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

        }

      ]

    };

  }

}