@nightingale-elements/nightingale-interpro-track - npm Package Compare versions

Comparing version 4.0.24-alpha.0 to 4.2.1-alpha.0

dist/index.d.ts

 import NightingaleInterproTrack from "./nightingale-interpro-track";
+export type { BaseGroup, LabelGroup } from "./nightingale-interpro-track";
 export default NightingaleInterproTrack;
 //# sourceMappingURL=index.d.ts.map

dist/index.js

@@ -1,2 +0,2 @@
-import{bindEvents as t,contrastingColor as e,getColor as n}from"@nightingale-elements/nightingale-new-core";import r,{DefaultLayout as i}from"@nightingale-elements/nightingale-track";function a(t,e,n,r){var i,a=arguments.length,o=a<3?e:null===r?r=Object.getOwnPropertyDescriptor(e,n):r;if("object"==typeof Reflect&&"function"==typeof Reflect.decorate)o=Reflect.decorate(t,e,n,r);else for(var s=t.length-1;s>=0;s--)(i=t[s])&&(o=(a<3?i(o):a>3?i(e,n,o):i(e,n))||o);return a>3&&o&&Object.defineProperty(e,n,o),o}function o(t,e,n,r){if("a"===n&&!r)throw new TypeError("Private accessor was defined without a getter");if("function"==typeof e?t!==e||!r:!e.has(t))throw new TypeError("Cannot read private member from an object whose class did not declare it");return"m"===n?r:"a"===n?r.call(t):r?r.value:e.get(t)}function s(t,e,n,r,i){if("m"===r)throw new TypeError("Private method is not writable");if("a"===r&&!i)throw new TypeError("Private accessor was defined without a setter");if("function"==typeof e?t!==e||!i:!e.has(t))throw new TypeError("Cannot write private member to an object whose class did not declare it");return"a"===r?i.call(t,n):i?i.value=n:e.set(t,n),n
+import{bindEvents as t,contrastingColor as e}from"@nightingale-elements/nightingale-new-core";import n,{DefaultLayout as r}from"@nightingale-elements/nightingale-track";function i(t,e,n,r){var i,a=arguments.length,o=a<3?e:null===r?r=Object.getOwnPropertyDescriptor(e,n):r;if("object"==typeof Reflect&&"function"==typeof Reflect.decorate)o=Reflect.decorate(t,e,n,r);else for(var s=t.length-1;s>=0;s--)(i=t[s])&&(o=(a<3?i(o):a>3?i(e,n,o):i(e,n))||o);return a>3&&o&&Object.defineProperty(e,n,o),o}function a(t,e,n,r){if("a"===n&&!r)throw new TypeError("Private accessor was defined without a getter");if("function"==typeof e?t!==e||!r:!e.has(t))throw new TypeError("Cannot read private member from an object whose class did not declare it");return"m"===n?r:"a"===n?r.call(t):r?r.value:e.get(t)}function o(t,e,n,r,i){if("m"===r)throw new TypeError("Private method is not writable");if("a"===r&&!i)throw new TypeError("Private accessor was defined without a setter");if("function"==typeof e?t!==e||!i:!e.has(t))throw new TypeError("Cannot write private member to an object whose class did not declare it");return"a"===r?i.call(t,n):i?i.value=n:e.set(t,n),n
 /**
@@ -6,3 +6,3 @@ * @license
  * SPDX-License-Identifier: BSD-3-Clause
- */}const u=(t,e)=>"method"===e.kind&&e.descriptor&&!("value"in e.descriptor)?{...e,finisher(n){n.createProperty(e.key,t)}}:{kind:"field",key:Symbol(),placement:"own",descriptor:{},originalKey:e.key,initializer(){"function"==typeof e.initializer&&(this[e.key]=e.initializer.call(this))},finisher(n){n.createProperty(e.key,t)}};
+ */}const s=(t,e)=>"method"===e.kind&&e.descriptor&&!("value"in e.descriptor)?{...e,finisher(n){n.createProperty(e.key,t)}}:{kind:"field",key:Symbol(),placement:"own",descriptor:{},originalKey:e.key,initializer(){"function"==typeof e.initializer&&(this[e.key]=e.initializer.call(this))},finisher(n){n.createProperty(e.key,t)}};
 /**
@@ -12,3 +12,3 @@ * @license
  * SPDX-License-Identifier: BSD-3-Clause
- */function l(t){return(e,n)=>void 0!==n?((t,e,n)=>{e.constructor.createProperty(n,t)})(t,e,n):u(t,e)
+ */function u(t){return(e,n)=>void 0!==n?((t,e,n)=>{e.constructor.createProperty(n,t)})(t,e,n):s(t,e)
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feature`)).call(t,this).on("click.expanded",((t,e)=>{e.feature.expanded=!e.feature.expanded,this.refresh()})),u.selectAll("text.child-label").data((t=>t.fragments.map((e=>({...e,feature:t.feature,fragments:t.fragments}))))).enter().append("text").attr("class","child-label").attr("dominant-baseline","middle").attr("text-anchor","middle").style("cursor","default").style("pointer-events","none"),o(this,Ur,Xr(s),"f"),zr({baseG:a(this,Ur,"f"),getResidueShape:t=>this.getResidueShape(t),getResidueTransform:t=>this.getResidueTransform(t),getResidueFill:t=>{var e;return this.getResidueFill(t,!!(null===(e=t.feature)||void 0===e?void 0:e.expanded))},element:this}),(null===(i=a(this,Br,"f"))||void 0===i?void 0:i.length)&&(({element:t,coverage:e})=>{var n,r,i;t.accession=(null===(r=null===(n=null==t?void 0:t.data)||void 0===n?void 0:n[0])||void 0===r?void 0:r.accession)||"_";const a=null===(i=t.svg)||void 0===i?void 0:i.append("defs").append("mask").attr("id",`mask-${t.accession}`);null==a||a.selectAll("rect").data(e).enter().append("rect").attr("y",0).attr("height",t.height)})({element:this,coverage:a(this,Br,"f")})}null===(s=this.svg)||void 0===s||s.attr("height",((null===(u=this.layoutObj)||void 0===u?void 0:u.maxYPos)||0)+this["margin-bottom"]),o(this,Ir,!0,"f")}getResidueShape(t){var e;return this.featureShape.getFeatureShape(this.getSingleBaseWidth(),(null===(e=this.layoutObj)||void 0===e?void 0:e.getFeatureHeight(`${t.accession}_${t.k}_${t.i}_${t.j}`))||0,t.end&&t.start?t.end-t.start+1:1,"rectangle")}getResidueTransform(t){var e;return`translate(${this.getXFromSeqPosition(t.start||1)},${this["margin-top"]+((null===(e=this.layoutObj)||void 0===e?void 0:e.getFeatureYPos(`${t.accession}_${t.k}_${t.i}_${t.j}`))||0)})`}getResidueFill(t,e){return e?this.getFeatureColor(t):"white"}getTextLabel(t){var e,n;return(null===(e=this.label)||void 0===e?void 0:e.length)?this.label.startsWith(".")?Yr(t,this.label.slice(1),null):this.label:(null===(n=null==t?void 0:t.feature)||void 0===n?void 0:n.accession)||null}refreshLabels(t,n=2){t.attr("x",(t=>{const e=Zr(this["display-start"],t.start),n=ti(this["display-end"],t.end,this.length);return this.getXFromSeqPosition(e+(n-e)/2||1)})).attr("y",(t=>{var e,n;return this["margin-top"]+((null===(e=this.layoutObj)||void 0===e?void 0:e.getFeatureYPos(t.feature))||0)+((null===(n=this.layoutObj)||void 0===n?void 0:n.getFeatureHeight(t.feature))||0)/2})).attr("fill",((t,n,r)=>{var i;return(null===(i=r[n].parentElement)||void 0===i?void 0:i.querySelector("path.feature"))?e(function(t){var e;if(Jr[t])return Jr[t];const n=document.createElement("div");n.style.color=t,document.body.appendChild(n);const r=window.getComputedStyle(n).color;document.body.removeChild(n);const i=(null===(e=null==r?void 0:r.match(/[.\d]+/g))||void 0===e?void 0:e.map(Number))||null;return Jr[t]=i,i}(this.getFeatureFillColor(t))):null})).attr("font-size",(t=>{var e;return((null===(e=this.layoutObj)||void 0===e?void 0:e.getFeatureHeight(t.feature))||2)-n})).text((t=>this["show-label"]?this.getTextLabel(t):null)).each(function(t,e,n,r,i){function a(a){var o,s,u;const l=function(t){return"string"==typeof t?new $t([[document.querySelector(t)]],[document.documentElement]):new $t([[t]],At)}(this),h=Zr(t,a.start),c=ti(e,a.end,n),f=r(c)-r(h),d=i(a.feature)/2;let p=(null===(s=null===(o=l.node())||void 0===o?void 0:o.getComputedTextLength)||void 0===s?void 0:s.call(o))||0,v=l.text();for(;p>f-2*d&&v.length>0;)v=v.slice(0,-1),l.text(v.length?v+"…":""),p=(null===(u=l.node())||void 0===u?void 0:u.getComputedTextLength())||0}return a}(this["display-start"],this["display-end"],this.length,(t=>this.getXFromSeqPosition(t)),(t=>{var e;return(null===(e=this.layoutObj)||void 0===e?void 0:e.getFeatureHeight(t))||0})))}refreshFeatures(t,e=!0){const n=new Set(t.data().map((t=>{var e;return null===(e=t.feature)||void 0===e?void 0:e.accession}))).size;t.attr("d",(t=>{var n;return this.featureShape.getFeatureShape(this.getSingleBaseWidth(),(null===(n=this.layoutObj)||void 0===n?void 0:n.getFeatureHeight(t.feature||""))||0,t.end&&t.start?t.end-t.start+1:1,e?this.getShape(t.shape?t:t.feature):"rectangle")})).style("fill",(t=>e?this.getFeatureColor(t.feature):"white")).attr("opacity",e?1:.8/n).style("stroke",(t=>e?this.getFeatureColor(t.feature):"none")).attr("transform",(t=>{var e;return`translate(${this.getXFromSeqPosition(t.start||1)},${this["margin-top"]+((null===(e=this.layoutObj)||void 0===e?void 0:e.getFeatureYPos(t.feature))||0)})`})).style("pointer-events",e?"auto":"none")}refreshCoverLine(t,e=!0){t.attr("x1",(t=>this.getXFromSeqPosition(t.start||1))).attr("x2",(t=>this.getXFromSeqPosition((t.end||0)+1))).attr("y1",(t=>{var e,n;return this["margin-top"]+((null===(e=this.layoutObj)||void 0===e?void 0:e.getFeatureYPos(t.feature))||0)+((null===(n=this.layoutObj)||void 0===n?void 0:n.getFeatureHeight(t.feature))||0)/2})).attr("y2",(t=>{var e,n;return this["margin-top"]+((null===(e=this.layoutObj)||void 0===e?void 0:e.getFeatureYPos(t.feature))||0)+((null===(n=this.layoutObj)||void 0===n?void 0:n.getFeatureHeight(t.feature))||0)/2})).attr("stroke",(t=>this.getFeatureColor(t.feature))).attr("visibility",e?"visible":"hidden")}refresh(){var t,e,n,r,i,o,s,u;if(a(this,Ir,"f")&&this.layoutObj){if(this.layoutObj.expanded=!!this.expanded,this.layoutObj.init(this.data,a(this,Wr,"f")),this.height=this.layoutObj.maxYPos,this.refreshCoverLine(null===(t=a(this,Dr,"f"))||void 0===t?void 0:t.selectAll("g.location-group line.cover")),this.refreshFeatures(null===(e=a(this,Dr,"f"))||void 0===e?void 0:e.selectAll("g.location-group path.feature")),this.refreshLabels(null===(n=a(this,Dr,"f"))||void 0===n?void 0:n.selectAll("g.location-group text.feature-label")),a(this,Vr,"f")&&Hr({baseG:a(this,Vr,"f"),expanded:!!this.expanded,getResidueShape:t=>this.getResidueShape(t),getResidueTransform:t=>this.getResidueTransform(t),getResidueFill:t=>this.getResidueFill(t,!!this.expanded)}),a(this,Wr,"f")){const t=null===(r=a(this,Gr,"f"))||void 0===r?void 0:r.select("g.children-group");null==t||t.attr("visibility",this.expanded?"visible":"hidden");const e=null==t?void 0:t.selectAll("g.child-group"),n=null==e?void 0:e.selectAll("g.child-location-group"),u=null==n?void 0:n.selectAll("line.cover"),l=null==n?void 0:n.selectAll("path.child-fragment");this.refreshCoverLine(u,this.expanded),this.refreshFeatures(l,this.expanded),this.refreshLabels(null==e?void 0:e.selectAll("g.child-location-group text.child-label"),0),null===(i=a(this,Ur,"f"))||void 0===i||i.attr("visibility",(()=>this.expanded?"visible":"hidden")),a(this,Ur,"f")&&Hr({baseG:a(this,Ur,"f"),expanded:!!this.expanded,getResidueShape:t=>this.getResidueShape(t),getResidueTransform:t=>this.getResidueTransform(t),getResidueFill:t=>{var e;return this.getResidueFill(t,!!(null===(e=t.feature)||void 0===e?void 0:e.expanded))}}),(null===(o=a(this,Br,"f"))||void 0===o?void 0:o.length)&&(({element:t,featuresG:e,contributorsLength:n})=>{var r;null==e||e.attr("mask",t.expanded?null:`url(#mask-${t.accession})`),null===(r=t.svg)||void 0===r||r.selectAll("defs mask rect").attr("x",(e=>t.getXFromSeqPosition(e.start))).attr("width",(e=>t.getSingleBaseWidth()*(e.end-e.start+1))).attr("height",t.height).attr("fill","white").attr("opacity",(t=>((t.value||0)/(n||1)+.3)/1.3))})({element:this,featuresG:a(this,Dr,"f"),contributorsLength:null===(s=a(this,Wr,"f"))||void 0===s?void 0:s.length})}null===(u=this.svg)||void 0===u||u.attr("height",this.layoutObj.maxYPos+this["margin-bottom"]),this.updateHighlight(),this.renderMarginOnGroup(this.margins)}}};function Zr(t,e){const n=t&&t>0?t:0;return Math.max(e||0,n)}function ti(t,e,n){const r=t&&t>0?t:n||0;return Math.min(e||0,r)}Wr=new WeakMap,Br=new WeakMap,Ir=new WeakMap,Gr=new WeakMap,Dr=new WeakMap,Vr=new WeakMap,Ur=new WeakMap,i([u({type:Boolean})],Qr.prototype,"expanded",void 0),i([u({type:Boolean})],Qr.prototype,"show-label",void 0),i([u({type:String})],Qr.prototype,"label",void 0),Qr=Kr=i([(t=>e=>"function"==typeof e?((t,e)=>(customElements.define(t,e),e))(t,e):((t,e)=>{const{kind:n,elements:r}=e;return{kind:n,elements:r,finisher(e){customElements.define(t,e)}}})(t,e))("nightingale-interpro-track")],Qr);var ei=Qr;export{ei as default};
 //# sourceMappingURL=index.js.map

dist/InterproEntryLayout.d.ts

@@ -21,3 +21,3 @@ import { DefaultLayout, Feature, FeatureLocation, LayoutOptions } from "@nightingale-elements/nightingale-track";
     residues: Residue[];
-    expanded: boolean;
+    expanded?: boolean;
     i?: number;
@@ -24,0 +24,0 @@ j?: number;

dist/nightingale-interpro-track.d.ts

@@ -8,5 +8,5 @@ import { Selection } from "d3";
     #private;
-    expanded: boolean;
-    "show-label": boolean;
-    label: string | null;
+    expanded?: boolean;
+    "show-label"?: boolean;
+    label?: string | null;
     layout: undefined;
@@ -32,2 +32,7 @@ protected layoutObj?: InterproEntryLayout;
 export default NightingaleInterproTrack;
+declare global {
+    interface HTMLElementTagNameMap {
+        "nightingale-interpro-track": NightingaleInterproTrack;
+    }
+}
 //# sourceMappingURL=nightingale-interpro-track.d.ts.map

package.json

 {
   "name": "@nightingale-elements/nightingale-interpro-track",
-  "version": "4.0.24-alpha.0",
+  "version": "4.2.1-alpha.0",
   "description": "Interpro extension of the track type.",
@@ -35,8 +35,8 @@ "files": [
   "dependencies": {
-    "@nightingale-elements/nightingale-new-core": "^4.0.24-alpha.0",
-    "@nightingale-elements/nightingale-track": "^4.0.24-alpha.0",
-    "d3": "7.8.2",
+    "@nightingale-elements/nightingale-new-core": "^4.2.0",
+    "@nightingale-elements/nightingale-track": "^4.2.1-alpha.0",
+    "d3": "7.8.3",
     "lodash-es": "^4.17.15"
   },
-  "gitHead": "7935a53b6f7736d5a9d4fd12d2f01612d6b9a93f"
+  "gitHead": "83029a091ebe9fa94512eaef3b8fe2a0f553c3ad"
 }

src/index.ts

 import NightingaleInterproTrack from "./nightingale-interpro-track";
+export type { BaseGroup, LabelGroup } from "./nightingale-interpro-track";
+
 export default NightingaleInterproTrack;

src/InterproEntryLayout.ts

@@ -30,3 +30,3 @@ /* eslint-disable no-param-reassign */
   residues: Residue[];
-  expanded: boolean;
+  expanded?: boolean;
   i?: number;
@@ -33,0 +33,0 @@ j?: number;

src/nightingale-interpro-track.ts

@@ -9,3 +9,2 @@ import { customElement, property } from "lit/decorators.js";
   contrastingColor,
-  getColor,
 } from "@nightingale-elements/nightingale-new-core";
@@ -39,10 +38,25 @@ import NightingaleTrack from "@nightingale-elements/nightingale-track";
 
+const colorCache: Record<string, number[] | null> = {};
+
+function colorKeywordToRGB(colorKeyword: string) {
+  if (colorCache[colorKeyword]) return colorCache[colorKeyword];
+
+  const el = document.createElement("div");
+  el.style.color = colorKeyword;
+  document.body.appendChild(el);
+  const rgbValue = window.getComputedStyle(el).color;
+  document.body.removeChild(el);
+  const res = rgbValue?.match(/[.\d]+/g)?.map(Number) || null;
+  colorCache[colorKeyword] = res;
+  return res;
+}
+
 @customElement("nightingale-interpro-track")
 class NightingaleInterproTrack extends NightingaleTrack {
   @property({ type: Boolean })
-  expanded = false;
+  expanded?: boolean = false;
   @property({ type: Boolean })
-  "show-label" = false;
+  "show-label"?: boolean = false;
   @property({ type: String })
-  label: string | null = null;
+  label?: string | null = null;
 
@@ -74,3 +88,3 @@ layout = undefined;
     if (!this.layoutObj) return;
-    this.layoutObj.expanded = this.expanded;
+    this.layoutObj.expanded = !!this.expanded;
     this.#childrenG = undefined;
@@ -109,3 +123,3 @@ super.createTrack();
       layoutHeight: this.height,
-      expanded: this.expanded,
+      expanded: !!this.expanded,
       padding: (this["margin-top"] + this["margin-bottom"]) / 2,
@@ -192,3 +206,3 @@ });
       getResidueTransform: (d) => this.getResidueTransform(d),
-      getResidueFill: (d) => this.getResidueFill(d, this.expanded),
+      getResidueFill: (d) => this.getResidueFill(d, !!this.expanded),
       element: this,
@@ -283,3 +297,3 @@ });
         getResidueTransform: (d) => this.getResidueTransform(d),
-        getResidueFill: (d) => this.getResidueFill(d, d.feature?.expanded),
+        getResidueFill: (d) => this.getResidueFill(d, !!d.feature?.expanded),
         element: this,
@@ -343,3 +357,3 @@ });
       )
-      .attr("fill", (_f, i, nodes) => {
+      .attr("fill", (f, i, nodes) => {
         const element = nodes[i];
@@ -349,3 +363,5 @@ const firstPath = element.parentElement?.querySelector("path.feature");
         if (firstPath) {
-          return contrastingColor(getColor(firstPath, "fill"));
+          return contrastingColor(
+            colorKeywordToRGB(this.getFeatureFillColor(f))
+          );
         }
@@ -386,3 +402,3 @@ return null;
       )
-      .attr("fill", (f) =>
+      .style("fill", (f) =>
         expanded ? this.getFeatureColor(f.feature as Feature) : "white"
@@ -432,3 +448,3 @@ )
     if (this.#haveCreatedFeatures && this.layoutObj) {
-      this.layoutObj.expanded = this.expanded;
+      this.layoutObj.expanded = !!this.expanded;
       this.layoutObj.init(this.data as InterProFeature[], this.#contributors);
@@ -453,6 +469,6 @@ this.height = this.layoutObj.maxYPos;
           baseG: this.#residuesG,
-          expanded: this.expanded,
+          expanded: !!this.expanded,
           getResidueShape: (d) => this.getResidueShape(d),
           getResidueTransform: (d) => this.getResidueTransform(d),
-          getResidueFill: (d) => this.getResidueFill(d, this.expanded),
+          getResidueFill: (d) => this.getResidueFill(d, !!this.expanded),
         });
@@ -493,6 +509,7 @@
             baseG: this.#childResiduesG,
-            expanded: this.expanded,
+            expanded: !!this.expanded,
             getResidueShape: (d) => this.getResidueShape(d),
             getResidueTransform: (d) => this.getResidueTransform(d),
-            getResidueFill: (d) => this.getResidueFill(d, d.feature?.expanded),
+            getResidueFill: (d) =>
+              this.getResidueFill(d, !!d.feature?.expanded),
           });
@@ -555,1 +572,7 @@
 export default NightingaleInterproTrack;
+
+declare global {
+  interface HTMLElementTagNameMap {
+    "nightingale-interpro-track": NightingaleInterproTrack;
+  }
+}

New alerts

Mixed license

License

(Experimental) Package contains multiple licenses.

Found 1 instance in 1 package

Fixed alerts

Mixed license

License

(Experimental) Package contains multiple licenses.

Found 1 instance in 1 package

Improved metrics

Total package byte prevSize

384142

increased by1.14%

Number of package files

25

increased by8.7%

Lines of code

1568

increased by1.75%

Dependency changes

• + Addedd3@7.8.3(transitive)

• - Removedd3@7.8.2(transitive)

• Updated@nightingale-elements/nightingale-new-core@^4.2.0

• Updated@nightingale-elements/nightingale-track@^4.2.1-alpha.0

• Updatedd3@7.8.3