@genome-spy/core 0.48.2 → 0.50.0

package/dist/src/marks/link.js

@@ -10,6 +10,9 @@ import { isChannelDefWithScale } from "../encoder/encoder.js";
 const LINK_SHAPES = ["arc", "dome", "diagonal", "line"];
 const ORIENTS = ["vertical", "horizontal"];
 
+/**
+ * @extends {Mark<import("../spec/mark.js").LinkProps>}
+ */
 export default class LinkMark extends Mark {
     /**
      * @param {import("../view/unitView.js").default} unitView
@@ -17,29 +20,27 @@ export default class LinkMark extends Mark {
     constructor(unitView) {
         super(unitView);
 
-        Object.defineProperties(
-            this.defaultProperties,
-            Object.getOwnPropertyDescriptors({
-                x: 0.0,
-                x2: undefined,
-                y: 0.0,
-                y2: undefined,
-                size: 1.0,
-                color: "black",
-                opacity: 1.0,
-
-                segments: 101, // Performance is affected more by the fill rate, i.e. number of pixels
-                arcHeightFactor: 1.0,
-                minArcHeight: 1.5,
-                minPickingSize: 3.0,
-                clampApex: false,
-                maxChordLength: 50000,
-                arcFadingDistance: false,
-
-                linkShape: "arc",
-                orient: "vertical",
-            })
-        );
+        this.augmentDefaultProperties({
+            x: 0.0,
+            x2: undefined,
+            y: 0.0,
+            y2: undefined,
+            size: 1.0,
+            color: "black",
+            opacity: 1.0,
+
+            segments: 101, // Performance is affected more by the fill rate, i.e. number of pixels
+            arcHeightFactor: 1.0,
+            minArcHeight: 1.5,
+            minPickingSize: 3.0,
+            clampApex: false,
+            maxChordLength: 50000,
+            arcFadingDistance: false,
+            noFadingOnPointSelection: true,
+
+            linkShape: "arc",
+            orient: "vertical",
+        });
 
         /**
          * Only available if "WebGL Draft Extensions" is enabled in chrome://flags
@@ -52,6 +53,9 @@ export default class LinkMark extends Mark {
         );
     }
 
+    /**
+     * @returns {import("../spec/channel.js").Channel[]}
+     */
     getAttributes() {
         return [
             "uniqueId",
@@ -61,7 +65,6 @@ export default class LinkMark extends Mark {
             "y",
             "y2",
             "size",
-            "height",
             "color",
             "opacity",
         ];
@@ -136,12 +139,21 @@ export default class LinkMark extends Mark {
         this.registerMarkUniformValue(
             "uSegmentBreaks",
             props.segments,
-            (x) => x + 1
+            (x) => x
+        );
+        this.registerMarkUniformValue(
+            "uNoFadingOnPointSelection",
+            props.noFadingOnPointSelection,
+            (x) => !!x
         );
     }
 
     updateGraphicsData() {
         const collector = this.unitView.getCollector();
+        if (!collector) {
+            console.debug("No collector");
+            return;
+        }
         const itemCount = collector.getItemCount();
 
         const builder = new LinkVertexBuilder({
@@ -195,6 +207,14 @@ export default class LinkMark extends Mark {
     render(options) {
         const gl = this.gl;
 
+        const getInstanceVertexCount = () => {
+            const breaks = /** @type {Float32Array} */ (
+                this.markUniformInfo.uniforms.uSegmentBreaks
+            )[0];
+
+            return (breaks + 1) * 2;
+        };
+
         return this._baseInstanceExt
             ? this.createRenderCallback((offset, count) => {
                   // Using the following extension, which, however, is only a draft and
@@ -204,9 +224,7 @@ export default class LinkMark extends Mark {
                   this._baseInstanceExt.drawArraysInstancedBaseInstanceWEBGL(
                       gl.TRIANGLE_STRIP,
                       0,
-                      /** @type {Float32Array} */ (
-                          this.markUniformInfo.uniforms.uSegmentBreaks
-                      )[0] * 2,
+                      getInstanceVertexCount(),
                       count,
                       offset
                   );
@@ -242,9 +260,7 @@ export default class LinkMark extends Mark {
                   gl.drawArraysInstanced(
                       gl.TRIANGLE_STRIP,
                       0,
-                      /** @type {Float32Array} */ (
-                          this.markUniformInfo.uniforms.uSegmentBreaks
-                      )[0] * 2,
+                      getInstanceVertexCount(),
                       count
                   );
               }, options);

package/dist/src/marks/link.vertex.glsl.js

@@ -1,2 +1,2 @@
-const shader = "out vec4 vColor;out float vSize;out float vNormalLengthInPixels;const int SHAPE_ARC=0;const int SHAPE_DOME=1;const int SHAPE_DIAGONAL=2;const int SHAPE_LINE=3;const int ORIENT_VERTICAL=0;const int ORIENT_HORIZONTAL=1;float distanceFromLine(vec2 pointOnLine1,vec2 pointOnLine2,vec2 point){vec2 a=point-pointOnLine1;vec2 b=pointOnLine2-pointOnLine1;vec2 proj=dot(a,b)/dot(b,b)*b;return length(a-proj);}bool isInsideViewport(vec2 point,float marginFactor){vec2 margin=uViewportSize*vec2(marginFactor);return point.x>=-margin.x&&point.x<=uViewportSize.x+margin.x&&point.y>=-margin.y&&point.y<=uViewportSize.y+margin.y;}void main(void){float pixelSize=1.0/uDevicePixelRatio;float opacity=getScaled_opacity()*uViewOpacity;vec2 p1,p2,p3,p4;vec2 a=applySampleFacet(vec2(getScaled_x(),getScaled_y()))*uViewportSize;vec2 b=applySampleFacet(vec2(getScaled_x2(),getScaled_y2()))*uViewportSize;if(uShape<=SHAPE_DOME){if(uShape==SHAPE_DOME){vec2 height=vec2(0.0);if(uOrient==ORIENT_VERTICAL){p1=vec2(min(a.x,b.x),b.y);p4=vec2(max(a.x,b.x),b.y);height=vec2(0.0,a.y-b.y);if(uClampApex){if(p4.x>0.0){p1.x=max(p1.x,-p4.x);}if(p1.x<uViewportSize.x){p4.x=min(p4.x,2.0*uViewportSize.x-p1.x);}}}else{p1=vec2(b.x,min(a.y,b.y));p4=vec2(b.x,max(a.y,b.y));height=vec2(a.x-b.x,0.0);if(uClampApex){if(p4.y>0.0){p1.y=max(p1.y,-p4.y);}if(p1.y<uViewportSize.y){p4.y=min(p4.y,2.0*uViewportSize.y-p1.y);}}}vec2 controlOffset=height/0.75;p2=p1+controlOffset;p3=p4+controlOffset;}if(uShape==SHAPE_ARC){p1=a;p4=b;vec2 chordVector=p4-p1;vec2 unitChordVector=normalize(chordVector);vec2 chordNormal=vec2(-unitChordVector.y,unitChordVector.x);float chordLength=length(chordVector);if(chordLength>uMaxChordLength){if(isInsideViewport(p1,2.0)){chordLength=uMaxChordLength;p4=p1+unitChordVector*uMaxChordLength;}else if(isInsideViewport(p4,2.0)){chordLength=uMaxChordLength;p1=p4-unitChordVector*uMaxChordLength;}}float height=max(chordLength/2.0*uArcHeightFactor,uMinArcHeight);vec2 controlOffset=chordNormal*height/0.75;p2=p1+controlOffset;p3=p4+controlOffset;}}else if(uShape==SHAPE_DIAGONAL){if(uOrient==ORIENT_VERTICAL){p1=a;p2=vec2(a.x,(a.y+b.y)/2.0);p3=vec2(b.x,(a.y+b.y)/2.0);p4=b;}else{p1=a;p2=vec2((a.x+b.x)/2.0,a.y);p3=vec2((a.x+b.x)/2.0,b.y);p4=b;}}else if(uShape==SHAPE_LINE){p1=a;p2=(a+b)/2.0;p3=p2;p4=b;}vec2 strip=vec2(float(gl_VertexID/2)/float(uSegmentBreaks),float(gl_VertexID % 2)-0.5);float t=smoothstep(0.0,1.0,strip.x);vec2 C1=p4-3.0*p3+3.0*p2-p1;vec2 C2=3.0*p3-6.0*p2+3.0*p1;vec2 C3=3.0*p2-3.0*p1;vec2 C4=p1;vec2 p;if(t==0.0){p=p1;}else if(t==1.0){p=p4;}else{p=C1*t*t*t+C2*t*t+C3*t+C4;}vec2 tangent=normalize(3.0*C1*t*t+2.0*C2*t+C3);vec2 normal=vec2(-tangent.y,tangent.x);float size=getScaled_size();if(size<pixelSize){opacity*=size/pixelSize;size=pixelSize;}float paddedSize=uPickingEnabled? max(size,uMinPickingSize): size+pixelSize;vNormalLengthInPixels=strip.y*paddedSize;if(uShape==SHAPE_ARC&&uArcFadingDistance[0]>0.0&&uArcFadingDistance[1]>0.0){float d=distanceFromLine(p1,p4,p);float distanceOpacity=smoothstep(uArcFadingDistance[1],uArcFadingDistance[0],d);opacity*=distanceOpacity;if(distanceOpacity<=0.0){vNormalLengthInPixels=0.0;}}p+=normal*vNormalLengthInPixels;gl_Position=pixelsToNdc(p);vec3 color=getScaled_color();vColor=vec4(color*opacity,opacity);vSize=paddedSize;setupPicking();}";
+const shader = "out vec4 vColor;out float vSize;out float vNormalLengthInPixels;out float vGamma;const int SHAPE_ARC=0;const int SHAPE_DOME=1;const int SHAPE_DIAGONAL=2;const int SHAPE_LINE=3;const int ORIENT_VERTICAL=0;const int ORIENT_HORIZONTAL=1;float distanceFromLine(vec2 pointOnLine1,vec2 pointOnLine2,vec2 point){vec2 a=point-pointOnLine1;vec2 b=pointOnLine2-pointOnLine1;vec2 proj=dot(a,b)/dot(b,b)*b;return length(a-proj);}bool isInsideViewport(vec2 point,float marginFactor){vec2 margin=uViewportSize*vec2(marginFactor);return point.x>=-margin.x&&point.x<=uViewportSize.x+margin.x&&point.y>=-margin.y&&point.y<=uViewportSize.y+margin.y;}void main(void){float pixelSize=1.0/uDevicePixelRatio;float opacity=getScaled_opacity()*uViewOpacity;vec2 p1,p2,p3,p4;vec2 a=applySampleFacet(vec2(getScaled_x(),getScaled_y()))*uViewportSize;vec2 b=applySampleFacet(vec2(getScaled_x2(),getScaled_y2()))*uViewportSize;if(uShape<=SHAPE_DOME){if(uShape==SHAPE_DOME){vec2 height=vec2(0.0);if(uOrient==ORIENT_VERTICAL){p1=vec2(min(a.x,b.x),b.y);p4=vec2(max(a.x,b.x),b.y);height=vec2(0.0,a.y-b.y);if(uClampApex){if(p4.x>0.0){p1.x=max(p1.x,-p4.x);}if(p1.x<uViewportSize.x){p4.x=min(p4.x,2.0*uViewportSize.x-p1.x);}}}else{p1=vec2(b.x,min(a.y,b.y));p4=vec2(b.x,max(a.y,b.y));height=vec2(a.x-b.x,0.0);if(uClampApex){if(p4.y>0.0){p1.y=max(p1.y,-p4.y);}if(p1.y<uViewportSize.y){p4.y=min(p4.y,2.0*uViewportSize.y-p1.y);}}}vec2 controlOffset=height/0.75;p2=p1+controlOffset;p3=p4+controlOffset;}if(uShape==SHAPE_ARC){p1=a;p4=b;vec2 chordVector=p4-p1;vec2 unitChordVector=normalize(chordVector);vec2 chordNormal=vec2(-unitChordVector.y,unitChordVector.x);float chordLength=length(chordVector);if(chordLength>uMaxChordLength){if(isInsideViewport(p1,2.0)){chordLength=uMaxChordLength;p4=p1+unitChordVector*uMaxChordLength;}else if(isInsideViewport(p4,2.0)){chordLength=uMaxChordLength;p1=p4-unitChordVector*uMaxChordLength;}}float height=max(chordLength/2.0*uArcHeightFactor,uMinArcHeight);vec2 controlOffset=chordNormal*height/0.75;p2=p1+controlOffset;p3=p4+controlOffset;}}else if(uShape==SHAPE_DIAGONAL){if(uOrient==ORIENT_VERTICAL){p1=a;p2=vec2(a.x,(a.y+b.y)/2.0);p3=vec2(b.x,(a.y+b.y)/2.0);p4=b;}else{p1=a;p2=vec2((a.x+b.x)/2.0,a.y);p3=vec2((a.x+b.x)/2.0,b.y);p4=b;}}else if(uShape==SHAPE_LINE){p1=a;p2=(a+b)/2.0;p3=p2;p4=b;}vec2 strip=vec2(float(gl_VertexID/2)/float(uSegmentBreaks),float(gl_VertexID % 2)-0.5);float t=smoothstep(0.0,1.0,strip.x);vec2 C1=p4-3.0*p3+3.0*p2-p1;vec2 C2=3.0*p3-6.0*p2+3.0*p1;vec2 C3=3.0*p2-3.0*p1;vec2 C4=p1;vec2 p;if(t==0.0){p=p1;}else if(t==1.0){p=p4;}else{p=C1*t*t*t+C2*t*t+C3*t+C4;}vec2 tangent=normalize(3.0*C1*t*t+2.0*C2*t+C3);vec2 normal=vec2(-tangent.y,tangent.x);float size=getScaled_size();if(size<pixelSize){opacity*=size/pixelSize;size=pixelSize;}float paddedSize=uPickingEnabled? max(size,uMinPickingSize): size+pixelSize;vNormalLengthInPixels=strip.y*paddedSize;if(uShape==SHAPE_ARC&&uArcFadingDistance[0]>0.0&&uArcFadingDistance[1]>0.0&&(!uNoFadingOnPointSelection||!isPointSelected())){float d=distanceFromLine(p1,p4,p);float distanceOpacity=smoothstep(uArcFadingDistance[1],uArcFadingDistance[0],d);opacity*=distanceOpacity;if(distanceOpacity<=0.0){vNormalLengthInPixels=0.0;}}p+=normal*vNormalLengthInPixels;gl_Position=pixelsToNdc(p);vec3 color=getScaled_color();vColor=vec4(color*opacity,opacity);vGamma=getGammaForColor(color);vSize=paddedSize;setupPicking();}";
 export default shader;

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

@@ -12,16 +12,18 @@ export const SAMPLE_FACET_TEXTURE: "SAMPLE_FACET_TEXTURE";
  * @callback DrawFunction
  * @param {number} offset
  * @param {number} count
- *
  */
-export default class Mark {
+/**
+ * @template {MarkProps} [P=MarkProps]
+ */
+export default class Mark<P extends import("../spec/mark.js").MarkProps = import("../spec/mark.js").MarkProps> {
     /**
      * @param {import("../view/unitView.js").default} unitView
      */
     constructor(unitView: import("../view/unitView.js").default);
     unitView: import("../view/unitView.js").default;
-    /** @type {Record<string, import("../types/encoder.js").Encoder>} */
-    encoders: Record<string, import("../types/encoder.js").Encoder>;
+    /** @type {Partial<Record<Channel, import("../types/encoder.js").Encoder>>} */
+    encoders: Partial<Record<import("../spec/channel.js").Channel, import("../types/encoder.js").Encoder>>;
     /**
      * @type {import("twgl.js").BufferInfo & { allocatedVertices?: number }}
      * @protected
@@ -69,28 +71,28 @@ export default class Mark {
     protected markUniformsAltered: boolean;
     /** @type {RangeMap<any>} keep track of facet locations within the vertex array */
     rangeMap: RangeMap<any>;
-    /** @type {MarkProps} */
-    defaultProperties: import("../spec/mark.js").MarkProps;
+    defaultProperties: P;
     /**
      * A properties object that contains the configured mark properties or
      * default values as fallback.
      *
-     * TODO: Proper and comprehensive typings for mark properties
-     *
-     * @type {Partial<MarkProps>}
+     * @type {P}
      * @readonly
      */
-    readonly properties: Partial<import("../spec/mark.js").MarkProps>;
+    readonly properties: P;
+    /**
+     * @param {Partial<P>} props
+     * @protected
+     */
+    protected augmentDefaultProperties(props: Partial<P>): void;
     get opaque(): boolean;
     /**
      * Returns attribute info for WebGL attributes that match visual channels.
      *
-     * Note: attributes and channels do not necessarily match.
-     * For example, rectangles have x, y, x2, and y2 channels but only x and y as attributes.
-     *
-     * @returns {string[]}
+     * @returns {import("../spec/channel.js").Channel[]}
+     * @protected
      */
-    getAttributes(): string[];
+    protected getAttributes(): import("../spec/channel.js").Channel[];
     /**
      * @returns {Channel[]}
      */
@@ -98,30 +100,30 @@ export default class Mark {
     /**
      * @returns {Encoding}
      */
-    getDefaultEncoding(): import("../spec/channel.js").Encoding<string>;
+    getDefaultEncoding(): import("../spec/channel.js").Encoding;
     /**
      * Adds intelligent defaults etc to the encoding.
      *
      * @param {Encoding} encoding
      * @returns {Encoding}
      */
-    fixEncoding(encoding: import("../spec/channel.js").Encoding<string>): import("../spec/channel.js").Encoding<string>;
+    fixEncoding(encoding: import("../spec/channel.js").Encoding): import("../spec/channel.js").Encoding;
     /**
      * Handles dynamic properties that are not bound to uniforms but need
      * to trigger a graphics update, i.e., rebuild the vertex buffer.
      *
-     * @param {(keyof MarkProps)[]} props
+     * @param {(keyof P)[]} props
      * @protected
      */
-    protected setupExprRefsNeedingGraphicsUpdate(props: (keyof import("../spec/mark.js").MarkProps)[]): void;
+    protected setupExprRefsNeedingGraphicsUpdate(props: (keyof P)[]): void;
     /**
      * Returns the encoding spec supplemented with mark's default encodings
      *
      * @returns {Encoding}
      */
-    get encoding(): import("../spec/channel.js").Encoding<string>;
+    get encoding(): import("../spec/channel.js").Encoding;
     getContext(): import("../types/viewContext.js").default;
-    getType(): import("../spec/mark.js").MarkType;
+    getType(): "link" | "rect" | "text" | "point" | "rule";
     initializeData(): void;
     /**
      * Initialize encoders that encode fields of the data (or constants) to
@@ -136,7 +138,7 @@ export default class Mark {
      * Update WebGL buffers from the data
      */
     updateGraphicsData(): void;
-    getSampleFacetMode(): "SAMPLE_FACET_TEXTURE" | "SAMPLE_FACET_UNIFORM";
+    getSampleFacetMode(): "SAMPLE_FACET_UNIFORM" | "SAMPLE_FACET_TEXTURE";
     /**
      *
      * @param {string} vertexShader
@@ -198,9 +200,6 @@ export default class Mark {
     isReady(): import("twgl.js").ProgramInfo;
     /**
      * Returns true if this mark instance participates in picking.
-     *
-     * TODO: Check if tooltip is enabled,
-     * TODO: Check if selection (when it's implemented) is enabled
      */
     isPickingParticipant(): boolean;
     /**

package/dist/src/marks/mark.d.ts.map

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