import { GeneAssembly } from '../../types';

export interface GenomicAnalysisResult {
  id: string;
  assemblyId: string;
  timestamp: string;
  metrics: {
    geneExpression: number[];
    regulatoryElements: string[];
    pathwayEnrichment: {
      pathway: string;
      score: number;
    }[];
    structuralVariants: {
      type: string;
      position: number;
      impact: number;
    }[];
  };
  predictions: {
    phenotype: string;
    probability: number;
    confidence: number;
  }[];
}

export class GenomicAnalysisPipeline {
  // Simulated quantum-enhanced analysis
  static async analyzeGeneAssembly(assembly: GeneAssembly): Promise<GenomicAnalysisResult> {
    // Simulate processing time
    await new Promise(resolve => setTimeout(resolve, 2000));

    const mockPathways = [
      'Photosynthesis',
      'Stress Response',
      'Growth Regulation',
      'Nutrient Uptake',
      'Secondary Metabolism'
    ];

    return {
      id: Math.random().toString(36).substr(2, 9),
      assemblyId: assembly.id,
      timestamp: new Date().toISOString(),
      metrics: {
        geneExpression: Array(10).fill(0).map(() => Math.random() * 2), // Fold change values
        regulatoryElements: [
          'Promoter_Region_1',
          'Enhancer_Element_A',
          'Silencer_Region_B',
          'TATA_Box_Modified'
        ],
        pathwayEnrichment: mockPathways.map(pathway => ({
          pathway,
          score: Math.random() * 0.5 + 0.5 // Score between 0.5 and 1.0
        })),
        structuralVariants: Array(3).fill(0).map(() => ({
          type: ['Insertion', 'Deletion', 'Inversion'][Math.floor(Math.random() * 3)],
          position: Math.floor(Math.random() * 1000000),
          impact: Math.random()
        }))
      },
      predictions: [
        {
          phenotype: 'Drought Resistance',
          probability: Math.random() * 0.3 + 0.7, // High probability 0.7-1.0
          confidence: Math.random() * 0.2 + 0.8 // High confidence 0.8-1.0
        },
        {
          phenotype: 'Growth Rate',
          probability: Math.random() * 0.4 + 0.6,
          confidence: Math.random() * 0.3 + 0.7
        },
        {
          phenotype: 'Yield Improvement',
          probability: Math.random() * 0.5 + 0.5,
          confidence: Math.random() * 0.4 + 0.6
        }
      ]
    };
  }
}