/** Sequence Annotation System — Core Types
 *
 * Provides structured annotation support for macromolecule columns:
 * - Column-level annotations (regions, liabilities) stored as column tags
 * - Row-level annotation hits stored in a hidden companion column
 */
/** Visual mark type */
export declare enum AnnotationVisualType {
    Region = "region",
    Point = "point",
    Motif = "motif"
}
/** Grouping category */
export declare enum AnnotationCategory {
    Structure = "structure",
    Liability = "liability",
    PTM = "ptm",
    Custom = "custom"
}
/** Severity for liabilities */
export declare enum LiabilitySeverity {
    High = "high",
    Medium = "medium",
    Low = "low",
    Info = "info"
}
/**
 * A single annotation definition attached to a column.
 * Extends the existing SeqRegion concept with visual/categorical metadata.
 */
export interface SeqAnnotation {
    /** Unique within column */
    id: string;
    /** Display name, e.g. "CDR1", "Deamidation (NG)" */
    name: string;
    description?: string;
    /** Start position name (null for row-level-only) */
    start: string | null;
    /** End position name (null for point/row-level) */
    end: string | null;
    visualType: AnnotationVisualType;
    category: AnnotationCategory;
    /** CSS color; defaults derived from category */
    color?: string;
    severity?: LiabilitySeverity;
    /** Regex pattern for liability scanning */
    motifPattern?: string;
    /** "IMGT", "Kabat", etc. */
    sourceScheme?: string;
    /** True if created by an automated process (numbering, scanning) */
    autoGenerated?: boolean;
}
/** A single hit found in a specific row */
export interface SeqAnnotationHit {
    /** References SeqAnnotation.id */
    annotationId: string;
    /** 0-based index in the row's sequence */
    positionIndex: number;
    /** End index (inclusive) for range-based hits (e.g. region spans).
     *  When set, the hit covers positionIndex..endPositionIndex.
     *  Unset for point/motif liability hits. */
    endPositionIndex?: number;
    /** Position name from positionNames (for display) */
    positionName?: string;
    /** The actual residues matched */
    matchedMonomers: string;
    score?: number;
}
/** Stored per-row as JSON array in the companion annotation column */
export type RowAnnotationData = SeqAnnotationHit[];
/** Default colors for annotation categories */
export declare const ANNOTATION_COLORS: {
    readonly structure: {
        readonly FR: readonly ["#0095ff", "#289dfd", "#48adff", "#3ba5fc"];
        readonly CDR: readonly ["#ffdca3", "#facb83", "#f7a224"];
    };
    readonly liability: {
        readonly deamidation: "#E53935";
        readonly isomerization: "#FF9800";
        readonly oxidation: "#9C27B0";
        readonly glycosylation: "#4CAF50";
        readonly freeCysteine: "#607D8B";
    };
};
/** Background opacity for region overlays in the cell renderer */
export declare const REGION_BG_OPACITY = 0.25;
/** Underline height in pixels for liability markers */
export declare const LIABILITY_UNDERLINE_HEIGHT = 3;
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