@genome-spy/core 0.39.0 → 0.41.0

package/dist/src/paramBroker.js

@@ -0,0 +1,102 @@
+import { isString } from "vega-util";
+import createFunction from "./utils/expression.js";
+
+/**
+ * A class that manages parameters and expressions. Still a work in progress.
+ *
+ * TODO: Write tests for this class.
+ *
+ * This should eventually handle the following:
+ * - Parameter registration
+ * - Dependency tracking
+ * - Calling observers when a parameter changes
+ * - Somehow saving parameter "state" (in bookmarks)
+ * - Maybe something else
+ */
+export default class ParamBroker {
+    /** @type {Map<string, any>} */
+    #params;
+
+    /** @type {Set<string>} */
+    #allocatedSetters;
+
+    /** @type {Record<string, any>} */
+    #proxy;
+
+    /** @type {Map<string, Set<() => void>>} */
+    #paramListeners;
+
+    constructor() {
+        this.#params = new Map();
+        this.#allocatedSetters = new Set();
+        this.#paramListeners = new Map();
+
+        this.#proxy = new Proxy(this.#params, {
+            get(target, prop) {
+                return isString(prop) ? target.get(prop) : undefined;
+            },
+        });
+    }
+
+    /**
+     *
+     * @param {string} paramName
+     * @returns {(value: any) => void}
+     */
+    allocateSetter(paramName) {
+        if (this.#allocatedSetters.has(paramName)) {
+            throw new Error(
+                "Setter already allocated for parameter: " + paramName
+            );
+        }
+
+        this.#allocatedSetters.add(paramName);
+
+        return (value) => {
+            this.#params.set(paramName, value);
+
+            const listeners = this.#paramListeners.get(paramName);
+            if (listeners) {
+                for (const listener of listeners) {
+                    listener();
+                }
+            }
+        };
+    }
+
+    // TODO: deallocateSetter
+
+    /**
+     * Parse expr and return a function that returns the value of the parameter.
+     *
+     * @param {string} expr
+     */
+    createExpression(expr) {
+        /** @type {import("./utils/expression.js").ExpressionFunction & { addListener: (listener: () => void) => void}} */
+        const fn = /** @type {any} */ (createFunction(expr, this.#proxy));
+
+        for (const g of fn.globals) {
+            if (!this.#allocatedSetters.has(g)) {
+                throw new Error(
+                    `Unknown variable "${g}" in expression: ${expr}`
+                );
+            }
+        }
+
+        /**
+         *
+         * @param {() => void} listener
+         */
+        fn.addListener = (listener) => {
+            for (const g of fn.globals) {
+                const listeners = this.#paramListeners.get(g) ?? new Set();
+                this.#paramListeners.set(g, listeners);
+                listeners.add(listener);
+            }
+        };
+
+        // TODO: remove listener
+
+        return fn;
+    }
+}

package/dist/src/spec/mark.d.ts

@@ -2,6 +2,15 @@ import { Scalar } from "./channel.js";
 import { Align, Baseline, FontStyle, FontWeight } from "./font.js";
 import { Tooltip } from "./tooltip.js";
 
+// TODO: This may not be the best place for this type.
+// Also, this is now similar to the ExprDef type in channel.d.ts
+export interface ExprRef {
+    /**
+     * The expression string.
+     */
+    expr: string;
+}
+
 export type MarkType = "rect" | "point" | "rule" | "text" | "link";
 
 export interface FillAndStrokeProps {
@@ -63,7 +72,7 @@ export interface RectProps extends SecondaryPositionProps {
      * **Default value:** `0`
      */
     // TODO: Rename to minCompensatedOpacity or something like that
-    minOpacity?: number;
+    minOpacity?: number | ExprRef;
 
     /**
      * The minimum width of a rectangle in pixels. The property clamps rectangles'
@@ -74,49 +83,49 @@ export interface RectProps extends SecondaryPositionProps {
      *
      * **Default value:** `1`
      */
-    minWidth?: number;
+    minWidth?: number | ExprRef;
 
     /**
      * The minimum height of a rectangle in pixels. The property clamps rectangles' heights.
      *
      * **Default value:** `0`
      */
-    minHeight?: number;
+    minHeight?: number | ExprRef;
 
     /**
      * Radius of the rounded corners.
      *
      * **Default value:** `0`
      */
-    cornerRadius?: number;
+    cornerRadius?: number | ExprRef;
 
     /**
      * Radius of the top left rounded corner. Has higher precedence than `cornerRadius`.
      *
      * **Default value:** (None)
      */
-    cornerRadiusTopLeft?: number;
+    cornerRadiusTopLeft?: number | ExprRef;
 
     /**
      * Radius of the top right rounded corner. Has higher precedence than `cornerRadius`.
      *
      * **Default value:** (None)
      */
-    cornerRadiusTopRight?: number;
+    cornerRadiusTopRight?: number | ExprRef;
 
     /**
      * Radius of the bottom left rounded corner. Has higher precedence than `cornerRadius`.
      *
      * **Default value:** (None)
      */
-    cornerRadiusBottomLeft?: number;
+    cornerRadiusBottomLeft?: number | ExprRef;
 
     /**
      * Radius of the bottom right rounded corner. Has higher precedence than `cornerRadius`.
      *
      * **Default value:** (None)
      */
-    cornerRadiusBottomRight?: number;
+    cornerRadiusBottomRight?: number | ExprRef;
 }
 
 export interface RuleProps extends SecondaryPositionProps {
@@ -126,7 +135,7 @@ export interface RuleProps extends SecondaryPositionProps {
      *
      * **Default value:** `0`
      */
-    minLength?: number;
+    minLength?: number | ExprRef;
 
     /**
      * An array of of alternating stroke and gap lengths or `null` for solid strokes.
@@ -147,7 +156,7 @@ export interface RuleProps extends SecondaryPositionProps {
      *
      * **Default value:** `"butt"`
      */
-    strokeCap?: "butt" | "square" | "round";
+    strokeCap?: "butt" | "square" | "round" | ExprRef;
 }
 
 export interface TextProps
@@ -333,7 +342,7 @@ export interface LinkProps extends SecondaryPositionProps {
      *
      * **Default value:** `"arc"`
      */
-    linkShape?: "arc" | "diagonal" | "line" | "dome";
+    linkShape?: "arc" | "diagonal" | "line" | "dome" | ExprRef;
 
     /**
      * The orientation of the link path. Either `"vertical"` or `"horizontal"`.
@@ -341,7 +350,7 @@ export interface LinkProps extends SecondaryPositionProps {
      *
      * **Default value:** `"vertical"`
      */
-    orient?: "vertical" | "horizontal";
+    orient?: "vertical" | "horizontal" | ExprRef;
 
     /**
      * Whether the apex of the `"dome"` shape is clamped to the viewport edge. When over a
@@ -350,7 +359,7 @@ export interface LinkProps extends SecondaryPositionProps {
      *
      * **Default value:** `false`
      */
-    clampApex?: boolean;
+    clampApex?: boolean | ExprRef;
 
     /**
      * The number of segments in the bézier curve. Affects the rendering quality and performance.
@@ -365,14 +374,35 @@ export interface LinkProps extends SecondaryPositionProps {
      *
      * **Default value:** `1.0`
      */
-    arcHeightFactor?: number;
+    arcHeightFactor?: number | ExprRef;
 
     /**
      * The minimum height of an `"arc"` shape. Makes very short links more clearly visible.
      *
      * **Default value:** `1.5`
      */
-    minArcHeight?: number;
+    minArcHeight?: number | ExprRef;
+
+    /**
+     * The maximum length of `"arc"` shape's chord in pixels. The chord is the line segment
+     * between the two points that define the arc. Limiting the chord length serves two purposes
+     * when zooming in close enough:
+     * 1) it prevents the arc from becoming a straight line and
+     * 2) it mitigates the limited precision of floating point numbers in arc rendering.
+     *
+     * **Default value:** `50000`
+     */
+    maxChordLength?: number | ExprRef;
+
+    /**
+     * The range of the `"arc"` shape's fading distance in pixels. This property allows for
+     * making the arc's opacity fade out as it extends away from the chord. The fading distance
+     * is interpolated from one to zero between the interval defined by this property.
+     * Both `false` and `[0, 0]` disable fading.
+     *
+     * **Default value:** `false`
+     */
+    arcFadingDistance?: [number, number] | false | ExprRef;
 
     /**
      * The minimum stroke width of the links when pointing with the mouse cursor.
@@ -380,7 +410,7 @@ export interface LinkProps extends SecondaryPositionProps {
      *
      * **Default value:** `3.0`
      */
-    minPickingSize?: number;
+    minPickingSize?: number | ExprRef;
 }
 
 // TODO: Mark-specific configs

package/dist/src/spec/view.d.ts

@@ -7,6 +7,7 @@ import {
     PrimaryPositionalChannel,
 } from "./channel.js";
 import {
+    ExprRef,
     FillAndStrokeProps,
     MarkConfigAndType,
     MarkType,
@@ -43,7 +44,7 @@ export interface DynamicOpacity {
     values: number[];
 }
 
-export type ViewOpacityDef = number | DynamicOpacity;
+export type ViewOpacityDef = number | DynamicOpacity | ExprRef;
 
 export interface Step {
     step: number;

package/dist/src/types/viewContext.d.ts

@@ -11,6 +11,7 @@ import { Datum } from "../data/flowNode.js";
 import { ImportSpec, ViewSpec } from "../spec/view.js";
 import ContainerView from "./containerView.js";
 import { BroadcastEventType } from "../genomeSpy.js";
+import ParamBroker from "../paramBroker.js";
 
 export interface Hover {
     mark: Mark;
@@ -28,6 +29,7 @@ export default interface ViewContext {
     genomeStore?: GenomeStore;
     fontManager: BmFontManager;
 
+    paramBroker: ParamBroker;
     devicePixelRatio: number;
 
     requestLayoutReflow: () => void;

package/dist/src/utils/expression.d.ts

@@ -1,9 +1,19 @@
 /**
+ * @typedef { object } ExpressionProps
+ * @prop { string[] } fields
+ * @prop { string[] } globals
+ * @prop { string } code
+ *
+ * @typedef { ((x: object) => any) & ExpressionProps } ExpressionFunction
  *
  * @param {string} expr
+ * @returns {ExpressionFunction}
  */
-export default function createFunction(expr: string, globalObject?: {}): {
-    (x: object): any;
+export default function createFunction(expr: string, globalObject?: {}): ExpressionFunction;
+export type ExpressionProps = {
     fields: string[];
+    globals: string[];
+    code: string;
 };
+export type ExpressionFunction = ((x: object) => any) & ExpressionProps;
 //# sourceMappingURL=expression.d.ts.map

package/dist/src/utils/expression.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"expression.d.ts","sourceRoot":"","sources":["../../../src/utils/expression.js"],"names":[],"mappings":"AAEA;;;GAGG;AACH,6CAFW,MAAM;QAqBwB,MAAM;;EAO9C"}
+{"version":3,"file":"expression.d.ts","sourceRoot":"","sources":["../../../src/utils/expression.js"],"names":[],"mappings":"AAyDA;;;;;;;;;;GAUG;AACH,6CAHW,MAAM,sBACJ,kBAAkB,CAyB9B;;YAhCU,MAAM,EAAE;aACR,MAAM,EAAE;UACR,MAAM;;sCAEE,MAAM,KAAK,GAAG"}

package/dist/src/utils/expression.js

@@ -1,17 +1,72 @@
-import { parseExpression, codegenExpression } from "vega-expression";
+import { parseExpression, codegenExpression, functions } from "vega-expression";
+import {
+    isArray,
+    isBoolean,
+    isNumber,
+    isObject,
+    isRegExp,
+    isString,
+    lerp,
+} from "vega-util";
+import smoothstep from "./smoothstep.js";
+import clamp from "./clamp.js";
+import linearstep from "./linearstep.js";
 
 /**
+ * Some bits are adapted from https://github.com/vega/vega/blob/main/packages/vega-functions/src/codegen.js
+ */
+const functionContext = {
+    clamp,
+    isArray,
+    isBoolean,
+    isDefined(/** @type {any} */ _) {
+        return _ !== undefined;
+    },
+    isNumber,
+    isObject,
+    isRegExp,
+    isString,
+    isValid(/** @type {any} */ _) {
+        // eslint-disable-next-line no-self-compare
+        return _ != null && _ === _;
+    },
+    lerp,
+    linearstep,
+    smoothstep,
+};
+
+/**
+ * @param {typeof codegenExpression} codegen
+ */
+function buildFunctions(codegen) {
+    const fn = functions(codegen);
+    // eslint-disable-next-line guard-for-in
+    for (const name in functionContext) {
+        fn[name] = `this.${name}`;
+    }
+    return fn;
+}
+
+const cg = codegenExpression({
+    forbidden: [],
+    allowed: ["datum"],
+    globalvar: "globalObject",
+    fieldvar: "datum",
+    functions: buildFunctions,
+});
+
+/**
+ * @typedef { object } ExpressionProps
+ * @prop { string[] } fields
+ * @prop { string[] } globals
+ * @prop { string } code
+ *
+ * @typedef { ((x: object) => any) & ExpressionProps } ExpressionFunction
  *
  * @param {string} expr
+ * @returns {ExpressionFunction}
  */
 export default function createFunction(expr, globalObject = {}) {
-    const cg = codegenExpression({
-        forbidden: [],
-        allowed: ["datum"],
-        globalvar: "globalObject",
-        fieldvar: "datum",
-    });
-
     try {
         const parsed = parseExpression(expr);
         const generatedCode = cg(parsed);
@@ -21,11 +76,15 @@ export default function createFunction(expr, globalObject = {}) {
             "datum",
             "globalObject",
             `"use strict"; return (${generatedCode.code});`
-        );
+        ).bind(functionContext);
 
+        /** @type { ExpressionFunction } */
         const exprFunction = /** @param {object} x */ (x) =>
             fn(x, globalObject);
         exprFunction.fields = generatedCode.fields;
+        exprFunction.globals = generatedCode.globals;
+        exprFunction.code = generatedCode.code;
+
         return exprFunction;
     } catch (e) {
         throw new Error(`Invalid expression: ${expr}, ${e.message}`);

package/dist/src/utils/linearstep.d.ts

@@ -0,0 +1,7 @@
+/**
+ * @param {number} edge0
+ * @param {number} edge1
+ * @param {number} x
+ */
+export default function linearstep(edge0: number, edge1: number, x: number): number;
+//# sourceMappingURL=linearstep.d.ts.map

package/dist/src/utils/linearstep.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"linearstep.d.ts","sourceRoot":"","sources":["../../../src/utils/linearstep.js"],"names":[],"mappings":"AAEA;;;;GAIG;AACH,0CAJW,MAAM,SACN,MAAM,KACN,MAAM,UAIhB"}

package/dist/src/utils/linearstep.js

@@ -0,0 +1,10 @@
+import clamp from "./clamp.js";
+
+/**
+ * @param {number} edge0
+ * @param {number} edge1
+ * @param {number} x
+ */
+export default function linearstep(edge0, edge1, x) {
+    return clamp((x - edge0) / (edge1 - edge0), 0.0, 1.0);
+}

package/dist/src/view/view.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"view.d.ts","sourceRoot":"","sources":["../../../src/view/view.js"],"names":[],"mappings":"AAyBA,oBAAoB;AACpB,sCAAuC;AACvC,0BAA0B;AAC1B,sCAAuC;AAKvC;;;;;;;;;;;;;;;;;;;;;;;;;;;GA2BG;AACH;IAeI;;;;;;;;;OASG;IACH,kBARW,OAAO,iBAAiB,EAAE,QAAQ,WAClC,OAAO,yBAAyB,EAAE,OAAO,gBACzC,OAAO,oBAAoB,EAAE,OAAO,cACpC,OAAO,WAAW,EAAE,OAAO,QAC3B,MAAM,YACN,WAAW,EAwCrB;IApDD;;OAEG;IACH,wBAFmB,MAAM,KAAE,MAAM,CAEQ;IAiBrC,mDAAsB;IACtB,mDAAgC;IAChC,iBAA4B;IAC5B,aAA6B;IAC7B,yCAAgB;IAEhB;QACI;;;WAGG;eADO,QAAQ,OAAO,OAAO,oBAAoB,EAAE,gBAAgB,EAAE,OAAO,sBAAsB,EAAE,OAAO,CAAC,CAAC;QAGhH;;;WAGG;cADO,QAAQ,OAAO,OAAO,oBAAoB,EAAE,wBAAwB,EAAE,OAAO,qBAAqB,EAAE,OAAO,CAAC,CAAC;MAG1H;IAID;;;;kCAxDE,OAAO;;;;kCAEP,OAAO;MA0DR;IAED;;;OAGG;IACH,WAFU,OAAO,OAAO,oBAAoB,EAAE,wBAAwB,EAAE,OAAO,CAAC,CAEzC;IAG3C,sBAIC;IAED;;;;OAIG;IACH,eAFa,OAAO,CAInB;IAED;;;;;OAKG;IACH,gBAFa,OAAO,CAMnB;IAED;;;;;OAKG;IACH,WAFa,cAAc,CAW1B;IAED;;OAEG;IACH,mBAFa,cAAc,CAkB1B;IAoED,+BAEC;IAED,2BAEC;IAED;;;;;;;;OAQG;IACH,aAFa,OAAO,CAMnB;IAED;;;;;;;OAOG;IACH,uBAFa,MAAM,CAMlB;IAED,wBAKC;IAkBD;;OAEG;IACH,6BAEC;IAED;;OAEG;IACH,2BAEC;IAED;;;;OAIG;IACH,yBAFW,gBAAgB,QAO1B;IAED;;;;OAIG;IACH,2BAHW,MAAM,kBACG,gBAAgB,KAAE,IAAI,QASzC;IAED;;;;;;;OAOG;IACH,+BALW,OAAO,uBAAuB,EAAE,OAAO,SAEvC,OAAO,8BAA8B,EAAE,OAAO,aAC9C,OAAO,QASjB;IAED;;;;;;;;;;OAUG;IACH,kCAJW,MAAM,YACN,wBAAwB,eACxB,OAAO,QAajB;IAED;;;;;;;OAOG;IACH,eAJW,OAAO,GACL,WAAW,CAmBvB;IAED;;OAEG;IACH,yBAOC;IAED;;OAEG;IACH,6BASC;IAED;;;OAGG;IACH,uBAEC;IA7ZyB,yJAIN;IAqapB;;;;;;OAMG;IACH,eAFY,OAAO,oBAAoB,EAAE,QAAQ,CAuBhD;IAED;;;;OAIG;IACH,+BAJW,IAAI,UAEM,MAAM,KAAE,GAAG,CAM/B;IAED;;;;;OAKG;IACH,6BAHW,IAAI,GACF,MAAM,EAAE,CASpB;IAED;;;;;;;;;;;;;;;OAeG;IACH,yBAFY,YAAY,CAIvB;IAED;;OAEG;IACH,4BAFW,OAAO,oBAAoB,EAAE,gBAAgB,0CAWvD;IAED;;OAEG;IACH,2BAFW,OAAO,oBAAoB,EAAE,iBAAiB,yCAWxD;IAED;;;;OAIG;IACH,iCAJW,OAAO,oBAAoB,EAAE,OAAO,GAAG,SAAS,kBAChD,OAAO,iBAAiB,EAAE,gBAAgB,GACxC,OAAO,iBAAiB,EAAE,kBAAkB,CAIxD;IAED;;;;OAIG;IACH,0CAJW,OAAO,oBAAoB,EAAE,OAAO,kBACpC,OAAO,iBAAiB,EAAE,gBAAgB,GACxC,OAAO,iBAAiB,EAAE,kBAAkB,CAQxD;IAED;;;;OAIG;IACH,8BAJW,OAAO,oBAAoB,EAAE,OAAO,kBACpC,OAAO,iBAAiB,EAAE,gBAAgB,GACxC,OAAO,iBAAiB,EAAE,kBAAkB,CAIxD;IAED;;OAEG;IACH,cAFa,MAAM,CAOlB;IAED;;OAEG;IACH,8BAEC;IAED,uBAKC;IAED;;;;;;OAMG;IACH,yBANW,GAAG,wCAQb;IAED;;;;OAIG;IACH,8BAHW,MAAM,cACN,MAAM,GAAG,SAAS,GAAG,WAAW,QAiB1C;IAED,4BAEC;IAED;;;;;OAKG;IACH,iCAFW,OAAO,8BAA8B,EAAE,OAAO,QAIxD;;CACJ;AAqEM,iCAHI,GAAG,0CAGkC;0BAnsBnC,8BAAsB,IAAI;qCAG5B,IAAI,KACF,WAAW;sBAEX,eAAe,GAAG;IAC9B,SAAgB,CAAC,SAAW,IAAI,KAAE,IAAI,CAAC;IACvC,cAAqB,CAAC,SAAW,IAAI,KAAE,IAAI,CAAC;IAC5C,aAAoB,CAAC,SAAW,IAAI,KAAE,IAAI,CAAA;CAAC;;;;;UAIlC,OAAO,iBAAiB,EAAE,kBAAkB;;;;cAC5C,GAAG;;gDAGF,OAAO,uBAAuB,EAAE,OAAO,SAEvC,OAAO,8BAA8B,EAAE,OAAO;;;;;+BAG/C,OAAO;;;;+BAEP,OAAO;;oBArDG,qBAAqB;+BADlC,wBAAwB"}

package/dist/src/view/view.js

@@ -16,6 +16,7 @@ import { appendToBaseUrl } from "../utils/url.js";
 import { isDiscrete, bandSpace } from "vega-scale";
 import { peek } from "../utils/arrayUtils.js";
 import ViewError from "./viewError.js";
+import { isExprRef } from "../marks/mark.js";
 
 // TODO: View classes have too many responsibilities. Come up with a way
 // to separate the concerns. However, most concerns are tightly tied to
@@ -723,6 +724,11 @@ function createViewOpacityFunction(view) {
 
                 return interpolate(unitsPerPixel) * parentOpacity;
             };
+        } else if (isExprRef(opacityDef)) {
+            const fn = view.context.paramBroker.createExpression(
+                opacityDef.expr
+            );
+            return (parentOpacity) => fn(null) * parentOpacity;
         }
     }
     return (parentOpacity) => parentOpacity;

package/package.json

@@ -7,7 +7,7 @@
   },
   "contributors": [],
   "license": "MIT",
-  "version": "0.39.0",
+  "version": "0.41.0",
   "jsdelivr": "dist/bundle/index.js",
   "unpkg": "dist/bundle/index.js",
   "browser": "dist/bundle/index.js",
@@ -65,5 +65,5 @@
     "vega-scale": "^7.1.1",
     "vega-util": "^1.16.0"
   },
-  "gitHead": "62718f51e03f665435dd2f3b557e20b42df1410e"
+  "gitHead": "b9e91be6b770d888429a3dc970c6468f776c76d4"
 }