higlass 1.13.4 → 1.13.6

package/app/scripts/utils/pixi-text-to-svg.js

@@ -1,10 +1,7 @@
-// @ts-nocheck
 /**
  * Export a PIXI text to an SVG element
- *
- * param {PIXI.Text} pixiText A PIXI.Text object that we want to create an SVG element for
- * returns {Element} A DOM SVG Element with all of the attributes set as to display
- * the given text.
+ * @param {import('pixi.js').Text} pixiText A PIXI.Text object that we want to create an SVG element for
+ * @returns { HTMLElement } A DOM SVG Element with all of the attributes set as to display the given text.
  */
 export const pixiTextToSvg = (pixiText) => {
   const g = document.createElement('g');
@@ -18,11 +15,10 @@ export const pixiTextToSvg = (pixiText) => {
     t.setAttribute('text-anchor', 'middle');
   }
 
-  t.setAttribute('font-family', pixiText.style.fontFamily);
-  t.setAttribute('font-size', pixiText.style.fontSize);
+  t.setAttribute('font-family', pixiText.style.fontFamily?.toString() ?? '');
+  t.setAttribute('font-size', pixiText.style.fontSize?.toString() ?? '');
   g.setAttribute('transform', `scale(${pixiText.scale.x},1)`);
-
-  t.setAttribute('fill', pixiText.style.fill);
+  t.setAttribute('fill', pixiText.style.fill?.toString() ?? '');
   t.innerHTML = pixiText.text;
 
   g.appendChild(t);

package/app/scripts/utils/range-query-2d.js

@@ -1,6 +1,6 @@
 // @ts-nocheck
-import addArrays from './add-arrays';
 import accessorTransposition from './accessor-transposition';
+import addArrays from './add-arrays';
 
 /**
  * Perform a 2D query on a 1D array
@@ -24,9 +24,9 @@ const rangeQuery2d = (
   xRange,
   yRange,
   mirrored,
-  /* eslint-disable-next-line default-param-last */
+  // biome-ignore lint/style/useDefaultParameterLast:
   xOff = 0,
-  /* eslint-disable-next-line default-param-last */
+  // biome-ignore lint/style/useDefaultParameterLast:
   yOff = 0,
   outList,
 ) => {

package/app/scripts/utils/reduce.js

@@ -1,10 +1,17 @@
-// @ts-nocheck
 /**
- * Pure functional reducer. Can be used for currying stuff. Check out `flatten.js`.
- * @param   {function}  f  Reducer function.
- * @return  {array}  Curried function that accepts an array to be reduced.
+ * Pure functional reducer. Can be used for currying stuff.
+ *
+ * @see {@link ./flatten.js}
+ *
+ * @template T
+ * @template U
+ *
+ * @param {(previousValue: U, currentValue: T, currentIndex: number, array: Array<T>) => U} callbackfn
+ * @param {U} initialValue
+ * @return {(x: Array<T>) => U}  Curried function that accepts an array to be reduced.
  */
-const reduce = (f) => (x) => Array.prototype.reduce.call(x, f);
+const reduce = (callbackfn, initialValue) => (x) =>
+  x.reduce(callbackfn, initialValue);
 
 // TODO(Trevor): Not referenced anywhere. Remove?
 export default reduce;

package/app/scripts/utils/segments-to-rows.js

@@ -1,18 +1,20 @@
-// @ts-nocheck
-import IntervalTree from './interval-tree';
-
+import { IntervalTree } from './interval-tree';
+
+/** @typedef {{ from:number, to: number }} Segment */
+
+/**
+ * Partition a list of segments into an array of rows containing the segments.
+ *
+ * WARNING: Sorts the `segments` array input _inplace_.
+ *
+ * @param {Array<Segment>} segments An array of segments (e.g. [{from: 10, to: 20}, {from: 18, to: 30}])
+ * @return: {Array<Array<Segment>>} non-overlapping rows of segments
+ */
 function segmentsToRows(segments) {
-  /**
-   * Partition a list of segments into an array of
-   * rows containing the segments.
-   *
-   * @param segments: An array of segments (e.g. [{from: 10, to: 20}, {from: 18, to: 30}])
-   * @return: An array of arrays of segments, representing
-   *          non-overlapping rows of segments
-   */
   // sort by the length of each segment
   segments.sort((a, b) => b.to - b.from - (a.to - a.from));
 
+  /** @type {Array<Array<Segment>>} */
   const rows = [[]];
   const rowIts = [new IntervalTree()];
 
@@ -23,6 +25,7 @@ function segmentsToRows(segments) {
     for (let j = 0; j < rows.length; j++) {
       const it = rowIts[j]; // an interval tree
 
+      /** @type {[number, number]} */
       const toCheck = [+segments[i].from, +segments[i].to];
       const occluded = it.intersects(toCheck);
 

package/app/scripts/utils/show-mouse-position.js

@@ -3,7 +3,7 @@ import { globalPubSub } from 'pub-sub-es';
 import hexStrToInt from './hex-string-to-int';
 
 // Configs
-import { GLOBALS } from '../configs';
+import GLOBALS from '../configs/globals';
 
 const COLOR = 0xaaaaaa;
 const ALPHA = 1.0;
@@ -119,6 +119,22 @@ const showMousePosition = (
       y = event.isFrom2dTrack ? event.dataY : event.dataX;
     }
 
+    // If a track is not 2d and is horizontal, the event.dataY
+    // value of the mouse pointer location should not be allowed
+    // to impact how other tracks globally render their mouse
+    // position (see https://github.com/higlass/higlass/issues/814).
+    // Likewise, if a track is not 2d and is vertical, the
+    // event.dataX value should not be used by other tracks for
+    // position reporting.
+
+    if (!event.isFrom2dTrack) {
+      if (!event.isFromVerticalTrack) {
+        y = Number.MIN_SAFE_INTEGER;
+      } else {
+        x = Number.MIN_SAFE_INTEGER;
+      }
+    }
+
     // 2d or central tracks are not offset and rather rely on a mask, i.e., the
     // top left *visible* position is *not* [0,0] but given by `getPosition()`.
     const offset = is2d ? getPosition() : [0, 0];

package/app/scripts/utils/svg-line.js

@@ -1,4 +1,3 @@
-// @ts-nocheck
 /**
  * Generate a SVG line
  * @param   {number}  x1  Start X
@@ -6,19 +5,19 @@
  * @param   {number}  x2  End X
  * @param   {number}  y2  End Y
  * @param   {number}  strokeWidth  Line width
- * @param   {number}  strokeColor  Color HEX string
- * @return  {object}  SVG line object
+ * @param   {string}  strokeColor  Color HEX string
+ * @return  {HTMLElement}  SVG line object
  */
 export const svgLine = (x1, y1, x2, y2, strokeWidth, strokeColor) => {
   const line = document.createElement('line');
 
-  line.setAttribute('x1', x1);
-  line.setAttribute('x2', x2);
-  line.setAttribute('y1', y1);
-  line.setAttribute('y2', y2);
+  line.setAttribute('x1', String(x1));
+  line.setAttribute('x2', String(x2));
+  line.setAttribute('y1', String(y1));
+  line.setAttribute('y2', String(y2));
 
   if (strokeWidth) {
-    line.setAttribute('stroke-width', strokeWidth);
+    line.setAttribute('stroke-width', String(strokeWidth));
   }
   if (strokeColor) {
     line.setAttribute('stroke', strokeColor);

package/app/scripts/utils/type-guards.js

@@ -1,9 +1,11 @@
+/** @import * as t from '../types' */
+
 /**
- * @param {import('../types').TrackConfig} trackConfig
- * @return {trackConfig is import('../types').CombinedTrackConfig}
+ * @param {t.TrackConfig} trackConfig
+ * @return {trackConfig is t.CombinedTrackConfig}
  */
 export function isCombinedTrackConfig(trackConfig) {
-  return trackConfig.type === 'combined';
+  return 'contents' in trackConfig && trackConfig.type === 'combined';
 }
 
 /**
@@ -23,17 +25,24 @@ export function isObject(obj) {
 }
 
 /**
- * @param {import('../types').TilesetInfo | undefined} info
- * @returns {info is import('../types').LegacyTilesetInfo}
+ * @param {t.TilesetInfo | undefined} info
+ * @returns {info is t.LegacyTilesetInfo}
  */
 export function isLegacyTilesetInfo(info) {
   return isObject(info) && 'max_width' in info;
 }
 
 /**
- * @param {import('../types').TilesetInfo | undefined} info
- * @returns {info is import('../types').ResolutionsTilesetInfo}
+ * @param {t.TilesetInfo | undefined | { error: string }} info
+ * @returns {info is t.ResolutionsTilesetInfo}
  */
 export function isResolutionsTilesetInfo(info) {
   return isObject(info) && 'resolutions' in info;
 }
+/**
+ * @param {t.TilesetInfo | undefined | { error: string }} info
+ * @returns {info is t.TilesetInfo}
+ */
+export function isTilesetInfo(info) {
+  return isObject(info) && !('error' in info);
+}

package/app/scripts/utils/visit-positioned-tracks.js

@@ -1,12 +1,14 @@
 import visitTracks from './visit-tracks';
 
-/** @typedef {{ [Key in import('../types').TrackPosition]: import('../types').TrackConfig[] }} PositionedTracks
- */
+/** @import { TrackConfig, TrackPosition, TrackVisitor } from '../types' */
+
+/** @typedef {{ [Key in TrackPosition]?: Array<TrackConfig> }} PositionedTracks */
 
 /**
  * Track visitor for positioned tracks, i.e., tracks with a position.
+ *
  * @param {PositionedTracks} positionedTracks - List of all positioned tracks from the view definition.
- * @param {import('../types').TrackVisitor} visitor - Callback function receiving individual tracks.
+ * @param {TrackVisitor} visitor - Callback function receiving individual tracks.
  * @param {boolean} inclCombinedTracks - If `true` recursively visit combined tracks.
  */
 const visitPositionedTracks = (
@@ -14,11 +16,11 @@ const visitPositionedTracks = (
   visitor,
   inclCombinedTracks = true,
 ) => {
-  /** @type {import('../types').TrackConfig[]} */
+  /** @type {Array<TrackConfig>} */
   const allTracks = [];
 
   for (const [stringPosition, tracks] of Object.entries(positionedTracks)) {
-    /** @type {import('../types').TrackPosition} */
+    /** @type {TrackPosition} */
     // @ts-expect-error - Typings for Object#entries don't have strong inference,
     // might change in the future.
     const position = stringPosition;

package/app/styles/d3-context-menu.css

@@ -24,7 +24,6 @@
 
 	-webkit-touch-callout: none; /* iOS Safari */
 	-webkit-user-select: none;   /* Chrome/Safari/Opera */
-	-khtml-user-select: none;    /* Konqueror */
 	-moz-user-select: none;      /* Firefox */
 	-ms-user-select: none;       /* Internet Explorer/Edge */
 	user-select: none;

package/app/styles/prism.css

@@ -45,6 +45,7 @@ pre[class*="language-"] {
 }
 
 :not(pre) > code[class*="language-"],
+/* biome-ignore lint/suspicious/noEmptyBlock: vendored */
 pre[class*="language-"] {
 }