siafun
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A collection of structure induction algorithms
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TypeScript
import { ArrayMap } from './quantizer';
import { OpsiatecOptions, OpsiatecResult } from './opsiatec';
import { SmithWatermanOptions, MultiSmithWatermanResult, IterativeSmithWatermanResult } from './sw-structure';
export declare type Point = number[];
export declare type PointSet = Point[];
export declare type Vector = number[];
export declare type Occurrence = Point[];
export interface Pattern {
points: PointSet;
vectors: Vector[];
occurrences: Occurrence[];
}
export interface StructureResult {
points: Point[];
patterns: Pattern[];
}
export interface MultiStructureResult extends StructureResult {
points2: Point[];
}
export interface MultiOpsiatecResult extends OpsiatecResult, MultiStructureResult {
}
export interface CacheableStructureOptions {
quantizerFunctions?: ArrayMap[];
cacheDir?: string;
loggingLevel?: number;
}
interface CosiatecIndexResult {
occurrences: number[][][];
numSiatecPatterns: number;
numOptimizedPatterns: number;
}
export declare function getCosiatecIndexOccurrences(points: number[][], options: OpsiatecOptions): CosiatecIndexResult;
export declare function getCosiatecOccurrences(points: Point[], options: OpsiatecOptions): number[][][][];
export declare function getCosiatec(points: Point[], options: OpsiatecOptions): OpsiatecResult;
export declare function getMultiCosiatec(points: Point[][], options: OpsiatecOptions): MultiOpsiatecResult;
export declare function getSiatecOccurrences(points: number[][], options: OpsiatecOptions): number[][][][];
export declare function getSmithWaterman(points: number[][], options: SmithWatermanOptions): IterativeSmithWatermanResult;
export declare function getDualSmithWaterman(points1: number[][], points2: number[][], options: SmithWatermanOptions): MultiSmithWatermanResult;
export declare function getStructure(points: number[][], options: OpsiatecOptions, minPatternLength?: number): number[];
export {};