/* ===== GLOBAL LAYOUT 3 - SLEEK & MODERN =====
   Contemporary design with refined aesthetics */

* {
    box-sizing: border-box;
}

body {
    font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', 'Inter', 'Roboto', sans-serif;
    margin: 0;
    display: grid;
    grid-template-areas: "header  header header" "content content content" "footer  footer footer";
    grid-template-columns: 220px 1fr;
    grid-template-rows: auto 1fr auto;
    min-height: 100vh;
    background: linear-gradient(135deg, #f8fafc 0%, #f1f5f9 100%);
    color: #1e293b;
}

/* ===== HEADER =====
   Modern top navigation with glass effect */

header {
    grid-area: header;
    background: linear-gradient(135deg, #0f172a 0%, #1e293b 100%);
    color: #f1f5f9;
    padding: 20px 32px;
    box-shadow: 0 8px 32px rgba(15, 23, 42, 0.12);
    backdrop-filter: blur(10px);
    position: sticky;
    top: 0;
    z-index: 100;
}

header h1 {
    margin: 0;
    font-size: 1.8rem;
    font-weight: 700;
    letter-spacing: -0.5px;
}

header a {
    text-decoration: none;
    color: #f1f5f9;
    transition: all 0.3s cubic-bezier(0.4, 0, 0.2, 1);
    display: inline-block;
}

header a:hover {
    color: #e0f2fe;
    transform: translateY(-1px);
}


/* ===== SIDEBAR =====
   Left navigation panel */

sidebar {
    grid-area: sidebar;
    background: linear-gradient(180deg, #ffffff 0%, #f8fafc 100%);
    padding: 24px 16px;
    border-right: 1px solid #e2e8f0;
    box-shadow: 2px 0 8px rgba(0, 0, 0, 0.04);
}

sidebar li {
    margin-bottom: 12px;
    list-style: none;
}

sidebar a {
    text-decoration: none;
    color: #475569;
    font-weight: 500;
    display: block;
    padding: 10px 12px;
    border-radius: 8px;
    transition: all 0.2s cubic-bezier(0.4, 0, 0.2, 1);
    border-left: 3px solid transparent;
}

sidebar a:hover {
    color: #0f172a;
    background-color: #e0f2fe;
    border-left-color: #0284c7;
    transform: translateX(4px);
}

/* ===== CONTENT AREA =====
   Main page content section */

content {
    grid-area: content;
    background: linear-gradient(135deg, #f8fafc 0%, #f1f5f9 100%);
    padding: 40px;
}

content p {
    line-height: 1.8;
    margin: 0 0 20px 0;
    color: #475569;
}

/* ===== FOOTER =====
   Bottom navigation bar */

footer {
    grid-area: footer;
    background: linear-gradient(135deg, #0f172a 0%, #1e293b 100%);
    color: #cbd5e1;
    text-align: center;
    padding: 20px 32px;
    font-size: 0.85rem;
    box-shadow: 0 -8px 32px rgba(15, 23, 42, 0.12);
}

/* ===== HEADINGS =====
   Text section headers */

h2, h3, h4 {
    margin-top: 0;
    color: #0f172a;
    font-weight: 700;
    letter-spacing: -0.3px;
}

h2 { font-size: 1.875rem; margin-bottom: 24px; }
h3 { font-size: 1.375rem; margin-bottom: 16px; }
h4 { font-size: 1.125rem; margin-bottom: 12px; }

/* ===== FORMS =====
   Input forms and their styling */

form {
    background: white;
    padding: 28px;
    border-radius: 12px;
    border: 1px solid #e2e8f0;
    margin-bottom: 24px;
    box-shadow: 0 1px 3px rgba(0, 0, 0, 0.1), 0 1px 2px rgba(0, 0, 0, 0.06);
    transition: all 0.3s cubic-bezier(0.4, 0, 0.2, 1);
}

form:hover {
    box-shadow: 0 4px 6px rgba(0, 0, 0, 0.07), 0 2px 4px rgba(0, 0, 0, 0.05);
    border-color: #cbd5e1;
}

form p {
    margin-bottom: 16px;
    font-weight: 600;
    color: #1e293b;
}

/* ===== FILE INPUT =====
   Large file upload area */

input[type="file"] {
    display: block;
    width: 100%;
    padding: 40px 20px;
    margin-bottom: 16px;
    border: 2px dashed #cbd5e1;
    border-radius: 12px;
    cursor: pointer;
    transition: all 0.3s cubic-bezier(0.4, 0, 0.2, 1);
    background: linear-gradient(135deg, #f8fafc 0%, #f1f5f9 100%);
    font-family: inherit;
    text-align: center;
    font-size: 1rem;
    color: #475569;
    font-weight: 500;
}

input[type="file"]::file-selector-button {
    background: linear-gradient(135deg, #0284c7 0%, #0369a1 100%);
    color: white;
    padding: 10px 20px;
    border: none;
    border-radius: 8px;
    cursor: pointer;
    font-weight: 600;
    font-size: 0.9rem;
    margin-right: 24px;
    transition: all 0.2s cubic-bezier(0.4, 0, 0.2, 1);
    box-shadow: 0 2px 8px rgba(2, 132, 199, 0.3);
}

input[type="file"]::file-selector-button:hover {
    transform: translateY(-2px);
    box-shadow: 0 4px 12px rgba(2, 132, 199, 0.4);
}

input[type="file"]:hover {
    border-color: #0284c7;
    background: linear-gradient(135deg, #f1f5f9 0%, #e0f2fe 100%);
    box-shadow: 0 4px 12px rgba(2, 132, 199, 0.08);
}

input[type="file"]:focus {
    outline: none;
    border-color: #0284c7;
    box-shadow: 0 0 0 4px rgba(2, 132, 199, 0.1);
}

/* ===== RADIO BUTTONS =====
   Styling for radio button groups */

.radio-group {
    margin-bottom: 20px;
    display: flex;
    align-items: center;
    gap: 20px;
    padding: 16px;
    background: #f8fafc;
    border-radius: 8px;
}

.radio-group label {
    display: inline-flex;
    align-items: center;
    cursor: pointer;
    font-weight: 500;
    gap: 8px;
    color: #475569;
}

input[type="radio"] {
    cursor: pointer;
    accent-color: #0284c7;
}

/* ===== BUTTONS =====
   All button styling and states */

button, input[type="submit"], input[type="button"] {
    font-family: inherit;
    padding: 11px 22px;
    border: none;
    border-radius: 8px;
    font-size: 1rem;
    font-weight: 600;
    cursor: pointer;
    transition: all 0.2s cubic-bezier(0.4, 0, 0.2, 1);
    display: inline-flex;
    align-items: center;
    justify-content: center;
    gap: 8px;
    white-space: nowrap;
    letter-spacing: 0.3px;
}

button[type="submit"], input[type="submit"], .submit {
    background: linear-gradient(135deg, #0284c7 0%, #0369a1 100%);
    color: white;
    box-shadow: 0 4px 12px rgba(2, 132, 199, 0.3);
}

button[type="submit"]:hover, input[type="submit"]:hover, .submit:hover {
    transform: translateY(-2px);
    box-shadow: 0 8px 20px rgba(2, 132, 199, 0.4);
}

button[type="submit"]:active, input[type="submit"]:active, .submit:active {
    transform: translateY(0);
}

button[type="submit"]:disabled, input[type="submit"]:disabled, .submit:disabled {
    opacity: 0.6;
    cursor: not-allowed;
    transform: none;
}

button.secondary, .secondary[type="submit"] {
    background-color: #e2e8f0;
    color: #475569;
    box-shadow: none;
}

button.secondary:hover, .secondary[type="submit"]:hover {
    background-color: #cbd5e1;
    color: #1e293b;
}

/* ===== ALIGNMENT CARDS =====
   Individual result cards */

.alignment-card {
    border: 1px solid #e2e8f0;
    border-radius: 12px;
    padding: 24px;
    transition: all 0.3s cubic-bezier(0.4, 0, 0.2, 1);
    cursor: pointer;
    background: white;
    overflow-x: auto;
    box-shadow: 0 1px 3px rgba(0, 0, 0, 0.08);
}

.alignment-card:hover {
    border-color: #0284c7;
    box-shadow: 0 8px 24px rgba(2, 132, 199, 0.15);
    transform: translateY(-4px);
}

.alignment-card h4 {
    color: #0284c7;
    margin-top: 0;
}

.alignment-card p {
    margin: 10px 0;
    color: #475569;
    line-height: 1.6;
}

.alignment-card pre {
    padding: 14px;
    margin: 12px 0;
    font-size: 0.9rem;
}

/* ===== GAP HIGHLIGHTING =====
   Highlights missing sections in sequences */

.gap {
    background-color: #fde047;
    padding: 0 2px;
    border-radius: 2px;
    color: #78350f;
}

/* ===== MESSAGE BOXES =====
   Styling for error and success messages */

.error-message, [style*="border: 3px solid red"] {
    background: linear-gradient(135deg, #fef2f2 0%, #fce7e6 100%);
    border: 1.5px solid #fca5a5 !important;
    border-radius: 10px !important;
    padding: 16px !important;
    margin-top: 16px !important;
    color: #991b1b;
    font-weight: 500;
}

.error-message p, [style*="border: 3px solid red"] p {
    margin: 0;
}

.success-message {
    background: linear-gradient(135deg, #f0fdf4 0%, #e7f5e3 100%);
    border: 1.5px solid #86efac;
    border-radius: 10px;
    padding: 16px;
    margin-top: 16px;
    color: #15803d;
    font-weight: 500;
}

/* ===== TABLES =====
   Data tables with headers and rows */

table {
    border-collapse: collapse;
    width: 100%;
    background-color: white;
    border-radius: 10px;
    overflow: hidden;
    box-shadow: 0 1px 3px rgba(0, 0, 0, 0.08);
}

th {
    background: linear-gradient(135deg, #0f172a 0%, #1e293b 100%);
    color: white;
    padding: 14px;
    font-weight: 600;
    letter-spacing: 0.3px;
}

th, td {
    text-align: center;
    border-bottom: 1px solid #e2e8f0;
    padding: 14px;
}

tr:hover {
    background-color: #f8fafc;
}

/* ===== LINKS =====
   Hyperlink styling */

a {
    color: #0284c7;
    text-decoration: none;
    transition: all 0.2s cubic-bezier(0.4, 0, 0.2, 1);
    font-weight: 500;
}

a:hover {
    color: #0369a1;
    text-decoration: underline;
    text-decoration-thickness: 2px;
    text-underline-offset: 4px;
}

/* ===== CODE BLOCKS =====
   Monospace code display areas */

pre {
    background: linear-gradient(135deg, #f8fafc 0%, #f1f5f9 100%);
    border: 1px solid #e2e8f0;
    border-radius: 8px;
    padding: 16px;
    font-family: 'Monaco', 'Courier New', 'JetBrains Mono', monospace;
    font-size: 0.95rem;
    overflow-x: auto;
    line-height: 1.5;
    color: #1e293b;
}

/* ===== SEQUENCE VIEWER =====
   Displays DNA/protein sequences in a scrollable container */

.sequence-viewer {
    border: 1px solid #e2e8f0;
    border-radius: 8px;
    overflow-x: auto;
    overflow-y: hidden;
    background: linear-gradient(135deg, #f8fafc 0%, #f1f5f9 100%);
}

.sequence-viewer pre {
    margin: 0;
    border: none;
    border-radius: 0;
    padding: 16px;
    overflow: visible;
    background-color: transparent;
    white-space: pre;
}

.sequence-viewer pre:not(:last-child) {
    border-bottom: 1px solid #e2e8f0;
}

.sequence-viewer pre:nth-child(2) {
    background-color: rgba(255, 255, 255, 0.5);
}

/* ===== SONIFICATION CONTAINER =====
   Layout for form and sound key side by side */

.sonification-container {
    display: flex;
    gap: 24px;
    align-items: flex-start;
}

.sonification-container form {
    flex: 4;
    margin: 0;
}

/* ===== SOUND KEY =====
   Legend showing audio symbols and their meanings */

.sound-key {
    flex: 0 0 auto;
    display: flex;
    flex-direction: column;
    gap: 16px;
    padding: 28px;
    background: #f8fafc;
    border-radius: 8px;
    border: 1px solid #e2e8f0;
    min-width: 220px;
}

.sound-key h4 {
    margin: 0 0 8px 0;
    color: #0f172a;
}

.sound-key h5 {
    margin: 12px 0 4px 0;
}

.sound-key-item {
    display: flex;
    align-items: center;
    gap: 8px;
    padding: 6px 0;
}

.sound-symbol {
    font-size: 1.5rem;
    display: flex;
    align-items: center;
    justify-content: center;
    flex-shrink: 0;
}

.sound-label {
    font-size: 0.85rem;
    color: #475569;
    font-weight: 500;
}

.sound-key-divider {
    border: none;
    border-top: 1px solid #cbd5e1;
    margin: 4px 0;
}

.sound-key-image {
    height: 2rem;
    width: auto;
    object-fit: contain;
}

/* ===== MIDI COMPONENTS =====
   Audio player and visualizer elements */

midi-player {
    margin: 24px 0;
}

midi-visualizer {
    margin: 24px 0;
    background-color: white;
    border: 1px solid #e2e8f0;
    border-radius: 10px;
    padding: 16px;
}

/* ===== CODON/BASE HIGHLIGHTING =====
   MIDI sync visualization */

.base {
    display: inline;
}

.base.active {
    background-color: #fbbf24;
    font-weight: bold;
    padding: 2px 4px;
    border-radius: 3px;
}

.codon {
    display: inline;
}

.codon.active {
    padding: 2px;
    border-radius: 3px;
}

.codon.match {
    background-color: #4caf50;
    color: white;
}

.codon.mismatch {
    background-color: #f44336;
    color: white;
}

.codon.stop-codon {
    color: #8b0000;
    font-weight: bold;
}

/* ===== RESPONSIVE DESIGN =====
   Styles that adapt to different screen sizes */

@media (max-width: 768px) {
    body {
        grid-template-areas: "header" "content" "footer";
        grid-template-columns: 1fr;
    }

    sidebar {
        display: none;
    }

    content {
        padding: 24px;
    }

    header {
        padding: 16px 20px;
    }

    header h1 {
        font-size: 1.4rem;
    }

    h2 { font-size: 1.5rem; }
    h3 { font-size: 1.125rem; }

    form {
        padding: 20px;
    }

    .alignment-card {
        padding: 16px;
    }

    pre {
        font-size: 0.85rem;
        padding: 12px;
    }

    button, input[type="submit"], input[type="button"] {
        padding: 10px 18px;
        font-size: 0.95rem;
    }

    table {
        font-size: 0.9rem;
    }

    th, td {
        padding: 10px;
    }
}

@media (max-width: 480px) {
    content {
        padding: 16px;
    }

    header {
        padding: 12px 16px;
    }

    header h1 {
        font-size: 1.2rem;
    }

    h2 { font-size: 1.25rem; }
    h3 { font-size: 1rem; }

    form {
        padding: 16px;
    }

    .alignment-card {
        padding: 12px;
    }

    pre {
        font-size: 0.8rem;
        padding: 8px;
    }

    button, input[type="submit"], input[type="button"] {
        padding: 8px 14px;
        font-size: 0.9rem;
        width: 100%;
    }

    .radio-group {
        flex-direction: column;
        gap: 12px;
    }

    .sonification-container {
        flex-direction: column;
        gap: 16px;
    }

    .sound-key {
        min-width: auto;
    }
}

@media print {
    header, footer, sidebar {
        display: none;
    }

    content {
        padding: 0;
        background-color: white;
    }

    .alignment-card {
        page-break-inside: avoid;
    }
}