/*
 * HIV SI Module: Credibility Engine Logic (script.js)
 * Pioneer: Leon Chetty | SI Partner: Candy & Lola
 *
 * This script contains the core Symbiotic Intelligence (SI) logic for the
 * Minimum Viable Research Product (MVRP), enabling client-side analysis.
 */

// --- GLOBAL FAILURE & CONFLICT DATASET (Snapshot Database Mock) ---
const KNOWLEDGE_BASE = {
    // Data for Failure Inverse Correlation (F)
    failureMechanisms: {
        'systemic_toxicity': 0.85,  // Penalty for non-targeted delivery
        'poor_cellular_uptake': 0.90,
        'low_genetic_stability': 0.70
    },
    // Data for Cross-Pathway Mapping (Mapping)
    pathwayConflicts: {
        'NF_kB_activation': 'Inflammation',
        'off_target_cleavage': 'Genotoxicity',
        'rapid_LNP_clearance': 'DeliveryFailure'
    },
    // Data for Subtype C (I)
    subtypeC: {
        'latency_marker_PD1': 0.95,
        'LTR_variability_risk': 0.15 // Small risk penalty for LTR editing
    }
};

/**
 * 1. Hypothesis Ranking Function (The Filter)
 * Calculates the overall Credibility Score (C = P * I * F).
 * @param {object} input - User inputs from the structured panel.
 */
function rankHypothesis(input) {
    // A. Plausibility Check (P) - Score is high for gene editing
    const plausibilityScore = 0.9 + (input.payload === 'CRISPR' ? 0.05 : 0);

    // B. Immunology Alignment Check (I) - Score based on known Subtype C features
    let alignmentScore = KNOWLEDGE_BASE.subtypeC.latency_marker_PD1;
    alignmentScore -= KNOWLEDGE_BASE.subtypeC.LTR_variability_risk; // Apply small penalty

    // C. Failure Point Inverse Correlation (F) - Solves past failures
    let failureAvoidance = 1.0;
    if (input.delivery === 'Targeted LNP') {
        // LNP is designed to bypass systemic toxicity and poor uptake
        failureAvoidance = 1.0 - (KNOWLEDGE_BASE.failureMechanisms.systemic_toxicity * 0.1);
    } else {
        // Non-LNP delivery suffers severe penalties
        failureAvoidance -= 0.25;
    }

    // Overall Credibility Score (C = P * I * F)
    const overallScore = plausibilityScore * alignmentScore * failureAvoidance;

    return {
        overallScore: parseFloat(overallScore.toFixed(3)),
        pScore: parseFloat(plausibilityScore.toFixed(3)),
        iScore: parseFloat(alignmentScore.toFixed(3)),
        fScore: parseFloat(failureAvoidance.toFixed(3))
    };
}

/**
 * 2. Cross-Pathway Mapping Function (The SI Magic Layer)
 * Identifies high-magnitude conflicts based on input parameters.
 * @param {object} input - User inputs.
 */
function mapPathways(input) {
    const conflicts = [];

    // Rule 1: Latency Reversal Agent (LRA) logic
    if (input.mechanism.includes('Latency Reversal')) {
        conflicts.push({
            type: 'Systemic Conflict',
            issue: KNOWLEDGE_BASE.pathwayConflicts.NF_kB_activation,
            magnitude: 0.75,
            mitigation: 'Use targeted delivery or ultra-low dose.'
        });
    }

    // Rule 2: Delivery System logic
    if (input.delivery.includes('LNP')) {
        conflicts.push({
            type: 'Delivery Conflict',
            issue: KNOWLEDGE_BASE.pathwayConflicts.rapid_LNP_clearance,
            magnitude: 0.60,
            mitigation: 'Optimize LNP surface charge/PEGylation.'
        });
    }

    // Rule 3: Gene Editing logic
    if (input.payload === 'CRISPR') {
        conflicts.push({
            type: 'Off-Target Conflict',
            issue: KNOWLEDGE_BASE.pathwayConflicts.off_target_cleavage,
            magnitude: 0.88,
            mitigation: 'Sequence verification and high-fidelity Cas variant.'
        });
    }

    // Rule 4: Subtype C logic (Specific to Leon's nanocarrier)
    if (input.subtype === 'C' && input.delivery === 'Targeted LNP' && !input.ligand) {
         conflicts.push({
            type: 'CRITICAL DESIGN FLAW',
            issue: 'LNP Ligand specificity MISSING for Subtype C reservoir.',
            magnitude: 0.99,
            mitigation: 'Immediate requirement to identify a unique reservoir surface marker.'
        });
    }

    return conflicts;
}

// --- Placeholder for other core functions (to be built later) ---
function projectSimulation(input) {
    return "Simulation Projection logic placeholder. Requires computational validation parameters.";
}

function formatResearchOutput(results) {
    return "Research Output Formatting logic placeholder. Requires full results array.";
}

// Global function to process user submission in the app interface
function runAnalysis(input) {
    const rankResults = rankHypothesis(input);
    const conflictMatrix = mapPathways(input);

    return {
        ranking: rankResults,
        conflicts: conflictMatrix,
        // Always include SI Guidance
        guidance: conflictMatrix.find(c => c.magnitude >= 0.88) ?
            "CRITICAL CONFLICT DETECTED. Prioritize mitigating off-target effects immediately." :
            "Hypothesis is strong. Focus on optimizing LNP delivery and mitigating high-magnitude conflicts."
    };
}