvc",
+]
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Cargo.toml

@@ -0,0 +1,7 @@
+[package]
+name = "pandora_lib_graph"
+version = "0.1.0"
+edition = "2021"
+
+[dependencies]
+pandora_lib_scan = { git = "https://git.t0m4.fr/Thomas/pandora_lib_scan.git" }

src/cytoband.rs

@@ -0,0 +1,319 @@
+use std::fs::File;
+use std::io::{BufRead, BufReader, Write};
+
+struct Range {
+    start: u32,
+    end: u32,
+    category: String,
+}
+
+struct SvgConfig {
+    width: u32,
+    height: u32,
+    tube_height: u32,
+    tube_y: i32,
+    above_height: u32,
+    below_height: u32,
+    rect_height: u32,
+}
+
+fn read_ranges(filename: &str, contig: &str) -> std::io::Result<Vec<Range>> {
+    let file = File::open(filename)?;
+    let reader = BufReader::new(file);
+    let mut ranges = Vec::new();
+
+    for line in reader.lines() {
+        let line = line?;
+        let parts: Vec<&str> = line.split('\t').collect();
+        if parts.len() >= 5 && parts[0] == contig {
+            ranges.push(Range {
+                start: parts[1].parse().unwrap_or(0),
+                end: parts[2].parse().unwrap_or(0),
+                category: parts[4].to_string(),
+            });
+        }
+    }
+
+    Ok(ranges)
+}
+
+fn calculate_svg_config(
+    width: u32,
+    height: u32,
+    additional_rects: &[AdditionalRect],
+) -> SvgConfig {
+    let max_above_level = additional_rects
+        .iter()
+        .filter_map(|r| {
+            if let RectPosition::Above(level) = r.position {
+                Some(level)
+            } else {
+                None
+            }
+        })
+        .max()
+        .unwrap_or(0);
+
+    let max_below_level = additional_rects
+        .iter()
+        .filter_map(|r| {
+            if let RectPosition::Below(level) = r.position {
+                Some(level)
+            } else {
+                None
+            }
+        })
+        .max()
+        .unwrap_or(0);
+
+    let height_lollipop = 25;
+    let tube_height = (height as f64 * 0.6) as u32;
+    let rect_height = 10;
+    let above_height = rect_height * (max_above_level + 1) + height_lollipop;
+    let below_height = rect_height * (max_below_level + 1) + height_lollipop;
+    let total_height = height + above_height + below_height;
+    SvgConfig {
+        width,
+        height: total_height,
+        tube_height,
+        tube_y: above_height as i32 + (height as i32 - tube_height as i32) / 2,
+        above_height,
+        below_height,
+        rect_height,
+    }
+}
+fn generate_svg_header(config: &SvgConfig) -> String {
+    format!(
+        r#"<svg width="{}" height="{}" xmlns="http://www.w3.org/2000/svg">
+        <defs>
+            <linearGradient id="tubeGradient" x1="0%" y1="0%" x2="0%" y2="100%">
+                <stop offset="0%" style="stop-color:rgb(240,240,240);stop-opacity:1" />
+                <stop offset="50%" style="stop-color:rgb(200,200,200);stop-opacity:1" />
+                <stop offset="100%" style="stop-color:rgb(180,180,180);stop-opacity:1" />
+            </linearGradient>
+            <clipPath id="tubeClip">
+                <rect x="0" y="0" width="{}" height="{}" rx="{}" ry="{}"/>
+            </clipPath>
+        </defs>"#,
+        config.width,
+        config.height,
+        config.width,
+        config.tube_height,
+        config.tube_height / 2,
+        config.tube_height / 2
+    )
+}
+
+fn generate_tube_base(config: &SvgConfig) -> String {
+    format!(
+        r#"<rect x="0" y="0" width="{}" height="{}" fill="url(#tubeGradient)" rx="{}" ry="{}"/>"#,
+        // r#"<rect x="0" y="0" width="{}" height="{}" fill="url(#tubeGradient)" stroke="black" stroke-width="1" rx="{}" ry="{}"/>"#,
+        config.width,
+        config.tube_height + 1,
+        config.tube_height / 2,
+        config.tube_height / 2
+    )
+}
+
+pub struct AdditionalRect {
+    pub start: u32,
+    pub end: u32,
+    pub color: String,
+    pub position: RectPosition,
+}
+
+pub enum RectPosition {
+    Above(u32), // The u32 represents the level (0 being just above the tube, 1 above that, etc.)
+    Below(u32), // The u32 represents the level (0 being just below the tube, 1 below that, etc.)
+}
+
+pub struct Lollipop {
+    pub position: u32,
+    pub above: bool,
+    pub letter: char,
+    pub color: String,
+}
+
+fn generate_lollipops(lollipops: &[Lollipop], config: &SvgConfig, scale_factor: f64) -> String {
+    let mut svg_content = String::new();
+    let stick_length = 30; // Length of the lollipop stick
+    let circle_radius = 10; // Radius of the lollipop circle
+
+    for lollipop in lollipops {
+        let x = (lollipop.position as f64 * scale_factor) as u32;
+        let pad = 5;
+        let (y_stick_start, y_stick_end, y_circle, y_text) = if lollipop.above {
+            (
+                config.tube_y,
+                config.tube_y - stick_length - pad,
+                config.tube_y - stick_length - pad - circle_radius,
+                config.tube_y - stick_length - pad - circle_radius,
+            )
+        } else {
+            let h = config.tube_height as i32;
+            (
+                config.tube_y + h,
+                config.tube_y + h + stick_length + pad,
+                config.tube_y + h + stick_length + pad + circle_radius,
+                config.tube_y + h + stick_length + pad + circle_radius,
+            )
+        };
+
+        // Draw the stick
+        svg_content.push_str(&format!(
+            r#"<line x1="{}" y1="{}" x2="{}" y2="{}" stroke="{}" stroke-width="1"/>"#,
+            x, y_stick_start, x, y_stick_end, lollipop.color
+        ));
+
+        // Draw the circle
+        svg_content.push_str(&format!(
+            r#"<circle cx="{}" cy="{}" r="{}" fill="{}"/>"#,
+            x, y_circle, circle_radius, lollipop.color
+        ));
+
+        // Add the letter
+        svg_content.push_str(&format!(
+            r#"<text x="{}" y="{}" fill="white" font-family="Arial" font-size="12" text-anchor="middle" dominant-baseline="central">{}</text>"#,
+            x, y_text, lollipop.letter
+        ));
+    }
+
+    svg_content
+}
+
+fn generate_chromosome_bands(ranges: &[Range], config: &SvgConfig, scale_factor: f64) -> String {
+    let mut bands = String::new();
+
+    for range in ranges {
+        let scaled_start = (range.start as f64 * scale_factor) as u32;
+        let scaled_width = ((range.end - range.start) as f64 * scale_factor) as u32;
+        let fill_color = match range.category.as_str() {
+            "gneg" => "rgb(255,255,255)",
+            "gpos25" => "rgb(192,192,192)",
+            "gpos50" => "rgb(128,128,128)",
+            "gpos75" => "rgb(64,64,64)",
+            "gpos100" => "rgb(0,0,0)",
+            _ => "rgb(162, 210, 255)",
+        };
+
+        bands.push_str(&format!(
+            r#"<rect x="{}" y="0" width="{}" height="{}" fill="{}" opacity="0.7"/>"#,
+            scaled_start, scaled_width, config.tube_height, fill_color
+        ));
+    }
+
+    bands
+}
+
+fn generate_tube_highlights(config: &SvgConfig) -> String {
+    format!(
+        r#"<rect x="0" y="0" width="{}" height="{}" fill="rgb(255,255,255)" opacity="0.3" rx="{}" ry="{}"/>
+        <rect x="0" y="{}" width="{}" height="{}" fill="rgb(0,0,0)" opacity="0.1" rx="{}" ry="{}"/>"#,
+        config.width,
+        config.tube_height / 6,
+        config.tube_height / 12,
+        config.tube_height / 12,
+        config.tube_height - config.tube_height / 12,
+        config.width,
+        config.tube_height / 12,
+        config.tube_height / 24,
+        config.tube_height / 24
+    )
+}
+
+
+fn generate_additional_rects<'a, I>(rects: I, config: &SvgConfig, scale_factor: f64) -> String
+where
+    I: IntoIterator<Item = &'a AdditionalRect>,
+{
+    let mut svg_content = String::new();
+    for rect in rects {
+        let scaled_start = (rect.start as f64 * scale_factor) as u32;
+        let scaled_width = ((rect.end - rect.start) as f64 * scale_factor) as u32;
+        let y = match rect.position {
+            RectPosition::Above(level) => config.above_height - (level + 1) * config.rect_height,
+            RectPosition::Below(level) => {
+                config.height - config.below_height + level * config.rect_height
+            }
+        };
+        svg_content.push_str(&format!(
+            r#"<rect x="{}" y="{}" width="{}" height="{}" fill="{}"/>"#,
+            scaled_start, y, scaled_width, config.rect_height, rect.color
+        ));
+    }
+    svg_content
+}
+
+fn create_chromosome_svg(
+    ranges: &[Range],
+    config: &SvgConfig,
+    total_range: u32,
+    additional_rects: &[AdditionalRect],
+    lollipops: &[Lollipop],
+) -> String {
+    let scale_factor = config.width as f64 / total_range as f64;
+
+    let mut svg_content = generate_svg_header(config);
+
+    // Draw all additional rectangles
+    svg_content.push_str(&generate_additional_rects(
+        additional_rects.iter(),
+        config,
+        scale_factor,
+    ));
+
+    // Start the transformed group
+    svg_content.push_str(&format!(
+        r#"<g transform="translate(0, {})">"#,
+        config.tube_y
+    ));
+
+    svg_content.push_str(&generate_tube_base(config));
+
+    // Clip the chromosome bands and highlights
+    svg_content.push_str(r#"<g clip-path="url(#tubeClip)">"#);
+    svg_content.push_str(&generate_chromosome_bands(ranges, config, scale_factor));
+    svg_content.push_str(&generate_tube_highlights(config));
+    svg_content.push_str("</g>");
+
+    // Add border on top of the tube
+    svg_content.push_str(&format!(
+        r#"<rect x="0" y="0" width="{}" height="{}" fill="none" 
+        stroke="black" stroke-width="1" rx="{}" ry="{}"/>"#,
+        config.width,
+        config.tube_height,
+        config.tube_height / 2,
+        config.tube_height / 2
+    ));
+
+    // Close the transformed group
+    svg_content.push_str("</g>");
+
+    // Draw lollipops
+    svg_content.push_str(&generate_lollipops(lollipops, config, scale_factor));
+
+    svg_content.push_str("</svg>");
+    svg_content
+}
+pub fn svg_chromosome(
+    contig: &str,
+    width: u32,
+    height: u32,
+    cytobands_path: &str,
+    svg_path: &str,
+    additional_rects: &[AdditionalRect],
+    lollipops: &[Lollipop],
+) -> std::io::Result<()> {
+    let ranges = read_ranges(cytobands_path, contig)?;
+    let total_range = ranges.iter().map(|r| r.end).max().unwrap_or(0);
+    let config = calculate_svg_config(width, height, additional_rects);
+
+    let svg_content = create_chromosome_svg(&ranges, &config, total_range, additional_rects, lollipops);
+
+    let mut output_file = File::create(svg_path)?;
+    output_file.write_all(svg_content.as_bytes())?;
+
+    println!("SVG file created: {svg_path}");
+
+    Ok(())
+}

src/lib.rs

@@ -0,0 +1,66 @@
+pub mod cytoband;
+
+#[cfg(test)]
+mod tests {
+    use cytoband::{svg_chromosome, AdditionalRect, Lollipop, RectPosition};
+
+    use super::*;
+
+    #[test]
+    fn it_works() {
+        let additional_rects = vec![
+            AdditionalRect {
+                start: 0,
+                end: 250000,
+                color: String::from("red"),
+                position: RectPosition::Above(0),
+            },
+            AdditionalRect {
+                start: 500000,
+                end: 1500000,
+                color: String::from("orange"),
+                position: RectPosition::Above(1),
+            },
+            AdditionalRect {
+                start: 2000000,
+                end: 30000000,
+                color: String::from("blue"),
+                position: RectPosition::Below(0),
+            },
+            AdditionalRect {
+                start: 1500000,
+                end: 2500000,
+                color: String::from("green"),
+                position: RectPosition::Below(1),
+            },
+            // Add more rectangles as needed
+        ];
+
+        let lollipops = vec![
+            Lollipop {
+                position: 5000000,
+                above: true,
+                letter: 'A',
+                color: String::from("red"),
+            },
+            Lollipop {
+                position: 20000000,
+                above: false,
+                letter: 'B',
+                color: String::from("blue"),
+            },
+            // Add more lollipops as needed
+        ];
+
+        svg_chromosome(
+            "chr2",
+            1000,
+            50,
+            "/data/ref/hs1/cytoBandMapped.bed",
+            "/data/chr1.svg",
+            &additional_rects,
+            &lollipops
+        )
+        .unwrap()
+    }
+}