// Global state management
const state = {
    isLoading: false,
    currentPdfUrl: null
};

// Add state management for the current paper
let currentPaperState = {
    pdfUrl: null,
    title: null
};

// Add state management for search results
let searchState = {
    lastResults: null,
    lastQuery: null
};

// Add missing sortBy variable
let sortBy = 'relevance'; // Default sort option

// Utility Functions
function getCsrfToken() {
    return document.querySelector('meta[name="csrf-token"]').getAttribute('content');
}

function showLoading() {
    const overlay = document.getElementById('loadingOverlay');
    overlay.classList.remove('hidden');
    state.isLoading = true;
}

function hideLoading() {
    const overlay = document.getElementById('loadingOverlay');
    overlay.classList.add('hidden');
    state.isLoading = false;
}

// Search Functionality
async function performSearch() {
    const searchQuery = document.getElementById('searchInput').value.trim();
    const maxResults = parseInt(document.getElementById('maxResults').value);

    if (!searchQuery) {
        alert('Please enter a search term');
        return;
    }

    // Show loading overlay
    document.getElementById('loadingOverlay').classList.remove('hidden');

    try {
        const response = await fetch('/search', {
            method: 'POST',
            headers: {
                'Content-Type': 'application/json',
                'X-CSRFToken': getCsrfToken()
            },
            body: JSON.stringify({
                paper_name: searchQuery,
                sort_by: sortBy,
                max_results: maxResults
            })
        });

        const data = await response.json();
        
        // Save the results to the state
        searchState.lastResults = data;
        searchState.lastQuery = searchQuery;

        // Get results section and clear it
        const resultsSection = document.getElementById('resultsSection');
        resultsSection.innerHTML = '';

        if (!response.ok) {
            throw new Error(data.error || 'Search failed');
        }

        // Show results section
        showResults();

        if (data.length === 0) {
            resultsSection.innerHTML = `
                <div class="no-results">
                    <p>No papers found matching your search.</p>
                </div>`;
            return;
        }

        // Create results container
        const resultsGrid = document.createElement('div');
        resultsGrid.className = 'results-grid';

        // Add each paper to the grid using the new function
        data.forEach(paper => {
            const paperCard = createPaperCard(paper);
            resultsGrid.appendChild(paperCard);
        });

        resultsSection.appendChild(resultsGrid);

    } catch (error) {
        console.error('Search error:', error);
        document.getElementById('resultsSection').innerHTML = `
            <div class="error-message">
                <p>Failed to search papers: ${error.message}</p>
            </div>`;
    } finally {
        // Hide loading overlay
        document.getElementById('loadingOverlay').classList.add('hidden');
    }
}

// Helper function to escape HTML and prevent XSS
function escapeHtml(unsafe) {
    return unsafe
        .replace(/&/g, "&amp;")
        .replace(/</g, "&lt;")
        .replace(/>/g, "&gt;")
        .replace(/"/g, "&quot;")
        .replace(/'/g, "&#039;");
}

// Display Functions
function displayResults(results) {
    const resultsSection = document.getElementById('resultsSection');
    resultsSection.innerHTML = '';

    const resultsGrid = document.createElement('div');
    resultsGrid.className = 'results-grid';

    results.forEach((paper, index) => {
        // Create paper card
        const paperCard = document.createElement('div');
        paperCard.className = 'paper-card';
        
        // Build the card HTML - removed save button
        paperCard.innerHTML = `
            <div class="paper-date">${paper.published}</div>
            <h2 class="paper-title">${paper.title}</h2>
            <div class="paper-author">${paper.authors}</div>
            <p class="paper-abstract">${paper.abstract}</p>
            <div class="paper-actions">
                <div class="action-row">
                    <button class="action-link view-pdf">VIEW PDF</button>
                    <button class="action-link arxiv">ARXIV</button>
                    <button class="action-button analyze">ANALYZE</button>
                </div>
            </div>
        `;

        // Add the paper card to the grid
        resultsGrid.appendChild(paperCard);

        // Add click handlers for remaining buttons
        const viewPdfButton = paperCard.querySelector('.view-pdf');
        viewPdfButton.addEventListener('click', () => window.open(paper.pdf_link, '_blank'));

        const arxivButton = paperCard.querySelector('.arxiv');
        arxivButton.addEventListener('click', () => window.open(paper.arxiv_link, '_blank'));

        const analyzeButton = paperCard.querySelector('.analyze');
        analyzeButton.addEventListener('click', () => analyzePaper(paper.pdf_link, paper.title));
    });

    resultsSection.appendChild(resultsGrid);
}

// Analysis Functions
async function analyzePaper(pdfUrl, paperTitle) {
    // Update current paper state
    currentPaperState.pdfUrl = pdfUrl;
    currentPaperState.title = paperTitle;

    // Show loading overlay
    showLoading();
    
    try {
        const response = await fetch('/perform-rag', {
            method: 'POST',
            headers: {
                'Content-Type': 'application/json',
                'X-CSRFToken': getCsrfToken()
            },
            body: JSON.stringify({
                pdf_url: pdfUrl,
                paper_title: paperTitle
            })
        });

        const data = await response.json();

        if (data.error) {
            throw new Error(data.error);
        }

        // Show results section with enhanced tab styling
        const resultsSection = document.getElementById('resultsSection');
        resultsSection.innerHTML = `
            <div class="analysis-container">
                <div class="analysis-header">
                    <button onclick="backToSearchResults()" class="back-button">
                        <span>←</span> Back to Results
                    </button>
                    <h2 class="current-paper-title">${paperTitle}</h2>
                </div>
                
                <div style="display: flex; gap: 0.75rem; margin-bottom: 2rem; padding: 0.5rem; background: rgba(15, 23, 42, 0.6); border-radius: 0.75rem; box-shadow: 0 4px 12px rgba(0, 0, 0, 0.15), inset 0 1px 0 rgba(255, 255, 255, 0.07); backdrop-filter: blur(10px); border: 1px solid rgba(99, 102, 241, 0.15); flex-wrap: wrap;">
                    <button id="paperAnalysisTab" 
                            style="flex: 1; min-width: 140px; padding: 0.85rem 1rem; background: linear-gradient(135deg, rgba(99, 102, 241, 0.25) 0%, rgba(79, 70, 229, 0.35) 100%); color: #ffffff; font-size: 0.95rem; font-weight: 600; cursor: pointer; border-radius: 0.6rem; transition: all 0.3s cubic-bezier(0.4, 0, 0.2, 1); white-space: nowrap; position: relative; box-shadow: 0 2px 10px rgba(99, 102, 241, 0.25), inset 0 1px 0 rgba(255, 255, 255, 0.1); border: none; outline: none; text-shadow: 0 1px 2px rgba(0, 0, 0, 0.2); letter-spacing: 0.3px; display: flex; align-items: center; justify-content: center; gap: 0.5rem;"
                            onclick="document.getElementById('analysisContent').style.display='block'; 
                                     document.getElementById('chatContent').style.display='none';
                                     this.style.background='linear-gradient(135deg, rgba(99, 102, 241, 0.25) 0%, rgba(79, 70, 229, 0.35) 100%)';
                                     this.style.boxShadow='0 2px 10px rgba(99, 102, 241, 0.25), inset 0 1px 0 rgba(255, 255, 255, 0.1)';
                                     this.style.color='#ffffff';
                                     document.getElementById('chatWithPaperTab').style.background='rgba(30, 41, 59, 0.4)';
                                     document.getElementById('chatWithPaperTab').style.boxShadow='none';
                                     document.getElementById('chatWithPaperTab').style.color='rgba(255, 255, 255, 0.6)';">
                        <svg xmlns="http://www.w3.org/2000/svg" width="18" height="18" viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="2" stroke-linecap="round" stroke-linejoin="round"><path d="M14 2H6a2 2 0 0 0-2 2v16a2 2 0 0 0 2 2h12a2 2 0 0 0 2-2V8z"></path><polyline points="14 2 14 8 20 8"></polyline><line x1="16" y1="13" x2="8" y2="13"></line><line x1="16" y1="17" x2="8" y2="17"></line><polyline points="10 9 9 9 8 9"></polyline></svg>
                        Paper Analysis
                    </button>
                    <button id="chatWithPaperTab" 
                            style="flex: 1; min-width: 140px; padding: 0.85rem 1rem; background: rgba(30, 41, 59, 0.4); color: rgba(255, 255, 255, 0.6); font-size: 0.95rem; font-weight: 600; cursor: pointer; border-radius: 0.6rem; transition: all 0.3s cubic-bezier(0.4, 0, 0.2, 1); white-space: nowrap; position: relative; box-shadow: none; border: none; outline: none; letter-spacing: 0.3px; display: flex; align-items: center; justify-content: center; gap: 0.5rem;"
                            onclick="document.getElementById('chatContent').style.display='block';
                                     document.getElementById('analysisContent').style.display='none';
                                     this.style.background='linear-gradient(135deg, rgba(99, 102, 241, 0.25) 0%, rgba(79, 70, 229, 0.35) 100%)';
                                     this.style.boxShadow='0 2px 10px rgba(99, 102, 241, 0.25), inset 0 1px 0 rgba(255, 255, 255, 0.1)';
                                     this.style.color='#ffffff';
                                     document.getElementById('paperAnalysisTab').style.background='rgba(30, 41, 59, 0.4)';
                                     document.getElementById('paperAnalysisTab').style.boxShadow='none';
                                     document.getElementById('paperAnalysisTab').style.color='rgba(255, 255, 255, 0.6)';">
                        <svg xmlns="http://www.w3.org/2000/svg" width="18" height="18" viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="2" stroke-linecap="round" stroke-linejoin="round"><path d="M21 15a2 2 0 0 1-2 2H7l-4 4V5a2 2 0 0 1 2-2h14a2 2 0 0 1 2 2z"></path><path d="M13 8l-5 5"></path><path d="M13 13l-5-5"></path></svg>
                        Chat with Paper
                    </button>
                </div>

                <div id="analysisContent" style="display: block; width: 100%; animation: fadeIn 0.4s cubic-bezier(0.4, 0, 0.2, 1);">
                    <div class="analysis-section">
                        <h3 style="font-size: 1.5rem; margin-bottom: 1.25rem; color: #f8fafc; font-weight: 600; display: flex; align-items: center; gap: 0.5rem;">
                            <svg xmlns="http://www.w3.org/2000/svg" width="22" height="22" viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="2" stroke-linecap="round" stroke-linejoin="round"><circle cx="12" cy="12" r="10"></circle><line x1="12" y1="16" x2="12" y2="12"></line><line x1="12" y1="8" x2="12.01" y2="8"></line></svg>
                            Research Paper Analysis
                        </h3>
                        <div class="analysis-content" style="background: rgba(15, 23, 42, 0.4); padding: 1.5rem; border-radius: 0.75rem; box-shadow: 0 4px 12px rgba(0, 0, 0, 0.1), inset 0 1px 0 rgba(255, 255, 255, 0.05); border: 1px solid rgba(99, 102, 241, 0.1);">
                            ${marked.parse(data.analysis.executive_summary)}
                        </div>
                    </div>
                </div>

                <div id="chatContent" style="display: none; width: 100%; animation: fadeIn 0.4s cubic-bezier(0.4, 0, 0.2, 1);">
                    <div class="chat-container" style="background: rgba(15, 23, 42, 0.4); border-radius: 0.75rem; box-shadow: 0 4px 12px rgba(0, 0, 0, 0.1), inset 0 1px 0 rgba(255, 255, 255, 0.05); border: 1px solid rgba(99, 102, 241, 0.1); overflow: hidden; display: flex; flex-direction: column; height: 500px;">
                        <div class="quick-questions" style="padding: 1rem; display: flex; gap: 0.5rem; overflow-x: auto; border-bottom: 1px solid rgba(255, 255, 255, 0.05); background: rgba(15, 23, 42, 0.6);">
                            <button class="quick-question-btn" style="padding: 0.6rem 1rem; background: rgba(99, 102, 241, 0.15); color: #d1d5db; border: 1px solid rgba(99, 102, 241, 0.2); border-radius: 2rem; font-size: 0.85rem; white-space: nowrap; transition: all 0.2s ease; cursor: pointer;" 
                                    onclick="handleQuickQuestion('What are the main findings?')"
                                    onmouseover="this.style.background='rgba(99, 102, 241, 0.25)'; this.style.color='white';"
                                    onmouseout="this.style.background='rgba(99, 102, 241, 0.15)'; this.style.color='#d1d5db';">
                                What are the main findings?
                            </button>
                            <button class="quick-question-btn" style="padding: 0.6rem 1rem; background: rgba(99, 102, 241, 0.15); color: #d1d5db; border: 1px solid rgba(99, 102, 241, 0.2); border-radius: 2rem; font-size: 0.85rem; white-space: nowrap; transition: all 0.2s ease; cursor: pointer;"
                                    onclick="handleQuickQuestion('Explain the methodology')"
                                    onmouseover="this.style.background='rgba(99, 102, 241, 0.25)'; this.style.color='white';"
                                    onmouseout="this.style.background='rgba(99, 102, 241, 0.15)'; this.style.color='#d1d5db';">
                                Explain the methodology
                            </button>
                            <button class="quick-question-btn" style="padding: 0.6rem 1rem; background: rgba(99, 102, 241, 0.15); color: #d1d5db; border: 1px solid rgba(99, 102, 241, 0.2); border-radius: 2rem; font-size: 0.85rem; white-space: nowrap; transition: all 0.2s ease; cursor: pointer;"
                                    onclick="handleQuickQuestion('Key contributions?')"
                                    onmouseover="this.style.background='rgba(99, 102, 241, 0.25)'; this.style.color='white';"
                                    onmouseout="this.style.background='rgba(99, 102, 241, 0.15)'; this.style.color='#d1d5db';">
                                Key contributions?
                            </button>
                            <button class="quick-question-btn" style="padding: 0.6rem 1rem; background: rgba(99, 102, 241, 0.15); color: #d1d5db; border: 1px solid rgba(99, 102, 241, 0.2); border-radius: 2rem; font-size: 0.85rem; white-space: nowrap; transition: all 0.2s ease; cursor: pointer;"
                                    onclick="handleQuickQuestion('Future research directions?')"
                                    onmouseover="this.style.background='rgba(99, 102, 241, 0.25)'; this.style.color='white';"
                                    onmouseout="this.style.background='rgba(99, 102, 241, 0.15)'; this.style.color='#d1d5db';">
                                Future research directions?
                            </button>
                        </div>
                        <div class="chat-messages" id="chatMessages" style="flex: 1; overflow-y: auto; padding: 1.25rem; display: flex; flex-direction: column; gap: 1rem;">
                            <div class="message-wrapper" style="display: flex; gap: 0.75rem; max-width: 85%;">
                                <div class="message-avatar ai-avatar" style="width: 36px; height: 36px; border-radius: 50%; background: linear-gradient(135deg, #6366f1 0%, #4f46e5 100%); display: flex; align-items: center; justify-content: center; font-weight: 600; color: white; font-size: 0.85rem; flex-shrink: 0;">AI</div>
                                <div class="message ai-message" style="background: rgba(30, 41, 59, 0.6); padding: 1rem; border-radius: 0 1rem 1rem 1rem; color: #e2e8f0; font-size: 0.95rem; line-height: 1.5; box-shadow: 0 2px 5px rgba(0, 0, 0, 0.1); border: 1px solid rgba(99, 102, 241, 0.1);">
                                    Hello! I'm here to help you understand this research paper better. 
                                    Feel free to ask any questions about the paper's content, methodology, 
                                    findings, or implications.
                                </div>
                            </div>
                        </div>
                        <div class="chat-input-area" style="padding: 1rem; border-top: 1px solid rgba(255, 255, 255, 0.05); background: rgba(15, 23, 42, 0.6); display: flex; gap: 0.75rem;">
                            <input type="text" 
                                   class="chat-input" 
                                   placeholder="Ask a question about the paper..." 
                                   id="chatInput"
                                   style="flex: 1; padding: 0.85rem 1.25rem; background: rgba(30, 41, 59, 0.6); border: 1px solid rgba(99, 102, 241, 0.2); border-radius: 0.5rem; color: white; font-size: 0.95rem; outline: none; transition: all 0.2s ease;"
                                   onfocus="this.style.borderColor='rgba(99, 102, 241, 0.5)'; this.style.boxShadow='0 0 0 2px rgba(99, 102, 241, 0.15)';"
                                   onblur="this.style.borderColor='rgba(99, 102, 241, 0.2)'; this.style.boxShadow='none';">
                            <button class="chat-send-button" 
                                    onclick="sendMessage()"
                                    style="padding: 0.85rem 1.5rem; background: linear-gradient(135deg, #6366f1 0%, #4f46e5 100%); color: white; border: none; border-radius: 0.5rem; font-weight: 600; cursor: pointer; display: flex; align-items: center; gap: 0.5rem; transition: all 0.2s ease; box-shadow: 0 2px 5px rgba(99, 102, 241, 0.3);"
                                    onmouseover="this.style.transform='translateY(-2px)'; this.style.boxShadow='0 4px 12px rgba(99, 102, 241, 0.4)';"
                                    onmouseout="this.style.transform='translateY(0)'; this.style.boxShadow='0 2px 5px rgba(99, 102, 241, 0.3)';">
                                <span>Send</span>
                                <svg width="16" height="16" viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="2">
                                    <path d="M22 2L11 13M22 2l-7 20-4-9-9-4 20-7z"/>
                                </svg>
                            </button>
                        </div>
                    </div>
                </div>
            </div>
        `;

        // Add event listener for Enter key in chat input
        const chatInput = document.getElementById('chatInput');
        if (chatInput) {
            chatInput.addEventListener('keypress', (e) => {
                if (e.key === 'Enter') {
                    sendMessage();
                }
            });
        }

        // Add animation keyframes
        const style = document.createElement('style');
        style.textContent = `
            @keyframes fadeIn {
                from { opacity: 0; transform: translateY(10px); }
                to { opacity: 1; transform: translateY(0); }
            }
        `;
        document.head.appendChild(style);

    } catch (error) {
        console.error('Analysis error:', error);
        document.getElementById('resultsSection').innerHTML = `
            <div class="error-message">
                Failed to analyze paper: ${error.message}
            </div>
        `;
    } finally {
        hideLoading();
    }
}

// Chat functionality
async function sendMessage() {
    const chatInput = document.getElementById('chatInput');
    const userMessage = chatInput.value.trim();
    
    if (!userMessage) return;
    
    // Clear input
    chatInput.value = '';
    
    // Add user message to chat
    addMessageToChat('user', userMessage);
    
    // Show typing indicator
    addTypingIndicator();
    
    try {
        console.log('Sending chat request with:', {
            question: userMessage,
            pdf_url: currentPaperState.pdfUrl
        });
        
        const response = await fetch('/chat-with-paper', {
            method: 'POST',
            headers: {
                'Content-Type': 'application/json',
                'X-CSRFToken': getCsrfToken()
            },
            body: JSON.stringify({
                question: userMessage,  // Changed from message to question
                pdf_url: currentPaperState.pdfUrl
                // Removed title parameter as it's not required by the backend
            })
        });
        
        // Remove typing indicator
        removeTypingIndicator();
        
        if (!response.ok) {
            const errorText = await response.text();
            console.error('Server error response:', errorText);
            throw new Error(`Server error: ${response.status} - ${errorText}`);
        }
        
        const data = await response.json();
        console.log('Received chat response:', data);
        
        if (data.error) {
            throw new Error(data.error);
        }
        
        // Add AI response to chat
        addMessageToChat('ai', data.response || data.message || data.answer || "I couldn't generate a proper response.");
        
        // Scroll to bottom of chat
        const chatMessages = document.getElementById('chatMessages');
        if (chatMessages) {
            chatMessages.scrollTop = chatMessages.scrollHeight;
        }
        
    } catch (error) {
        console.error('Chat error:', error);
        removeTypingIndicator();
        addMessageToChat('ai', `I'm sorry, I encountered an error: ${error.message}. Please try again.`);
    }
}

// Handle quick questions
function handleQuickQuestion(question) {
    const chatInput = document.getElementById('chatInput');
    if (chatInput) {
        chatInput.value = question;
        sendMessage();
    }
}

// Add message to chat
function addMessageToChat(sender, message) {
    const chatMessages = document.getElementById('chatMessages');
    if (!chatMessages) return;
    
    const messageWrapper = document.createElement('div');
    messageWrapper.className = 'message-wrapper';
    
    const avatar = document.createElement('div');
    avatar.className = sender === 'user' ? 'message-avatar user-avatar' : 'message-avatar ai-avatar';
    avatar.textContent = sender === 'user' ? 'You' : 'AI';
    
    const messageElement = document.createElement('div');
    messageElement.className = sender === 'user' ? 'message user-message' : 'message ai-message';
    
    // Safely handle the message content
    if (typeof message === 'string') {
        // For AI messages, use marked to parse markdown
        if (sender === 'ai') {
            try {
                messageElement.innerHTML = marked.parse(message);
            } catch (e) {
                console.error('Error parsing markdown:', e);
                messageElement.textContent = message;
            }
        } else {
            // For user messages, just use text
            messageElement.textContent = message;
        }
    } else {
        // Handle non-string messages safely
        messageElement.textContent = JSON.stringify(message);
    }
    
    messageWrapper.appendChild(avatar);
    messageWrapper.appendChild(messageElement);
    chatMessages.appendChild(messageWrapper);
    
    // Scroll to bottom
    chatMessages.scrollTop = chatMessages.scrollHeight;
    
    // Add improved message styling if it doesn't exist
    if (!document.getElementById('improved-message-style')) {
        const style = document.createElement('style');
        style.id = 'improved-message-style';
        style.textContent = `
            .message-wrapper {
                display: flex;
                margin-bottom: 16px;
                max-width: 100%;
                animation: fadeIn 0.3s ease;
            }
            
            .message-avatar {
                width: 36px;
                height: 36px;
                border-radius: 50%;
                display: flex;
                align-items: center;
                justify-content: center;
                font-weight: 600;
                font-size: 0.85rem;
                flex-shrink: 0;
                margin-right: 12px;
            }
            
            .user-avatar {
                background: linear-gradient(135deg, #10b981 0%, #059669 100%);
                color: white;
            }
            
            .ai-avatar {
                background: linear-gradient(135deg, #6366f1 0%, #4f46e5 100%);
                color: white;
            }
            
            .message {
                padding: 16px;
                border-radius: 12px;
                font-size: 0.95rem;
                line-height: 1.6;
                max-width: calc(100% - 60px);
                overflow-wrap: break-word;
                box-shadow: 0 2px 5px rgba(0, 0, 0, 0.1);
            }
            
            .user-message {
                background: rgba(16, 185, 129, 0.1);
                color: #e2e8f0;
                border: 1px solid rgba(16, 185, 129, 0.2);
                border-radius: 12px 12px 2px 12px;
                align-self: flex-end;
            }
            
            .ai-message {
                background: rgba(99, 102, 241, 0.1);
                color: #e2e8f0;
                border: 1px solid rgba(99, 102, 241, 0.2);
                border-radius: 2px 12px 12px 12px;
            }
            
            /* Style for markdown content in AI messages */
            .ai-message p {
                margin: 0 0 12px 0;
            }
            
            .ai-message p:last-child {
                margin-bottom: 0;
            }
            
            .ai-message ul, .ai-message ol {
                margin: 12px 0;
                padding-left: 24px;
            }
            
            .ai-message li {
                margin-bottom: 6px;
            }
            
            .ai-message h1, .ai-message h2, .ai-message h3, .ai-message h4 {
                margin: 16px 0 12px 0;
                font-weight: 600;
                line-height: 1.3;
            }
            
            .ai-message h1 {
                font-size: 1.4rem;
            }
            
            .ai-message h2 {
                font-size: 1.3rem;
            }
            
            .ai-message h3 {
                font-size: 1.2rem;
            }
            
            .ai-message h4 {
                font-size: 1.1rem;
            }
            
            .ai-message code {
                background: rgba(30, 41, 59, 0.5);
                padding: 2px 6px;
                border-radius: 4px;
                font-family: monospace;
                font-size: 0.9em;
            }
            
            .ai-message pre {
                background: rgba(30, 41, 59, 0.5);
                padding: 12px;
                border-radius: 8px;
                overflow-x: auto;
                margin: 12px 0;
                border: 1px solid rgba(99, 102, 241, 0.2);
            }
            
            .ai-message pre code {
                background: transparent;
                padding: 0;
                border-radius: 0;
                display: block;
                line-height: 1.5;
            }
            
            .ai-message blockquote {
                border-left: 4px solid rgba(99, 102, 241, 0.4);
                padding-left: 12px;
                margin: 12px 0;
                font-style: italic;
                color: #94a3b8;
            }
            
            .ai-message a {
                color: #818cf8;
                text-decoration: underline;
                text-underline-offset: 2px;
            }
            
            .ai-message a:hover {
                color: #a5b4fc;
            }
            
            .ai-message table {
                border-collapse: collapse;
                width: 100%;
                margin: 16px 0;
                font-size: 0.9em;
            }
            
            .ai-message th, .ai-message td {
                border: 1px solid rgba(99, 102, 241, 0.2);
                padding: 8px 12px;
                text-align: left;
            }
            
            .ai-message th {
                background: rgba(99, 102, 241, 0.1);
                font-weight: 600;
            }
            
            /* Responsive adjustments */
            @media (max-width: 768px) {
                .message {
                    padding: 14px;
                    font-size: 0.9rem;
                    line-height: 1.5;
                }
                
                .message-avatar {
                    width: 32px;
                    height: 32px;
                    font-size: 0.75rem;
                    margin-right: 10px;
                }
                
                .ai-message pre {
                    padding: 10px;
                }
            }
        `;
        document.head.appendChild(style);
    }
}

// Add typing indicator
function addTypingIndicator() {
    const chatMessages = document.getElementById('chatMessages');
    if (!chatMessages) return;
    
    const typingIndicator = document.createElement('div');
    typingIndicator.className = 'message-wrapper typing-indicator';
    typingIndicator.innerHTML = `
        <div class="message-avatar ai-avatar">AI</div>
        <div class="message ai-message typing-message">
            <div class="typing-dots">
                <span></span>
                <span></span>
                <span></span>
            </div>
        </div>
    `;
    
    chatMessages.appendChild(typingIndicator);
    chatMessages.scrollTop = chatMessages.scrollHeight;
    
    // Add the CSS for the typing animation if it doesn't exist
    if (!document.getElementById('typing-animation-style')) {
        const style = document.createElement('style');
        style.id = 'typing-animation-style';
        style.textContent = `
            .typing-message {
                padding: 10px 15px;
                min-height: 20px;
                display: flex;
                align-items: center;
            }
            
            .typing-dots {
                display: flex;
                align-items: center;
                height: 20px;
            }
            
            .typing-dots span {
                display: inline-block;
                width: 8px;
                height: 8px;
                border-radius: 50%;
                background-color: rgba(255, 255, 255, 0.7);
                margin: 0 3px;
                animation: typingAnimation 1.4s infinite ease-in-out;
            }
            
            .typing-dots span:nth-child(1) {
                animation-delay: 0s;
            }
            
            .typing-dots span:nth-child(2) {
                animation-delay: 0.2s;
            }
            
            .typing-dots span:nth-child(3) {
                animation-delay: 0.4s;
            }
            
            @keyframes typingAnimation {
                0%, 60%, 100% {
                    transform: translateY(0);
                    opacity: 0.6;
                }
                30% {
                    transform: translateY(-5px);
                    opacity: 1;
                }
            }
            
            /* Make the typing indicator look better on mobile */
            @media (max-width: 768px) {
                .typing-dots span {
                    width: 6px;
                    height: 6px;
                    margin: 0 2px;
                }
                
                .typing-message {
                    padding: 8px 12px;
                }
            }
        `;
        document.head.appendChild(style);
    }
}

// Remove typing indicator
function removeTypingIndicator() {
    const typingIndicator = document.querySelector('.typing-indicator');
    if (typingIndicator) {
        // Add a fade-out effect
        typingIndicator.style.transition = 'opacity 0.3s ease';
        typingIndicator.style.opacity = '0';
        
        // Remove after animation completes
        setTimeout(() => {
            if (typingIndicator.parentNode) {
                typingIndicator.parentNode.removeChild(typingIndicator);
            }
        }, 300);
    }
}

// Create chat interface HTML
function createChatInterface() {
    return `
        <div class="chat-container">
            <div class="quick-questions">
                <button class="quick-question-btn" onclick="handleQuickQuestion('What are the main findings?')">
                    Main findings
                </button>
                <button class="quick-question-btn" onclick="handleQuickQuestion('Explain the methodology')">
                    Methodology
                </button>
                <button class="quick-question-btn" onclick="handleQuickQuestion('Key contributions?')">
                    Key contributions
                </button>
                <button class="quick-question-btn" onclick="handleQuickQuestion('Future research directions?')">
                    Future directions
                </button>
            </div>
            <div class="chat-messages" id="chatMessages">
                <div class="message-wrapper">
                    <div class="message-avatar ai-avatar">AI</div>
                    <div class="message ai-message">
                        Hello! I'm here to help you understand this research paper better. 
                        Feel free to ask any questions about the paper's content, methodology, 
                        findings, or implications.
                    </div>
                </div>
            </div>
            <div class="chat-input-area">
                <input type="text" 
                       class="chat-input" 
                       placeholder="Ask a question about the paper..." 
                       id="chatInput">
                <button class="chat-send-button" onclick="sendMessage()">
                    <span>Send</span>
                    <svg width="16" height="16" viewBox="0 0 24 24" fill="none" stroke="currentColor" stroke-width="2">
                        <path d="M22 2L11 13M22 2l-7 20-4-9-9-4 20-7z"/>
                    </svg>
                </button>
            </div>
        </div>
    `;
}

// Navigation Functions
function showHome() {
    hideAllSections();
    document.getElementById('homeSection').classList.add('active');
    document.getElementById('backButton').style.display = 'none';
}

function showResults() {
    hideAllSections();
    document.getElementById('resultsSection').classList.add('active');
    document.getElementById('currentSection').textContent = 'Search Results';
    document.getElementById('backButton').style.display = 'block';
}

function hideAllSections() {
    const sections = ['homeSection', 'historySection', 'savedSection', 'resultsSection'];
    sections.forEach(section => {
        document.getElementById(section).classList.remove('active');
    });
}

function goBack() {
    showHome();
}

// Load search history
function loadSearchHistory() {
    const historyGrid = document.getElementById('searchHistory');
    try {
        const history = JSON.parse(localStorage.getItem('searchHistory') || '[]');
        
        if (history.length === 0) {
            historyGrid.innerHTML = '<p class="no-history">No search history yet</p>';
            return;
        }

        historyGrid.innerHTML = '';
        history.forEach(item => {
            const historyCard = document.createElement('div');
            historyCard.className = 'history-card';
            historyCard.innerHTML = `
                <h3>${item.query}</h3>
                <p class="timestamp">${new Date(item.timestamp).toLocaleDateString()}</p>
                <button onclick="repeatSearch('${item.query}')" class="action-button">Search Again</button>
            `;
            historyGrid.appendChild(historyCard);
        });
    } catch (error) {
        console.error('Error loading history:', error);
        historyGrid.innerHTML = '<p class="error-message">Error loading history</p>';
    }
}

// Add notification system
function showNotification(message, type = 'info') {
    const notification = document.createElement('div');
    notification.className = `notification ${type}`;
    notification.textContent = message;
    document.body.appendChild(notification);
    
    setTimeout(() => {
        notification.classList.add('show');
        setTimeout(() => {
            notification.classList.remove('show');
            setTimeout(() => notification.remove(), 300);
        }, 2000);
    }, 100);
}

// Add history functionality
function saveToHistory(query, results) {
    try {
        const history = JSON.parse(localStorage.getItem('searchHistory') || '[]');
        history.unshift({
            query,
            timestamp: new Date().toISOString(),
            results: results.slice(0, 3) // Save only first 3 results to save space
        });
        // Keep only last 10 searches
        localStorage.setItem('searchHistory', JSON.stringify(history.slice(0, 10)));
    } catch (error) {
        console.error('Error saving to history:', error);
    }
}

// Add function to repeat search from history
function repeatSearch(query) {
    const searchInput = document.getElementById('searchInput');
    searchInput.value = query;
    showHome();
    performSearch();
}

// Add tab switching functionality
function switchTab(tabName) {
    // Update tab buttons
    document.querySelectorAll('.tab-button').forEach(button => {
        button.classList.remove('active');
        if (button.textContent.toLowerCase().includes(tabName)) {
            button.classList.add('active');
        }
    });

    // Update tab content
    document.querySelectorAll('.tab-content').forEach(content => {
        content.classList.remove('active');
    });
    document.getElementById(`${tabName}Tab`).classList.add('active');
}

// Add function to return to search results
function showSearchResults() {
    if (lastSearchResults) {
        displayResults(lastSearchResults);
        // Update navigation state
        document.getElementById('currentSection').textContent = 'Search Results';
    } else {
        showHome();
    }
}

// Add function to handle back to search
function backToSearchResults() {
    if (searchState.lastResults) {
        const resultsSection = document.getElementById('resultsSection');
        resultsSection.innerHTML = '';

        // Create results container
        const resultsGrid = document.createElement('div');
        resultsGrid.className = 'results-grid';

        // Recreate the results from the saved state using the new function
        searchState.lastResults.forEach(paper => {
            const paperCard = createPaperCard(paper);
            resultsGrid.appendChild(paperCard);
        });

        resultsSection.appendChild(resultsGrid);
    } else {
        // If no previous results, redirect to home
        showHome();
    }
}

// Add function to handle search history
function updateSearchHistory(searchTerm) {
    try {
        let searches = JSON.parse(localStorage.getItem('recentSearches') || '[]');
        
        // Add new search with timestamp
        searches.unshift({
            term: searchTerm,
            date: new Date().toISOString()
        });
        
        // Keep only the most recent 9 searches
        searches = searches.slice(0, 9);
        
        localStorage.setItem('recentSearches', JSON.stringify(searches));
        displaySearchHistory();
    } catch (error) {
        console.error('Error updating search history:', error);
    }
}

// Add function to display search history
function displaySearchHistory() {
    const historyContainer = document.getElementById('searchHistory');
    if (!historyContainer) return;

    try {
        const searches = JSON.parse(localStorage.getItem('recentSearches') || '[]');
        
        historyContainer.innerHTML = `
            <h2 class="history-title">Recent Searches</h2>
            <div class="search-history-grid">
                ${searches.map(search => `
                    <div class="history-item">
                        <h3 class="search-term">${search.term}</h3>
                        <div class="search-date">
                            ${new Date(search.date).toLocaleDateString('en-GB')}
                        </div>
                        <button 
                            onclick="searchAgain('${search.term}')" 
                            class="search-again-btn">
                            SEARCH AGAIN
                        </button>
                    </div>
                `).join('')}
            </div>
        `;
    } catch (error) {
        console.error('Error displaying search history:', error);
    }
}

// Add function to handle search again
function searchAgain(term) {
    document.getElementById('searchInput').value = term;
    handleSearch(term);
}

// Update the search container HTML in your JavaScript
function initializeSearchInterface() {
    const searchSection = document.querySelector('.search-section');
    if (searchSection) {
        searchSection.innerHTML = `
            <div class="search-container">
                <input 
                    type="text" 
                    id="searchInput" 
                    class="search-input" 
                    placeholder="Enter research paper title"
                    autocomplete="off"
                >
                <select id="maxResults" class="filter-select">
                    <option value="10">10 results</option>
                    <option value="25">25 results</option>
                    <option value="50">50 results</option>
                </select>
                <button id="searchButton" class="search-button">
                    SCAN
                </button>
            </div>
        `;

        // Add event listeners
        const searchInput = document.getElementById('searchInput');
        const searchButton = document.getElementById('searchButton');

        searchInput.addEventListener('keypress', (e) => {
            if (e.key === 'Enter') {
                performSearch();
            }
        });

        searchButton.addEventListener('click', performSearch);
    }
}

// Event Listeners
document.addEventListener('DOMContentLoaded', () => {
    // Navigation initialization
    showHome();
    
    initializeSearchInterface();
    
    // Search button click
    const searchButton = document.getElementById('searchButton');
    searchButton.addEventListener('click', performSearch);
    
    // Search input enter key
    const searchInput = document.getElementById('searchInput');
    searchInput.addEventListener('keypress', (e) => {
        if (e.key === 'Enter') {
            performSearch();
        }
    });
});

function addThinkingMessage(id) {
    const chatMessages = document.getElementById('chatMessages');
    const thinkingDiv = document.createElement('div');
    thinkingDiv.id = id;
    thinkingDiv.className = 'message-wrapper thinking-indicator';
    thinkingDiv.innerHTML = `
        <div class="message-avatar ai-avatar">AI</div>
        <div class="message ai-message ai-thinking">
            <div class="ai-thinking-dots">
                <div class="ai-thinking-dot"></div>
                <div class="ai-thinking-dot"></div>
                <div class="ai-thinking-dot"></div>
            </div>
        </div>
    `;
    chatMessages.appendChild(thinkingDiv);
    chatMessages.scrollTop = chatMessages.scrollHeight;
    return thinkingDiv;
}

// Add new function to remove thinking message
function removeThinkingMessage(id) {
    const thinkingDiv = document.getElementById(id);
    if (thinkingDiv) {
        thinkingDiv.remove();
    }
}

// Function to create consistent paper cards with properly styled buttons
function createPaperCard(paper) {
    const paperCard = document.createElement('div');
    paperCard.className = 'paper-card';
    
    // Format the paper data with proper HTML structure
    paperCard.innerHTML = `
        <div class="paper-header">
            <div class="paper-date">${escapeHtml(paper.published)}</div>
            <div class="paper-category">Category: ${escapeHtml(paper.category || 'N/A')}</div>
        </div>
        <h3 class="paper-title">${escapeHtml(paper.title)}</h3>
        <div class="paper-authors">Authors: ${escapeHtml(paper.authors)}</div>
        <p class="paper-abstract">${escapeHtml(paper.abstract.substring(0, 200))}${paper.abstract.length > 200 ? '...' : ''}</p>
        <div class="paper-actions">
            <a href="${paper.pdf_link}" target="_blank" class="paper-button pdf-button">PDF</a>
            <a href="${paper.arxiv_link}" target="_blank" class="paper-button arxiv-button">ARXIV</a>
            <button onclick="analyzePaper('${paper.pdf_link}', '${escapeHtml(paper.title)}')" class="paper-button analyze-button">Analyze</button>
        </div>
    `;
    
    return paperCard;
}

// Add comprehensive button styling
const buttonStyle = document.createElement('style');
buttonStyle.id = 'paper-buttons-style';
buttonStyle.textContent = `
    .paper-card {
        background: rgba(15, 23, 42, 0.6);
        border-radius: 0.75rem;
        padding: 1.5rem;
        margin-bottom: 1.5rem;
        box-shadow: 0 4px 12px rgba(0, 0, 0, 0.1);
        border: 1px solid rgba(99, 102, 241, 0.1);
        transition: transform 0.3s ease, box-shadow 0.3s ease;
    }
    
    .paper-card:hover {
        transform: translateY(-5px);
        box-shadow: 0 8px 24px rgba(0, 0, 0, 0.15);
    }
    
    .paper-actions {
        display: flex;
        justify-content: center;
        gap: 0.75rem;
        margin-top: 1.25rem;
    }
    
    .paper-button {
        display: inline-flex;
        align-items: center;
        justify-content: center;
        padding: 0.75rem 1.5rem;
        border-radius: 0.5rem;
        font-weight: 600;
        font-size: 0.9rem;
        cursor: pointer;
        transition: all 0.2s ease;
        text-decoration: none;
        border: none;
        min-width: 100px;
        letter-spacing: 0.5px;
    }
    
    .pdf-button {
        background: rgba(30, 41, 59, 0.8);
        color: #e2e8f0;
        box-shadow: 0 2px 4px rgba(0, 0, 0, 0.2);
    }
    
    .pdf-button:hover {
        background: rgba(44, 55, 74, 0.9);
        transform: translateY(-2px);
        box-shadow: 0 4px 8px rgba(0, 0, 0, 0.25);
    }
    
    .arxiv-button {
        background: rgba(99, 102, 241, 0.2);
        color: #e2e8f0;
        box-shadow: 0 2px 4px rgba(99, 102, 241, 0.15);
    }
    
    .arxiv-button:hover {
        background: rgba(99, 102, 241, 0.3);
        transform: translateY(-2px);
        box-shadow: 0 4px 8px rgba(99, 102, 241, 0.25);
    }
    
    .analyze-button {
        background: linear-gradient(135deg, #6366f1 0%, #4f46e5 100%);
        color: white;
        box-shadow: 0 2px 4px rgba(99, 102, 241, 0.3);
    }
    
    .analyze-button:hover {
        transform: translateY(-2px);
        box-shadow: 0 4px 8px rgba(99, 102, 241, 0.4);
        background: linear-gradient(135deg, #818cf8 0%, #6366f1 100%);
    }
`;
document.head.appendChild(buttonStyle);