mzcore 0.1.0 - Docs.rs

#![allow(clippy::missing_panics_doc)]
use base64::Engine;
use swash::{CacheKey, FontRef, scale::ScaleContext};

use crate::glycan::{
    GlycanDirection, GlycanPosition, GlycanRoot, GlycanStructure, render::element::GlycanSelection,
};
use std::{
    fmt::Write,
    io::BufWriter,
    path::{Path, PathBuf},
};

pub(super) struct Font {
    // Full content of the font file
    data: Vec<u8>,
    // Offset to the table directory
    offset: u32,
    // Cache key
    key: CacheKey,
}

impl Font {
    pub(super) fn from_file(path: PathBuf, index: usize) -> Option<Self> {
        // Read the full font file
        let data = std::fs::read(path).ok()?;
        // Create a temporary font reference for the first font in the file.
        // This will do some basic validation, compute the necessary offset
        // and generate a fresh cache key for us.
        let font = FontRef::from_index(&data, index)?;
        let (offset, key) = (font.offset, font.key);
        // Return our struct with the original file data and copies of the
        // offset and key from the font reference
        Some(Self { data, offset, key })
    }

    // Create the transient font reference for accessing this crate's
    // functionality.
    pub(super) fn as_ref(&self) -> FontRef<'_> {
        // Note that you'll want to initialize the struct directly here as
        // using any of the FontRef constructors will generate a new key which,
        // while completely safe, will nullify the performance optimizations of
        // the caching mechanisms used in this crate.
        FontRef {
            data: &self.data,
            offset: self.offset,
            key: self.key,
        }
    }
}

#[test]
fn test_rendering() {
    const COLUMN_SIZE: f32 = 30.0;
    const SUGAR_SIZE: f32 = 15.0;
    const STROKE_SIZE: f32 = 1.5;

    let font = Font::from_file(
        std::fs::read_dir(
            directories::UserDirs::font_dir(
                &directories::UserDirs::new().expect("Could not find user directories"),
            )
            .unwrap_or_else(|| Path::new("C:/WINDOWS/Fonts")), // Font directory not defined for windows
        )
        .expect("Could not open font directory")
        .find(|p| {
            p.as_ref()
                .is_ok_and(|p| p.file_name().eq_ignore_ascii_case("times.ttf"))
        })
        .expect("No font files")
        .expect("Could not open font file")
        .path(),
        0,
    )
    .expect("Invalid font");

    let mut html = String::new();
    let mut footnotes = Vec::new();
    write!(&mut html, "<html lang=\"en\"><head><meta charset=\"UTF-8\"><meta name=\"viewport\" content=\"width=device-width, initial-scale=1.0\"><title>Glycan render test</title></head><body>").unwrap();

    let codes = [
        (
            "G01670UQ",
            "Neu5Ac(a2-6)Gal(b1-4)GlcNAc(b1-2)Man(a1-3)[Gal(b1-4)GlcNAc(b1-2)Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(?1-",
        ),
        ("G13523IF", "Fuc(?1-?)Gal(?1-?)GalNAc(?1-"),
        ("G00613DO", "GlcN(b1-4)GlcNAc(b1-4)GlcNAc(b1-4)GlcNAc6S(?1-"),
        (
            "G00621IU",
            "Neu5Gc(a2-3/6)Gal(b1-4)[Fuc(a1-3)]GlcNAc(b1-2)[Gal(a1-3)Gal(b1-4)GlcNAc(b1-4)]Man(a1-3)[Neu5Ac(a2-8)Neu5Ac(a2-3/6)Gal(b1-4)GlcNAc(b1-3)Gal(b1-4)GlcNAc(b1-2)[Neu5Ac(a2-3/6)Gal(b1-4)[Fuc(a1-3)]GlcNAc(b1-6)]Man(a1-6)]Man(b1-4)GlcNAc(b1-4)[Fuc(a1-6)]GlcNAc(?1-",
        ),
        ("G01464QV", "Rha2,3,4Ac3(a1-2)[Xyl(b1-3)]Ara(a1-"),
        (
            "G04421VO",
            "Fruf(b2-1a)[Glc(a1-2)Glc(a1-2)Glc(a1-2)Glc(a1-2)Glc(a1-2)Glc(a1-2)]Glc",
        ),
        (
            "G04458LN",
            "Kdn(a2-3)Gal(b1-4)ManNAc(b1-2)[Kdn(a2-3)Gal(b1-4)GlcNAc(b1-4)]Man(a1-3)[GlcNAc(b1-4)][Kdn(a2-3)Gal(b1-4)GlcNAc(b1-2)[Neu5Gc(a2-3)Gal(b1-4)GlcNAc(b1-6)]Man(a1-6)]Man(b1-4)GlcNAc(b1-4)[Fuc(a1-6)]GlcNAc(b1-",
        ),
        ("G69524KC", "Xyl(?1-?)Ara(?1-?)[Gal(?1-?)]GlcA"),
        (
            "G37707YH",
            "Fuc(a1-2)Gal(b1-4)[Fuc(a1-3)]GlcNAc(b1-2)[Gal(a1-3)Gal(b1-4)GlcNAc(b1-4)]Man(a1-3)[GlcNAc(b1-4)][Neu5Gc(a2-3/6)Gal(b1-4)[Fuc(a1-3)]GlcNAc(b1-3)Gal(b1-4)GlcNAc(b1-2)[Neu5Ac(a2-3/6)Gal(b1-4)[Fuc(a1-3)]GlcNAc(b1-6)]Man(a1-6)]Man(b1-4)GlcNAc(b1-4)[Fuc(a1-6)]GlcNAc(?1-",
        ),
        (
            "G07370RP",
            "Rha(a1-3)Qui(b1-4)Rha(a1-2)Glc(b1-2)[Rha(a1-6)]Glc(b1-",
        ),
        ("G11504PZ", "Dig3CMe(b1-3)Oli(b1-3)Oli(b1-"),
        ("G64699IM", "GlcA(b1-3)GalNAc(b1-4)4eLeg?5,7Ac2(a2-"),
        (
            "G14402AU",
            "D-Araf(b1-5)Dha(?2-3)[GalA(a1-4)GalA(a1-4)]GalA(a1-4)GalA",
        ),
        ("G08395BZ", "Glc(b1-2a)[Ido(b1-3)]Psif"),
        (
            "G49642ZT",
            "Man(?1-?)[Man(?1-?)]Man(?1-?)[Man(?1-?)]Man(?1-?)GlcNAc(?1-?)[Fuc(?1-?)][Fuc(?1-?)]GlcNAc(?1-",
        ),
        (
            "G59426OB",
            "Hex(?1-?)HexNAc(?1-?)HexA(?1-?)Gal(?1-?)GalNAc-ol",
        ),
        (
            "G75424NV",
            "Hex?(?1-?)Hex?NAc(?1-?)[Hex?NAc(?1-?)]Hex?(?1-?)[Hex?(?1-?)[Hex?(?1-?)]Hex?(?1-?)][Hex?NAc(?1-?)]Hex?(?1-?)Hex?NAc(?1-?)Hex?NAc(?1-",
        ),
        (
            "G36128WO",
            "Ido(b1-3)ManNAc(?1-3)[Ido(b1-3)L-AllNAc(b1-3)Ido(b1-4)AltNAc(b1-6)]Tal(b1-4)D-Ido(?1-",
        ),
        (
            "G83422GV",
            "L-6dTal(a1-3)[Fuc(a1-2)Gal(b1-4)GlcNAc(b1-3)Gal(b1-4)]GlcNAc(b1-3)Gal(b1-3)[Neu5Ac(a2-3)Gal(b1-4)[Fuc(a1-3)]GlcNAc(b1-6)]GalNAc(a1-",
        ),
        ("G09073GJ", "GalNAc(?1-?)GlcA2,3NAc2(?1-?)D-FucNAc"),
        (
            "G00069DT",
            "Neu(a2-3)Gal(b1-4)GlcNAc(b1-3)Gal(b1-4)GlcNAc(b1-3)Gal(b1-4)Glc(b1-",
        ),
        (
            "G00468KU",
            "GlcNAc(b1-2)Man(a1-3)[GlcNAc(b1-4)][Man(a1-?)Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(?1-",
        ),
        (
            "G75079FY",
            "Neu5Ac(?2-?)Gal(?1-?)GlcNAc(?1-?)Man(?1-?)[Neu5Ac(?2-?)Gal(?1-?)GlcNAc(?1-?)Man(?1-?)][GlcNAc(?1-?)]Man(?1-?)GlcNAc(?1-?)[Fuc(?1-?)]GlcNAc",
        ),
    ];

    let mut context = ScaleContext::new();
    for (index, (_, iupac)) in codes.iter().enumerate() {
        let structure = GlycanStructure::from_short_iupac(iupac, 0..iupac.len(), 0).unwrap();
        let rendered = structure
            .render(
                GlycanRoot::Text("pep".to_string()),
                COLUMN_SIZE,
                SUGAR_SIZE,
                STROKE_SIZE,
                if index % 3 == 0 {
                    GlycanDirection::LeftToRight
                } else {
                    GlycanDirection::TopDown
                },
                GlycanSelection::FULL,
                [66, 66, 66],
                [255, 255, 255],
                &mut footnotes,
            )
            .unwrap();
        rendered.to_svg(&mut html).unwrap();
        let (bitmap, width) = rendered.to_bitmap(
            if index % 2 == 0 {
                zeno::Format::subpixel_bgra()
            } else {
                zeno::Format::Alpha
            },
            font.as_ref(),
            &mut context,
        );
        let mut buffer = Vec::new();
        let mut w = BufWriter::new(&mut buffer);
        let mut encoder =
            png::Encoder::new(&mut w, width as u32, (bitmap.len() / 4 / width) as u32);
        encoder.set_color(png::ColorType::Rgba);
        encoder.set_depth(png::BitDepth::Eight);
        let mut writer = encoder.write_header().unwrap();
        writer.write_image_data(&bitmap).unwrap();
        drop(writer);
        drop(w);

        write!(&mut html, "<img src=\"data:image/png;base64, ").unwrap();
        base64::engine::general_purpose::STANDARD.encode_string(&buffer, &mut html);
        write!(&mut html, "\"/>").unwrap();
    }

    for (index, selection) in [
        (
            0,
            GlycanSelection::Subtree(
                Some(&GlycanPosition {
                    inner_depth: 2,
                    series_number: 2,
                    branch: Vec::new(),
                    attachment: None,
                }),
                &[],
            ),
        ),
        (
            0,
            GlycanSelection::Subtree(
                Some(&GlycanPosition {
                    inner_depth: 2,
                    series_number: 2,
                    branch: Vec::new(),
                    attachment: None,
                }),
                &[GlycanPosition {
                    inner_depth: 4,
                    series_number: 4,
                    branch: vec![(1, 1)],
                    attachment: None,
                }],
            ),
        ),
        (
            0,
            GlycanSelection::Subtree(
                Some(&GlycanPosition {
                    inner_depth: 2,
                    series_number: 2,
                    branch: Vec::new(),
                    attachment: None,
                }),
                &[
                    GlycanPosition {
                        inner_depth: 5,
                        series_number: 5,
                        branch: vec![(0, 0)],
                        attachment: None,
                    },
                    GlycanPosition {
                        inner_depth: 3,
                        series_number: 3,
                        branch: vec![(1, 1)],
                        attachment: None,
                    },
                ],
            ),
        ),
        (
            0,
            GlycanSelection::Subtree(
                Some(&GlycanPosition {
                    inner_depth: 4,
                    series_number: 4,
                    branch: vec![(1, 1)],
                    attachment: None,
                }),
                &[],
            ),
        ),
        (
            14,
            GlycanSelection::Subtree(
                Some(&GlycanPosition {
                    inner_depth: 0,
                    series_number: 0,
                    branch: Vec::new(),
                    attachment: None,
                }),
                &[GlycanPosition {
                    inner_depth: 1,
                    series_number: 1,
                    branch: vec![(0, 0)],
                    attachment: None,
                }],
            ),
        ),
        (
            14,
            GlycanSelection::Subtree(
                Some(&GlycanPosition {
                    inner_depth: 1,
                    series_number: 1,
                    branch: vec![(0, 0)],
                    attachment: None,
                }),
                &[GlycanPosition {
                    inner_depth: 2,
                    series_number: 2,
                    branch: vec![(0, 0)],
                    attachment: None,
                }],
            ),
        ),
        (
            16,
            GlycanSelection::Subtree(
                Some(&GlycanPosition {
                    inner_depth: 1,
                    series_number: 1,
                    branch: Vec::new(),
                    attachment: None,
                }),
                &[
                    GlycanPosition {
                        inner_depth: 3,
                        series_number: 3,
                        branch: vec![(0, 0)],
                        attachment: None,
                    },
                    GlycanPosition {
                        inner_depth: 4,
                        series_number: 4,
                        branch: vec![(1, 1), (1, 1)],
                        attachment: None,
                    },
                ],
            ),
        ),
        (
            18,
            GlycanSelection::Subtree(
                Some(&GlycanPosition {
                    inner_depth: 1,
                    series_number: 1,
                    branch: vec![(0, 0)],
                    attachment: None,
                }),
                &[
                    GlycanPosition {
                        inner_depth: 3,
                        series_number: 3,
                        branch: vec![(0, 0), (0, 0)],
                        attachment: None,
                    },
                    GlycanPosition {
                        inner_depth: 6,
                        series_number: 6,
                        branch: vec![(0, 0), (1, 1)],
                        attachment: None,
                    },
                ],
            ),
        ),
        (
            1,
            GlycanSelection::Subtree(
                None,
                &[GlycanPosition {
                    inner_depth: 1,
                    series_number: 1,
                    branch: Vec::new(),
                    attachment: None,
                }],
            ),
        ),
        (
            1,
            GlycanSelection::Subtree(
                None,
                &[GlycanPosition {
                    inner_depth: 2,
                    series_number: 2,
                    branch: Vec::new(),
                    attachment: None,
                }],
            ),
        ),
        (
            // Y5
            21,
            GlycanSelection::Subtree(
                None,
                &[GlycanPosition {
                    inner_depth: 0,
                    series_number: 5,
                    branch: Vec::new(),
                    attachment: None,
                }],
            ),
        ),
        (
            // B3Y1gY2bY2a
            21,
            GlycanSelection::Subtree(
                Some(&GlycanPosition {
                    inner_depth: 2,
                    series_number: 3,
                    branch: vec![],
                    attachment: None,
                }),
                &[
                    GlycanPosition {
                        inner_depth: 3,
                        series_number: 1,
                        branch: vec![(1, 2)],
                        attachment: None,
                    },
                    GlycanPosition {
                        inner_depth: 3,
                        series_number: 2,
                        branch: vec![(2, 1)],
                        attachment: None,
                    },
                    GlycanPosition {
                        inner_depth: 3,
                        series_number: 2,
                        branch: vec![(0, 0)],
                        attachment: None,
                    },
                ],
            ),
        ),
        (
            // B2aY1a
            21,
            GlycanSelection::Subtree(
                Some(&GlycanPosition {
                    inner_depth: 3,
                    series_number: 2,
                    branch: vec![(0, 0)],
                    attachment: None,
                }),
                &[GlycanPosition {
                    inner_depth: 4,
                    series_number: 1,
                    branch: vec![(0, 0)],
                    attachment: None,
                }],
            ),
        ),
        (
            // B2bY1b
            21,
            GlycanSelection::Subtree(
                Some(&GlycanPosition {
                    inner_depth: 3,
                    series_number: 2,
                    branch: vec![(2, 1)],
                    attachment: None,
                }),
                &[GlycanPosition {
                    inner_depth: 4,
                    series_number: 1,
                    branch: vec![(2, 1)],
                    attachment: None,
                }],
            ),
        ),
        (
            // B1b
            21,
            GlycanSelection::Subtree(
                Some(&GlycanPosition {
                    inner_depth: 4,
                    series_number: 1,
                    branch: vec![(2, 1)],
                    attachment: None,
                }),
                &[],
            ),
        ),
        (
            // dHex3
            21,
            GlycanSelection::SingleSugar(&GlycanPosition {
                inner_depth: 2,
                series_number: 3,
                branch: vec![],
                attachment: None,
            }),
        ),
        (
            // dHex2a
            21,
            GlycanSelection::SingleSugar(&GlycanPosition {
                inner_depth: 3,
                series_number: 2,
                branch: vec![(0, 0)],
                attachment: None,
            }),
        ),
        (
            // dHex2b
            21,
            GlycanSelection::SingleSugar(&GlycanPosition {
                inner_depth: 3,
                series_number: 2,
                branch: vec![(2, 1)],
                attachment: None,
            }),
        ),
        (
            // dHex1b
            21,
            GlycanSelection::SingleSugar(&GlycanPosition {
                inner_depth: 4,
                series_number: 1,
                branch: vec![(2, 1)],
                attachment: None,
            }),
        ),
        (
            // B4a'
            22,
            GlycanSelection::Subtree(
                Some(&GlycanPosition {
                    inner_depth: 3,
                    series_number: 4,
                    branch: vec![(0, 0), (1, 1)],
                    attachment: None,
                }),
                &[],
            ),
        ),
    ] {
        let structure =
            GlycanStructure::from_short_iupac(codes[index].1, 0..codes[index].1.len(), 0).unwrap();
        if let Some(rendered) = structure.render(
            GlycanRoot::Symbol,
            COLUMN_SIZE,
            SUGAR_SIZE,
            STROKE_SIZE,
            GlycanDirection::TopDown,
            selection,
            [0, 0, 0],
            [255, 255, 255],
            &mut footnotes,
        ) {
            rendered.to_svg(&mut html).unwrap();
            let (bitmap, width) = rendered.to_bitmap(
                if index % 2 == 0 {
                    zeno::Format::subpixel_bgra()
                } else {
                    zeno::Format::Alpha
                },
                font.as_ref(),
                &mut context,
            );
            let mut buffer = Vec::new();
            let mut w = BufWriter::new(&mut buffer);
            let mut encoder =
                png::Encoder::new(&mut w, width as u32, (bitmap.len() / 4 / width) as u32);
            encoder.set_color(png::ColorType::Rgba);
            encoder.set_depth(png::BitDepth::Eight);
            let mut writer = encoder.write_header().unwrap();
            writer.write_image_data(&bitmap).unwrap();
            drop(writer);
            drop(w);

            write!(&mut html, "<img src=\"data:image/png;base64, ").unwrap();
            base64::engine::general_purpose::STANDARD.encode_string(&buffer, &mut html);
            write!(&mut html, "\"/>").unwrap();
        } else {
            write!(&mut html, "Render error: invalid root").unwrap();
        }
    }

    let structure = GlycanStructure::from_short_iupac(codes[0].1, 0..codes[0].1.len(), 0).unwrap();
    for root in [
        GlycanRoot::None,
        GlycanRoot::Line,
        GlycanRoot::Symbol,
        GlycanRoot::Text("pep".to_string()),
        GlycanRoot::Text("N".to_string()),
        GlycanRoot::Text("Arg".to_string()),
    ] {
        let rendered = structure
            .render(
                root,
                COLUMN_SIZE,
                SUGAR_SIZE,
                STROKE_SIZE,
                GlycanDirection::TopDown,
                GlycanSelection::FULL,
                [0, 0, 0],
                [255, 255, 255],
                &mut footnotes,
            )
            .unwrap();
        rendered.to_svg(&mut html).unwrap();
    }

    write!(&mut html, "<hr>").unwrap();
    if !footnotes.is_empty() {
        write!(&mut html, "<ol>").unwrap();
        for note in footnotes {
            write!(&mut html, "<li>{note}</li>").unwrap();
        }
        write!(&mut html, "</ol><hr>").unwrap();
    }
    for (code, _) in &codes {
        write!(
            &mut html,
            "<image src=\"https://image.glycosmos.org/snfg/png/{code}\"/>"
        )
        .unwrap();
    }
    write!(&mut html, "</body></html>").unwrap();
    std::fs::write("../rendered_glycans.html", html).unwrap();
}