gosling.js 0.15.0 → 0.17.0

package/dist/gosling.js

@@ -34,7 +34,7 @@ import "bezier-js";
 import { scaleLinear, scaleSequential, scaleOrdinal, scaleBand } from "d3-scale";
 import { sampleSize, isEqual, uniqBy, cloneDeepWith } from "lodash-es";
 import { interpolateViridis } from "d3-scale-chromatic";
-import { A as Ajv, I as IsChannelDeep, r as resolveSuperposedTracks, t as traverseTracks, a as IsTemplateTrack, g as getTextStyle, c as computeChromSizes, b as cartesianToPolar, u as uuid, R as RADIAN_GAP, v as valueToRadian, p as pointsToDegree, d as commonjsGlobal, e as RemoteFile, f as IsOneOfFilter, h as IsRangeFilter, i as IsIncludeFilter, j as getChannelKeysByAggregateFnc, k as getChannelKeysByType, s as sanitizeChrName, l as filterUsingGenoPos, m as IsDataDeepTileset, n as IsDomainChr, o as IsDomainInterval, q as IsDomainChrInterval, S as SUPPORTED_CHANNELS, w as insertItemToArray, x as getAutoCompleteId, y as IsChannelValue, z as getValueUsingChannel, B as rectProperty, C as pointProperty, D as barProperty, E as IsStackedChannel, F as IsDomainArray, P as PREDEFINED_COLOR_STR_MAP, G as IsRangeArray, H as Is2DTrack, J as isTabularDataFetcher, K as drawPreEmbellishment, L as drawMark, M as drawPostEmbellishment, N as getRelativeGenomicPosition, O as hasDataTransform, Q as IsXAxis, T as IsMouseEventsDeep, U as colorToHex, V as flatArrayToPairArray, W as DEWFAULT_TITLE_PADDING_ON_TOP_AND_BOTTOM, X as traverseTracksAndViews, Y as traverseViewArrangements, Z as DEFAULT_VIEW_SPACING, _ as DEFAULT_INNER_RADIUS_PROP, $ as IsDummyTrack, a0 as IsOverlaidTrack, a1 as IsYAxis, a2 as DEFAULT_CIRCULAR_VIEW_PADDING, a3 as IsDataDeep, a4 as IsHiGlassMatrix, a5 as getHiGlassColorRange, a6 as DEFAULT_TEXT_STYLE, a7 as overrideDataTemplates, a8 as traverseToFixSpecDownstream, a9 as GenomicPositionHelper, aa as isObject } from "./exported-utils-d4f1abea.js";
+import { A as Ajv, I as IsChannelDeep, r as resolveSuperposedTracks, t as traverseTracks, a as IsTemplateTrack, g as getTextStyle, c as computeChromSizes, b as cartesianToPolar, u as uuid, R as RADIAN_GAP, v as valueToRadian, p as pointsToDegree, d as commonjsGlobal, e as RemoteFile, f as IsOneOfFilter, h as IsRangeFilter, i as IsIncludeFilter, j as getChannelKeysByAggregateFnc, k as getChannelKeysByType, s as sanitizeChrName, l as filterUsingGenoPos, m as IsDataDeepTileset, n as IsDomainChr, o as IsDomainInterval, q as IsDomainChrInterval, S as SUPPORTED_CHANNELS, w as insertItemToArray, x as getAutoCompleteObject, y as IsChannelValue, z as getValueUsingChannel, B as rectProperty, C as pointProperty, D as barProperty, E as IsStackedChannel, F as IsDomainArray, P as PREDEFINED_COLOR_STR_MAP, G as IsRangeArray, H as Is2DTrack, J as isTabularDataFetcher, K as drawPreEmbellishment, L as drawMark, M as drawPostEmbellishment, N as getRelativeGenomicPosition, O as hasDataTransform, Q as IsXAxis, T as IsMouseEventsDeep, U as colorToHex, V as flatArrayToPairArray, W as DEWFAULT_TITLE_PADDING_ON_TOP_AND_BOTTOM, X as traverseTracksAndViews, Y as traverseViewArrangements, Z as DEFAULT_VIEW_SPACING, _ as DEFAULT_INNER_RADIUS_PROP, $ as IsDummyTrack, a0 as IsOverlaidTrack, a1 as IsYAxis, a2 as DEFAULT_CIRCULAR_VIEW_PADDING, a3 as IsDataDeep, a4 as IsHiGlassMatrix, a5 as getHiGlassColorRange, a6 as DEFAULT_TEXT_STYLE, a7 as overrideDataTemplates, a8 as traverseToFixSpecDownstream, a9 as GenomicPositionHelper, aa as isObject } from "./exported-utils-c7f92c46.js";
 import higlassRegister from "higlass-register";
 import { TextTrack } from "higlass-text";
 import RBush from "rbush";
@@ -52,7 +52,7 @@ import require$$0 from "react-dom";
 import { HiGlassComponent } from "higlass";
 import { ResizeSensor } from "css-element-queries";
 const name = "gosling.js";
-const version = "0.15.0";
+const version = "0.17.0";
 const $ref$2 = "#/definitions/GoslingSpec";
 const $schema$2 = "http://json-schema.org/draft-07/schema#";
 const definitions$2 = {
@@ -23122,12 +23122,7 @@ const HIGLASS_AXIS_SIZE = 30;
 const getViewTemplate = (assembly) => {
   return {
     genomePositionSearchBoxVisible: false,
-    genomePositionSearchBox: {
-      autocompleteServer: "https://higlass.io/api/v1",
-      autocompleteId: getAutoCompleteId(assembly),
-      chromInfoServer: "https://higlass.io/api/v1",
-      chromInfoId: assembly != null ? assembly : "hg38"
-    },
+    genomePositionSearchBox: getAutoCompleteObject(assembly),
     layout: { w: 12, h: 12, x: 0, y: 0 },
     tracks: {
       top: [],
@@ -23764,7 +23759,7 @@ class GoslingTrackModel {
     this.theme = theme != null ? theme : getTheme();
     this.dataAggregated = data;
     this.specOriginal = spec;
-    this.specComplete = structuredClone(spec);
+    this.specComplete = JSON.parse(JSON.stringify(spec));
     this.channelScales = {};
     this.mouseEventModel = new MouseEventModel();
     const validity = this.validateSpec();
@@ -24432,11 +24427,11 @@ const config$1 = {
   }
 };
 const factory$1 = (HGC, context, options) => {
-  var _assembly2, _processedTileInfo, _mouseDownX, _mouseDownY, _isRangeBrushActivated, _gBrush, _loadingTextStyleObj, _loadingTextBg, _loadingText, _tilesToId, tilesToId_fn, _binsPerTile, binsPerTile_get, _generateTabularData, generateTabularData_fn, _onMouseDown, onMouseDown_fn, _onMouseMove, onMouseMove_fn, _onMouseUp, onMouseUp_fn, _onMouseOut, onMouseOut_fn, _getElementsWithinMouse, getElementsWithinMouse_fn, _publishTrackEvents, publishTrackEvents_fn, _onRangeBrush, onRangeBrush_fn, _highlightMarks, highlightMarks_fn, _publishOnNewTrack, publishOnNewTrack_fn, _hasStretchableGraphics, hasStretchableGraphics_fn, _isTooStretched, isTooStretched_fn;
+  var _assembly2, _processedTileInfo, _mouseDownX, _mouseDownY, _isRangeBrushActivated, _gBrush, _loadingTextStyleObj, _loadingTextBg, _loadingText, _processedTileMap, _tilesToId, tilesToId_fn, _binsPerTile, binsPerTile_get, _generateTabularData, generateTabularData_fn, _onMouseDown, onMouseDown_fn, _onMouseMove, onMouseMove_fn, _onMouseUp, onMouseUp_fn, _onMouseOut, onMouseOut_fn, _getElementsWithinMouse, getElementsWithinMouse_fn, _publishTrackEvents, publishTrackEvents_fn, _onRangeBrush, onRangeBrush_fn, _highlightMarks, highlightMarks_fn, _publishOnNewTrack, publishOnNewTrack_fn, _hasStretchableGraphics, hasStretchableGraphics_fn, _isTooStretched, isTooStretched_fn;
   const { tileProxy } = HGC.services;
-  const { BarTrack } = HGC.tracks;
+  const { TiledPixiTrack } = HGC.tracks;
   const loadingTextStyle = getTextStyle({ color: "black", size: 12 });
-  const _GoslingTrackClass = class _GoslingTrackClass extends BarTrack {
+  const _GoslingTrackClass = class _GoslingTrackClass extends TiledPixiTrack {
     /* *
      *
      *  Constructor
@@ -24450,11 +24445,6 @@ const factory$1 = (HGC, context, options) => {
        * Construct tabular data from a higlass tileset and a gosling track model.
        */
       __privateAdd(this, _generateTabularData);
-      /* *
-       *
-       *  Mouse methods
-       *
-       * */
       __privateAdd(this, _onMouseDown);
       __privateAdd(this, _onMouseMove);
       __privateAdd(this, _onMouseUp);
@@ -24486,8 +24476,7 @@ const factory$1 = (HGC, context, options) => {
        */
       __privateAdd(this, _hasStretchableGraphics);
       /**
-       * Used in drawTile()
-       * Checks if the tile Graphic is too stretched. If so, it returns true.
+       * Used in drawTile(). Checks if the tile Graphic is too stretched. If so, it returns true.
        * @param stretchFactor The factor by which the tile is stretched
        * @returns True if the tile is too stretched, false otherwise
        */
@@ -24523,7 +24512,10 @@ const factory$1 = (HGC, context, options) => {
       __privateAdd(this, _loadingText, new HGC.libraries.PIXI.Text("", loadingTextStyle));
       __publicField(this, "prevVisibleAndFetchedTiles");
       __publicField(this, "resolvedTracks");
+      // This is used to persist processed tile data across draw() calls.
+      __privateAdd(this, _processedTileMap, /* @__PURE__ */ new WeakMap());
       __publicField(this, "hideMousePosition");
+      const { isShowGlobalMousePosition } = context;
       context.dataFetcher.track = this;
       __privateSet(this, _processedTileInfo, {});
       __privateSet(this, _assembly2, this.options.spec.assembly);
@@ -24559,15 +24551,11 @@ const factory$1 = (HGC, context, options) => {
       });
       this.pMask.on("mouseout", __privateMethod(this, _onMouseOut, onMouseOut_fn).bind(this));
       this.flipText = this.options.spec.orientation === "vertical";
-      if (this.hideMousePosition) {
-        this.hideMousePosition();
-        this.hideMousePosition = void 0;
-      }
       if (((_d = this.options) == null ? void 0 : _d.showMousePosition) && !this.hideMousePosition) {
         this.hideMousePosition = HGC.utils.showMousePosition(
           this,
           Is2DTrack(this.getResolvedTracks()[0]),
-          this.isShowGlobalMousePosition()
+          isShowGlobalMousePosition()
         );
       }
       this.pLabel.removeChild(this.trackNotFoundText);
@@ -24601,6 +24589,11 @@ const factory$1 = (HGC, context, options) => {
         const isBamDataFetcher = this.dataFetcher instanceof BamDataFetcher;
         this.processAllTiles(isBamDataFetcher);
         super.draw();
+        Object.values(this.fetchedTiles).forEach((tile) => {
+          if (!tile.drawnAtScale)
+            return;
+          [tile.graphics.scale.x, tile.graphics.position.x] = this.getXScaleAndOffset(tile.drawnAtScale);
+        });
         this.prevVisibleAndFetchedTiles = this.visibleAndFetchedTiles();
       };
       if (isTabularDataFetcher(this.dataFetcher) && !isEqual(this.visibleAndFetchedTiles(), this.prevVisibleAndFetchedTiles)) {
@@ -24614,6 +24607,17 @@ const factory$1 = (HGC, context, options) => {
         this.firstDraw = false;
       }
     }
+    /**
+     * Copied from BarTrack
+     */
+    getXScaleAndOffset(drawnAtScale) {
+      const dA = drawnAtScale.domain();
+      const dB = this._xScale.domain();
+      const tileK = (dA[1] - dA[0]) / (dB[1] - dB[0]);
+      const newRange = this._xScale.domain().map(drawnAtScale);
+      const posOffset = newRange[0];
+      return [tileK, -posOffset * tileK];
+    }
     /*
      * Do whatever is necessary before rendering a new tile. This function is called from `receivedTiles()`.
      * Overrides initTile in BarTrack
@@ -24654,7 +24658,8 @@ const factory$1 = (HGC, context, options) => {
       this.pBackground.clear();
       this.pBackground.removeChildren();
       this.pBorder.clear();
-      this.pBorder.removeChildren();
+      const children = this.pBorder.removeChildren();
+      children.forEach((c) => c.destroy());
       this.displayedLegends = [];
       tileInfo.goslingModels.forEach((model) => {
         const trackWidth = this.dimensions[0];
@@ -24679,6 +24684,7 @@ const factory$1 = (HGC, context, options) => {
       this.getResolvedTracks(true);
       this.clearMouseEventData();
       this.textsBeingUsed = 0;
+      __privateSet(this, _processedTileMap, /* @__PURE__ */ new WeakMap());
       this.processAllTiles(true);
       this.draw();
       this.forceDraw();
@@ -24725,6 +24731,7 @@ const factory$1 = (HGC, context, options) => {
     setPosition(newPosition) {
       super.setPosition(newPosition);
       [this.pMain.position.x, this.pMain.position.y] = this.position;
+      [this.pMouseOver.position.x, this.pMouseOver.position.y] = this.position;
       this.mRangeBrush.setOffset(...newPosition);
     }
     /**
@@ -24790,6 +24797,9 @@ const factory$1 = (HGC, context, options) => {
       var _a, _b;
       this.tileSize = (_b = (_a = this.tilesetInfo) == null ? void 0 : _a.tile_size) != null ? _b : 1024;
       const tiles = this.visibleAndFetchedTiles();
+      if (tiles.every((tile) => __privateGet(this, _processedTileMap).get(tile) !== void 0)) {
+        return;
+      }
       tiles.forEach((tile) => __privateMethod(this, _generateTabularData, generateTabularData_fn).call(this, tile, force));
       this.combineAllTilesIfNeeded();
       const models = tiles.flatMap((tile) => this.transformDataAndCreateModels(tile));
@@ -24798,6 +24808,9 @@ const factory$1 = (HGC, context, options) => {
       if (flatTileData.length !== 0) {
         this.options.siblingIds.forEach((id) => publish("rawData", { id, data: flatTileData }));
       }
+      tiles.forEach((tile) => {
+        __privateGet(this, _processedTileMap).set(tile, true);
+      });
     }
     /**
      * This is currently for testing the new way of rendering visual elements. Called by this.draw()
@@ -24821,7 +24834,7 @@ const factory$1 = (HGC, context, options) => {
       callback();
     }
     /**
-     * Overrides method in Tiled1DPixiTrack. It is called in the constructor, `super(context, options)`.
+     * This method is called in the TiledPixiTrack constructor `super(context, options)`.
      * So be aware to use defined variables.
      */
     calculateVisibleTiles() {
@@ -24866,7 +24879,7 @@ const factory$1 = (HGC, context, options) => {
         } else {
           const xTiles = tileProxy.calculateTiles(
             zoomLevel,
-            this.relevantScale(),
+            this._xScale,
             this.tilesetInfo.min_pos[0],
             this.tilesetInfo.max_pos[0],
             this.tilesetInfo.max_zoom,
@@ -24890,7 +24903,31 @@ const factory$1 = (HGC, context, options) => {
       }
     }
     /**
-     * Get the tile's position in its coordinate system. Overrides method in Tiled1DPixiTrack.
+     * Copied from HorizontalTiled1DPixiTrack
+     */
+    calculateZoomLevel() {
+      if (!this.tilesetInfo) {
+        throw Error("tilesetInfo not parsed");
+      }
+      if ("resolutions" in this.tilesetInfo) {
+        const zoomIndexX = tileProxy.calculateZoomLevelFromResolutions(
+          this.tilesetInfo.resolutions,
+          this._xScale
+        );
+        return zoomIndexX;
+      }
+      const xZoomLevel = tileProxy.calculateZoomLevel(
+        this._xScale,
+        this.tilesetInfo.min_pos[0],
+        this.tilesetInfo.max_pos[0],
+        this.tilesetInfo.bins_per_dimension || this.tilesetInfo.tile_size
+      );
+      let zoomLevel = Math.min(xZoomLevel, this.maxZoom);
+      zoomLevel = Math.max(zoomLevel, 0);
+      return zoomLevel;
+    }
+    /**
+     * Get the tile's position in its coordinate system. Based on method in Tiled1DPixiTrack
      */
     getTilePosAndDimensions(zoomLevel, tilePos) {
       if (!this.tilesetInfo) {
@@ -24927,7 +24964,7 @@ const factory$1 = (HGC, context, options) => {
       }
     }
     /**
-     * Gets the indices of the visible data a tile. Overrides method in Tiled1DPixiTrack
+     * Gets the indices of the visible data a tile. Based on method in Tiled1DPixiTrack
      */
     getIndicesOfVisibleDataInTile(tile) {
       const visible = this._xScale.range();
@@ -24945,7 +24982,6 @@ const factory$1 = (HGC, context, options) => {
     }
     /**
      * Overrides method in TiledPixiTrack
-     * @param loadedTiles
      */
     receivedTiles(loadedTiles) {
       super.receivedTiles(loadedTiles);
@@ -24998,6 +25034,18 @@ const factory$1 = (HGC, context, options) => {
       const isBamDataFetcher = this.dataFetcher instanceof BamDataFetcher;
       return includesDisplaceTransform && !hasDenseTiles() && !isBamDataFetcher;
     }
+    /**
+     * Copied from Tiled1DPixiTrack. The ID of the local tile
+     */
+    tileToLocalId(tile) {
+      return `${tile.join(".")}`;
+    }
+    /**
+     * Copied from Tiled1DPixiTrack. The ID of the tile on the server.
+     */
+    tileToRemoteId(tile) {
+      return `${tile.join(".")}`;
+    }
     /**
      * Creates an array of SingleTracks if there are overlaid tracks.
      * This method cannot be private because it is called by functions which are called by super.draw();
@@ -25076,7 +25124,7 @@ const factory$1 = (HGC, context, options) => {
         } catch (e) {
         }
         const [trackWidth, trackHeight] = this.dimensions;
-        const axisSize = IsXAxis(resolvedSpec) ? HIGLASS_AXIS_SIZE : 0;
+        const axisSize = IsXAxis(resolvedSpec) && this.options.spec.layout === "linear" ? HIGLASS_AXIS_SIZE : 0;
         const [w, h] = [trackWidth, trackHeight + axisSize];
         const circularFactor = Math.min(w, h) / Math.min(resolvedSpec.width, resolvedSpec.height);
         if (resolvedSpec.innerRadius) {
@@ -25092,9 +25140,20 @@ const factory$1 = (HGC, context, options) => {
       });
       return tileInfo.goslingModels;
     }
+    /* *
+     *
+     *  Mouse methods
+     *
+     * */
+    /**
+     * This is for the HiGlass mouseMoveZoom event. However, GoslingTrack has its own way of handling mouse events.
+     */
+    mouseMoveZoomHandler() {
+      return;
+    }
     // set in HorizontalTiled1DPixiTrack
     /**
-     * Overrides method in HorizontalLine1DPixiTrack
+     * Called by showHoverMenu() in HiGlassComponent
      */
     getMouseOverHtml(mouseX, mouseY) {
       var _a, _b, _c, _d, _e;
@@ -25248,6 +25307,7 @@ const factory$1 = (HGC, context, options) => {
   _loadingTextStyleObj = new WeakMap();
   _loadingTextBg = new WeakMap();
   _loadingText = new WeakMap();
+  _processedTileMap = new WeakMap();
   _tilesToId = new WeakSet();
   tilesToId_fn = function(xTiles, yTiles, zoomLevel) {
     if (!yTiles) {