const pptxgen = require("pptxgenjs");

const pres = new pptxgen();
pres.layout = "LAYOUT_16x9";
pres.title = "Introduction to Genetics";
pres.author = "Genetics Template";

// ─── COLOR PALETTE ────────────────────────────────────────────────────────────
// Deep navy dominant, teal accent, amber highlight, light slate text
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// ─── HELPER: section label pill ───────────────────────────────────────────────
function sectionPill(slide, label, x, y) {
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}

// ─── SLIDE 1: TITLE ───────────────────────────────────────────────────────────
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}

// ─── SLIDE 2: TABLE OF CONTENTS ───────────────────────────────────────────────
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  const topics = [
    ["01", "DNA Structure & Replication"],
    ["02", "Genes & the Genome"],
    ["03", "Mendelian Inheritance"],
    ["04", "Non-Mendelian Inheritance"],
    ["05", "Mutations & Genetic Variation"],
    ["06", "Genetic Technologies"],
  ];

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}

// ─── SLIDE 3: DNA STRUCTURE ────────────────────────────────────────────────────
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  sectionPill(sl, "DNA STRUCTURE & REPLICATION", 0.45, 0.22);
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  // Key fact cards
  const cards = [
    { icon: "🧬", title: "Structure", body: "DNA is a double helix made of two antiparallel polynucleotide strands wound around each other, stabilised by hydrogen bonds between complementary bases." },
    { icon: "🔗", title: "Base Pairing", body: "Adenine (A) pairs with Thymine (T) via 2 H-bonds; Guanine (G) pairs with Cytosine (C) via 3 H-bonds. This is Chargaff's Rule." },
    { icon: "⚙️", title: "Replication", body: "Semi-conservative: each strand acts as a template. Key enzymes: Helicase (unwinds), Primase (primer), DNA Polymerase III (synthesis 5'→3'), Ligase (seals)." },
  ];

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}

// ─── SLIDE 4: GENES & GENOME ───────────────────────────────────────────────────
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  sl.addText("02", { x: 8.8, y: 0.2, w: 0.8, h: 0.4, fontSize: 22, bold: true, color: C.divider, align: "right" });

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  sl.addText("From DNA to Protein", { x: 0.45, y: 0.6, w: 8, h: 0.65, fontSize: 30, bold: true, color: C.white });
  sl.addShape(pres.ShapeType.rect, { x: 0.45, y: 1.3, w: 9, h: 0.03, fill: { color: C.divider }, line: { color: C.divider } });

  // Left column: key definitions
  const defs = [
    ["Gene", "A segment of DNA that encodes a functional product (protein or RNA)."],
    ["Genome", "The complete set of genetic material in an organism (~3 billion bp in humans)."],
    ["Locus", "The fixed position of a gene on a chromosome."],
    ["Allele", "Alternative forms of a gene at a given locus."],
    ["Genotype", "The genetic makeup of an individual (e.g. Aa, BB)."],
    ["Phenotype", "The observable traits produced by genotype × environment."],
  ];

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}

// ─── SLIDE 5: MENDELIAN INHERITANCE ───────────────────────────────────────────
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  sl.addText("Mendel's Laws", { x: 0.45, y: 0.6, w: 8, h: 0.65, fontSize: 30, bold: true, color: C.white });
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  // Three law cards (horizontal)
  const laws = [
    { num: "I", name: "Law of Segregation", body: "Allele pairs separate during gamete formation. Each gamete carries only one allele for each gene." },
    { num: "II", name: "Law of Independent Assortment", body: "Genes on different chromosomes assort independently. Produces 9:3:3:1 ratio in dihybrid crosses." },
    { num: "III", name: "Law of Dominance", body: "One allele can mask the expression of another. Dominant (uppercase) is expressed; recessive (lowercase) is masked." },
  ];

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  // Punnett square example
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  sl.addText("AA  :  Aa  :  Aa  :  aa   →   Phenotype ratio 3:1  |  Genotype ratio 1:2:1", {
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  sl.addText("Dominant phenotype (AA + Aa) = 75%   |   Recessive phenotype (aa) = 25%", {
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}

// ─── SLIDE 6: NON-MENDELIAN INHERITANCE ──────────────────────────────────────
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  sl.addShape(pres.ShapeType.rect, { x: 0, y: 0, w: 0.18, h: 5.625, fill: { color: C.teal }, line: { color: C.teal } });
  sl.addText("04", { x: 8.8, y: 0.2, w: 0.8, h: 0.4, fontSize: 22, bold: true, color: C.divider, align: "right" });

  sectionPill(sl, "NON-MENDELIAN INHERITANCE", 0.45, 0.22);
  sl.addText("Beyond Mendel", { x: 0.45, y: 0.6, w: 8, h: 0.65, fontSize: 30, bold: true, color: C.white });
  sl.addShape(pres.ShapeType.rect, { x: 0.45, y: 1.3, w: 9, h: 0.03, fill: { color: C.divider }, line: { color: C.divider } });

  const patterns = [
    ["Incomplete Dominance", "Neither allele is fully dominant. Heterozygote shows intermediate phenotype (e.g. red × white = pink flowers in snapdragons)."],
    ["Codominance", "Both alleles are equally expressed simultaneously (e.g. ABO blood type AB; both A and B antigens present)."],
    ["Multiple Alleles", "More than two alleles exist for a gene in the population (e.g. ABO locus has I^A, I^B, and i alleles)."],
    ["Polygenic Traits", "Phenotype controlled by multiple genes, producing a continuous distribution (e.g. skin colour, height, IQ)."],
    ["Epistasis", "One gene masks or modifies the expression of another (e.g. coat colour in Labrador retrievers: 9:3:4 ratio)."],
    ["Sex-Linkage", "Genes on X or Y chromosome. X-linked recessive traits are more prevalent in males (e.g. haemophilia, colour blindness)."],
  ];

  patterns.forEach(([term, body], i) => {
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    sl.addText(term, { x: x + 0.2, y: y + 0.1, w: 4.35, h: 0.38, fontSize: 11.5, bold: true, color: C.amber });
    sl.addText(body, { x: x + 0.2, y: y + 0.5, w: 4.3, h: 0.65, fontSize: 9.5, color: C.lightSlate, wrap: true });
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}

// ─── SLIDE 7: MUTATIONS & VARIATION ──────────────────────────────────────────
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  sl.addText("05", { x: 8.8, y: 0.2, w: 0.8, h: 0.4, fontSize: 22, bold: true, color: C.divider, align: "right" });

  sectionPill(sl, "MUTATIONS & GENETIC VARIATION", 0.45, 0.22);
  sl.addText("Mutations", { x: 0.45, y: 0.6, w: 8, h: 0.65, fontSize: 30, bold: true, color: C.white });
  sl.addShape(pres.ShapeType.rect, { x: 0.45, y: 1.3, w: 9, h: 0.03, fill: { color: C.divider }, line: { color: C.divider } });

  // Two-column layout: left = point mutations, right = chromosomal
  // Left header
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  const pointMuts = [
    ["Silent", "Codon changes but same amino acid (synonymous)."],
    ["Missense", "Codon changes → different amino acid (e.g. sickle cell: Glu→Val)."],
    ["Nonsense", "Codon changes → stop codon → truncated protein."],
    ["Frameshift", "Insertion or deletion shifts the reading frame downstream."],
  ];
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    sl.addText(type, { x: 0.5, y: y + 0.05, w: 1.2, h: 0.28, fontSize: 10.5, bold: true, color: C.amber });
    sl.addText(desc, { x: 0.5, y: y + 0.32, w: 4.1, h: 0.32, fontSize: 9.5, color: C.lightSlate });
  });

  // Right header
  sl.addShape(pres.ShapeType.rect, { x: 5.15, y: 1.42, w: 4.4, h: 0.38, fill: { color: C.navyMid }, line: { color: C.navyMid } });
  sl.addText("CHROMOSOMAL MUTATIONS", { x: 5.15, y: 1.42, w: 4.4, h: 0.38, fontSize: 11, bold: true, color: C.teal, align: "center", valign: "middle", charSpacing: 1.5 });

  const chromMuts = [
    ["Deletion", "Loss of a chromosomal segment (e.g. cri du chat syndrome, del 5p)."],
    ["Duplication", "Extra copy of a segment → gene dosage imbalance."],
    ["Inversion", "Segment reversed within same chromosome; may disrupt genes."],
    ["Translocation", "Segment moves to a non-homologous chromosome (e.g. Philadelphia chromosome t(9;22))."],
  ];
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    const y = 1.92 + i * 0.78;
    sl.addShape(pres.ShapeType.roundRect, { x: 5.15, y, w: 4.4, h: 0.68, fill: { color: C.cardBg }, line: { color: C.divider }, rectRadius: 0.08 });
    sl.addText(type, { x: 5.27, y: y + 0.05, w: 1.5, h: 0.28, fontSize: 10.5, bold: true, color: C.amber });
    sl.addText(desc, { x: 5.27, y: y + 0.32, w: 4.1, h: 0.32, fontSize: 9.5, color: C.lightSlate });
  });
}

// ─── SLIDE 8: GENETIC TECHNOLOGIES ───────────────────────────────────────────
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  sl.addShape(pres.ShapeType.rect, { x: 0, y: 0, w: 0.18, h: 5.625, fill: { color: C.teal }, line: { color: C.teal } });
  sl.addText("06", { x: 8.8, y: 0.2, w: 0.8, h: 0.4, fontSize: 22, bold: true, color: C.divider, align: "right" });

  sectionPill(sl, "GENETIC TECHNOLOGIES", 0.45, 0.22);
  sl.addText("Modern Tools", { x: 0.45, y: 0.6, w: 8, h: 0.65, fontSize: 30, bold: true, color: C.white });
  sl.addShape(pres.ShapeType.rect, { x: 0.45, y: 1.3, w: 9, h: 0.03, fill: { color: C.divider }, line: { color: C.divider } });

  const tools = [
    { icon: "🔬", name: "PCR", desc: "Polymerase Chain Reaction amplifies specific DNA sequences exponentially using thermocycling: denature → anneal primers → extend." },
    { icon: "✂️", name: "CRISPR-Cas9", desc: "Precise genome editing using guide RNA to direct the Cas9 nuclease to cut a target sequence; enables knock-in, knock-out, and repair." },
    { icon: "📊", name: "DNA Sequencing", desc: "Sanger (chain-termination) and Next-Gen Sequencing (NGS) methods determine the nucleotide sequence of DNA fragments rapidly." },
    { icon: "🔭", name: "Gel Electrophoresis", desc: "Separates DNA fragments by size through an agarose gel under electric current. Smaller fragments migrate further." },
    { icon: "🗺️", name: "SNP Genotyping", desc: "Single Nucleotide Polymorphisms used in GWAS studies to identify loci associated with complex diseases or traits." },
    { icon: "🧪", name: "Gene Therapy", desc: "Introduces functional genes into cells to correct genetic disorders. Uses viral vectors (e.g. AAV) or lipid nanoparticles for delivery." },
  ];

  tools.forEach((tool, i) => {
    const col = i % 3;
    const row = Math.floor(i / 3);
    const x = 0.38 + col * 3.2;
    const y = 1.5 + row * 1.95;

    sl.addShape(pres.ShapeType.roundRect, { x, y, w: 3.0, h: 1.78, fill: { color: C.cardBg }, line: { color: C.teal, size: 0.6 }, rectRadius: 0.1 });
    sl.addText(tool.icon, { x, y: y + 0.1, w: 3.0, h: 0.42, fontSize: 20, align: "center" });
    sl.addText(tool.name, { x, y: y + 0.52, w: 3.0, h: 0.32, fontSize: 12, bold: true, color: C.white, align: "center" });
    sl.addText(tool.desc, { x: x + 0.12, y: y + 0.86, w: 2.76, h: 0.88, fontSize: 9, color: C.lightSlate, align: "left", wrap: true });
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}

// ─── SLIDE 9: KEY VOCABULARY ──────────────────────────────────────────────────
{
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  const vocab = [
    ["Homozygous", "Two identical alleles at a locus (AA or aa)"],
    ["Heterozygous", "Two different alleles at a locus (Aa)"],
    ["Diploid (2n)", "Two sets of chromosomes (46 in humans)"],
    ["Haploid (n)", "One set of chromosomes (23 in gametes)"],
    ["Mitosis", "Cell division → two genetically identical daughter cells"],
    ["Meiosis", "Cell division → four genetically unique haploid gametes"],
    ["Crossing Over", "Recombination between homologous chromosomes in meiosis I"],
    ["Linkage", "Genes close together on the same chromosome; tend to inherit together"],
    ["Hardy-Weinberg", "p² + 2pq + q² = 1; allele frequencies stay constant in ideal populations"],
    ["Penetrance", "Proportion of individuals with a genotype who show the associated phenotype"],
  ];

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    sl.addText(def, { x: x + 0.15, y: y + 0.36, w: 4.3, h: 0.3, fontSize: 9.5, color: C.lightSlate });
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// ─── SLIDE 10: CLOSING / THANK YOU ────────────────────────────────────────────
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  sl.addText("Questions & Discussion", { x: 2.5, y: 2.75, w: 7, h: 0.55, fontSize: 18, color: C.lightSlate, align: "center", italic: true });

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// ─── WRITE FILE ───────────────────────────────────────────────────────────────
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