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web_structure.txt
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Directory: .
==================================================
File: ./web/all_files.py
--------------------------------------------------
import os
def save_directory_structure_and_files(root_dir, output_file):
with open(output_file, 'w', encoding='utf-8') as out:
for dirpath, dirnames, filenames in os.walk(root_dir):
# Write the directory name
rel_path = os.path.relpath(dirpath, root_dir)
out.write(f"Directory: {rel_path}\n")
out.write("=" * 50 + "\n")
# Write file names and contents
for file in filenames:
file_path = os.path.join(dirpath, file)
out.write(f"File: {file_path}\n") # Include full file path
out.write("-" * 50 + "\n")
try:
with open(file_path, 'r', encoding='utf-8') as f:
out.write(f.read())
except Exception as e:
out.write(f"[Could not read file: {e}]\n")
out.write("\n" + "-" * 50 + "\n")
out.write("\n")
if __name__ == "__main__":
root_directory = "./web"
output_text_file = "web_structure.txt"
save_directory_structure_and_files(root_directory, output_text_file)
print(f"Directory structure and files saved to {output_text_file}")
--------------------------------------------------
File: ./web/index.html
--------------------------------------------------
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>DNAnalyzer - DNA Sequence Analysis with Machine Learning</title>
<meta name="description" content="DNAnalyzer is a powerful, privacy-focused DNA analysis tool using advanced machine learning for accurate, on-device genomic analysis.">
<!-- Stylesheets -->
<link rel="stylesheet" href="style.css">
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.0/css/all.min.css">
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<h1>Revolutionizing <span>DNA analysis</span> with machine learning</h1>
<p class="hero-subtitle">Powerful, privacy-focused DNA analysis using advanced ML algorithms designed for both researchers and individuals.</p>
<div class="hero-buttons">
<a href="analyzer/analyzer.html" class="btn btn-primary">
<i class="fas fa-dna btn-icon"></i> Try DNA Analysis
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</div>
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<div class="stat-number" id="statSequences">7M+</div>
<div class="stat-label">DNA Sequences</div>
</div>
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<div class="stat-number" id="statUsers">46+</div>
<div class="stat-label">Contributors</div>
</div>
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<div class="stat-number">86</div>
<div class="stat-label">Discord Members</div>
</div>
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</section>
<!-- Features Overview -->
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<h2>Why Choose <span class="gradient-text">DNAnalyzer</span>?</h2>
<p>Our cutting-edge technology provides unparalleled accuracy and insights while keeping your data secure.</p>
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</div>
<h3 class="card-title">Privacy-First Analysis</h3>
<p>Your genetic data never leaves your device. All computation is performed locally using our advanced on-device ML models.</p>
</div>
<div class="card">
<div class="card-icon">
<i class="fas fa-dna"></i>
</div>
<h3 class="card-title">Advanced DNA Analysis</h3>
<p>Identify open reading frames, high coverage regions, protein sequences, and transcription factor binding sites with precision.</p>
</div>
<div class="card">
<div class="card-icon">
<i class="fas fa-brain"></i>
</div>
<h3 class="card-title">Machine Learning Powered</h3>
<p>Our cutting-edge neural networks provide insights and pattern recognition beyond traditional analytics capabilities.</p>
</div>
</div>
</div>
</section>
<!-- Workflow Section -->
<section class="section section-bg-gradient">
<div class="container">
<div class="section-title">
<h2>How It Works</h2>
<p>A simple three-step process to analyze your DNA sequences</p>
</div>
<div class="steps-container">
<div class="step-item">
<div class="step-content">
<h3>Upload Your Sequence</h3>
<p>Upload your DNA sequence file in FASTA or FASTQ format. Your data stays on your device.</p>
</div>
</div>
<div class="step-item">
<div class="step-content">
<h3>Select Analysis Options</h3>
<p>Choose from a variety of analysis options, including codon detection, coverage analysis, and protein prediction.</p>
</div>
</div>
<div class="step-item">
<div class="step-content">
<h3>Get Comprehensive Results</h3>
<p>Receive detailed insights with visualizations and downloadable reports for your research.</p>
</div>
</div>
</div>
</div>
</section>
<!-- Feature Details Section -->
<section class="section">
<div class="container">
<div class="section-title">
<h2>Powerful Analysis Features</h2>
<p>Comprehensive tools designed for researchers, students, and enthusiasts</p>
</div>
<div class="feature-card">
<div class="feature-icon feature-icon-blue">
<i class="fas fa-search"></i>
</div>
<div class="feature-content">
<h3>Open Reading Frame Identification</h3>
<p>Scans DNA for start and stop codons to identify protein-coding sequences (open reading frames). Recognizes canonical start codons (e.g., ATG) and stop codons to pinpoint the locations of putative proteins within a genome.</p>
</div>
</div>
<div class="feature-card">
<div class="feature-icon feature-icon-magenta">
<i class="fas fa-chart-bar"></i>
</div>
<div class="feature-content">
<h3>GC-Rich Region Detection</h3>
<p>Locates high coverage (GC-rich) regions in the DNA, often associated with gene-dense areas and promoter regions. Flags GC-rich stretches to help identify potential regulatory regions.</p>
</div>
</div>
<div class="feature-card">
<div class="feature-icon feature-icon-orange">
<i class="fas fa-microscope"></i>
</div>
<div class="feature-content">
<h3>Core Promoter Element Identification</h3>
<p>Scans for known core promoter motifs in the DNA sequence, such as the TATA box, BRE, INR, and DPE motifs. Detecting these elements can indicate the presence of gene promoters, helping you locate potential gene start sites.</p>
</div>
</div>
</div>
</section>
<!-- CTA Section -->
<section class="section section-bg-dark">
<div class="container text-center">
<h2>Ready to Start Analyzing?</h2>
<p class="mb-xl">Join thousands of researchers and scientists using DNAnalyzer for their genetic analysis needs.</p>
<div class="hero-buttons" style="justify-content: center;">
<a href="analyzer/analyzer.html" class="btn btn-primary">
<i class="fas fa-dna btn-icon"></i> Start Analyzing
</a>
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<i class="fas fa-book btn-icon"></i> Read Documentation
</a>
</div>
</div>
</section>
<!-- Disclaimer Section -->
<section class="section section-bg-dark disclaimer-section">
<div class="container">
<div class="disclaimer-content">
<h4 class="disclaimer-title">DNAnalyzer Disclaimer</h4>
<div class="disclaimer-text">
<p><strong>Limitation of Liability:</strong> The DNAnalyzer tool is intended for research, educational, and informational purposes only. The machine learning-based DNA analysis provides computational predictions that should not be used for medical diagnosis, clinical interpretation, or treatment decisions. DNAnalyzer is not a substitute for professional medical advice, diagnosis, or treatment.</p>
<p><strong>Analysis Limitations:</strong> DNAnalyzer's computational analysis, including open reading frame identification, GC-rich region detection, and promoter element identification, is based on algorithmic predictions using machine learning models trained on public datasets. Results may vary in accuracy depending on the quality of input data, sequence type, and other biological factors. The absence of identified genomic features does not rule out their presence, and the identification of features does not guarantee their biological relevance or function.</p>
<p><strong>Privacy Notice:</strong> While DNAnalyzer processes DNA sequences locally on your device to maximize privacy, users should exercise caution when uploading sensitive genetic information. We recommend against uploading human genomic data with identifiable personal information. DNAnalyzer is not responsible for any privacy implications resulting from user actions.</p>
<p><strong>Research Use Only:</strong> Results generated by DNAnalyzer should be experimentally validated before being used in research publications or academic work. Citations of DNAnalyzer should acknowledge its computational nature and inherent limitations.</p>
<p><strong>No Warranty:</strong> DNAnalyzer is provided "as is" without warranty of any kind, express or implied. The creators and contributors of DNAnalyzer disclaim all warranties, including but not limited to accuracy, reliability, and fitness for a particular purpose. In no event shall the creators, contributors, or copyright holders be liable for any claim, damages, or other liability arising from the use of this software.</p>
</div>
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</section>
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<footer class="footer">
<div class="container">
<div class="footer-grid">
<div class="footer-brand">
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<h4>Product</h4>
<ul>
<li><a href="features/features.html">Features</a></li>
<li><a href="analyzer/analyzer.html">DNA Analyzer</a></li>
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<li><a href="docs/docs.html">Documentation</a></li>
</ul>
</div>
<div class="footer-nav">
<h4>Resources</h4>
<ul>
<li><a href="docs/getting-started.md">Getting Started</a></li>
<li><a href="docs/citations.md">Citations</a></li>
<li><a href="docs/research/genes.md">Gene Research</a></li>
<li><a href="docs/samples/cli-arguments-examples.md">CLI Examples</a></li>
</ul>
</div>
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<h4>Community</h4>
<ul>
<li><a href="https://github.com/VerisimilitudeX/DNAnalyzer">GitHub</a></li>
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<li><a href="docs/contributing/CONTRIBUTING.md">Contributing</a></li>
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Copyright © Piyush Acharya 2025. DNAnalyzer is a fiscally sponsored 501(c)(3) nonprofit (EIN: 81-2908499). MIT License.
</div>
<div class="footer-links">
<a href="LICENSE.md">License</a>
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<a href="CITATION.cff">Citation</a>
</div>
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</footer>
<!-- JavaScript -->
<script src="index.js"></script>
</body>
</html>
--------------------------------------------------
File: ./web/humans.txt
--------------------------------------------------
[email protected] is built by a large team of engineers, designers, researchers, robots, and others in many different sites across the globe. It is updated continuously, and built with more tools and technologies than we can shake a stick at. If you'd like to help us out, see www.github.com/VerisimilitudeX/DNAnalyzer. We're always looking for more talent, and we're always looking for more ideas. If you have any suggestions, please let us know! We're always looking for ways to improve the site. If you have any questions, please feel free to contact us at [email protected]. We'd love to hear from you!
--------------------------------------------------
File: ./web/index.js
--------------------------------------------------
/**
* DNAnalyzer Main JavaScript
* Handles animations, interactivity and UI functionality
*/
document.addEventListener('DOMContentLoaded', function() {
// Initialize DNA Helix animation
initDNAHelix();
// Initialize mobile menu toggle
initMobileMenu();
// Initialize navbar scroll effect
initNavbarScroll();
// Initialize stats counter animation
initStatsAnimation();
});
/**
* Initialize the DNA Helix animation on the homepage
*/
function initDNAHelix() {
const dnaHelix = document.getElementById('dnaHelix');
if (!dnaHelix) return;
const numBases = 15;
const basePairs = [
['A', 'T'],
['T', 'A'],
['G', 'C'],
['C', 'G']
];
// Create base pairs
for (let i = 0; i < numBases; i++) {
const pairIndex = Math.floor(Math.random() * basePairs.length);
const [leftBase, rightBase] = basePairs[pairIndex];
const basePair = document.createElement('div');
basePair.className = 'base-pair';
basePair.style.top = `${i * 40}px`;
basePair.style.animationDelay = `${i * 0.2}s`;
const leftBaseElem = document.createElement('div');
leftBaseElem.className = 'base left-base';
leftBaseElem.textContent = leftBase;
leftBaseElem.style.animationDelay = `${i * 0.2}s`;
const rightBaseElem = document.createElement('div');
rightBaseElem.className = 'base right-base';
rightBaseElem.textContent = rightBase;
rightBaseElem.style.animationDelay = `${i * 0.2}s`;
const connector = document.createElement('div');
connector.className = 'base-connector';
connector.style.animationDelay = `${i * 0.2}s`;
basePair.appendChild(leftBaseElem);
basePair.appendChild(connector);
basePair.appendChild(rightBaseElem);
dnaHelix.appendChild(basePair);
}
}
/**
* Initialize the mobile menu toggle functionality
*/
function initMobileMenu() {
const mobileToggle = document.getElementById('mobileToggle');
const navLinks = document.getElementById('navLinks');
if (!mobileToggle || !navLinks) return;
mobileToggle.addEventListener('click', function() {
navLinks.classList.toggle('active');
// Change the icon based on the state
const icon = mobileToggle.querySelector('i');
if (navLinks.classList.contains('active')) {
icon.classList.remove('fa-bars');
icon.classList.add('fa-times');
} else {
icon.classList.remove('fa-times');
icon.classList.add('fa-bars');
}
});
// Close the mobile menu when clicking a link
const links = navLinks.querySelectorAll('a');
links.forEach(link => {
link.addEventListener('click', function() {
navLinks.classList.remove('active');
const icon = mobileToggle.querySelector('i');
icon.classList.remove('fa-times');
icon.classList.add('fa-bars');
});
});
}
/**
* Initialize the navbar scroll effect
*/
function initNavbarScroll() {
const navbar = document.getElementById('navbar');
if (!navbar) return;
window.addEventListener('scroll', function() {
if (window.scrollY > 50) {
navbar.classList.add('scrolled');
} else {
navbar.classList.remove('scrolled');
}
});
}
/**
* Animate number counting from 0 to target
* @param {HTMLElement} element - The element containing the number
* @param {number} target - The target number to count to
* @param {string} suffix - Optional suffix like '%' or 'M'
* @param {number} duration - Animation duration in milliseconds
*/
function animateNumber(element, target, suffix = '', duration = 2000) {
if (!element) return;
let start = 0;
let startTime = null;
const targetNum = parseFloat(target);
function easeOutQuart(x) {
return 1 - Math.pow(1 - x, 4);
}
function animate(timestamp) {
if (!startTime) startTime = timestamp;
const progress = Math.min((timestamp - startTime) / duration, 1);
const easedProgress = easeOutQuart(progress);
let currentValue = Math.floor(easedProgress * targetNum);
// Handle special cases
if (suffix === '%') {
const decimal = (easedProgress * targetNum) % 1;
if (decimal > 0) {
currentValue = (easedProgress * targetNum).toFixed(1);
}
}
element.textContent = `${currentValue}${suffix}`;
if (progress < 1) {
requestAnimationFrame(animate);
} else {
element.textContent = `${target}${suffix}`;
}
}
requestAnimationFrame(animate);
}
/**
* Initialize the stats counter animation with Intersection Observer
*/
function initStatsAnimation() {
const statsSection = document.querySelector('.stats-section');
if (!statsSection) return;
const statElements = {
accuracy: { elem: document.getElementById('statAccuracy'), target: '141', suffix: '' },
sequences: { elem: document.getElementById('statSequences'), target: '7', suffix: 'M+' },
users: { elem: document.getElementById('statUsers'), target: '46', suffix: '+' }
};
let animated = false;
const observer = new IntersectionObserver((entries) => {
entries.forEach(entry => {
if (entry.isIntersecting && !animated) {
// Animate each stat with staggered delays
Object.values(statElements).forEach((stat, index) => {
setTimeout(() => {
if (stat.elem) {
animateNumber(stat.elem, stat.target, stat.suffix, 2000);
}
}, index * 200);
});
animated = true;
observer.unobserve(statsSection);
}
});
}, { threshold: 0.5 });
observer.observe(statsSection);
}
/**
* Add smooth scrolling for anchor links
*/
document.querySelectorAll('a[href^="#"]').forEach(anchor => {
anchor.addEventListener('click', function(e) {
const targetId = this.getAttribute('href');
if (targetId === '#') return; // Skip if it's just "#"
const targetElement = document.querySelector(targetId);
if (targetElement) {
e.preventDefault();
window.scrollTo({
top: targetElement.offsetTop - 100,
behavior: 'smooth'
});
}
});
});
/**
* Add intersection observer for animating sections as they come into view
*/
const animateSections = document.querySelectorAll('.section, .feature-card, .card');
const observerOptions = {
threshold: 0.1,
rootMargin: '0px 0px -100px 0px'
};
const sectionObserver = new IntersectionObserver((entries) => {
entries.forEach(entry => {
if (entry.isIntersecting) {
entry.target.style.opacity = '1';
entry.target.style.transform = 'translateY(0)';
sectionObserver.unobserve(entry.target);
}
});
}, observerOptions);
animateSections.forEach(section => {
section.style.opacity = '0';
section.style.transform = 'translateY(20px)';
section.style.transition = 'opacity 0.6s ease, transform 0.6s ease';
sectionObserver.observe(section);
});
--------------------------------------------------
File: ./web/style.css
--------------------------------------------------
/* DNAnalyzer - Main Stylesheet
* Global styles for all pages
*/
:root {
/* Brand colors from logo */
--magenta: #ff0066;
--blue: #00a4ef;
--orange: #f48022;
--white: #ffffff;
--dark-bg: #001427;
/* Additional UI colors */
--dark-blue: #051e3e;
--light-blue: #2596be;
--light-gray: #f5f5f7;
--medium-gray: #86868b;
--dark-gray: #333333;
/* Functional colors */
--success: #34c759;
--warning: #ff9500;
--error: #ff3b30;
/* Typography */
--font-heading: 'Inter', -apple-system, BlinkMacSystemFont, sans-serif;
--font-body: 'Inter', -apple-system, BlinkMacSystemFont, sans-serif;
--font-mono: 'IBM Plex Mono', monospace;
/* Spacing */
--space-xs: 0.25rem;
--space-sm: 0.5rem;
--space-md: 1rem;
--space-lg: 1.5rem;
--space-xl: 2rem;
--space-xxl: 3rem;
/* Border radius */
--radius-sm: 4px;
--radius-md: 8px;
--radius-lg: 12px;
--radius-xl: 20px;
/* Shadows */
--shadow-sm: 0 2px 5px rgba(0, 0, 0, 0.1);
--shadow-md: 0 4px 12px rgba(0, 0, 0, 0.15);
--shadow-lg: 0 8px 20px rgba(0, 0, 0, 0.2);
/* Transitions */
--transition-fast: 0.2s ease;
--transition-normal: 0.3s ease;
--transition-slow: 0.5s ease;
/* Z-index layers */
--z-tooltip: 100;
--z-navbar: 200;
--z-modal: 300;
}
/* Reset & Base Styles */
*,
*::before,
*::after {
box-sizing: border-box;
margin: 0;
padding: 0;
}
html {
font-size: 16px;
scroll-behavior: smooth;
}
body {
font-family: var(--font-body);
background-color: var(--dark-bg);
color: var(--white);
line-height: 1.6;
overflow-x: hidden;
min-height: 100vh;
display: flex;
flex-direction: column;
-webkit-font-smoothing: antialiased;
-moz-osx-font-smoothing: grayscale;
}
h1, h2, h3, h4, h5, h6 {
font-family: var(--font-heading);
line-height: 1.2;
font-weight: 700;
margin-bottom: var(--space-md);
}
h1 {
font-size: 3.5rem;
margin-bottom: var(--space-lg);
}
h2 {
font-size: 2.5rem;
margin-bottom: var(--space-lg);
}
h3 {
font-size: 1.75rem;
}
h4 {
font-size: 1.375rem;
}
p {
margin-bottom: var(--space-md);
color: rgba(255, 255, 255, 0.85);
}
a {
color: var(--blue);
text-decoration: none;
transition: color var(--transition-fast);
}
a:hover {
color: var(--light-blue);
}
img {
max-width: 100%;
height: auto;
}
button {
font-family: var(--font-body);
cursor: pointer;
}
code, pre {
font-family: var(--font-mono);
}
ul, ol {
padding-left: var(--space-lg);
margin-bottom: var(--space-md);
}
/* Container */
.container {
width: 100%;
max-width: 1200px;
margin: 0 auto;
padding: 0 var(--space-lg);
}
.container-sm {
max-width: 800px;
}
.container-lg {
max-width: 1400px;
}
/* Navbar */
.navbar {
position: fixed;
top: 0;
left: 0;
right: 0;
background: rgba(0, 20, 39, 0.8);
backdrop-filter: blur(10px);
-webkit-backdrop-filter: blur(10px);
border-bottom: 1px solid rgba(255, 255, 255, 0.08);
z-index: var(--z-navbar);
padding: var(--space-md) 0;
transition: all var(--transition-normal);
}
.navbar.scrolled {
padding: var(--space-sm) 0;
}
.navbar-container {
display: flex;
align-items: center;
justify-content: space-between;
}
.logo {
display: flex;
align-items: center;
}
.logo img {
height: 36px;
margin-right: var(--space-sm);
}
.logo-text {
font-size: 1.25rem;
font-weight: 700;
color: var(--white);
}
.nav-links {
display: flex;
align-items: center;
list-style: none;
margin: 0;
padding: 0;
}
.nav-links li {
margin: 0 var(--space-md);
}
.nav-links a {
color: var(--white);
font-weight: 500;
position: relative;
padding: var(--space-xs) 0;
}
.nav-links a::after {
content: '';
position: absolute;
width: 0;
height: 2px;
bottom: 0;
left: 0;
background: linear-gradient(90deg, var(--magenta), var(--blue));
transition: width var(--transition-normal);
}
.nav-links a:hover::after,
.nav-links a.active::after {
width: 100%;
}
.nav-buttons {
display: flex;
align-items: center;
}
.mobile-toggle {
display: none;
background: none;
border: none;
color: var(--white);
font-size: 1.5rem;
}
/* Buttons */
.btn {
display: inline-flex;
align-items: center;
justify-content: center;
padding: 0.75rem 1.5rem;
border-radius: var(--radius-md);
font-weight: 600;
transition: all var(--transition-fast);
border: none;
text-align: center;
cursor: pointer;
}
.btn-primary {
background: linear-gradient(135deg, var(--magenta), var(--blue));
color: var(--white);
}
.btn-primary:hover {
transform: translateY(-2px);
box-shadow: 0 5px 15px rgba(0, 164, 239, 0.4);
color: var(--white);
}
.btn-secondary {
background: rgba(255, 255, 255, 0.1);
color: var(--white);
border: 1px solid rgba(255, 255, 255, 0.2);
}
.btn-secondary:hover {
background: rgba(255, 255, 255, 0.15);
transform: translateY(-2px);
color: var(--white);
}
.btn-sm {
padding: 0.5rem 1rem;
font-size: 0.875rem;
}
.btn-lg {
padding: 1rem 2rem;
font-size: 1.125rem;
}
.btn-icon {
margin-right: var(--space-xs);
}
.btn-github {
background: #24292e;
color: var(--white);
}
.btn-github:hover {
background: #2c3440;
color: var(--white);
}
.btn-discord {
background: #5865F2;
color: var(--white);
}
.btn-discord:hover {
background: #4752c4;
color: var(--white);
}
/* Hero section */
.hero {
padding: 160px 0 100px;
position: relative;
overflow: hidden;
}
.hero-content {
display: grid;
grid-template-columns: 1fr 1fr;
gap: var(--space-xxl);
align-items: center;
}
.hero-headings {
position: relative;
z-index: 2;
}
.hero h1 {
margin-bottom: var(--space-md);
letter-spacing: -0.02em;
line-height: 1.1;
}
.hero h1 span {
background: linear-gradient(135deg, var(--magenta), var(--blue));
-webkit-background-clip: text;
background-clip: text;
-webkit-text-fill-color: transparent;
}
.hero-subtitle {
font-size: 1.25rem;
margin-bottom: var(--space-xl);
color: rgba(255, 255, 255, 0.85);
max-width: 500px;
}
.hero-buttons {
display: flex;
gap: var(--space-md);
margin-bottom: var(--space-xl);
}
.hero-animation {
position: relative;
width: 100%;
height: 500px;
display: flex;
align-items: center;
justify-content: center;
}
/* DNA Helix Animation */
.dna-helix {
position: relative;
width: 100%;
height: 100%;
transform-style: preserve-3d;
perspective: 1200px;
}
.base-pair {
position: absolute;
width: 100%;
height: 30px;