siafun
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A collection of structure induction algorithms
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TypeScript
import { StructureResult, MultiStructureResult, CacheableStructureOptions } from './structure';
import { SmithWatermanResult } from './smith-waterman';
export interface IterativeSmithWatermanResult extends StructureResult {
matrices: SmithWatermanResult[];
segmentMatrix: number[][];
}
export interface MultiSmithWatermanResult extends MultiStructureResult, IterativeSmithWatermanResult {
}
export interface SmithWatermanOptions extends CacheableStructureOptions {
maxIterations?: number;
maxThreshold?: number;
endThreshold?: number;
minSegmentLength?: number;
similarityThreshold?: number;
onlyDiagonals?: boolean;
nLongest?: number;
fillGaps?: boolean;
maxGapSize?: number;
maxGaps?: number;
maxGapRatio?: number;
minDistance?: number;
cacheDir?: string;
}
export declare function getSimpleSmithWatermanPath(points: number[][], points2: number[][], options: SmithWatermanOptions): [number, number][];
export declare function getMultiSWOccurrences(points: number[][], points2: number[][], options: SmithWatermanOptions): MultiSmithWatermanResult;
export declare function getSmithWatermanOccurrences(points: number[][], options: SmithWatermanOptions): IterativeSmithWatermanResult;
export declare function getPaddedArea(points: number[][], padding: number, symmetric: boolean, maxX: number, maxY: number): number[][];