// Research Radar - Enhanced Interactive JavaScript
class ResearchRadar {
    constructor() {
        this.currentSection = 'search';
        this.currentPage = 'landing';
        this.isLoading = false;
        this.chatHistory = [];
        this.currentDocumentId = null;
        this.uploadProgress = 0;
        this.searchCache = new Map();
        
        this.init();
    }

    init() {
        this.setupEventListeners();
        this.setupDragAndDrop();
        this.initializeChat();
        this.setupChatInput();
        this.setupSearchSuggestions();
        this.updateStatusIndicator();
        this.setupPageNavigation();
        this.setupEnhancedChat();
        this.setupMobileNav();
        this.setupVhUnit();
    }

    setupEventListeners() {
        console.log('Setting up event listeners...');
        
        // Landing page CTA buttons - Critical buttons that need to work
        this.setupLandingPageButtons();
        
        // Navigation for app page
        const navLinks = document.querySelectorAll('.app-nav .nav-link');
        console.log(`Found ${navLinks.length} navigation links`);
        navLinks.forEach(link => {
            link.addEventListener('click', (e) => {
                e.preventDefault();
                const section = link.dataset.section;
                console.log(`Navigation clicked: ${section}`);
                if (section) {
                this.switchSection(section);
                }
            });
        });

        // Quick search cards
        const quickSearchCards = document.querySelectorAll('.quick-search-card');
        console.log(`Found ${quickSearchCards.length} quick search cards`);
        quickSearchCards.forEach(card => {
            card.addEventListener('click', (e) => {
                const query = card.dataset.query;
                console.log(`Quick search card clicked: ${query}`);
                if (query) {
                    const searchInput = document.getElementById('searchInput');
                    if (searchInput) {
                        searchInput.value = query;
                        this.searchPapers();
                    }
                }
            });
        });

        // Chat suggestions
        document.querySelectorAll('.suggestion-chip').forEach(chip => {
            chip.addEventListener('click', (e) => {
                const question = chip.dataset.question;
                if (question) {
                    document.getElementById('chatInput').value = question;
                    this.sendChatMessage();
                }
            });
        });

        // Example URLs
        document.querySelectorAll('.example-url').forEach(btn => {
            btn.addEventListener('click', (e) => {
                const url = btn.dataset.url;
                if (url) {
                    document.getElementById('paperUrl').value = url;
                }
            });
        });

        // Clear chat button
        const clearBtn = document.getElementById('chatClearBtn');
        if (clearBtn) {
            clearBtn.addEventListener('click', () => this.clearChat());
        }

        // Search functionality
        const searchBtn = document.getElementById('searchBtn');
        const searchInput = document.getElementById('searchInput');
        
        console.log('Search button found:', !!searchBtn);
        console.log('Search input found:', !!searchInput);
        
        if (searchBtn) {
            searchBtn.addEventListener('click', () => {
                console.log('Search button clicked!');
                this.searchPapers();
            });
        }
        
        if (searchInput) {
            searchInput.addEventListener('keypress', (e) => {
                if (e.key === 'Enter') {
                    console.log('Search input Enter pressed!');
                    this.searchPapers();
                }
            });
        }

        // File upload
        const fileInput = document.getElementById('fileInput');
        console.log('File input found:', !!fileInput);
        if (fileInput) {
            fileInput.addEventListener('change', (e) => {
                console.log('File input changed!');
                this.handleFileUpload(e);
            });
        }

        // URL analysis
        const analyzeUrlBtn = document.getElementById('analyzeUrlBtn');
        const paperUrlInput = document.getElementById('paperUrl');
        
        console.log('Analyze URL button found:', !!analyzeUrlBtn);
        console.log('Paper URL input found:', !!paperUrlInput);
        
        if (analyzeUrlBtn) {
            analyzeUrlBtn.addEventListener('click', () => {
                console.log('Analyze URL button clicked!');
                this.analyzePaperUrl();
            });
        }
        
        if (paperUrlInput) {
            paperUrlInput.addEventListener('keypress', (e) => {
                if (e.key === 'Enter') {
                    console.log('Paper URL input Enter pressed!');
                    this.analyzePaperUrl();
                }
            });
        }

        // Chat functionality
        const chatSendBtn = document.getElementById('chatSendBtn');
        const chatInput = document.getElementById('chatInput');
        const chatSendBtnPanel = document.getElementById('chatSendBtnPanel');
        const chatInputPanel = document.getElementById('chatInputPanel');
        
        if (chatSendBtn) {
            chatSendBtn.addEventListener('click', () => this.sendChatMessage());
        }
        
        if (chatInput) {
            chatInput.addEventListener('keypress', (e) => {
                if (e.key === 'Enter') {
                    this.sendChatMessage();
                }
            });
        }

        // Panel chat functionality
        if (chatSendBtnPanel) {
            chatSendBtnPanel.addEventListener('click', () => this.sendChatMessagePanel());
        }
        
        if (chatInputPanel) {
            chatInputPanel.addEventListener('keypress', (e) => {
                if (e.key === 'Enter' && !e.shiftKey) {
                    e.preventDefault();
                    this.sendChatMessagePanel();
                }
            });
        }
    }

    setupLandingPageButtons() {
        console.log('Setting up landing page buttons...');
        
        // Get Started button (nav)
        const getStartedBtn = document.querySelector('.nav-cta-btn');
        console.log('Get Started button found:', !!getStartedBtn);
        if (getStartedBtn) {
            // Remove existing onclick to prevent conflicts
            getStartedBtn.removeAttribute('onclick');
            getStartedBtn.addEventListener('click', (e) => {
                e.preventDefault();
                console.log('Get Started button clicked!');
                this.navigateToApp('search');
            });
        }

        // Start Exploring button
        const startExploringBtn = document.querySelector('.cta-button.primary');
        console.log('Start Exploring button found:', !!startExploringBtn);
        if (startExploringBtn) {
            // Remove existing onclick to prevent conflicts
            startExploringBtn.removeAttribute('onclick');
            startExploringBtn.addEventListener('click', (e) => {
                e.preventDefault();
                console.log('Start Exploring button clicked!');
                this.navigateToApp('search');
            });
        }

        // Upload Paper button
        const uploadPaperBtn = document.querySelector('.cta-button.secondary');
        console.log('Upload Paper button found:', !!uploadPaperBtn);
        if (uploadPaperBtn) {
            // Remove existing onclick to prevent conflicts
            uploadPaperBtn.removeAttribute('onclick');
            uploadPaperBtn.addEventListener('click', (e) => {
                e.preventDefault();
                console.log('Upload Paper button clicked!');
                this.navigateToApp('upload');
            });
        }

        // Back to Landing button
        const backToLandingBtn = document.querySelector('.back-to-landing');
        console.log('Back to Landing button found:', !!backToLandingBtn);
        if (backToLandingBtn) {
            // Remove existing onclick to prevent conflicts
            backToLandingBtn.removeAttribute('onclick');
            backToLandingBtn.addEventListener('click', (e) => {
                e.preventDefault();
                console.log('Back to Landing button clicked!');
                this.navigateToLanding();
            });
        }

        // Brand logo that navigates to landing
        const brandLogo = document.querySelector('.app-nav .nav-brand');
        console.log('Brand logo found:', !!brandLogo);
        if (brandLogo) {
            // Remove existing onclick to prevent conflicts
            brandLogo.removeAttribute('onclick');
            brandLogo.addEventListener('click', (e) => {
                e.preventDefault();
                console.log('Brand logo clicked!');
                this.navigateToLanding();
            });
        }
    }

    setupDragAndDrop() {
        const uploadZone = document.getElementById('uploadZone');
        if (!uploadZone) return;

        ['dragenter', 'dragover', 'dragleave', 'drop'].forEach(eventName => {
            uploadZone.addEventListener(eventName, this.preventDefaults, false);
        });

        ['dragenter', 'dragover'].forEach(eventName => {
            uploadZone.addEventListener(eventName, () => {
                uploadZone.classList.add('drag-over');
            }, false);
        });

        ['dragleave', 'drop'].forEach(eventName => {
            uploadZone.addEventListener(eventName, () => {
                uploadZone.classList.remove('drag-over');
            }, false);
        });

        uploadZone.addEventListener('drop', (e) => {
            const files = e.dataTransfer.files;
            if (files.length > 0) {
                this.processFile(files[0]);
            }
        }, false);
    }

    preventDefaults(e) {
        e.preventDefault();
        e.stopPropagation();
    }

    switchSection(sectionName) {
        // Update navigation
        document.querySelectorAll('.nav-link').forEach(link => {
            link.classList.remove('active');
        });
        
        document.querySelector(`[data-section="${sectionName}"]`).classList.add('active');

        // Update sections
        document.querySelectorAll('.section').forEach(section => {
            section.classList.remove('active');
        });
        
        document.getElementById(sectionName).classList.add('active');
        
        this.currentSection = sectionName;
    }

    showLoading(show = true) {
        const overlay = document.getElementById('loadingOverlay');
        if (overlay) {
            if (show) {
                overlay.classList.add('active');
                this.isLoading = true;
            } else {
                overlay.classList.remove('active');
                this.isLoading = false;
            }
        }
    }

    showToast(message, type = 'info') {
        const container = document.getElementById('toastContainer');
        if (!container) return;

        const toast = document.createElement('div');
        toast.className = `toast ${type}`;
        toast.innerHTML = `
            <div style="display: flex; align-items: center; gap: 0.5rem;">
                <i class="fas fa-${this.getToastIcon(type)}"></i>
                <span>${message}</span>
            </div>
        `;

        container.appendChild(toast);

        // Auto remove after 5 seconds
        setTimeout(() => {
            if (toast.parentNode) {
                toast.style.animation = 'toastSlideOut 0.3s ease-out forwards';
                setTimeout(() => {
                    container.removeChild(toast);
                }, 300);
            }
        }, 5000);
    }

    getToastIcon(type) {
        const icons = {
            'success': 'check-circle',
            'error': 'exclamation-circle',
            'warning': 'exclamation-triangle',
            'info': 'info-circle'
        };
        return icons[type] || 'info-circle';
    }

    async searchPapers() {
        const searchInput = document.getElementById('searchInput');
        const query = searchInput.value.trim();
        
        if (!query) {
            this.showToast('Please enter a search query', 'warning');
            return;
        }

        this.showLoading(true);
        
        try {
            const response = await fetch('/search', {
                method: 'POST',
                headers: {
                    'Content-Type': 'application/json',
                },
                body: JSON.stringify({ query })
            });

            const data = await response.json();
            
            if (response.ok) {
                this.displaySearchResults(data.papers);
                this.showToast(`Found ${data.papers.length} papers`, 'success');
            } else {
                throw new Error(data.error || 'Search failed');
            }
        } catch (error) {
            console.error('Search error:', error);
            this.showToast(error.message, 'error');
        } finally {
            this.showLoading(false);
        }
    }

    displaySearchResults(papers) {
        const container = document.getElementById('searchResults');
        if (!container) return;

        // Keep papers for later access (e.g., openSummaryChat after ingest/summarize)
        this.lastSearchResults = papers;

        if (papers.length === 0) {
            container.innerHTML = `
                <div class="result-card">
                    <p style="text-align: center; color: var(--text-secondary);">
                        <i class="fas fa-search" style="font-size: 2rem; margin-bottom: 1rem; display: block;"></i>
                        No papers found. Try different keywords.
                    </p>
                </div>
            `;
            return;
        }

        container.innerHTML = papers.map((paper, index) => `
            <div class="paper-card">
                <h3 class="paper-title">${this.escapeHtml(paper.title)}</h3>
                <div class="paper-authors">
                    <i class="fas fa-users"></i>
                    ${paper.authors.slice(0, 3).map(author => this.escapeHtml(author)).join(', ')}
                    ${paper.authors.length > 3 ? ` and ${paper.authors.length - 3} others` : ''}
                </div>
                <div class="paper-meta">
                    <span><i class="fas fa-calendar"></i> ${paper.published}</span>
                    <span><i class="fas fa-tag"></i> ${this.escapeHtml(paper.category)}</span>
                </div>
                <div class="paper-summary">
                    ${this.truncateText(this.escapeHtml(paper.summary), 300)}
                </div>
                <div class="paper-actions">
                    <button class="btn-primary generate-summary-btn" data-paper-url="${paper.url}" data-paper-pdf-url="${paper.pdf_url}" data-paper-index="${index}">
                        <i class="fas fa-magic"></i> Generate Summary
                    </button>
                    <a href="${paper.pdf_url}" target="_blank" class="btn-secondary">
                        <i class="fas fa-file-pdf"></i> View PDF
                    </a>
                    <a href="${paper.url}" target="_blank" class="btn-secondary">
                        <i class="fas fa-external-link-alt"></i> arXiv Page
                    </a>
                </div>
            </div>
        `).join('');

        // Add event listeners to Generate Summary buttons
        this.setupGenerateSummaryButtons();
    }

    setupGenerateSummaryButtons() {
        console.log('Setting up Generate Summary buttons...');
        
        const generateButtons = document.querySelectorAll('.generate-summary-btn');
        console.log(`Found ${generateButtons.length} Generate Summary buttons`);
        
        generateButtons.forEach(button => {
            button.addEventListener('click', async (e) => {
                e.preventDefault();
                const paperUrl = button.dataset.paperUrl;
                const paperIndex = button.dataset.paperIndex;
                const pdfUrl = button.dataset.paperPdfUrl;
                const paper = this.lastSearchResults && typeof Number(paperIndex) === 'number'
                    ? this.lastSearchResults[Number(paperIndex)]
                    : null;
                
                console.log(`Generate Summary button clicked for paper: ${paperUrl}`);
                
                if (paperUrl) {
                    // Disable button and show loading state
                    button.disabled = true;
                    button.innerHTML = '<i class="fas fa-spinner fa-spin"></i> Generating...';
                    
                    try {
                        // Ingest the paper PDF first, then summarize from doc_id
                        const ingestRes = await fetch('/ingest-paper', {
                            method: 'POST',
                            headers: { 'Content-Type': 'application/json' },
                            body: JSON.stringify({ pdf_url: pdfUrl, url: paperUrl })
                        });
                        const ingestData = await ingestRes.json();
                        if (!ingestRes.ok || !ingestData.success) {
                            throw new Error(ingestData.error || 'Failed to ingest paper');
                        }
                        const docId = ingestData.doc_id;
                        // Persist active document in UI
                        this.setActiveDocument(docId);
                        // Now summarize using doc_id (backend will fetch all chunks from Qdrant)
                        const sumRes = await fetch('/summarize-paper', {
                            method: 'POST',
                            headers: { 'Content-Type': 'application/json' },
                            body: JSON.stringify({ doc_id: docId })
                        });
                        const sumData = await sumRes.json();
                        if (!sumRes.ok || !sumData.success) {
                            throw new Error(sumData.error || 'Failed to generate summary');
                        }
                        // Open summary + chat view
                        const paperData = paper || { title: '', authors: [], published: '', category: '' };
                        this.openSummaryChat({ title: paperData.title, authors: paperData.authors, published: paperData.published, category: paperData.category }, sumData.summary);
                    } catch (error) {
                        console.error('Error generating summary:', error);
                        this.showToast('Failed to generate summary. Please try again.', 'error');
                    } finally {
                        // Re-enable button
                        button.disabled = false;
                        button.innerHTML = '<i class="fas fa-magic"></i> Generate Summary';
                    }
                } else {
                    console.error('No paper URL found for Generate Summary button');
                    this.showToast('Error: Paper URL not found', 'error');
                }
            });
        });
    }

    async handleFileUpload(event) {
        const file = event.target.files[0];
        if (file) {
            await this.processFile(file);
        }
    }

    async processFile(file) {
        // Validate file
        const allowedTypes = ['application/pdf', 'text/plain', 'application/vnd.openxmlformats-officedocument.wordprocessingml.document'];
        const maxSize = 16 * 1024 * 1024; // 16MB

        if (!allowedTypes.includes(file.type)) {
            this.showToast('Invalid file type. Please upload PDF, TXT, or DOCX files.', 'error');
            return;
        }

        if (file.size > maxSize) {
            this.showToast('File too large. Maximum size is 16MB.', 'error');
            return;
        }

        this.showLoading(true);

        try {
            const formData = new FormData();
            formData.append('file', file);

            const response = await fetch('/upload', {
                method: 'POST',
                body: formData
            });

            const data = await response.json();

            if (response.ok) {
                this.displayUploadResult(data);
                this.showToast('File processed successfully!', 'success');
            } else {
                throw new Error(data.error || 'Upload failed');
            }
        } catch (error) {
            console.error('Upload error:', error);
            this.showToast(error.message, 'error');
        } finally {
            this.showLoading(false);
            // Reset file input
            document.getElementById('fileInput').value = '';
        }
    }

    displayUploadResult(data) {
        // Create paper data object for the uploaded file
        const paperData = {
            title: data.filename || 'Uploaded Document',
            authors: ['Uploaded by User'],
            published: new Date().toLocaleDateString(),
            category: 'Uploaded Document',
            filename: data.filename,
            word_count: data.word_count
        };

        // Store the document ID for chat functionality
        this.currentDocumentId = data.doc_id;

        // Open the Summary + Chat panel with the uploaded document
        this.openSummaryChat(paperData, data.summary);
    }

    async analyzePaperUrl() {
        const urlInput = document.getElementById('paperUrl');
        const url = urlInput.value.trim();

        if (!url) {
            this.showToast('Please enter a paper URL', 'warning');
            return;
        }

        // Basic URL validation
        if (!url.includes('arxiv.org')) {
            this.showToast('Please enter a valid arXiv URL', 'warning');
            return;
        }

        this.showLoading(true);

        try {
            const response = await fetch('/summarize-paper', {
                method: 'POST',
                headers: {
                    'Content-Type': 'application/json',
                },
                body: JSON.stringify({ url })
            });

            const data = await response.json();

            if (response.ok) {
                this.displayPaperAnalysis(data);
                this.showToast('Paper analyzed successfully!', 'success');
                urlInput.value = ''; // Clear input
            } else {
                throw new Error(data.error || 'Analysis failed');
            }
        } catch (error) {
            console.error('Analysis error:', error);
            this.showToast(error.message, 'error');
        } finally {
            this.showLoading(false);
        }
    }

    displayPaperAnalysis(data) {
        // Store the document ID for chat functionality
        this.currentDocumentId = data.doc_id;

        // Open the Summary + Chat panel with the analyzed paper
        this.openSummaryChat(data.paper, data.summary);
    }

    async summarizePaper(paperUrl) {
        // Deprecated in favor of ingest -> summarize flow
        return this.showToast('Summarization flow updated. Please use Generate Summary button.', 'info');
    }

    openSummaryChat(paperData, summaryText) {
        // Hide current section and show summary-chat
        document.querySelectorAll('.section').forEach(section => {
            section.style.display = 'none';
        });
        
        const summarySection = document.getElementById('summary-chat');
        summarySection.style.display = 'block';
        
        // Update paper information
        document.getElementById('paperTitle').textContent = paperData.title || 'Research Paper';
        document.getElementById('paperAuthor').textContent = paperData.authors ? paperData.authors.join(', ') : 'Unknown Author';
        document.getElementById('paperDate').textContent = paperData.published || new Date().getFullYear();
        document.getElementById('paperCategory').textContent = paperData.category || 'Research';
        
        // Show summary
        this.displaySummaryInPanel(summaryText);
        
        // Setup chat panel
        this.setupChatPanel();
        
        // Store current paper data for chat context
        this.currentPaper = paperData;

        // Default to Chat tab for immediate Q&A after tabs are in DOM
        setTimeout(() => {
            try { switchTab('chat'); } catch (_) {}
            const chatInput = document.getElementById('chatInputPanel');
            if (chatInput) chatInput.focus();
        }, 150);
    }

    displaySummaryInPanel(summaryText) {
        const summaryLoading = document.getElementById('summaryLoading');
        const summaryTextEl = document.getElementById('summaryText');
        
        // Hide loading and show summary
        summaryLoading.style.display = 'none';
        summaryTextEl.style.display = 'block';
        summaryTextEl.innerHTML = this.formatSummaryText(summaryText);
        
        // Update stats
        this.updateSummaryStats(summaryText);
    }

    formatSummaryText(text) {
        // Convert plain text to formatted HTML
        return text
            .replace(/\n\n/g, '</p><p>')
            .replace(/\n/g, '<br>')
            .replace(/\*\*(.*?)\*\*/g, '<strong>$1</strong>')
            .replace(/\*(.*?)\*/g, '<em>$1</em>')
            .replace(/^/, '<p>')
            .replace(/$/, '</p>');
    }

    updateSummaryStats(text) {
        const wordCount = text.split(/\s+/).length;
        const readingTime = Math.ceil(wordCount / 200); // Average reading speed
        const compressionRatio = Math.round((1 - (text.length / (text.length * 3))) * 100); // Estimate
        
        const wc = document.getElementById('wordCount');
        const rt = document.getElementById('readingTime');
        const cr = document.getElementById('compressionRatio');
        if (wc) wc.textContent = wordCount.toLocaleString();
        if (rt) rt.textContent = `${readingTime} min`;
        if (cr) cr.textContent = `${compressionRatio}%`;
    }

    setupChatPanel() {
        const chatInput = document.getElementById('chatInputPanel');
        const sendBtn = document.getElementById('chatSendBtnPanel');
        
        // Clear any existing event listeners
        const newChatInput = chatInput.cloneNode(true);
        chatInput.parentNode.replaceChild(newChatInput, chatInput);
        
        const newSendBtn = sendBtn.cloneNode(true);
        sendBtn.parentNode.replaceChild(newSendBtn, sendBtn);
        
        // Add new event listeners
        newChatInput.addEventListener('keydown', (e) => {
            if (e.key === 'Enter' && !e.shiftKey) {
                e.preventDefault();
                this.sendChatMessagePanel();
            }
        });
        
        newChatInput.addEventListener('input', () => {
            this.autoResizeTextarea(newChatInput);
        });
        
        newSendBtn.addEventListener('click', () => {
            this.sendChatMessagePanel();
        });
    }

    sendChatMessagePanel() {
        const chatInput = document.getElementById('chatInputPanel');
        const message = chatInput.value.trim();
        
        if (!message) return;
        
        // Add user message
        this.addChatMessagePanel(message, 'user');
        
        // Clear input
        chatInput.value = '';
        this.autoResizeTextarea(chatInput);
        
        // Show typing indicator and send to backend
        this.showChatTypingPanel();
        this.sendChatToBackend(message);
    }

    addChatMessagePanel(message, sender) {
        const chatPanel = document.getElementById('chatMessagesPanel');
        
        // Remove welcome message if it exists
        const welcome = chatPanel.querySelector('.chat-welcome');
        if (welcome && sender === 'user') {
            welcome.remove();
        }
        
        const messageDiv = document.createElement('div');
        messageDiv.className = `chat-message-panel ${sender}`;
        
        const currentTime = new Date().toLocaleTimeString([], { 
            hour: '2-digit', 
            minute: '2-digit' 
        });
        
        messageDiv.innerHTML = `
            <div class="message-avatar-panel ${sender}">
                <i class="fas fa-${sender === 'user' ? 'user' : 'robot'}"></i>
                </div>
            <div class="message-content-panel ${sender}">
                <div class="message-bubble ${sender}">
                    ${sender === 'bot' ? message : this.escapeHtml(message)}
                    </div>
                <div class="message-time-panel">${currentTime}</div>
                    </div>
        `;
        
        chatPanel.appendChild(messageDiv);
        chatPanel.scrollTop = chatPanel.scrollHeight;
    }

    showChatTypingPanel() {
        const chatPanel = document.getElementById('chatMessagesPanel');
        
        const typingDiv = document.createElement('div');
        typingDiv.className = 'chat-message-panel bot';
        typingDiv.id = 'typingIndicatorPanel';
        
        typingDiv.innerHTML = `
            <div class="message-avatar-panel bot">
                <i class="fas fa-robot"></i>
            </div>
            <div class="message-content-panel bot">
                <div class="message-bubble bot">
                    <div class="typing-dots">
                        <div class="dot"></div>
                        <div class="dot"></div>
                        <div class="dot"></div>
                    </div>
                    <span style="margin-left: 0.5rem; font-style: italic;">AI is thinking...</span>
                </div>
            </div>
        `;

        chatPanel.appendChild(typingDiv);
        chatPanel.scrollTop = chatPanel.scrollHeight;
    }

    hideChatTypingPanel() {
        const typingIndicator = document.getElementById('typingIndicatorPanel');
        if (typingIndicator) {
            typingIndicator.remove();
        }
    }

    sendChatToBackend(message) {
        fetch('/chat', {
            method: 'POST',
            headers: {
                'Content-Type': 'application/json',
            },
            body: JSON.stringify({ message: message })
        })
        .then(response => response.json())
        .then(data => {
            this.hideChatTypingPanel();
            
            if (data.success) {
                this.addChatMessagePanel(data.response, 'bot');
            } else {
                this.addChatMessagePanel(
                    `I apologize, but I encountered an error: ${data.error || 'Unknown error'}. Please try again.`,
                    'bot'
                );
            }
        })
        .catch(error => {
            console.error('Chat error:', error);
            this.hideChatTypingPanel();
            this.addChatMessagePanel(
                'I apologize, but I\'m having trouble connecting right now. Please check your connection and try again.',
                'bot'
            );
        });
    }

    initializeChat() {
        this.chatHistory = [];
    }

    async sendChatMessage() {
        // Redirect to the enhanced chat functionality
        this.sendMessage();
    }

    addChatMessage(message, sender) {
        // Redirect to the enhanced chat message functionality
        this.addMessageToChat(message, sender);
    }

    // Utility functions
    escapeHtml(text) {
        const div = document.createElement('div');
        div.textContent = text;
        return div.innerHTML;
    }

    truncateText(text, maxLength) {
        if (text.length <= maxLength) return text;
        return text.substr(0, maxLength) + '...';
    }

    // Enhanced UI Methods (Legacy - now handled by setupEnhancedChat)
    setupChatInput() {
        // This is now handled by the enhanced chat setup
        this.setupEnhancedChat();
    }

    setupSearchSuggestions() {
        const searchInput = document.getElementById('searchInput');
        const suggestions = document.getElementById('searchSuggestions');
        
        // Initialize enhanced search features
        this.initializeQuickSearchCards();
        this.initializeSearchTips();
        this.initializeRecentSearches();
        this.initializeAdvancedFilters();
        
        if (searchInput && suggestions) {
            searchInput.addEventListener('input', (e) => this.handleSearchInput(e));
            searchInput.addEventListener('focus', () => this.showSearchSuggestions());
            searchInput.addEventListener('blur', () => this.hideSearchSuggestions());

            // Handle suggestion clicks
            suggestions.querySelectorAll('.suggestion-item').forEach(item => {
                item.addEventListener('click', () => {
                    const query = item.dataset.query;
                    if (query) {
                        searchInput.value = query;
                        suggestions.classList.remove('show');
                        this.searchPapers();
                        this.addToRecentSearches(query);
                    }
                });
            });
        }
    }

    initializeQuickSearchCards() {
        const quickSearchCards = document.querySelectorAll('.quick-search-card');
        quickSearchCards.forEach(card => {
            card.addEventListener('click', () => {
                const query = card.dataset.query;
                if (query) {
                    const searchInput = document.getElementById('searchInput');
                    if (searchInput) {
                        searchInput.value = query;
                        this.searchPapers();
                        this.addToRecentSearches(query);
                    }
                }
            });
        });
    }

    initializeSearchTips() {
        const tipsToggle = document.querySelector('.tips-toggle');
        const tipsContent = document.querySelector('.tips-content');
        
        if (tipsToggle && tipsContent) {
            tipsToggle.addEventListener('click', () => {
                tipsContent.classList.toggle('show');
                const icon = tipsToggle.querySelector('i');
                if (icon) {
                    icon.classList.toggle('fa-chevron-down');
                    icon.classList.toggle('fa-chevron-up');
                }
            });
        }
    }

    initializeRecentSearches() {
        this.loadRecentSearches();
    }

    initializeAdvancedFilters() {
        // Advanced filters toggle is handled by global function
    }

    handleSearchInput(e) {
        const query = e.target.value.trim();
        
        if (query.length > 2) {
            this.updateSearchSuggestions(query);
            this.showSearchSuggestions();
        } else if (query.length === 0) {
            this.showSearchSuggestions();
        } else {
            this.hideSearchSuggestions();
        }
    }

    updateSearchSuggestions(query) {
        const searchSuggestions = document.getElementById('searchSuggestions');
        if (!searchSuggestions) return;
        
        // Generate dynamic suggestions based on the query
        const suggestions = [
            { text: query, count: '~1.2k papers' },
            { text: query + ' applications', count: '~800 papers' },
            { text: query + ' algorithms', count: '~650 papers' },
            { text: query + ' recent advances', count: '~420 papers' }
        ];
        
        const suggestionsSection = searchSuggestions.querySelector('.suggestions-section');
        if (suggestionsSection) {
            const suggestionItems = suggestions.map(s => `
                <div class="suggestion-item" data-query="${s.text}">
                    <i class="fas fa-search"></i>
                    <span>${s.text}</span>
                    <small>${s.count}</small>
                </div>
            `).join('');
            
            suggestionsSection.innerHTML = `
                <h4>Suggestions</h4>
                ${suggestionItems}
            `;
            
            // Re-attach event listeners
            suggestionsSection.querySelectorAll('.suggestion-item').forEach(item => {
                item.addEventListener('click', () => {
                    const query = item.dataset.query;
                    if (query) {
                        const searchInput = document.getElementById('searchInput');
                        if (searchInput) {
                            searchInput.value = query;
                            this.searchPapers();
                            this.hideSearchSuggestions();
                            this.addToRecentSearches(query);
                        }
                    }
                });
            });
        }
    }

    showSearchSuggestions() {
        const searchSuggestions = document.getElementById('searchSuggestions');
        if (searchSuggestions) {
            searchSuggestions.classList.add('show');
        }
    }

    hideSearchSuggestions() {
        setTimeout(() => {
            const searchSuggestions = document.getElementById('searchSuggestions');
            if (searchSuggestions) {
                searchSuggestions.classList.remove('show');
            }
        }, 200);
    }

    addToRecentSearches(query) {
        let recentSearches = JSON.parse(localStorage.getItem('recentSearches') || '[]');
        
        // Remove if already exists
        recentSearches = recentSearches.filter(search => search !== query);
        
        // Add to beginning
        recentSearches.unshift(query);
        
        // Keep only last 5
        recentSearches = recentSearches.slice(0, 5);
        
        localStorage.setItem('recentSearches', JSON.stringify(recentSearches));
        this.updateRecentSearchesDisplay();
    }

    loadRecentSearches() {
        const recentSearches = JSON.parse(localStorage.getItem('recentSearches') || '[]');
        if (recentSearches.length > 0) {
            this.updateRecentSearchesDisplay();
        }
    }

    updateRecentSearchesDisplay() {
        const recentSearches = JSON.parse(localStorage.getItem('recentSearches') || '[]');
        const recentSearchesContainer = document.getElementById('recentSearches');
        const recentSearchItems = document.getElementById('recentSearchItems');
        
        if (recentSearches.length > 0 && recentSearchesContainer && recentSearchItems) {
            const recentHTML = recentSearches.map(search => `
                <div class="suggestion-item" data-query="${search}">
                    <i class="fas fa-history"></i>
                    <span>${search}</span>
                </div>
            `).join('');
            
            recentSearchItems.innerHTML = recentHTML;
            recentSearchesContainer.style.display = 'block';
            
            // Attach event listeners
            recentSearchItems.querySelectorAll('.suggestion-item').forEach(item => {
                item.addEventListener('click', () => {
                    const query = item.dataset.query;
                    if (query) {
                        const searchInput = document.getElementById('searchInput');
                        if (searchInput) {
                            searchInput.value = query;
                            this.searchPapers();
                        }
                    }
                });
            });
        }
    }

    updateStatusIndicator() {
        const indicator = document.getElementById('statusIndicator');
        const chatStatus = document.getElementById('chatStatus');
        
        if (indicator) {
            const statusText = indicator.querySelector('.status-text');
            const statusDot = indicator.querySelector('.status-dot');
            
            if (this.currentDocumentId) {
                statusText.textContent = 'Document Active';
                statusDot.style.background = 'var(--success-color)';
            } else {
                statusText.textContent = 'Ready';
                statusDot.style.background = 'var(--warning-color)';
            }
        }

        if (chatStatus) {
            const statusIndicator = chatStatus.querySelector('.status-indicator');
            if (this.currentDocumentId) {
                statusIndicator.classList.remove('offline');
                statusIndicator.classList.add('online');
                statusIndicator.querySelector('span').textContent = 'Document loaded';
            } else {
                statusIndicator.classList.remove('online');
                statusIndicator.classList.add('offline');
                statusIndicator.querySelector('span').textContent = 'No document selected';
            }
        }
    }

    updateUploadProgress(percentage, step) {
        const progressContainer = document.getElementById('uploadProgress');
        const progressFill = document.getElementById('progressFill');
        const progressPercentage = document.getElementById('progressPercentage');
        const progressSubtitle = document.getElementById('progressSubtitle');
        const progressTime = document.getElementById('progressTime');

        if (progressContainer && progressFill && progressPercentage) {
            progressContainer.style.display = 'block';
            progressFill.style.width = `${percentage}%`;
            progressPercentage.textContent = `${percentage}%`;

            // Update subtitle and time estimate
            const subtitles = [
                'Preparing your document for analysis...',
                'Uploading your document securely...',
                'Extracting text and content...',
                'AI analyzing document structure...',
                'Analysis complete! Ready for questions.'
            ];

            if (progressSubtitle && step <= subtitles.length) {
                progressSubtitle.textContent = subtitles[step - 1] || subtitles[0];
            }

            if (progressTime) {
                if (percentage < 100) {
                    const remainingTime = Math.max(1, Math.round((100 - percentage) / 10));
                    progressTime.textContent = `~${remainingTime}s remaining`;
                } else {
                    progressTime.textContent = 'Complete!';
                }
            }

            // Update steps with enhanced system
            const steps = progressContainer.querySelectorAll('.progress-step');
            steps.forEach((stepEl, index) => {
                const stepNumber = parseInt(stepEl.dataset.step);
                if (stepNumber <= step) {
                    stepEl.classList.add('active');
                } else {
                    stepEl.classList.remove('active');
                }
            });

            if (percentage === 100) {
                setTimeout(() => {
                    progressContainer.style.display = 'none';
                }, 3000);
            }
        }
    }

    autoResizeTextarea(event) {
        const textarea = event.target;
        textarea.style.height = 'auto';
        const newHeight = Math.min(textarea.scrollHeight, 120);
        textarea.style.height = newHeight + 'px';
    }

    clearChat() {
        const chatMessages = document.getElementById('chatMessages');
        if (chatMessages) {
            // Keep the welcome message
            const welcomeMessage = chatMessages.querySelector('.welcome-message');
            chatMessages.innerHTML = '';
            if (welcomeMessage) {
                chatMessages.appendChild(welcomeMessage);
            }
        }
        this.chatHistory = [];
        this.showToast('Chat cleared', 'success');
    }

    setActiveDocument(docId) {
        this.currentDocumentId = docId;
        this.updateStatusIndicator();
        
        // Show chat indicator
        const chatIndicator = document.getElementById('chatIndicator');
        if (chatIndicator) {
            chatIndicator.classList.add('active');
        }
    }

    // Override the original methods to include enhanced functionality
    async processFile(file) {
        if (!file || !this.allowed_file(file.name)) {
            this.showToast('Please select a valid file (PDF, TXT, or DOCX)', 'error');
            return;
        }

        const formData = new FormData();
        formData.append('file', file);

        this.showLoading(true);
        this.updateUploadProgress(25, 1);

        try {
            this.updateUploadProgress(50, 2);
            
            const response = await fetch('/upload', {
                method: 'POST',
                body: formData
            });

            this.updateUploadProgress(75, 3);

            const data = await response.json();

            if (response.ok) {
                this.updateUploadProgress(100, 4);
                this.displayUploadResult(data);
                this.setActiveDocument(data.doc_id);
                this.showToast('File uploaded and analyzed successfully!', 'success');
            } else {
                throw new Error(data.error || 'Upload failed');
            }
        } catch (error) {
            console.error('Upload error:', error);
            this.showToast(error.message, 'error');
            this.updateUploadProgress(0, 0);
        } finally {
            this.showLoading(false);
        }
    }

    allowed_file(filename) {
        const allowedExtensions = ['pdf', 'txt', 'docx'];
        const extension = filename.split('.').pop().toLowerCase();
        return allowedExtensions.includes(extension);
    }

    // Page Navigation Methods
    setupPageNavigation() {
        // Handle smooth scrolling for landing page links
        document.querySelectorAll('a[href^="#"]').forEach(anchor => {
            anchor.addEventListener('click', function (e) {
                e.preventDefault();
                const target = document.querySelector(this.getAttribute('href'));
                if (target && target.closest('#landingPage')) {
                    target.scrollIntoView({
                        behavior: 'smooth',
                        block: 'start'
                    });
                }
            });
        });
    }

    setupMobileNav() {
        // Toggle landing nav links
        document.querySelectorAll('.navbar .mobile-nav-toggle').forEach(toggle => {
            toggle.addEventListener('click', () => {
                const container = toggle.closest('.navbar').querySelector('.landing-nav-links, .nav-links');
                if (container) {
                    container.classList.toggle('show');
                }
            });
        });
        // Close menu on link click (mobile)
        document.querySelectorAll('.landing-nav-links .nav-link').forEach(link => {
            link.addEventListener('click', () => {
                const links = document.querySelector('.landing-nav-links');
                links && links.classList.remove('show');
            });
        });
    }

    setupVhUnit() {
        const setVh = () => {
            const vh = window.innerHeight * 0.01;
            document.documentElement.style.setProperty('--vh', `${vh}px`);
        };
        setVh();
        window.addEventListener('resize', setVh);
        window.addEventListener('orientationchange', setVh);
    }

    // Removed split-mode; tabs-only behavior
    setupViewToggle() {
        // Strict tabs: only one panel visible
        document.querySelectorAll('.tab-btn').forEach(btn => {
            btn.classList.remove('active');
        });
        document.querySelectorAll('.tab-content').forEach(content => {
            content.classList.remove('active');
        });
        document.querySelector(`[data-tab="summary"]`)?.classList.add('active');
        document.getElementById('summary-tab')?.classList.add('active');
        history.replaceState(null, null, `#summary`);
        const tabDisplayName = 'Summary';
        showToast(`Focused ${tabDisplayName}`, 'info');
    }

    navigateToApp(section = 'search') {
        // Hide landing page
        const landingPage = document.getElementById('landingPage');
        const appPage = document.getElementById('appPage');
        
        if (landingPage && appPage) {
            landingPage.classList.remove('active');
            appPage.classList.add('active');
            
            this.currentPage = 'app';
            
            // Switch to the specified section
            this.switchSection(section);
            
            // Show toast message
            this.showToast(`Welcome to Research Radar! ${section === 'search' ? 'Start searching for papers' : 'Upload your documents'}`, 'success');
            
            // Focus on the relevant input
            setTimeout(() => {
                if (section === 'search') {
                    const searchInput = document.getElementById('searchInput');
                    if (searchInput) searchInput.focus();
                } else if (section === 'upload') {
                    // Auto-focus on upload section
                    document.getElementById('upload').scrollIntoView({ behavior: 'smooth' });
                }
            }, 500);
        }
    }

    navigateToLanding() {
        const landingPage = document.getElementById('landingPage');
        const appPage = document.getElementById('appPage');
        
        if (landingPage && appPage) {
            appPage.classList.remove('active');
            landingPage.classList.add('active');
            
            this.currentPage = 'landing';
            
            // Scroll to top
            window.scrollTo({ top: 0, behavior: 'smooth' });
            
            this.showToast('Welcome back to the homepage!', 'info');
        }
    }

    // Enhanced section switching for app page
    switchSection(sectionName) {
        if (this.currentPage !== 'app') return;

        // Update navigation
        document.querySelectorAll('.app-nav .nav-link').forEach(link => {
            link.classList.remove('active');
        });
        
        const activeLink = document.querySelector(`.app-nav [data-section="${sectionName}"]`);
        if (activeLink) {
            activeLink.classList.add('active');
        }

        // Update sections
        document.querySelectorAll('#appPage .section').forEach(section => {
            section.classList.remove('active');
        });
        
        const targetSection = document.getElementById(sectionName);
        if (targetSection) {
            targetSection.classList.add('active');
        }
        
        this.currentSection = sectionName;
        
        // Add section-specific functionality
        this.onSectionChange(sectionName);
    }

    onSectionChange(sectionName) {
        switch(sectionName) {
            case 'search':
                // Focus search input after animation
                setTimeout(() => {
                    const searchInput = document.getElementById('searchInput');
                    if (searchInput) searchInput.focus();
                }, 300);
                break;
            case 'upload':
                // Reset upload progress
                this.updateUploadProgress(0, 0);
                break;
            case 'mypapers':
                // Load papers when section is accessed
                this.loadMyPapers();
                break;
            case 'chat':
                // Focus chat input
                setTimeout(() => {
                    const chatInput = document.getElementById('chatInput');
                    if (chatInput) chatInput.focus();
                }, 300);
                break;
        }
    }

    // Enhanced Chat Functionality
    setupEnhancedChat() {
        this.messageCount = 0;
        this.sessionStartTime = Date.now();
        this.updateChatStats();
        this.setupChatSuggestions();
        this.setupChatInput();
        this.setupQuickActions();
        this.startSessionTimer();
    }

    setupChatSuggestions() {
        // Handle suggestion chips
        document.querySelectorAll('.suggestion-chip-enhanced').forEach(chip => {
            chip.addEventListener('click', (e) => {
                const question = e.currentTarget.dataset.question;
                if (question) {
                    const chatInput = document.getElementById('chatInput');
                    chatInput.value = question;
            chatInput.focus();
                    this.autoResizeTextarea(chatInput);
                }
            });
        });
    }

    setupChatInput() {
        const chatInput = document.getElementById('chatInput');
        const sendBtn = document.getElementById('chatSendBtn');
        const clearBtn = document.getElementById('chatClearBtn');

        // Auto-resize textarea
        chatInput.addEventListener('input', () => {
            this.autoResizeTextarea(chatInput);
        });

        // Handle Enter key
        chatInput.addEventListener('keydown', (e) => {
            if (e.key === 'Enter' && !e.shiftKey) {
                e.preventDefault();
                this.sendMessage();
            } else if (e.key === 'Enter' && e.shiftKey) {
                // Allow new line
            }
        });

        // Send button
        sendBtn.addEventListener('click', () => {
            this.sendMessage();
        });

        // Clear chat
        clearBtn.addEventListener('click', () => {
            this.clearChat();
        });

        // Attach button (placeholder)
        document.getElementById('attachBtn')?.addEventListener('click', () => {
            this.showNotification('File attachment coming soon!', 'info');
        });

        // Emoji button (placeholder)
        document.getElementById('emojiBtn')?.addEventListener('click', () => {
            this.showNotification('Emoji picker coming soon!', 'info');
        });
    }

    setupQuickActions() {
        // Quick action buttons in status card
        document.querySelectorAll('.quick-action-btn').forEach(btn => {
            btn.addEventListener('click', (e) => {
                e.stopPropagation();
            });
        });
    }

    autoResizeTextarea(textarea) {
        textarea.style.height = 'auto';
        textarea.style.height = Math.min(textarea.scrollHeight, 120) + 'px';
    }

    sendMessage() {
        const chatInput = document.getElementById('chatInput');
        const message = chatInput.value.trim();
        
        if (!message) return;

        // Add user message to chat
        this.addMessageToChat(message, 'user');
        
        // Clear input
        chatInput.value = '';
        this.autoResizeTextarea(chatInput);
        
        // Show typing indicator
        this.showTypingIndicator();
        
        // Update stats
        this.messageCount++;
        this.updateChatStats();
        
        // Send to backend
        this.sendChatMessage(message);
    }

    addMessageToChat(message, sender = 'user') {
        const chatMessages = document.getElementById('chatMessages');
        const messageDiv = document.createElement('div');
        
        const currentTime = new Date().toLocaleTimeString([], { 
            hour: '2-digit', 
            minute: '2-digit' 
        });
        
        if (sender === 'user') {
            messageDiv.className = 'chat-message user-message';
        messageDiv.innerHTML = `
                <div class="message-avatar-enhanced">
                    <div class="avatar-icon user-avatar">
                        <i class="fas fa-user"></i>
            </div>
                </div>
                <div class="message-content-enhanced">
                    <div class="message-header">
                        <span class="message-sender">You</span>
                        <span class="message-time">${currentTime}</span>
                    </div>
                    <div class="message-text">
                <p>${this.escapeHtml(message)}</p>
                    </div>
            </div>
        `;
        } else {
            messageDiv.className = 'chat-message bot-message';
            messageDiv.innerHTML = `
                <div class="message-avatar-enhanced">
                    <div class="avatar-icon">
                        <i class="fas fa-robot"></i>
                    </div>
                    <div class="avatar-status online"></div>
                </div>
                <div class="message-content-enhanced">
                    <div class="message-header">
                        <span class="message-sender">Research Assistant</span>
                        <span class="message-time">${currentTime}</span>
                        <span class="message-badge ai">AI</span>
                    </div>
                    <div class="message-text">
                        <div class="message-content">${message}</div>
                    </div>
                </div>
            `;
        }

        // Remove welcome message if it's the first user message
        const welcomeMessage = chatMessages.querySelector('.welcome-message-enhanced');
        if (welcomeMessage && sender === 'user') {
            welcomeMessage.style.animation = 'fadeOut 0.3s ease-out forwards';
            setTimeout(() => {
                welcomeMessage.remove();
            }, 300);
        }

        chatMessages.appendChild(messageDiv);
        
        // Scroll to bottom
        const container = document.querySelector('.chat-messages-container');
        container.scrollTop = container.scrollHeight;

        // Update chat status
        this.updateChatStatus('active');
    }

    showTypingIndicator() {
        const loadingIndicator = document.getElementById('chatLoading');
        loadingIndicator.style.display = 'flex';
        
        // Scroll to show typing indicator
        const container = document.querySelector('.chat-messages-container');
        setTimeout(() => {
            container.scrollTop = container.scrollHeight;
        }, 100);
    }

    hideTypingIndicator() {
        const loadingIndicator = document.getElementById('chatLoading');
        loadingIndicator.style.display = 'none';
    }

    clearChat() {
        if (confirm('Are you sure you want to clear the chat history?')) {
            const chatMessages = document.getElementById('chatMessages');
            chatMessages.innerHTML = `
                <div class="chat-message bot-message welcome-message-enhanced">
                    <div class="message-avatar-enhanced">
                        <div class="avatar-icon">
                            <i class="fas fa-robot"></i>
                        </div>
                        <div class="avatar-status online"></div>
                    </div>
                    <div class="message-content-enhanced">
                        <div class="message-header">
                            <span class="message-sender">Research Assistant</span>
                            <span class="message-time">Just now</span>
                            <span class="message-badge ai">AI</span>
                        </div>
                        <div class="message-text">
                            <div class="welcome-intro">
                                <h3>👋 Welcome back to Research Radar!</h3>
                                <p>Chat cleared. I'm ready to help you with your research questions.</p>
                            </div>
                        </div>
                    </div>
                </div>
            `;
            
            this.messageCount = 0;
            this.updateChatStats();
            this.updateChatStatus('ready');
            this.showNotification('Chat cleared successfully', 'success');
        }
    }

    updateChatStats() {
        const messageCountEl = document.getElementById('messageCount');
        const sessionTimeEl = document.getElementById('sessionTime');
        
        if (messageCountEl) {
            messageCountEl.textContent = this.messageCount;
        }
    }

    startSessionTimer() {
        setInterval(() => {
            const sessionTimeEl = document.getElementById('sessionTime');
            if (sessionTimeEl) {
                const elapsed = Math.floor((Date.now() - this.sessionStartTime) / 1000);
                const minutes = Math.floor(elapsed / 60);
                const seconds = elapsed % 60;
                sessionTimeEl.textContent = `${minutes}:${seconds.toString().padStart(2, '0')}`;
            }
        }, 1000);
    }

    updateChatStatus(status) {
        const statusTitle = document.getElementById('statusTitle');
        const statusDescription = document.getElementById('statusDescription');
        
        switch (status) {
            case 'ready':
                statusTitle.textContent = 'Ready to Chat';
                statusDescription.textContent = 'Upload a document or search for papers to get started';
                break;
            case 'active':
                statusTitle.textContent = 'Chat Active';
                statusDescription.textContent = 'AI assistant is ready to answer your questions';
                break;
            case 'processing':
                statusTitle.textContent = 'Processing...';
                statusDescription.textContent = 'AI is analyzing your question';
                break;
        }
    }

    sendChatMessage(message) {
        this.updateChatStatus('processing');
        
        fetch('/chat', {
            method: 'POST',
            headers: {
                'Content-Type': 'application/json',
            },
            body: JSON.stringify({ message: message })
        })
        .then(response => response.json())
        .then(data => {
            this.hideTypingIndicator();
            
            if (data.success) {
                this.addMessageToChat(data.response, 'bot');
                this.messageCount++;
                this.updateChatStats();
            } else {
                this.addMessageToChat(
                    `I apologize, but I encountered an error: ${data.error || 'Unknown error'}. Please try again.`,
                    'bot'
                );
            }
            
            this.updateChatStatus('active');
        })
        .catch(error => {
            console.error('Chat error:', error);
            this.hideTypingIndicator();
            this.addMessageToChat(
                'I apologize, but I\'m having trouble connecting right now. Please check your connection and try again.',
                'bot'
            );
            this.updateChatStatus('ready');
        });
    }

    escapeHtml(text) {
        const div = document.createElement('div');
        div.textContent = text;
        return div.innerHTML;
    }

    // Global functions for HTML onclick handlers
    toggleSuggestions() {
        const content = document.getElementById('suggestionsContent');
        const toggle = document.querySelector('.suggestions-toggle i');
        
        if (content.classList.contains('collapsed')) {
            content.classList.remove('collapsed');
            toggle.className = 'fas fa-chevron-up';
        } else {
            content.classList.add('collapsed');
            toggle.className = 'fas fa-chevron-down';
        }
    }

    showQuickActions() {
        const quickActions = document.getElementById('chatQuickActions');
        quickActions.style.display = 'block';
        quickActions.style.animation = 'slideUp 0.3s ease-out';
    }

    hideQuickActions() {
        const quickActions = document.getElementById('chatQuickActions');
        quickActions.style.animation = 'slideDown 0.3s ease-out';
        setTimeout(() => {
            quickActions.style.display = 'none';
        }, 300);
    }

    generateSummary() {
        this.addMessageToChat('Please generate a summary of the current document.', 'user');
        this.sendChatMessage('Please generate a summary of the current document.');
        this.hideQuickActions();
    }

    extractKeyPoints() {
        this.addMessageToChat('What are the key points from this paper?', 'user');
        this.sendChatMessage('What are the key points from this paper?');
        this.hideQuickActions();
    }

    findRelatedPapers() {
        this.addMessageToChat('Can you suggest related papers to this research?', 'user');
        this.sendChatMessage('Can you suggest related papers to this research?');
        this.hideQuickActions();
    }

    exportChat() {
        // Get all messages
        const messages = document.querySelectorAll('.chat-message');
        let chatText = 'Research Radar Chat Export\n';
        chatText += '='.repeat(50) + '\n\n';
        
        messages.forEach(message => {
            const sender = message.querySelector('.message-sender')?.textContent || 'Unknown';
            const time = message.querySelector('.message-time')?.textContent || '';
            const text = message.querySelector('.message-text')?.textContent || '';
            
            if (text.trim()) {
                chatText += `[${time}] ${sender}:\n${text.trim()}\n\n`;
            }
        });
        
        // Create and download file
        const blob = new Blob([chatText], { type: 'text/plain' });
        const url = URL.createObjectURL(blob);
        const a = document.createElement('a');
        a.href = url;
        a.download = `research-radar-chat-${new Date().toISOString().split('T')[0]}.txt`;
        document.body.appendChild(a);
        a.click();
        document.body.removeChild(a);
        URL.revokeObjectURL(url);
        
        this.showNotification('Chat exported successfully!', 'success');
        this.hideQuickActions();
    }

    // Summary + Chat Functionality
    openSummaryChat(paperData, summaryText) {
        console.log('openSummaryChat called with:', { paperData, summaryText });
        
        // Hide current section and show summary-chat
        document.querySelectorAll('.section').forEach(section => {
            section.style.display = 'none';
        });
        
        const summarySection = document.getElementById('summary-chat');
        if (!summarySection) {
            console.error('summary-chat section not found!');
            this.showToast('Error: Summary section not found', 'error');
            return;
        }
        summarySection.style.display = 'block';
        
        // Update paper information
        document.getElementById('paperTitle').textContent = paperData.title || 'Research Paper';
        document.getElementById('paperAuthor').textContent = paperData.authors ? paperData.authors.join(', ') : 'Unknown Author';
        document.getElementById('paperDate').textContent = paperData.published || new Date().getFullYear();
        document.getElementById('paperCategory').textContent = paperData.category || 'Research';
        
        // Show summary
        this.displaySummaryInPanel(summaryText);
        
        // Setup chat panel
        this.setupChatPanel();
        
        // Store current paper data for chat context
        this.currentPaper = paperData;

        // Default to Chat tab for immediate Q&A after tabs are in DOM
        setTimeout(() => {
            try { switchTab('chat'); } catch (_) {}
            const chatInput = document.getElementById('chatInputPanel');
            if (chatInput) chatInput.focus();
        }, 150);
    }

    displaySummaryInPanel(summaryText) {
        const summaryLoading = document.getElementById('summaryLoading');
        const summaryTextEl = document.getElementById('summaryText');
        
        // Hide loading and show summary
        summaryLoading.style.display = 'none';
        summaryTextEl.style.display = 'block';
        summaryTextEl.innerHTML = this.formatSummaryText(summaryText);
        
        // Update stats
        this.updateSummaryStats(summaryText);
    }

    formatSummaryText(text) {
        // Convert plain text to formatted HTML
        return text
            .replace(/\n\n/g, '</p><p>')
            .replace(/\n/g, '<br>')
            .replace(/\*\*(.*?)\*\*/g, '<strong>$1</strong>')
            .replace(/\*(.*?)\*/g, '<em>$1</em>')
            .replace(/^/, '<p>')
            .replace(/$/, '</p>');
    }

    updateSummaryStats(text) {
        const wordCount = text.split(/\s+/).length;
        const readingTime = Math.ceil(wordCount / 200); // Average reading speed
        const compressionRatio = Math.round((1 - (text.length / (text.length * 3))) * 100); // Estimate
        
        const wc = document.getElementById('wordCount');
        const rt = document.getElementById('readingTime');
        const cr = document.getElementById('compressionRatio');
        if (wc) wc.textContent = wordCount.toLocaleString();
        if (rt) rt.textContent = `${readingTime} min`;
        if (cr) cr.textContent = `${compressionRatio}%`;
    }

    setupChatPanel() {
        const chatInput = document.getElementById('chatInputPanel');
        const sendBtn = document.getElementById('chatSendBtnPanel');
        
        if (!chatInput || !sendBtn) return;
        
        // Clear any existing event listeners by cloning
        const newChatInput = chatInput.cloneNode(true);
        chatInput.parentNode.replaceChild(newChatInput, chatInput);
        
        const newSendBtn = sendBtn.cloneNode(true);
        sendBtn.parentNode.replaceChild(newSendBtn, sendBtn);
        
        // Add new event listeners
        newChatInput.addEventListener('keydown', (e) => {
            if (e.key === 'Enter' && !e.shiftKey) {
                e.preventDefault();
                this.sendChatMessagePanel();
            }
        });
        
        newChatInput.addEventListener('input', () => {
            this.autoResizeTextarea(newChatInput);
        });
        
        newSendBtn.addEventListener('click', () => {
            this.sendChatMessagePanel();
        });
    }

    sendChatMessagePanel() {
        const chatInput = document.getElementById('chatInputPanel');
        const message = chatInput.value.trim();
        
        if (!message) return;
        
        // Add user message
        this.addChatMessagePanel(message, 'user');
        
        // Clear input
        chatInput.value = '';
        this.autoResizeTextarea(chatInput);
        
        // Show typing indicator and send to backend
        this.showChatTypingPanel();
        this.sendChatToBackend(message);
    }

    addChatMessagePanel(message, sender) {
        const chatPanel = document.getElementById('chatMessagesPanel');
        
        // Remove welcome message if it exists
        const welcome = chatPanel.querySelector('.chat-welcome');
        if (welcome && sender === 'user') {
            welcome.remove();
        }
        
        const messageDiv = document.createElement('div');
        messageDiv.className = `chat-message-panel ${sender}`;
        
        const currentTime = new Date().toLocaleTimeString([], { 
            hour: '2-digit', 
            minute: '2-digit' 
        });
        
        messageDiv.innerHTML = `
            <div class="message-avatar-panel ${sender}">
                <i class="fas fa-${sender === 'user' ? 'user' : 'robot'}"></i>
            </div>
            <div class="message-content-panel ${sender}">
                <div class="message-bubble ${sender}">
                    ${sender === 'bot' ? message : this.escapeHtml(message)}
                </div>
                <div class="message-time-panel">${currentTime}</div>
            </div>
        `;
        
        chatPanel.appendChild(messageDiv);
        chatPanel.scrollTop = chatPanel.scrollHeight;
    }

    showChatTypingPanel() {
        const chatPanel = document.getElementById('chatMessagesPanel');
        
        const typingDiv = document.createElement('div');
        typingDiv.className = 'chat-message-panel bot';
        typingDiv.id = 'typingIndicatorPanel';
        
        typingDiv.innerHTML = `
            <div class="message-avatar-panel bot">
                <i class="fas fa-robot"></i>
            </div>
            <div class="message-content-panel bot">
                <div class="message-bubble bot">
                    <div class="typing-dots">
                        <div class="dot"></div>
                        <div class="dot"></div>
                        <div class="dot"></div>
                    </div>
                    <span style="margin-left: 0.5rem; font-style: italic;">AI is thinking...</span>
                </div>
            </div>
        `;
        
        chatPanel.appendChild(typingDiv);
        chatPanel.scrollTop = chatPanel.scrollHeight;
    }

    hideChatTypingPanel() {
        const typingIndicator = document.getElementById('typingIndicatorPanel');
        if (typingIndicator) {
            typingIndicator.remove();
        }
    }

    sendChatToBackend(message) {
        fetch('/chat', {
            method: 'POST',
            headers: {
                'Content-Type': 'application/json',
            },
            body: JSON.stringify({ message: message })
        })
        .then(response => response.json())
        .then(data => {
            this.hideChatTypingPanel();
            
            if (data.success) {
                this.addChatMessagePanel(data.response, 'bot');
            } else {
                this.addChatMessagePanel(
                    `I apologize, but I encountered an error: ${data.error || 'Unknown error'}. Please try again.`,
                    'bot'
                );
            }
        })
        .catch(error => {
            console.error('Chat error:', error);
            this.hideChatTypingPanel();
            this.addChatMessagePanel(
                'I apologize, but I\'m having trouble connecting right now. Please check your connection and try again.',
                'bot'
            );
        });
    }

    // My Papers functionality
    async loadMyPapers() {
        const loadingEl = document.getElementById('mypapersLoading');
        const emptyEl = document.getElementById('mypapersEmpty');
        const gridEl = document.getElementById('papersGrid');
        
        if (loadingEl) loadingEl.style.display = 'block';
        if (emptyEl) emptyEl.style.display = 'none';
        if (gridEl) gridEl.innerHTML = '';
        
        try {
            const response = await fetch('/documents');
            const data = await response.json();
            
            if (response.ok && data.success) {
                this.displayMyPapers(data.documents);
            } else {
                throw new Error(data.error || 'Failed to load papers');
            }
        } catch (error) {
            console.error('Error loading papers:', error);
            this.showToast('Failed to load papers', 'error');
            if (emptyEl) emptyEl.style.display = 'block';
        } finally {
            if (loadingEl) loadingEl.style.display = 'none';
        }
    }

    displayMyPapers(documents) {
        const emptyEl = document.getElementById('mypapersEmpty');
        const gridEl = document.getElementById('papersGrid');
        
        if (!documents || documents.length === 0) {
            if (emptyEl) emptyEl.style.display = 'block';
            if (gridEl) gridEl.innerHTML = '';
            return;
        }
        
        if (emptyEl) emptyEl.style.display = 'none';
        if (!gridEl) return;
        
        gridEl.innerHTML = documents.map(doc => this.createPaperCard(doc)).join('');
        
        // Add event listeners to the buttons after creating them
        this.setupMyPapersButtons();
    }

    setupMyPapersButtons() {
        console.log('Setting up My Papers buttons...');
        
        // Add event listeners to Open buttons
        const openButtons = document.querySelectorAll('.paper-action-btn.primary');
        console.log(`Found ${openButtons.length} Open buttons`);
        
        openButtons.forEach(button => {
            button.addEventListener('click', (e) => {
                e.preventDefault();
                const docId = button.getAttribute('data-doc-id');
                console.log('Open button clicked for docId:', docId);
                this.openPaperFromMyPapers(docId);
            });
        });

        // Add event listeners to Delete buttons
        const deleteButtons = document.querySelectorAll('.paper-action-btn.secondary');
        console.log(`Found ${deleteButtons.length} Delete buttons`);
        
        deleteButtons.forEach(button => {
            button.addEventListener('click', (e) => {
                e.preventDefault();
                const docId = button.getAttribute('data-doc-id');
                console.log('Delete button clicked for docId:', docId);
                this.deletePaper(docId);
            });
        });
    }

    createPaperCard(doc) {
        const icon = this.getDocumentIcon(doc.type);
        const authors = Array.isArray(doc.authors) ? doc.authors.join(', ') : doc.authors || 'Unknown';
        const date = doc.upload_date || doc.published || 'Unknown Date';
        
        return `
            <div class="paper-card-mypapers" data-doc-id="${doc.document_id}">
                <div class="paper-card-header">
                    <div class="paper-card-icon">
                        <i class="${icon}"></i>
                    </div>
                    <div class="paper-card-content">
                        <div class="paper-card-title">${this.escapeHtml(doc.title)}</div>
                        <div class="paper-card-meta">
                            <span><i class="fas fa-users"></i> ${this.escapeHtml(authors)}</span>
                            <span><i class="fas fa-calendar"></i> ${this.escapeHtml(date)}</span>
                            ${doc.word_count ? `<span><i class="fas fa-file-text"></i> ${doc.word_count.toLocaleString()} words</span>` : ''}
                        </div>
                    </div>
                </div>
                <div class="paper-card-actions">
                    <button class="paper-action-btn primary" data-doc-id="${doc.document_id}">
                        <i class="fas fa-eye"></i>
                        <span>Open</span>
                    </button>
                    <button class="paper-action-btn secondary" data-doc-id="${doc.document_id}">
                        <i class="fas fa-trash"></i>
                        <span>Delete</span>
                    </button>
                </div>
            </div>
        `;
    }

    getDocumentIcon(type) {
        switch (type) {
            case 'arxiv_paper': return 'fas fa-graduation-cap';
            case 'uploaded_document': return 'fas fa-file-upload';
            default: return 'fas fa-file-alt';
        }
    }

    async openPaperFromMyPapers(docId) {
        console.log('ResearchRadar.openPaperFromMyPapers called with docId:', docId);
        try {
            // Set the document as active for chat
            this.currentDocumentId = docId;
            
            // Fetch document summary
            console.log('Fetching document summary...');
            const response = await fetch(`/documents/${docId}/summary`);
            const data = await response.json();
            
            console.log('Summary response:', data);
            
            if (response.ok && data.success) {
                // Activate the document for chat
                await fetch(`/documents/${docId}/activate`, {
                    method: 'POST',
                    headers: { 'Content-Type': 'application/json' }
                });
                
                // Redirect to summary and chat page
                console.log('Redirecting to summary and chat...');
                this.openSummaryChat(data.document, data.summary);
                this.showToast('Paper loaded successfully', 'success');
            } else {
                throw new Error(data.error || 'Failed to load paper');
            }
        } catch (error) {
            console.error('Error opening paper:', error);
            this.showToast('Failed to open paper', 'error');
        }
    }

    async deletePaper(docId) {
        console.log('ResearchRadar.deletePaper called with docId:', docId);
        if (!confirm('Are you sure you want to delete this paper? This action cannot be undone.')) {
            return;
        }
        
        try {
            console.log('Deleting document...');
            const response = await fetch(`/documents/${docId}`, {
                method: 'DELETE',
                headers: { 'Content-Type': 'application/json' }
            });
            
            const data = await response.json();
            console.log('Delete response:', data);
            
            if (response.ok && data.success) {
                const card = document.querySelector(`[data-doc-id="${docId}"]`);
                if (card) {
                    card.remove();
                }
                this.showToast('Paper deleted successfully', 'success');
            } else {
                throw new Error(data.error || 'Failed to delete paper');
            }
        } catch (error) {
            console.error('Error deleting paper:', error);
            this.showToast('Failed to delete paper', 'error');
        }
    }

    async clearAllPapers() {
        if (!confirm('Are you sure you want to clear all papers? This action cannot be undone.')) {
            return;
        }
        
        try {
            const response = await fetch('/documents', {
                method: 'DELETE',
                headers: { 'Content-Type': 'application/json' }
            });
            
            const data = await response.json();
            
            if (response.ok && data.success) {
                const gridEl = document.getElementById('papersGrid');
                if (gridEl) {
                    gridEl.innerHTML = '';
                    document.getElementById('mypapersEmpty').style.display = 'block';
                }
                this.showToast('All papers cleared successfully', 'success');
            } else {
                throw new Error(data.error || 'Failed to clear papers');
            }
        } catch (error) {
            console.error('Error clearing papers:', error);
            this.showToast('Failed to clear papers', 'error');
        }
    }
}



// Global navigation functions
function navigateToApp(section = 'search') {
    console.log(`Global navigateToApp called with section: ${section}`);
    
    if (window.researchRadar) {
        console.log('Using ResearchRadar instance');
        window.researchRadar.navigateToApp(section);
    } else {
        console.log('ResearchRadar instance not ready, using fallback navigation');
        // Fallback navigation if ResearchRadar isn't ready yet
        const landingPage = document.getElementById('landingPage');
        const appPage = document.getElementById('appPage');
        
        if (landingPage && appPage) {
            landingPage.classList.remove('active');
            appPage.classList.add('active');
            
            // Switch to the requested section
            setTimeout(() => {
                const sections = document.querySelectorAll('.section');
                sections.forEach(s => s.classList.remove('active'));
                
                const targetSection = document.getElementById(section);
                if (targetSection) {
                    targetSection.classList.add('active');
                }
                
                // Update navigation
                const navLinks = document.querySelectorAll('.nav-link');
                navLinks.forEach(link => link.classList.remove('active'));
                
                const activeNavLink = document.querySelector(`[data-section="${section}"]`);
                if (activeNavLink) {
                    activeNavLink.classList.add('active');
                }
            }, 50);
        }
    }
}

function navigateToLanding() {
    console.log('Global navigateToLanding called');
    
    if (window.researchRadar) {
        console.log('Using ResearchRadar instance');
        window.researchRadar.navigateToLanding();
    } else {
        console.log('ResearchRadar instance not ready, using fallback navigation');
        // Fallback navigation if ResearchRadar isn't ready yet
        const landingPage = document.getElementById('landingPage');
        const appPage = document.getElementById('appPage');
        
        if (landingPage && appPage) {
            appPage.classList.remove('active');
            landingPage.classList.add('active');
        }
    }
}

// Global chat functions
function toggleSuggestions() {
    if (window.researchRadar) {
        window.researchRadar.toggleSuggestions();
    }
}

function showQuickActions() {
    if (window.researchRadar) {
        window.researchRadar.showQuickActions();
    }
}

function hideQuickActions() {
    if (window.researchRadar) {
        window.researchRadar.hideQuickActions();
    }
}

function generateSummary() {
    if (window.researchRadar) {
        window.researchRadar.generateSummary();
    }
}

function extractKeyPoints() {
    if (window.researchRadar) {
        window.researchRadar.extractKeyPoints();
    }
}

function findRelatedPapers() {
    if (window.researchRadar) {
        window.researchRadar.findRelatedPapers();
    }
}

// Global functions for My Papers buttons
function openPaperFromMyPapers(docId) {
    console.log('Global openPaperFromMyPapers called with docId:', docId);
    
    // Wait for ResearchRadar to be available
    const waitForResearchRadar = () => {
        if (window.researchRadar) {
            window.researchRadar.openPaperFromMyPapers(docId);
        } else {
            console.log('ResearchRadar not ready, waiting...');
            setTimeout(waitForResearchRadar, 100);
        }
    };
    
    waitForResearchRadar();
}

function deletePaperFromMyPapers(docId) {
    console.log('Global deletePaperFromMyPapers called with docId:', docId);
    
    // Wait for ResearchRadar to be available
    const waitForResearchRadar = () => {
        if (window.researchRadar) {
            window.researchRadar.deletePaper(docId);
        } else {
            console.log('ResearchRadar not ready, waiting...');
            setTimeout(waitForResearchRadar, 100);
        }
    };
    
    waitForResearchRadar();
}

function exportChat() {
    if (window.researchRadar) {
        window.researchRadar.exportChat();
    }
}

// Enhanced Search Functions
function toggleAdvancedSearch() {
    const advancedFilters = document.getElementById('advancedFilters');
    const toggleBtn = document.querySelector('.advanced-search-btn');
    
    if (advancedFilters) {
        const isShowing = advancedFilters.classList.toggle('show');
        
        if (toggleBtn) {
            const icon = toggleBtn.querySelector('i');
            if (icon) {
                if (isShowing) {
                    icon.classList.remove('fa-sliders-h');
                    icon.classList.add('fa-times');
                    toggleBtn.classList.add('active');
                } else {
                    icon.classList.remove('fa-times');
                    icon.classList.add('fa-sliders-h');
                    toggleBtn.classList.remove('active');
                }
            }
        }
    }
}

function toggleSearchTips() {
    const tipsContent = document.querySelector('.tips-content');
    const tipsToggle = document.querySelector('.tips-toggle');
    
    if (tipsContent) {
        tipsContent.classList.toggle('show');
        
        if (tipsToggle) {
            const icon = tipsToggle.querySelector('i');
            if (icon) {
                icon.classList.toggle('fa-chevron-down');
                icon.classList.toggle('fa-chevron-up');
            }
        }
    }
}

function clearSearchHistory() {
    localStorage.removeItem('recentSearches');
    const recentSearchesContainer = document.getElementById('recentSearches');
    if (recentSearchesContainer) {
        recentSearchesContainer.style.display = 'none';
    }
    
    if (window.researchRadar) {
        window.researchRadar.showToast('Search history cleared', 'success');
    }
}

// Enhanced Upload Functions
function toggleUploadTips() {
    const tipsContent = document.getElementById('uploadTipsContent');
    const tipsToggle = document.querySelector('.upload-tips .tips-toggle');
    
    if (tipsContent) {
        tipsContent.classList.toggle('show');
        
        if (tipsToggle) {
            const icon = tipsToggle.querySelector('i');
            if (icon) {
                icon.classList.toggle('fa-chevron-down');
                icon.classList.toggle('fa-chevron-up');
            }
        }
    }
}

// Additional missing functions for summary-chat functionality
function goBackToSearch() {
    console.log('Global goBackToSearch called');
    
    if (window.researchRadar) {
        console.log('Using ResearchRadar instance for goBackToSearch');
        
        // Hide summary-chat section
        const summarySection = document.getElementById('summary-chat');
        if (summarySection) {
            summarySection.classList.remove('active');
            summarySection.style.display = 'none';
        }
        
        // Show search section and restore navigation
        window.researchRadar.switchSection('search');
        
        console.log('Successfully returned to search section');
    } else {
        console.log('ResearchRadar instance not ready, using fallback navigation');
        
        // Fallback navigation
        const summarySection = document.getElementById('summary-chat');
        const searchSection = document.getElementById('search');
        
        if (summarySection) {
            summarySection.classList.remove('active');
            summarySection.style.display = 'none';
        }
        
        if (searchSection) {
            searchSection.classList.add('active');
            searchSection.style.display = 'block';
        }
        
        // Update navigation
        const navLinks = document.querySelectorAll('.nav-link');
        navLinks.forEach(link => link.classList.remove('active'));
        
        const searchNavLink = document.querySelector('[data-section="search"]');
        if (searchNavLink) {
            searchNavLink.classList.add('active');
        }
    }
}

function exportSummaryChat() {
    console.log('Exporting summary and chat...');
    if (window.researchRadar) {
        window.researchRadar.showToast('Export feature coming soon!', 'info');
    }
}

function shareSummary() {
    console.log('Sharing summary...');
    if (window.researchRadar) {
        window.researchRadar.showToast('Share feature coming soon!', 'info');
    }
}

function regenerateSummary() {
    console.log('Regenerating summary...');
    if (window.researchRadar) {
        window.researchRadar.showToast('Regenerating summary...', 'info');
    }
}

function copySummary() {
    const summaryText = document.getElementById('summaryText');
    if (summaryText) {
        navigator.clipboard.writeText(summaryText.textContent).then(() => {
            if (window.researchRadar) {
                window.researchRadar.showToast('Summary copied to clipboard!', 'success');
            }
        });
    }
}

function askQuickQuestion(question) {
    const chatInput = document.getElementById('chatInputPanel');
    if (chatInput) {
        chatInput.value = question;
        chatInput.focus();
    }
}

// Global summarize paper function (fallback for any remaining onclick handlers)
function summarizePaper(paperUrl) {
    console.log(`Global summarizePaper called with URL: ${paperUrl}`);
    
    if (window.researchRadar) {
        console.log('Using ResearchRadar instance for summarizePaper');
        window.researchRadar.summarizePaper(paperUrl);
    } else {
        console.error('ResearchRadar instance not available for summarizePaper');
        alert('Application not ready. Please try again in a moment.');
    }
}

// Immediate setup for critical buttons (before full initialization)
function setupCriticalButtons() {
    console.log('Setting up critical buttons immediately...');
    
    // Set up the main navigation buttons with fallback functions
    const buttons = [
        { selector: '.nav-cta-btn', action: () => navigateToApp('search'), name: 'Get Started' },
        { selector: '.cta-button.primary', action: () => navigateToApp('search'), name: 'Start Exploring' },
        { selector: '.cta-button.secondary', action: () => navigateToApp('upload'), name: 'Upload Paper' },
        { selector: '.back-to-landing', action: () => navigateToLanding(), name: 'Back to Landing' },
        { selector: '.app-nav .nav-brand', action: () => navigateToLanding(), name: 'Brand Logo' }
    ];
    
    buttons.forEach(({ selector, action, name }) => {
        const button = document.querySelector(selector);
        if (button) {
            console.log(`✅ Setting up ${name} button`);
            button.removeAttribute('onclick');
            button.addEventListener('click', (e) => {
                e.preventDefault();
                console.log(`${name} button clicked!`);
                action();
            });
        } else {
            console.log(`❌ ${name} button not found`);
        }
    });
    
    // Also setup summary page buttons if they exist
    setupSummaryPageButtonsGlobal();
}

// Global function to setup summary page buttons
function setupSummaryPageButtonsGlobal() {
    console.log('Setting up summary page buttons globally...');
    
    // Summary page buttons with fallback functions
    const summaryButtons = [
        { selector: '.back-btn', action: () => goBackToSearch(), name: 'Back to Search' },
        { selector: '.summary-action-btn[title*="Copy"]', action: () => copySummary(), name: 'Copy Summary' },
        { selector: '.summary-action-btn[title*="Regenerate"]', action: () => regenerateSummary(), name: 'Regenerate Summary' },
        { selector: '.action-btn-header[title*="Export"]', action: () => exportSummaryChat(), name: 'Export Summary' },
        { selector: '.action-btn-header[title*="Share"]', action: () => shareSummary(), name: 'Share Summary' }
    ];
    
    summaryButtons.forEach(({ selector, action, name }) => {
        const button = document.querySelector(selector);
        if (button) {
            console.log(`✅ Setting up ${name} button`);
            button.removeAttribute('onclick');
            // Clone button to remove all existing event listeners
            const newButton = button.cloneNode(true);
            button.parentNode.replaceChild(newButton, button);
            
            newButton.addEventListener('click', (e) => {
                e.preventDefault();
                console.log(`${name} button clicked!`);
                action();
            });
        } else {
            console.log(`❌ ${name} button not found`);
        }
    });
    
    // Setup quick question buttons
    const quickQuestionBtns = document.querySelectorAll('.quick-question-btn');
    console.log(`Found ${quickQuestionBtns.length} quick question buttons`);
    quickQuestionBtns.forEach((btn, index) => {
        btn.removeAttribute('onclick');
        // Clone button to remove existing listeners
        const newBtn = btn.cloneNode(true);
        btn.parentNode.replaceChild(newBtn, btn);
        
        newBtn.addEventListener('click', (e) => {
            e.preventDefault();
            const question = newBtn.textContent.trim();
            console.log(`Quick question button ${index + 1} clicked: ${question}`);
            askQuickQuestion(question);
        });
    });
}

// Run critical setup immediately if DOM is already loaded
if (document.readyState === 'loading') {
    document.addEventListener('DOMContentLoaded', setupCriticalButtons);
} else {
    setupCriticalButtons();
}

// Initialize the application when DOM is loaded
document.addEventListener('DOMContentLoaded', () => {
    console.log('DOM Content Loaded - Initializing Research Radar...');
    
    // Small delay to ensure all elements are rendered
    setTimeout(() => {
    window.researchRadar = new ResearchRadar();
    console.log('🚀 Research Radar - Application initialized successfully!');
        
        // Test if critical elements exist
        const testElements = [
            'searchInput',
            'searchBtn', 
            'analyzeUrlBtn',
            'fileInput',
            'searchResults'
        ];
        
        testElements.forEach(id => {
            const element = document.getElementById(id);
            console.log(`Element ${id}:`, element ? 'Found' : 'Not found');
        });
        
        // Test if Generate Summary buttons exist (they might be created dynamically)
        setTimeout(() => {
            const generateButtons = document.querySelectorAll('.generate-summary-btn');
            console.log(`Dynamic Generate Summary buttons found: ${generateButtons.length}`);
        }, 1000);
        
    }, 100);
});
// Add some additional CSS for animations
const additionalCSS = `
@keyframes toastSlideOut {
    to {
        opacity: 0;
        transform: translateX(100%);
    }
}
`;

const styleSheet = document.createElement('style');
styleSheet.textContent = additionalCSS;
document.head.appendChild(styleSheet); 

// Tab switching functionality
function switchTab(tabName) {
    // Strict tabs: only one panel visible
    document.querySelectorAll('.tab-btn').forEach(btn => {
        btn.classList.remove('active');
    });
    document.querySelectorAll('.tab-content').forEach(content => {
        content.classList.remove('active');
    });
    document.querySelector(`[data-tab="${tabName}"]`)?.classList.add('active');
    document.getElementById(`${tabName}-tab`)?.classList.add('active');
    if (tabName === 'chat') {
        setTimeout(() => {
            const chatInput = document.getElementById('chatInputPanel');
            if (chatInput) chatInput.focus();
        }, 100);
    }
    history.replaceState(null, null, `#${tabName}`);
    const tabDisplayName = tabName === 'summary' ? 'Summary' : 'Chat';
    showToast(`Switched to ${tabDisplayName} tab`, 'info');
}

// Initialize tab from URL hash
function initializeTabFromHash() {
    const hash = window.location.hash.substring(1);
    if (hash === 'summary' || hash === 'chat') {
        switchTab(hash);
    }
}

// Quick question functionality
function askQuickQuestion(question) {
    const chatInput = document.getElementById('chatInputPanel');
    if (chatInput) {
        chatInput.value = question;
        chatInput.focus();
    }
}

// Enhanced chat input functionality
function initializeChatInput() {
    const chatInput = document.getElementById('chatInputPanel');
    const sendBtn = document.getElementById('chatSendBtnPanel');
    
    if (chatInput && sendBtn) {
        // Auto-resize textarea
        chatInput.addEventListener('input', function() {
            this.style.height = 'auto';
            this.style.height = Math.min(this.scrollHeight, 120) + 'px';
        });
        
        // Handle Enter key
        chatInput.addEventListener('keydown', function(e) {
            if (e.key === 'Enter') {
                if (e.ctrlKey || e.metaKey) {
                    // Ctrl+Enter or Cmd+Enter to send
                    e.preventDefault();
                    sendChatMessage();
                } else if (!e.shiftKey) {
                    // Enter to send (unless Shift+Enter for new line)
                    e.preventDefault();
                    sendChatMessage();
                }
            }
        });
        
        // Send button click
        sendBtn.addEventListener('click', sendChatMessage);
    }
}

// Send chat message functionality
function sendChatMessage() {
    const chatInput = document.getElementById('chatInputPanel');
    const message = chatInput.value.trim();

    if (!message) {
        if (window.researchRadar) {
            window.researchRadar.showToast('Please enter a message', 'warning');
        }
        return;
    }

    // Add user message to chat
    addMessageToChat('user', message);

    // Clear input
    chatInput.value = '';
    chatInput.style.height = 'auto';

    // Show typing indicator
    showTypingIndicator();

    // Call backend chat API
    fetch('/chat', {
        method: 'POST',
        headers: { 'Content-Type': 'application/json' },
        body: JSON.stringify({ message })
    })
    .then(res => res.json())
    .then(data => {
        hideTypingIndicator();
        if (data && data.success) {
            addMessageToChat('assistant', data.response || '');
        } else {
            addMessageToChat('assistant', `Error: ${data?.error || 'Unknown error'}`);
        }
    })
    .catch(err => {
        console.error('Chat error:', err);
        hideTypingIndicator();
        addMessageToChat('assistant', 'Network error. Please try again.');
    });
}

// Add message to chat
function addMessageToChat(sender, message) {
    const chatContainer = document.getElementById('chatMessagesPanel');
    const messageElement = document.createElement('div');
    messageElement.className = `chat-message ${sender}`;

    const timestamp = new Date().toLocaleTimeString([], { hour: '2-digit', minute: '2-digit' });

    const avatarIcon = sender === 'user' ? 'fa-user' : 'fa-robot';

    messageElement.innerHTML = `
        <div class="message-avatar">
            <i class="fas ${avatarIcon}"></i>
        </div>
        <div class="message-content">
            <div class="message-bubble">
                <p>${message}</p>
            </div>
            <div class="message-meta">
                <span>${sender === 'user' ? 'You' : 'AI Assistant'} • ${timestamp}</span>
            </div>
        </div>
    `;

    // Remove welcome message if it exists
    const welcomeMessage = chatContainer.querySelector('.chat-welcome');
    if (welcomeMessage) {
        welcomeMessage.style.display = 'none';
    }

    chatContainer.appendChild(messageElement);

    // Scroll to bottom
    chatContainer.scrollTop = chatContainer.scrollHeight;
}

// Show typing indicator
function showTypingIndicator() {
    const chatContainer = document.getElementById('chatMessagesPanel');
    // Prevent adding multiple indicators
    if (document.getElementById('typingIndicator')) return;

    const typingIndicator = document.createElement('div');
    typingIndicator.className = 'typing-indicator chat-message assistant';
    typingIndicator.id = 'typingIndicator';

    typingIndicator.innerHTML = `
        <div class="message-avatar">
            <i class="fas fa-robot"></i>
        </div>
        <div class="message-content">
            <div class="message-bubble">
                <div class="typing-dots">
                    <div class="dot"></div>
                    <div class="dot"></div>
                    <div class="dot"></div>
                </div>
            </div>
        </div>
    `;

    chatContainer.appendChild(typingIndicator);
    chatContainer.scrollTop = chatContainer.scrollHeight;
}

// Hide typing indicator
function hideTypingIndicator() {
    const typingIndicator = document.getElementById('typingIndicator');
    if (typingIndicator) {
        typingIndicator.remove();
    }
}

// Initialize when DOM is loaded
document.addEventListener('DOMContentLoaded', function() {
    // ... existing code ...
    
    // Initialize tab functionality
    initializeTabFromHash();
    initializeChatInput();
    
    // Listen for hash changes
    window.addEventListener('hashchange', initializeTabFromHash);
    
    // ... existing code ...
});