/**
 * MSA Coordinate Systems:
 *
 * 1. **Global Column (globalCol)**: The column index in the full, unfiltered MSA.
 *    Range: 0 to (MSA width - 1)
 *    This is the "true" column position before any gap-hiding is applied.
 *
 * 2. **Visible Column (visibleCol)**: The column index after hiding gappy columns.
 *    Range: 0 to (numColumns - 1) where numColumns = MSA width - blanks.length
 *    This is what the user sees on screen when "Hide columns w/ N% gaps" is enabled.
 *    When gap hiding is disabled, visibleCol === globalCol.
 *
 * 3. **Sequence Position (seqPos)**: The position within a specific row's ungapped sequence.
 *    Range: 0 to (ungapped sequence length - 1)
 *    This counts only non-gap characters ('-' and '.' are gaps).
 *    Each row can have different seqPos values for the same globalCol due to gaps.
 */
/**
 * Convert a visible column index to a global column index.
 * This is used when translating mouse/screen coordinates to MSA coordinates.
 *
 * @param blanks - Sorted array of global column indices that are hidden
 * @param visibleCol - The visible column index (what the user sees on screen)
 * @returns The corresponding global column index in the full MSA
 */
export declare function visibleColToGlobalCol(blanks: number[], visibleCol: number): number;
/**
 * Convert a global column index to a visible column index.
 * This is the inverse of visibleColToGlobalCol.
 *
 * @param blanks - Sorted array of global column indices that are hidden
 * @param globalCol - The global column index in the full MSA
 * @returns The visible column index, or undefined if the column is hidden
 */
export declare function globalColToVisibleCol(blanks: number[], globalCol: number): number | undefined;
/**
 * Convert a global column index to a row-specific sequence position.
 * This counts non-gap characters up to the given global column.
 *
 * @param seq - The row's sequence string (including gaps)
 * @param globalCol - The global column index
 * @returns The sequence position (count of non-gap characters before this column)
 */
export declare function globalColToSeqPos(seq: string, globalCol: number): number;
/**
 * Convert a visible column to a row-specific sequence position.
 * Returns undefined if the position is a gap in the sequence.
 *
 * @param seq - The row's sequence string (including gaps)
 * @param blanks - Sorted array of global column indices that are hidden
 * @param visibleCol - The visible column index
 * @returns The sequence position, or undefined if it's a gap
 */
export declare function visibleColToSeqPos({ seq, blanks, visibleCol, }: {
    seq: string;
    blanks: number[];
    visibleCol: number;
}): number | undefined;
/**
 * Convert a visible column to a row-specific sequence position, with row lookup.
 *
 * @param rowName - The name of the row
 * @param visibleCol - The visible column index
 * @param rowMap - Map from row name to sequence string
 * @param blanks - Sorted array of global column indices that are hidden
 * @returns The sequence position, or undefined if row not found or position is a gap
 */
export declare function visibleColToSeqPosForRow({ rowName, visibleCol, rowMap, blanks, }: {
    rowName: string;
    visibleCol: number;
    rowMap: Map<string, string>;
    blanks: number[];
}): number | undefined;