vista/index.html at master · edilytics/vista · GitHub

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<!DOCTYPE html>
<html lang="en">
<head>
    <meta charset="UTF-8">
    <meta name="viewport" content="width=device-width, initial-scale=1.0">
    <title>Vista - DNA Alignment Visualization</title>
    <link rel="stylesheet" href="style.css">
</head>
<body>
    <header>
        <h1>Vista</h1>
        <p>DNA Sequence Alignment Visualization</p>
    </header>

    <main>
        <section id="visualization">
            <div class="viz-header">
                <h2>Alignment Visualization</h2>
                <button id="reset-zoom" class="reset-button">Reset Zoom</button>
            </div>
            <div id="alignment-container">
                <!-- DNA alignment will render here -->
            </div>
            <div id="navigation-slider">
                <div id="slider-track">
                    <div id="slider-viewport"></div>
                </div>
            </div>
        </section>

        <section id="controls">
            <div class="section-header">
                <h2>Parameters</h2>
                <button id="toggle-controls" class="collapse-button">▼</button>
            </div>
            <div id="sequence-inputs" class="collapsible-content">
                <div class="sequence-input-group">
                    <label for="name1">Sequence 1 Name:</label>
                    <input type="text" id="name1" placeholder="Sequence 1" class="name-input">
                    <label for="seq1">Sequence 1:</label>
                    <textarea id="seq1" rows="3" placeholder="Enter DNA sequence (A, T, C, G, or -)"></textarea>
                </div>
                <div class="sequence-input-group">
                    <label for="name2">Sequence 2 Name:</label>
                    <input type="text" id="name2" placeholder="Sequence 2" class="name-input">
                    <label for="seq2">Sequence 2:</label>
                    <textarea id="seq2" rows="3" placeholder="Enter DNA sequence (A, T, C, G, or -)"></textarea>
                </div>

                <!-- sgRNA Settings -->
                <div class="sgrna-settings">
                    <h3>sgRNA Settings (Optional)</h3>
                    <div class="sequence-input-group">
                        <label for="sgrnas">sgRNA Sequences (comma-separated):</label>
                        <textarea id="sgrnas" rows="2" placeholder="e.g., ATCGATCGATCGATCG,GCTAGCTAGCTAGCTA"></textarea>
                    </div>
                    <div class="sgrna-params">
                        <div class="param-group">
                            <label for="cut-site">Cut Site Offset:</label>
                            <input type="number" id="cut-site" value="-3" class="param-input">
                            <span class="param-help">Position relative to sgRNA 3' end</span>
                        </div>
                        <div class="param-group">
                            <label for="score-cutoff">Score Cutoff (%):</label>
                            <input type="number" id="score-cutoff" value="80" min="0" max="100" class="param-input">
                            <span class="param-help">Minimum match percentage</span>
                        </div>
                    </div>
                </div>

                <!-- Annotations -->
                <div class="annotations-settings">
                    <h3>Annotations (Optional)</h3>
                    <div id="annotations-list" class="annotations-list">
                        <!-- Annotations will be rendered here -->
                    </div>
                    <div class="annotation-add">
                        <div class="annotation-inputs">
                            <select id="annotation-seq" class="annotation-select">
                                <option value="seq1">Reference</option>
                                <option value="seq2">Amplicon 1</option>
                            </select>
                            <input type="number" id="annotation-start" placeholder="Start" min="0" class="annotation-input">
                            <input type="number" id="annotation-end" placeholder="End" min="0" class="annotation-input">
                            <input type="text" id="annotation-text" placeholder="Annotation text" class="annotation-input annotation-text-input">
                            <button id="add-annotation" class="add-annotation-button">Add</button>
                        </div>
                    </div>
                </div>
            </div>
        </section>

        <!-- sgRNA Results Sidebar -->
        <section id="sgrna-results" class="sgrna-sidebar hidden">
            <div class="sidebar-header">
                <h2>sgRNA Alignment Results</h2>
                <button id="toggle-sidebar" class="collapse-button">▼</button>
            </div>
            <div id="sgrna-results-content" class="sidebar-content">
                <!-- Results will be rendered here -->
            </div>
        </section>
    </main>

    <!-- Application scripts -->
    <script src="js/alignment.js"></script>
    <script src="js/sgrna-alignment.js"></script>
    <script src="js/annotations.js"></script>
    <script src="js/dna-alignment.js"></script>
    <script src="js/main.js"></script>
</body>
</html>