jbrowse-plugin-msaview 1.0.17 → 1.0.18

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Files changed (9) hide show
  1. package/CHANGELOG.md +4 -0
  2. package/dist/jbrowse-plugin-msaview.cjs.development.js +1 -1
  3. package/dist/jbrowse-plugin-msaview.cjs.production.min.js +1 -1
  4. package/dist/jbrowse-plugin-msaview.esm.js +1 -1
  5. package/dist/jbrowse-plugin-msaview.umd.development.js +61 -43
  6. package/dist/jbrowse-plugin-msaview.umd.development.js.map +1 -1
  7. package/dist/jbrowse-plugin-msaview.umd.production.min.js +1 -1
  8. package/dist/jbrowse-plugin-msaview.umd.production.min.js.map +1 -1
  9. package/package.json +1 -1
package/dist/jbrowse-plugin-msaview.umd.production.min.js CHANGED
@@ -1,2 +1,2 @@
1
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Redistributions of source code must retain the above copyright notice, this\nlist of conditions and the following disclaimer.\n\n2. Redistributions in binary form must reproduce the above copyright notice,\nthis list of conditions and the following disclaimer in the documentation and/or\nother materials provided with the distribution.\n\n3. Neither the name of the copyright holder nor the names of its contributors\nmay be used to endorse or promote products derived from this software without\nspecific prior written permission.\n\nTHIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND\nANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED\nWARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE\nDISCLAIMED. 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t,n=e[0]/255,r=e[1]/255,o=e[2]/255;return[100*((1-n-(t=Math.min(1-n,1-r,1-o)))/(1-t)||0),100*((1-r-t)/(1-t)||0),100*((1-o-t)/(1-t)||0),100*t]},r.rgb.keyword=function(e){var n=t[e];if(n)return n;var r,o,a,i=Infinity;for(var l in Oe)if(Oe.hasOwnProperty(l)){var s=(o=e,a=Oe[l],Math.pow(o[0]-a[0],2)+Math.pow(o[1]-a[1],2)+Math.pow(o[2]-a[2],2));s<i&&(i=s,r=l)}return r},r.keyword.rgb=function(e){return Oe[e]},r.rgb.xyz=function(e){var t=e[0]/255,n=e[1]/255,r=e[2]/255;return[100*(.4124*(t=t>.04045?Math.pow((t+.055)/1.055,2.4):t/12.92)+.3576*(n=n>.04045?Math.pow((n+.055)/1.055,2.4):n/12.92)+.1805*(r=r>.04045?Math.pow((r+.055)/1.055,2.4):r/12.92)),100*(.2126*t+.7152*n+.0722*r),100*(.0193*t+.1192*n+.9505*r)]},r.rgb.lab=function(e){var t=r.rgb.xyz(e),n=t[0],o=t[1],a=t[2];return o/=100,a/=108.883,n=(n/=95.047)>.008856?Math.pow(n,1/3):7.787*n+16/116,[116*(o=o>.008856?Math.pow(o,1/3):7.787*o+16/116)-16,500*(n-o),200*(o-(a=a>.008856?Math.pow(a,1/3):7.787*a+16/116))]},r.hsl.rgb=function(e){var t,n,r,o,a,i=e[0]/360,l=e[1]/100,s=e[2]/100;if(0===l)return[a=255*s,a,a];t=2*s-(n=s<.5?s*(1+l):s+l-s*l),o=[0,0,0];for(var c=0;c<3;c++)(r=i+1/3*-(c-1))<0&&r++,r>1&&r--,o[c]=255*(a=6*r<1?t+6*(n-t)*r:2*r<1?n:3*r<2?t+(n-t)*(2/3-r)*6:t);return o},r.hsl.hsv=function(e){var t=e[0],n=e[1]/100,r=e[2]/100,o=n,a=Math.max(r,.01);return n*=(r*=2)<=1?r:2-r,o*=a<=1?a:2-a,[t,100*(0===r?2*o/(a+o):2*n/(r+n)),(r+n)/2*100]},r.hsv.rgb=function(e){var t=e[0]/60,n=e[1]/100,r=e[2]/100,o=Math.floor(t)%6,a=t-Math.floor(t),i=255*r*(1-n),l=255*r*(1-n*a),s=255*r*(1-n*(1-a));switch(r*=255,o){case 0:return[r,s,i];case 1:return[l,r,i];case 2:return[i,r,s];case 3:return[i,l,r];case 4:return[s,i,r];case 5:return[r,i,l]}},r.hsv.hsl=function(e){var t,n,r,o=e[0],a=e[1]/100,i=e[2]/100,l=Math.max(i,.01);return r=(2-a)*i,n=a*l,[o,100*(n=(n/=(t=(2-a)*l)<=1?t:2-t)||0),100*(r/=2)]},r.hwb.rgb=function(e){var t,n,r,o,a,i,l,s=e[0]/360,c=e[1]/100,u=e[2]/100,f=c+u;switch(f>1&&(c/=f,u/=f),r=6*s-(t=Math.floor(6*s)),0!=(1&t)&&(r=1-r),o=c+r*((n=1-u)-c),t){default:case 6:case 0:a=n,i=o,l=c;break;case 1:a=o,i=n,l=c;break;case 2:a=c,i=n,l=o;break;case 3:a=c,i=o,l=n;break;case 4:a=o,i=c,l=n;break;case 5:a=n,i=c,l=o}return[255*a,255*i,255*l]},r.cmyk.rgb=function(e){var t=e[1]/100,n=e[2]/100,r=e[3]/100;return[255*(1-Math.min(1,e[0]/100*(1-r)+r)),255*(1-Math.min(1,t*(1-r)+r)),255*(1-Math.min(1,n*(1-r)+r))]},r.xyz.rgb=function(e){var t,n,r,o=e[0]/100,a=e[1]/100,i=e[2]/100;return n=-.9689*o+1.8758*a+.0415*i,r=.0557*o+-.204*a+1.057*i,t=(t=3.2406*o+-1.5372*a+-.4986*i)>.0031308?1.055*Math.pow(t,1/2.4)-.055:12.92*t,n=n>.0031308?1.055*Math.pow(n,1/2.4)-.055:12.92*n,r=r>.0031308?1.055*Math.pow(r,1/2.4)-.055:12.92*r,[255*(t=Math.min(Math.max(0,t),1)),255*(n=Math.min(Math.max(0,n),1)),255*(r=Math.min(Math.max(0,r),1))]},r.xyz.lab=function(e){var t=e[0],n=e[1],r=e[2];return n/=100,r/=108.883,t=(t/=95.047)>.008856?Math.pow(t,1/3):7.787*t+16/116,[116*(n=n>.008856?Math.pow(n,1/3):7.787*n+16/116)-16,500*(t-n),200*(n-(r=r>.008856?Math.pow(r,1/3):7.787*r+16/116))]},r.lab.xyz=function(e){var t,n,r;t=e[1]/500+(n=(e[0]+16)/116),r=n-e[2]/200;var o=Math.pow(n,3),a=Math.pow(t,3),i=Math.pow(r,3);return n=o>.008856?o:(n-16/116)/7.787,t=a>.008856?a:(t-16/116)/7.787,r=i>.008856?i:(r-16/116)/7.787,[t*=95.047,n*=100,r*=108.883]},r.lab.lch=function(e){var t,n=e[0],r=e[1],o=e[2];return(t=360*Math.atan2(o,r)/2/Math.PI)<0&&(t+=360),[n,Math.sqrt(r*r+o*o),t]},r.lch.lab=function(e){var t,n=e[1];return t=e[2]/360*2*Math.PI,[e[0],n*Math.cos(t),n*Math.sin(t)]},r.rgb.ansi16=function(e){var t=e[0],n=e[1],o=e[2],a=1 in arguments?arguments[1]:r.rgb.hsv(e)[2];if(0===(a=Math.round(a/50)))return 30;var i=30+(Math.round(o/255)<<2|Math.round(n/255)<<1|Math.round(t/255));return 2===a&&(i+=60),i},r.hsv.ansi16=function(e){return r.rgb.ansi16(r.hsv.rgb(e),e[2])},r.rgb.ansi256=function(e){var t=e[0],n=e[1],r=e[2];return t===n&&n===r?t<8?16:t>248?231:Math.round((t-8)/247*24)+232:16+36*Math.round(t/255*5)+6*Math.round(n/255*5)+Math.round(r/255*5)},r.ansi16.rgb=function(e){var t=e%10;if(0===t||7===t)return e>50&&(t+=3.5),[t=t/10.5*255,t,t];var n=.5*(1+~~(e>50));return[(1&t)*n*255,(t>>1&1)*n*255,(t>>2&1)*n*255]},r.ansi256.rgb=function(e){if(e>=232){var t=10*(e-232)+8;return[t,t,t]}var n;return e-=16,[Math.floor(e/36)/5*255,Math.floor((n=e%36)/6)/5*255,n%6/5*255]},r.rgb.hex=function(e){var t=(((255&Math.round(e[0]))<<16)+((255&Math.round(e[1]))<<8)+(255&Math.round(e[2]))).toString(16).toUpperCase();return"000000".substring(t.length)+t},r.hex.rgb=function(e){var t=e.toString(16).match(/[a-f0-9]{6}|[a-f0-9]{3}/i);if(!t)return[0,0,0];var n=t[0];3===t[0].length&&(n=n.split("").map((function(e){return e+e})).join(""));var r=parseInt(n,16);return[r>>16&255,r>>8&255,255&r]},r.rgb.hcg=function(e){var t,n=e[0]/255,r=e[1]/255,o=e[2]/255,a=Math.max(Math.max(n,r),o),i=Math.min(Math.min(n,r),o),l=a-i;return t=l<=0?0:a===n?(r-o)/l%6:a===r?2+(o-n)/l:4+(n-r)/l+4,t/=6,[360*(t%=1),100*l,100*(l<1?i/(1-l):0)]},r.hsl.hcg=function(e){var t,n=e[1]/100,r=e[2]/100,o=0;return(t=r<.5?2*n*r:2*n*(1-r))<1&&(o=(r-.5*t)/(1-t)),[e[0],100*t,100*o]},r.hsv.hcg=function(e){var t=e[2]/100,n=e[1]/100*t,r=0;return n<1&&(r=(t-n)/(1-n)),[e[0],100*n,100*r]},r.hcg.rgb=function(e){var t=e[1]/100,n=e[2]/100;if(0===t)return[255*n,255*n,255*n];var r,o=[0,0,0],a=e[0]/360%1*6,i=a%1,l=1-i;switch(Math.floor(a)){case 0:o[0]=1,o[1]=i,o[2]=0;break;case 1:o[0]=l,o[1]=1,o[2]=0;break;case 2:o[0]=0,o[1]=1,o[2]=i;break;case 3:o[0]=0,o[1]=l,o[2]=1;break;case 4:o[0]=i,o[1]=0,o[2]=1;break;default:o[0]=1,o[1]=0,o[2]=l}return[255*(t*o[0]+(r=(1-t)*n)),255*(t*o[1]+r),255*(t*o[2]+r)]},r.hcg.hsv=function(e){var t=e[1]/100,n=t+e[2]/100*(1-t),r=0;return n>0&&(r=t/n),[e[0],100*r,100*n]},r.hcg.hsl=function(e){var t=e[1]/100,n=e[2]/100*(1-t)+.5*t,r=0;return n>0&&n<.5?r=t/(2*n):n>=.5&&n<1&&(r=t/(2*(1-n))),[e[0],100*r,100*n]},r.hcg.hwb=function(e){var t=e[1]/100,n=t+e[2]/100*(1-t);return[e[0],100*(n-t),100*(1-n)]},r.hwb.hcg=function(e){var t=1-e[2]/100,n=t-e[1]/100,r=0;return n<1&&(r=(t-n)/(1-n)),[e[0],100*n,100*r]},r.apple.rgb=function(e){return[e[0]/65535*255,e[1]/65535*255,e[2]/65535*255]},r.rgb.apple=function(e){return[e[0]/255*65535,e[1]/255*65535,e[2]/255*65535]},r.gray.rgb=function(e){return[e[0]/100*255,e[0]/100*255,e[0]/100*255]},r.gray.hsl=r.gray.hsv=function(e){return[0,0,e[0]]},r.gray.hwb=function(e){return[0,100,e[0]]},r.gray.cmyk=function(e){return[0,0,0,e[0]]},r.gray.lab=function(e){return[e[0],0,0]},r.gray.hex=function(e){var t=255&Math.round(e[0]/100*255),n=((t<<16)+(t<<8)+t).toString(16).toUpperCase();return"000000".substring(n.length)+n},r.rgb.gray=function(e){return[(e[0]+e[1]+e[2])/3/255*100]}}));function De(e,t){return function(n){return t(e(n))}}function Ne(e,t){for(var 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0:t.getTree())||{noTree:!0}},get rowNames(){return this.hierarchy.leaves().map((function(e){return e.data.name}))},get mouseOverRowName(){return void 0!==e.mouseRow?this.rowNames[e.mouseRow]:void 0},getMouseOverResidue:function(e){return this.columns[e]},get root(){var t=Ft(this.tree,(function(e){return e.branchset})).sum((function(e){return e.branchset?0:1})).sort((function(e,t){return function(e,t){return e<t?-1:e>t?1:e>=t?0:NaN}(e.data.length||1,t.data.length||1)}));if(e.showOnly){var n=t.find((function(t){return t.data.id===e.showOnly}));n&&(t=n)}return e.collapsed.length&&e.collapsed.map((function(e){return t.find((function(t){return t.data.id===e}))})).filter((function(e){return!!e})).map((function(e){return Rn(e)})),t},get structures(){var e;return(null===(e=this.MSA)||void 0===e?void 0:e.getStructures())||{}},get inverseStructures(){var e=Object.entries(this.structures).map((function(e){var t=e[0];return e[1].map((function(e){return[e.pdb,{id:t}]}))})).flat();return Object.fromEntries(e)},get msaAreaWidth(){return e.width-e.treeAreaWidth},get blanks(){for(var e,t=this,n=[],r=this.hierarchy.leaves().map((function(e){var n;return null===(n=t.MSA)||void 0===n?void 0:n.getRow(e.data.name)})).filter((function(e){return!!e})),o=0;o<(null===(e=r[0])||void 0===e?void 0:e.length);o++){for(var a=0,i=0;i<r.length;i++)"-"===r[i][o]&&a++;a===r.length&&n.push(o)}return n},get rows(){var e=this;return this.hierarchy.leaves().map((function(t){var n,r=t.data;return[r.name,null===(n=e.MSA)||void 0===n?void 0:n.getRow(r.name)]})).filter((function(e){return!!e[1]}))},get columns(){var e=this.columns2d;return Object.fromEntries(this.rows.map((function(t,n){return[t[0],e[n]]})))},get columns2d(){for(var e=this.rows.map((function(e){return e[1]})),t=[],n=0;n<e.length;n++)t.push(Pn(this.blanks,e[n]));return t},get colStats(){for(var e=[],t=this.columns2d,n=0;n<t.length;n++)for(var r=0;r<t[n].length;r++){var o=e[r]||{};o[t[n][r]]||(o[t[n][r]]=0),o[t[n][r]]++,e[r]=o}return e},get hierarchy(){var t=this.root;return function(){var e=Dt,t=1,n=1,r=!1;function o(o){var a,i=0;o.eachAfter((function(t){var n=t.children;n?(t.x=function(e){return e.reduce(Nt,0)/e.length}(n),t.y=function(e){return 1+e.reduce(jt,0)}(n)):(t.x=a?i+=e(t,a):0,t.y=0,a=t)}));var l=function(e){for(var t;t=e.children;)e=t[0];return e}(o),s=function(e){for(var t;t=e.children;)e=t[t.length-1];return e}(o),c=l.x-e(l,s)/2,u=s.x+e(s,l)/2;return o.eachAfter(r?function(e){e.x=(e.x-o.x)*t,e.y=(o.y-e.y)*n}:function(e){e.x=(e.x-c)/(u-c)*t,e.y=(1-(o.y?e.y/o.y:1))*n})}return o.separation=function(t){return arguments.length?(e=t,o):e},o.size=function(e){return arguments.length?(r=!1,t=+e[0],n=+e[1],o):r?null:[t,n]},o.nodeSize=function(e){return arguments.length?(r=!0,t=+e[0],n=+e[1],o):r?[t,n]:null},o}().size([this.totalHeight,e.treeWidth]).separation((function(){return 1}))(t),function e(t,n,r){var o;t.len=(n+=Math.max(t.data.length||0,0))*r,null===(o=t.children)||void 0===o||o.forEach((function(t){e(t,n,r)}))}(t,t.data.length=0,e.treeWidth/On(t)),t},get totalHeight(){return this.root.leaves().length*e.rowHeight}}})).actions((function(e){return{addUniprotTrack:function(t){e.boxTracks.find((function(e){return e.name===t.name}))?e.turnedOffTracks.has(t.name)&&this.toggleTrack(t.name):e.boxTracks.push(kn(kn({},t),{id:t.name,associatedRowName:t.name}))},doScrollY:function(t){e.scrollY=Dn(10-e.totalHeight,e.scrollY+t,0)},doScrollX:function(t){e.scrollX=Dn(e.msaAreaWidth-100-e.numColumns,e.scrollX+t,0)},setMouseoveredColumn:function(t,n,r){var o,a=0,i=0,l=(e.inverseStructures[r.slice(0,-4)]||{}).id,s=null===(o=e.MSA)||void 0===o?void 0:o.getRow(l);if(s){for(i=0;i<s.length&&a<t;i++)"-"!==s[i]&&a++;e.mouseCol=a+1}else e.mouseCol=void 0},toggleTrack:function(t){e.turnedOffTracks.has(t)?e.turnedOffTracks.delete(t):e.turnedOffTracks.set(t,!0)}}})).views((function(e){return{get secondaryStructureConsensus(){var t;return null===(t=e.MSA)||void 0===t?void 0:t.secondaryStructureConsensus},get seqConsensus(){var t;return null===(t=e.MSA)||void 0===t?void 0:t.seqConsensus},get conservation(){var t=e.columns2d;if(t.length)for(var n=0;n<t[0].length;n++)for(var r=[],o=0;o<t.length;o++)r.push(t[o][n]);return["a"]},get tracks(){var t=e.blanks,n=e.MSA?e.MSA.tracks.map((function(n){var r=n.data;return{model:kn(kn({},n),{data:r?Pn(t,r):void 0,height:e.rowHeight}),ReactComponent:Sn}})):[],r=e.boxTracks.filter((function(t){return!!e.rows.find((function(e){return e[0]===t.name}))})).map((function(e){return{model:e,ReactComponent:An}})),o=e.annotatedRegions.length>0?[{model:{features:e.annotatedRegions,height:100,id:"annotations",name:"User-created annotations",data:e.annotatedRegions.map((function(e){var t=e.attributes?Object.entries(e.attributes).map((function(e){var t=e[1];return"".concat(e[0],"=").concat(t.join(","))})).join(";"):".";return["MSA_refcoord",".",".",e.start,e.end,".",".",".",t].join("\t")})).join("\n")},ReactComponent:An}]:[];return Cn(Cn(Cn([],n,!0),r,!0),o,!0)},get turnedOnTracks(){return this.tracks.filter((function(t){return!e.turnedOffTracks.has(t.model.id)}))},pxToBp:function(t){return Math.floor((t-e.scrollX)/e.colWidth)},rowSpecificBpToPx:function(t,n){var r,o=e.blanks,a=e.rows[e.rowNames.indexOf(t)][1],i=n-((null===(r=e.getRowDetails(t).range)||void 0===r?void 0:r.start)||0);if(i<0)return 0;for(var l=0,s=0;s<a.length&&("-"===a[s]||l++!==i);s++);for(var c=0,u=0;u<a.length;u++)-1!==o.indexOf(u)&&u<s+1&&c++;return s-c},globalBpToPx:function(t){for(var n,r=0,o=0;o<(null===(n=e.rows[0])||void 0===n?void 0:n[1].length);o++)-1!==e.blanks.indexOf(o)&&o<t+1&&r++;return t-r},relativePxToBp:function(t,n){for(var r=e.rows[e.rowNames.indexOf(t)][1],o=0,a=0;a<n;a++)if("-"!==r[a])o++;else if(o>=n)break;return o},getPos:function(t){for(var n=0,r=0,o=0;r<t;r++,n++)for(;n===e.blanks[o];)o++,n++;return n}}})).actions((function(e){return{addAnnotation:function(t,n,r){e.annotatedRegions.push({start:e.getPos(t),end:e.getPos(n),attributes:r})},setOffsets:function(t,n){e.annotPos={left:t,right:n}},clearAnnotPos:function(){e.annotPos=void 0}}})),Fn=u.types.snapshotProcessor(u.types.compose(hn,In),{postProcessor:function(e){var t=e.data,n=t.tree,r=t.msa,o=function(e,t){var n={};for(var r in e)Object.prototype.hasOwnProperty.call(e,r)&&t.indexOf(r)<0&&(n[r]=e[r]);if(null!=e&&"function"==typeof Object.getOwnPropertySymbols){var o=0;for(r=Object.getOwnPropertySymbols(e);o<r.length;o++)t.indexOf(r[o])<0&&Object.prototype.propertyIsEnumerable.call(e,r[o])&&(n[r[o]]=e[r[o]])}return n}(e,["data"]);return kn({data:kn(kn({},!e.treeFilehandle&&{tree:n}),!e.msaFilehandle&&{msa:r})},o)}}),_n={__proto__:null,MSAModel:Fn,MSAView:Rt},Bn=A(k((function(e,t){Object.defineProperty(t,"__esModule",{value:!0}),t.default=void 0;var n=C(p),r=(0,L(P).default)(n.createElement("path",{d:"M20 2H4c-1.1 0-2 .9-2 2v16c0 1.1.9 2 2 2h16c1.1 0 2-.9 2-2V4c0-1.1-.9-2-2-2zM8 20H4v-4h4v4zm0-6H4v-4h4v4zm0-6H4V4h4v4zm6 12h-4v-4h4v4zm0-6h-4v-4h4v4zm0-6h-4V4h4v4zm6 12h-4v-4h4v4zm0-6h-4v-4h4v4zm0-6h-4V4h4v4z"}),"GridOn");t.default=r})));e.default=function(e){!function(e,t){if("function"!=typeof t&&null!==t)throw new TypeError("Super expression must either be null or a function");e.prototype=Object.create(t&&t.prototype,{constructor:{value:e,writable:!0,configurable:!0}}),t&&w(e,t)}(o,e);var t,r=S(o);function o(){var e;return b(this,o),(e=r.apply(this,arguments)).name="MsaViewPlugin",e.version="1.0.18",e}return(t=[{key:"install",value:function(e){console.log({MSA:_n}),e.addViewType((function(){return new m({name:"MsaView",stateModel:Fn,ReactComponent:Rt})}))}},{key:"configure",value:function(e){n.isAbstractMenuManager(e.rootModel)&&e.rootModel.appendToSubMenu(["Add"],{label:"Multiple sequence alignment view",icon:Bn,onClick:function(e){e.addView("MsaView",{})}})}}])&&function(e,t){for(var n=0;n<t.length;n++){var r=t[n];r.enumerable=r.enumerable||!1,r.configurable=!0,"value"in r&&(r.writable=!0),Object.defineProperty(e,r.key,r)}}(o.prototype,t),o}(t),Object.defineProperty(e,"__esModule",{value:!0})}));
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