protvista-coloured-sequence - npm Package Compare versions

Comparing version 2.6.1 to 2.7.0

dist/protvista-coloured-sequence.js

@@ -1,2 +0,2 @@
-var ProtvistaColouredSequence=function(t){var e={};function r(n){if(e[n])return e[n].exports;var o=e[n]={i:n,l:!1,exports:{}};return t[n].call(o.exports,o,o.exports,r),o.l=!0,o.exports}return r.m=t,r.c=e,r.d=function(t,e,n){r.o(t,e)||Object.defineProperty(t,e,{enumerable:!0,get:n})},r.r=function(t){"undefined"!=typeof Symbol&&Symbol.toStringTag&&Object.defineProperty(t,Symbol.toStringTag,{value:"Module"}),Object.defineProperty(t,"__esModule",{value:!0})},r.t=function(t,e){if(1&e&&(t=r(t)),8&e)return t;if(4&e&&"object"==typeof t&&t&&t.__esModule)return t;var n=Object.create(null);if(r.r(n),Object.defineProperty(n,"default",{enumerable:!0,value:t}),2&e&&"string"!=typeof t)for(var o in t)r.d(n,o,function(e){return t[e]}.bind(null,o));return n},r.n=function(t){var e=t&&t.__esModule?function(){return t.default}:function(){return t};return r.d(e,"a",e),e},r.o=function(t,e){return Object.prototype.hasOwnProperty.call(t,e)},r.p="",r(r.s=12)}([function(t,e){t.exports=d3},function(t,e){t.exports=ProtvistaSequence},function(t,e){t.exports=ProtvistaUtils},function(t,e){t.exports=function(t,e){if(!(t instanceof e))throw new TypeError("Cannot call a class as a function")}},function(t,e){function r(t,e){for(var r=0;r<e.length;r++){var n=e[r];n.enumerable=n.enumerable||!1,n.configurable=!0,"value"in n&&(n.writable=!0),Object.defineProperty(t,n.key,n)}}t.exports=function(t,e,n){return e&&r(t.prototype,e),n&&r(t,n),t}},function(t,e,r){var n=r(13),o=r(14);t.exports=function(t,e){return!e||"object"!==n(e)&&"function"!=typeof e?o(t):e}},function(t,e){function r(e){return t.exports=r=Object.setPrototypeOf?Object.getPrototypeOf:function(t){return t.__proto__||Object.getPrototypeOf(t)},r(e)}t.exports=r},function(t,e,r){var n=r(15);t.exports=function(t,e){if("function"!=typeof e&&null!==e)throw new TypeError("Super expression must either be null or a function");t.prototype=Object.create(e&&e.prototype,{constructor:{value:t,writable:!0,configurable:!0}}),e&&n(t,e)}},function(t){t.exports=JSON.parse('{"I":-0.31,"L":-0.56,"F":-1.13,"V":0.07,"M":-0.23,"P":0.45,"W":-1.85,"H":0.17,"T":0.14,"E":-0.01,"Q":0.58,"C":-0.24,"Y":-0.94,"A":0.17,"S":0.13,"N":0.42,"D":-0.07,"R":0.81,"G":0.01,"K":0.99}')},function(t){t.exports=JSON.parse('{"I":-1.12,"L":-1.25,"F":-1.71,"V":-0.46,"M":-0.67,"P":0.14,"W":-2.09,"H":0.11,"T":0.25,"E":0.11,"Q":0.77,"C":-0.02,"Y":-0.71,"A":0.5,"S":0.46,"N":0.85,"D":0.43,"R":1.15,"G":3.63,"K":3.64}')},function(t){t.exports=JSON.parse('{"I":-0.81,"L":-0.69,"F":-0.58,"V":-0.53,"M":-0.44,"P":-0.31,"W":-0.24,"H":-0.06,"T":0.11,"E":0.12,"Q":0.19,"C":0.22,"Y":0.23,"A":0.33,"S":0.33,"N":0.43,"D":0.5,"R":1.14,"G":1.61,"K":2.41}')},function(t){t.exports=JSON.parse('{"I":6.04,"L":6.04,"F":5.91,"V":6.02,"M":5.74,"P":6.3,"W":5.88,"H":7.64,"T":5.6,"E":3.08,"Q":5.65,"C":5.02,"Y":5.63,"A":6.11,"S":5.68,"N":5.41,"D":2.87,"R":10.76,"G":6.06,"K":9.47}')},function(t,e,r){t.exports=r(16)},function(t,e){function r(t){return(r="function"==typeof Symbol&&"symbol"==typeof Symbol.iterator?function(t){return typeof t}:function(t){return t&&"function"==typeof Symbol&&t.constructor===Symbol&&t!==Symbol.prototype?"symbol":typeof t})(t)}function n(e){return"function"==typeof Symbol&&"symbol"===r(Symbol.iterator)?t.exports=n=function(t){return r(t)}:t.exports=n=function(t){return t&&"function"==typeof Symbol&&t.constructor===Symbol&&t!==Symbol.prototype?"symbol":r(t)},n(e)}t.exports=n},function(t,e){t.exports=function(t){if(void 0===t)throw new ReferenceError("this hasn't been initialised - super() hasn't been called");return t}},function(t,e){function r(e,n){return t.exports=r=Object.setPrototypeOf||function(t,e){return t.__proto__=e,t},r(e,n)}t.exports=r},function(t,e,r){"use strict";r.r(e);var n=r(3),o=r.n(n),i=r(4),s=r.n(i),a=r(5),c=r.n(a),u=r(6),l=r.n(u),f=r(7),p=r.n(f),h=r(0),d=r(1),y=r.n(d),b=r(2),g=r(8),v=r(9),m=r(10),S=r(11),_=["hydrophobicity-interface-scale","hydrophobicity-octanol-scale","hydrophobicity-scale","isoelectric-point-scale"],x={domain:[-2,2],range:["#ffdd00","#0000FF"]},O=function(t){function e(){return o()(this,e),c()(this,l()(e).apply(this,arguments))}return p()(e,t),s()(e,[{key:"_createSequence",value:function(){this.svg=Object(h.select)(this).append("div").attr("class","").append("svg").attr("id","").attr("width",this.width).attr("height",this._height),this.uniqueID=Math.random().toString(36).substring(7),this.gradient=this.svg.append("defs").append("linearGradient").attr("id","scale-gradient-".concat(this.uniqueID)),this.seq_g=this.svg.append("g").attr("class","background"),this.seq_greadient=this.svg.append("rect").attr("class","seq-gradient").style("pointer-events","none"),this._getCharWidth(),this.trackHighlighter.appendHighlightTo(this.svg),this.refresh()}},{key:"getScaleFromAttribute",value:function(){var t=null;if(_.indexOf(this._scale)>=0)switch(this._scale){case"hydrophobicity-scale":return m;case"hydrophobicity-interface-scale":return g;case"isoelectric-point-scale":return S;case"hydrophobicity-octanol-scale":return v;default:return null}if(/([ILFVMPWHTEQCYASNDRGK]:-?\d+\.?\d*)(,[ILFVMPWHTEQCYASNDRGK]:-?\d+\.?\d*)*/.test(this._scale))try{t=Object(b.String2Object)(this._scale,{keyFormatter:function(t){return t.toUpperCase()},valueFormatter:function(t){return parseFloat(t)}})}catch(t){console.error("Couldn't parse the given scale ".concat(this._scale),t)}return t}},{key:"refresh",value:function(){var t=this;if(this.seq_g){var e=this.getScaleFromAttribute();if(null===e)return void console.error("The attribute scale is not valid.");var r=Object(h.scaleLinear)();this.colorScale=x,this._color_range&&(this.colorScale=Object(b.ColorScaleParser)(this._color_range)),r.domain(this.colorScale.domain).range(this.colorScale.range);var n=this.getSingleBaseWidth(),o=Math.round(Math.max(0,this._displaystart-2)),i=Math.round(Math.min(this.sequence.length,this._displayend+1)),s=this.sequence.slice(o,i).split("").map(function(t,n){var i=t.toUpperCase()in e?e[t.toUpperCase()]:0;return{start:1+o+n,end:1+o+n,aa:t,value:i,colour:r(i)}});this.residues=this.seq_g.selectAll("rect.base_bg").data(n<8?[]:s,function(t){return t.start}),this.residues.enter().append("rect").attr("class","base_bg feature").attr("data-base",function(t){return t.aa}).attr("data-pos",function(t){return t.start}).attr("height",this._height).merge(this.residues).attr("width",n).attr("fill",function(t){return t.colour}).attr("x",function(e){var r=e.start;return t.getXFromSeqPosition(r)}).call(this.bindEvents,this),this.residues.exit().remove();var a=this.gradient.selectAll("stop").data(this.sequence.split(""));a.enter().append("stop").merge(a).attr("offset",function(e,r){return(r+.5)/t.sequence.length}).attr("stop-color",function(t){return r(t.toUpperCase()in e?e[t.toUpperCase()]:0)}),this.gradient.exit().remove(),this.seq_greadient.attr("x",this.getXFromSeqPosition(1)).attr("y",0).attr("height",this._height).attr("width",this.getXFromSeqPosition(this.sequence.length)-this.getXFromSeqPosition(0)).style("opacity",n<8?1:8/n).attr("fill","url(#scale-gradient-".concat(this.uniqueID,")")),this._updateHighlight()}}}],[{key:"observedAttributes",get:function(){return y.a.observedAttributes.concat("scale","color_range")}}]),e}(y.a),P=function(){customElements.define("protvista-coloured-sequence",O)};window.customElements?P():document.addEventListener("WebComponentsReady",function(){P()})}]);
+var ProtvistaColouredSequence=function(t){var e={};function r(n){if(e[n])return e[n].exports;var o=e[n]={i:n,l:!1,exports:{}};return t[n].call(o.exports,o,o.exports,r),o.l=!0,o.exports}return r.m=t,r.c=e,r.d=function(t,e,n){r.o(t,e)||Object.defineProperty(t,e,{enumerable:!0,get:n})},r.r=function(t){"undefined"!=typeof Symbol&&Symbol.toStringTag&&Object.defineProperty(t,Symbol.toStringTag,{value:"Module"}),Object.defineProperty(t,"__esModule",{value:!0})},r.t=function(t,e){if(1&e&&(t=r(t)),8&e)return t;if(4&e&&"object"==typeof t&&t&&t.__esModule)return t;var n=Object.create(null);if(r.r(n),Object.defineProperty(n,"default",{enumerable:!0,value:t}),2&e&&"string"!=typeof t)for(var o in t)r.d(n,o,function(e){return t[e]}.bind(null,o));return n},r.n=function(t){var e=t&&t.__esModule?function(){return t.default}:function(){return t};return r.d(e,"a",e),e},r.o=function(t,e){return Object.prototype.hasOwnProperty.call(t,e)},r.p="",r(r.s=12)}([function(t,e){t.exports=d3},function(t,e){t.exports=ProtvistaSequence},function(t,e){t.exports=ProtvistaUtils},function(t,e){t.exports=function(t,e){if(!(t instanceof e))throw new TypeError("Cannot call a class as a function")}},function(t,e){function r(t,e){for(var r=0;r<e.length;r++){var n=e[r];n.enumerable=n.enumerable||!1,n.configurable=!0,"value"in n&&(n.writable=!0),Object.defineProperty(t,n.key,n)}}t.exports=function(t,e,n){return e&&r(t.prototype,e),n&&r(t,n),t}},function(t,e,r){var n=r(13),o=r(14);t.exports=function(t,e){return!e||"object"!==n(e)&&"function"!=typeof e?o(t):e}},function(t,e){function r(e){return t.exports=r=Object.setPrototypeOf?Object.getPrototypeOf:function(t){return t.__proto__||Object.getPrototypeOf(t)},r(e)}t.exports=r},function(t,e,r){var n=r(15);t.exports=function(t,e){if("function"!=typeof e&&null!==e)throw new TypeError("Super expression must either be null or a function");t.prototype=Object.create(e&&e.prototype,{constructor:{value:t,writable:!0,configurable:!0}}),e&&n(t,e)}},function(t){t.exports=JSON.parse('{"I":-0.31,"L":-0.56,"F":-1.13,"V":0.07,"M":-0.23,"P":0.45,"W":-1.85,"H":0.17,"T":0.14,"E":-0.01,"Q":0.58,"C":-0.24,"Y":-0.94,"A":0.17,"S":0.13,"N":0.42,"D":-0.07,"R":0.81,"G":0.01,"K":0.99}')},function(t){t.exports=JSON.parse('{"I":-1.12,"L":-1.25,"F":-1.71,"V":-0.46,"M":-0.67,"P":0.14,"W":-2.09,"H":0.11,"T":0.25,"E":0.11,"Q":0.77,"C":-0.02,"Y":-0.71,"A":0.5,"S":0.46,"N":0.85,"D":0.43,"R":1.15,"G":3.63,"K":3.64}')},function(t){t.exports=JSON.parse('{"I":-0.81,"L":-0.69,"F":-0.58,"V":-0.53,"M":-0.44,"P":-0.31,"W":-0.24,"H":-0.06,"T":0.11,"E":0.12,"Q":0.19,"C":0.22,"Y":0.23,"A":0.33,"S":0.33,"N":0.43,"D":0.5,"R":1.14,"G":1.61,"K":2.41}')},function(t){t.exports=JSON.parse('{"I":6.04,"L":6.04,"F":5.91,"V":6.02,"M":5.74,"P":6.3,"W":5.88,"H":7.64,"T":5.6,"E":3.08,"Q":5.65,"C":5.02,"Y":5.63,"A":6.11,"S":5.68,"N":5.41,"D":2.87,"R":10.76,"G":6.06,"K":9.47}')},function(t,e,r){t.exports=r(16)},function(t,e){function r(t){return(r="function"==typeof Symbol&&"symbol"==typeof Symbol.iterator?function(t){return typeof t}:function(t){return t&&"function"==typeof Symbol&&t.constructor===Symbol&&t!==Symbol.prototype?"symbol":typeof t})(t)}function n(e){return"function"==typeof Symbol&&"symbol"===r(Symbol.iterator)?t.exports=n=function(t){return r(t)}:t.exports=n=function(t){return t&&"function"==typeof Symbol&&t.constructor===Symbol&&t!==Symbol.prototype?"symbol":r(t)},n(e)}t.exports=n},function(t,e){t.exports=function(t){if(void 0===t)throw new ReferenceError("this hasn't been initialised - super() hasn't been called");return t}},function(t,e){function r(e,n){return t.exports=r=Object.setPrototypeOf||function(t,e){return t.__proto__=e,t},r(e,n)}t.exports=r},function(t,e,r){"use strict";r.r(e);var n=r(3),o=r.n(n),i=r(4),s=r.n(i),a=r(5),c=r.n(a),u=r(6),l=r.n(u),f=r(7),p=r.n(f),h=r(0),d=r(1),y=r.n(d),b=r(2),g=r(8),v=r(9),m=r(10),S=r(11),_=["hydrophobicity-interface-scale","hydrophobicity-octanol-scale","hydrophobicity-scale","isoelectric-point-scale"],x={domain:[-2,2],range:["#ffdd00","#0000FF"]},O=function(t){function e(){return o()(this,e),c()(this,l()(e).apply(this,arguments))}return p()(e,t),s()(e,[{key:"_createSequence",value:function(){this.svg=Object(h.select)(this).append("div").attr("class","").append("svg").attr("id","").attr("width",this.width).attr("height",this._height),this.uniqueID=Math.random().toString(36).substring(7),this.gradient=this.svg.append("defs").append("linearGradient").attr("id","scale-gradient-".concat(this.uniqueID)),this.seq_g=this.svg.append("g").attr("class","background"),this.seq_greadient=this.svg.append("rect").attr("class","seq-gradient").style("pointer-events","none"),this._getCharSize(),this.trackHighlighter.appendHighlightTo(this.svg),this.refresh()}},{key:"getScaleFromAttribute",value:function(){var t=null;if(_.indexOf(this._scale)>=0)switch(this._scale){case"hydrophobicity-scale":return m;case"hydrophobicity-interface-scale":return g;case"isoelectric-point-scale":return S;case"hydrophobicity-octanol-scale":return v;default:return null}if(/([ILFVMPWHTEQCYASNDRGK]:-?\d+\.?\d*)(,[ILFVMPWHTEQCYASNDRGK]:-?\d+\.?\d*)*/.test(this._scale))try{t=Object(b.String2Object)(this._scale,{keyFormatter:function(t){return t.toUpperCase()},valueFormatter:function(t){return parseFloat(t)}})}catch(t){console.error("Couldn't parse the given scale ".concat(this._scale),t)}return t}},{key:"refresh",value:function(){var t=this;if(this.seq_g){var e=this.getScaleFromAttribute();if(null===e)return void console.error("The attribute scale is not valid.");var r=Object(h.scaleLinear)();this.colorScale=x,this._color_range&&(this.colorScale=Object(b.ColorScaleParser)(this._color_range)),r.domain(this.colorScale.domain).range(this.colorScale.range);var n=this.getSingleBaseWidth(),o=Math.round(Math.max(0,this._displaystart-2)),i=Math.round(Math.min(this.sequence.length,this._displayend+1)),s=this.sequence.slice(o,i).split("").map(function(t,n){var i=t.toUpperCase()in e?e[t.toUpperCase()]:0;return{start:1+o+n,end:1+o+n,aa:t,value:i,colour:r(i)}});this.residues=this.seq_g.selectAll("rect.base_bg").data(n<8?[]:s,function(t){return t.start}),this.residues.enter().append("rect").attr("class","base_bg feature").attr("data-base",function(t){return t.aa}).attr("data-pos",function(t){return t.start}).attr("height",this._height).merge(this.residues).attr("width",n).attr("fill",function(t){return t.colour}).attr("x",function(e){var r=e.start;return t.getXFromSeqPosition(r)}).call(this.bindEvents,this),this.residues.exit().remove();var a=this.gradient.selectAll("stop").data(this.sequence.split(""));a.enter().append("stop").merge(a).attr("offset",function(e,r){return(r+.5)/t.sequence.length}).attr("stop-color",function(t){return r(t.toUpperCase()in e?e[t.toUpperCase()]:0)}),this.gradient.exit().remove(),this.seq_greadient.attr("x",this.getXFromSeqPosition(1)).attr("y",0).attr("height",this._height).attr("width",this.getXFromSeqPosition(this.sequence.length)-this.getXFromSeqPosition(0)).style("opacity",n<8?1:8/n).attr("fill","url(#scale-gradient-".concat(this.uniqueID,")")),this._updateHighlight()}}}],[{key:"observedAttributes",get:function(){return y.a.observedAttributes.concat("scale","color_range")}}]),e}(y.a),P=function(){customElements.define("protvista-coloured-sequence",O)};window.customElements?P():document.addEventListener("WebComponentsReady",function(){P()})}]);
 //# sourceMappingURL=protvista-coloured-sequence.js.map

package.json

 {
   "name": "protvista-coloured-sequence",
-  "version": "2.6.1",
+  "version": "2.7.0",
   "description": "Track that colors each base by a given function. The default function is hydrophobicity",
@@ -14,3 +14,3 @@ "files": [
   "dependencies": {
-    "protvista-sequence": "^2.6.1",
+    "protvista-sequence": "^2.7.0",
     "protvista-utils": "^2.3.0"
@@ -37,3 +37,3 @@ },
   },
-  "gitHead": "e2d43c39b15f9a84c88c20caf7a07ffcf5f9c5a8"
+  "gitHead": "5e555eaa38d9facc16ee276eaa4abd47c15a3a74"
 }

src/protvista-coloured-sequence.js

@@ -57,3 +57,3 @@ import { select, scaleLinear } from "d3";
 
-    this._getCharWidth();
+    this._getCharSize();
 
@@ -60,0 +60,0 @@ this.trackHighlighter.appendHighlightTo(this.svg);

New alerts

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Found 1 instance in 1 package

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A new npm collaborator published a version of the package for the first time. New collaborators are usually benign additions to a project, but do indicate a change to the security surface area of a package.

Found 1 instance in 1 package

Fixed alerts

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This package is not allowed per your license policy. Review the package's license to ensure compliance.

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Total package byte prevSize

39000

decreased by-0.01%

Number of medium supply chain risk alerts

1

increased byInfinity%

Dependency changes

• Updatedprotvista-sequence@^2.7.0