@genome-spy/core 0.39.0 → 0.40.0

package/dist/schema.json

@@ -2457,6 +2457,23 @@
           "description": "The rotation angle in degrees.\n\n**Default value:** `0`",
           "type": "number"
         },
+        "arcFadingDistance": {
+          "anyOf": [
+            {
+              "items": {
+                "type": "number"
+              },
+              "maxItems": 2,
+              "minItems": 2,
+              "type": "array"
+            },
+            {
+              "const": false,
+              "type": "boolean"
+            }
+          ],
+          "description": "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.\n\n**Default value:** `false`"
+        },
         "arcHeightFactor": {
           "description": "Scaling factor for the `\"arc`\" shape's height. The default value `1.0` produces roughly circular arcs.\n\n**Default value:** `1.0`",
           "type": "number"
@@ -2578,6 +2595,10 @@
           "description": "Stretch letters so that they can be used with [sequence logos](https://en.wikipedia.org/wiki/Sequence_logo), etc...",
           "type": "boolean"
         },
+        "maxChordLength": {
+          "description": "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.\n\n**Default value:** `50000`",
+          "type": "number"
+        },
         "minArcHeight": {
           "description": "The minimum height of an `\"arc\"` shape. Makes very short links more clearly visible.\n\n**Default value:** `1.5`",
           "type": "number"

package/dist/src/gl/includes/scales.glsl.js

@@ -1,2 +1,2 @@
-const shader = "const float inf=1.0/0.0;vec3 getDiscreteColor(sampler2D s,int index){return texelFetch(s,ivec2(index % textureSize(s,0).x,0),0).rgb;}vec3 getInterpolatedColor(sampler2D s,float unitValue){return texture(s,vec2(unitValue,0.0)).rgb;}float clampToRange(float value,vec2 range){return clamp(value,min(range[0],range[1]),max(range[0],range[1]));}float scaleIdentity(float value){return value;}float scaleLinear(float value,vec2 domain,vec2 range){float domainSpan=domain[1]-domain[0];float rangeSpan=range[1]-range[0];return(value-domain[0])/domainSpan*rangeSpan+range[0];}float scaleLog(float value,vec2 domain,vec2 range,float base){return scaleLinear(log(value)/log(base),log(domain)/log(base),range);}float symlog(float value,float constant){return sign(value)*log(abs(value/constant)+1.0);}float scaleSymlog(float value,vec2 domain,vec2 range,float constant){return scaleLinear(symlog(value,constant),vec2(symlog(domain[0],constant),symlog(domain[1],constant)),range);}float scalePow(float value,vec2 domain,vec2 range,float exponent){return scaleLinear(pow(abs(value),exponent)*sign(value),pow(abs(domain),vec2(exponent))*sign(domain),range);}float scaleBand(float value,vec2 domainExtent,vec2 range,float paddingInner,float paddingOuter,float align,float band){float start=range[0];float stop=range[1];float rangeSpan=stop-start;float n=domainExtent[1]-domainExtent[0];paddingInner=int(n)>1 ? paddingInner : 0.0;float step=rangeSpan/max(1.0,n-paddingInner+paddingOuter*2.0);start+=(rangeSpan-step*(n-paddingInner))*align;float bandwidth=step*(1.0-paddingInner);return start+(value-domainExtent[0])*step+bandwidth*band;}float scaleBandHp(vec2 value,vec3 domainExtent,vec2 range,float paddingInner,float paddingOuter,float align,float band){float start=range[0];float stop=range[1];float rangeSpan=stop-start;vec2 domainStart=domainExtent.xy;float n=domainExtent[2];float step=rangeSpan/max(1.0,n-paddingInner+paddingOuter*2.0);start+=(rangeSpan-step*(n-paddingInner))*align;float bandwidth=step*(1.0-paddingInner);float hi=max(value[0]-domainStart[0],-inf);float lo=max(value[1]-domainStart[1],-inf);return dot(vec4(start,hi,lo,bandwidth),vec4(1.0,step,step,band));}";
+const shader = "uniform highp float uZero;vec3 getDiscreteColor(sampler2D s,int index){return texelFetch(s,ivec2(index % textureSize(s,0).x,0),0).rgb;}vec3 getInterpolatedColor(sampler2D s,float unitValue){return texture(s,vec2(unitValue,0.0)).rgb;}float clampToRange(float value,vec2 range){return clamp(value,min(range[0],range[1]),max(range[0],range[1]));}float scaleIdentity(float value){return value;}float scaleLinear(float value,vec2 domain,vec2 range){float domainSpan=domain[1]-domain[0];float rangeSpan=range[1]-range[0];return(value-domain[0])/domainSpan*rangeSpan+range[0];}float scaleLog(float value,vec2 domain,vec2 range,float base){return scaleLinear(log(value)/log(base),log(domain)/log(base),range);}float symlog(float value,float constant){return sign(value)*log(abs(value/constant)+1.0);}float scaleSymlog(float value,vec2 domain,vec2 range,float constant){return scaleLinear(symlog(value,constant),vec2(symlog(domain[0],constant),symlog(domain[1],constant)),range);}float scalePow(float value,vec2 domain,vec2 range,float exponent){return scaleLinear(pow(abs(value),exponent)*sign(value),pow(abs(domain),vec2(exponent))*sign(domain),range);}float scaleBand(float value,vec2 domainExtent,vec2 range,float paddingInner,float paddingOuter,float align,float band){float start=range[0];float stop=range[1];float rangeSpan=stop-start;float n=domainExtent[1]-domainExtent[0];paddingInner=int(n)>1 ? paddingInner : 0.0;float step=rangeSpan/max(1.0,n-paddingInner+paddingOuter*2.0);start+=(rangeSpan-step*(n-paddingInner))*align;float bandwidth=step*(1.0-paddingInner);return start+(value-domainExtent[0])*step+bandwidth*band;}float scaleBandHp(vec2 value,vec3 domainExtent,vec2 range,float paddingInner,float paddingOuter,float align,float band){float start=range[0];float stop=range[1];float rangeSpan=stop-start;vec2 domainStart=domainExtent.xy;float n=domainExtent[2];float step=rangeSpan/max(1.0,n-paddingInner+paddingOuter*2.0);start+=(rangeSpan-step*(n-paddingInner))*align;float bandwidth=step*(1.0-paddingInner);float inf=1.0/uZero;float hi=max(value[0]-domainStart[0],-inf);float lo=max(value[1]-domainStart[1],-inf);return dot(vec4(start,hi,lo,bandwidth),vec4(1.0,step,step,band));}";
 export default shader;

package/dist/src/gl/link.fragment.glsl.js

@@ -1,2 +1,2 @@
-const shader = "in lowp vec4 vColor;in float vSize;in float vNormalLengthInPixels;out lowp vec4 fragColor;void main(void){float dpr=uDevicePixelRatio;float distance=abs(vNormalLengthInPixels);float opacity=clamp(((vSize/2.0-distance)*dpr),0.0,1.0);fragColor=vColor*opacity;if(uPickingEnabled){fragColor=vPickingColor;}}";
+const shader = "in vec4 vColor;in float vSize;in float vNormalLengthInPixels;out lowp vec4 fragColor;void main(void){float dpr=uDevicePixelRatio;float distance=abs(vNormalLengthInPixels);float opacity=clamp(((vSize/2.0-distance)*dpr),0.0,1.0);fragColor=vColor*opacity;if(uPickingEnabled){fragColor=vPickingColor;}}";
 export default shader;

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

@@ -1,2 +1,2 @@
-const shader = "uniform float uArcHeightFactor;uniform float uMinArcHeight;uniform float uMinPickingSize;uniform int uShape;uniform int uOrient;uniform bool uClampApex;in vec2 strip;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;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 height=max(length(chordVector)/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;}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;p+=normal*vNormalLengthInPixels;gl_Position=pixelsToNdc(p);vec3 color=getScaled_color();vColor=vec4(color*opacity,opacity);vSize=paddedSize;setupPicking();}";
+const shader = "uniform float uArcHeightFactor;uniform float uMinArcHeight;uniform float uMinPickingSize;uniform int uShape;uniform int uOrient;uniform bool uClampApex;uniform float uMaxChordLength;uniform vec2 uArcFadingDistance;in vec2 strip;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;}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();}";
 export default shader;

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

@@ -1 +1 @@
-{"version":3,"file":"link.d.ts","sourceRoot":"","sources":["../../../src/marks/link.js"],"names":[],"mappings":"AAWA;IAsHQ;;;;;;MAKC;CAkDR;iBAnLgB,WAAW"}
+{"version":3,"file":"link.d.ts","sourceRoot":"","sources":["../../../src/marks/link.js"],"names":[],"mappings":"AAWA;IA0HQ;;;;;;MAKC;CAkDR;iBAvLgB,WAAW"}

package/dist/src/marks/link.js

@@ -32,6 +32,8 @@ export default class LinkMark extends Mark {
                 minArcHeight: 1.5,
                 minPickingSize: 3.0,
                 clampApex: false,
+                maxChordLength: 50000,
+                arcFadingDistance: false,
 
                 linkShape: "arc",
                 orient: "vertical",
@@ -103,6 +105,8 @@ export default class LinkMark extends Mark {
             uShape: LINK_SHAPES.indexOf(props.linkShape),
             uOrient: ORIENTS.indexOf(props.orient),
             uClampApex: !!props.clampApex,
+            uMaxChordLength: props.maxChordLength,
+            uArcFadingDistance: props.arcFadingDistance || [0, 0],
         });
     }
 

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

@@ -115,10 +115,7 @@ export default class Mark {
         program: WebGLProgram;
         getProgramErrors: () => {
             message: string;
-            detail: string; /**
-             *
-             * @param {any} vertexData TODO: Extract type from VertexBuilder
-             */
+            detail: string;
         };
     };
     /**

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

@@ -1 +1 @@
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package/dist/src/marks/mark.js

@@ -441,6 +441,7 @@ export default class Mark {
             // left pos, left height, right pos, right height
             uSampleFacet: [0, 1, 0, 1],
             uTransitionOffset: 0.0,
+            uZero: 0.0,
         });
     }
 

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

@@ -374,6 +374,27 @@ export interface LinkProps extends SecondaryPositionProps {
      */
     minArcHeight?: number;
 
+    /**
+     * 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;
+
+    /**
+     * 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;
+
     /**
      * The minimum stroke width of the links when pointing with the mouse cursor.
      * Allows making very thin links easier to point at.

package/package.json

@@ -7,7 +7,7 @@
   },
   "contributors": [],
   "license": "MIT",
-  "version": "0.39.0",
+  "version": "0.40.0",
   "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": "74d4f6721b31c1916051f868e95be7d83d8d6369"
 }