@jbrowse/plugin-wiggle 3.2.0 → 3.4.0

package/esm/WiggleRPC/cluster.d.ts

@@ -1,17 +0,0 @@
-export declare function euclideanDistance(a: number[], b: number[]): number;
-export declare function averageDistance(setA: number[], setB: number[], distances: number[][]): number;
-export declare function clusterData({ data, distance, linkage, onProgress, stopToken, }: {
-    data: number[][];
-    distance?: (a: number[], b: number[]) => number;
-    linkage?: (a: number[], b: number[], distances: number[][]) => number;
-    onProgress?: (a: number) => void;
-    stopToken?: string;
-}): {
-    clusters: {
-        height: number;
-        indexes: number[];
-    } | undefined;
-    distances: number[][];
-    order: number[];
-    clustersGivenK: number[][][];
-};

package/esm/WiggleRPC/cluster.js

@@ -1,79 +0,0 @@
-import { checkStopToken } from '@jbrowse/core/util/stopToken';
-export function euclideanDistance(a, b) {
-    const size = Math.min(a.length, b.length);
-    let sum = 0;
-    for (let index = 0; index < size; index++) {
-        sum += (a[index] - b[index]) * (a[index] - b[index]);
-    }
-    return Math.sqrt(sum);
-}
-export function averageDistance(setA, setB, distances) {
-    let distance = 0;
-    for (const a of setA) {
-        for (const b of setB) {
-            distance += distances[a][b];
-        }
-    }
-    return distance / setA.length / setB.length;
-}
-function updateProgress(stepNumber, stepProgress, onProgress) {
-    onProgress(stepNumber / 2 + stepProgress / 2);
-}
-export function clusterData({ data, distance = euclideanDistance, linkage = averageDistance, onProgress, stopToken, }) {
-    const distances = data.map((datum, index) => {
-        if (onProgress) {
-            updateProgress(0, index / (data.length - 1), onProgress);
-        }
-        return data.map(otherDatum => distance(datum, otherDatum));
-    });
-    const clusters = data.map((_datum, index) => ({
-        height: 0,
-        indexes: [Number(index)],
-    }));
-    let clustersGivenK = [];
-    let start = performance.now();
-    for (let iteration = 0; iteration < data.length; iteration++) {
-        if (performance.now() - start > 2000) {
-            checkStopToken(stopToken);
-            start = performance.now();
-        }
-        if (onProgress) {
-            updateProgress(1, (iteration + 1) / data.length, onProgress);
-        }
-        clustersGivenK.push(clusters.map(cluster => cluster.indexes));
-        if (iteration >= data.length - 1) {
-            break;
-        }
-        let nearestDistance = Infinity;
-        let nearestRow = 0;
-        let nearestCol = 0;
-        for (let row = 0; row < clusters.length; row++) {
-            for (let col = row + 1; col < clusters.length; col++) {
-                const distance = linkage(clusters[row].indexes, clusters[col].indexes, distances);
-                if (distance < nearestDistance) {
-                    nearestDistance = distance;
-                    nearestRow = row;
-                    nearestCol = col;
-                }
-            }
-        }
-        const newCluster = {
-            indexes: [
-                ...clusters[nearestRow].indexes,
-                ...clusters[nearestCol].indexes,
-            ],
-            height: nearestDistance,
-            children: [clusters[nearestRow], clusters[nearestCol]],
-        };
-        clusters.splice(Math.max(nearestRow, nearestCol), 1);
-        clusters.splice(Math.min(nearestRow, nearestCol), 1);
-        clusters.push(newCluster);
-    }
-    clustersGivenK = [[], ...clustersGivenK.reverse()];
-    return {
-        clusters: clusters[0],
-        distances: distances,
-        order: clusters[0].indexes,
-        clustersGivenK: clustersGivenK,
-    };
-}