higlass 1.13.2 → 1.13.3

package/app/scripts/utils/DenseDataExtrema1D.js

@@ -1,27 +1,36 @@
 import { NUM_PRECOMP_SUBSETS_PER_1D_TTILE } from '../configs';
 
+/**
+ * @template {ArrayLike<number>} [T=ArrayLike<number>]
+ */
 class DenseDataExtrema1D {
   /**
    * This module efficiently computes extrema of arbitrary subsets of a given data array.
    * The array is subdivided into 'numSubsets' subsets where extrema are precomputed.
    * These values are used to compute extrema given arbitrary start and end indices via
    * the getMinNonZeroInSubset and getMaxNonZeroInSubset methods.
-   * @param   {array}  data
+   * @param {T}  data
    */
   constructor(data) {
+    /** @type {number} */
     this.epsilon = 1e-6;
+    /** @type {T} */
     this.data = data;
 
+    /** @type {number} */
     this.tileSize = this.data.length; // might not be a power of 2
+    /** @type {number} */
     this.paddedTileSize = 2 ** Math.ceil(Math.log2(this.tileSize));
 
     // This controls how many subsets are created and precomputed.
     // Setting numSubsets to 1, is equivalent to no precomputation in
     // most cases
+    /** @type {number} */
     this.numSubsets = Math.min(
       NUM_PRECOMP_SUBSETS_PER_1D_TTILE,
       this.paddedTileSize,
     );
+    /** @type {number} */
     this.subsetSize = this.paddedTileSize / this.numSubsets;
 
     this.subsetMinimums = this.computeSubsetNonZeroMinimums();
@@ -33,8 +42,9 @@ class DenseDataExtrema1D {
   /**
    * Computes the non-zero minimum in a subset using precomputed values,
    * if possible. data[end] is not considered.
-   * @param   {array}  indexBounds  [start, end]
-   * @return  {number}  non-zero minium of the subset
+   *
+   * @param {[start: number, end: number]} indexBounds
+   * @return {number} non-zero minium of the subset
    */
   getMinNonZeroInSubset(indexBounds) {
     const start = indexBounds[0];
@@ -79,10 +89,10 @@ class DenseDataExtrema1D {
   }
 
   /**
-   * Computes the non-zero maximum in a subset using precomputed values,
-   * if possible
-   * @param   {array}  indexBounds  [start, end]
-   * @return  {number}  non-zero maxium of the subset
+   * Computes the non-zero maximum in a subset using precomputed values, if possible
+   *
+   * @param {[start: number, end: number]}  indexBounds
+   * @return {number} non-zero maxium of the subset
    */
   getMaxNonZeroInSubset(indexBounds) {
     const start = indexBounds[0];
@@ -128,10 +138,11 @@ class DenseDataExtrema1D {
 
   /**
    * Precomputes non-zero minimums of subsets of the given data vector
-   * @return  {array}  array containing minimums of the regularly subdivided
-   *                   data vector
+   *
+   * @returns {Array<number>} - Minimums of the regularly subdivided data vector
    */
   computeSubsetNonZeroMinimums() {
+    /** @type {Array<number>} */
     const minimums = [];
 
     for (let i = 0; i < this.numSubsets; i++) {
@@ -159,10 +170,10 @@ class DenseDataExtrema1D {
 
   /**
    * Precomputes non-zero maximums of subsets of the given data vector
-   * @return  {array}  array containing maximums of the regularly subdivided
-   *                   data vector
+   * @return {Array<number>} Maximums of the regularly subdivided data vector
    */
   computeSubsetNonZeroMaximums() {
+    /** @type {Array<number>} */
     const maximums = [];
 
     for (let i = 0; i < this.numSubsets; i++) {
@@ -190,7 +201,8 @@ class DenseDataExtrema1D {
 
   /**
    * Computes the non-zero minimum in the entire data array using precomputed values
-   * @return  {number}  non-zeros maximum of the data
+   *
+   * @return {number} Non-zeros maximum of the data
    */
   getMinNonZeroInTile() {
     return Math.min(...this.subsetMinimums);
@@ -198,7 +210,8 @@ class DenseDataExtrema1D {
 
   /**
    * Computes the non-zero maximum in the entire data array using precomputed values
-   * @return  {number}  non-zeros maximum of the data
+   *
+   * @return {number} Non-zeros maximum of the data
    */
   getMaxNonZeroInTile() {
     return Math.max(...this.subsetMaximums);
@@ -208,9 +221,9 @@ class DenseDataExtrema1D {
    * Calculate the minimum non-zero value in the data from start
    * to end. No precomputations are used to compute the min.
    *
-   * @param {Float32Array} data
-   * @param {int} start
-   * @param {int} end
+   * @param {ArrayLike<number>} data
+   * @param {number} start
+   * @param {number} end
    * @return {number} non-zero min in subset
    */
   minNonZero(data, start, end) {
@@ -235,9 +248,9 @@ class DenseDataExtrema1D {
    * Calculate the maximum non-zero value in the data from start
    * to end. No precomputations are used to compute the max.
    *
-   * @param {Float32Array} data
- ` * @param {int} start
-   * @param {int} end
+   * @param {ArrayLike<number>} data
+   * @param {number} start
+   * @param {number} end
    * @return {number} non-zero max in subset
    */
   maxNonZero(data, start, end) {

package/app/scripts/utils/DenseDataExtrema2D.js

@@ -1,7 +1,12 @@
 import ndarray from 'ndarray';
-
 import { NUM_PRECOMP_SUBSETS_PER_2D_TTILE } from '../configs';
 
+/**
+ * @typedef View2D
+ * @property {(i: number, j: number) => number} get
+ * @property {(i: number, j: number, v: number) => void} set
+ */
+
 class DenseDataExtrema2D {
   /**
    * This module efficiently computes extrema of subsets of a given data matrix.
@@ -9,11 +14,12 @@ class DenseDataExtrema2D {
    * These values are used to efficiently approximate extrema given arbitrary subsets.
    * Larger values of 'numSubsets' lead to more accurate approximations (more expensive).
    *
-   * @param   {array}  data array of quadratic length
+   * @param {ArrayLike<number>} data array of quadratic length
    */
   constructor(data) {
+    /** @type {number} */
     this.epsilon = 1e-6;
-
+    /** @type {number} */
     this.tileSize = Math.sqrt(data.length);
 
     if (!Number.isSafeInteger(this.tileSize)) {
@@ -23,25 +29,33 @@ class DenseDataExtrema2D {
     }
 
     // if this.numSubsets == this.tilesize the extrema are computed exactly (expensive).
+    /** @type {number} */
     this.numSubsets = Math.min(NUM_PRECOMP_SUBSETS_PER_2D_TTILE, this.tileSize);
+    /** @type {number} */
     this.subsetSize = this.tileSize / this.numSubsets;
 
     // Convert data to 2d array
+    /** @type {View2D} */
     const dataMatrix = ndarray(Array.from(data), [
       this.tileSize,
       this.tileSize,
     ]);
 
+    /** @type {View2D} */
     this.subsetMinimums = this.computeSubsetNonZeroMinimums(dataMatrix);
+    /** @type {View2D} */
     this.subsetMaximums = this.computeSubsetNonZeroMaximums(dataMatrix);
+    /** @type {number} */
     this.minNonZeroInTile = this.getMinNonZeroInTile();
+    /** @type {number} */
     this.maxNonZeroInTile = this.getMaxNonZeroInTile();
   }
 
   /**
    * Computes an approximation of the non-zero minimum in a subset
-   * @param   {array}  indexBounds  [startX, startY, endX, endY]
-   * @return  {number}  non-zero minium of the subset
+   *
+   * @param {[startX: number, startY: number, endX: number, endY: number]} indexBounds
+   * @return {number} Non-zero minium of the subset
    */
   getMinNonZeroInSubset(indexBounds) {
     const startX = indexBounds[0];
@@ -69,8 +83,9 @@ class DenseDataExtrema2D {
 
   /**
    * Computes an approximation of the non-zero maximum in a subset
-   * @param   {array}  indexBounds  [startX, startY, endX, endY]
-   * @return  {number}  non-zero maxium of the subset
+   *
+   * @param {[startX: number, startY: number, endX: number, endY: number]} indexBounds
+   * @return {number} Non-zero maxium of the subset
    */
   getMaxNonZeroInSubset(indexBounds) {
     const startX = indexBounds[0];
@@ -98,13 +113,14 @@ class DenseDataExtrema2D {
 
   /**
    * Precomputes non-zero minimums of subsets of a given matrix
-   * @param   {ndarray}  dataMatrix
-   * @return  {ndarray}  matrix containing minimums of the dataMatrix
-   *                     after subdivision using a regular grid
+   * @param {View2D} dataMatrix
+   * @return {View2D} Matrix containing minimums of the dataMatrix after subdivision using a regular grid
    */
   computeSubsetNonZeroMinimums(dataMatrix) {
-    let minimums = new Array(this.numSubsets ** 2);
-    minimums = ndarray(minimums, [this.numSubsets, this.numSubsets]);
+    const minimums = ndarray(new Array(this.numSubsets ** 2), [
+      this.numSubsets,
+      this.numSubsets,
+    ]);
 
     for (let i = 0; i < this.numSubsets; i++) {
       for (let j = 0; j < this.numSubsets; j++) {
@@ -123,13 +139,15 @@ class DenseDataExtrema2D {
 
   /**
    * Precomputes non-zero maximums of subsets of a given matrix
-   * @param   {ndarray}  dataMatrix
-   * @return  {ndarray}  matrix containing maximums of the dataMatrix
-   *                     after subdivision using a regular grid
+   *
+   * @param {View2D} dataMatrix
+   * @return {View2D} Matrix containing maximums of the dataMatrix after subdivision using a regular grid
    */
   computeSubsetNonZeroMaximums(dataMatrix) {
-    let maximums = new Array(this.numSubsets ** 2);
-    maximums = ndarray(maximums, [this.numSubsets, this.numSubsets]);
+    const maximums = ndarray(new Array(this.numSubsets ** 2), [
+      this.numSubsets,
+      this.numSubsets,
+    ]);
 
     for (let i = 0; i < this.numSubsets; i++) {
       for (let j = 0; j < this.numSubsets; j++) {
@@ -148,12 +166,12 @@ class DenseDataExtrema2D {
 
   /**
    * Computes the non-zero minimum of a subset of a matrix (ndarray)
-   * @param   {ndarray}  arr
-   * @param   {int}  rowOffset Starting row of the subset
-   * @param   {int}  colOffset Starting column of the subset
-   * @param   {int}  width Width (num columns) of the subset
-   * @param   {int}  height Height (num rows) of the subset
-   * @return  {number}  non-zeros minimum of the subset
+   * @param {View2D} arr
+   * @param {number} rowOffset - Starting row of the subset
+   * @param {number} colOffset - Starting column of the subset
+   * @param {number} width - Width (num columns) of the subset
+   * @param {number} height - Height (num rows) of the subset
+   * @return {number} Non-zeros - minimum of the subset
    */
   getMinNonZeroInNdarraySubset(arr, rowOffset, colOffset, width, height) {
     let curMin = Number.MAX_SAFE_INTEGER;
@@ -175,12 +193,12 @@ class DenseDataExtrema2D {
 
   /**
    * Computes the non-zero maximum of a subset of a matrix (ndarray)
-   * @param   {ndarray}  arr
-   * @param   {int}  rowOffset Starting row of the subset
-   * @param   {int}  colOffset Starting column of the subset
-   * @param   {int}  width Width (num columns) of the subset
-   * @param   {int}  height Height (num rows) of the subset
-   * @return  {number}  non-zeros maximum of the subset
+   * @param {View2D} arr
+   * @param {number} rowOffset - Starting row of the subset
+   * @param {number} colOffset - Starting column of the subset
+   * @param {number} width - Width (num columns) of the subset
+   * @param {number} height - Height (num rows) of the subset
+   * @return {number} Non-zeros maximum of the subset
    */
   getMaxNonZeroInNdarraySubset(arr, rowOffset, colOffset, width, height) {
     let curMax = Number.MIN_SAFE_INTEGER;
@@ -211,7 +229,8 @@ class DenseDataExtrema2D {
 
   /**
    * Computes the non-zero minimum in the entire data array using precomputed values
-   * @return  {number}  non-zeros minimum of the data
+   *
+   * @return {number} Non-zeros minimum of the data
    */
   getMinNonZeroInTile() {
     return this.getMinNonZeroInNdarraySubset(
@@ -225,7 +244,8 @@ class DenseDataExtrema2D {
 
   /**
    * Computes the non-zero maximum in the entire data array using precomputed values
-   * @return  {number}  non-zeros maximum of the data
+   *
+   * @return {number} Non-zeros maximum of the data
    */
   getMaxNonZeroInTile() {
     return this.getMaxNonZeroInNdarraySubset(

package/app/scripts/utils/LruCache.js

@@ -1,3 +1,4 @@
+// @ts-nocheck
 /**
  * A doubly linked list-based Least Recently Used (LRU) cache. Will keep most
  * recently used items while discarding least recently used items when its limit

package/app/scripts/utils/abs-to-chr.js

@@ -1,4 +1,3 @@
-// @ts-check
 import chromInfoBisector from './chrom-info-bisector';
 
 /**

package/app/scripts/utils/accessor-transposition.js

@@ -1,5 +1,3 @@
-// @ts-check
-
 /**
  * Factory function for a transposition accessor for a 2D matrix in form of a 1D
  * array.

package/app/scripts/utils/add-arrays.js

@@ -1,5 +1,3 @@
-// @ts-check
-
 /** @type {<T>(index: T) => T} */
 const identity = (i) => i;
 

package/app/scripts/utils/add-class.js

@@ -1,4 +1,3 @@
-// @ts-check
 import hasClass from './has-class';
 
 const XMLNS = 'http://www.w3.org/2000/svg';

package/app/scripts/utils/add-event-listener-once.js

@@ -1,5 +1,3 @@
-// @ts-check
-
 /**
  * Add an event listener that fires only once and auto-removes itself
  *

package/app/scripts/utils/background-task-scheduler.js

@@ -1,5 +1,3 @@
-// @ts-check
-
 /**
  * @template T
  * @typedef DataTask

package/app/scripts/utils/base64-to-canvas.js

@@ -1,5 +1,3 @@
-// @ts-check
-
 /**
  * Convert a base64 encoded image into a canvas object.
  * @param {string} base64 - Base64 string encoding the image.

package/app/scripts/utils/chr-to-abs.js

@@ -1,5 +1,3 @@
-// @ts-check
-
 /**
  * Convert a chromosome position to an absolute genome position.
  *

package/app/scripts/utils/chrom-info-bisector.js

@@ -1,4 +1,3 @@
-// @ts-check
 import { bisector } from 'd3-array';
 
 const chromInfoBisector = bisector(

package/app/scripts/utils/clone-event.js

@@ -1,5 +1,3 @@
-// @ts-check
-
 /**
  * Clone an event by invoking the source event's constructor and passing in the source event.
  *

package/app/scripts/utils/color-domain-to-rgba-array.js

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import { scaleLinear } from 'd3-scale';
 import { range } from 'd3-array';
 import { rgb } from 'd3-color';

package/app/scripts/utils/color-to-hex.js

@@ -1,4 +1,3 @@
-// @ts-check
 import { color } from 'd3-color';
 
 // Configs

package/app/scripts/utils/color-to-rgba.js

@@ -1,4 +1,3 @@
-// @ts-check
 import { color } from 'd3-color';
 
 /**

package/app/scripts/utils/data-to-genomic-loci.js

@@ -1,4 +1,3 @@
-// @ts-check
 import absToChr from './abs-to-chr';
 
 /** @typedef {[startChromName: string, startChromPos: number, endChromName: string, endChromPos: number]} GenomicLoci */

package/app/scripts/utils/debounce.js

@@ -1,5 +1,3 @@
-// @ts-check
-
 /**
  * Debounce a function call
  *

package/app/scripts/utils/dec-to-hex-str.js

@@ -1,4 +1,3 @@
-// @ts-check
 /**
  * Converts a decimal number to a hex string.
  *

package/app/scripts/utils/dict-from-tuples.js

@@ -1,5 +1,3 @@
-// @ts-check
-
 /**
  * Create a dictionary from a list of [key, value] pairs.
  *

package/app/scripts/utils/dict-items.js

@@ -1,5 +1,3 @@
-// @ts-check
-
 /**
  * @template T
  * @typedef {Array<{ [Key in keyof T]: [Key, T[Key]] }[keyof T]>} DictItems

package/app/scripts/utils/dict-keys.js

@@ -1,5 +1,3 @@
-// @ts-check
-
 /**
  * Return an array of keys that are present in this dictionary
  *

package/app/scripts/utils/dict-values.js

@@ -1,5 +1,3 @@
-// @ts-check
-
 /**
  * Return an array of values that are present in this dictionary
  *

package/app/scripts/utils/download.js

@@ -1,5 +1,3 @@
-// @ts-check
-
 /**
  * Download a file to the user's computer.
  * @param {string} filename - Name of the file to download

package/app/scripts/utils/expand-combined-tracks.js

@@ -1,3 +1,4 @@
+// @ts-nocheck
 /**
  * Go through a list of tracks and expand combined
  * tracks.

package/app/scripts/utils/fill-in-min-widths.js

@@ -1,3 +1,4 @@
+// @ts-nocheck
 // Configs
 import {
   MIN_HORIZONTAL_HEIGHT,

package/app/scripts/utils/flatten.js

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import reduce from './reduce';
 
 /**

package/app/scripts/utils/for-each.js

@@ -1,4 +1,3 @@
-// @ts-check
 /**
  * Functional version of `Array.forEach`. More flexible and applicable to other array-like data types.
  *

package/app/scripts/utils/forward-event.js

@@ -1,4 +1,3 @@
-// @ts-check
 import cloneEvent from './clone-event';
 
 /**

package/app/scripts/utils/genome-loci-to-pixels.js

@@ -1,4 +1,3 @@
-// @ts-check
 import chrToAbs from './chr-to-abs';
 
 /**

package/app/scripts/utils/genomic-range-to-chromosome-chunks.js

@@ -1,5 +1,3 @@
-// @ts-check
-
 /**
  * Using the [genomicStart, genomicEnd] range, get an array of "chromosome chunks",
  * where each chunk range starts and ends with the same chromosome.

package/app/scripts/utils/get-aggregation-function.js

@@ -1,20 +1,15 @@
-// @ts-check
 import { mean, sum, variance, deviation } from 'd3-array';
 
+/** @typedef {(values: number[]) => number | undefined} Aggregation */
+
 /**
  * Get an aggregation function from a function name.
- * @template {'mean' | 'sum' | 'variance' | 'deviation'} Type
- * @param {Type} name - The name of an aggregation function
- * ('mean', 'sum', 'variance', 'deviation'). If an unknown string is passed,
- * the mean function will be used, and a console warning will be thrown.
- * @returns {{
- *  mean: typeof mean,
- *  sum: typeof sum,
- *  variance: typeof variance,
- *  deviation: typeof deviation,
- * }[Type]} The function of interest as determined by the string,
+ * @param {'mean' | 'sum' | 'variance' | 'deviation'} name - The type of aggregation.
+ * If an unknown string is passed, the mean function will be used (and a warning will be logged).
+ * @returns {Aggregation} The function of interest as determined by the string,
  */
 const getAggregationFunction = (name) => {
+  /** @type {Aggregation} */
   let aggFunc;
   const lowerCaseName = name ? name.toLowerCase() : name;
   switch (lowerCaseName) {
@@ -36,7 +31,6 @@ const getAggregationFunction = (name) => {
         'Encountered an unsupported selectedRowsAggregationMode option.',
       );
   }
-  // @ts-expect-error - TS can't infer type-mapping
   return aggFunc;
 };
 

package/app/scripts/utils/get-default-track-for-datatype.js

@@ -1,3 +1,4 @@
+// @ts-nocheck
 // Configs
 import { DEFAULT_TRACKS_FOR_DATATYPE } from '../configs';
 

package/app/scripts/utils/get-element-dim.js

@@ -1,4 +1,3 @@
-// @ts-check
 import { ElementResizeListener } from '../services';
 
 /**

package/app/scripts/utils/get-higlass-components.js

@@ -1,3 +1,4 @@
+// @ts-nocheck
 export const getTrackObjectFromHGC = (hgc, viewUid, trackUid) => {
   let newViewUid = viewUid;
   let newTrackUid = trackUid;

package/app/scripts/utils/get-track-by-uid.js

@@ -1,3 +1,4 @@
+// @ts-nocheck
 /**
  * Return the track object for the track corresponding to this uid
  *

package/app/scripts/utils/get-track-conf-from-hgc.js

@@ -1,3 +1,4 @@
+// @ts-nocheck
 /**
  * Get a track's config (not the track object) from a higlass component.
  *

package/app/scripts/utils/get-track-obj-by-id.js

@@ -1,3 +1,4 @@
+// @ts-nocheck
 const getTrackObjById = (tiledPlots, viewId, trackId) => {
   const tiledPlot = viewId ? tiledPlots[viewId] : Object.values(tiledPlots)[0];
 

package/app/scripts/utils/get-track-position-by-uid.js

@@ -1,3 +1,4 @@
+// @ts-nocheck
 import visitPositionedTracks from './visit-positioned-tracks';
 
 /**

package/app/scripts/utils/get-xylofon.js

@@ -1,3 +1,4 @@
+// @ts-nocheck
 /* global XYLOPHON:false */
 
 import map from './map';

package/app/scripts/utils/gradient.js

@@ -1,5 +1,3 @@
-// @ts-check
-
 /**
  * @param {{ from: number, color: string }[]} steps
  * @param {number} width

package/app/scripts/utils/has-class.js

@@ -1,5 +1,3 @@
-// @ts-check
-
 const XMLNS = 'http://www.w3.org/2000/svg';
 
 /**

package/app/scripts/utils/has-parent.js

@@ -1,3 +1,4 @@
+// @ts-nocheck
 /**
  * Test whether a DOM element is the parent of another DOM element.
  *

package/app/scripts/utils/hex-string-to-int.js

@@ -1,4 +1,3 @@
-// @ts-check
 /**
  * Convert a HEX string into a HEX integer.
  *

package/app/scripts/utils/index.js

@@ -1,4 +1,3 @@
-// @ts-check
 export { default as absToChr } from './abs-to-chr';
 export { default as accessorTransposition } from './accessor-transposition';
 export { default as addArrays } from './add-arrays';

package/app/scripts/utils/interval-tree.js

@@ -1,3 +1,4 @@
+// @ts-nocheck
 function IntervalTreeNode(start, end, left, right) {
   /**
    * Node interval.

package/app/scripts/utils/into-the-void.js

@@ -1,4 +1,3 @@
-// @ts-check
 /**
  * An adventure into the abyss of void!
  * @type {(...args: any[]) => void}  The explorers find nothing but void.

package/app/scripts/utils/is-track-or-child-track.js

@@ -1,4 +1,3 @@
-// @ts-check
 import CombinedTrack from '../CombinedTrack';
 
 /**

package/app/scripts/utils/is-track-range-selectable.js

@@ -1,4 +1,3 @@
-// @ts-check
 import or from './or';
 
 /**

package/app/scripts/utils/is-within.js

@@ -1,5 +1,3 @@
-// @ts-check
-
 /**
  * Check if a 2D or 1D point is within a rectangle or range
  * @param {number} x - The point's X coordinate.