protvista-utils - npm Package Compare versions

Comparing version 3.0.0 to 3.2.13

dist/protvista-utils.js

@@ -1,2 +0,2 @@
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Region: ").concat(t));return{start:u,end:c,color:s}})):this.segments=[]}}]),t}(),s=function(t,e){return t?e?"".concat(t,",").concat(e):t:e},h=function(){function t(e){var n=e.element,r=e.min,i=e.max;l()(this,t),this.element=n,this.element._highlightcolor="#FFEB3B66",this.region=new c({min:r,max:i}),this.fixedHighlight=null}return u()(t,[{key:"setAttributesInElement",value:function(){this.region.decode(this.element.getAttribute("highlight")),0===this.region.segments.length&&(this.element._highlightstart=Number(this.element.getAttribute("highlightstart")),this.element._highlightend=Number(this.element.getAttribute("highlightend")),this.element._highlightcolor=this.element.getAttribute("highlightcolor")||"#FFEB3B66",null!==this.element._highlightstart&&null!==this.element._highlightend&&"number"==typeof this.element._highlightstart&&"number"==typeof this.element._highlightend&&(this.element._highlight="".concat(this.element._highlightstart,":").concat(this.element._highlightend),this.region.decode(s(this.fixedHighlight,this.element._highlight))))}},{key:"setFloatAttribute",value:function(t,e){var n=parseFloat(e);this.element["_".concat(t)]=Number.isNaN(n)?e:n}},{key:"changedCallBack",value:function(t,e){switch(t){case"highlightstart":case"highlightend":this.setFloatAttribute(t,e),this.element._highlight=Number.isNaN(this.element._highlightstart)||Number.isNaN(this.element._highlightend)||void 0===this.element._highlightstart||void 0===this.element._highlightend||null===this.element._highlightstart||null===this.element._highlightend?"":"".concat(Math.max(this.region.min,this.element._highlightstart),":").concat(Math.min(this.region.max,this.element._highlightend));break;default:this.element._highlight=e}this.region.decode(s(this.fixedHighlight,this.element._highlight)),this.element.refresh()}},{key:"setFixedHighlight",value:function(t){this.fixedHighlight=t,this.region.decode(s(t,this.element._highlight)),this.element.refresh()}},{key:"appendHighlightTo",value:function(t){this.highlighted=t.append("g").attr("class","highlighted")}},{key:"updateHighlight",value:function(){var t=this,e=this.highlighted.selectAll("rect").data(this.region.segments);e.enter().append("rect").style("pointer-events","none").merge(e).attr("fill",(function(e){return e.color?e.color:t.element._highlightcolor})).attr("height",this.element._height).attr("x",(function(e){return t.element.getXFromSeqPosition(e.start)})).attr("width",(function(e){return t.element.getSingleBaseWidth()*(e.end-e.start+1)})),e.exit().remove()}},{key:"max",set:function(t){this.region.max=t}}]),t}();function f(t){var e=document.createElement("div");return e.style.borderColor="",e.style.borderColor=t,""!==e.style.borderColor}var g=function(t){return t},m=function(){function t(e){l()(this,t),this.element=e,this.timeStampWheelOutside=0,this.resetScrollableTimeout=null}return u()(t,[{key:"setElementScrollable",value:function(t){this.element.setAttribute("scrollable",t)}},{key:"startResetScrollableTimer",value:function(){var t=this;this.resetScrollableTimeout&&clearTimeout(this.resetScrollableTimeout),this.resetScrollableTimeout=setTimeout((function(){t.setElementScrollable(!0),t.resetScrollableTimeout=null}),400)}},{key:"blockScroll",value:function(t){this.timeStampWheelOutside=t,this.setElementScrollable(!1),this.startResetScrollableTimer()}},{key:"isWheelEventInsideElement",value:function(t,e){var n=this.element.getBoundingClientRect(),r=n.height,i=n.width,o=n.x,l=n.y;return t>o&&e<o+i&&e>l&&e<l+r}},{key:"wheel",value:function(t){var e=t.x,n=t.y,r=t.timeStamp;this.isWheelEventInsideElement(e,n)?r<this.timeStampWheelOutside+400?this.blockScroll(r):this.setElementScrollable(!0):this.blockScroll(r)}}]),t}(),p=n(3),d=n.n(p),b=n(4),y=n.n(b),v=n(8),x=n.n(v),S=n(9),w=n.n(S),_=n(2),j=n.n(_);function E(t,e){var n;if("undefined"==typeof Symbol||null==t[Symbol.iterator]){if(Array.isArray(t)||(n=function(t,e){if(!t)return;if("string"==typeof t)return O(t,e);var n=Object.prototype.toString.call(t).slice(8,-1);"Object"===n&&t.constructor&&(n=t.constructor.name);if("Map"===n||"Set"===n)return Array.from(t);if("Arguments"===n||/^(?:Ui|I)nt(?:8|16|32)(?:Clamped)?Array$/.test(n))return O(t,e)}(t))||e&&t&&"number"==typeof t.length){n&&(t=n);var r=0,i=function(){};return{s:i,n:function(){return r>=t.length?{done:!0}:{done:!1,value:t[r++]}},e:function(t){throw t},f:i}}throw new TypeError("Invalid attempt to iterate non-iterable instance.\nIn order to be iterable, non-array objects must have a [Symbol.iterator]() method.")}var o,l=!0,a=!1;return{s:function(){n=t[Symbol.iterator]()},n:function(){var t=n.next();return l=t.done,t},e:function(t){a=!0,o=t},f:function(){try{l||null==n.return||n.return()}finally{if(a)throw o}}}}function O(t,e){(null==e||e>t.length)&&(e=t.length);for(var n=0,r=new Array(e);n<e;n++)r[n]=t[n];return r}function k(t){var e=function(){if("undefined"==typeof Reflect||!Reflect.construct)return!1;if(Reflect.construct.sham)return!1;if("function"==typeof Proxy)return!0;try{return Date.prototype.toString.call(Reflect.construct(Date,[],(function(){}))),!0}catch(t){return!1}}();return function(){var n,r=j()(t);if(e){var i=j()(this).constructor;n=Reflect.construct(r,arguments,i)}else n=r.apply(this,arguments);return w()(this,n)}}var A=["left","right","top","bottom"],T=A.map((function(t){return"margin".concat(t)})),N=c,P=h,R=function(){var t=arguments.length>0&&void 0!==arguments[0]?arguments[0]:null,e=[],n=[];if(null!==t&&"string"!=typeof t)throw new Error("The attribute text has to be of type string");if(t&&""!==t.trim()){var r=t.split(",").map((function(t){return t.split(":")}));if(r.length<2)throw new Error("There should be at least 2 points to create a scale");e=r.map((function(t){var e=t[0].trim().toUpperCase();if(!f(e))throw new Error("The color '".concat(e," is not valid'"));return e})),n=r.map((function(t,e){var n=parseFloat(t[1]);if(Number.isNaN(n))throw new Error("The second part of every point should be a number. Error in point ".concat(e,": ").concat(t));return n}))}return{range:e,domain:n}},C=function(){var t=arguments.length>0&&void 0!==arguments[0]?arguments[0]:null,e=arguments.length>1&&void 0!==arguments[1]?arguments[1]:{},n=e.keyFormatter,r=void 0===n?g:n,i=e.valueFormatter,o=void 0===i?g:i;if(null!==t&&"string"!=typeof t)throw new Error("The attribute text has to be of type string");if(t&&""!==t.trim()){var l=t.split(",").map((function(t){return t.split(":")})),a={};return l.forEach((function(t){if(2!==t.length)throw new Error("Bad block: ".concat(t.join(":"),"\n The blocks of the string should follow the format KEY:VALUE"));a[r(t[0])]=o(t[1])})),a}return{}},F=m,I=function(t){var e,n=arguments.length>1&&void 0!==arguments[1]?arguments[1]:{initialValue:{top:0,bottom:0,left:0,right:0}},r=function(t){x()(r,t);var e=k(r);function r(){var t;return l()(this,r),(t=e.call(this)).margin=n.initialValue,t}return u()(r,[{key:"attributeChangedCallback",value:function(t,e,n){e!==n&&T.includes(t)&&(this[t]=n),y()(j()(r.prototype),"attributeChangedCallback",this).call(this,t,e,n)}}],[{key:"observedAttributes",get:function(){return[].concat(d()(y()(j()(r),"observedAttributes",this)),d()(T))}}]),r}(t),i=E(A);try{var o=function(){var t=e.value;Object.defineProperty(r.prototype,"margin".concat(t),{get:function(){return this.margin[t]||0},set:function(e){this.margin[t]=+e}})};for(i.s();!(e=i.n()).done;)o()}catch(t){i.e(t)}finally{i.f()}return r}}])}));
 //# sourceMappingURL=protvista-utils.js.map

package.json

 {
   "name": "protvista-utils",
-  "version": "3.0.0",
+  "version": "3.2.13",
   "description": "Collection of utilities for ProtVista components",
@@ -29,3 +29,3 @@ "files": [
   "license": "ISC",
-  "gitHead": "750856a787e184ab73d6677d5cef2d64fbf918e1"
+  "gitHead": "563f7872ea6e92d7dc343cadcc7c4ed887c39d80"
 }

src/Region.js

@@ -11,7 +11,7 @@ export default class Region {
     return this.segments
-      .map(({ start, end }) => {
-        if (full) return `${start}:${end}`;
+      .map(({ start, end, color }) => {
+        if (full) return `${start}:${end}${color ? `:${color}` : ""}`;
         const s = start === this.min ? "" : start;
         const e = end === this.max ? "" : end;
-        return `${s}:${e}`;
+        return `${s}:${e}${color ? `:${color}` : ""}`;
       })
@@ -27,10 +27,11 @@ .join(",");
     }
-    this.segments = this.regionString.split(",").map(region => {
-      const [_start, _end, _] = region.split(":");
+    this.segments = this.regionString.split(",").map((region) => {
+      const [_start, _end, _color, _] = region.split(":");
       if (typeof _ !== "undefined")
         throw new Error(
-          `there should be at most 1 ':' per region. Region: ${region}`
+          `there should be at most 2 ':' per region. Region: ${region}`
         );
       let start = _start ? Number(_start) : this.min;
       let end = _end ? Number(_end) : this.max;
+      const color = _color !== "" ? _color : undefined;
       if (start > end) [start, end] = [end, start];
@@ -47,5 +48,11 @@ if (start < this.min) start = this.min;
         );
+      if (color && !color.match(/^#[0-9a-f]{6,8}$/i))
+        throw new Error(
+          `The parsed value of ${_color} is not a color in hex format. Region: ${region}`
+        );
+
       return {
         start,
-        end
+        end,
+        color,
       };
@@ -52,0 +59,0 @@ });

src/region.test.js

@@ -19,2 +19,10 @@ /* eslint-disable no-empty */
   });
+
+  test("encode whole region with default color", () => {
+    const region = new Region();
+    region.decode("::");
+    expect(region.segments).toMatchSnapshot();
+    expect(region.encode(true)).toEqual("-Infinity:Infinity");
+    expect(region.encode(false)).toEqual(":");
+  });
   test("encode simple region", () => {
@@ -27,2 +35,23 @@ const region = new Region();
   });
+  test("encode simple region with color", () => {
+    const region = new Region();
+    region.decode("2:10:#00EE55");
+    expect(region.segments).toMatchSnapshot();
+    expect(region.encode(true)).toEqual("2:10:#00EE55");
+    expect(region.encode(false)).toEqual("2:10:#00EE55");
+  });
+  test("encode simple region with color alpha", () => {
+    const region = new Region();
+    region.decode("2:10:#00EE55A0");
+    expect(region.segments).toMatchSnapshot();
+    expect(region.encode(true)).toEqual("2:10:#00EE55A0");
+    expect(region.encode(false)).toEqual("2:10:#00EE55A0");
+  });
+  test("encode whole region with color", () => {
+    const region = new Region();
+    region.decode("::#00EE55");
+    expect(region.segments).toMatchSnapshot();
+    expect(region.encode(true)).toEqual("-Infinity:Infinity:#00EE55");
+    expect(region.encode(false)).toEqual("::#00EE55");
+  });
   test("encode multiple region", () => {
@@ -33,5 +62,16 @@ const region = new Region({ min: 1, max: 100 });
     expect(region.segments).toMatchSnapshot();
-    expect(region.encode(true)).toEqual(txt);
+    expect(region.encode(true)).toEqual("1:5,10:20,30:50,50:100");
     expect(region.encode()).toEqual(":5,10:20,30:50,50:");
   });
+  test("encode multiple region with color", () => {
+    const region = new Region({ min: 1, max: 100 });
+    const txt = "1:5:#00EE55,10:20,30:50:#00E800AA,50:100";
+    region.decode(txt);
+    expect(region.segments).toMatchSnapshot();
+    expect(region.encode(true)).toEqual(
+      "1:5:#00EE55,10:20,30:50:#00E800AA,50:100"
+    );
+    expect(region.encode()).toEqual(":5:#00EE55,10:20,30:50:#00E800AA,50:");
+  });
+
   test("encode multiple and complex region", () => {
@@ -44,2 +84,14 @@ const region = new Region({ min: 1, max: 100 });
   });
+
+  test("encode multiple and complex region with color", () => {
+    const region = new Region({ min: 1, max: 100 });
+    region.decode("::#00EE55,:20:#00E800AA,30::#00EE55,50:100,,0:200");
+    expect(region.segments).toMatchSnapshot();
+    expect(region.encode(true)).toEqual(
+      "1:100:#00EE55,1:20:#00E800AA,30:100:#00EE55,50:100,1:100,1:100"
+    );
+    expect(region.encode()).toEqual(
+      "::#00EE55,:20:#00E800AA,30::#00EE55,50:,:,:"
+    );
+  });
 });
@@ -53,2 +105,3 @@
     expect(region.min).toEqual(-Infinity);
+    expect(region.color).toEqual(undefined);
 
@@ -69,4 +122,14 @@ region.decode(null);
     expect(region.segments[0].end).toEqual(5);
+    expect(region.segments[0].color).toEqual(undefined);
   });
 
+  test("decode simple region with color", () => {
+    const region = new Region();
+    region.decode("1:5:#AAAAAA");
+    expect(region.segments.length).toEqual(1);
+    expect(region.segments[0].start).toEqual(1);
+    expect(region.segments[0].end).toEqual(5);
+    expect(region.segments[0].color).toEqual("#AAAAAA");
+  });
+
   test("decode multiple region", () => {
@@ -78,6 +141,20 @@ const region = new Region();
     expect(region.segments[0].end).toEqual(5);
+    expect(region.segments[0].color).toEqual(undefined);
     expect(region.segments[1].start).toEqual(10);
     expect(region.segments[1].end).toEqual(15);
+    expect(region.segments[1].color).toEqual(undefined);
   });
 
+  test("decode multiple region with color", () => {
+    const region = new Region();
+    region.decode("1:5:#AAAAAA,10:15:#AAAAAA00");
+    expect(region.segments.length).toEqual(2);
+    expect(region.segments[0].start).toEqual(1);
+    expect(region.segments[0].end).toEqual(5);
+    expect(region.segments[0].color).toEqual("#AAAAAA");
+    expect(region.segments[1].start).toEqual(10);
+    expect(region.segments[1].end).toEqual(15);
+    expect(region.segments[1].color).toEqual("#AAAAAA00");
+  });
+
   test("decode region missing start and not initialised min", () => {
@@ -89,2 +166,3 @@ const region = new Region();
     expect(region.segments[0].end).toEqual(5);
+    expect(region.segments[0].color).toEqual(undefined);
   });
@@ -98,2 +176,3 @@
     expect(region.segments[0].end).toEqual(Infinity);
+    expect(region.segments[0].color).toEqual(undefined);
 
@@ -104,2 +183,3 @@ region.decode("1");
     expect(region.segments[0].end).toEqual(Infinity);
+    expect(region.segments[0].color).toEqual(undefined);
   });
@@ -113,2 +193,3 @@
     expect(region.segments[0].end).toEqual(5);
+    expect(region.segments[0].color).toEqual(undefined);
   });
@@ -122,2 +203,3 @@
     expect(region.segments[0].end).toEqual(10);
+    expect(region.segments[0].color).toEqual(undefined);
 
@@ -128,2 +210,3 @@ region.decode("1");
     expect(region.segments[0].end).toEqual(10);
+    expect(region.segments[0].color).toEqual(undefined);
   });
@@ -137,4 +220,14 @@
     expect(region.segments[0].end).toEqual(5);
+    expect(region.segments[0].color).toEqual(undefined);
   });
 
+  test("decode region with inverted values with color", () => {
+    const region = new Region();
+    region.decode("5:1:#000000");
+    expect(region.segments.length).toEqual(1);
+    expect(region.segments[0].start).toEqual(1);
+    expect(region.segments[0].end).toEqual(5);
+    expect(region.segments[0].color).toEqual("#000000");
+  });
+
   test("Fails decoding because of non-numeric chars", () => {
@@ -156,9 +249,33 @@ const region = new Region();
 
-  test("Fails decoding because there should be at most 1 ':' per region", () => {
+  test("Fails decoding because there should be at most 2 ':' per region", () => {
     const region = new Region();
     try {
-      region.decode("1:3:4");
+      region.decode("1:3:#000000:5");
       fail("The decoding should fails");
     } catch (e) {}
   });
+
+  test("Fails decoding because of wrong color format", () => {
+    const region = new Region();
+    try {
+      region.decode("2:10:#00ET5S");
+      fail("The decoding should fails");
+    } catch (e) {}
+    try {
+      region.decode("2:10:#000000000");
+      fail("The decoding should fails");
+    } catch (e) {}
+    try {
+      region.decode("2:10:aeghh");
+      fail("The decoding should fails");
+    } catch (e) {}
+    try {
+      region.decode("::dggS");
+      fail("The decoding should fails");
+    } catch (e) {}
+    try {
+      region.decode("::#000000II");
+      fail("The decoding should fails");
+    } catch (e) {}
+  });
 });

src/TrackHighlighter.js

 import Region from "./Region";
 
+const DEFAULT_HIGLIGHT_COLOR = "#FFEB3B66";
+
 const combineRegions = (region1, region2) => {
@@ -11,2 +13,3 @@ if (!region1) return region2;
     this.element = element;
+    this.element._highlightcolor = DEFAULT_HIGLIGHT_COLOR;
     this.region = new Region({ min, max });
@@ -29,2 +32,4 @@ this.fixedHighlight = null;
       );
+      this.element._highlightcolor =
+        this.element.getAttribute("highlightcolor") || DEFAULT_HIGLIGHT_COLOR;
       if (
@@ -93,11 +98,10 @@ this.element._highlightstart !== null &&
       .append("rect")
-      .style("opacity", 0.5)
-      .attr("fill", "rgba(255, 235, 59, 0.8)")
       .style("pointer-events", "none")
       .merge(highlighs)
+      .attr("fill", (d) => (d.color ? d.color : this.element._highlightcolor))
       .attr("height", this.element._height)
-      .attr("x", d => this.element.getXFromSeqPosition(d.start))
+      .attr("x", (d) => this.element.getXFromSeqPosition(d.start))
       .attr(
         "width",
-        d => this.element.getSingleBaseWidth() * (d.end - d.start + 1)
+        (d) => this.element.getSingleBaseWidth() * (d.end - d.start + 1)
       );
@@ -104,0 +108,0 @@ highlighs.exit().remove();

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