evolution/src/lib/neatArena/genome.ts

/**
 * NEAT Genome Implementation
 * 
 * Represents a neural network genome with node genes and connection genes.
 * Implements the core NEAT genome structure as described in the original paper.
 */

export type NodeType = 'input' | 'hidden' | 'output';
export type ActivationFunction = 'tanh' | 'sigmoid' | 'relu' | 'linear';

/**
 * Node gene - represents a neuron
 */
export interface NodeGene {
    id: number;
    type: NodeType;
    activation: ActivationFunction;
}

/**
 * Connection gene - represents a synapse
 */
export interface ConnectionGene {
    innovation: number;
    from: number;
    to: number;
    weight: number;
    enabled: boolean;
}

/**
 * Complete genome
 */
/**
 * Complete genome
 */
export interface Genome {
    id: number;
    nodes: NodeGene[];
    connections: ConnectionGene[];
    fitness: number;
}

/**
 * Global innovation tracker for historical markings
 */
export class InnovationTracker {
    private currentInnovation: number = 0;
    private innovationHistory: Map<string, number> = new Map();

    /**
     * Get or create innovation number for a connection
     */
    getInnovation(from: number, to: number): number {
        const key = `${from}->${to}`;
        
        if (this.innovationHistory.has(key)) {
            return this.innovationHistory.get(key)!;
        }
        
        const innovation = this.currentInnovation++;
        this.innovationHistory.set(key, innovation);
        return innovation;
    }

    /**
     * Reset innovation tracking (useful for new experiments)
     */
    reset(): void {
        this.currentInnovation = 0;
        this.innovationHistory.clear();
    }

    /**
     * Get current innovation count
     */
    getCurrentInnovation(): number {
        return this.currentInnovation;
    }
}

let nextGenomeId = 0;

/**
 * Create a minimal genome with only input and output nodes, fully connected
 */
export function createMinimalGenome(
    inputCount: number,
    outputCount: number,
    innovationTracker: InnovationTracker
): Genome {
    const nodes: NodeGene[] = [];
    const connections: ConnectionGene[] = [];

    // Create input nodes (IDs 0 to inputCount-1)
    // PLUS one extra for Bias
    for (let i = 0; i < inputCount + 1; i++) {
        nodes.push({
            id: i,
            type: 'input',
            activation: 'linear',
        });
    }

    // Create output nodes (IDs starting from inputCount + 1)
    // Fix: Bias node uses ID `inputCount`, so outputs must start at `inputCount + 1`
    for (let i = 0; i < outputCount; i++) {
        nodes.push({
            id: inputCount + 1 + i,
            type: 'output',
            activation: 'tanh',
        });
    }

    // Create fully connected minimal genome
    // Iterate through all inputs INCLUDING Bias
    for (let i = 0; i < inputCount + 1; i++) {
        const inputNode = i; 
        
        for (let o = 0; o < outputCount; o++) {
            const outputNode = inputCount + 1 + o; // target the shifted output IDs
            const innovation = innovationTracker.getInnovation(inputNode, outputNode);
            
            let weight = (Math.random() * 2.0) - 1.0; 

            // FORCE AGGRESSION:
            // If connection is from BIAS node (index == inputCount) TO SHOOT node (index 3 of output)
            // Warning: Output indices are 0..4 relative to output block.
            // Shoot is 4th output (moveX, moveY, turn, shoot, reserved).
            if (inputNode === inputCount && o === 3) {
                weight = 1.0 + Math.random(); // Range [1.0, 2.0] -> Strong Positive Bias
            }

            connections.push({
                innovation,
                from: inputNode,
                to: outputNode,
                weight,
                enabled: true,
            });
        }
    }

    return {
        id: nextGenomeId++,
        nodes,
        connections,
        fitness: 0,
    };
}

/**
 * Clone a genome (deep copy)
 */
export function cloneGenome(genome: Genome): Genome {
    return {
        id: nextGenomeId++,
        nodes: genome.nodes.map(n => ({ ...n })),
        connections: genome.connections.map(c => ({ ...c })),
        fitness: genome.fitness,
    };
}

/**
 * Get next available node ID
 */
export function getNextNodeId(genome: Genome): number {
    return Math.max(...genome.nodes.map(n => n.id)) + 1;
}

/**
 * Check if a connection already exists
 */
export function connectionExists(genome: Genome, from: number, to: number): boolean {
    return genome.connections.some(c => c.from === from && c.to === to);
}

/**
 * Check if adding a connection would create a cycle (for feedforward networks)
 */
export function wouldCreateCycle(genome: Genome, from: number, to: number): boolean {
    // Build adjacency list
    const adj = new Map<number, number[]>();
    for (const node of genome.nodes) {
        adj.set(node.id, []);
    }
    
    for (const conn of genome.connections) {
        if (!conn.enabled) continue;
        if (!adj.has(conn.from)) adj.set(conn.from, []);
        adj.get(conn.from)!.push(conn.to);
    }
    
    // Add the proposed connection
    if (!adj.has(from)) adj.set(from, []);
    adj.get(from)!.push(to);
    
    // DFS to detect cycle
    const visited = new Set<number>();
    const recStack = new Set<number>();
    
    const hasCycle = (nodeId: number): boolean => {
        visited.add(nodeId);
        recStack.add(nodeId);
        
        const neighbors = adj.get(nodeId) || [];
        for (const neighbor of neighbors) {
            if (!visited.has(neighbor)) {
                if (hasCycle(neighbor)) return true;
            } else if (recStack.has(neighbor)) {
                return true;
            }
        }
        
        recStack.delete(nodeId);
        return false;
    };
    
    // Check from the 'from' node
    return hasCycle(from);
}

/**
 * Serialize genome to JSON
 */
export function serializeGenome(genome: Genome): string {
    return JSON.stringify(genome, null, 2);
}

/**
 * Deserialize genome from JSON
 */
export function deserializeGenome(json: string): Genome {
    return JSON.parse(json);
}