types.ts

export interface SequenceInfo {
  length_bp: number;
  gc_content: number;
  notes: string;
}

export interface Motif {
  family: string;
  position_start: number;
  position_end: number;
  strand: '+' | '-';
  role: 'activator' | 'repressor' | 'cofactor' | 'unknown';
}

export interface ElementAnnotation {
  element_type: 'promoter' | 'enhancer' | 'insulator' | 'utr' | 'intron' | 'intergenic' | 'ambiguous';
  rationale: string;
  motifs: Motif[];
  baseline_effect?: string;
}

export interface VariantImpact {
  variant_id: string;
  position: number;
  ref: string;
  alt: string;
  motif_effect: 'motif_gain' | 'motif_loss' | 'motif_shift' | 'neutral_or_uncertain';
  affected_motif_families: string[];
  predicted_direction: 'up' | 'down' | 'ambiguous';
  confidence: 'high' | 'medium' | 'low';
  confidence_rationale: string;
  impact_summary: string;
}

export interface TFNetworkNode {
  id: string;
  type: 'tf' | 'element' | 'gene';
}

export interface TFNetworkEdge {
  source: string;
  target: string;
  interaction: 'activates' | 'represses' | 'modulates';
}

export interface TFNetwork {
  nodes: TFNetworkNode[];
  edges: TFNetworkEdge[];
  network_summary: string;
}

export interface QuizQuestion {
  question: string;
  options: string[];
  correctAnswerIndex: number;
  explanation: string;
}

export interface TeachingContent {
  enabled: boolean;
  explanation: string;
  quiz_questions?: QuizQuestion[];
}

export interface Citation {
  id: string;
  authors: string;
  year: number;
  title: string;
  journal: string;
  relevance: string;
}

export interface RegulatoryAnalysisResult {
  sequence_info: SequenceInfo;
  element_annotation: ElementAnnotation;
  variant_impacts: VariantImpact[];
  tf_network: TFNetwork;
  teaching: TeachingContent;
  image_context?: {
    tracks_identified: string[];
    observations: string;
    correlation_with_sequence: string;
  };
  citations: Citation[];
}

export interface RegulatoryInput {
  sequence: string;
  coordinates: string;
  variants: string; // Line separated or CSV
  mode: 'mechanistic' | 'teaching';
  browserImage: File | null;
}

export interface AnalysisInput {
  imageFile: File | null;
  genomicText: string;
  clinicalText: string;
}

export type AnalysisResult = RegulatoryAnalysisResult;

// Perturbation Sandbox Types
export interface MotifDelta {
  family: string;
  change_type: 'loss' | 'gain' | 'retained';
  significance: 'high' | 'medium' | 'low';
}

export interface PerturbationResult {
  wt_regulatory_score: number; // 0-100
  mutant_regulatory_score: number; // 0-100
  score_rationale: string;
  motif_deltas: MotifDelta[];
  functional_consequence: string; // The "Diagnosis" of the mutation
  network_impact: {
    lost_edges: string[];
    gained_edges: string[];
  };
}

// Evolution Viewer Types
export interface EvolutionaryRegion {
  start_index: number;
  end_index: number;
  conservation_score: number; // 0.0 to 1.0 (1.0 = highly conserved)
  evolutionary_logic: string; // e.g., "Purifying selection on E-Box core"
}

export interface EvolutionaryScenario {
  title: string;
  prompt: string; // "What if this motif evolved?"
  prediction: string;
}

export interface EvolutionaryAnalysisResult {
  regions: EvolutionaryRegion[];
  motif_ages: {
    family: string;
    age_category: 'Ancient (Vertebrate)' | 'Intermediate (Mammalian)' | 'Recent (Primate/Specific)';
    rationale: string;
  }[];
  scenarios: EvolutionaryScenario[];
  evolutionary_narrative: string;
}

export interface ClinicalTrial {
  id: string;
  title: string;
  phase: string;
  matchScore: number;
  institution: string;
  location: string;
  rationale: string;
}

// Sketch Interpretation Types
export interface SketchInteraction {
  source: string;
  target: string;
  type: 'activation' | 'repression';
}

export interface SketchVariantSensitivity {
  position: number;
  effect: string;
}

export interface SketchInferredMotif {
  tf_family: string;
  confidence: string;
}

export interface SketchAnalysisResult {
  regulatory_class: string;
  reasoning: string;
  motifs: SketchInferredMotif[];
  chromatin_state: string;
  interactions: SketchInteraction[];
  prototype_sequence: string;
  sensitive_positions: SketchVariantSensitivity[];
}

// Regulatory Remix Types
export interface RemixDesign {
  label: string;
  new_sequence: string;
  predicted_class: string;
  explanation: string;
  motif_changes: {
    gained: string[];
    lost: string[];
  };
}