From 4b603dc9a499022cb2cac1e0375e9af3b512983b Mon Sep 17 00:00:00 2001
From: colin-combe <colin.combe@ed.ac.uk>
Date: Tue, 19 Oct 2021 15:33:50 +0100
Subject: [PATCH 1/2] fix for collapsing proteins from table (keep them on
 screen)

---
 dist/complexviewer.js               |  2 +-
 package.json                        |  2 +-
 src/js/app.js                       |  2 +-
 src/js/viz/interactor/interactor.js |  6 +++++-
 src/js/viz/interactor/polymer.js    | 15 +++++++++++++++
 5 files changed, 23 insertions(+), 4 deletions(-)

diff --git a/dist/complexviewer.js b/dist/complexviewer.js
index fa49406..a09b40c 100644
--- a/dist/complexviewer.js
+++ b/dist/complexviewer.js
@@ -22,4 +22,4 @@
  *
  * Date: 2021-02-16
  */
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h=[],p=0;c.forEach((function(a){0===a.type?(h.push(a.s),p++):p--,0==p&&(t.nudgeSegs(n,r,e,h,i,o),h=[])}))}},t.prototype.routeEdges=function(e,n,r,i){var o=this,a=e.map((function(t){return o.route(r(t),i(t))})),s=t.orderEdges(a),u=a.map((function(e){return t.makeSegments(e)}));return t.nudgeSegments(u,"x","y",s,n),t.nudgeSegments(u,"y","x",s,n),t.unreverseEdges(u,a),u},t.unreverseEdges=function(t,e){t.forEach((function(t,n){e[n].reversed&&(t.reverse(),t.forEach((function(t){t.reverse()})))}))},t.angleBetween2Lines=function(t,e){var n=Math.atan2(t[0].y-t[1].y,t[0].x-t[1].x),r=Math.atan2(e[0].y-e[1].y,e[0].x-e[1].x),i=n-r;return(i>Math.PI||i<-Math.PI)&&(i=r-n),i},t.isLeft=function(t,e,n){return(e.x-t.x)*(n.y-t.y)-(e.y-t.y)*(n.x-t.x)<=0},t.getOrder=function(t){for(var e={},n=0;n<t.length;n++){var r=t[n];void 0===e[r.l]&&(e[r.l]={}),e[r.l][r.r]=!0}return function(t,n){return void 0!==e[t]&&e[t][n]}},t.orderEdges=function(e){for(var n=[],r=0;r<e.length-1;r++)for(var i=r+1;i<e.length;i++){var 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a||r.node&&r.node.id in a)}));for(var s=1;s<r.ports.length;s++){var u=r.ports[0].id,c=r.ports[s].id;this.passableEdges.push({source:u,target:c,length:0})}for(s=1;s<i.ports.length;s++)u=i.ports[0].id,c=i.ports[s].id,this.passableEdges.push({source:u,target:c,length:0});var l=new o.Calculator(this.verts.length,this.passableEdges,(function(t){return t.source}),(function(t){return t.target}),(function(t){return t.length})).PathFromNodeToNodeWithPrevCost(r.ports[0].id,i.ports[0].id,(function(t,e,o){var a=n.verts[t],s=n.verts[e],u=n.verts[o],c=Math.abs(u.x-a.x),l=Math.abs(u.y-a.y);return a.node===r&&a.node===s.node||s.node===i&&s.node===u.node?0:c>1&&l>1?1e3:0})).reverse().map((function(t){return n.verts[t]}));return l.push(this.nodes[i.id].ports[0]),l.filter((function(t,e){return!(e<l.length-1&&l[e+1].node===r&&t.node===r||e>0&&t.node===i&&l[e-1].node===i)}))},t.getRoutePath=function(e,n,r,i){var o,a,s,u={routepath:"M "+e[0][0].x+" "+e[0][0].y+" ",arrowpath:""};if(e.length>1)for(var c=0;c<e.length;c++){var l=(o=e[c])[1].x,f=o[1].y,h=l-o[0].x,p=f-o[0].y;if(c<e.length-1){Math.abs(h)>0?l-=h/Math.abs(h)*n:f-=p/Math.abs(p)*n,u.routepath+="L "+l+" "+f+" ";var d=e[c+1],y=d[0].x,g=d[0].y;h=d[1].x-y,p=d[1].y-g;var v,x,m=t.angleBetween2Lines(o,d)<0?1:0;Math.abs(h)>0?(v=y+h/Math.abs(h)*n,x=g):(v=y,x=g+p/Math.abs(p)*n);var b=Math.abs(v-l),w=Math.abs(x-f);u.routepath+="A "+b+" "+w+" 0 0 "+m+" "+v+" "+x+" "}else{var k=[l,f];Math.abs(h)>0?(a=[l-=h/Math.abs(h)*i,f+r],s=[l,f-r]):(a=[l+r,f-=p/Math.abs(p)*i],s=[l-r,f]),u.routepath+="L "+l+" "+f+" ",i>0&&(u.arrowpath="M "+k[0]+" "+k[1]+" L "+a[0]+" "+a[1]+" L "+s[0]+" "+s[1])}}else l=(o=e[0])[1].x,f=o[1].y,h=l-o[0].x,p=f-o[0].y,k=[l,f],Math.abs(h)>0?(a=[l-=h/Math.abs(h)*i,f+r],s=[l,f-r]):(a=[l+r,f-=p/Math.abs(p)*i],s=[l-r,f]),u.routepath+="L "+l+" "+f+" ",i>0&&(u.arrowpath="M "+k[0]+" "+k[1]+" L "+a[0]+" "+a[1]+" L "+s[0]+" "+s[1]);return 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n=e.x-t.width/2,r=e.y-t.height/2,i=t.x-n+c/2-f/2,o=t.y-r+l/2-h/2;t.array.forEach((function(t){t.x+=i,t.y+=o}))}))}(t))},n.separateGraphs=function(t,e){for(var n={},r={},i=[],o=0,a=0;a<e.length;a++){var s=e[a],u=s.source,c=s.target;r[u.index]?r[u.index].push(c):r[u.index]=[c],r[c.index]?r[c.index].push(u):r[c.index]=[u]}for(a=0;a<t.length;a++){var l=t[a];n[l.index]||f(l,!0)}function f(t,e){if(void 0===n[t.index]){e&&(o++,i.push({array:[]})),n[t.index]=o,i[o-1].array.push(t);var a=r[t.index];if(a)for(var s=0;s<a.length;s++)f(a[s],!1)}}return i}},{}],11:[function(t,e,n){"use strict";Object.defineProperty(n,"__esModule",{value:!0});var r,i=t("./powergraph"),o=t("./linklengths"),a=t("./descent"),s=t("./rectangle"),u=t("./shortestpaths"),c=t("./geom"),l=t("./handledisconnected");function f(t){return void 0!==t.leaves||void 0!==t.groups}!function(t){t[t.start=0]="start",t[t.tick=1]="tick",t[t.end=2]="end"}(r=n.EventType||(n.EventType={}));var h=function(){function t(){var e=this;this._canvasSize=[1,1],this._linkDistance=20,this._defaultNodeSize=10,this._linkLengthCalculator=null,this._linkType=null,this._avoidOverlaps=!1,this._handleDisconnected=!0,this._running=!1,this._nodes=[],this._groups=[],this._rootGroup=null,this._links=[],this._constraints=[],this._distanceMatrix=null,this._descent=null,this._directedLinkConstraints=null,this._threshold=.01,this._visibilityGraph=null,this._groupCompactness=1e-6,this.event=null,this.linkAccessor={getSourceIndex:t.getSourceIndex,getTargetIndex:t.getTargetIndex,setLength:t.setLinkLength,getType:function(t){return"function"==typeof e._linkType?e._linkType(t):0}}}return t.prototype.on=function(t,e){return this.event||(this.event={}),"string"==typeof t?this.event[r[t]]=e:this.event[t]=e,this},t.prototype.trigger=function(t){this.event&&void 0!==this.event[t.type]&&this.event[t.type](t)},t.prototype.kick=function(){for(;!this.tick(););},t.prototype.tick=function(){if(this._alpha<this._threshold)return this._running=!1,this.trigger({type:r.end,alpha:this._alpha=0,stress:this._lastStress}),!0;var t,e,n=this._nodes.length;for(this._links.length,this._descent.locks.clear(),e=0;e<n;++e)if((t=this._nodes[e]).fixed){void 0!==t.px&&void 0!==t.py||(t.px=t.x,t.py=t.y);var i=[t.px,t.py];this._descent.locks.add(e,i)}var o=this._descent.rungeKutta();return 0===o?this._alpha=0:void 0!==this._lastStress&&(this._alpha=o),this._lastStress=o,this.updateNodePositions(),this.trigger({type:r.tick,alpha:this._alpha,stress:this._lastStress}),!1},t.prototype.updateNodePositions=function(){for(var t,e=this._descent.x[0],n=this._descent.x[1],r=this._nodes.length;r--;)(t=this._nodes[r]).x=e[r],t.y=n[r]},t.prototype.nodes=function(t){if(!t){if(0===this._nodes.length&&this._links.length>0){var e=0;this._links.forEach((function(t){e=Math.max(e,t.source,t.target)})),this._nodes=new Array(++e);for(var n=0;n<e;++n)this._nodes[n]={}}return this._nodes}return this._nodes=t,this},t.prototype.groups=function(t){var e=this;return t?(this._groups=t,this._rootGroup={},this._groups.forEach((function(t){void 0===t.padding&&(t.padding=1),void 0!==t.leaves&&t.leaves.forEach((function(n,r){"number"==typeof n&&((t.leaves[r]=e._nodes[n]).parent=t)})),void 0!==t.groups&&t.groups.forEach((function(n,r){"number"==typeof n&&((t.groups[r]=e._groups[n]).parent=t)}))})),this._rootGroup.leaves=this._nodes.filter((function(t){return void 0===t.parent})),this._rootGroup.groups=this._groups.filter((function(t){return void 0===t.parent})),this):this._groups},t.prototype.powerGraphGroups=function(t){var e=i.getGroups(this._nodes,this._links,this.linkAccessor,this._rootGroup);return this.groups(e.groups),t(e),this},t.prototype.avoidOverlaps=function(t){return arguments.length?(this._avoidOverlaps=t,this):this._avoidOverlaps},t.prototype.handleDisconnected=function(t){return arguments.length?(this._handleDisconnected=t,this):this._handleDisconnected},t.prototype.flowLayout=function(t,e){return arguments.length||(t="y"),this._directedLinkConstraints={axis:t,getMinSeparation:"number"==typeof e?function(){return e}:e},this},t.prototype.links=function(t){return arguments.length?(this._links=t,this):this._links},t.prototype.constraints=function(t){return arguments.length?(this._constraints=t,this):this._constraints},t.prototype.distanceMatrix=function(t){return arguments.length?(this._distanceMatrix=t,this):this._distanceMatrix},t.prototype.size=function(t){return t?(this._canvasSize=t,this):this._canvasSize},t.prototype.defaultNodeSize=function(t){return t?(this._defaultNodeSize=t,this):this._defaultNodeSize},t.prototype.groupCompactness=function(t){return t?(this._groupCompactness=t,this):this._groupCompactness},t.prototype.linkDistance=function(t){return t?(this._linkDistance="function"==typeof t?t:+t,this._linkLengthCalculator=null,this):this._linkDistance},t.prototype.linkType=function(t){return this._linkType=t,this},t.prototype.convergenceThreshold=function(t){return t?(this._threshold="function"==typeof t?t:+t,this):this._threshold},t.prototype.alpha=function(t){return arguments.length?(t=+t,this._alpha?this._alpha=t>0?t:0:t>0&&(this._running||(this._running=!0,this.trigger({type:r.start,alpha:this._alpha=t}),this.kick())),this):this._alpha},t.prototype.getLinkLength=function(t){return"function"==typeof this._linkDistance?+this._linkDistance(t):this._linkDistance},t.setLinkLength=function(t,e){t.length=e},t.prototype.getLinkType=function(t){return"function"==typeof this._linkType?this._linkType(t):0},t.prototype.symmetricDiffLinkLengths=function(t,e){var n=this;return void 0===e&&(e=1),this.linkDistance((function(e){return t*e.length})),this._linkLengthCalculator=function(){return o.symmetricDiffLinkLengths(n._links,n.linkAccessor,e)},this},t.prototype.jaccardLinkLengths=function(t,e){var n=this;return void 0===e&&(e=1),this.linkDistance((function(e){return t*e.length})),this._linkLengthCalculator=function(){return o.jaccardLinkLengths(n._links,n.linkAccessor,e)},this},t.prototype.start=function(e,n,r,i,c,l){var f=this;void 0===e&&(e=0),void 0===n&&(n=0),void 0===r&&(r=0),void 0===i&&(i=0),void 0===c&&(c=!0),void 0===l&&(l=!0);var h,p=this.nodes().length,d=p+2*this._groups.length,y=(this._links.length,this._canvasSize[0]),g=this._canvasSize[1],v=new Array(d),x=new Array(d),m=null,b=this._avoidOverlaps;this._nodes.forEach((function(t,e){t.index=e,void 0===t.x&&(t.x=y/2,t.y=g/2),v[e]=t.x,x[e]=t.y})),this._linkLengthCalculator&&this._linkLengthCalculator(),this._distanceMatrix?h=this._distanceMatrix:(h=new u.Calculator(d,this._links,t.getSourceIndex,t.getTargetIndex,(function(t){return f.getLinkLength(t)})).DistanceMatrix(),m=a.Descent.createSquareMatrix(d,(function(){return 2})),this._links.forEach((function(t){"number"==typeof t.source&&(t.source=f._nodes[t.source]),"number"==typeof t.target&&(t.target=f._nodes[t.target])})),this._links.forEach((function(e){var n=t.getSourceIndex(e),r=t.getTargetIndex(e);m[n][r]=m[r][n]=e.weight||1})));var w=a.Descent.createSquareMatrix(d,(function(t,e){return h[t][e]}));if(this._rootGroup&&void 0!==this._rootGroup.groups){var k=p;this._groups.forEach((function(t){!function(t,e,n,r){m[t][e]=m[e][t]=n,w[t][e]=w[e][t]=r}(k,k+1,f._groupCompactness,.1),void 0===t.bounds?(v[k]=y/2,x[k++]=g/2,v[k]=y/2,x[k++]=g/2):(v[k]=t.bounds.x,x[k++]=t.bounds.y,v[k]=t.bounds.X,x[k++]=t.bounds.Y)}))}else this._rootGroup={leaves:this._nodes,groups:[]};var S=this._constraints||[];for(this._directedLinkConstraints&&(this.linkAccessor.getMinSeparation=this._directedLinkConstraints.getMinSeparation,S=S.concat(o.generateDirectedEdgeConstraints(p,this._links,this._directedLinkConstraints.axis,this.linkAccessor))),this.avoidOverlaps(!1),this._descent=new a.Descent([v,x],w),this._descent.locks.clear(),k=0;k<p;++k){var _=this._nodes[k];if(_.fixed){_.px=_.x,_.py=_.y;var M=[_.x,_.y];this._descent.locks.add(k,M)}}if(this._descent.threshold=this._threshold,this.initialLayout(e,v,x),S.length>0&&(this._descent.project=new s.Projection(this._nodes,this._groups,this._rootGroup,S).projectFunctions()),this._descent.run(n),this.separateOverlappingComponents(y,g,l),this.avoidOverlaps(b),b&&(this._nodes.forEach((function(t,e){t.x=v[e],t.y=x[e]})),this._descent.project=new s.Projection(this._nodes,this._groups,this._rootGroup,S,!0).projectFunctions(),this._nodes.forEach((function(t,e){v[e]=t.x,x[e]=t.y}))),this._descent.G=m,this._descent.run(r),i){this._descent.snapStrength=1e3,this._descent.snapGridSize=this._nodes[0].width,this._descent.numGridSnapNodes=p,this._descent.scaleSnapByMaxH=p!=d;var E=a.Descent.createSquareMatrix(d,(function(t,e){return t>=p||e>=p?m[t][e]:0}));this._descent.G=E,this._descent.run(i)}return this.updateNodePositions(),this.separateOverlappingComponents(y,g,l),c?this.resume():this},t.prototype.initialLayout=function(e,n,r){if(this._groups.length>0&&e>0){var i=this._nodes.length,o=this._links.map((function(t){return{source:t.source.index,target:t.target.index}})),a=this._nodes.map((function(t){return{index:t.index}}));this._groups.forEach((function(t,e){a.push({index:t.index=i+e})})),this._groups.forEach((function(t,e){void 0!==t.leaves&&t.leaves.forEach((function(e){return o.push({source:t.index,target:e.index})})),void 0!==t.groups&&t.groups.forEach((function(e){return o.push({source:t.index,target:e.index})}))})),(new t).size(this.size()).nodes(a).links(o).avoidOverlaps(!1).linkDistance(this.linkDistance()).symmetricDiffLinkLengths(5).convergenceThreshold(1e-4).start(e,0,0,0,!1),this._nodes.forEach((function(t){n[t.index]=a[t.index].x,r[t.index]=a[t.index].y}))}else this._descent.run(e)},t.prototype.separateOverlappingComponents=function(t,e,n){var r=this;if(void 0===n&&(n=!0),!this._distanceMatrix&&this._handleDisconnected){var i=this._descent.x[0],o=this._descent.x[1];this._nodes.forEach((function(t,e){t.x=i[e],t.y=o[e]}));var a=l.separateGraphs(this._nodes,this._links);l.applyPacking(a,t,e,this._defaultNodeSize,e/t,n),this._nodes.forEach((function(t,e){r._descent.x[0][e]=t.x,r._descent.x[1][e]=t.y,t.bounds&&(t.bounds.setXCentre(t.x),t.bounds.setYCentre(t.y))}))}},t.prototype.resume=function(){return this.alpha(.1)},t.prototype.stop=function(){return this.alpha(0)},t.prototype.prepareEdgeRouting=function(t){void 0===t&&(t=0),this._visibilityGraph=new c.TangentVisibilityGraph(this._nodes.map((function(e){return e.bounds.inflate(-t).vertices()})))},t.prototype.routeEdge=function(t,e,n){void 0===e&&(e=5);var r=[],i=new c.TangentVisibilityGraph(this._visibilityGraph.P,{V:this._visibilityGraph.V,E:this._visibilityGraph.E}),o={x:t.source.x,y:t.source.y},a={x:t.target.x,y:t.target.y},l=i.addPoint(o,t.source.index),f=i.addPoint(a,t.target.index);i.addEdgeIfVisible(o,a,t.source.index,t.target.index),void 0!==n&&n(i);var h=new u.Calculator(i.V.length,i.E,(function(t){return t.source.id}),(function(t){return t.target.id}),(function(t){return t.length()})).PathFromNodeToNode(l.id,f.id);if(1===h.length||h.length===i.V.length){var p=s.makeEdgeBetween(t.source.innerBounds,t.target.innerBounds,e);r=[p.sourceIntersection,p.arrowStart]}else{for(var d=h.length-2,y=i.V[h[d]].p,g=i.V[h[0]].p,v=(r=[t.source.innerBounds.rayIntersection(y.x,y.y)],d);v>=0;--v)r.push(i.V[h[v]].p);r.push(s.makeEdgeTo(g,t.target.innerBounds,e))}return r},t.getSourceIndex=function(t){return"number"==typeof t.source?t.source:t.source.index},t.getTargetIndex=function(t){return"number"==typeof t.target?t.target:t.target.index},t.linkId=function(e){return t.getSourceIndex(e)+"-"+t.getTargetIndex(e)},t.dragStart=function(e){f(e)?t.storeOffset(e,t.dragOrigin(e)):(t.stopNode(e),e.fixed|=2)},t.stopNode=function(t){t.px=t.x,t.py=t.y},t.storeOffset=function(e,n){void 0!==e.leaves&&e.leaves.forEach((function(e){e.fixed|=2,t.stopNode(e),e._dragGroupOffsetX=e.x-n.x,e._dragGroupOffsetY=e.y-n.y})),void 0!==e.groups&&e.groups.forEach((function(e){return t.storeOffset(e,n)}))},t.dragOrigin=function(t){return f(t)?{x:t.bounds.cx(),y:t.bounds.cy()}:t},t.drag=function(e,n){f(e)?(void 0!==e.leaves&&e.leaves.forEach((function(t){e.bounds.setXCentre(n.x),e.bounds.setYCentre(n.y),t.px=t._dragGroupOffsetX+n.x,t.py=t._dragGroupOffsetY+n.y})),void 0!==e.groups&&e.groups.forEach((function(e){return t.drag(e,n)}))):(e.px=n.x,e.py=n.y)},t.dragEnd=function(e){f(e)?(void 0!==e.leaves&&e.leaves.forEach((function(e){t.dragEnd(e),delete e._dragGroupOffsetX,delete e._dragGroupOffsetY})),void 0!==e.groups&&e.groups.forEach(t.dragEnd)):e.fixed&=-7},t.mouseOver=function(t){t.fixed|=4,t.px=t.x,t.py=t.y},t.mouseOut=function(t){t.fixed&=-5},t}();n.Layout=h},{"./descent":7,"./geom":8,"./handledisconnected":10,"./linklengths":13,"./powergraph":14,"./rectangle":17,"./shortestpaths":18}],12:[function(t,e,n){"use strict";Object.defineProperty(n,"__esModule",{value:!0});var r=t("./shortestpaths"),i=t("./descent"),o=t("./rectangle"),a=t("./linklengths"),s=function(){function t(t,e){this.source=t,this.target=e}return t.prototype.actualLength=function(t){var e=this;return Math.sqrt(t.reduce((function(t,n){var r=n[e.target]-n[e.source];return t+r*r}),0))},t}();n.Link3D=s;var u=function(t,e,n){void 0===t&&(t=0),void 0===e&&(e=0),void 0===n&&(n=0),this.x=t,this.y=e,this.z=n};n.Node3D=u;var c=function(){function t(e,n,r){var i=this;void 0===r&&(r=1),this.nodes=e,this.links=n,this.idealLinkLength=r,this.constraints=null,this.useJaccardLinkLengths=!0,this.result=new Array(t.k);for(var o=0;o<t.k;++o)this.result[o]=new Array(e.length);e.forEach((function(e,n){for(var r=0,o=t.dims;r<o.length;r++){var a=o[r];void 0===e[a]&&(e[a]=Math.random())}i.result[0][n]=e.x,i.result[1][n]=e.y,i.result[2][n]=e.z}))}return t.prototype.linkLength=function(t){return t.actualLength(this.result)},t.prototype.start=function(t){var e=this;void 0===t&&(t=100);var n=this.nodes.length,s=new l;this.useJaccardLinkLengths&&a.jaccardLinkLengths(this.links,s,1.5),this.links.forEach((function(t){return t.length*=e.idealLinkLength}));var u=new r.Calculator(n,this.links,(function(t){return t.source}),(function(t){return t.target}),(function(t){return t.length})).DistanceMatrix(),c=i.Descent.createSquareMatrix(n,(function(t,e){return u[t][e]})),f=i.Descent.createSquareMatrix(n,(function(){return 2}));this.links.forEach((function(t){var e=t.source,n=t.target;return f[e][n]=f[n][e]=1})),this.descent=new i.Descent(this.result,c),this.descent.threshold=.001,this.descent.G=f,this.constraints&&(this.descent.project=new o.Projection(this.nodes,null,null,this.constraints).projectFunctions());for(var h=0;h<this.nodes.length;h++){var p=this.nodes[h];p.fixed&&this.descent.locks.add(h,[p.x,p.y,p.z])}return this.descent.run(t),this},t.prototype.tick=function(){this.descent.locks.clear();for(var t=0;t<this.nodes.length;t++){var e=this.nodes[t];e.fixed&&this.descent.locks.add(t,[e.x,e.y,e.z])}return this.descent.rungeKutta()},t.dims=["x","y","z"],t.k=t.dims.length,t}();n.Layout3D=c;var l=function(){function t(){}return t.prototype.getSourceIndex=function(t){return t.source},t.prototype.getTargetIndex=function(t){return t.target},t.prototype.getLength=function(t){return t.length},t.prototype.setLength=function(t,e){t.length=e},t}()},{"./descent":7,"./linklengths":13,"./rectangle":17,"./shortestpaths":18}],13:[function(t,e,n){"use strict";function r(t,e){var n={};for(var r in t)n[r]={};for(var r in e)n[r]={};return Object.keys(n).length}function i(t,e){var n=0;for(var r in t)void 0!==e[r]&&++n;return n}function o(t,e,n,r){var i=function(t,e){var n={},r=function(t,e){void 0===n[t]&&(n[t]={}),n[t][e]={}};return t.forEach((function(t){var n=e.getSourceIndex(t),i=e.getTargetIndex(t);r(n,i),r(i,n)})),n}(t,r);t.forEach((function(t){var o=i[r.getSourceIndex(t)],a=i[r.getTargetIndex(t)];r.setLength(t,1+e*n(o,a))}))}function a(t,e,n){var r=[],i=0,o=[],a=[];function s(t){t.index=t.lowlink=i++,o.push(t),t.onStack=!0;for(var e=0,n=t.out;e<n.length;e++){var r=n[e];void 0===r.index?(s(r),t.lowlink=Math.min(t.lowlink,r.lowlink)):r.onStack&&(t.lowlink=Math.min(t.lowlink,r.index))}if(t.lowlink===t.index){for(var u=[];o.length&&((r=o.pop()).onStack=!1,u.push(r),r!==t););a.push(u.map((function(t){return t.id})))}}for(var u=0;u<t;u++)r.push({id:u,out:[]});for(var c=0,l=e;c<l.length;c++){var f=l[c],h=r[n.getSourceIndex(f)],p=r[n.getTargetIndex(f)];h.out.push(p)}for(var d=0,y=r;d<y.length;d++){var g=y[d];void 0===g.index&&s(g)}return a}Object.defineProperty(n,"__esModule",{value:!0}),n.symmetricDiffLinkLengths=function(t,e,n){void 0===n&&(n=1),o(t,n,(function(t,e){return Math.sqrt(r(t,e)-i(t,e))}),e)},n.jaccardLinkLengths=function(t,e,n){void 0===n&&(n=1),o(t,n,(function(t,e){return Math.min(Object.keys(t).length,Object.keys(e).length)<1.1?0:i(t,e)/r(t,e)}),e)},n.generateDirectedEdgeConstraints=function(t,e,n,r){var i=a(t,e,r),o={};i.forEach((function(t,e){return t.forEach((function(t){return o[t]=e}))}));var s=[];return e.forEach((function(t){var e=r.getSourceIndex(t),i=r.getTargetIndex(t);o[e]!==o[i]&&s.push({axis:n,left:e,right:i,gap:r.getMinSeparation(t)})})),s},n.stronglyConnectedComponents=a},{}],14:[function(t,e,n){"use strict";Object.defineProperty(n,"__esModule",{value:!0});var r=function(t,e,n){this.source=t,this.target=e,this.type=n};n.PowerEdge=r;var i=function(){function t(t,e,n,r){var i=this;if(this.linkAccessor=n,this.modules=new Array(t),this.roots=[],r)this.initModulesFromGroup(r);else{this.roots.push(new s);for(var a=0;a<t;++a)this.roots[0].add(this.modules[a]=new o(a))}this.R=e.length,e.forEach((function(t){var e=i.modules[n.getSourceIndex(t)],r=i.modules[n.getTargetIndex(t)],o=n.getType(t);e.outgoing.add(o,r),r.incoming.add(o,e)}))}return t.prototype.initModulesFromGroup=function(t){var e=new s;this.roots.push(e);for(var n=0;n<t.leaves.length;++n){var r=t.leaves[n],i=new o(r.id);this.modules[r.id]=i,e.add(i)}if(t.groups)for(var a=0;a<t.groups.length;++a){var c=t.groups[a],l={};for(var f in c)"leaves"!==f&&"groups"!==f&&c.hasOwnProperty(f)&&(l[f]=c[f]);e.add(new o(-1-a,new u,new u,this.initModulesFromGroup(c),l))}return e},t.prototype.merge=function(t,e,n){void 0===n&&(n=0);var r=t.incoming.intersection(e.incoming),i=t.outgoing.intersection(e.outgoing),a=new s;a.add(t),a.add(e);var u=new o(this.modules.length,i,r,a);this.modules.push(u);var c=function(n,r,i){n.forAll((function(n,o){n.forAll((function(n){var a=n[r];a.add(o,u),a.remove(o,t),a.remove(o,e),t[i].remove(o,n),e[i].remove(o,n)}))}))};return c(i,"incoming","outgoing"),c(r,"outgoing","incoming"),this.R-=r.count()+i.count(),this.roots[n].remove(t),this.roots[n].remove(e),this.roots[n].add(u),u},t.prototype.rootMerges=function(t){void 0===t&&(t=0);for(var e=this.roots[t].modules(),n=e.length,r=new Array(n*(n-1)),i=0,o=0,a=n-1;o<a;++o)for(var s=o+1;s<n;++s){var u=e[o],c=e[s];r[i]={id:i,nEdges:this.nEdges(u,c),a:u,b:c},i++}return r},t.prototype.greedyMerge=function(){for(var t=0;t<this.roots.length;++t)if(!(this.roots[t].modules().length<2)){var e=this.rootMerges(t).sort((function(t,e){return t.nEdges==e.nEdges?t.id-e.id:t.nEdges-e.nEdges}))[0];if(!(e.nEdges>=this.R))return this.merge(e.a,e.b,t),!0}},t.prototype.nEdges=function(t,e){var n=t.incoming.intersection(e.incoming),r=t.outgoing.intersection(e.outgoing);return this.R-n.count()-r.count()},t.prototype.getGroupHierarchy=function(t){var e=this,n=[];return function t(e,n,r){e.forAll((function(e){if(e.isLeaf())n.leaves||(n.leaves=[]),n.leaves.push(e.id);else{var i=n;if(e.gid=r.length,!e.isIsland()||e.isPredefined()){if(i={id:e.gid},e.isPredefined())for(var o in e.definition)i[o]=e.definition[o];n.groups||(n.groups=[]),n.groups.push(e.gid),r.push(i)}t(e.children,i,r)}}))}(this.roots[0],{},n),this.allEdges().forEach((function(i){var o=e.modules[i.source],a=e.modules[i.target];t.push(new r(void 0===o.gid?i.source:n[o.gid],void 0===a.gid?i.target:n[a.gid],i.type))})),n},t.prototype.allEdges=function(){var e=[];return t.getEdges(this.roots[0],e),e},t.getEdges=function(e,n){e.forAll((function(e){e.getEdges(n),t.getEdges(e.children,n)}))},t}();n.Configuration=i;var o=function(){function t(t,e,n,r,i){void 0===e&&(e=new u),void 0===n&&(n=new u),void 0===r&&(r=new s),this.id=t,this.outgoing=e,this.incoming=n,this.children=r,this.definition=i}return t.prototype.getEdges=function(t){var e=this;this.outgoing.forAll((function(n,i){n.forAll((function(n){t.push(new r(e.id,n.id,i))}))}))},t.prototype.isLeaf=function(){return 0===this.children.count()},t.prototype.isIsland=function(){return 0===this.outgoing.count()&&0===this.incoming.count()},t.prototype.isPredefined=function(){return void 0!==this.definition},t}();function a(t,e){var n={};for(var r in t)r in e&&(n[r]=t[r]);return n}n.Module=o;var s=function(){function t(){this.table={}}return t.prototype.count=function(){return Object.keys(this.table).length},t.prototype.intersection=function(e){var n=new t;return n.table=a(this.table,e.table),n},t.prototype.intersectionCount=function(t){return this.intersection(t).count()},t.prototype.contains=function(t){return t in this.table},t.prototype.add=function(t){this.table[t.id]=t},t.prototype.remove=function(t){delete this.table[t.id]},t.prototype.forAll=function(t){for(var e in this.table)t(this.table[e])},t.prototype.modules=function(){var t=[];return 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null;for(;null!==t.left;)t=t.left;return t.data},t.prototype.max=function(){var t=this._root;if(null===t)return null;for(;null!==t.right;)t=t.right;return t.data},t.prototype.iterator=function(){return new a(this)},t.prototype.each=function(t){for(var e,n=this.iterator();null!==(e=n.next());)t(e)},t.prototype.reach=function(t){for(var e,n=this.iterator();null!==(e=n.prev());)t(e)},t.prototype._bound=function(t,e){for(var n=this._root,r=this.iterator();null!==n;){var i=this._comparator(t,n.data);if(0===i)return r._cursor=n,r;r._ancestors.push(n),n=n.get_child(i>0)}for(var o=r._ancestors.length-1;o>=0;--o)if(e(t,(n=r._ancestors[o]).data)>0)return r._cursor=n,r._ancestors.length=o,r;return r._ancestors.length=0,r},t}();n.TreeBase=o;var a=function(){function t(t){this._tree=t,this._ancestors=[],this._cursor=null}return t.prototype.data=function(){return null!==this._cursor?this._cursor.data:null},t.prototype.next=function(){if(null===this._cursor){var 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r=t("./pqueue"),i=function(t,e){this.id=t,this.distance=e},o=function(t){this.id=t,this.neighbours=[]},a=function(t,e,n){this.node=t,this.prev=e,this.d=n},s=function(){function t(t,e,n,r,a){this.n=t,this.es=e,this.neighbours=new Array(this.n);for(var s=this.n;s--;)this.neighbours[s]=new o(s);for(s=this.es.length;s--;){var u=this.es[s],c=n(u),l=r(u),f=a(u);this.neighbours[c].neighbours.push(new i(l,f)),this.neighbours[l].neighbours.push(new i(c,f))}}return t.prototype.DistanceMatrix=function(){for(var t=new Array(this.n),e=0;e<this.n;++e)t[e]=this.dijkstraNeighbours(e);return t},t.prototype.DistancesFromNode=function(t){return this.dijkstraNeighbours(t)},t.prototype.PathFromNodeToNode=function(t,e){return this.dijkstraNeighbours(t,e)},t.prototype.PathFromNodeToNodeWithPrevCost=function(t,e,n){var i=new r.PriorityQueue((function(t,e){return t.d<=e.d})),o=this.neighbours[t],s=new a(o,null,0),u={};for(i.push(s);!i.empty()&&(o=(s=i.pop()).node).id!==e;)for(var 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2*this.weight*(this.position()-this.desiredPosition)},t.prototype.position=function(){return(this.block.ps.scale*this.block.posn+this.offset)/this.scale},t.prototype.visitNeighbours=function(t,e){var n=function(n,r){return n.active&&t!==r&&e(n,r)};this.cOut.forEach((function(t){return n(t,t.right)})),this.cIn.forEach((function(t){return n(t,t.left)}))},t}();n.Variable=o;var a=function(){function t(t){this.vars=[],t.offset=0,this.ps=new r(t.scale),this.addVariable(t)}return t.prototype.addVariable=function(t){t.block=this,this.vars.push(t),this.ps.addVariable(t),this.posn=this.ps.getPosn()},t.prototype.updateWeightedPosition=function(){this.ps.AB=this.ps.AD=this.ps.A2=0;for(var t=0,e=this.vars.length;t<e;++t)this.ps.addVariable(this.vars[t]);this.posn=this.ps.getPosn()},t.prototype.compute_lm=function(t,e,n){var r=this,i=t.dfdv();return t.visitNeighbours(e,(function(e,o){var a=r.compute_lm(o,t,n);o===e.right?(i+=a*e.left.scale,e.lm=a):(i+=a*e.right.scale,e.lm=-a),n(e)})),i/t.scale},t.prototype.populateSplitBlock=function(t,e){var n=this;t.visitNeighbours(e,(function(e,r){r.offset=t.offset+(r===e.right?e.gap:-e.gap),n.addVariable(r),n.populateSplitBlock(r,t)}))},t.prototype.traverse=function(t,e,n,r){var i=this;void 0===n&&(n=this.vars[0]),void 0===r&&(r=null),n.visitNeighbours(r,(function(r,o){e.push(t(r)),i.traverse(t,e,o,n)}))},t.prototype.findMinLM=function(){var t=null;return this.compute_lm(this.vars[0],null,(function(e){!e.equality&&(null===t||e.lm<t.lm)&&(t=e)})),t},t.prototype.findMinLMBetween=function(t,e){this.compute_lm(t,null,(function(){}));var n=null;return this.findPath(t,null,e,(function(t,e){!t.equality&&t.right===e&&(null===n||t.lm<n.lm)&&(n=t)})),n},t.prototype.findPath=function(t,e,n,r){var i=this,o=!1;return t.visitNeighbours(e,(function(e,a){o||a!==n&&!i.findPath(a,t,n,r)||(o=!0,r(e,a))})),o},t.prototype.isActiveDirectedPathBetween=function(t,e){if(t===e)return!0;for(var n=t.cOut.length;n--;){var r=t.cOut[n];if(r.active&&this.isActiveDirectedPathBetween(r.right,e))return!0}return!1},t.split=function(e){return e.active=!1,[t.createSplitBlock(e.left),t.createSplitBlock(e.right)]},t.createSplitBlock=function(e){var n=new t(e);return n.populateSplitBlock(e,null),n},t.prototype.splitBetween=function(e,n){var r=this.findMinLMBetween(e,n);if(null!==r){var i=t.split(r);return{constraint:r,lb:i[0],rb:i[1]}}return null},t.prototype.mergeAcross=function(t,e,n){e.active=!0;for(var r=0,i=t.vars.length;r<i;++r){var o=t.vars[r];o.offset+=n,this.addVariable(o)}this.posn=this.ps.getPosn()},t.prototype.cost=function(){for(var t=0,e=this.vars.length;e--;){var n=this.vars[e],r=n.position()-n.desiredPosition;t+=r*r*n.weight}return t},t}();n.Block=a;var s=function(){function t(t){this.vs=t;var e=t.length;for(this.list=new Array(e);e--;){var n=new a(t[e]);this.list[e]=n,n.blockInd=e}}return t.prototype.cost=function(){for(var t=0,e=this.list.length;e--;)t+=this.list[e].cost();return t},t.prototype.insert=function(t){t.blockInd=this.list.length,this.list.push(t)},t.prototype.remove=function(t){var e=this.list.length-1,n=this.list[e];this.list.length=e,t!==n&&(this.list[t.blockInd]=n,n.blockInd=t.blockInd)},t.prototype.merge=function(t){var e=t.left.block,n=t.right.block,r=t.right.offset-t.left.offset-t.gap;e.vars.length<n.vars.length?(n.mergeAcross(e,t,r),this.remove(e)):(e.mergeAcross(n,t,-r),this.remove(n))},t.prototype.forEach=function(t){this.list.forEach(t)},t.prototype.updateBlockPositions=function(){this.list.forEach((function(t){return t.updateWeightedPosition()}))},t.prototype.split=function(t){var e=this;this.updateBlockPositions(),this.list.forEach((function(n){var r=n.findMinLM();null!==r&&r.lm<u.LAGRANGIAN_TOLERANCE&&(n=r.left.block,a.split(r).forEach((function(t){return e.insert(t)})),e.remove(n),t.push(r))}))},t}();n.Blocks=s;var u=function(){function t(t,e){this.vs=t,this.cs=e,this.vs=t,t.forEach((function(t){t.cIn=[],t.cOut=[]})),this.cs=e,e.forEach((function(t){t.left.cOut.push(t),t.right.cIn.push(t)})),this.inactive=e.map((function(t){return t.active=!1,t})),this.bs=null}return t.prototype.cost=function(){return this.bs.cost()},t.prototype.setStartingPositions=function(t){this.inactive=this.cs.map((function(t){return t.active=!1,t})),this.bs=new s(this.vs),this.bs.forEach((function(e,n){return e.posn=t[n]}))},t.prototype.setDesiredPositions=function(t){this.vs.forEach((function(e,n){return e.desiredPosition=t[n]}))},t.prototype.mostViolated=function(){for(var e=Number.MAX_VALUE,n=null,r=this.inactive,i=r.length,o=i,a=0;a<i;++a){var s=r[a];if(!s.unsatisfiable){var u=s.slack();if((s.equality||u<e)&&(e=u,n=s,o=a,s.equality))break}}return 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e,n,r,o=A(a);function a(){var t;return function(t,e){if(!(t instanceof e))throw new TypeError("Cannot call a class as a function")}(this,a),(t=o.call(this)).nTermFeatures=[],t.cTermFeatures=[],t}return e=a,(n=[{key:"getSymbolRadius",value:function(){return 15}},{key:"showHighlight",value:function(t){this.highlight.setAttribute("stroke-opacity",t?"1":"0")}},{key:"setStickScale",value:function(t,e){var n=this.stickZoom,r=this.ix-e.x,i=r*t/n-r,o=this.ix+i;this.stickZoom=t,this.scale(),this.setPosition(o,this.iy),this.setAllLinkCoordinates()}},{key:"scale",value:function(){var t=this.size*this.stickZoom;if(this.expanded){var e=i.transform(this.labelSVG.getAttribute("transform")),n=this.app.svgElement.createSVGMatrix().rotate(e.rotate).translate(-(this.size/2*this.stickZoom+(this.nTermFeatures.length>0?25:10)),this.labelY);this.labelSVG.transform.baseVal.initialize(this.app.svgElement.createSVGTransformFromMatrix(n)),this.updateAnnotationRectanglesNoTransition(),i.select(this.background).attr("width",t).attr("x",this.getResXWithStickZoom(.5)),i.select(this.outline).attr("width",t).attr("x",this.getResXWithStickZoom(.5)),i.select(this.highlight).attr("width",t+5).attr("x",this.getResXWithStickZoom(.5)-2.5),this.setScaleGroup()}}},{key:"setScaleGroup",value:function(){this.upperGroup.appendChild(this.ticks),this.ticks.textContent="",this.scaleLabels=[];for(var t=-1,e=this.getResXWithStickZoom(this.size),n=1;n<=this.size;n++){if(1===n||n%100==0&&200*this.stickZoom>a.minXDist||n%10==0&&20*this.stickZoom>a.minXDist){var r=this.getResXWithStickZoom(n);(this.stickZoom>=8||1!==n)&&c(this,r),0==(t=(t+1)%2)&&r+a.minXDist<e&&u(this,n,r)}if(this.stickZoom>=8){var i=document.createElementNS(d,"g");i.setAttribute("transform","translate("+this.getResXWithStickZoom(n)+" 0)");var o=document.createElementNS(d,"text");o.classList.add("label","sequence"),o.setAttribute("x","0"),o.setAttribute("y","3"),o.appendChild(document.createTextNode(this.sequence[n-1]));var s=document.createElementNS(d,"text");s.classList.add("label","sequence-outline"),s.setAttribute("x","0"),s.setAttribute("y","3"),s.appendChild(document.createTextNode(this.sequence[n-1])),i.appendChild(s),this.scaleLabels.push(s),i.appendChild(o),this.scaleLabels.push(o),this.ticks.appendChild(i)}}function u(t,e,n){var r=document.createElementNS(d,"g");r.setAttribute("transform","translate("+n+" 0)");var i=document.createElementNS(d,"text");i.classList.add("label","scale-label"),i.setAttribute("x","0"),i.setAttribute("y",a.STICKHEIGHT+4),i.appendChild(document.createTextNode(e)),r.appendChild(i),t.scaleLabels.push(i),t.ticks.appendChild(r)}function c(t,e){var n=document.createElementNS(d,"line");n.classList.add("tick"),n.setAttribute("x1",e),n.setAttribute("y1","5"),n.setAttribute("x2",e),n.setAttribute("y2","10"),t.ticks.appendChild(n)}u(this,this.size,e),this.stickZoom>=8&&c(this,e)}},{key:"setExpanded",value:function(t,e){!0!==this.busy&&(t?this.toStick(!0):this.toCircle(!0,e))}},{key:"toCircle",value:function(){var t=!(arguments.length>0&&void 0!==arguments[0])||arguments[0],e=arguments.length>1?arguments[1]:void 0,n=t?a.transitionTime:0;this.postAnimExpanded=!1,this.busy=!0;var r=this.getSymbolRadius();i.select(this.background).transition().attr("x",-r).attr("y",-r).attr("width",2*r).attr("height",2*r).attr("rx",r).attr("ry",r).duration(n),i.select(this.outline).transition().attr("x",-r).attr("y",-r).attr("width",2*r).attr("height",2*r).attr("rx",r).attr("ry",r).duration(n),i.select(this.highlight).transition().attr("width",2*r+5).attr("height",2*r+5).attr("x",-r-2.5).attr("y",-r-2.5).attr("rx",r+2.5).attr("ry",r+2.5).duration(n);var o=i.interpolate(this.stickZoom,0),s=i.transform(this.labelSVG.getAttribute("transform")),u=s.translate[0],c=i.interpolate(u,-(r+5)),l=null;null!=e&&(l=i.interpolate(this.ix,e.x));var f=this;i.select(this.ticks).transition().attr("opacity",0).duration(n/4).each("end",(function(){i.select(this).selectAll("*").remove()}));var h=this.stickZoom,p=this.rotation,d=i.ease("cubic-in-out");if(t){var y,g=k(this.annotationSets);try{for(g.s();!(y=g.n()).done;){var v=w(y.value,2),x=v[0],m=v[1];if(!0===this.app.annotationSetsShown.get(x)){var b,S=k(m);try{for(S.s();!(b=S.n()).done;){var _=b.value;if(_.fuzzyStart){var M=_.fuzzyStart;i.select(M).transition().attr("d",this.getAnnotationPieSlicePath(_.seqDatum.uncertainBegin,_.seqDatum.begin,_,!1)).duration(n)}if(_.certain){var E=_.certain;i.select(E).transition().attr("d",this.getAnnotationPieSlicePath(_.seqDatum.begin,_.seqDatum.end,_,!1)).duration(n)}if(_.fuzzyEnd){var A=_.fuzzyEnd;i.select(A).transition().attr("d",this.getAnnotationPieSlicePath(_.seqDatum.end,_.seqDatum.uncertainEnd,_,!1)).duration(n)}}}catch(t){S.e(t)}finally{S.f()}}}}catch(t){g.e(t)}finally{g.f()}i.timer((function(t){return C(t/n)}))}else C(1);function C(t){var e=i.transform(f.labelSVG.getAttribute("transform")),n=f.app.svgElement.createSVGMatrix().rotate(e.rotate).translate(c(d(t)),f.labelY);if(f.labelSVG.transform.baseVal.initialize(f.app.svgElement.createSVGTransformFromMatrix(n)),null!==l&&f.setPosition(l(d(t)),f.iy),f.stickZoom=o(d(t)),f.setAllLinkCoordinates(),1===t){f.expanded=!1,f.checkLinks();var r,a=k(f.annotationSets);try{for(a.s();!(r=a.n()).done;){var s=w(r.value,2),u=s[0],y=s[1];if(!0===f.app.annotationSetsShown.get(u)){var g,v=k(y);try{for(v.s();!(g=v.n()).done;){var x=g.value;if(x.fuzzyStart){var m=x.fuzzyStart;i.select(m).attr("d",f.getAnnotationPieSlicePath(x.seqDatum.uncertainBegin,x.seqDatum.begin,x))}if(x.certain){var b=x.certain;i.select(b).attr("d",f.getAnnotationPieSlicePath(x.seqDatum.begin,x.seqDatum.end,x))}if(x.fuzzyEnd){var S=x.fuzzyEnd;i.select(S).attr("d",f.getAnnotationPieSlicePath(x.seqDatum.end,x.seqDatum.uncertainEnd,x))}}}catch(t){v.e(t)}finally{v.f()}}}}catch(t){a.e(t)}finally{a.f()}return f.stickZoom=h,f.rotation=p,f.busy=!1,!0}return!!(t>1||isNaN(t))&&C(1)}}},{key:"toStick",value:function(){var t=!(arguments.length>0&&void 0!==arguments[0])||arguments[0],e=t?a.transitionTime:0;this.busy=!0,this.expanded=!0,this.postAnimExpanded=!0;var n=this.size*this.stickZoom,r=this.getSymbolRadius(),o=i.interpolate(2*r,n),s=i.interpolate(0,this.stickZoom),u=i.interpolate(-(r+5),-(this.size/2*this.stickZoom+(this.nTermFeatures.length>0?25:10))),c=this.stickZoom;this.stickZoom=0,this.checkLinks(),this.stickZoom=c,i.select(this.background).transition().attr("height",a.STICKHEIGHT).attr("y",-a.STICKHEIGHT/2).attr("rx",0).attr("ry",0).duration(e),i.select(this.outline).transition().attr("height",a.STICKHEIGHT).attr("y",-a.STICKHEIGHT/2).attr("rx",0).attr("ry",0).duration(e),i.select(this.highlight).transition().attr("width",n+5).attr("height",a.STICKHEIGHT+5).attr("x",this.getResXWithStickZoom(.5)-2.5).attr("y",-a.STICKHEIGHT/2-2.5).attr("rx",0).attr("ry",0).duration(e);var l=this,f=i.ease("cubic-in-out");if(t){var h,p=k(this.annotationSets);try{for(p.s();!(h=p.n()).done;){var d=w(h.value,2),y=d[0],g=d[1];if(!0===this.app.annotationSetsShown.get(y)){var v,x=k(g);try{for(x.s();!(v=x.n()).done;){var m=v.value;if(m.fuzzyStart){var b=m.fuzzyStart;b.setAttribute("d",this.getAnnotationPieSlicePath(m.seqDatum.uncertainBegin,m.seqDatum.begin,m,!1)),i.select(b).transition().attr("d",this.getAnnotationRectPath(m.seqDatum.uncertainBegin,m.seqDatum.begin,m)).duration(a.transitionTime)}if(m.certain){var S=m.certain,_=m.seqDatum.begin,M=m.seqDatum.end;m.seqDatum.uncertainBegin&&(_+=1),m.seqDatum.uncertainEnd&&(M-=1),S.setAttribute("d",this.getAnnotationPieSlicePath(_,M,m,!1)),i.select(S).transition().attr("d",this.getAnnotationRectPath(_,M,m)).duration(a.transitionTime)}if(m.fuzzyEnd){var E=m.fuzzyEnd;E.setAttribute("d",this.getAnnotationPieSlicePath(m.seqDatum.end,m.seqDatum.uncertainEnd,m,!1)),i.select(E).transition().attr("d",this.getAnnotationRectPath(m.seqDatum.end,m.seqDatum.uncertainEnd,m)).duration(a.transitionTime)}}}catch(t){x.e(t)}finally{x.f()}}}}catch(t){p.e(t)}finally{p.f()}i.timer((function(t){return A(t/e)}))}else A(1);function A(t){var e=i.transform(l.labelSVG.getAttribute("transform")),n=l.app.svgElement.createSVGMatrix().rotate(e.rotate).translate(u(f(t)),l.labelY);l.labelSVG.transform.baseVal.initialize(l.app.svgElement.createSVGTransformFromMatrix(n));var r=o(f(t));return i.select(l.highlight).attr("width",r).attr("x",-r/2+.5*l.stickZoom),i.select(l.outline).attr("width",r).attr("x",-r/2+.5*l.stickZoom),i.select(l.background).attr("width",r).attr("x",-r/2+.5*l.stickZoom),l.stickZoom=s(f(t)),l.setAllLinkCoordinates(),1===t?(l.updateAnnotationRectanglesNoTransition(),l.busy=!1,!0):!!(t>1||isNaN(t))&&A(1)}i.select(this.ticks).attr("opacity",0),this.setScaleGroup(),i.select(this.ticks).transition().attr("opacity",1).delay(.8*e).duration(e/2)}},{key:"updateAnnotationRectanglesNoTransition",value:function(){var t,e=k(this.annotationSets);try{for(e.s();!(t=e.n()).done;){var n=w(t.value,2),r=n[0],o=n[1];if(!0===this.app.annotationSetsShown.get(r)){var a,s=k(o);try{for(s.s();!(a=s.n()).done;){var u=a.value;if(u.fuzzyStart){var c=u.fuzzyStart;i.select(c).attr("d",this.getAnnotationRectPath(u.seqDatum.uncertainBegin,u.seqDatum.begin,u))}if(u.certain){var l=u.seqDatum.begin,f=u.seqDatum.end;u.seqDatum.uncertainBegin&&(l+=1),u.seqDatum.uncertainEnd&&(f-=1),u.certain.setAttribute("d",this.getAnnotationRectPath(l,f,u))}if(u.fuzzyEnd){var h=u.fuzzyEnd;i.select(h).attr("d",this.getAnnotationRectPath(u.seqDatum.end,u.seqDatum.uncertainEnd,u))}}}catch(t){s.e(t)}finally{s.f()}}}}catch(t){e.e(t)}finally{e.f()}}},{key:"getResXWithStickZoom",value:function(t){return"n-n"===t?-this.size/2*this.stickZoom-20:"c-c"===t?this.size/2*this.stickZoom+20:(t-this.size/2)*this.stickZoom}},{key:"getResidueCoordinates",value:function(t,e){void 0===t&&console.error("ERROR: residue number is undefined");var n,r=this.getResXWithStickZoom(1*t);if(0!==r){var i=Math.abs(r),o=Math.acos(r/i),a=this.rotation/360*Math.PI*2;r=i*Math.cos(a+o),n=i*Math.sin(a+o),void 0!==e&&(r+=e*Math.cos(a+Math.PI/2),n+=e*Math.sin(a+Math.PI/2))}else n=e;return[r+=this.ix,n+=this.iy]}},{key:"clearPositionalFeatures",value:function(){this.annotations=[],this.annotationTypes=[],this.annotationsSvgGroup.textContent="",this.nTermFeatures=[],this.cTermFeatures=[]}},{key:"updatePositionalFeatures",value:function(){var t=this,e=function(e){var n=e.target.correspondingUseElement?e.target.correspondingUseElement:e.target;t.app.preventDefaultsAndStopPropagation(e),t.app.setTooltip(n.name,n.getAttribute("fill")),t.showHighlight(!0)},n=-1,r=[];function i(t,e){var n,r=k(t);try{for(r.s();!(n=r.n()).done;)if(n.value.seqDatum.overlaps(e.seqDatum))return!0}catch(t){r.e(t)}finally{r.f()}return!1}var o,a=k(this.annotationSets);try{for(a.s();!(o=a.n()).done;){var s=w(o.value,2),u=s[0],c=s[1];if(!0===this.app.annotationSetsShown.get(u)){c&&c.length>0&&(r[++n]=[]);var l,f=new Set,h=k(Array.from(c.values()).sort((function(t,e){var n=t.description,r=e.description;return n<r?-1:n>r?1:0})));try{for(h.s();!(l=h.n()).done;){var p=l.value;if(!f.has(p.toString()))if(f.add(p.toString()),"n-n"===p.seqDatum.sequenceDatumString||"c-c"===p.seqDatum.sequenceDatumString)"n-n"===p.seqDatum.sequenceDatumString?(p.rung=this.nTermFeatures.length,this.nTermFeatures.push(p)):(p.rung=this.cTermFeatures.length,this.cTermFeatures.push(p));else{var y=r[n];i(y,p)&&(r[++n]=[],y=r[n]),p.rung=n,y.push(p)}}}catch(t){h.e(t)}finally{h.f()}}}}catch(t){a.e(t)}finally{a.f()}this.rungCount=n+1;var g,v=k(this.annotationSets);try{for(v.s();!(g=v.n()).done;){var x=w(g.value,2),m=x[0],b=x[1];if(!0===this.app.annotationSetsShown.get(m)){var S,_=new Set,M=k(b.values());try{for(M.s();!(S=M.n()).done;){var E=S.value;if(!_.has(E.toString())){_.add(E.toString());var A=E.toString();if(E.seqDatum.uncertainBegin&&(E.fuzzyStart=document.createElementNS(d,"path"),this.expanded?E.fuzzyStart.setAttribute("d",this.getAnnotationRectPath(E.seqDatum.uncertainBegin,E.seqDatum.begin,E)):E.fuzzyStart.setAttribute("d",this.getAnnotationPieSlicePath(E.seqDatum.uncertainBegin,E.seqDatum.begin,E)),E.fuzzyStart.setAttribute("stroke-width","1"),E.fuzzyStart.name=A,E.fuzzyStart.onmouseover=e,this.annotationsSvgGroup.appendChild(E.fuzzyStart)),E.seqDatum.begin&&E.seqDatum.end){E.certain=document.createElementNS(d,"path");var C=E.seqDatum.begin,L=E.seqDatum.end;E.seqDatum.uncertainBegin&&(C+=1),E.seqDatum.uncertainEnd&&(L-=1),this.expanded?E.certain.setAttribute("d",this.getAnnotationRectPath(C,L,E)):E.certain.setAttribute("d",this.getAnnotationPieSlicePath(C,L,E)),E.certain.setAttribute("stroke-width","1"),E.certain.name=A,E.certain.onmouseover=e,this.annotationsSvgGroup.appendChild(E.certain)}E.seqDatum.uncertainEnd&&(E.fuzzyEnd=document.createElementNS(d,"path"),this.expanded?E.fuzzyEnd.setAttribute("d",this.getAnnotationRectPath(E.seqDatum.end,E.seqDatum.uncertainEnd,E)):E.fuzzyEnd.setAttribute("d",this.getAnnotationPieSlicePath(E.seqDatum.end,E.seqDatum.uncertainEnd,E)),E.fuzzyEnd.setAttribute("stroke-width","1"),E.fuzzyEnd.name=A,E.fuzzyEnd.onmouseover=e,this.annotationsSvgGroup.appendChild(E.fuzzyEnd))}}}catch(t){M.e(t)}finally{M.f()}}}}catch(t){v.e(t)}finally{v.f()}this.scale()}},{key:"getAnnotationPieSlicePath",value:function(t,e,n){var r,i,o,s,u,c=!(arguments.length>3&&void 0!==arguments[3])||arguments[3],l=this.getSymbolRadius(),f=n.rung;-1===f?(i=0,r=l):r=(i=f*(o=l/this.rungCount))+o,"n-n"===t?(s=-20,u=0):"c-c"===e?(s=0,u=20):(s=(t-1)/this.size*360,u=(e-1)/this.size*360);var h=0;(u-s>180||u===s)&&(h=1);var d=p([0,i],[0,0],s-180),y=p([0,r],[0,0],s-180),g=p([0,r],[0,0],u-180),v=p([0,i],[0,0],u-180),x="M"+d[0]+","+d[1]+" L"+y[0]+","+y[1];if(c)x+=" A"+r+","+r+" 0 "+h+" 1 "+g[0]+","+g[1];else for(var m=0;m<=a.stepsInArc;m++){var b=s+(u-s)/a.stepsInArc*m,w=p([0,r],[0,0],b-180);x+=" L"+w[0]+","+w[1]}if(c)x+=" L"+v[0]+","+v[1],x+=" A"+i+","+i+" 0 "+h+" 0 "+d[0]+","+d[1];else for(var k=a.stepsInArc;k>=0;k--){var S=s+(u-s)/a.stepsInArc*k,_=p([0,i],[0,0],S-180);x+=" L"+_[0]+","+_[1]}return x+=" Z"}},{key:"getAnnotationRectPath",value:function(t,e,n){var 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t=this.participants.length,e=0;e<t;e++)if(this.participants[e].expanded)return!0;return!1}},{key:"show",value:function(){this.setLinkCoordinates();var t=this.app.res_resLinks;this.participants[0]===this.participants[1]&&(t=this.app.selfRes_resLinks),t.appendChild(this.glyph),t.appendChild(this.uncertainGlyph)}},{key:"hide",value:function(){this.glyph.remove(),this.uncertainGlyph.remove()}},{key:"setLinkCoordinates",value:function(){function t(t){return!isNaN(parseFloat(t))&&isFinite(t)}function e(t,e,n,r,i,o,a){var s,u;return i.expanded?(s=i.getResidueCoordinates(n,o),u=i.getResidueCoordinates(r,o)):u=s=i.getPosition(a)," Q"+e[0]+","+e[1]+" "+s[0]+","+s[1]+" L"+u[0]+","+u[1]+" Q"+e[0]+","+e[1]+" "+t[0]+","+t[1]}function n(t,e){for(var n=null,r=null,i=t.length,o=0;o<i;o++){var a=t[o];if(!isNaN(parseFloat(a.begin))&&isFinite(a.begin)){var s=1*a.begin;(null===n||s<n)&&(n=s)}if(!isNaN(parseFloat(a.uncertainBegin))&&isFinite(a.uncertainBegin)){var u=1*a.uncertainBegin;(null===n||u<n)&&(n=u)}if(!isNaN(parseFloat(a.end))&&isFinite(a.end)){var c=1*a.end;(null===r||c>r)&&(r=c)}if(!isNaN(parseFloat(a.uncertainEnd))&&isFinite(a.uncertainEnd)){var l=1*a.uncertainEnd;(null===r||l>r)&&(r=l)}}return e.getResidueCoordinates((n+r)/2,0)}var r,i,o=this.fromSequenceData[0].participant,a=this.toSequenceData[0].participant;o.expanded&&(r=n(this.fromSequenceData,o)),a.expanded&&(i=n(this.toSequenceData,a)),o.expanded||(r=o.getPosition(i)),a.expanded||(i=a.getPosition(r));var s=r,u=i,c=r[0]-i[0],l=r[1]-i[1],f=Math.atan2(l,c)/(2*Math.PI)*360;f<0&&(f+=360);var h=f-o.rotation;h<0&&(h+=360);var p=10;h<180&&(p=-10);var d=o.rotation/360*Math.PI*2;h>180&&(d-=Math.PI),(h=f-a.rotation)<0&&(h+=360);var y=10;h>180&&(y=-10);var g=a.rotation/360*Math.PI*2;h<180&&(g-=Math.PI);var v=[r[0]+30*Math.sin(d)*this.app.z,r[1]-30*Math.cos(d)*this.app.z];o.expanded||(v=r);var x=[i[0]+30*Math.sin(g)*this.app.z,i[1]-30*Math.cos(g)*this.app.z];a.expanded||(x=i);for(var m,b=[(v[0]+x[0])/2,(v[1]+x[1])/2],w=this.fromSequenceData.length,k=this.toSequenceData.length,S="M"+b[0]+","+b[1],_="M"+b[0]+","+b[1],M=0;M<w;M++)(t((m=this.fromSequenceData[M]).begin)&&t(m.end)||"protein"!==o.type)&&(S+=e(b,v,m.begin,m.end,o,p,u)),t(m.uncertainBegin)&&(_+=e(b,v,m.uncertainBegin,m.begin,o,p,u)),t(m.uncertainEnd)&&(_+=e(b,v,m.end,m.uncertainEnd,o,p,u));for(var E=0;E<k;E++)(t((m=this.toSequenceData[E]).begin)&&t(m.end)||"protein"!==a.type)&&(S+=e(b,x,m.begin,m.end,a,y,s)),t(m.uncertainBegin)&&(_+=e(b,x,m.uncertainBegin,m.begin,a,y,s)),t(m.uncertainEnd)&&(_+=e(b,x,m.end,m.uncertainEnd,a,y,s));this.glyph||this.initSVG(),this.glyph.setAttribute("d",S),this.uncertainGlyph.setAttribute("d",_)}}])&&Yt(e.prototype,n),r&&Yt(e,r),o}(zt);function te(t){return(te="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 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se(t){return(se=Object.setPrototypeOf?Object.getPrototypeOf:function(t){return t.__proto__||Object.getPrototypeOf(t)})(t)}var ue=function(t){!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&&ie(t,e)}(o,t);var e,n,r,i=oe(o);function o(t,e,n,r){var a;return function(t,e){if(!(t instanceof e))throw new TypeError("Cannot call a class as a function")}(this,o),(a=i.call(this)).id=t,a.participants=[n,r],a.sequenceLinks=new Map,a.app=e,a.line=document.createElementNS(d,"line"),a.highlightLine=document.createElementNS(d,"line"),a.initSVG(),a}return e=o,(n=[{key:"check",value:function(){return 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c=s(this.participants[1]);c&&(a=c)}this.line.setAttribute("x1",o[0]),this.line.setAttribute("y1",o[1]),this.highlightLine.setAttribute("x1",o[0]),this.highlightLine.setAttribute("y1",o[1]),this.line.setAttribute("x2",a[0]),this.line.setAttribute("y2",a[1]),this.highlightLine.setAttribute("x2",a[0]),this.highlightLine.setAttribute("y2",a[1])}}])&&re(e.prototype,n),r&&re(e,r),o}(zt);function ce(t){return(ce="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 le(t,e){for(var n=0;n<e.length;n++){var r=e[n];r.enumerable=r.enumerable||!1,r.configurable=!0,"value"in r&&(r.writable=!0),Object.defineProperty(t,r.key,r)}}function fe(t,e){return(fe=Object.setPrototypeOf||function(t,e){return t.__proto__=e,t})(t,e)}function he(t){var e=function(){if("undefined"==typeof 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0!==arguments[1]?arguments[1]:4;De(this,t),this.el=e,this.el.textContent="",this.maxCountInitiallyExpanded=n,this.d3cola=u.d3adaptor().groupCompactness(Number.MIN_VALUE).avoidOverlaps(!0);var o=i.select(this.el).append("div").classed("custom-menu-margin",!0).append("div").classed("custom-menu",!0).append("ul"),a=this,s=o.append("li").classed("collapse",!0);s.text("Collapse"),s[0][0].onclick=function(t){a.collapseProtein(t)};var c=o.append("li").text("Scale: "),l=c.selectAll("ul.custom-menu").data(t.barScales).enter().append("div").attr("class","bar-scale").append("label");l.append("span").text((function(t){return 8===t?"AA":t})),l.append("input").attr("class",(function(t){return"scaleButton scaleButton_"+100*t})).attr("name","scaleButtons").attr("type","radio").on("change",(function(t){a.preventDefaultsAndStopPropagation(t),a.contextMenuProt.setStickScale(t,a.contextMenuPoint)}));var f=i.select(".custom-menu-margin").node();f.onmouseout=function(t){var e=t.relatedTarget;do{if(e===this)return;e=e.parentNode}while(e);a.contextMenuProt=null,i.select(this).style("display","none")},this.svgElement=document.createElementNS(d,"svg"),this.svgElement.classList.add("complexViewerSVG"),this.svgElement.onmousedown=function(t){a.mouseDown(t)},this.svgElement.onmousemove=function(t){a.move(t)},this.svgElement.onmouseup=function(t){a.mouseUp(t)},this.svgElement.onmouseout=function(t){a.mouseOut(t)},this.svgElement.ontouchstart=function(t){a.touchStart(t)},this.svgElement.ontouchmove=function(t){a.move(t)},this.svgElement.ontouchend=function(t){a.mouseUp(t)},this.lastMouseUp=(new Date).getTime(),this.el.oncontextmenu=function(t){return t.preventDefault&&t.preventDefault(),t.returnValue=!1,!1};var h=/Firefox/i.test(navigator.userAgent)?"DOMMouseScroll":"mousewheel";document.attachEvent?this.svgElement.attachEvent("on"+h,(function(t){a.mouseWheel(t)})):document.addEventListener&&this.svgElement.addEventListener(h,(function(t){a.mouseWheel(t)}),!1),this.hoverListeners=new Set,this.expandListeners=new Set,this.el.appendChild(this.svgElement),this.container=document.createElementNS(d,"g"),this.container.setAttribute("id","container");var p=i.select(this.svgElement);this.defs=p.append("defs"),this.acknowledgement=document.createElementNS(d,"g");var y=document.createElementNS(d,"text");y.innerHTML="<a href='https://academic.oup.com/bioinformatics/article/33/22/3673/4061280' target='_blank'><tspan x='0' dy='1.2em' style='text-decoration: underline'>ComplexViewer "+r.version+"</tspan></a><tspan x='0' dy='1.2em'>by <a href='https://rappsilberlab.org/' target='_blank'>Rappsilber 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g=document.createTextNode("tooltip");this.tooltip.classList.add("label","tooltip"),this.tooltip.appendChild(g),this.tooltip_bg=document.createElementNS(d,"rect"),this.tooltip_bg.classList.add("tooltip-background"),this.tooltip_subBg=document.createElementNS(d,"rect"),this.tooltip_subBg.classList.add("tooltip-sub-background"),this.svgElement.appendChild(this.tooltip_subBg),this.svgElement.appendChild(this.tooltip_bg),this.svgElement.appendChild(this.tooltip),this.annotationSetsShown=new Map,this.annotationSetsShown.set("Interactor",!1),this.annotationSetsShown.set("UniprotKB",!1),this.annotationSetsShown.set("Superfamily",!1),this.annotationSetsShown.set("MI Features",!0),this.clear()}var e,n,o;return e=t,(n=[{key:"clear",value:function(){this.d3cola.stop(),this.naryLinks.textContent="",this.p_pLinksWide.textContent="",this.highlights.textContent="",this.p_pLinks.textContent="",this.res_resLinks.textContent="",this.proteinUpper.textContent="",this.selfRes_resLinks.textContent="",this.dragElement=null,this.dragStart=null,this.participants=new Map,this.allNaryLinks=new Map,this.allBinaryLinks=new Map,this.allUnaryLinks=new Map,this.allSequenceLinks=new Map,this.complexes=[];var e,n=[],r=Te(a);try{for(r.s();!(e=r.n()).done;){var o=e.value,s=i.hsl(o);s.l=.9,n.push(s+"")}}catch(t){r.e(t)}finally{r.f()}Xt.naryColors=i.scale.ordinal().range(n),this.z=1,this.hideTooltip(),this.state=t.STATES.MOUSE_UP}},{key:"collapseProtein",value:function(){i.select(".custom-menu-margin").style("display","none"),this.contextMenuProt.setExpanded(!1,this.contextMenuPoint),this.contextMenuProt=null,this.notifyExpandListeners()}},{key:"init",value:function(){this.d3cola.stop();var e,n=0,r=Te(this.participants.values());try{for(r.s();!(e=r.n()).done;){var o=e.value;o.size>n&&(n=o.size)}}catch(t){r.e(t)}finally{r.f()}var a,s,u,c=.8*this.svgElement.parentNode.clientWidth/n;this.defaultBarScale=(a=t.barScales,s=c,0===(u=(0,i.bisector((function(t){return t})).left)(a,s))||1===u?a[1]:u===a.length?a[a.length-1]:a[u-1]);var l,f=Te(this.participants.values());try{for(f.s();!(l=f.n()).done;){var h=l.value;"complex"!==h.type&&(h.setPosition(-500,-500),this.proteinUpper.appendChild(h.upperGroup))}}catch(t){f.e(t)}finally{f.f()}var p,d=Te(this.participants.values());try{for(d.s();!(p=d.n()).done;){var y=p.value;"protein"===y.type&&(y.stickZoom=this.defaultBarScale,this.participants.size<this.maxCountInitiallyExpanded&&y.toStick(!1))}}catch(t){d.e(t)}finally{d.f()}this.updateAnnotations();var g=this;!function(t,e){var n,r=Array.from(t.participants.values()).filter((function(t){return"protein"===t.type})),i=0,o=r.length,a=Me(r);try{for(a.s();!(n=a.n()).done;){var s=n.value,u=new RegExp("[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}![-]","i").exec(s.json.identifier.id);u&&u[0]===s.json.identifier.id.trim()&&(Ce(s,(function(){++i===o&&e()})),Ae(s,(function(){++i===o&&e()})))}}catch(t){a.e(t)}finally{a.f()}}(this,(function(){g.updateAnnotations()})),this.checkLinks(),this.autoLayout()}},{key:"zoomToExtent",value:function(){var t=this.svgElement.parentNode.clientWidth,e=this.svgElement.parentNode.clientHeight,n=this.container.getBBox(),r=(t/n.width).toFixed(4),i=(e/n.height).toFixed(4);if((i<r?i:r)<1){var o;r=(t-40)/n.width,(o=(i=(e-40)/n.height)<r?i:r)>this.z&&(o=this.z);var a=-n.x+20/o,s=-n.y+20/o;this.container.setAttribute("transform","scale("+o+") translate("+a+" "+s+") "),this.z=this.container.getCTM().inverse().a}else{var u=t-n.width,c=e-n.height,l=u/2-n.x,f=c/2-n.y;this.container.setAttribute("transform","scale(1) translate("+l+" "+f+")"),this.z=1}this.acknowledgement.setAttribute("transform","translate("+(t-150)+", "+(e-30)+")")}},{key:"autoLayout",value:function(){this.d3cola.stop();var t,e=[],n=[],r=this,o=Te(this.participants.values());try{for(o.s();!(t=o.n()).done;){var a=t.value;"complex"!==a.type&&(n.push(a),a.binaryLinks.size>2&&e.push(a)),delete a.x,delete a.y,delete a.px,delete a.py,delete a.bounds,a.fixed=0}}catch(t){o.e(t)}finally{o.f()}var s=n.length<30?30:20,u=this.svgElement.parentNode.clientWidth,c=this.svgElement.parentNode.clientHeight;function l(t){var e,n=[],i={},o=0,a=Te(t);try{for(a.s();!(e=a.n()).done;)i[e.value.id]=o,o++}catch(t){a.e(t)}finally{a.f()}var s,u=Te(r.allBinaryLinks.values());try{for(u.s();!(s=u.n()).done;){var c=s.value,l=c.participants[0],f=c.participants[1];if(l!==f&&-1!==t.indexOf(l)&&-1!==t.indexOf(f)){var h={};h.source=i[l.id],h.target=i[f.id],h.id=c.id,n.push(h)}}}catch(t){u.e(t)}finally{u.f()}return n}this.d3cola.size([c-40,u-40]).symmetricDiffLinkLengths(s),h(e,l(e),!0);var f=l(n);function h(t,e,n){var o;if(delete r.d3cola._lastStress,delete r.d3cola._alpha,delete r.d3cola._descent,delete r.d3cola._rootGroup,r.d3cola.nodes(t).links(e),r.debug&&((o=i.select(r.container).selectAll(".node").data(t)).enter().append("rect").classed("node",!0).attr({rx:5,ry:5}).style("stroke","red").style("fill","none"),o.exit().remove()),n)r.d3cola.groups([]).start(23,10,0,0,!1);else{var a=[];if(r.complexes){var s,u=Te(r.complexes);try{for(u.s();!(s=u.n()).done;){var c=s.value;c.leaves=[],c.groups=[];var l,f=Te(c.naryLink.participants);try{for(f.s();!(l=f.n()).done;){var h=l.value;"complex"!==h.type&&c.leaves.push(t.indexOf(h))}}catch(t){f.e(t)}finally{f.f()}a.push(c)}}catch(t){u.e(t)}finally{u.f()}var p,d=Te(r.complexes);try{for(d.s();!(p=d.n()).done;){var y,g=p.value,v=Te(g.naryLink.participants);try{for(v.s();!(y=v.n()).done;){var x=y.value;"complex"===x.type&&g.groups.push(a.indexOf(x))}}catch(t){v.e(t)}finally{v.f()}}}catch(t){d.e(t)}finally{d.f()}}r.d3cola.groups(a).start(0,10,1,0,!0).on("tick",(function(){var t,e=Te(r.d3cola.nodes());try{for(e.s();!(t=e.n()).done;){var n=t.value;n.setPositionFromCola(n.x,n.y)}}catch(t){e.e(t)}finally{e.f()}r.setAllLinkCoordinates(),r.zoomToExtent(),r.debug&&o.attr({x:function(t){return t.bounds.x},y:function(t){return t.bounds.y},width:function(t){return t.bounds.width()},height:function(t){return t.bounds.height()}})}))}}h(n,f,!0),h(n,f,!1)}},{key:"getSVG",value:function(){var t=[i.select(this.el).selectAll("svg").node()],e=l.capture(t);return l.makeXMLStr(new XMLSerializer,e[0])}},{key:"readMIJSON",value:function(t){var e=!(arguments.length>1&&void 0!==arguments[1])||arguments[1];_e(t,this,e),this.init()}},{key:"checkLinks",value:function(){var t,e=Te(this.allNaryLinks.values());try{for(e.s();!(t=e.n()).done;)t.value.check()}catch(t){e.e(t)}finally{e.f()}var n,r=Te(this.allBinaryLinks.values());try{for(r.s();!(n=r.n()).done;)n.value.check()}catch(t){r.e(t)}finally{r.f()}var i,o=Te(this.allUnaryLinks.values());try{for(o.s();!(i=o.n()).done;)i.value.check()}catch(t){o.e(t)}finally{o.f()}var a,s=Te(this.allSequenceLinks.values());try{for(s.s();!(a=s.n()).done;)a.value.check()}catch(t){s.e(t)}finally{s.f()}}},{key:"setAllLinkCoordinates",value:function(){var t,e=Te(this.allNaryLinks.values());try{for(e.s();!(t=e.n()).done;)t.value.setLinkCoordinates()}catch(t){e.e(t)}finally{e.f()}var n,r=Te(this.allBinaryLinks.values());try{for(r.s();!(n=r.n()).done;)n.value.setLinkCoordinates()}catch(t){r.e(t)}finally{r.f()}var i,o=Te(this.allUnaryLinks.values());try{for(o.s();!(i=o.n()).done;)i.value.setLinkCoordinates()}catch(t){o.e(t)}finally{o.f()}var a,s=Te(this.allSequenceLinks.values());try{for(s.s();!(a=s.n()).done;)a.value.setLinkCoordinates()}catch(t){s.e(t)}finally{s.f()}}},{key:"showTooltip",value:function(t){var e,n,r=this.tooltip.getComputedTextLength()+16,i=this.svgElement.parentNode.clientWidth,o=this.svgElement.parentNode.clientHeight;e=t.x+20+r<i?t.x:i-r-20,n=t.y+60<o?t.y:o-60,this.tooltip.setAttribute("x",e+22),this.tooltip.setAttribute("y",n+47),this.tooltip_bg.setAttribute("x",e+16),this.tooltip_bg.setAttribute("y",n+28),this.tooltip_subBg.setAttribute("x",e+16),this.tooltip_subBg.setAttribute("y",n+28)}},{key:"setTooltip",value:function(t,e){if(t){this.tooltip.firstChild.data=t.toString().replace(/&(quot);/g,'"'),this.tooltip.setAttribute("display","block");var n=this.tooltip.getComputedTextLength();this.tooltip_bg.setAttribute("width",n+16),this.tooltip_subBg.setAttribute("width",n+16),void 0!==e&&null!=e?(this.tooltip_bg.setAttribute("fill",e),this.tooltip_bg.setAttribute("stroke",e),this.tooltip_bg.setAttribute("fill-opacity","0.0")):(this.tooltip_bg.setAttribute("fill","white"),this.tooltip_bg.setAttribute("stroke","grey")),this.tooltip_bg.setAttribute("height","28"),this.tooltip_subBg.setAttribute("height","28"),this.tooltip_bg.setAttribute("display","block"),this.tooltip_subBg.setAttribute("display","block")}else this.hideTooltip()}},{key:"hideTooltip",value:function(){this.tooltip.setAttribute("display","none"),this.tooltip_bg.setAttribute("display","none"),this.tooltip_subBg.setAttribute("display","none")}},{key:"setAnnotations",value:function(t){t=t.toUpperCase();var e,n=Te(this.annotationSetsShown.keys());try{for(n.s();!(e=n.n()).done;){var r=e.value;this.annotationSetsShown.set(r,t===r)}}catch(t){n.e(t)}finally{n.f()}return this.updateAnnotations(),this.getColorKeyJson()}},{key:"showAnnotations",value:function(t,e){return this.annotationSetsShown.set(t,e),this.updateAnnotations(),this.getColorKeyJson()}},{key:"updateAnnotations",value:function(){this.defs.textContent="",this.uncertainCategories=new Set,this.certainCategories=new Set,delete this.featureColors;var t,e,n=new Set,r=Te(this.participants.values());try{for(r.s();!(t=r.n()).done;){var o,a=Te(t.value.annotationSets);try{for(a.s();!(o=a.n()).done;){var u=Ne(o.value,2),l=u[0],f=u[1];if(!0===this.annotationSetsShown.get(l)){var h,p=Te(f.values());try{for(p.s();!(h=p.n()).done;){var d=h.value;n.add(d.description)}}catch(t){p.e(t)}finally{p.f()}}}}catch(t){a.e(t)}finally{a.f()}}}catch(t){r.e(t)}finally{r.f()}e=n.size<11?i.scale.ordinal().range(s):i.scale.category20();var y=this;function g(t,e){var n=y.defs.append("pattern").attr("id",t).attr("patternUnits","userSpaceOnUse").attr("x",0).attr("y",0).attr("width",12).attr("height",12).attr("patternTransform","rotate(45)");n.append("rect").attr("x",0).attr("y",2).attr("width",12).attr("height",4).attr("fill",e),n.append("rect").attr("x",0).attr("y",8).attr("width",12).attr("height",4).attr("fill",e)}var v,x=Te(this.participants.values());try{for(x.s();!(v=x.n()).done;){var m=v.value;if("protein"===m.type){m.clearPositionalFeatures(),m.updatePositionalFeatures();var b,w=Te(m.annotationSets);try{for(w.s();!(b=w.n()).done;){var k=Ne(b.value,2),S=k[0],_=k[1];if(!0===this.annotationSetsShown.get(S)){var M,E=Te(_);try{for(E.s();!(M=E.n()).done;){var A=M.value,C=void 0;if(C="No annotations"===A.description?"#eeeeee":e(A.description),A.certain&&(A.certain.setAttribute("fill",C),A.certain.setAttribute("stroke",C),this.certainCategories.add(A.description)),A.fuzzyStart||A.fuzzyEnd){if(!this.uncertainCategories.has(name)){var L=new c(C),N="rgba("+L.r+","+L.g+","+L.b+", 0.6)";g("hatched_"+A.description+"_"+C.toString(),N),this.uncertainCategories.add(A.description)}var T="url('#hatched_"+A.description+"_"+C.toString()+"')";A.fuzzyStart&&(A.fuzzyStart.setAttribute("fill",T),A.fuzzyStart.setAttribute("stroke",C)),A.fuzzyEnd&&(A.fuzzyEnd.setAttribute("fill",T),A.fuzzyEnd.setAttribute("stroke",C))}}}catch(t){E.e(t)}finally{E.f()}}}}catch(t){w.e(t)}finally{w.f()}}}}catch(t){x.e(t)}finally{x.f()}this.featureColors=e}},{key:"getColorKeyJson",value:function(){var t,e={Complex:[]},n=Te(Xt.naryColors.domain());try{for(n.s();!(t=n.n()).done;){var r=t.value;e.Complex.push({name:r,certain:{color:Xt.naryColors(r)}})}}catch(t){n.e(t)}finally{n.f()}if(this.featureColors){var i,o=Te(this.annotationSetsShown);try{for(o.s();!(i=o.n()).done;){var a=Ne(i.value,2),s=a[0];if(a[1]){var u,l=[],f=new Set,h=Te(this.participants.values());try{for(h.s();!(u=h.n()).done;){var p=u.value;if("protein"===p.type){var 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null!==t&&t.apply(this,arguments)||this}return i(e,t),e}(a);n.TVGPoint=x;var m=function(t,e,n,r){this.id=t,this.polyid=e,this.polyvertid=n,this.p=r,r.vv=this};n.VisibilityVertex=m;var b=function(){function t(t,e){this.source=t,this.target=e}return t.prototype.length=function(){var t=this.source.p.x-this.target.p.x,e=this.source.p.y-this.target.p.y;return Math.sqrt(t*t+e*e)},t}();n.VisibilityEdge=b;var w=function(){function t(t,e){if(this.P=t,this.V=[],this.E=[],e)this.V=e.V.slice(0),this.E=e.E.slice(0);else{for(var n=t.length,r=0;r<n;r++){for(var i=t[r],o=0;o<i.length;++o){var a=i[o],s=new m(this.V.length,r,o,a);this.V.push(s),o>0&&this.E.push(new b(i[o-1].vv,s))}i.length>1&&this.E.push(new b(i[0].vv,i[i.length-1].vv))}for(r=0;r<n-1;r++){var u=t[r];for(o=r+1;o<n;o++){var c=t[o],l=S(u,c);for(var f in l){var h=l[f],p=u[h.t1],d=c[h.t2];this.addEdgeIfVisible(p,d,r,o)}}}}}return t.prototype.addEdgeIfVisible=function(t,e,n,r){this.intersectsPolys(new s(t.x,t.y,e.x,e.y),n,r)||this.E.push(new b(t.vv,e.vv))},t.prototype.addPoint=function(t,e){var n,r,i,o=this.P.length;this.V.push(new m(this.V.length,o,0,t));for(var a=0;a<o;++a)if(a!==e){var s=this.P[a],u=(n=t,i=void 0,(i=(r=s).slice(0)).push(r[0]),{rtan:h(n,i),ltan:p(n,i)});this.addEdgeIfVisible(t,s[u.ltan],e,a),this.addEdgeIfVisible(t,s[u.rtan],e,a)}return t.vv},t.prototype.intersectsPolys=function(t,e,n){for(var r=0,i=this.P.length;r<i;++r)if(r!=e&&r!=n&&k(t,this.P[r]).length>0)return!0;return!1},t}();function k(t,e){for(var n=[],r=1,i=e.length;r<i;++r){var a=o.Rectangle.lineIntersection(t.x1,t.y1,t.x2,t.y2,e[r-1].x,e[r-1].y,e[r].x,e[r].y);a&&n.push(a)}return n}function S(t,e){for(var n=t.length-1,r=e.length-1,i=new v,o=0;o<=n;++o)for(var a=0;a<=r;++a){var s=t[0==o?n:o-1],u=t[o],l=t[o==n?0:o+1],f=e[0==a?r:a-1],h=e[a],p=e[a==r?0:a+1],d=c(s,u,h),y=c(u,f,h),x=c(u,h,p),m=c(f,h,u),b=c(h,s,u),w=c(h,u,l);d>=0&&y>=0&&x<0&&m>=0&&b>=0&&w<0?i.ll=new g(o,a):d<=0&&y<=0&&x>0&&m<=0&&b<=0&&w>0?i.rr=new 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r=t.findMatch(e,n),i=n.slice(0).reverse(),o=t.findMatch(e,i);r.length>=o.length?(this.length=r.length,this.si=r.si,this.ti=r.ti,this.reversed=!1):(this.length=o.length,this.si=o.si,this.ti=n.length-o.ti-o.length,this.reversed=!0)}return t.findMatch=function(t,e){for(var n=t.length,r=e.length,i={length:0,si:-1,ti:-1},o=new Array(n),a=0;a<n;a++){o[a]=new Array(r);for(var s=0;s<r;s++)if(t[a]===e[s]){var u=o[a][s]=0===a||0===s?1:o[a-1][s-1]+1;u>i.length&&(i.length=u,i.si=a-u+1,i.ti=s-u+1)}else o[a][s]=0}return i},t.prototype.getSequence=function(){return this.length>=0?this.s.slice(this.si,this.si+this.length):[]},t}();n.LongestCommonSubsequence=u;var c=function(){function t(t,e,n){var i=this;void 0===n&&(n=12),this.originalnodes=t,this.groupPadding=n,this.leaves=null,this.nodes=t.map((function(t,n){return new a(n,e.getBounds(t),e.getChildren(t))})),this.leaves=this.nodes.filter((function(t){return t.leaf})),this.groups=this.nodes.filter((function(t){return!t.leaf})),this.cols=this.getGridLines("x"),this.rows=this.getGridLines("y"),this.groups.forEach((function(t){return t.children.forEach((function(e){return i.nodes[e].parent=t}))})),this.root={children:[]},this.nodes.forEach((function(t){void 0===t.parent&&(t.parent=i.root,i.root.children.push(t.id)),t.ports=[]})),this.backToFront=this.nodes.slice(0),this.backToFront.sort((function(t,e){return i.getDepth(t)-i.getDepth(e)})),this.backToFront.slice(0).reverse().filter((function(t){return!t.leaf})).forEach((function(t){var e=r.Rectangle.empty();t.children.forEach((function(t){return e=e.union(i.nodes[t].rect)})),t.rect=e.inflate(i.groupPadding)}));var o=this.midPoints(this.cols.map((function(t){return t.pos}))),u=this.midPoints(this.rows.map((function(t){return t.pos}))),c=o[0],l=o[o.length-1],f=u[0],h=u[u.length-1],p=this.rows.map((function(t){return{x1:c,x2:l,y1:t.pos,y2:t.pos}})).concat(u.map((function(t){return{x1:c,x2:l,y1:t,y2:t}}))),d=this.cols.map((function(t){return{x1:t.pos,x2:t.pos,y1:f,y2:h}})).concat(o.map((function(t){return{x1:t,x2:t,y1:f,y2:h}}))),y=p.concat(d);y.forEach((function(t){return t.verts=[]})),this.verts=[],this.edges=[],p.forEach((function(t){return d.forEach((function(e){var n=new s(i.verts.length,e.x1,t.y1);t.verts.push(n),e.verts.push(n),i.verts.push(n);for(var r=i.backToFront.length;r-- >0;){var o=i.backToFront[r],a=o.rect,u=Math.abs(n.x-a.cx()),c=Math.abs(n.y-a.cy());if(u<a.width()/2&&c<a.height()/2){n.node=o;break}}}))})),y.forEach((function(t,e){i.nodes.forEach((function(e,n){e.rect.lineIntersections(t.x1,t.y1,t.x2,t.y2).forEach((function(n,r){var o=new s(i.verts.length,n.x,n.y,e,t);i.verts.push(o),t.verts.push(o),e.ports.push(o)}))}));var n=Math.abs(t.y1-t.y2)<.1,r=function(t,e){return n?e.x-t.x:e.y-t.y};t.verts.sort(r);for(var o=1;o<t.verts.length;o++){var a=t.verts[o-1],u=t.verts[o];a.node&&a.node===u.node&&a.node.leaf||i.edges.push({source:a.id,target:u.id,length:Math.abs(r(a,u))})}}))}return t.prototype.avg=function(t){return t.reduce((function(t,e){return t+e}))/t.length},t.prototype.getGridLines=function(t){for(var e=[],n=this.leaves.slice(0,this.leaves.length);n.length>0;){var r=n.filter((function(e){return e.rect["overlap"+t.toUpperCase()](n[0].rect)})),i={nodes:r,pos:this.avg(r.map((function(e){return e.rect["c"+t]()})))};e.push(i),i.nodes.forEach((function(t){return n.splice(n.indexOf(t),1)}))}return e.sort((function(t,e){return t.pos-e.pos})),e},t.prototype.getDepth=function(t){for(var e=0;t.parent!==this.root;)e++,t=t.parent;return e},t.prototype.midPoints=function(t){for(var e=t[1]-t[0],n=[t[0]-e/2],r=1;r<t.length;r++)n.push((t[r]+t[r-1])/2);return n.push(t[t.length-1]+e/2),n},t.prototype.findLineage=function(t){var e=[t];do{t=t.parent,e.push(t)}while(t!==this.root);return e.reverse()},t.prototype.findAncestorPathBetween=function(t,e){for(var n=this.findLineage(t),r=this.findLineage(e),i=0;n[i]===r[i];)i++;return{commonAncestor:n[i-1],lineages:n.slice(i).concat(r.slice(i))}},t.prototype.siblingObstacles=function(t,e){var n=this,r=this.findAncestorPathBetween(t,e),i={};r.lineages.forEach((function(t){return i[t.id]={}}));var o=r.commonAncestor.children.filter((function(t){return!(t in i)}));return r.lineages.filter((function(t){return t.parent!==r.commonAncestor})).forEach((function(t){return o=o.concat(t.parent.children.filter((function(e){return e!==t.id})))})),o.map((function(t){return n.nodes[t]}))},t.getSegmentSets=function(t,e,n){for(var r=[],i=0;i<t.length;i++)for(var o=t[i],a=0;a<o.length;a++){(f=o[a]).edgeid=i,f.i=a;var s=f[1][e]-f[0][e];Math.abs(s)<.1&&r.push(f)}r.sort((function(t,n){return t[0][e]-n[0][e]}));for(var u=[],c=null,l=0;l<r.length;l++){var f=r[l];(!c||Math.abs(f[0][e]-c.pos)>.1)&&(c={pos:f[0][e],segments:[]},u.push(c)),c.segments.push(f)}return u},t.nudgeSegs=function(t,e,n,r,o,a){var s=r.length;if(!(s<=1)){for(var u=r.map((function(e){return new i.Variable(e[0][t])})),c=[],l=0;l<s;l++)for(var f=0;f<s;f++)if(l!==f){var h=r[l],p=r[f],d=h.edgeid,y=p.edgeid,g=-1,v=-1;"x"==t?o(d,y)&&(h[0][e]<h[1][e]?(g=f,v=l):(g=l,v=f)):o(d,y)&&(h[0][e]<h[1][e]?(g=l,v=f):(g=f,v=l)),g>=0&&c.push(new i.Constraint(u[g],u[v],a))}new i.Solver(u,c).solve(),u.forEach((function(e,i){var o=r[i],a=e.position();o[0][t]=o[1][t]=a;var s=n[o.edgeid];o.i>0&&(s[o.i-1][1][t]=a),o.i<s.length-1&&(s[o.i+1][0][t]=a)}))}},t.nudgeSegments=function(e,n,r,i,o){for(var a=t.getSegmentSets(e,n,r),s=0;s<a.length;s++){for(var u=a[s],c=[],l=0;l<u.segments.length;l++){var f=u.segments[l];c.push({type:0,s:f,pos:Math.min(f[0][r],f[1][r])}),c.push({type:1,s:f,pos:Math.max(f[0][r],f[1][r])})}c.sort((function(t,e){return t.pos-e.pos+t.type-e.type}));var h=[],p=0;c.forEach((function(a){0===a.type?(h.push(a.s),p++):p--,0==p&&(t.nudgeSegs(n,r,e,h,i,o),h=[])}))}},t.prototype.routeEdges=function(e,n,r,i){var o=this,a=e.map((function(t){return o.route(r(t),i(t))})),s=t.orderEdges(a),u=a.map((function(e){return t.makeSegments(e)}));return t.nudgeSegments(u,"x","y",s,n),t.nudgeSegments(u,"y","x",s,n),t.unreverseEdges(u,a),u},t.unreverseEdges=function(t,e){t.forEach((function(t,n){e[n].reversed&&(t.reverse(),t.forEach((function(t){t.reverse()})))}))},t.angleBetween2Lines=function(t,e){var n=Math.atan2(t[0].y-t[1].y,t[0].x-t[1].x),r=Math.atan2(e[0].y-e[1].y,e[0].x-e[1].x),i=n-r;return(i>Math.PI||i<-Math.PI)&&(i=r-n),i},t.isLeft=function(t,e,n){return(e.x-t.x)*(n.y-t.y)-(e.y-t.y)*(n.x-t.x)<=0},t.getOrder=function(t){for(var e={},n=0;n<t.length;n++){var r=t[n];void 0===e[r.l]&&(e[r.l]={}),e[r.l][r.r]=!0}return function(t,n){return void 0!==e[t]&&e[t][n]}},t.orderEdges=function(e){for(var n=[],r=0;r<e.length-1;r++)for(var i=r+1;i<e.length;i++){var o,a,s,c=e[r],l=e[i],f=new u(c,l);0!==f.length&&(f.reversed&&(l.reverse(),l.reversed=!0,f=new u(c,l)),(f.si<=0||f.ti<=0)&&(f.si+f.length>=c.length||f.ti+f.length>=l.length)?n.push({l:r,r:i}):(f.si+f.length>=c.length||f.ti+f.length>=l.length?(o=c[f.si+1],s=c[f.si-1],a=l[f.ti-1]):(o=c[f.si+f.length-2],a=c[f.si+f.length],s=l[f.ti+f.length]),t.isLeft(o,a,s)?n.push({l:i,r:r}):n.push({l:r,r:i})))}return t.getOrder(n)},t.makeSegments=function(t){function e(t){return{x:t.x,y:t.y}}for(var n=function(t,e,n){return Math.abs((e.x-t.x)*(n.y-t.y)-(e.y-t.y)*(n.x-t.x))<.001},r=[],i=e(t[0]),o=1;o<t.length;o++){var a=e(t[o]),s=o<t.length-1?t[o+1]:null;s&&n(i,a,s)||(r.push([i,a]),i=a)}return r},t.prototype.route=function(t,e){var n=this,r=this.nodes[t],i=this.nodes[e];this.obstacles=this.siblingObstacles(r,i);var a={};this.obstacles.forEach((function(t){return a[t.id]=t})),this.passableEdges=this.edges.filter((function(t){var e=n.verts[t.source],r=n.verts[t.target];return!(e.node&&e.node.id in a||r.node&&r.node.id in a)}));for(var s=1;s<r.ports.length;s++){var u=r.ports[0].id,c=r.ports[s].id;this.passableEdges.push({source:u,target:c,length:0})}for(s=1;s<i.ports.length;s++)u=i.ports[0].id,c=i.ports[s].id,this.passableEdges.push({source:u,target:c,length:0});var l=new o.Calculator(this.verts.length,this.passableEdges,(function(t){return t.source}),(function(t){return t.target}),(function(t){return t.length})).PathFromNodeToNodeWithPrevCost(r.ports[0].id,i.ports[0].id,(function(t,e,o){var a=n.verts[t],s=n.verts[e],u=n.verts[o],c=Math.abs(u.x-a.x),l=Math.abs(u.y-a.y);return a.node===r&&a.node===s.node||s.node===i&&s.node===u.node?0:c>1&&l>1?1e3:0})).reverse().map((function(t){return n.verts[t]}));return l.push(this.nodes[i.id].ports[0]),l.filter((function(t,e){return!(e<l.length-1&&l[e+1].node===r&&t.node===r||e>0&&t.node===i&&l[e-1].node===i)}))},t.getRoutePath=function(e,n,r,i){var o,a,s,u={routepath:"M "+e[0][0].x+" "+e[0][0].y+" ",arrowpath:""};if(e.length>1)for(var c=0;c<e.length;c++){var l=(o=e[c])[1].x,f=o[1].y,h=l-o[0].x,p=f-o[0].y;if(c<e.length-1){Math.abs(h)>0?l-=h/Math.abs(h)*n:f-=p/Math.abs(p)*n,u.routepath+="L "+l+" "+f+" ";var d=e[c+1],y=d[0].x,g=d[0].y;h=d[1].x-y,p=d[1].y-g;var v,x,m=t.angleBetween2Lines(o,d)<0?1:0;Math.abs(h)>0?(v=y+h/Math.abs(h)*n,x=g):(v=y,x=g+p/Math.abs(p)*n);var b=Math.abs(v-l),w=Math.abs(x-f);u.routepath+="A "+b+" "+w+" 0 0 "+m+" "+v+" "+x+" "}else{var k=[l,f];Math.abs(h)>0?(a=[l-=h/Math.abs(h)*i,f+r],s=[l,f-r]):(a=[l+r,f-=p/Math.abs(p)*i],s=[l-r,f]),u.routepath+="L "+l+" "+f+" ",i>0&&(u.arrowpath="M "+k[0]+" "+k[1]+" L "+a[0]+" "+a[1]+" L "+s[0]+" "+s[1])}}else l=(o=e[0])[1].x,f=o[1].y,h=l-o[0].x,p=f-o[0].y,k=[l,f],Math.abs(h)>0?(a=[l-=h/Math.abs(h)*i,f+r],s=[l,f-r]):(a=[l+r,f-=p/Math.abs(p)*i],s=[l-r,f]),u.routepath+="L "+l+" "+f+" ",i>0&&(u.arrowpath="M "+k[0]+" "+k[1]+" L "+a[0]+" "+a[1]+" L "+s[0]+" "+s[1]);return u},t}();n.GridRouter=c},{"./rectangle":17,"./shortestpaths":18,"./vpsc":19}],10:[function(t,e,n){"use strict";Object.defineProperty(n,"__esModule",{value:!0});var r=10,i=(1+Math.sqrt(5))/2,o=1e-4;n.applyPacking=function(t,e,n,a,s,u){void 0===s&&(s=1),void 0===u&&(u=!0);var c=e,l=n,f=(s=void 0!==s?s:1,a=void 0!==a?a:0,0),h=0,p=0,d=0,y=[];function g(t,e){y=[],f=0,h=0,d=0;for(var n=0;n<t.length;n++)v(t[n],e);return Math.abs(f/h-s)}function v(t,e){for(var n=void 0,i=0;i<y.length;i++)if(y[i].space_left>=t.height&&y[i].x+y[i].width+t.width+r-e<=o){n=y[i];break}y.push(t),void 0!==n?(t.x=n.x+n.width+r,t.y=n.bottom,t.space_left=t.height,t.bottom=t.y,n.space_left-=t.height+r,n.bottom+=t.height+r):(t.y=d,d+=t.height+r,t.x=0,t.bottom=t.y,t.space_left=t.height),t.y+t.height-h>-o&&(h=t.y+t.height-0),t.x+t.width-f>-o&&(f=t.x+t.width-0)}0!=t.length&&(function(t){t.forEach((function(t){var e,n,r,i,o;e=t,n=Number.MAX_VALUE,r=Number.MAX_VALUE,i=0,o=0,e.array.forEach((function(t){var e=void 0!==t.width?t.width:a,s=void 0!==t.height?t.height:a;e/=2,s/=2,i=Math.max(t.x+e,i),n=Math.min(t.x-e,n),o=Math.max(t.y+s,o),r=Math.min(t.y-s,r)})),e.width=i-n,e.height=o-r}))}(t),function(t,e){var n=Number.POSITIVE_INFINITY,a=0;t.sort((function(t,e){return e.height-t.height})),p=t.reduce((function(t,e){return t.width<e.width?t.width:e.width}));for(var s=v=p,u=x=function(t){var e=0;return t.forEach((function(t){return e+=t.width+r})),e}(t),c=0,l=Number.MAX_VALUE,f=Number.MAX_VALUE,h=-1,d=Number.MAX_VALUE,y=Number.MAX_VALUE;d>p||y>o;){if(1!=h){var v=u-(u-s)/i;l=g(t,v)}if(0!=h){var x=s+(u-s)/i;f=g(t,x)}if(d=Math.abs(v-x),y=Math.abs(l-f),l<n&&(n=l,a=v),f<n&&(n=f,a=x),l>f?(s=v,v=x,l=f,h=1):(u=x,x=v,f=l,h=0),c++>100)break}g(t,a)}(t),u&&function(t){t.forEach((function(t){var e={x:0,y:0};t.array.forEach((function(t){e.x+=t.x,e.y+=t.y})),e.x/=t.array.length,e.y/=t.array.length;var n=e.x-t.width/2,r=e.y-t.height/2,i=t.x-n+c/2-f/2,o=t.y-r+l/2-h/2;t.array.forEach((function(t){t.x+=i,t.y+=o}))}))}(t))},n.separateGraphs=function(t,e){for(var n={},r={},i=[],o=0,a=0;a<e.length;a++){var s=e[a],u=s.source,c=s.target;r[u.index]?r[u.index].push(c):r[u.index]=[c],r[c.index]?r[c.index].push(u):r[c.index]=[u]}for(a=0;a<t.length;a++){var l=t[a];n[l.index]||f(l,!0)}function f(t,e){if(void 0===n[t.index]){e&&(o++,i.push({array:[]})),n[t.index]=o,i[o-1].array.push(t);var a=r[t.index];if(a)for(var s=0;s<a.length;s++)f(a[s],!1)}}return i}},{}],11:[function(t,e,n){"use strict";Object.defineProperty(n,"__esModule",{value:!0});var r,i=t("./powergraph"),o=t("./linklengths"),a=t("./descent"),s=t("./rectangle"),u=t("./shortestpaths"),c=t("./geom"),l=t("./handledisconnected");function f(t){return void 0!==t.leaves||void 0!==t.groups}!function(t){t[t.start=0]="start",t[t.tick=1]="tick",t[t.end=2]="end"}(r=n.EventType||(n.EventType={}));var h=function(){function t(){var e=this;this._canvasSize=[1,1],this._linkDistance=20,this._defaultNodeSize=10,this._linkLengthCalculator=null,this._linkType=null,this._avoidOverlaps=!1,this._handleDisconnected=!0,this._running=!1,this._nodes=[],this._groups=[],this._rootGroup=null,this._links=[],this._constraints=[],this._distanceMatrix=null,this._descent=null,this._directedLinkConstraints=null,this._threshold=.01,this._visibilityGraph=null,this._groupCompactness=1e-6,this.event=null,this.linkAccessor={getSourceIndex:t.getSourceIndex,getTargetIndex:t.getTargetIndex,setLength:t.setLinkLength,getType:function(t){return"function"==typeof e._linkType?e._linkType(t):0}}}return t.prototype.on=function(t,e){return this.event||(this.event={}),"string"==typeof t?this.event[r[t]]=e:this.event[t]=e,this},t.prototype.trigger=function(t){this.event&&void 0!==this.event[t.type]&&this.event[t.type](t)},t.prototype.kick=function(){for(;!this.tick(););},t.prototype.tick=function(){if(this._alpha<this._threshold)return this._running=!1,this.trigger({type:r.end,alpha:this._alpha=0,stress:this._lastStress}),!0;var t,e,n=this._nodes.length;for(this._links.length,this._descent.locks.clear(),e=0;e<n;++e)if((t=this._nodes[e]).fixed){void 0!==t.px&&void 0!==t.py||(t.px=t.x,t.py=t.y);var i=[t.px,t.py];this._descent.locks.add(e,i)}var o=this._descent.rungeKutta();return 0===o?this._alpha=0:void 0!==this._lastStress&&(this._alpha=o),this._lastStress=o,this.updateNodePositions(),this.trigger({type:r.tick,alpha:this._alpha,stress:this._lastStress}),!1},t.prototype.updateNodePositions=function(){for(var t,e=this._descent.x[0],n=this._descent.x[1],r=this._nodes.length;r--;)(t=this._nodes[r]).x=e[r],t.y=n[r]},t.prototype.nodes=function(t){if(!t){if(0===this._nodes.length&&this._links.length>0){var e=0;this._links.forEach((function(t){e=Math.max(e,t.source,t.target)})),this._nodes=new Array(++e);for(var n=0;n<e;++n)this._nodes[n]={}}return this._nodes}return this._nodes=t,this},t.prototype.groups=function(t){var e=this;return t?(this._groups=t,this._rootGroup={},this._groups.forEach((function(t){void 0===t.padding&&(t.padding=1),void 0!==t.leaves&&t.leaves.forEach((function(n,r){"number"==typeof n&&((t.leaves[r]=e._nodes[n]).parent=t)})),void 0!==t.groups&&t.groups.forEach((function(n,r){"number"==typeof n&&((t.groups[r]=e._groups[n]).parent=t)}))})),this._rootGroup.leaves=this._nodes.filter((function(t){return void 0===t.parent})),this._rootGroup.groups=this._groups.filter((function(t){return void 0===t.parent})),this):this._groups},t.prototype.powerGraphGroups=function(t){var e=i.getGroups(this._nodes,this._links,this.linkAccessor,this._rootGroup);return this.groups(e.groups),t(e),this},t.prototype.avoidOverlaps=function(t){return arguments.length?(this._avoidOverlaps=t,this):this._avoidOverlaps},t.prototype.handleDisconnected=function(t){return arguments.length?(this._handleDisconnected=t,this):this._handleDisconnected},t.prototype.flowLayout=function(t,e){return arguments.length||(t="y"),this._directedLinkConstraints={axis:t,getMinSeparation:"number"==typeof e?function(){return e}:e},this},t.prototype.links=function(t){return arguments.length?(this._links=t,this):this._links},t.prototype.constraints=function(t){return arguments.length?(this._constraints=t,this):this._constraints},t.prototype.distanceMatrix=function(t){return arguments.length?(this._distanceMatrix=t,this):this._distanceMatrix},t.prototype.size=function(t){return t?(this._canvasSize=t,this):this._canvasSize},t.prototype.defaultNodeSize=function(t){return t?(this._defaultNodeSize=t,this):this._defaultNodeSize},t.prototype.groupCompactness=function(t){return t?(this._groupCompactness=t,this):this._groupCompactness},t.prototype.linkDistance=function(t){return t?(this._linkDistance="function"==typeof t?t:+t,this._linkLengthCalculator=null,this):this._linkDistance},t.prototype.linkType=function(t){return this._linkType=t,this},t.prototype.convergenceThreshold=function(t){return t?(this._threshold="function"==typeof t?t:+t,this):this._threshold},t.prototype.alpha=function(t){return arguments.length?(t=+t,this._alpha?this._alpha=t>0?t:0:t>0&&(this._running||(this._running=!0,this.trigger({type:r.start,alpha:this._alpha=t}),this.kick())),this):this._alpha},t.prototype.getLinkLength=function(t){return"function"==typeof this._linkDistance?+this._linkDistance(t):this._linkDistance},t.setLinkLength=function(t,e){t.length=e},t.prototype.getLinkType=function(t){return"function"==typeof this._linkType?this._linkType(t):0},t.prototype.symmetricDiffLinkLengths=function(t,e){var n=this;return void 0===e&&(e=1),this.linkDistance((function(e){return t*e.length})),this._linkLengthCalculator=function(){return o.symmetricDiffLinkLengths(n._links,n.linkAccessor,e)},this},t.prototype.jaccardLinkLengths=function(t,e){var n=this;return void 0===e&&(e=1),this.linkDistance((function(e){return t*e.length})),this._linkLengthCalculator=function(){return o.jaccardLinkLengths(n._links,n.linkAccessor,e)},this},t.prototype.start=function(e,n,r,i,c,l){var f=this;void 0===e&&(e=0),void 0===n&&(n=0),void 0===r&&(r=0),void 0===i&&(i=0),void 0===c&&(c=!0),void 0===l&&(l=!0);var h,p=this.nodes().length,d=p+2*this._groups.length,y=(this._links.length,this._canvasSize[0]),g=this._canvasSize[1],v=new Array(d),x=new Array(d),m=null,b=this._avoidOverlaps;this._nodes.forEach((function(t,e){t.index=e,void 0===t.x&&(t.x=y/2,t.y=g/2),v[e]=t.x,x[e]=t.y})),this._linkLengthCalculator&&this._linkLengthCalculator(),this._distanceMatrix?h=this._distanceMatrix:(h=new u.Calculator(d,this._links,t.getSourceIndex,t.getTargetIndex,(function(t){return f.getLinkLength(t)})).DistanceMatrix(),m=a.Descent.createSquareMatrix(d,(function(){return 2})),this._links.forEach((function(t){"number"==typeof t.source&&(t.source=f._nodes[t.source]),"number"==typeof t.target&&(t.target=f._nodes[t.target])})),this._links.forEach((function(e){var n=t.getSourceIndex(e),r=t.getTargetIndex(e);m[n][r]=m[r][n]=e.weight||1})));var w=a.Descent.createSquareMatrix(d,(function(t,e){return h[t][e]}));if(this._rootGroup&&void 0!==this._rootGroup.groups){var k=p;this._groups.forEach((function(t){!function(t,e,n,r){m[t][e]=m[e][t]=n,w[t][e]=w[e][t]=r}(k,k+1,f._groupCompactness,.1),void 0===t.bounds?(v[k]=y/2,x[k++]=g/2,v[k]=y/2,x[k++]=g/2):(v[k]=t.bounds.x,x[k++]=t.bounds.y,v[k]=t.bounds.X,x[k++]=t.bounds.Y)}))}else this._rootGroup={leaves:this._nodes,groups:[]};var S=this._constraints||[];for(this._directedLinkConstraints&&(this.linkAccessor.getMinSeparation=this._directedLinkConstraints.getMinSeparation,S=S.concat(o.generateDirectedEdgeConstraints(p,this._links,this._directedLinkConstraints.axis,this.linkAccessor))),this.avoidOverlaps(!1),this._descent=new a.Descent([v,x],w),this._descent.locks.clear(),k=0;k<p;++k){var _=this._nodes[k];if(_.fixed){_.px=_.x,_.py=_.y;var M=[_.x,_.y];this._descent.locks.add(k,M)}}if(this._descent.threshold=this._threshold,this.initialLayout(e,v,x),S.length>0&&(this._descent.project=new s.Projection(this._nodes,this._groups,this._rootGroup,S).projectFunctions()),this._descent.run(n),this.separateOverlappingComponents(y,g,l),this.avoidOverlaps(b),b&&(this._nodes.forEach((function(t,e){t.x=v[e],t.y=x[e]})),this._descent.project=new s.Projection(this._nodes,this._groups,this._rootGroup,S,!0).projectFunctions(),this._nodes.forEach((function(t,e){v[e]=t.x,x[e]=t.y}))),this._descent.G=m,this._descent.run(r),i){this._descent.snapStrength=1e3,this._descent.snapGridSize=this._nodes[0].width,this._descent.numGridSnapNodes=p,this._descent.scaleSnapByMaxH=p!=d;var E=a.Descent.createSquareMatrix(d,(function(t,e){return t>=p||e>=p?m[t][e]:0}));this._descent.G=E,this._descent.run(i)}return this.updateNodePositions(),this.separateOverlappingComponents(y,g,l),c?this.resume():this},t.prototype.initialLayout=function(e,n,r){if(this._groups.length>0&&e>0){var i=this._nodes.length,o=this._links.map((function(t){return{source:t.source.index,target:t.target.index}})),a=this._nodes.map((function(t){return{index:t.index}}));this._groups.forEach((function(t,e){a.push({index:t.index=i+e})})),this._groups.forEach((function(t,e){void 0!==t.leaves&&t.leaves.forEach((function(e){return o.push({source:t.index,target:e.index})})),void 0!==t.groups&&t.groups.forEach((function(e){return o.push({source:t.index,target:e.index})}))})),(new t).size(this.size()).nodes(a).links(o).avoidOverlaps(!1).linkDistance(this.linkDistance()).symmetricDiffLinkLengths(5).convergenceThreshold(1e-4).start(e,0,0,0,!1),this._nodes.forEach((function(t){n[t.index]=a[t.index].x,r[t.index]=a[t.index].y}))}else this._descent.run(e)},t.prototype.separateOverlappingComponents=function(t,e,n){var r=this;if(void 0===n&&(n=!0),!this._distanceMatrix&&this._handleDisconnected){var i=this._descent.x[0],o=this._descent.x[1];this._nodes.forEach((function(t,e){t.x=i[e],t.y=o[e]}));var a=l.separateGraphs(this._nodes,this._links);l.applyPacking(a,t,e,this._defaultNodeSize,e/t,n),this._nodes.forEach((function(t,e){r._descent.x[0][e]=t.x,r._descent.x[1][e]=t.y,t.bounds&&(t.bounds.setXCentre(t.x),t.bounds.setYCentre(t.y))}))}},t.prototype.resume=function(){return this.alpha(.1)},t.prototype.stop=function(){return this.alpha(0)},t.prototype.prepareEdgeRouting=function(t){void 0===t&&(t=0),this._visibilityGraph=new c.TangentVisibilityGraph(this._nodes.map((function(e){return e.bounds.inflate(-t).vertices()})))},t.prototype.routeEdge=function(t,e,n){void 0===e&&(e=5);var r=[],i=new c.TangentVisibilityGraph(this._visibilityGraph.P,{V:this._visibilityGraph.V,E:this._visibilityGraph.E}),o={x:t.source.x,y:t.source.y},a={x:t.target.x,y:t.target.y},l=i.addPoint(o,t.source.index),f=i.addPoint(a,t.target.index);i.addEdgeIfVisible(o,a,t.source.index,t.target.index),void 0!==n&&n(i);var h=new u.Calculator(i.V.length,i.E,(function(t){return t.source.id}),(function(t){return t.target.id}),(function(t){return t.length()})).PathFromNodeToNode(l.id,f.id);if(1===h.length||h.length===i.V.length){var p=s.makeEdgeBetween(t.source.innerBounds,t.target.innerBounds,e);r=[p.sourceIntersection,p.arrowStart]}else{for(var d=h.length-2,y=i.V[h[d]].p,g=i.V[h[0]].p,v=(r=[t.source.innerBounds.rayIntersection(y.x,y.y)],d);v>=0;--v)r.push(i.V[h[v]].p);r.push(s.makeEdgeTo(g,t.target.innerBounds,e))}return r},t.getSourceIndex=function(t){return"number"==typeof t.source?t.source:t.source.index},t.getTargetIndex=function(t){return"number"==typeof t.target?t.target:t.target.index},t.linkId=function(e){return t.getSourceIndex(e)+"-"+t.getTargetIndex(e)},t.dragStart=function(e){f(e)?t.storeOffset(e,t.dragOrigin(e)):(t.stopNode(e),e.fixed|=2)},t.stopNode=function(t){t.px=t.x,t.py=t.y},t.storeOffset=function(e,n){void 0!==e.leaves&&e.leaves.forEach((function(e){e.fixed|=2,t.stopNode(e),e._dragGroupOffsetX=e.x-n.x,e._dragGroupOffsetY=e.y-n.y})),void 0!==e.groups&&e.groups.forEach((function(e){return t.storeOffset(e,n)}))},t.dragOrigin=function(t){return f(t)?{x:t.bounds.cx(),y:t.bounds.cy()}:t},t.drag=function(e,n){f(e)?(void 0!==e.leaves&&e.leaves.forEach((function(t){e.bounds.setXCentre(n.x),e.bounds.setYCentre(n.y),t.px=t._dragGroupOffsetX+n.x,t.py=t._dragGroupOffsetY+n.y})),void 0!==e.groups&&e.groups.forEach((function(e){return t.drag(e,n)}))):(e.px=n.x,e.py=n.y)},t.dragEnd=function(e){f(e)?(void 0!==e.leaves&&e.leaves.forEach((function(e){t.dragEnd(e),delete e._dragGroupOffsetX,delete e._dragGroupOffsetY})),void 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o=0;o<t.k;++o)this.result[o]=new Array(e.length);e.forEach((function(e,n){for(var r=0,o=t.dims;r<o.length;r++){var a=o[r];void 0===e[a]&&(e[a]=Math.random())}i.result[0][n]=e.x,i.result[1][n]=e.y,i.result[2][n]=e.z}))}return t.prototype.linkLength=function(t){return t.actualLength(this.result)},t.prototype.start=function(t){var e=this;void 0===t&&(t=100);var n=this.nodes.length,s=new l;this.useJaccardLinkLengths&&a.jaccardLinkLengths(this.links,s,1.5),this.links.forEach((function(t){return t.length*=e.idealLinkLength}));var u=new r.Calculator(n,this.links,(function(t){return t.source}),(function(t){return t.target}),(function(t){return t.length})).DistanceMatrix(),c=i.Descent.createSquareMatrix(n,(function(t,e){return u[t][e]})),f=i.Descent.createSquareMatrix(n,(function(){return 2}));this.links.forEach((function(t){var e=t.source,n=t.target;return f[e][n]=f[n][e]=1})),this.descent=new 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t(t,e,n,r){this.x=t,this.X=e,this.y=n,this.Y=r}return t.empty=function(){return new t(Number.POSITIVE_INFINITY,Number.NEGATIVE_INFINITY,Number.POSITIVE_INFINITY,Number.NEGATIVE_INFINITY)},t.prototype.cx=function(){return(this.x+this.X)/2},t.prototype.cy=function(){return(this.y+this.Y)/2},t.prototype.overlapX=function(t){var e=this.cx(),n=t.cx();return e<=n&&t.x<this.X?this.X-t.x:n<=e&&this.x<t.X?t.X-this.x:0},t.prototype.overlapY=function(t){var e=this.cy(),n=t.cy();return e<=n&&t.y<this.Y?this.Y-t.y:n<=e&&this.y<t.Y?t.Y-this.y:0},t.prototype.setXCentre=function(t){var e=t-this.cx();this.x+=e,this.X+=e},t.prototype.setYCentre=function(t){var e=t-this.cy();this.y+=e,this.Y+=e},t.prototype.width=function(){return this.X-this.x},t.prototype.height=function(){return this.Y-this.y},t.prototype.union=function(e){return new t(Math.min(this.x,e.x),Math.max(this.X,e.X),Math.min(this.y,e.y),Math.max(this.Y,e.Y))},t.prototype.lineIntersections=function(e,n,r,i){for(var o=[[this.x,this.y,this.X,this.y],[this.X,this.y,this.X,this.Y],[this.X,this.Y,this.x,this.Y],[this.x,this.Y,this.x,this.y]],a=[],s=0;s<4;++s){var u=t.lineIntersection(e,n,r,i,o[s][0],o[s][1],o[s][2],o[s][3]);null!==u&&a.push({x:u.x,y:u.y})}return a},t.prototype.rayIntersection=function(t,e){var n=this.lineIntersections(this.cx(),this.cy(),t,e);return n.length>0?n[0]:null},t.prototype.vertices=function(){return[{x:this.x,y:this.y},{x:this.X,y:this.y},{x:this.X,y:this.Y},{x:this.x,y:this.Y}]},t.lineIntersection=function(t,e,n,r,i,o,a,s){var u=n-t,c=a-i,l=r-e,f=s-o,h=f*u-c*l;if(0==h)return null;var p=t-i,d=e-o,y=(c*d-f*p)/h,g=(u*d-l*p)/h;return y>=0&&y<=1&&g>=0&&g<=1?{x:t+y*u,y:e+y*l}:null},t.prototype.inflate=function(e){return new t(this.x-e,this.X+e,this.y-e,this.Y+e)},t}();n.Rectangle=u,n.makeEdgeBetween=function(t,e,n){var r=t.rayIntersection(e.cx(),e.cy())||{x:t.cx(),y:t.cy()},i=e.rayIntersection(t.cx(),t.cy())||{x:e.cx(),y:e.cy()},o=i.x-r.x,a=i.y-r.y,s=Math.sqrt(o*o+a*a),u=s-n;return{sourceIntersection:r,targetIntersection:i,arrowStart:{x:r.x+u*o/s,y:r.y+u*a/s}}},n.makeEdgeTo=function(t,e,n){var r=e.rayIntersection(t.x,t.y);r||(r={x:e.cx(),y:e.cy()});var i=r.x-t.x,o=r.y-t.y,a=Math.sqrt(i*i+o*o);return{x:r.x-n*i/a,y:r.y-n*o/a}};var c=function(t,e,n){this.v=t,this.r=e,this.pos=n,this.prev=h(),this.next=h()},l=function(t,e,n){this.isOpen=t,this.v=e,this.pos=n};function f(t,e){return t.pos>e.pos?1:t.pos<e.pos||t.isOpen?-1:e.isOpen?1:0}function h(){return new a.RBTree((function(t,e){return t.pos-e.pos}))}var p={getCentre:function(t){return t.cx()},getOpen:function(t){return t.y},getClose:function(t){return t.Y},getSize:function(t){return t.width()},makeRect:function(t,e,n,r){return new u(n-r/2,n+r/2,t,e)},findNeighbours:function(t,e){var n=function(n,r){for(var i,o=e.findIter(t);null!==(i=o[n]());){var a=i.r.overlapX(t.r);if((a<=0||a<=i.r.overlapY(t.r))&&(t[n].insert(i),i[r].insert(t)),a<=0)break}};n("next","prev"),n("prev","next")}},d={getCentre:function(t){return t.cy()},getOpen:function(t){return t.x},getClose:function(t){return t.X},getSize:function(t){return t.height()},makeRect:function(t,e,n,r){return new u(t,e,n-r/2,n+r/2)},findNeighbours:function(t,e){var n=function(n,r){var i=e.findIter(t)[n]();null!==i&&i.r.overlapX(t.r)>0&&(t[n].insert(i),i[r].insert(t))};n("next","prev"),n("prev","next")}};function y(t,e,n,r){void 0===r&&(r=!1);var i=t.padding,o=void 0!==t.groups?t.groups.length:0,a=void 0!==t.leaves?t.leaves.length:0,s=o?t.groups.reduce((function(t,r){return t.concat(y(r,e,n,!0))}),[]):[],u=(r?2:0)+a+o,c=new Array(u),l=new Array(u),f=0,h=function(t,e){l[f]=t,c[f++]=e};if(r){var p=t.bounds,d=e.getCentre(p),v=e.getSize(p)/2,x=e.getOpen(p),m=e.getClose(p),b=d-v+i/2,w=d+v-i/2;t.minVar.desiredPosition=b,h(e.makeRect(x,m,b,i),t.minVar),t.maxVar.desiredPosition=w,h(e.makeRect(x,m,w,i),t.maxVar)}a&&t.leaves.forEach((function(t){return h(t.bounds,t.variable)})),o&&t.groups.forEach((function(t){var n=t.bounds;h(e.makeRect(e.getOpen(n),e.getClose(n),e.getCentre(n),e.getSize(n)),t.minVar)}));var k=g(l,c,e,n);return o&&(c.forEach((function(t){t.cOut=[],t.cIn=[]})),k.forEach((function(t){t.left.cOut.push(t),t.right.cIn.push(t)})),t.groups.forEach((function(t){var n=(t.padding-e.getSize(t.bounds))/2;t.minVar.cIn.forEach((function(t){return t.gap+=n})),t.minVar.cOut.forEach((function(e){e.left=t.maxVar,e.gap+=n}))}))),s.concat(k)}function g(t,e,n,r){var i,a=t.length,s=2*a;console.assert(e.length>=a);var u=new Array(s);for(i=0;i<a;++i){var p=t[i],d=new c(e[i],p,n.getCentre(p));u[i]=new l(!0,d,n.getOpen(p)),u[i+a]=new l(!1,d,n.getClose(p))}u.sort(f);var y=new Array,g=h();for(i=0;i<s;++i){var v=u[i];if(d=v.v,v.isOpen)g.insert(d),n.findNeighbours(d,g);else{g.remove(d);var x=function(t,e){var i=(n.getSize(t.r)+n.getSize(e.r))/2+r;y.push(new o.Constraint(t.v,e.v,i))},m=function(t,e,n){for(var r,i=d[t].iterator();null!==(r=i[t]());)n(r,d),r[e].remove(d)};m("prev","next",(function(t,e){return x(t,e)})),m("next","prev",(function(t,e){return x(e,t)}))}}return console.assert(0===g.size),y}function v(t,e){return g(t,e,p,1e-6)}function x(t,e){return g(t,e,d,1e-6)}function m(t){return y(t,p,1e-6)}function b(t){return y(t,d,1e-6)}n.generateXConstraints=v,n.generateYConstraints=x,n.generateXGroupConstraints=m,n.generateYGroupConstraints=b,n.removeOverlaps=function(t){var e=t.map((function(t){return new o.Variable(t.cx())})),n=v(t,e),r=new o.Solver(e,n);r.solve(),e.forEach((function(e,n){return t[n].setXCentre(e.position())})),e=t.map((function(t){return new o.Variable(t.cy())})),n=x(t,e),(r=new o.Solver(e,n)).solve(),e.forEach((function(e,n){return t[n].setYCentre(e.position())}))};var w=function(t){function e(e,n){var r=t.call(this,0,n)||this;return r.index=e,r}return i(e,t),e}(o.Variable);n.IndexedVariable=w;var k=function(){function t(t,e,n,r,i){var o=this;if(void 0===n&&(n=null),void 0===r&&(r=null),void 0===i&&(i=!1),this.nodes=t,this.groups=e,this.rootGroup=n,this.avoidOverlaps=i,this.variables=t.map((function(t,e){return t.variable=new w(e,1)})),r&&this.createConstraints(r),i&&n&&void 0!==n.groups){t.forEach((function(t){if(t.width&&t.height){var e=t.width/2,n=t.height/2;t.bounds=new u(t.x-e,t.x+e,t.y-n,t.y+n)}else t.bounds=new u(t.x,t.x,t.y,t.y)})),s(n);var a=t.length;e.forEach((function(t){o.variables[a]=t.minVar=new w(a++,void 0!==t.stiffness?t.stiffness:.01),o.variables[a]=t.maxVar=new w(a++,void 0!==t.stiffness?t.stiffness:.01)}))}}return t.prototype.createSeparation=function(t){return new o.Constraint(this.nodes[t.left].variable,this.nodes[t.right].variable,t.gap,void 0!==t.equality&&t.equality)},t.prototype.makeFeasible=function(t){var e=this;if(this.avoidOverlaps){var n="x",r="width";"x"===t.axis&&(n="y",r="height");var i=t.offsets.map((function(t){return e.nodes[t.node]})).sort((function(t,e){return t[n]-e[n]})),o=null;i.forEach((function(t){if(o){var e=o[n]+o[r];e>t[n]&&(t[n]=e)}o=t}))}},t.prototype.createAlignment=function(t){var e=this,n=this.nodes[t.offsets[0].node].variable;this.makeFeasible(t);var r="x"===t.axis?this.xConstraints:this.yConstraints;t.offsets.slice(1).forEach((function(t){var i=e.nodes[t.node].variable;r.push(new o.Constraint(n,i,t.offset,!0))}))},t.prototype.createConstraints=function(t){var e=this,n=function(t){return void 0===t.type||"separation"===t.type};this.xConstraints=t.filter((function(t){return"x"===t.axis&&n(t)})).map((function(t){return e.createSeparation(t)})),this.yConstraints=t.filter((function(t){return"y"===t.axis&&n(t)})).map((function(t){return e.createSeparation(t)})),t.filter((function(t){return"alignment"===t.type})).forEach((function(t){return e.createAlignment(t)}))},t.prototype.setupVariablesAndBounds=function(t,e,n,r){this.nodes.forEach((function(i,o){i.fixed?(i.variable.weight=i.fixedWeight?i.fixedWeight:1e3,n[o]=r(i)):i.variable.weight=1;var a=(i.width||0)/2,s=(i.height||0)/2,c=t[o],l=e[o];i.bounds=new u(c-a,c+a,l-s,l+s)}))},t.prototype.xProject=function(t,e,n){(this.rootGroup||this.avoidOverlaps||this.xConstraints)&&this.project(t,e,t,n,(function(t){return t.px}),this.xConstraints,m,(function(t){return t.bounds.setXCentre(n[t.variable.index]=t.variable.position())}),(function(t){var e=n[t.minVar.index]=t.minVar.position(),r=n[t.maxVar.index]=t.maxVar.position(),i=t.padding/2;t.bounds.x=e-i,t.bounds.X=r+i}))},t.prototype.yProject=function(t,e,n){(this.rootGroup||this.yConstraints)&&this.project(t,e,e,n,(function(t){return t.py}),this.yConstraints,b,(function(t){return t.bounds.setYCentre(n[t.variable.index]=t.variable.position())}),(function(t){var e=n[t.minVar.index]=t.minVar.position(),r=n[t.maxVar.index]=t.maxVar.position(),i=t.padding/2;t.bounds.y=e-i,t.bounds.Y=r+i}))},t.prototype.projectFunctions=function(){var t=this;return[function(e,n,r){return t.xProject(e,n,r)},function(e,n,r){return t.yProject(e,n,r)}]},t.prototype.project=function(t,e,n,r,i,o,a,u,c){this.setupVariablesAndBounds(t,e,r,i),this.rootGroup&&this.avoidOverlaps&&(s(this.rootGroup),o=o.concat(a(this.rootGroup))),this.solve(this.variables,o,n,r),this.nodes.forEach(u),this.rootGroup&&this.avoidOverlaps&&(this.groups.forEach(c),s(this.rootGroup))},t.prototype.solve=function(t,e,n,r){var i=new o.Solver(t,e);i.setStartingPositions(n),i.setDesiredPositions(r),i.solve()},t}();n.Projection=k},{"./rbtree":16,"./vpsc":19}],18:[function(t,e,n){"use strict";Object.defineProperty(n,"__esModule",{value:!0});var r=t("./pqueue"),i=function(t,e){this.id=t,this.distance=e},o=function(t){this.id=t,this.neighbours=[]},a=function(t,e,n){this.node=t,this.prev=e,this.d=n},s=function(){function t(t,e,n,r,a){this.n=t,this.es=e,this.neighbours=new Array(this.n);for(var s=this.n;s--;)this.neighbours[s]=new o(s);for(s=this.es.length;s--;){var u=this.es[s],c=n(u),l=r(u),f=a(u);this.neighbours[c].neighbours.push(new i(l,f)),this.neighbours[l].neighbours.push(new i(c,f))}}return t.prototype.DistanceMatrix=function(){for(var t=new Array(this.n),e=0;e<this.n;++e)t[e]=this.dijkstraNeighbours(e);return t},t.prototype.DistancesFromNode=function(t){return this.dijkstraNeighbours(t)},t.prototype.PathFromNodeToNode=function(t,e){return this.dijkstraNeighbours(t,e)},t.prototype.PathFromNodeToNodeWithPrevCost=function(t,e,n){var i=new r.PriorityQueue((function(t,e){return t.d<=e.d})),o=this.neighbours[t],s=new a(o,null,0),u={};for(i.push(s);!i.empty()&&(o=(s=i.pop()).node).id!==e;)for(var c=o.neighbours.length;c--;){var l=o.neighbours[c],f=this.neighbours[l.id];if(!s.prev||f.id!==s.prev.node.id){var h=f.id+","+o.id;if(!(h in u&&u[h]<=s.d)){var p=s.prev?n(s.prev.node.id,o.id,f.id):0,d=s.d+l.distance+p;u[h]=d,i.push(new a(f,s,d))}}}for(var y=[];s.prev;)s=s.prev,y.push(s.node.id);return y},t.prototype.dijkstraNeighbours=function(t,e){void 0===e&&(e=-1);for(var n=new r.PriorityQueue((function(t,e){return t.d<=e.d})),i=this.neighbours.length,o=new Array(i);i--;){var a=this.neighbours[i];a.d=i===t?0:Number.POSITIVE_INFINITY,a.q=n.push(a)}for(;!n.empty();){var s=n.pop();if(o[s.id]=s.d,s.id===e){for(var u=[],c=s;void 0!==c.prev;)u.push(c.prev.id),c=c.prev;return u}for(i=s.neighbours.length;i--;){var l=s.neighbours[i],f=(c=this.neighbours[l.id],s.d+l.distance);s.d!==Number.MAX_VALUE&&c.d>f&&(c.d=f,c.prev=s,n.reduceKey(c.q,c,(function(t,e){return t.q=e})))}}return o},t}();n.Calculator=s},{"./pqueue":15}],19:[function(t,e,n){"use 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2*this.weight*(this.position()-this.desiredPosition)},t.prototype.position=function(){return(this.block.ps.scale*this.block.posn+this.offset)/this.scale},t.prototype.visitNeighbours=function(t,e){var n=function(n,r){return n.active&&t!==r&&e(n,r)};this.cOut.forEach((function(t){return n(t,t.right)})),this.cIn.forEach((function(t){return n(t,t.left)}))},t}();n.Variable=o;var a=function(){function t(t){this.vars=[],t.offset=0,this.ps=new r(t.scale),this.addVariable(t)}return t.prototype.addVariable=function(t){t.block=this,this.vars.push(t),this.ps.addVariable(t),this.posn=this.ps.getPosn()},t.prototype.updateWeightedPosition=function(){this.ps.AB=this.ps.AD=this.ps.A2=0;for(var t=0,e=this.vars.length;t<e;++t)this.ps.addVariable(this.vars[t]);this.posn=this.ps.getPosn()},t.prototype.compute_lm=function(t,e,n){var r=this,i=t.dfdv();return t.visitNeighbours(e,(function(e,o){var 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t=this;this.upperGroup.onmousedown=function(e){t.mouseDown(e)},this.upperGroup.onmouseenter=function(e){t.mouseOver(e)},this.upperGroup.onmouseleave=function(e){t.mouseOut(e)},this.upperGroup.ontouchstart=function(e){t.touchStart(e)}}},{key:"addStoichiometryLabel",value:function(t){this.labelSVG&&(this.labelSVG.childNodes[0].data=this.labelSVG.childNodes[0].data+" ["+t+"]")}},{key:"mouseDown",value:function(t){return this.app.preventDefaultsAndStopPropagation(t),this.app.d3cola.stop(),this.app.dragElement=this,this.app.dragStart=t,!1}},{key:"touchStart",value:function(t){return this.app.preventDefaultsAndStopPropagation(t),this.app.d3cola.stop(),this.app.dragElement=this,this.app.dragStart=t,!1}},{key:"mouseOver",value:function(t){return this.app.preventDefaultsAndStopPropagation(t),this.showHighlight(!0),this.app.notifyHoverListeners([this.json]),!1}},{key:"mouseOut",value:function(t){return this.app.preventDefaultsAndStopPropagation(t),this.showHighlight(!1),this.app.hideTooltip(),this.app.notifyHoverListeners([]),!1}},{key:"getSymbolRadius",value:function(){return 15}},{key:"showHighlight",value:function(){}},{key:"getPosition",value:function(){return[this.ix,this.iy]}},{key:"setPositionFromCola",value:function(){this.px=this.x,this.py=this.y;var t=this.width/2-this.getSymbolRadius();this.expanded&&(t-=this.size/2*this.stickZoom),this.setPosition(this.x+t,this.y)}},{key:"setPosition",value:function(t,e){this.ix=t,this.iy=e,this.upperGroup.setAttribute("transform","translate("+this.ix+" "+this.iy+")")}},{key:"changePosition",value:function(t,e){this.ix-=t,this.iy-=e,this.upperGroup.setAttribute("transform","translate("+this.ix+" "+this.iy+")")}},{key:"getAggregateSelfLinkPath",value:function(){var t=this.getSymbolRadius()+7,e=m(t,70),n=m(t,20),r=m(t,85),i=m(t,5);return"M 0,0 Q "+r.x+","+-r.y+" "+e.x+","+-e.y+" A "+t+" "+t+" 0 0 1 "+n.x+","+-n.y+" Q "+i.x+","+-i.y+" 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e,n,r,o=A(a);function a(){var t;return function(t,e){if(!(t instanceof e))throw new TypeError("Cannot call a class as a function")}(this,a),(t=o.call(this)).nTermFeatures=[],t.cTermFeatures=[],t}return e=a,(n=[{key:"getSymbolRadius",value:function(){return 15}},{key:"showHighlight",value:function(t){this.highlight.setAttribute("stroke-opacity",t?"1":"0")}},{key:"setStickScale",value:function(t,e){var n=this.stickZoom,r=this.ix-e.x,i=r*t/n-r,o=this.ix+i;this.stickZoom=t,this.scale(),this.setPosition(o,this.iy),this.setAllLinkCoordinates()}},{key:"scale",value:function(){var t=this.size*this.stickZoom;if(this.expanded){var e=i.transform(this.labelSVG.getAttribute("transform")),n=this.app.svgElement.createSVGMatrix().rotate(e.rotate).translate(-(this.size/2*this.stickZoom+(this.nTermFeatures.length>0?25:10)),this.labelY);this.labelSVG.transform.baseVal.initialize(this.app.svgElement.createSVGTransformFromMatrix(n)),this.updateAnnotationRectanglesNoTransition(),i.select(this.background).attr("width",t).attr("x",this.getResXWithStickZoom(.5)),i.select(this.outline).attr("width",t).attr("x",this.getResXWithStickZoom(.5)),i.select(this.highlight).attr("width",t+5).attr("x",this.getResXWithStickZoom(.5)-2.5),this.setScaleGroup()}}},{key:"setScaleGroup",value:function(){this.upperGroup.appendChild(this.ticks),this.ticks.textContent="",this.scaleLabels=[];for(var t=-1,e=this.getResXWithStickZoom(this.size),n=1;n<=this.size;n++){if(1===n||n%100==0&&200*this.stickZoom>a.minXDist||n%10==0&&20*this.stickZoom>a.minXDist){var r=this.getResXWithStickZoom(n);(this.stickZoom>=8||1!==n)&&c(this,r),0==(t=(t+1)%2)&&r+a.minXDist<e&&u(this,n,r)}if(this.stickZoom>=8){var i=document.createElementNS(d,"g");i.setAttribute("transform","translate("+this.getResXWithStickZoom(n)+" 0)");var o=document.createElementNS(d,"text");o.classList.add("label","sequence"),o.setAttribute("x","0"),o.setAttribute("y","3"),o.appendChild(document.createTextNode(this.sequence[n-1]));var s=document.createElementNS(d,"text");s.classList.add("label","sequence-outline"),s.setAttribute("x","0"),s.setAttribute("y","3"),s.appendChild(document.createTextNode(this.sequence[n-1])),i.appendChild(s),this.scaleLabels.push(s),i.appendChild(o),this.scaleLabels.push(o),this.ticks.appendChild(i)}}function u(t,e,n){var r=document.createElementNS(d,"g");r.setAttribute("transform","translate("+n+" 0)");var i=document.createElementNS(d,"text");i.classList.add("label","scale-label"),i.setAttribute("x","0"),i.setAttribute("y",a.STICKHEIGHT+4),i.appendChild(document.createTextNode(e)),r.appendChild(i),t.scaleLabels.push(i),t.ticks.appendChild(r)}function c(t,e){var n=document.createElementNS(d,"line");n.classList.add("tick"),n.setAttribute("x1",e),n.setAttribute("y1","5"),n.setAttribute("x2",e),n.setAttribute("y2","10"),t.ticks.appendChild(n)}u(this,this.size,e),this.stickZoom>=8&&c(this,e)}},{key:"setExpanded",value:function(t,e){!0!==this.busy&&(t?this.toStick(!0):this.toCircle(!0,e))}},{key:"toCircle",value:function(){var t=!(arguments.length>0&&void 0!==arguments[0])||arguments[0],e=arguments.length>1?arguments[1]:void 0;if(!e){var n=this.app.svgElement.parentNode.clientWidth,r=this.app.container.getCTM().inverse(),o=this.app.container.getCTM().inverse().a;this.ix<r.e&&(console.log("off left edge"),e={x:r.e+(this.getSymbolRadius()+15+this.labelSVG.getComputedTextLength()),y:this.iy}),this.ix>r.e+n*o&&(console.log("off right edge"),e={x:r.e+n*o-(this.getSymbolRadius()+5),y:this.iy})}var s=t?a.transitionTime:0;this.postAnimExpanded=!1,this.busy=!0;var u=this.getSymbolRadius();i.select(this.background).transition().attr("x",-u).attr("y",-u).attr("width",2*u).attr("height",2*u).attr("rx",u).attr("ry",u).duration(s),i.select(this.outline).transition().attr("x",-u).attr("y",-u).attr("width",2*u).attr("height",2*u).attr("rx",u).attr("ry",u).duration(s),i.select(this.highlight).transition().attr("width",2*u+5).attr("height",2*u+5).attr("x",-u-2.5).attr("y",-u-2.5).attr("rx",u+2.5).attr("ry",u+2.5).duration(s);var c=i.interpolate(this.stickZoom,0),l=i.transform(this.labelSVG.getAttribute("transform")),f=l.translate[0],h=i.interpolate(f,-(u+5)),p=null;null!=e&&(p=i.interpolate(this.ix,e.x));var d=this;i.select(this.ticks).transition().attr("opacity",0).duration(s/4).each("end",(function(){i.select(this).selectAll("*").remove()}));var y=this.stickZoom,g=this.rotation,v=i.ease("cubic-in-out");if(t){var x,m=k(this.annotationSets);try{for(m.s();!(x=m.n()).done;){var b=w(x.value,2),S=b[0],_=b[1];if(!0===this.app.annotationSetsShown.get(S)){var M,E=k(_);try{for(E.s();!(M=E.n()).done;){var A=M.value;if(A.fuzzyStart){var C=A.fuzzyStart;i.select(C).transition().attr("d",this.getAnnotationPieSlicePath(A.seqDatum.uncertainBegin,A.seqDatum.begin,A,!1)).duration(s)}if(A.certain){var L=A.certain;i.select(L).transition().attr("d",this.getAnnotationPieSlicePath(A.seqDatum.begin,A.seqDatum.end,A,!1)).duration(s)}if(A.fuzzyEnd){var N=A.fuzzyEnd;i.select(N).transition().attr("d",this.getAnnotationPieSlicePath(A.seqDatum.end,A.seqDatum.uncertainEnd,A,!1)).duration(s)}}}catch(t){E.e(t)}finally{E.f()}}}}catch(t){m.e(t)}finally{m.f()}i.timer((function(t){return T(t/s)}))}else T(1);function T(t){var e=i.transform(d.labelSVG.getAttribute("transform")),n=d.app.svgElement.createSVGMatrix().rotate(e.rotate).translate(h(v(t)),d.labelY);if(d.labelSVG.transform.baseVal.initialize(d.app.svgElement.createSVGTransformFromMatrix(n)),null!==p&&d.setPosition(p(v(t)),d.iy),d.stickZoom=c(v(t)),d.setAllLinkCoordinates(),1===t){d.expanded=!1,d.checkLinks();var r,o=k(d.annotationSets);try{for(o.s();!(r=o.n()).done;){var a=w(r.value,2),s=a[0],u=a[1];if(!0===d.app.annotationSetsShown.get(s)){var l,f=k(u);try{for(f.s();!(l=f.n()).done;){var x=l.value;if(x.fuzzyStart){var m=x.fuzzyStart;i.select(m).attr("d",d.getAnnotationPieSlicePath(x.seqDatum.uncertainBegin,x.seqDatum.begin,x))}if(x.certain){var b=x.certain;i.select(b).attr("d",d.getAnnotationPieSlicePath(x.seqDatum.begin,x.seqDatum.end,x))}if(x.fuzzyEnd){var S=x.fuzzyEnd;i.select(S).attr("d",d.getAnnotationPieSlicePath(x.seqDatum.end,x.seqDatum.uncertainEnd,x))}}}catch(t){f.e(t)}finally{f.f()}}}}catch(t){o.e(t)}finally{o.f()}return d.stickZoom=y,d.rotation=g,d.busy=!1,!0}return!!(t>1||isNaN(t))&&T(1)}}},{key:"toStick",value:function(){var t=!(arguments.length>0&&void 0!==arguments[0])||arguments[0],e=t?a.transitionTime:0;this.busy=!0,this.expanded=!0,this.postAnimExpanded=!0;var n=this.size*this.stickZoom,r=this.getSymbolRadius(),o=i.interpolate(2*r,n),s=i.interpolate(0,this.stickZoom),u=i.interpolate(-(r+5),-(this.size/2*this.stickZoom+(this.nTermFeatures.length>0?25:10))),c=this.stickZoom;this.stickZoom=0,this.checkLinks(),this.stickZoom=c,i.select(this.background).transition().attr("height",a.STICKHEIGHT).attr("y",-a.STICKHEIGHT/2).attr("rx",0).attr("ry",0).duration(e),i.select(this.outline).transition().attr("height",a.STICKHEIGHT).attr("y",-a.STICKHEIGHT/2).attr("rx",0).attr("ry",0).duration(e),i.select(this.highlight).transition().attr("width",n+5).attr("height",a.STICKHEIGHT+5).attr("x",this.getResXWithStickZoom(.5)-2.5).attr("y",-a.STICKHEIGHT/2-2.5).attr("rx",0).attr("ry",0).duration(e);var l=this,f=i.ease("cubic-in-out");if(t){var h,p=k(this.annotationSets);try{for(p.s();!(h=p.n()).done;){var d=w(h.value,2),y=d[0],g=d[1];if(!0===this.app.annotationSetsShown.get(y)){var v,x=k(g);try{for(x.s();!(v=x.n()).done;){var m=v.value;if(m.fuzzyStart){var b=m.fuzzyStart;b.setAttribute("d",this.getAnnotationPieSlicePath(m.seqDatum.uncertainBegin,m.seqDatum.begin,m,!1)),i.select(b).transition().attr("d",this.getAnnotationRectPath(m.seqDatum.uncertainBegin,m.seqDatum.begin,m)).duration(a.transitionTime)}if(m.certain){var S=m.certain,_=m.seqDatum.begin,M=m.seqDatum.end;m.seqDatum.uncertainBegin&&(_+=1),m.seqDatum.uncertainEnd&&(M-=1),S.setAttribute("d",this.getAnnotationPieSlicePath(_,M,m,!1)),i.select(S).transition().attr("d",this.getAnnotationRectPath(_,M,m)).duration(a.transitionTime)}if(m.fuzzyEnd){var E=m.fuzzyEnd;E.setAttribute("d",this.getAnnotationPieSlicePath(m.seqDatum.end,m.seqDatum.uncertainEnd,m,!1)),i.select(E).transition().attr("d",this.getAnnotationRectPath(m.seqDatum.end,m.seqDatum.uncertainEnd,m)).duration(a.transitionTime)}}}catch(t){x.e(t)}finally{x.f()}}}}catch(t){p.e(t)}finally{p.f()}i.timer((function(t){return A(t/e)}))}else A(1);function A(t){var e=i.transform(l.labelSVG.getAttribute("transform")),n=l.app.svgElement.createSVGMatrix().rotate(e.rotate).translate(u(f(t)),l.labelY);l.labelSVG.transform.baseVal.initialize(l.app.svgElement.createSVGTransformFromMatrix(n));var r=o(f(t));return i.select(l.highlight).attr("width",r).attr("x",-r/2+.5*l.stickZoom),i.select(l.outline).attr("width",r).attr("x",-r/2+.5*l.stickZoom),i.select(l.background).attr("width",r).attr("x",-r/2+.5*l.stickZoom),l.stickZoom=s(f(t)),l.setAllLinkCoordinates(),1===t?(l.updateAnnotationRectanglesNoTransition(),l.busy=!1,!0):!!(t>1||isNaN(t))&&A(1)}i.select(this.ticks).attr("opacity",0),this.setScaleGroup(),i.select(this.ticks).transition().attr("opacity",1).delay(.8*e).duration(e/2)}},{key:"updateAnnotationRectanglesNoTransition",value:function(){var t,e=k(this.annotationSets);try{for(e.s();!(t=e.n()).done;){var n=w(t.value,2),r=n[0],o=n[1];if(!0===this.app.annotationSetsShown.get(r)){var a,s=k(o);try{for(s.s();!(a=s.n()).done;){var u=a.value;if(u.fuzzyStart){var c=u.fuzzyStart;i.select(c).attr("d",this.getAnnotationRectPath(u.seqDatum.uncertainBegin,u.seqDatum.begin,u))}if(u.certain){var l=u.seqDatum.begin,f=u.seqDatum.end;u.seqDatum.uncertainBegin&&(l+=1),u.seqDatum.uncertainEnd&&(f-=1),u.certain.setAttribute("d",this.getAnnotationRectPath(l,f,u))}if(u.fuzzyEnd){var h=u.fuzzyEnd;i.select(h).attr("d",this.getAnnotationRectPath(u.seqDatum.end,u.seqDatum.uncertainEnd,u))}}}catch(t){s.e(t)}finally{s.f()}}}}catch(t){e.e(t)}finally{e.f()}}},{key:"getResXWithStickZoom",value:function(t){return"n-n"===t?-this.size/2*this.stickZoom-20:"c-c"===t?this.size/2*this.stickZoom+20:(t-this.size/2)*this.stickZoom}},{key:"getResidueCoordinates",value:function(t,e){void 0===t&&console.error("ERROR: residue number is undefined");var n,r=this.getResXWithStickZoom(1*t);if(0!==r){var i=Math.abs(r),o=Math.acos(r/i),a=this.rotation/360*Math.PI*2;r=i*Math.cos(a+o),n=i*Math.sin(a+o),void 0!==e&&(r+=e*Math.cos(a+Math.PI/2),n+=e*Math.sin(a+Math.PI/2))}else n=e;return[r+=this.ix,n+=this.iy]}},{key:"clearPositionalFeatures",value:function(){this.annotations=[],this.annotationTypes=[],this.annotationsSvgGroup.textContent="",this.nTermFeatures=[],this.cTermFeatures=[]}},{key:"updatePositionalFeatures",value:function(){var t=this,e=function(e){var n=e.target.correspondingUseElement?e.target.correspondingUseElement:e.target;t.app.preventDefaultsAndStopPropagation(e),t.app.setTooltip(n.name,n.getAttribute("fill")),t.showHighlight(!0)},n=-1,r=[];function i(t,e){var n,r=k(t);try{for(r.s();!(n=r.n()).done;)if(n.value.seqDatum.overlaps(e.seqDatum))return!0}catch(t){r.e(t)}finally{r.f()}return!1}var o,a=k(this.annotationSets);try{for(a.s();!(o=a.n()).done;){var s=w(o.value,2),u=s[0],c=s[1];if(!0===this.app.annotationSetsShown.get(u)){c&&c.length>0&&(r[++n]=[]);var l,f=new Set,h=k(Array.from(c.values()).sort((function(t,e){var n=t.description,r=e.description;return n<r?-1:n>r?1:0})));try{for(h.s();!(l=h.n()).done;){var 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t=this.participants.length,e=0;e<t;e++)if(this.participants[e].expanded)return!0;return!1}},{key:"show",value:function(){this.setLinkCoordinates();var t=this.app.res_resLinks;this.participants[0]===this.participants[1]&&(t=this.app.selfRes_resLinks),t.appendChild(this.glyph),t.appendChild(this.uncertainGlyph)}},{key:"hide",value:function(){this.glyph.remove(),this.uncertainGlyph.remove()}},{key:"setLinkCoordinates",value:function(){function t(t){return!isNaN(parseFloat(t))&&isFinite(t)}function e(t,e,n,r,i,o,a){var s,u;return i.expanded?(s=i.getResidueCoordinates(n,o),u=i.getResidueCoordinates(r,o)):u=s=i.getPosition(a)," Q"+e[0]+","+e[1]+" "+s[0]+","+s[1]+" L"+u[0]+","+u[1]+" Q"+e[0]+","+e[1]+" "+t[0]+","+t[1]}function n(t,e){for(var n=null,r=null,i=t.length,o=0;o<i;o++){var a=t[o];if(!isNaN(parseFloat(a.begin))&&isFinite(a.begin)){var s=1*a.begin;(null===n||s<n)&&(n=s)}if(!isNaN(parseFloat(a.uncertainBegin))&&isFinite(a.uncertainBegin)){var u=1*a.uncertainBegin;(null===n||u<n)&&(n=u)}if(!isNaN(parseFloat(a.end))&&isFinite(a.end)){var c=1*a.end;(null===r||c>r)&&(r=c)}if(!isNaN(parseFloat(a.uncertainEnd))&&isFinite(a.uncertainEnd)){var l=1*a.uncertainEnd;(null===r||l>r)&&(r=l)}}return e.getResidueCoordinates((n+r)/2,0)}var r,i,o=this.fromSequenceData[0].participant,a=this.toSequenceData[0].participant;o.expanded&&(r=n(this.fromSequenceData,o)),a.expanded&&(i=n(this.toSequenceData,a)),o.expanded||(r=o.getPosition(i)),a.expanded||(i=a.getPosition(r));var s=r,u=i,c=r[0]-i[0],l=r[1]-i[1],f=Math.atan2(l,c)/(2*Math.PI)*360;f<0&&(f+=360);var h=f-o.rotation;h<0&&(h+=360);var p=10;h<180&&(p=-10);var d=o.rotation/360*Math.PI*2;h>180&&(d-=Math.PI),(h=f-a.rotation)<0&&(h+=360);var y=10;h>180&&(y=-10);var g=a.rotation/360*Math.PI*2;h<180&&(g-=Math.PI);var v=[r[0]+30*Math.sin(d)*this.app.z,r[1]-30*Math.cos(d)*this.app.z];o.expanded||(v=r);var x=[i[0]+30*Math.sin(g)*this.app.z,i[1]-30*Math.cos(g)*this.app.z];a.expanded||(x=i);for(var m,b=[(v[0]+x[0])/2,(v[1]+x[1])/2],w=this.fromSequenceData.length,k=this.toSequenceData.length,S="M"+b[0]+","+b[1],_="M"+b[0]+","+b[1],M=0;M<w;M++)(t((m=this.fromSequenceData[M]).begin)&&t(m.end)||"protein"!==o.type)&&(S+=e(b,v,m.begin,m.end,o,p,u)),t(m.uncertainBegin)&&(_+=e(b,v,m.uncertainBegin,m.begin,o,p,u)),t(m.uncertainEnd)&&(_+=e(b,v,m.end,m.uncertainEnd,o,p,u));for(var E=0;E<k;E++)(t((m=this.toSequenceData[E]).begin)&&t(m.end)||"protein"!==a.type)&&(S+=e(b,x,m.begin,m.end,a,y,s)),t(m.uncertainBegin)&&(_+=e(b,x,m.uncertainBegin,m.begin,a,y,s)),t(m.uncertainEnd)&&(_+=e(b,x,m.end,m.uncertainEnd,a,y,s));this.glyph||this.initSVG(),this.glyph.setAttribute("d",S),this.uncertainGlyph.setAttribute("d",_)}}])&&Yt(e.prototype,n),r&&Yt(e,r),o}(zt);function te(t){return(te="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 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i,o=Te(this.allUnaryLinks.values());try{for(o.s();!(i=o.n()).done;)i.value.check()}catch(t){o.e(t)}finally{o.f()}var a,s=Te(this.allSequenceLinks.values());try{for(s.s();!(a=s.n()).done;)a.value.check()}catch(t){s.e(t)}finally{s.f()}}},{key:"setAllLinkCoordinates",value:function(){var t,e=Te(this.allNaryLinks.values());try{for(e.s();!(t=e.n()).done;)t.value.setLinkCoordinates()}catch(t){e.e(t)}finally{e.f()}var n,r=Te(this.allBinaryLinks.values());try{for(r.s();!(n=r.n()).done;)n.value.setLinkCoordinates()}catch(t){r.e(t)}finally{r.f()}var i,o=Te(this.allUnaryLinks.values());try{for(o.s();!(i=o.n()).done;)i.value.setLinkCoordinates()}catch(t){o.e(t)}finally{o.f()}var a,s=Te(this.allSequenceLinks.values());try{for(s.s();!(a=s.n()).done;)a.value.setLinkCoordinates()}catch(t){s.e(t)}finally{s.f()}}},{key:"showTooltip",value:function(t){var e,n,r=this.tooltip.getComputedTextLength()+16,i=this.svgElement.parentNode.clientWidth,o=this.svgElement.parentNode.clientHeight;e=t.x+20+r<i?t.x:i-r-20,n=t.y+60<o?t.y:o-60,this.tooltip.setAttribute("x",e+22),this.tooltip.setAttribute("y",n+47),this.tooltip_bg.setAttribute("x",e+16),this.tooltip_bg.setAttribute("y",n+28),this.tooltip_subBg.setAttribute("x",e+16),this.tooltip_subBg.setAttribute("y",n+28)}},{key:"setTooltip",value:function(t,e){if(t){this.tooltip.firstChild.data=t.toString().replace(/&(quot);/g,'"'),this.tooltip.setAttribute("display","block");var n=this.tooltip.getComputedTextLength();this.tooltip_bg.setAttribute("width",n+16),this.tooltip_subBg.setAttribute("width",n+16),void 0!==e&&null!=e?(this.tooltip_bg.setAttribute("fill",e),this.tooltip_bg.setAttribute("stroke",e),this.tooltip_bg.setAttribute("fill-opacity","0.0")):(this.tooltip_bg.setAttribute("fill","white"),this.tooltip_bg.setAttribute("stroke","grey")),this.tooltip_bg.setAttribute("height","28"),this.tooltip_subBg.setAttribute("height","28"),this.tooltip_bg.setAttribute("display","block"),this.tooltip_subBg.setAttribute("display","block")}else this.hideTooltip()}},{key:"hideTooltip",value:function(){this.tooltip.setAttribute("display","none"),this.tooltip_bg.setAttribute("display","none"),this.tooltip_subBg.setAttribute("display","none")}},{key:"setAnnotations",value:function(t){t=t.toUpperCase();var e,n=Te(this.annotationSetsShown.keys());try{for(n.s();!(e=n.n()).done;){var r=e.value;this.annotationSetsShown.set(r,t===r)}}catch(t){n.e(t)}finally{n.f()}return this.updateAnnotations(),this.getColorKeyJson()}},{key:"showAnnotations",value:function(t,e){return this.annotationSetsShown.set(t,e),this.updateAnnotations(),this.getColorKeyJson()}},{key:"updateAnnotations",value:function(){this.defs.textContent="",this.uncertainCategories=new Set,this.certainCategories=new Set,delete this.featureColors;var t,e,n=new Set,r=Te(this.participants.values());try{for(r.s();!(t=r.n()).done;){var o,a=Te(t.value.annotationSets);try{for(a.s();!(o=a.n()).done;){var u=Ne(o.value,2),l=u[0],f=u[1];if(!0===this.annotationSetsShown.get(l)){var h,p=Te(f.values());try{for(p.s();!(h=p.n()).done;){var d=h.value;n.add(d.description)}}catch(t){p.e(t)}finally{p.f()}}}}catch(t){a.e(t)}finally{a.f()}}}catch(t){r.e(t)}finally{r.f()}e=n.size<11?i.scale.ordinal().range(s):i.scale.category20();var y=this;function g(t,e){var n=y.defs.append("pattern").attr("id",t).attr("patternUnits","userSpaceOnUse").attr("x",0).attr("y",0).attr("width",12).attr("height",12).attr("patternTransform","rotate(45)");n.append("rect").attr("x",0).attr("y",2).attr("width",12).attr("height",4).attr("fill",e),n.append("rect").attr("x",0).attr("y",8).attr("width",12).attr("height",4).attr("fill",e)}var v,x=Te(this.participants.values());try{for(x.s();!(v=x.n()).done;){var m=v.value;if("protein"===m.type){m.clearPositionalFeatures(),m.updatePositionalFeatures();var b,w=Te(m.annotationSets);try{for(w.s();!(b=w.n()).done;){var k=Ne(b.value,2),S=k[0],_=k[1];if(!0===this.annotationSetsShown.get(S)){var M,E=Te(_);try{for(E.s();!(M=E.n()).done;){var A=M.value,C=void 0;if(C="No annotations"===A.description?"#eeeeee":e(A.description),A.certain&&(A.certain.setAttribute("fill",C),A.certain.setAttribute("stroke",C),this.certainCategories.add(A.description)),A.fuzzyStart||A.fuzzyEnd){if(!this.uncertainCategories.has(name)){var L=new c(C),N="rgba("+L.r+","+L.g+","+L.b+", 0.6)";g("hatched_"+A.description+"_"+C.toString(),N),this.uncertainCategories.add(A.description)}var T="url('#hatched_"+A.description+"_"+C.toString()+"')";A.fuzzyStart&&(A.fuzzyStart.setAttribute("fill",T),A.fuzzyStart.setAttribute("stroke",C)),A.fuzzyEnd&&(A.fuzzyEnd.setAttribute("fill",T),A.fuzzyEnd.setAttribute("stroke",C))}}}catch(t){E.e(t)}finally{E.f()}}}}catch(t){w.e(t)}finally{w.f()}}}}catch(t){x.e(t)}finally{x.f()}this.featureColors=e}},{key:"getColorKeyJson",value:function(){var t,e={Complex:[]},n=Te(Xt.naryColors.domain());try{for(n.s();!(t=n.n()).done;){var r=t.value;e.Complex.push({name:r,certain:{color:Xt.naryColors(r)}})}}catch(t){n.e(t)}finally{n.f()}if(this.featureColors){var i,o=Te(this.annotationSetsShown);try{for(o.s();!(i=o.n()).done;){var a=Ne(i.value,2),s=a[0];if(a[1]){var u,l=[],f=new Set,h=Te(this.participants.values());try{for(h.s();!(u=h.n()).done;){var p=u.value;if("protein"===p.type){var d=p.annotationSets.get(s);if(d){var y,g=Te(d);try{for(g.s();!(y=g.n()).done;){var v=y.value.description;if(!f.has(v)){f.add(v);var x={name:v};if(this.certainCategories.has(v)&&(x.certain={color:this.featureColors(v)}),this.uncertainCategories.has(v)){var m=new c(this.featureColors(v)),b="rgba("+m.r+","+m.g+","+m.b+", 0.6)";x.uncertain={color:b}}l.push(x)}}}catch(t){g.e(t)}finally{g.f()}}}}}catch(t){h.e(t)}finally{h.f()}e[s]=l}}}catch(t){o.e(t)}finally{o.f()}}return e}},{key:"collapseAll",value:function(){var t,e=Te(this.participants.values());try{for(e.s();!(t=e.n()).done;){var n=t.value;n.expanded&&n.toCircle(!1)}}catch(t){e.e(t)}finally{e.f()}this.autoLayout(),this.notifyExpandListeners()}},{key:"expandAll",value:function(){var t,e=Te(this.participants.values());try{for(e.s();!(t=e.n()).done;){var n=t.value;"protein"!==n.type||n.expanded||n.toStick(!1)}}catch(t){e.e(t)}finally{e.f()}this.autoLayout(),this.notifyExpandListeners()}},{key:"expandAndCollapseSelection",value:function(t){var e,n=Te(this.participants.values());try{for(n.s();!(e=n.n()).done;){var r=e.value,i=r.json.identifier.id;t.includes(i)?r.expanded||r.setExpanded(!0):r.expanded&&r.setExpanded(!1)}}catch(t){n.e(t)}finally{n.f()}this.notifyExpandListeners()}},{key:"addHoverListener",value:function(t){this.hoverListeners.add(t)}},{key:"removeHoverListener",value:function(t){this.hoverListeners.remove(t)}},{key:"notifyHoverListeners",value:function(t){var e,n=Te(this.hoverListeners);try{for(n.s();!(e=n.n()).done;)(0,e.value)(t)}catch(t){n.e(t)}finally{n.f()}}},{key:"addExpandListener",value:function(t){this.expandListeners.add(t)}},{key:"removeExpandListener",value:function(t){this.expandListeners.remove(t)}},{key:"notifyExpandListeners",value:function(){var t,e=this.getExpandedParticipants(),n=Te(this.expandListeners);try{for(n.s();!(t=n.n()).done;)(0,t.value)(e)}catch(t){n.e(t)}finally{n.f()}}},{key:"getExpandedParticipants",value:function(){var t,e=[],n=Te(this.participants.values());try{for(n.s();!(t=n.n()).done;){var r=t.value;r.postAnimExpanded&&e.push(r.json)}}catch(t){n.e(t)}finally{n.f()}return e}},{key:"setCTM",value:function(t,e){var n="matrix("+e.a+","+e.b+","+e.c+","+e.d+","+e.e+","+e.f+")";t.setAttribute("transform",n)}},{key:"mouseDown",value:function(e){e.preventDefault(),this.d3cola.stop(),this.dragStart=e,this.state=t.STATES.SELECT_PAN,i.select(".custom-menu-margin").style("display","none")}},{key:"touchStart",value:function(e){e.preventDefault(),this.d3cola.stop(),this.dragStart=e,this.state=t.STATES.SELECT_PAN,i.select(".custom-menu-margin").style("display","none")}},{key:"move",value:function(e){var n=this.getEventPoint(e),r=n.matrixTransform(this.container.getCTM().inverse());if(r.x)if(this.dragStart){this.hideTooltip();var i=this.getEventPoint(this.dragStart).matrixTransform(this.container.getCTM().inverse());if(null!=this.dragElement){var o=i.x-r.x,a=i.y-r.y;if(this.state===t.STATES.DRAGGING){if(this.dragElement.ix)this.dragElement.changePosition(o,a),this.dragElement.setAllLinkCoordinates();else{var s,u=Te(this.dragElement.participants);try{for(u.s();!(s=u.n()).done;)s.value.changePosition(o,a)}catch(t){u.e(t)}finally{u.f()}this.setAllLinkCoordinates()}this.dragStart=e}else Math.sqrt(o*o+a*a)>5*this.z&&(this.state=t.STATES.DRAGGING)}else this.state===t.STATES.SELECT_PAN&&(this.setCTM(this.container,this.container.getCTM().translate(r.x-i.x,r.y-i.y)),this.dragStart=e)}else this.showTooltip(n)}},{key:"mouseUp",value:function(e){this.preventDefaultsAndStopPropagation(e);var n=(new Date).getTime();if(n-this.lastMouseUp>150&&this.dragElement&&"protein"===this.dragElement.type&&this.state!==t.STATES.DRAGGING&&!this.dragElement.busy)if(this.dragElement.expanded){this.contextMenuProt=this.dragElement;var r=this.getEventPoint(e);this.contextMenuPoint=r.matrixTransform(this.container.getCTM().inverse());var o,a,s=i.select(".custom-menu-margin");e.pageX?(o=e.pageX,a=e.pageY):(o=this.dragStart.touches[0].pageX,a=this.dragStart.touches[0].pageY),s.style("top",a-20+"px").style("left",o-20+"px").style("display","block"),i.select(".scaleButton_"+100*this.dragElement.stickZoom).property("checked",!0)}else this.dragElement.setExpanded(!0),this.notifyExpandListeners();return this.dragElement=null,this.dragStart=null,this.state=t.STATES.MOUSE_UP,this.lastMouseUp=n,!1}},{key:"mouseWheel",value:function(t){this.preventDefaultsAndStopPropagation(t),this.d3cola.stop();var e=1+(t.wheelDelta?t.wheelDelta/3600:t.detail/-90),n=this.container,r=this.getEventPoint(t).matrixTransform(n.getCTM().inverse()),i=this.svgElement.createSVGMatrix().translate(r.x,r.y).scale(e).translate(-r.x,-r.y);return this.setCTM(n,n.getCTM().multiply(i)),!1}},{key:"mouseOut",value:function(){this.hideTooltip()}},{key:"getEventPoint",value:function(t){var e=this.svgElement.createSVGPoint();return e.x=t.pageX-Le(this.el).offset().left,e.y=t.pageY-Le(this.el).offset().top,e}},{key:"preventDefaultsAndStopPropagation",value:function(t){t.stopPropagation&&t.stopPropagation(),null!=t.cancelBubble&&(t.cancelBubble=!0),t.preventDefault&&t.preventDefault()}},{key:"downloadSVG",value:function(t){t||(t="complexViewer");var e=this.getSVG(),n=function(t){var e,n=[];try{e=new TextEncoder("utf-8")}catch(t){e=void 0}if(e)n=e.encode(t);else for(var r=0;r<t.length;r++){var i=t.charCodeAt(r);i<128?n.push(i):i<2048?n.push(192|i>>6,128|63&i):i<55296||i>=57344?n.push(224|i>>12,128|i>>6&63,128|63&i):(r++,i=65536+((1023&i)<<10|1023&t.charCodeAt(r)),n.push(240|i>>18,128|i>>12&63,128|i>>6&63,128|63&i))}return new Blob([new Uint8Array(n)],{type:"image/svg+xml;charset=utf-8"})}(e);if(navigator.msSaveOrOpenBlob)navigator.msSaveOrOpenBlob(n,t);else{var r=document.createElement("a");r.href=window.URL.createObjectURL(n),r.download=t,r.style.display="none",document.body.appendChild(r),r.click(),document.body.removeChild(r),window.URL.revokeObjectURL(r.href)}n=null}}])&&je(e.prototype,n),o&&je(e,o),t}();Ie.STATES={MOUSE_UP:0,SELECT_PAN:1,DRAGGING:2},Ie.barScales=[.01,.2,1,2,4,8]}])}));
\ No newline at end of file
diff --git a/package.json b/package.json
index 14ed188..cbc0bdb 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "complexviewer",
-  "version": "2.1.15",
+  "version": "2.1.16",
   "description": "A network visualisation that displays molecular interaction data, including detailed residue-level information such as binding sites. Used in EBI's Complex Portal and elsewhere.",
   "author": {
     "name": "Colin Combe",
diff --git a/src/js/app.js b/src/js/app.js
index 92ede1b..2eda614 100644
--- a/src/js/app.js
+++ b/src/js/app.js
@@ -239,7 +239,7 @@ export class App {
 
     collapseProtein() {
         d3.select(".custom-menu-margin").style("display", "none");
-        this.contextMenuProt.setExpanded(false, this.contextMenuPoint);
+        this.contextMenuProt.setExpanded(false);//, this.contextMenuPoint);
         this.contextMenuProt = null;
         this.notifyExpandListeners();
     }
diff --git a/src/js/viz/interactor/interactor.js b/src/js/viz/interactor/interactor.js
index eb2983e..b022ed1 100644
--- a/src/js/viz/interactor/interactor.js
+++ b/src/js/viz/interactor/interactor.js
@@ -148,8 +148,12 @@ export class Interactor {
         //remember previous position
         this.px = this.x;
         this.py = this.y;
-
         let xOffset = (this.width / 2 - (this.getSymbolRadius()));
+        /*
+        // let xOffset = (15 + this.labelSVG.getComputedTextLength()) / 2;
+        // would also work because
+        // width = (2 * this.getSymbolRadius()) + 15 + this.labelSVG.getComputedTextLength();
+        */
         if (this.expanded) {
             xOffset = xOffset - (this.size / 2 * this.stickZoom);
         }
diff --git a/src/js/viz/interactor/polymer.js b/src/js/viz/interactor/polymer.js
index 45d1067..d372a8d 100644
--- a/src/js/viz/interactor/polymer.js
+++ b/src/js/viz/interactor/polymer.js
@@ -159,6 +159,21 @@ export class Polymer extends Interactor {
     }
 
     toCircle(transition = true, svgP) {
+
+        if (!svgP) {
+            const width = this.app.svgElement.parentNode.clientWidth;
+            const ctm = this.app.container.getCTM().inverse();
+            const z = this.app.container.getCTM().inverse().a;
+            if (this.ix < ctm.e){
+                console.log("off left edge");
+                svgP = {x:ctm.e  + ((this.getSymbolRadius() + 15 + this.labelSVG.getComputedTextLength())), y:this.iy};
+            }
+            if (this.ix > ctm.e + (width * z)){
+                console.log("off right edge");
+                svgP = {x:ctm.e + (width * z)  - ((this.getSymbolRadius() + 5)), y:this.iy};
+            }
+        }
+
         const transitionTime = transition ? Polymer.transitionTime : 0;
         this.postAnimExpanded = false; // bit of a hack, used for updating listeners before anim complete, todo - is there better way
         this.busy = true;

From 2f1ad6fd152fc01a8e43fe72607b0e491ed0a5ab Mon Sep 17 00:00:00 2001
From: colin-combe <colin.combe@ed.ac.uk>
Date: Tue, 19 Oct 2021 15:36:35 +0100
Subject: [PATCH 2/2] undo temp change

---
 dist/complexviewer.js | 2 +-
 src/js/app.js         | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/dist/complexviewer.js b/dist/complexviewer.js
index a09b40c..e9a1f52 100644
--- a/dist/complexviewer.js
+++ b/dist/complexviewer.js
@@ -22,4 +22,4 @@
  *
  * Date: 2021-02-16
  */
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o=0;o<r;++o)e[i][o]=t[i][o]},t.prototype.stepAndProject=function(e,n,r,i){t.copy(e,n),this.takeDescentStep(n[0],r[0],i),this.project&&this.project[0](e[0],e[1],n[0]),this.takeDescentStep(n[1],r[1],i),this.project&&this.project[1](n[0],e[1],n[1]);for(var o=2;o<this.k;o++)this.takeDescentStep(n[o],r[o],i)},t.mApply=function(t,e,n){for(var r=t;r-- >0;)for(var i=e;i-- >0;)n(r,i)},t.prototype.matrixApply=function(e){t.mApply(this.k,this.n,e)},t.prototype.computeNextPosition=function(t,e){var n=this;this.computeDerivatives(t);var r=this.computeStepSize(this.g);if(this.stepAndProject(t,e,this.g,r),this.project){this.matrixApply((function(r,i){return n.e[r][i]=t[r][i]-e[r][i]}));var i=this.computeStepSize(this.e);i=Math.max(.2,Math.min(i,1)),this.stepAndProject(t,e,this.e,i)}},t.prototype.run=function(t){for(var e=Number.MAX_VALUE,n=!1;!n&&t-- >0;){var r=this.rungeKutta();n=Math.abs(e/r-1)<this.threshold,e=r}return e},t.prototype.rungeKutta=function(){var e=this;this.computeNextPosition(this.x,this.a),t.mid(this.x,this.a,this.ia),this.computeNextPosition(this.ia,this.b),t.mid(this.x,this.b,this.ib),this.computeNextPosition(this.ib,this.c),this.computeNextPosition(this.c,this.d);var n=0;return this.matrixApply((function(t,r){var i=(e.a[t][r]+2*e.b[t][r]+2*e.c[t][r]+e.d[t][r])/6,o=e.x[t][r]-i;n+=o*o,e.x[t][r]=i})),n},t.mid=function(e,n,r){t.mApply(e.length,e[0].length,(function(t,i){return r[t][i]=e[t][i]+(n[t][i]-e[t][i])/2}))},t.prototype.takeDescentStep=function(t,e,n){for(var r=0;r<this.n;++r)t[r]=t[r]-n*e[r]},t.prototype.computeStress=function(){for(var t=0,e=0,n=this.n-1;e<n;++e)for(var r=e+1,i=this.n;r<i;++r){for(var o=0,a=0;a<this.k;++a){var s=this.x[a][e]-this.x[a][r];o+=s*s}o=Math.sqrt(o);var u=this.D[e][r];if(isFinite(u)){var c=u-o;t+=c*c/(u*u)}}return t},t.zeroDistance=1e-10,t}();n.Descent=i;var o=function(){function t(t){void 0===t&&(t=1),this.seed=t,this.a=214013,this.c=2531011,this.m=2147483648,this.range=32767}return 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n?e.x-t.x:e.y-t.y};t.verts.sort(r);for(var o=1;o<t.verts.length;o++){var a=t.verts[o-1],u=t.verts[o];a.node&&a.node===u.node&&a.node.leaf||i.edges.push({source:a.id,target:u.id,length:Math.abs(r(a,u))})}}))}return t.prototype.avg=function(t){return t.reduce((function(t,e){return t+e}))/t.length},t.prototype.getGridLines=function(t){for(var e=[],n=this.leaves.slice(0,this.leaves.length);n.length>0;){var r=n.filter((function(e){return e.rect["overlap"+t.toUpperCase()](n[0].rect)})),i={nodes:r,pos:this.avg(r.map((function(e){return e.rect["c"+t]()})))};e.push(i),i.nodes.forEach((function(t){return n.splice(n.indexOf(t),1)}))}return e.sort((function(t,e){return t.pos-e.pos})),e},t.prototype.getDepth=function(t){for(var e=0;t.parent!==this.root;)e++,t=t.parent;return e},t.prototype.midPoints=function(t){for(var e=t[1]-t[0],n=[t[0]-e/2],r=1;r<t.length;r++)n.push((t[r]+t[r-1])/2);return n.push(t[t.length-1]+e/2),n},t.prototype.findLineage=function(t){var e=[t];do{t=t.parent,e.push(t)}while(t!==this.root);return e.reverse()},t.prototype.findAncestorPathBetween=function(t,e){for(var n=this.findLineage(t),r=this.findLineage(e),i=0;n[i]===r[i];)i++;return{commonAncestor:n[i-1],lineages:n.slice(i).concat(r.slice(i))}},t.prototype.siblingObstacles=function(t,e){var n=this,r=this.findAncestorPathBetween(t,e),i={};r.lineages.forEach((function(t){return i[t.id]={}}));var o=r.commonAncestor.children.filter((function(t){return!(t in i)}));return r.lineages.filter((function(t){return t.parent!==r.commonAncestor})).forEach((function(t){return o=o.concat(t.parent.children.filter((function(e){return e!==t.id})))})),o.map((function(t){return n.nodes[t]}))},t.getSegmentSets=function(t,e,n){for(var r=[],i=0;i<t.length;i++)for(var o=t[i],a=0;a<o.length;a++){(f=o[a]).edgeid=i,f.i=a;var s=f[1][e]-f[0][e];Math.abs(s)<.1&&r.push(f)}r.sort((function(t,n){return t[0][e]-n[0][e]}));for(var u=[],c=null,l=0;l<r.length;l++){var f=r[l];(!c||Math.abs(f[0][e]-c.pos)>.1)&&(c={pos:f[0][e],segments:[]},u.push(c)),c.segments.push(f)}return u},t.nudgeSegs=function(t,e,n,r,o,a){var s=r.length;if(!(s<=1)){for(var u=r.map((function(e){return new i.Variable(e[0][t])})),c=[],l=0;l<s;l++)for(var f=0;f<s;f++)if(l!==f){var h=r[l],p=r[f],d=h.edgeid,y=p.edgeid,g=-1,v=-1;"x"==t?o(d,y)&&(h[0][e]<h[1][e]?(g=f,v=l):(g=l,v=f)):o(d,y)&&(h[0][e]<h[1][e]?(g=l,v=f):(g=f,v=l)),g>=0&&c.push(new i.Constraint(u[g],u[v],a))}new i.Solver(u,c).solve(),u.forEach((function(e,i){var o=r[i],a=e.position();o[0][t]=o[1][t]=a;var s=n[o.edgeid];o.i>0&&(s[o.i-1][1][t]=a),o.i<s.length-1&&(s[o.i+1][0][t]=a)}))}},t.nudgeSegments=function(e,n,r,i,o){for(var a=t.getSegmentSets(e,n,r),s=0;s<a.length;s++){for(var u=a[s],c=[],l=0;l<u.segments.length;l++){var f=u.segments[l];c.push({type:0,s:f,pos:Math.min(f[0][r],f[1][r])}),c.push({type:1,s:f,pos:Math.max(f[0][r],f[1][r])})}c.sort((function(t,e){return t.pos-e.pos+t.type-e.type}));var h=[],p=0;c.forEach((function(a){0===a.type?(h.push(a.s),p++):p--,0==p&&(t.nudgeSegs(n,r,e,h,i,o),h=[])}))}},t.prototype.routeEdges=function(e,n,r,i){var o=this,a=e.map((function(t){return o.route(r(t),i(t))})),s=t.orderEdges(a),u=a.map((function(e){return t.makeSegments(e)}));return t.nudgeSegments(u,"x","y",s,n),t.nudgeSegments(u,"y","x",s,n),t.unreverseEdges(u,a),u},t.unreverseEdges=function(t,e){t.forEach((function(t,n){e[n].reversed&&(t.reverse(),t.forEach((function(t){t.reverse()})))}))},t.angleBetween2Lines=function(t,e){var n=Math.atan2(t[0].y-t[1].y,t[0].x-t[1].x),r=Math.atan2(e[0].y-e[1].y,e[0].x-e[1].x),i=n-r;return(i>Math.PI||i<-Math.PI)&&(i=r-n),i},t.isLeft=function(t,e,n){return(e.x-t.x)*(n.y-t.y)-(e.y-t.y)*(n.x-t.x)<=0},t.getOrder=function(t){for(var e={},n=0;n<t.length;n++){var r=t[n];void 0===e[r.l]&&(e[r.l]={}),e[r.l][r.r]=!0}return function(t,n){return void 0!==e[t]&&e[t][n]}},t.orderEdges=function(e){for(var n=[],r=0;r<e.length-1;r++)for(var i=r+1;i<e.length;i++){var o,a,s,c=e[r],l=e[i],f=new u(c,l);0!==f.length&&(f.reversed&&(l.reverse(),l.reversed=!0,f=new u(c,l)),(f.si<=0||f.ti<=0)&&(f.si+f.length>=c.length||f.ti+f.length>=l.length)?n.push({l:r,r:i}):(f.si+f.length>=c.length||f.ti+f.length>=l.length?(o=c[f.si+1],s=c[f.si-1],a=l[f.ti-1]):(o=c[f.si+f.length-2],a=c[f.si+f.length],s=l[f.ti+f.length]),t.isLeft(o,a,s)?n.push({l:i,r:r}):n.push({l:r,r:i})))}return t.getOrder(n)},t.makeSegments=function(t){function e(t){return{x:t.x,y:t.y}}for(var n=function(t,e,n){return Math.abs((e.x-t.x)*(n.y-t.y)-(e.y-t.y)*(n.x-t.x))<.001},r=[],i=e(t[0]),o=1;o<t.length;o++){var a=e(t[o]),s=o<t.length-1?t[o+1]:null;s&&n(i,a,s)||(r.push([i,a]),i=a)}return r},t.prototype.route=function(t,e){var n=this,r=this.nodes[t],i=this.nodes[e];this.obstacles=this.siblingObstacles(r,i);var a={};this.obstacles.forEach((function(t){return a[t.id]=t})),this.passableEdges=this.edges.filter((function(t){var e=n.verts[t.source],r=n.verts[t.target];return!(e.node&&e.node.id in a||r.node&&r.node.id in a)}));for(var s=1;s<r.ports.length;s++){var u=r.ports[0].id,c=r.ports[s].id;this.passableEdges.push({source:u,target:c,length:0})}for(s=1;s<i.ports.length;s++)u=i.ports[0].id,c=i.ports[s].id,this.passableEdges.push({source:u,target:c,length:0});var l=new o.Calculator(this.verts.length,this.passableEdges,(function(t){return t.source}),(function(t){return t.target}),(function(t){return t.length})).PathFromNodeToNodeWithPrevCost(r.ports[0].id,i.ports[0].id,(function(t,e,o){var a=n.verts[t],s=n.verts[e],u=n.verts[o],c=Math.abs(u.x-a.x),l=Math.abs(u.y-a.y);return a.node===r&&a.node===s.node||s.node===i&&s.node===u.node?0:c>1&&l>1?1e3:0})).reverse().map((function(t){return n.verts[t]}));return l.push(this.nodes[i.id].ports[0]),l.filter((function(t,e){return!(e<l.length-1&&l[e+1].node===r&&t.node===r||e>0&&t.node===i&&l[e-1].node===i)}))},t.getRoutePath=function(e,n,r,i){var o,a,s,u={routepath:"M "+e[0][0].x+" "+e[0][0].y+" ",arrowpath:""};if(e.length>1)for(var c=0;c<e.length;c++){var l=(o=e[c])[1].x,f=o[1].y,h=l-o[0].x,p=f-o[0].y;if(c<e.length-1){Math.abs(h)>0?l-=h/Math.abs(h)*n:f-=p/Math.abs(p)*n,u.routepath+="L "+l+" "+f+" ";var d=e[c+1],y=d[0].x,g=d[0].y;h=d[1].x-y,p=d[1].y-g;var v,x,m=t.angleBetween2Lines(o,d)<0?1:0;Math.abs(h)>0?(v=y+h/Math.abs(h)*n,x=g):(v=y,x=g+p/Math.abs(p)*n);var b=Math.abs(v-l),w=Math.abs(x-f);u.routepath+="A "+b+" "+w+" 0 0 "+m+" "+v+" "+x+" "}else{var k=[l,f];Math.abs(h)>0?(a=[l-=h/Math.abs(h)*i,f+r],s=[l,f-r]):(a=[l+r,f-=p/Math.abs(p)*i],s=[l-r,f]),u.routepath+="L "+l+" "+f+" ",i>0&&(u.arrowpath="M "+k[0]+" "+k[1]+" L "+a[0]+" "+a[1]+" L "+s[0]+" "+s[1])}}else l=(o=e[0])[1].x,f=o[1].y,h=l-o[0].x,p=f-o[0].y,k=[l,f],Math.abs(h)>0?(a=[l-=h/Math.abs(h)*i,f+r],s=[l,f-r]):(a=[l+r,f-=p/Math.abs(p)*i],s=[l-r,f]),u.routepath+="L "+l+" "+f+" ",i>0&&(u.arrowpath="M "+k[0]+" "+k[1]+" L "+a[0]+" "+a[1]+" L "+s[0]+" "+s[1]);return 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t?(this._threshold="function"==typeof t?t:+t,this):this._threshold},t.prototype.alpha=function(t){return arguments.length?(t=+t,this._alpha?this._alpha=t>0?t:0:t>0&&(this._running||(this._running=!0,this.trigger({type:r.start,alpha:this._alpha=t}),this.kick())),this):this._alpha},t.prototype.getLinkLength=function(t){return"function"==typeof this._linkDistance?+this._linkDistance(t):this._linkDistance},t.setLinkLength=function(t,e){t.length=e},t.prototype.getLinkType=function(t){return"function"==typeof this._linkType?this._linkType(t):0},t.prototype.symmetricDiffLinkLengths=function(t,e){var n=this;return void 0===e&&(e=1),this.linkDistance((function(e){return t*e.length})),this._linkLengthCalculator=function(){return o.symmetricDiffLinkLengths(n._links,n.linkAccessor,e)},this},t.prototype.jaccardLinkLengths=function(t,e){var n=this;return void 0===e&&(e=1),this.linkDistance((function(e){return t*e.length})),this._linkLengthCalculator=function(){return o.jaccardLinkLengths(n._links,n.linkAccessor,e)},this},t.prototype.start=function(e,n,r,i,c,l){var f=this;void 0===e&&(e=0),void 0===n&&(n=0),void 0===r&&(r=0),void 0===i&&(i=0),void 0===c&&(c=!0),void 0===l&&(l=!0);var h,p=this.nodes().length,d=p+2*this._groups.length,y=(this._links.length,this._canvasSize[0]),g=this._canvasSize[1],v=new Array(d),x=new Array(d),m=null,b=this._avoidOverlaps;this._nodes.forEach((function(t,e){t.index=e,void 0===t.x&&(t.x=y/2,t.y=g/2),v[e]=t.x,x[e]=t.y})),this._linkLengthCalculator&&this._linkLengthCalculator(),this._distanceMatrix?h=this._distanceMatrix:(h=new u.Calculator(d,this._links,t.getSourceIndex,t.getTargetIndex,(function(t){return f.getLinkLength(t)})).DistanceMatrix(),m=a.Descent.createSquareMatrix(d,(function(){return 2})),this._links.forEach((function(t){"number"==typeof t.source&&(t.source=f._nodes[t.source]),"number"==typeof t.target&&(t.target=f._nodes[t.target])})),this._links.forEach((function(e){var n=t.getSourceIndex(e),r=t.getTargetIndex(e);m[n][r]=m[r][n]=e.weight||1})));var w=a.Descent.createSquareMatrix(d,(function(t,e){return h[t][e]}));if(this._rootGroup&&void 0!==this._rootGroup.groups){var k=p;this._groups.forEach((function(t){!function(t,e,n,r){m[t][e]=m[e][t]=n,w[t][e]=w[e][t]=r}(k,k+1,f._groupCompactness,.1),void 0===t.bounds?(v[k]=y/2,x[k++]=g/2,v[k]=y/2,x[k++]=g/2):(v[k]=t.bounds.x,x[k++]=t.bounds.y,v[k]=t.bounds.X,x[k++]=t.bounds.Y)}))}else this._rootGroup={leaves:this._nodes,groups:[]};var S=this._constraints||[];for(this._directedLinkConstraints&&(this.linkAccessor.getMinSeparation=this._directedLinkConstraints.getMinSeparation,S=S.concat(o.generateDirectedEdgeConstraints(p,this._links,this._directedLinkConstraints.axis,this.linkAccessor))),this.avoidOverlaps(!1),this._descent=new a.Descent([v,x],w),this._descent.locks.clear(),k=0;k<p;++k){var _=this._nodes[k];if(_.fixed){_.px=_.x,_.py=_.y;var M=[_.x,_.y];this._descent.locks.add(k,M)}}if(this._descent.threshold=this._threshold,this.initialLayout(e,v,x),S.length>0&&(this._descent.project=new s.Projection(this._nodes,this._groups,this._rootGroup,S).projectFunctions()),this._descent.run(n),this.separateOverlappingComponents(y,g,l),this.avoidOverlaps(b),b&&(this._nodes.forEach((function(t,e){t.x=v[e],t.y=x[e]})),this._descent.project=new s.Projection(this._nodes,this._groups,this._rootGroup,S,!0).projectFunctions(),this._nodes.forEach((function(t,e){v[e]=t.x,x[e]=t.y}))),this._descent.G=m,this._descent.run(r),i){this._descent.snapStrength=1e3,this._descent.snapGridSize=this._nodes[0].width,this._descent.numGridSnapNodes=p,this._descent.scaleSnapByMaxH=p!=d;var E=a.Descent.createSquareMatrix(d,(function(t,e){return t>=p||e>=p?m[t][e]:0}));this._descent.G=E,this._descent.run(i)}return this.updateNodePositions(),this.separateOverlappingComponents(y,g,l),c?this.resume():this},t.prototype.initialLayout=function(e,n,r){if(this._groups.length>0&&e>0){var i=this._nodes.length,o=this._links.map((function(t){return{source:t.source.index,target:t.target.index}})),a=this._nodes.map((function(t){return{index:t.index}}));this._groups.forEach((function(t,e){a.push({index:t.index=i+e})})),this._groups.forEach((function(t,e){void 0!==t.leaves&&t.leaves.forEach((function(e){return o.push({source:t.index,target:e.index})})),void 0!==t.groups&&t.groups.forEach((function(e){return o.push({source:t.index,target:e.index})}))})),(new t).size(this.size()).nodes(a).links(o).avoidOverlaps(!1).linkDistance(this.linkDistance()).symmetricDiffLinkLengths(5).convergenceThreshold(1e-4).start(e,0,0,0,!1),this._nodes.forEach((function(t){n[t.index]=a[t.index].x,r[t.index]=a[t.index].y}))}else this._descent.run(e)},t.prototype.separateOverlappingComponents=function(t,e,n){var r=this;if(void 0===n&&(n=!0),!this._distanceMatrix&&this._handleDisconnected){var i=this._descent.x[0],o=this._descent.x[1];this._nodes.forEach((function(t,e){t.x=i[e],t.y=o[e]}));var a=l.separateGraphs(this._nodes,this._links);l.applyPacking(a,t,e,this._defaultNodeSize,e/t,n),this._nodes.forEach((function(t,e){r._descent.x[0][e]=t.x,r._descent.x[1][e]=t.y,t.bounds&&(t.bounds.setXCentre(t.x),t.bounds.setYCentre(t.y))}))}},t.prototype.resume=function(){return this.alpha(.1)},t.prototype.stop=function(){return this.alpha(0)},t.prototype.prepareEdgeRouting=function(t){void 0===t&&(t=0),this._visibilityGraph=new c.TangentVisibilityGraph(this._nodes.map((function(e){return e.bounds.inflate(-t).vertices()})))},t.prototype.routeEdge=function(t,e,n){void 0===e&&(e=5);var r=[],i=new c.TangentVisibilityGraph(this._visibilityGraph.P,{V:this._visibilityGraph.V,E:this._visibilityGraph.E}),o={x:t.source.x,y:t.source.y},a={x:t.target.x,y:t.target.y},l=i.addPoint(o,t.source.index),f=i.addPoint(a,t.target.index);i.addEdgeIfVisible(o,a,t.source.index,t.target.index),void 0!==n&&n(i);var h=new u.Calculator(i.V.length,i.E,(function(t){return t.source.id}),(function(t){return t.target.id}),(function(t){return t.length()})).PathFromNodeToNode(l.id,f.id);if(1===h.length||h.length===i.V.length){var p=s.makeEdgeBetween(t.source.innerBounds,t.target.innerBounds,e);r=[p.sourceIntersection,p.arrowStart]}else{for(var d=h.length-2,y=i.V[h[d]].p,g=i.V[h[0]].p,v=(r=[t.source.innerBounds.rayIntersection(y.x,y.y)],d);v>=0;--v)r.push(i.V[h[v]].p);r.push(s.makeEdgeTo(g,t.target.innerBounds,e))}return r},t.getSourceIndex=function(t){return"number"==typeof t.source?t.source:t.source.index},t.getTargetIndex=function(t){return"number"==typeof t.target?t.target:t.target.index},t.linkId=function(e){return t.getSourceIndex(e)+"-"+t.getTargetIndex(e)},t.dragStart=function(e){f(e)?t.storeOffset(e,t.dragOrigin(e)):(t.stopNode(e),e.fixed|=2)},t.stopNode=function(t){t.px=t.x,t.py=t.y},t.storeOffset=function(e,n){void 0!==e.leaves&&e.leaves.forEach((function(e){e.fixed|=2,t.stopNode(e),e._dragGroupOffsetX=e.x-n.x,e._dragGroupOffsetY=e.y-n.y})),void 0!==e.groups&&e.groups.forEach((function(e){return t.storeOffset(e,n)}))},t.dragOrigin=function(t){return f(t)?{x:t.bounds.cx(),y:t.bounds.cy()}:t},t.drag=function(e,n){f(e)?(void 0!==e.leaves&&e.leaves.forEach((function(t){e.bounds.setXCentre(n.x),e.bounds.setYCentre(n.y),t.px=t._dragGroupOffsetX+n.x,t.py=t._dragGroupOffsetY+n.y})),void 0!==e.groups&&e.groups.forEach((function(e){return t.drag(e,n)}))):(e.px=n.x,e.py=n.y)},t.dragEnd=function(e){f(e)?(void 0!==e.leaves&&e.leaves.forEach((function(e){t.dragEnd(e),delete e._dragGroupOffsetX,delete e._dragGroupOffsetY})),void 0!==e.groups&&e.groups.forEach(t.dragEnd)):e.fixed&=-7},t.mouseOver=function(t){t.fixed|=4,t.px=t.x,t.py=t.y},t.mouseOut=function(t){t.fixed&=-5},t}();n.Layout=h},{"./descent":7,"./geom":8,"./handledisconnected":10,"./linklengths":13,"./powergraph":14,"./rectangle":17,"./shortestpaths":18}],12:[function(t,e,n){"use strict";Object.defineProperty(n,"__esModule",{value:!0});var r=t("./shortestpaths"),i=t("./descent"),o=t("./rectangle"),a=t("./linklengths"),s=function(){function t(t,e){this.source=t,this.target=e}return t.prototype.actualLength=function(t){var e=this;return Math.sqrt(t.reduce((function(t,n){var r=n[e.target]-n[e.source];return t+r*r}),0))},t}();n.Link3D=s;var u=function(t,e,n){void 0===t&&(t=0),void 0===e&&(e=0),void 0===n&&(n=0),this.x=t,this.y=e,this.z=n};n.Node3D=u;var c=function(){function t(e,n,r){var i=this;void 0===r&&(r=1),this.nodes=e,this.links=n,this.idealLinkLength=r,this.constraints=null,this.useJaccardLinkLengths=!0,this.result=new Array(t.k);for(var o=0;o<t.k;++o)this.result[o]=new Array(e.length);e.forEach((function(e,n){for(var r=0,o=t.dims;r<o.length;r++){var a=o[r];void 0===e[a]&&(e[a]=Math.random())}i.result[0][n]=e.x,i.result[1][n]=e.y,i.result[2][n]=e.z}))}return t.prototype.linkLength=function(t){return t.actualLength(this.result)},t.prototype.start=function(t){var e=this;void 0===t&&(t=100);var n=this.nodes.length,s=new l;this.useJaccardLinkLengths&&a.jaccardLinkLengths(this.links,s,1.5),this.links.forEach((function(t){return t.length*=e.idealLinkLength}));var u=new r.Calculator(n,this.links,(function(t){return t.source}),(function(t){return t.target}),(function(t){return t.length})).DistanceMatrix(),c=i.Descent.createSquareMatrix(n,(function(t,e){return u[t][e]})),f=i.Descent.createSquareMatrix(n,(function(){return 2}));this.links.forEach((function(t){var e=t.source,n=t.target;return f[e][n]=f[n][e]=1})),this.descent=new i.Descent(this.result,c),this.descent.threshold=.001,this.descent.G=f,this.constraints&&(this.descent.project=new o.Projection(this.nodes,null,null,this.constraints).projectFunctions());for(var h=0;h<this.nodes.length;h++){var p=this.nodes[h];p.fixed&&this.descent.locks.add(h,[p.x,p.y,p.z])}return this.descent.run(t),this},t.prototype.tick=function(){this.descent.locks.clear();for(var t=0;t<this.nodes.length;t++){var e=this.nodes[t];e.fixed&&this.descent.locks.add(t,[e.x,e.y,e.z])}return this.descent.rungeKutta()},t.dims=["x","y","z"],t.k=t.dims.length,t}();n.Layout3D=c;var l=function(){function t(){}return t.prototype.getSourceIndex=function(t){return t.source},t.prototype.getTargetIndex=function(t){return t.target},t.prototype.getLength=function(t){return t.length},t.prototype.setLength=function(t,e){t.length=e},t}()},{"./descent":7,"./linklengths":13,"./rectangle":17,"./shortestpaths":18}],13:[function(t,e,n){"use strict";function r(t,e){var n={};for(var r in t)n[r]={};for(var r in e)n[r]={};return Object.keys(n).length}function i(t,e){var n=0;for(var r in t)void 0!==e[r]&&++n;return n}function o(t,e,n,r){var i=function(t,e){var n={},r=function(t,e){void 0===n[t]&&(n[t]={}),n[t][e]={}};return t.forEach((function(t){var n=e.getSourceIndex(t),i=e.getTargetIndex(t);r(n,i),r(i,n)})),n}(t,r);t.forEach((function(t){var o=i[r.getSourceIndex(t)],a=i[r.getTargetIndex(t)];r.setLength(t,1+e*n(o,a))}))}function a(t,e,n){var r=[],i=0,o=[],a=[];function s(t){t.index=t.lowlink=i++,o.push(t),t.onStack=!0;for(var e=0,n=t.out;e<n.length;e++){var r=n[e];void 0===r.index?(s(r),t.lowlink=Math.min(t.lowlink,r.lowlink)):r.onStack&&(t.lowlink=Math.min(t.lowlink,r.index))}if(t.lowlink===t.index){for(var u=[];o.length&&((r=o.pop()).onStack=!1,u.push(r),r!==t););a.push(u.map((function(t){return t.id})))}}for(var u=0;u<t;u++)r.push({id:u,out:[]});for(var c=0,l=e;c<l.length;c++){var f=l[c],h=r[n.getSourceIndex(f)],p=r[n.getTargetIndex(f)];h.out.push(p)}for(var d=0,y=r;d<y.length;d++){var g=y[d];void 0===g.index&&s(g)}return a}Object.defineProperty(n,"__esModule",{value:!0}),n.symmetricDiffLinkLengths=function(t,e,n){void 0===n&&(n=1),o(t,n,(function(t,e){return Math.sqrt(r(t,e)-i(t,e))}),e)},n.jaccardLinkLengths=function(t,e,n){void 0===n&&(n=1),o(t,n,(function(t,e){return Math.min(Object.keys(t).length,Object.keys(e).length)<1.1?0:i(t,e)/r(t,e)}),e)},n.generateDirectedEdgeConstraints=function(t,e,n,r){var i=a(t,e,r),o={};i.forEach((function(t,e){return t.forEach((function(t){return o[t]=e}))}));var s=[];return e.forEach((function(t){var e=r.getSourceIndex(t),i=r.getTargetIndex(t);o[e]!==o[i]&&s.push({axis:n,left:e,right:i,gap:r.getMinSeparation(t)})})),s},n.stronglyConnectedComponents=a},{}],14:[function(t,e,n){"use strict";Object.defineProperty(n,"__esModule",{value:!0});var r=function(t,e,n){this.source=t,this.target=e,this.type=n};n.PowerEdge=r;var i=function(){function t(t,e,n,r){var i=this;if(this.linkAccessor=n,this.modules=new Array(t),this.roots=[],r)this.initModulesFromGroup(r);else{this.roots.push(new s);for(var a=0;a<t;++a)this.roots[0].add(this.modules[a]=new o(a))}this.R=e.length,e.forEach((function(t){var e=i.modules[n.getSourceIndex(t)],r=i.modules[n.getTargetIndex(t)],o=n.getType(t);e.outgoing.add(o,r),r.incoming.add(o,e)}))}return t.prototype.initModulesFromGroup=function(t){var e=new s;this.roots.push(e);for(var n=0;n<t.leaves.length;++n){var r=t.leaves[n],i=new o(r.id);this.modules[r.id]=i,e.add(i)}if(t.groups)for(var a=0;a<t.groups.length;++a){var c=t.groups[a],l={};for(var f in c)"leaves"!==f&&"groups"!==f&&c.hasOwnProperty(f)&&(l[f]=c[f]);e.add(new o(-1-a,new u,new u,this.initModulesFromGroup(c),l))}return e},t.prototype.merge=function(t,e,n){void 0===n&&(n=0);var r=t.incoming.intersection(e.incoming),i=t.outgoing.intersection(e.outgoing),a=new s;a.add(t),a.add(e);var u=new o(this.modules.length,i,r,a);this.modules.push(u);var c=function(n,r,i){n.forAll((function(n,o){n.forAll((function(n){var a=n[r];a.add(o,u),a.remove(o,t),a.remove(o,e),t[i].remove(o,n),e[i].remove(o,n)}))}))};return c(i,"incoming","outgoing"),c(r,"outgoing","incoming"),this.R-=r.count()+i.count(),this.roots[n].remove(t),this.roots[n].remove(e),this.roots[n].add(u),u},t.prototype.rootMerges=function(t){void 0===t&&(t=0);for(var e=this.roots[t].modules(),n=e.length,r=new Array(n*(n-1)),i=0,o=0,a=n-1;o<a;++o)for(var s=o+1;s<n;++s){var u=e[o],c=e[s];r[i]={id:i,nEdges:this.nEdges(u,c),a:u,b:c},i++}return r},t.prototype.greedyMerge=function(){for(var t=0;t<this.roots.length;++t)if(!(this.roots[t].modules().length<2)){var e=this.rootMerges(t).sort((function(t,e){return t.nEdges==e.nEdges?t.id-e.id:t.nEdges-e.nEdges}))[0];if(!(e.nEdges>=this.R))return this.merge(e.a,e.b,t),!0}},t.prototype.nEdges=function(t,e){var n=t.incoming.intersection(e.incoming),r=t.outgoing.intersection(e.outgoing);return this.R-n.count()-r.count()},t.prototype.getGroupHierarchy=function(t){var e=this,n=[];return function t(e,n,r){e.forAll((function(e){if(e.isLeaf())n.leaves||(n.leaves=[]),n.leaves.push(e.id);else{var i=n;if(e.gid=r.length,!e.isIsland()||e.isPredefined()){if(i={id:e.gid},e.isPredefined())for(var o in e.definition)i[o]=e.definition[o];n.groups||(n.groups=[]),n.groups.push(e.gid),r.push(i)}t(e.children,i,r)}}))}(this.roots[0],{},n),this.allEdges().forEach((function(i){var o=e.modules[i.source],a=e.modules[i.target];t.push(new r(void 0===o.gid?i.source:n[o.gid],void 0===a.gid?i.target:n[a.gid],i.type))})),n},t.prototype.allEdges=function(){var e=[];return t.getEdges(this.roots[0],e),e},t.getEdges=function(e,n){e.forAll((function(e){e.getEdges(n),t.getEdges(e.children,n)}))},t}();n.Configuration=i;var o=function(){function t(t,e,n,r,i){void 0===e&&(e=new u),void 0===n&&(n=new u),void 0===r&&(r=new s),this.id=t,this.outgoing=e,this.incoming=n,this.children=r,this.definition=i}return t.prototype.getEdges=function(t){var e=this;this.outgoing.forAll((function(n,i){n.forAll((function(n){t.push(new r(e.id,n.id,i))}))}))},t.prototype.isLeaf=function(){return 0===this.children.count()},t.prototype.isIsland=function(){return 0===this.outgoing.count()&&0===this.incoming.count()},t.prototype.isPredefined=function(){return void 0!==this.definition},t}();function a(t,e){var n={};for(var r in t)r in e&&(n[r]=t[r]);return n}n.Module=o;var s=function(){function t(){this.table={}}return t.prototype.count=function(){return Object.keys(this.table).length},t.prototype.intersection=function(e){var n=new t;return n.table=a(this.table,e.table),n},t.prototype.intersectionCount=function(t){return this.intersection(t).count()},t.prototype.contains=function(t){return t in this.table},t.prototype.add=function(t){this.table[t.id]=t},t.prototype.remove=function(t){delete this.table[t.id]},t.prototype.forAll=function(t){for(var e in this.table)t(this.table[e])},t.prototype.modules=function(){var t=[];return this.forAll((function(e){e.isPredefined()||t.push(e)})),t},t}();n.ModuleSet=s;var u=function(){function t(){this.sets={},this.n=0}return t.prototype.count=function(){return this.n},t.prototype.contains=function(t){var e=!1;return this.forAllModules((function(n){e||n.id!=t||(e=!0)})),e},t.prototype.add=function(t,e){(t in this.sets?this.sets[t]:this.sets[t]=new s).add(e),++this.n},t.prototype.remove=function(t,e){var n=this.sets[t];n.remove(e),0===n.count()&&delete this.sets[t],--this.n},t.prototype.forAll=function(t){for(var e in this.sets)t(this.sets[e],Number(e))},t.prototype.forAllModules=function(t){this.forAll((function(e,n){return e.forAll(t)}))},t.prototype.intersection=function(e){var n=new t;return this.forAll((function(t,r){if(r in e.sets){var i=t.intersection(e.sets[r]),o=i.count();o>0&&(n.sets[r]=i,n.n+=o)}})),n},t}();n.LinkSets=u,n.getGroups=function(t,e,n,r){for(var o=t.length,a=new i(o,e,n,r);a.greedyMerge(););var s=[],u=a.getGroupHierarchy(s);return 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d.stickZoom=y,d.rotation=g,d.busy=!1,!0}return!!(t>1||isNaN(t))&&T(1)}}},{key:"toStick",value:function(){var t=!(arguments.length>0&&void 0!==arguments[0])||arguments[0],e=t?a.transitionTime:0;this.busy=!0,this.expanded=!0,this.postAnimExpanded=!0;var n=this.size*this.stickZoom,r=this.getSymbolRadius(),o=i.interpolate(2*r,n),s=i.interpolate(0,this.stickZoom),u=i.interpolate(-(r+5),-(this.size/2*this.stickZoom+(this.nTermFeatures.length>0?25:10))),c=this.stickZoom;this.stickZoom=0,this.checkLinks(),this.stickZoom=c,i.select(this.background).transition().attr("height",a.STICKHEIGHT).attr("y",-a.STICKHEIGHT/2).attr("rx",0).attr("ry",0).duration(e),i.select(this.outline).transition().attr("height",a.STICKHEIGHT).attr("y",-a.STICKHEIGHT/2).attr("rx",0).attr("ry",0).duration(e),i.select(this.highlight).transition().attr("width",n+5).attr("height",a.STICKHEIGHT+5).attr("x",this.getResXWithStickZoom(.5)-2.5).attr("y",-a.STICKHEIGHT/2-2.5).attr("rx",0).attr("ry",0).duration(e);var 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E=m.fuzzyEnd;E.setAttribute("d",this.getAnnotationPieSlicePath(m.seqDatum.end,m.seqDatum.uncertainEnd,m,!1)),i.select(E).transition().attr("d",this.getAnnotationRectPath(m.seqDatum.end,m.seqDatum.uncertainEnd,m)).duration(a.transitionTime)}}}catch(t){x.e(t)}finally{x.f()}}}}catch(t){p.e(t)}finally{p.f()}i.timer((function(t){return A(t/e)}))}else A(1);function A(t){var e=i.transform(l.labelSVG.getAttribute("transform")),n=l.app.svgElement.createSVGMatrix().rotate(e.rotate).translate(u(f(t)),l.labelY);l.labelSVG.transform.baseVal.initialize(l.app.svgElement.createSVGTransformFromMatrix(n));var r=o(f(t));return i.select(l.highlight).attr("width",r).attr("x",-r/2+.5*l.stickZoom),i.select(l.outline).attr("width",r).attr("x",-r/2+.5*l.stickZoom),i.select(l.background).attr("width",r).attr("x",-r/2+.5*l.stickZoom),l.stickZoom=s(f(t)),l.setAllLinkCoordinates(),1===t?(l.updateAnnotationRectanglesNoTransition(),l.busy=!1,!0):!!(t>1||isNaN(t))&&A(1)}i.select(this.ticks).attr("opacity",0),this.setScaleGroup(),i.select(this.ticks).transition().attr("opacity",1).delay(.8*e).duration(e/2)}},{key:"updateAnnotationRectanglesNoTransition",value:function(){var t,e=k(this.annotationSets);try{for(e.s();!(t=e.n()).done;){var n=w(t.value,2),r=n[0],o=n[1];if(!0===this.app.annotationSetsShown.get(r)){var a,s=k(o);try{for(s.s();!(a=s.n()).done;){var u=a.value;if(u.fuzzyStart){var c=u.fuzzyStart;i.select(c).attr("d",this.getAnnotationRectPath(u.seqDatum.uncertainBegin,u.seqDatum.begin,u))}if(u.certain){var l=u.seqDatum.begin,f=u.seqDatum.end;u.seqDatum.uncertainBegin&&(l+=1),u.seqDatum.uncertainEnd&&(f-=1),u.certain.setAttribute("d",this.getAnnotationRectPath(l,f,u))}if(u.fuzzyEnd){var h=u.fuzzyEnd;i.select(h).attr("d",this.getAnnotationRectPath(u.seqDatum.end,u.seqDatum.uncertainEnd,u))}}}catch(t){s.e(t)}finally{s.f()}}}}catch(t){e.e(t)}finally{e.f()}}},{key:"getResXWithStickZoom",value:function(t){return"n-n"===t?-this.size/2*this.stickZoom-20:"c-c"===t?this.size/2*this.stickZoom+20:(t-this.size/2)*this.stickZoom}},{key:"getResidueCoordinates",value:function(t,e){void 0===t&&console.error("ERROR: residue number is undefined");var n,r=this.getResXWithStickZoom(1*t);if(0!==r){var i=Math.abs(r),o=Math.acos(r/i),a=this.rotation/360*Math.PI*2;r=i*Math.cos(a+o),n=i*Math.sin(a+o),void 0!==e&&(r+=e*Math.cos(a+Math.PI/2),n+=e*Math.sin(a+Math.PI/2))}else 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p=l.value;if(!f.has(p.toString()))if(f.add(p.toString()),"n-n"===p.seqDatum.sequenceDatumString||"c-c"===p.seqDatum.sequenceDatumString)"n-n"===p.seqDatum.sequenceDatumString?(p.rung=this.nTermFeatures.length,this.nTermFeatures.push(p)):(p.rung=this.cTermFeatures.length,this.cTermFeatures.push(p));else{var y=r[n];i(y,p)&&(r[++n]=[],y=r[n]),p.rung=n,y.push(p)}}}catch(t){h.e(t)}finally{h.f()}}}}catch(t){a.e(t)}finally{a.f()}this.rungCount=n+1;var g,v=k(this.annotationSets);try{for(v.s();!(g=v.n()).done;){var x=w(g.value,2),m=x[0],b=x[1];if(!0===this.app.annotationSetsShown.get(m)){var S,_=new Set,M=k(b.values());try{for(M.s();!(S=M.n()).done;){var E=S.value;if(!_.has(E.toString())){_.add(E.toString());var 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C=E.seqDatum.begin,L=E.seqDatum.end;E.seqDatum.uncertainBegin&&(C+=1),E.seqDatum.uncertainEnd&&(L-=1),this.expanded?E.certain.setAttribute("d",this.getAnnotationRectPath(C,L,E)):E.certain.setAttribute("d",this.getAnnotationPieSlicePath(C,L,E)),E.certain.setAttribute("stroke-width","1"),E.certain.name=A,E.certain.onmouseover=e,this.annotationsSvgGroup.appendChild(E.certain)}E.seqDatum.uncertainEnd&&(E.fuzzyEnd=document.createElementNS(d,"path"),this.expanded?E.fuzzyEnd.setAttribute("d",this.getAnnotationRectPath(E.seqDatum.end,E.seqDatum.uncertainEnd,E)):E.fuzzyEnd.setAttribute("d",this.getAnnotationPieSlicePath(E.seqDatum.end,E.seqDatum.uncertainEnd,E)),E.fuzzyEnd.setAttribute("stroke-width","1"),E.fuzzyEnd.name=A,E.fuzzyEnd.onmouseover=e,this.annotationsSvgGroup.appendChild(E.fuzzyEnd))}}}catch(t){M.e(t)}finally{M.f()}}}}catch(t){v.e(t)}finally{v.f()}this.scale()}},{key:"getAnnotationPieSlicePath",value:function(t,e,n){var r,i,o,s,u,c=!(arguments.length>3&&void 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g=document.createTextNode("tooltip");this.tooltip.classList.add("label","tooltip"),this.tooltip.appendChild(g),this.tooltip_bg=document.createElementNS(d,"rect"),this.tooltip_bg.classList.add("tooltip-background"),this.tooltip_subBg=document.createElementNS(d,"rect"),this.tooltip_subBg.classList.add("tooltip-sub-background"),this.svgElement.appendChild(this.tooltip_subBg),this.svgElement.appendChild(this.tooltip_bg),this.svgElement.appendChild(this.tooltip),this.annotationSetsShown=new Map,this.annotationSetsShown.set("Interactor",!1),this.annotationSetsShown.set("UniprotKB",!1),this.annotationSetsShown.set("Superfamily",!1),this.annotationSetsShown.set("MI Features",!0),this.clear()}var e,n,o;return e=t,(n=[{key:"clear",value:function(){this.d3cola.stop(),this.naryLinks.textContent="",this.p_pLinksWide.textContent="",this.highlights.textContent="",this.p_pLinks.textContent="",this.res_resLinks.textContent="",this.proteinUpper.textContent="",this.selfRes_resLinks.textContent="",this.dragElement=null,this.dragStart=null,this.participants=new Map,this.allNaryLinks=new Map,this.allBinaryLinks=new Map,this.allUnaryLinks=new Map,this.allSequenceLinks=new Map,this.complexes=[];var e,n=[],r=Te(a);try{for(r.s();!(e=r.n()).done;){var o=e.value,s=i.hsl(o);s.l=.9,n.push(s+"")}}catch(t){r.e(t)}finally{r.f()}Xt.naryColors=i.scale.ordinal().range(n),this.z=1,this.hideTooltip(),this.state=t.STATES.MOUSE_UP}},{key:"collapseProtein",value:function(){i.select(".custom-menu-margin").style("display","none"),this.contextMenuProt.setExpanded(!1),this.contextMenuProt=null,this.notifyExpandListeners()}},{key:"init",value:function(){this.d3cola.stop();var e,n=0,r=Te(this.participants.values());try{for(r.s();!(e=r.n()).done;){var o=e.value;o.size>n&&(n=o.size)}}catch(t){r.e(t)}finally{r.f()}var a,s,u,c=.8*this.svgElement.parentNode.clientWidth/n;this.defaultBarScale=(a=t.barScales,s=c,0===(u=(0,i.bisector((function(t){return t})).left)(a,s))||1===u?a[1]:u===a.length?a[a.length-1]:a[u-1]);var l,f=Te(this.participants.values());try{for(f.s();!(l=f.n()).done;){var h=l.value;"complex"!==h.type&&(h.setPosition(-500,-500),this.proteinUpper.appendChild(h.upperGroup))}}catch(t){f.e(t)}finally{f.f()}var p,d=Te(this.participants.values());try{for(d.s();!(p=d.n()).done;){var y=p.value;"protein"===y.type&&(y.stickZoom=this.defaultBarScale,this.participants.size<this.maxCountInitiallyExpanded&&y.toStick(!1))}}catch(t){d.e(t)}finally{d.f()}this.updateAnnotations();var g=this;!function(t,e){var n,r=Array.from(t.participants.values()).filter((function(t){return"protein"===t.type})),i=0,o=r.length,a=Me(r);try{for(a.s();!(n=a.n()).done;){var s=n.value,u=new RegExp("[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}![-]","i").exec(s.json.identifier.id);u&&u[0]===s.json.identifier.id.trim()&&(Ce(s,(function(){++i===o&&e()})),Ae(s,(function(){++i===o&&e()})))}}catch(t){a.e(t)}finally{a.f()}}(this,(function(){g.updateAnnotations()})),this.checkLinks(),this.autoLayout()}},{key:"zoomToExtent",value:function(){var t=this.svgElement.parentNode.clientWidth,e=this.svgElement.parentNode.clientHeight,n=this.container.getBBox(),r=(t/n.width).toFixed(4),i=(e/n.height).toFixed(4);if((i<r?i:r)<1){var o;r=(t-40)/n.width,(o=(i=(e-40)/n.height)<r?i:r)>this.z&&(o=this.z);var a=-n.x+20/o,s=-n.y+20/o;this.container.setAttribute("transform","scale("+o+") translate("+a+" "+s+") "),this.z=this.container.getCTM().inverse().a}else{var u=t-n.width,c=e-n.height,l=u/2-n.x,f=c/2-n.y;this.container.setAttribute("transform","scale(1) translate("+l+" "+f+")"),this.z=1}this.acknowledgement.setAttribute("transform","translate("+(t-150)+", "+(e-30)+")")}},{key:"autoLayout",value:function(){this.d3cola.stop();var t,e=[],n=[],r=this,o=Te(this.participants.values());try{for(o.s();!(t=o.n()).done;){var a=t.value;"complex"!==a.type&&(n.push(a),a.binaryLinks.size>2&&e.push(a)),delete a.x,delete a.y,delete a.px,delete a.py,delete a.bounds,a.fixed=0}}catch(t){o.e(t)}finally{o.f()}var s=n.length<30?30:20,u=this.svgElement.parentNode.clientWidth,c=this.svgElement.parentNode.clientHeight;function l(t){var e,n=[],i={},o=0,a=Te(t);try{for(a.s();!(e=a.n()).done;)i[e.value.id]=o,o++}catch(t){a.e(t)}finally{a.f()}var s,u=Te(r.allBinaryLinks.values());try{for(u.s();!(s=u.n()).done;){var c=s.value,l=c.participants[0],f=c.participants[1];if(l!==f&&-1!==t.indexOf(l)&&-1!==t.indexOf(f)){var h={};h.source=i[l.id],h.target=i[f.id],h.id=c.id,n.push(h)}}}catch(t){u.e(t)}finally{u.f()}return n}this.d3cola.size([c-40,u-40]).symmetricDiffLinkLengths(s),h(e,l(e),!0);var f=l(n);function h(t,e,n){var o;if(delete r.d3cola._lastStress,delete r.d3cola._alpha,delete r.d3cola._descent,delete r.d3cola._rootGroup,r.d3cola.nodes(t).links(e),r.debug&&((o=i.select(r.container).selectAll(".node").data(t)).enter().append("rect").classed("node",!0).attr({rx:5,ry:5}).style("stroke","red").style("fill","none"),o.exit().remove()),n)r.d3cola.groups([]).start(23,10,0,0,!1);else{var a=[];if(r.complexes){var s,u=Te(r.complexes);try{for(u.s();!(s=u.n()).done;){var c=s.value;c.leaves=[],c.groups=[];var l,f=Te(c.naryLink.participants);try{for(f.s();!(l=f.n()).done;){var h=l.value;"complex"!==h.type&&c.leaves.push(t.indexOf(h))}}catch(t){f.e(t)}finally{f.f()}a.push(c)}}catch(t){u.e(t)}finally{u.f()}var p,d=Te(r.complexes);try{for(d.s();!(p=d.n()).done;){var y,g=p.value,v=Te(g.naryLink.participants);try{for(v.s();!(y=v.n()).done;){var x=y.value;"complex"===x.type&&g.groups.push(a.indexOf(x))}}catch(t){v.e(t)}finally{v.f()}}}catch(t){d.e(t)}finally{d.f()}}r.d3cola.groups(a).start(0,10,1,0,!0).on("tick",(function(){var t,e=Te(r.d3cola.nodes());try{for(e.s();!(t=e.n()).done;){var n=t.value;n.setPositionFromCola(n.x,n.y)}}catch(t){e.e(t)}finally{e.f()}r.setAllLinkCoordinates(),r.zoomToExtent(),r.debug&&o.attr({x:function(t){return t.bounds.x},y:function(t){return t.bounds.y},width:function(t){return t.bounds.width()},height:function(t){return t.bounds.height()}})}))}}h(n,f,!0),h(n,f,!1)}},{key:"getSVG",value:function(){var t=[i.select(this.el).selectAll("svg").node()],e=l.capture(t);return l.makeXMLStr(new XMLSerializer,e[0])}},{key:"readMIJSON",value:function(t){var e=!(arguments.length>1&&void 0!==arguments[1])||arguments[1];_e(t,this,e),this.init()}},{key:"checkLinks",value:function(){var t,e=Te(this.allNaryLinks.values());try{for(e.s();!(t=e.n()).done;)t.value.check()}catch(t){e.e(t)}finally{e.f()}var n,r=Te(this.allBinaryLinks.values());try{for(r.s();!(n=r.n()).done;)n.value.check()}catch(t){r.e(t)}finally{r.f()}var i,o=Te(this.allUnaryLinks.values());try{for(o.s();!(i=o.n()).done;)i.value.check()}catch(t){o.e(t)}finally{o.f()}var a,s=Te(this.allSequenceLinks.values());try{for(s.s();!(a=s.n()).done;)a.value.check()}catch(t){s.e(t)}finally{s.f()}}},{key:"setAllLinkCoordinates",value:function(){var t,e=Te(this.allNaryLinks.values());try{for(e.s();!(t=e.n()).done;)t.value.setLinkCoordinates()}catch(t){e.e(t)}finally{e.f()}var n,r=Te(this.allBinaryLinks.values());try{for(r.s();!(n=r.n()).done;)n.value.setLinkCoordinates()}catch(t){r.e(t)}finally{r.f()}var i,o=Te(this.allUnaryLinks.values());try{for(o.s();!(i=o.n()).done;)i.value.setLinkCoordinates()}catch(t){o.e(t)}finally{o.f()}var a,s=Te(this.allSequenceLinks.values());try{for(s.s();!(a=s.n()).done;)a.value.setLinkCoordinates()}catch(t){s.e(t)}finally{s.f()}}},{key:"showTooltip",value:function(t){var e,n,r=this.tooltip.getComputedTextLength()+16,i=this.svgElement.parentNode.clientWidth,o=this.svgElement.parentNode.clientHeight;e=t.x+20+r<i?t.x:i-r-20,n=t.y+60<o?t.y:o-60,this.tooltip.setAttribute("x",e+22),this.tooltip.setAttribute("y",n+47),this.tooltip_bg.setAttribute("x",e+16),this.tooltip_bg.setAttribute("y",n+28),this.tooltip_subBg.setAttribute("x",e+16),this.tooltip_subBg.setAttribute("y",n+28)}},{key:"setTooltip",value:function(t,e){if(t){this.tooltip.firstChild.data=t.toString().replace(/&(quot);/g,'"'),this.tooltip.setAttribute("display","block");var n=this.tooltip.getComputedTextLength();this.tooltip_bg.setAttribute("width",n+16),this.tooltip_subBg.setAttribute("width",n+16),void 0!==e&&null!=e?(this.tooltip_bg.setAttribute("fill",e),this.tooltip_bg.setAttribute("stroke",e),this.tooltip_bg.setAttribute("fill-opacity","0.0")):(this.tooltip_bg.setAttribute("fill","white"),this.tooltip_bg.setAttribute("stroke","grey")),this.tooltip_bg.setAttribute("height","28"),this.tooltip_subBg.setAttribute("height","28"),this.tooltip_bg.setAttribute("display","block"),this.tooltip_subBg.setAttribute("display","block")}else this.hideTooltip()}},{key:"hideTooltip",value:function(){this.tooltip.setAttribute("display","none"),this.tooltip_bg.setAttribute("display","none"),this.tooltip_subBg.setAttribute("display","none")}},{key:"setAnnotations",value:function(t){t=t.toUpperCase();var e,n=Te(this.annotationSetsShown.keys());try{for(n.s();!(e=n.n()).done;){var r=e.value;this.annotationSetsShown.set(r,t===r)}}catch(t){n.e(t)}finally{n.f()}return this.updateAnnotations(),this.getColorKeyJson()}},{key:"showAnnotations",value:function(t,e){return this.annotationSetsShown.set(t,e),this.updateAnnotations(),this.getColorKeyJson()}},{key:"updateAnnotations",value:function(){this.defs.textContent="",this.uncertainCategories=new Set,this.certainCategories=new Set,delete this.featureColors;var t,e,n=new Set,r=Te(this.participants.values());try{for(r.s();!(t=r.n()).done;){var o,a=Te(t.value.annotationSets);try{for(a.s();!(o=a.n()).done;){var u=Ne(o.value,2),l=u[0],f=u[1];if(!0===this.annotationSetsShown.get(l)){var h,p=Te(f.values());try{for(p.s();!(h=p.n()).done;){var d=h.value;n.add(d.description)}}catch(t){p.e(t)}finally{p.f()}}}}catch(t){a.e(t)}finally{a.f()}}}catch(t){r.e(t)}finally{r.f()}e=n.size<11?i.scale.ordinal().range(s):i.scale.category20();var y=this;function g(t,e){var n=y.defs.append("pattern").attr("id",t).attr("patternUnits","userSpaceOnUse").attr("x",0).attr("y",0).attr("width",12).attr("height",12).attr("patternTransform","rotate(45)");n.append("rect").attr("x",0).attr("y",2).attr("width",12).attr("height",4).attr("fill",e),n.append("rect").attr("x",0).attr("y",8).attr("width",12).attr("height",4).attr("fill",e)}var v,x=Te(this.participants.values());try{for(x.s();!(v=x.n()).done;){var m=v.value;if("protein"===m.type){m.clearPositionalFeatures(),m.updatePositionalFeatures();var b,w=Te(m.annotationSets);try{for(w.s();!(b=w.n()).done;){var k=Ne(b.value,2),S=k[0],_=k[1];if(!0===this.annotationSetsShown.get(S)){var M,E=Te(_);try{for(E.s();!(M=E.n()).done;){var A=M.value,C=void 0;if(C="No annotations"===A.description?"#eeeeee":e(A.description),A.certain&&(A.certain.setAttribute("fill",C),A.certain.setAttribute("stroke",C),this.certainCategories.add(A.description)),A.fuzzyStart||A.fuzzyEnd){if(!this.uncertainCategories.has(name)){var L=new c(C),N="rgba("+L.r+","+L.g+","+L.b+", 0.6)";g("hatched_"+A.description+"_"+C.toString(),N),this.uncertainCategories.add(A.description)}var T="url('#hatched_"+A.description+"_"+C.toString()+"')";A.fuzzyStart&&(A.fuzzyStart.setAttribute("fill",T),A.fuzzyStart.setAttribute("stroke",C)),A.fuzzyEnd&&(A.fuzzyEnd.setAttribute("fill",T),A.fuzzyEnd.setAttribute("stroke",C))}}}catch(t){E.e(t)}finally{E.f()}}}}catch(t){w.e(t)}finally{w.f()}}}}catch(t){x.e(t)}finally{x.f()}this.featureColors=e}},{key:"getColorKeyJson",value:function(){var t,e={Complex:[]},n=Te(Xt.naryColors.domain());try{for(n.s();!(t=n.n()).done;){var r=t.value;e.Complex.push({name:r,certain:{color:Xt.naryColors(r)}})}}catch(t){n.e(t)}finally{n.f()}if(this.featureColors){var i,o=Te(this.annotationSetsShown);try{for(o.s();!(i=o.n()).done;){var a=Ne(i.value,2),s=a[0];if(a[1]){var u,l=[],f=new Set,h=Te(this.participants.values());try{for(h.s();!(u=h.n()).done;){var p=u.value;if("protein"===p.type){var d=p.annotationSets.get(s);if(d){var y,g=Te(d);try{for(g.s();!(y=g.n()).done;){var v=y.value.description;if(!f.has(v)){f.add(v);var x={name:v};if(this.certainCategories.has(v)&&(x.certain={color:this.featureColors(v)}),this.uncertainCategories.has(v)){var m=new c(this.featureColors(v)),b="rgba("+m.r+","+m.g+","+m.b+", 0.6)";x.uncertain={color:b}}l.push(x)}}}catch(t){g.e(t)}finally{g.f()}}}}}catch(t){h.e(t)}finally{h.f()}e[s]=l}}}catch(t){o.e(t)}finally{o.f()}}return e}},{key:"collapseAll",value:function(){var t,e=Te(this.participants.values());try{for(e.s();!(t=e.n()).done;){var n=t.value;n.expanded&&n.toCircle(!1)}}catch(t){e.e(t)}finally{e.f()}this.autoLayout(),this.notifyExpandListeners()}},{key:"expandAll",value:function(){var t,e=Te(this.participants.values());try{for(e.s();!(t=e.n()).done;){var n=t.value;"protein"!==n.type||n.expanded||n.toStick(!1)}}catch(t){e.e(t)}finally{e.f()}this.autoLayout(),this.notifyExpandListeners()}},{key:"expandAndCollapseSelection",value:function(t){var e,n=Te(this.participants.values());try{for(n.s();!(e=n.n()).done;){var r=e.value,i=r.json.identifier.id;t.includes(i)?r.expanded||r.setExpanded(!0):r.expanded&&r.setExpanded(!1)}}catch(t){n.e(t)}finally{n.f()}this.notifyExpandListeners()}},{key:"addHoverListener",value:function(t){this.hoverListeners.add(t)}},{key:"removeHoverListener",value:function(t){this.hoverListeners.remove(t)}},{key:"notifyHoverListeners",value:function(t){var e,n=Te(this.hoverListeners);try{for(n.s();!(e=n.n()).done;)(0,e.value)(t)}catch(t){n.e(t)}finally{n.f()}}},{key:"addExpandListener",value:function(t){this.expandListeners.add(t)}},{key:"removeExpandListener",value:function(t){this.expandListeners.remove(t)}},{key:"notifyExpandListeners",value:function(){var t,e=this.getExpandedParticipants(),n=Te(this.expandListeners);try{for(n.s();!(t=n.n()).done;)(0,t.value)(e)}catch(t){n.e(t)}finally{n.f()}}},{key:"getExpandedParticipants",value:function(){var t,e=[],n=Te(this.participants.values());try{for(n.s();!(t=n.n()).done;){var r=t.value;r.postAnimExpanded&&e.push(r.json)}}catch(t){n.e(t)}finally{n.f()}return e}},{key:"setCTM",value:function(t,e){var n="matrix("+e.a+","+e.b+","+e.c+","+e.d+","+e.e+","+e.f+")";t.setAttribute("transform",n)}},{key:"mouseDown",value:function(e){e.preventDefault(),this.d3cola.stop(),this.dragStart=e,this.state=t.STATES.SELECT_PAN,i.select(".custom-menu-margin").style("display","none")}},{key:"touchStart",value:function(e){e.preventDefault(),this.d3cola.stop(),this.dragStart=e,this.state=t.STATES.SELECT_PAN,i.select(".custom-menu-margin").style("display","none")}},{key:"move",value:function(e){var n=this.getEventPoint(e),r=n.matrixTransform(this.container.getCTM().inverse());if(r.x)if(this.dragStart){this.hideTooltip();var i=this.getEventPoint(this.dragStart).matrixTransform(this.container.getCTM().inverse());if(null!=this.dragElement){var o=i.x-r.x,a=i.y-r.y;if(this.state===t.STATES.DRAGGING){if(this.dragElement.ix)this.dragElement.changePosition(o,a),this.dragElement.setAllLinkCoordinates();else{var s,u=Te(this.dragElement.participants);try{for(u.s();!(s=u.n()).done;)s.value.changePosition(o,a)}catch(t){u.e(t)}finally{u.f()}this.setAllLinkCoordinates()}this.dragStart=e}else Math.sqrt(o*o+a*a)>5*this.z&&(this.state=t.STATES.DRAGGING)}else this.state===t.STATES.SELECT_PAN&&(this.setCTM(this.container,this.container.getCTM().translate(r.x-i.x,r.y-i.y)),this.dragStart=e)}else this.showTooltip(n)}},{key:"mouseUp",value:function(e){this.preventDefaultsAndStopPropagation(e);var n=(new Date).getTime();if(n-this.lastMouseUp>150&&this.dragElement&&"protein"===this.dragElement.type&&this.state!==t.STATES.DRAGGING&&!this.dragElement.busy)if(this.dragElement.expanded){this.contextMenuProt=this.dragElement;var r=this.getEventPoint(e);this.contextMenuPoint=r.matrixTransform(this.container.getCTM().inverse());var o,a,s=i.select(".custom-menu-margin");e.pageX?(o=e.pageX,a=e.pageY):(o=this.dragStart.touches[0].pageX,a=this.dragStart.touches[0].pageY),s.style("top",a-20+"px").style("left",o-20+"px").style("display","block"),i.select(".scaleButton_"+100*this.dragElement.stickZoom).property("checked",!0)}else this.dragElement.setExpanded(!0),this.notifyExpandListeners();return this.dragElement=null,this.dragStart=null,this.state=t.STATES.MOUSE_UP,this.lastMouseUp=n,!1}},{key:"mouseWheel",value:function(t){this.preventDefaultsAndStopPropagation(t),this.d3cola.stop();var e=1+(t.wheelDelta?t.wheelDelta/3600:t.detail/-90),n=this.container,r=this.getEventPoint(t).matrixTransform(n.getCTM().inverse()),i=this.svgElement.createSVGMatrix().translate(r.x,r.y).scale(e).translate(-r.x,-r.y);return this.setCTM(n,n.getCTM().multiply(i)),!1}},{key:"mouseOut",value:function(){this.hideTooltip()}},{key:"getEventPoint",value:function(t){var e=this.svgElement.createSVGPoint();return e.x=t.pageX-Le(this.el).offset().left,e.y=t.pageY-Le(this.el).offset().top,e}},{key:"preventDefaultsAndStopPropagation",value:function(t){t.stopPropagation&&t.stopPropagation(),null!=t.cancelBubble&&(t.cancelBubble=!0),t.preventDefault&&t.preventDefault()}},{key:"downloadSVG",value:function(t){t||(t="complexViewer");var e=this.getSVG(),n=function(t){var e,n=[];try{e=new TextEncoder("utf-8")}catch(t){e=void 0}if(e)n=e.encode(t);else for(var r=0;r<t.length;r++){var i=t.charCodeAt(r);i<128?n.push(i):i<2048?n.push(192|i>>6,128|63&i):i<55296||i>=57344?n.push(224|i>>12,128|i>>6&63,128|63&i):(r++,i=65536+((1023&i)<<10|1023&t.charCodeAt(r)),n.push(240|i>>18,128|i>>12&63,128|i>>6&63,128|63&i))}return new Blob([new Uint8Array(n)],{type:"image/svg+xml;charset=utf-8"})}(e);if(navigator.msSaveOrOpenBlob)navigator.msSaveOrOpenBlob(n,t);else{var r=document.createElement("a");r.href=window.URL.createObjectURL(n),r.download=t,r.style.display="none",document.body.appendChild(r),r.click(),document.body.removeChild(r),window.URL.revokeObjectURL(r.href)}n=null}}])&&je(e.prototype,n),o&&je(e,o),t}();Ie.STATES={MOUSE_UP:0,SELECT_PAN:1,DRAGGING:2},Ie.barScales=[.01,.2,1,2,4,8]}])}));
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h=[],p=0;c.forEach((function(a){0===a.type?(h.push(a.s),p++):p--,0==p&&(t.nudgeSegs(n,r,e,h,i,o),h=[])}))}},t.prototype.routeEdges=function(e,n,r,i){var o=this,a=e.map((function(t){return o.route(r(t),i(t))})),s=t.orderEdges(a),u=a.map((function(e){return t.makeSegments(e)}));return t.nudgeSegments(u,"x","y",s,n),t.nudgeSegments(u,"y","x",s,n),t.unreverseEdges(u,a),u},t.unreverseEdges=function(t,e){t.forEach((function(t,n){e[n].reversed&&(t.reverse(),t.forEach((function(t){t.reverse()})))}))},t.angleBetween2Lines=function(t,e){var n=Math.atan2(t[0].y-t[1].y,t[0].x-t[1].x),r=Math.atan2(e[0].y-e[1].y,e[0].x-e[1].x),i=n-r;return(i>Math.PI||i<-Math.PI)&&(i=r-n),i},t.isLeft=function(t,e,n){return(e.x-t.x)*(n.y-t.y)-(e.y-t.y)*(n.x-t.x)<=0},t.getOrder=function(t){for(var e={},n=0;n<t.length;n++){var r=t[n];void 0===e[r.l]&&(e[r.l]={}),e[r.l][r.r]=!0}return function(t,n){return void 0!==e[t]&&e[t][n]}},t.orderEdges=function(e){for(var n=[],r=0;r<e.length-1;r++)for(var i=r+1;i<e.length;i++){var 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a||r.node&&r.node.id in a)}));for(var s=1;s<r.ports.length;s++){var u=r.ports[0].id,c=r.ports[s].id;this.passableEdges.push({source:u,target:c,length:0})}for(s=1;s<i.ports.length;s++)u=i.ports[0].id,c=i.ports[s].id,this.passableEdges.push({source:u,target:c,length:0});var l=new o.Calculator(this.verts.length,this.passableEdges,(function(t){return t.source}),(function(t){return t.target}),(function(t){return t.length})).PathFromNodeToNodeWithPrevCost(r.ports[0].id,i.ports[0].id,(function(t,e,o){var a=n.verts[t],s=n.verts[e],u=n.verts[o],c=Math.abs(u.x-a.x),l=Math.abs(u.y-a.y);return a.node===r&&a.node===s.node||s.node===i&&s.node===u.node?0:c>1&&l>1?1e3:0})).reverse().map((function(t){return n.verts[t]}));return l.push(this.nodes[i.id].ports[0]),l.filter((function(t,e){return!(e<l.length-1&&l[e+1].node===r&&t.node===r||e>0&&t.node===i&&l[e-1].node===i)}))},t.getRoutePath=function(e,n,r,i){var o,a,s,u={routepath:"M "+e[0][0].x+" "+e[0][0].y+" ",arrowpath:""};if(e.length>1)for(var c=0;c<e.length;c++){var l=(o=e[c])[1].x,f=o[1].y,h=l-o[0].x,p=f-o[0].y;if(c<e.length-1){Math.abs(h)>0?l-=h/Math.abs(h)*n:f-=p/Math.abs(p)*n,u.routepath+="L "+l+" "+f+" ";var d=e[c+1],y=d[0].x,g=d[0].y;h=d[1].x-y,p=d[1].y-g;var v,x,m=t.angleBetween2Lines(o,d)<0?1:0;Math.abs(h)>0?(v=y+h/Math.abs(h)*n,x=g):(v=y,x=g+p/Math.abs(p)*n);var b=Math.abs(v-l),w=Math.abs(x-f);u.routepath+="A "+b+" "+w+" 0 0 "+m+" "+v+" "+x+" "}else{var k=[l,f];Math.abs(h)>0?(a=[l-=h/Math.abs(h)*i,f+r],s=[l,f-r]):(a=[l+r,f-=p/Math.abs(p)*i],s=[l-r,f]),u.routepath+="L "+l+" "+f+" ",i>0&&(u.arrowpath="M "+k[0]+" "+k[1]+" L "+a[0]+" "+a[1]+" L "+s[0]+" "+s[1])}}else l=(o=e[0])[1].x,f=o[1].y,h=l-o[0].x,p=f-o[0].y,k=[l,f],Math.abs(h)>0?(a=[l-=h/Math.abs(h)*i,f+r],s=[l,f-r]):(a=[l+r,f-=p/Math.abs(p)*i],s=[l-r,f]),u.routepath+="L "+l+" "+f+" ",i>0&&(u.arrowpath="M "+k[0]+" "+k[1]+" L "+a[0]+" "+a[1]+" L "+s[0]+" "+s[1]);return 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n=e.x-t.width/2,r=e.y-t.height/2,i=t.x-n+c/2-f/2,o=t.y-r+l/2-h/2;t.array.forEach((function(t){t.x+=i,t.y+=o}))}))}(t))},n.separateGraphs=function(t,e){for(var n={},r={},i=[],o=0,a=0;a<e.length;a++){var s=e[a],u=s.source,c=s.target;r[u.index]?r[u.index].push(c):r[u.index]=[c],r[c.index]?r[c.index].push(u):r[c.index]=[u]}for(a=0;a<t.length;a++){var l=t[a];n[l.index]||f(l,!0)}function f(t,e){if(void 0===n[t.index]){e&&(o++,i.push({array:[]})),n[t.index]=o,i[o-1].array.push(t);var a=r[t.index];if(a)for(var s=0;s<a.length;s++)f(a[s],!1)}}return i}},{}],11:[function(t,e,n){"use strict";Object.defineProperty(n,"__esModule",{value:!0});var r,i=t("./powergraph"),o=t("./linklengths"),a=t("./descent"),s=t("./rectangle"),u=t("./shortestpaths"),c=t("./geom"),l=t("./handledisconnected");function f(t){return void 0!==t.leaves||void 0!==t.groups}!function(t){t[t.start=0]="start",t[t.tick=1]="tick",t[t.end=2]="end"}(r=n.EventType||(n.EventType={}));var h=function(){function t(){var e=this;this._canvasSize=[1,1],this._linkDistance=20,this._defaultNodeSize=10,this._linkLengthCalculator=null,this._linkType=null,this._avoidOverlaps=!1,this._handleDisconnected=!0,this._running=!1,this._nodes=[],this._groups=[],this._rootGroup=null,this._links=[],this._constraints=[],this._distanceMatrix=null,this._descent=null,this._directedLinkConstraints=null,this._threshold=.01,this._visibilityGraph=null,this._groupCompactness=1e-6,this.event=null,this.linkAccessor={getSourceIndex:t.getSourceIndex,getTargetIndex:t.getTargetIndex,setLength:t.setLinkLength,getType:function(t){return"function"==typeof e._linkType?e._linkType(t):0}}}return t.prototype.on=function(t,e){return this.event||(this.event={}),"string"==typeof t?this.event[r[t]]=e:this.event[t]=e,this},t.prototype.trigger=function(t){this.event&&void 0!==this.event[t.type]&&this.event[t.type](t)},t.prototype.kick=function(){for(;!this.tick(););},t.prototype.tick=function(){if(this._alpha<this._threshold)return this._running=!1,this.trigger({type:r.end,alpha:this._alpha=0,stress:this._lastStress}),!0;var t,e,n=this._nodes.length;for(this._links.length,this._descent.locks.clear(),e=0;e<n;++e)if((t=this._nodes[e]).fixed){void 0!==t.px&&void 0!==t.py||(t.px=t.x,t.py=t.y);var i=[t.px,t.py];this._descent.locks.add(e,i)}var o=this._descent.rungeKutta();return 0===o?this._alpha=0:void 0!==this._lastStress&&(this._alpha=o),this._lastStress=o,this.updateNodePositions(),this.trigger({type:r.tick,alpha:this._alpha,stress:this._lastStress}),!1},t.prototype.updateNodePositions=function(){for(var t,e=this._descent.x[0],n=this._descent.x[1],r=this._nodes.length;r--;)(t=this._nodes[r]).x=e[r],t.y=n[r]},t.prototype.nodes=function(t){if(!t){if(0===this._nodes.length&&this._links.length>0){var e=0;this._links.forEach((function(t){e=Math.max(e,t.source,t.target)})),this._nodes=new Array(++e);for(var n=0;n<e;++n)this._nodes[n]={}}return this._nodes}return this._nodes=t,this},t.prototype.groups=function(t){var e=this;return t?(this._groups=t,this._rootGroup={},this._groups.forEach((function(t){void 0===t.padding&&(t.padding=1),void 0!==t.leaves&&t.leaves.forEach((function(n,r){"number"==typeof n&&((t.leaves[r]=e._nodes[n]).parent=t)})),void 0!==t.groups&&t.groups.forEach((function(n,r){"number"==typeof n&&((t.groups[r]=e._groups[n]).parent=t)}))})),this._rootGroup.leaves=this._nodes.filter((function(t){return void 0===t.parent})),this._rootGroup.groups=this._groups.filter((function(t){return void 0===t.parent})),this):this._groups},t.prototype.powerGraphGroups=function(t){var e=i.getGroups(this._nodes,this._links,this.linkAccessor,this._rootGroup);return this.groups(e.groups),t(e),this},t.prototype.avoidOverlaps=function(t){return arguments.length?(this._avoidOverlaps=t,this):this._avoidOverlaps},t.prototype.handleDisconnected=function(t){return arguments.length?(this._handleDisconnected=t,this):this._handleDisconnected},t.prototype.flowLayout=function(t,e){return arguments.length||(t="y"),this._directedLinkConstraints={axis:t,getMinSeparation:"number"==typeof e?function(){return e}:e},this},t.prototype.links=function(t){return arguments.length?(this._links=t,this):this._links},t.prototype.constraints=function(t){return arguments.length?(this._constraints=t,this):this._constraints},t.prototype.distanceMatrix=function(t){return arguments.length?(this._distanceMatrix=t,this):this._distanceMatrix},t.prototype.size=function(t){return t?(this._canvasSize=t,this):this._canvasSize},t.prototype.defaultNodeSize=function(t){return t?(this._defaultNodeSize=t,this):this._defaultNodeSize},t.prototype.groupCompactness=function(t){return t?(this._groupCompactness=t,this):this._groupCompactness},t.prototype.linkDistance=function(t){return t?(this._linkDistance="function"==typeof t?t:+t,this._linkLengthCalculator=null,this):this._linkDistance},t.prototype.linkType=function(t){return this._linkType=t,this},t.prototype.convergenceThreshold=function(t){return t?(this._threshold="function"==typeof t?t:+t,this):this._threshold},t.prototype.alpha=function(t){return arguments.length?(t=+t,this._alpha?this._alpha=t>0?t:0:t>0&&(this._running||(this._running=!0,this.trigger({type:r.start,alpha:this._alpha=t}),this.kick())),this):this._alpha},t.prototype.getLinkLength=function(t){return"function"==typeof this._linkDistance?+this._linkDistance(t):this._linkDistance},t.setLinkLength=function(t,e){t.length=e},t.prototype.getLinkType=function(t){return"function"==typeof this._linkType?this._linkType(t):0},t.prototype.symmetricDiffLinkLengths=function(t,e){var n=this;return void 0===e&&(e=1),this.linkDistance((function(e){return t*e.length})),this._linkLengthCalculator=function(){return o.symmetricDiffLinkLengths(n._links,n.linkAccessor,e)},this},t.prototype.jaccardLinkLengths=function(t,e){var n=this;return void 0===e&&(e=1),this.linkDistance((function(e){return t*e.length})),this._linkLengthCalculator=function(){return o.jaccardLinkLengths(n._links,n.linkAccessor,e)},this},t.prototype.start=function(e,n,r,i,c,l){var f=this;void 0===e&&(e=0),void 0===n&&(n=0),void 0===r&&(r=0),void 0===i&&(i=0),void 0===c&&(c=!0),void 0===l&&(l=!0);var h,p=this.nodes().length,d=p+2*this._groups.length,y=(this._links.length,this._canvasSize[0]),g=this._canvasSize[1],v=new Array(d),x=new Array(d),m=null,b=this._avoidOverlaps;this._nodes.forEach((function(t,e){t.index=e,void 0===t.x&&(t.x=y/2,t.y=g/2),v[e]=t.x,x[e]=t.y})),this._linkLengthCalculator&&this._linkLengthCalculator(),this._distanceMatrix?h=this._distanceMatrix:(h=new u.Calculator(d,this._links,t.getSourceIndex,t.getTargetIndex,(function(t){return f.getLinkLength(t)})).DistanceMatrix(),m=a.Descent.createSquareMatrix(d,(function(){return 2})),this._links.forEach((function(t){"number"==typeof t.source&&(t.source=f._nodes[t.source]),"number"==typeof t.target&&(t.target=f._nodes[t.target])})),this._links.forEach((function(e){var n=t.getSourceIndex(e),r=t.getTargetIndex(e);m[n][r]=m[r][n]=e.weight||1})));var w=a.Descent.createSquareMatrix(d,(function(t,e){return h[t][e]}));if(this._rootGroup&&void 0!==this._rootGroup.groups){var k=p;this._groups.forEach((function(t){!function(t,e,n,r){m[t][e]=m[e][t]=n,w[t][e]=w[e][t]=r}(k,k+1,f._groupCompactness,.1),void 0===t.bounds?(v[k]=y/2,x[k++]=g/2,v[k]=y/2,x[k++]=g/2):(v[k]=t.bounds.x,x[k++]=t.bounds.y,v[k]=t.bounds.X,x[k++]=t.bounds.Y)}))}else this._rootGroup={leaves:this._nodes,groups:[]};var S=this._constraints||[];for(this._directedLinkConstraints&&(this.linkAccessor.getMinSeparation=this._directedLinkConstraints.getMinSeparation,S=S.concat(o.generateDirectedEdgeConstraints(p,this._links,this._directedLinkConstraints.axis,this.linkAccessor))),this.avoidOverlaps(!1),this._descent=new a.Descent([v,x],w),this._descent.locks.clear(),k=0;k<p;++k){var _=this._nodes[k];if(_.fixed){_.px=_.x,_.py=_.y;var M=[_.x,_.y];this._descent.locks.add(k,M)}}if(this._descent.threshold=this._threshold,this.initialLayout(e,v,x),S.length>0&&(this._descent.project=new s.Projection(this._nodes,this._groups,this._rootGroup,S).projectFunctions()),this._descent.run(n),this.separateOverlappingComponents(y,g,l),this.avoidOverlaps(b),b&&(this._nodes.forEach((function(t,e){t.x=v[e],t.y=x[e]})),this._descent.project=new s.Projection(this._nodes,this._groups,this._rootGroup,S,!0).projectFunctions(),this._nodes.forEach((function(t,e){v[e]=t.x,x[e]=t.y}))),this._descent.G=m,this._descent.run(r),i){this._descent.snapStrength=1e3,this._descent.snapGridSize=this._nodes[0].width,this._descent.numGridSnapNodes=p,this._descent.scaleSnapByMaxH=p!=d;var E=a.Descent.createSquareMatrix(d,(function(t,e){return t>=p||e>=p?m[t][e]:0}));this._descent.G=E,this._descent.run(i)}return this.updateNodePositions(),this.separateOverlappingComponents(y,g,l),c?this.resume():this},t.prototype.initialLayout=function(e,n,r){if(this._groups.length>0&&e>0){var i=this._nodes.length,o=this._links.map((function(t){return{source:t.source.index,target:t.target.index}})),a=this._nodes.map((function(t){return{index:t.index}}));this._groups.forEach((function(t,e){a.push({index:t.index=i+e})})),this._groups.forEach((function(t,e){void 0!==t.leaves&&t.leaves.forEach((function(e){return o.push({source:t.index,target:e.index})})),void 0!==t.groups&&t.groups.forEach((function(e){return o.push({source:t.index,target:e.index})}))})),(new t).size(this.size()).nodes(a).links(o).avoidOverlaps(!1).linkDistance(this.linkDistance()).symmetricDiffLinkLengths(5).convergenceThreshold(1e-4).start(e,0,0,0,!1),this._nodes.forEach((function(t){n[t.index]=a[t.index].x,r[t.index]=a[t.index].y}))}else this._descent.run(e)},t.prototype.separateOverlappingComponents=function(t,e,n){var r=this;if(void 0===n&&(n=!0),!this._distanceMatrix&&this._handleDisconnected){var i=this._descent.x[0],o=this._descent.x[1];this._nodes.forEach((function(t,e){t.x=i[e],t.y=o[e]}));var a=l.separateGraphs(this._nodes,this._links);l.applyPacking(a,t,e,this._defaultNodeSize,e/t,n),this._nodes.forEach((function(t,e){r._descent.x[0][e]=t.x,r._descent.x[1][e]=t.y,t.bounds&&(t.bounds.setXCentre(t.x),t.bounds.setYCentre(t.y))}))}},t.prototype.resume=function(){return this.alpha(.1)},t.prototype.stop=function(){return this.alpha(0)},t.prototype.prepareEdgeRouting=function(t){void 0===t&&(t=0),this._visibilityGraph=new c.TangentVisibilityGraph(this._nodes.map((function(e){return e.bounds.inflate(-t).vertices()})))},t.prototype.routeEdge=function(t,e,n){void 0===e&&(e=5);var r=[],i=new c.TangentVisibilityGraph(this._visibilityGraph.P,{V:this._visibilityGraph.V,E:this._visibilityGraph.E}),o={x:t.source.x,y:t.source.y},a={x:t.target.x,y:t.target.y},l=i.addPoint(o,t.source.index),f=i.addPoint(a,t.target.index);i.addEdgeIfVisible(o,a,t.source.index,t.target.index),void 0!==n&&n(i);var h=new u.Calculator(i.V.length,i.E,(function(t){return t.source.id}),(function(t){return t.target.id}),(function(t){return t.length()})).PathFromNodeToNode(l.id,f.id);if(1===h.length||h.length===i.V.length){var p=s.makeEdgeBetween(t.source.innerBounds,t.target.innerBounds,e);r=[p.sourceIntersection,p.arrowStart]}else{for(var d=h.length-2,y=i.V[h[d]].p,g=i.V[h[0]].p,v=(r=[t.source.innerBounds.rayIntersection(y.x,y.y)],d);v>=0;--v)r.push(i.V[h[v]].p);r.push(s.makeEdgeTo(g,t.target.innerBounds,e))}return r},t.getSourceIndex=function(t){return"number"==typeof t.source?t.source:t.source.index},t.getTargetIndex=function(t){return"number"==typeof t.target?t.target:t.target.index},t.linkId=function(e){return t.getSourceIndex(e)+"-"+t.getTargetIndex(e)},t.dragStart=function(e){f(e)?t.storeOffset(e,t.dragOrigin(e)):(t.stopNode(e),e.fixed|=2)},t.stopNode=function(t){t.px=t.x,t.py=t.y},t.storeOffset=function(e,n){void 0!==e.leaves&&e.leaves.forEach((function(e){e.fixed|=2,t.stopNode(e),e._dragGroupOffsetX=e.x-n.x,e._dragGroupOffsetY=e.y-n.y})),void 0!==e.groups&&e.groups.forEach((function(e){return t.storeOffset(e,n)}))},t.dragOrigin=function(t){return f(t)?{x:t.bounds.cx(),y:t.bounds.cy()}:t},t.drag=function(e,n){f(e)?(void 0!==e.leaves&&e.leaves.forEach((function(t){e.bounds.setXCentre(n.x),e.bounds.setYCentre(n.y),t.px=t._dragGroupOffsetX+n.x,t.py=t._dragGroupOffsetY+n.y})),void 0!==e.groups&&e.groups.forEach((function(e){return t.drag(e,n)}))):(e.px=n.x,e.py=n.y)},t.dragEnd=function(e){f(e)?(void 0!==e.leaves&&e.leaves.forEach((function(e){t.dragEnd(e),delete e._dragGroupOffsetX,delete e._dragGroupOffsetY})),void 0!==e.groups&&e.groups.forEach(t.dragEnd)):e.fixed&=-7},t.mouseOver=function(t){t.fixed|=4,t.px=t.x,t.py=t.y},t.mouseOut=function(t){t.fixed&=-5},t}();n.Layout=h},{"./descent":7,"./geom":8,"./handledisconnected":10,"./linklengths":13,"./powergraph":14,"./rectangle":17,"./shortestpaths":18}],12:[function(t,e,n){"use strict";Object.defineProperty(n,"__esModule",{value:!0});var r=t("./shortestpaths"),i=t("./descent"),o=t("./rectangle"),a=t("./linklengths"),s=function(){function t(t,e){this.source=t,this.target=e}return t.prototype.actualLength=function(t){var e=this;return Math.sqrt(t.reduce((function(t,n){var r=n[e.target]-n[e.source];return t+r*r}),0))},t}();n.Link3D=s;var u=function(t,e,n){void 0===t&&(t=0),void 0===e&&(e=0),void 0===n&&(n=0),this.x=t,this.y=e,this.z=n};n.Node3D=u;var c=function(){function t(e,n,r){var i=this;void 0===r&&(r=1),this.nodes=e,this.links=n,this.idealLinkLength=r,this.constraints=null,this.useJaccardLinkLengths=!0,this.result=new Array(t.k);for(var o=0;o<t.k;++o)this.result[o]=new Array(e.length);e.forEach((function(e,n){for(var r=0,o=t.dims;r<o.length;r++){var a=o[r];void 0===e[a]&&(e[a]=Math.random())}i.result[0][n]=e.x,i.result[1][n]=e.y,i.result[2][n]=e.z}))}return t.prototype.linkLength=function(t){return t.actualLength(this.result)},t.prototype.start=function(t){var e=this;void 0===t&&(t=100);var n=this.nodes.length,s=new l;this.useJaccardLinkLengths&&a.jaccardLinkLengths(this.links,s,1.5),this.links.forEach((function(t){return t.length*=e.idealLinkLength}));var u=new r.Calculator(n,this.links,(function(t){return t.source}),(function(t){return t.target}),(function(t){return t.length})).DistanceMatrix(),c=i.Descent.createSquareMatrix(n,(function(t,e){return u[t][e]})),f=i.Descent.createSquareMatrix(n,(function(){return 2}));this.links.forEach((function(t){var e=t.source,n=t.target;return f[e][n]=f[n][e]=1})),this.descent=new i.Descent(this.result,c),this.descent.threshold=.001,this.descent.G=f,this.constraints&&(this.descent.project=new o.Projection(this.nodes,null,null,this.constraints).projectFunctions());for(var h=0;h<this.nodes.length;h++){var p=this.nodes[h];p.fixed&&this.descent.locks.add(h,[p.x,p.y,p.z])}return this.descent.run(t),this},t.prototype.tick=function(){this.descent.locks.clear();for(var t=0;t<this.nodes.length;t++){var e=this.nodes[t];e.fixed&&this.descent.locks.add(t,[e.x,e.y,e.z])}return this.descent.rungeKutta()},t.dims=["x","y","z"],t.k=t.dims.length,t}();n.Layout3D=c;var l=function(){function t(){}return t.prototype.getSourceIndex=function(t){return t.source},t.prototype.getTargetIndex=function(t){return t.target},t.prototype.getLength=function(t){return t.length},t.prototype.setLength=function(t,e){t.length=e},t}()},{"./descent":7,"./linklengths":13,"./rectangle":17,"./shortestpaths":18}],13:[function(t,e,n){"use strict";function r(t,e){var n={};for(var r in t)n[r]={};for(var r in e)n[r]={};return Object.keys(n).length}function i(t,e){var n=0;for(var r in t)void 0!==e[r]&&++n;return n}function o(t,e,n,r){var i=function(t,e){var n={},r=function(t,e){void 0===n[t]&&(n[t]={}),n[t][e]={}};return t.forEach((function(t){var n=e.getSourceIndex(t),i=e.getTargetIndex(t);r(n,i),r(i,n)})),n}(t,r);t.forEach((function(t){var o=i[r.getSourceIndex(t)],a=i[r.getTargetIndex(t)];r.setLength(t,1+e*n(o,a))}))}function a(t,e,n){var r=[],i=0,o=[],a=[];function s(t){t.index=t.lowlink=i++,o.push(t),t.onStack=!0;for(var e=0,n=t.out;e<n.length;e++){var r=n[e];void 0===r.index?(s(r),t.lowlink=Math.min(t.lowlink,r.lowlink)):r.onStack&&(t.lowlink=Math.min(t.lowlink,r.index))}if(t.lowlink===t.index){for(var u=[];o.length&&((r=o.pop()).onStack=!1,u.push(r),r!==t););a.push(u.map((function(t){return t.id})))}}for(var u=0;u<t;u++)r.push({id:u,out:[]});for(var c=0,l=e;c<l.length;c++){var f=l[c],h=r[n.getSourceIndex(f)],p=r[n.getTargetIndex(f)];h.out.push(p)}for(var d=0,y=r;d<y.length;d++){var g=y[d];void 0===g.index&&s(g)}return a}Object.defineProperty(n,"__esModule",{value:!0}),n.symmetricDiffLinkLengths=function(t,e,n){void 0===n&&(n=1),o(t,n,(function(t,e){return Math.sqrt(r(t,e)-i(t,e))}),e)},n.jaccardLinkLengths=function(t,e,n){void 0===n&&(n=1),o(t,n,(function(t,e){return Math.min(Object.keys(t).length,Object.keys(e).length)<1.1?0:i(t,e)/r(t,e)}),e)},n.generateDirectedEdgeConstraints=function(t,e,n,r){var i=a(t,e,r),o={};i.forEach((function(t,e){return t.forEach((function(t){return o[t]=e}))}));var s=[];return e.forEach((function(t){var e=r.getSourceIndex(t),i=r.getTargetIndex(t);o[e]!==o[i]&&s.push({axis:n,left:e,right:i,gap:r.getMinSeparation(t)})})),s},n.stronglyConnectedComponents=a},{}],14:[function(t,e,n){"use strict";Object.defineProperty(n,"__esModule",{value:!0});var r=function(t,e,n){this.source=t,this.target=e,this.type=n};n.PowerEdge=r;var i=function(){function t(t,e,n,r){var i=this;if(this.linkAccessor=n,this.modules=new Array(t),this.roots=[],r)this.initModulesFromGroup(r);else{this.roots.push(new s);for(var a=0;a<t;++a)this.roots[0].add(this.modules[a]=new o(a))}this.R=e.length,e.forEach((function(t){var e=i.modules[n.getSourceIndex(t)],r=i.modules[n.getTargetIndex(t)],o=n.getType(t);e.outgoing.add(o,r),r.incoming.add(o,e)}))}return t.prototype.initModulesFromGroup=function(t){var e=new s;this.roots.push(e);for(var n=0;n<t.leaves.length;++n){var r=t.leaves[n],i=new o(r.id);this.modules[r.id]=i,e.add(i)}if(t.groups)for(var a=0;a<t.groups.length;++a){var c=t.groups[a],l={};for(var f in c)"leaves"!==f&&"groups"!==f&&c.hasOwnProperty(f)&&(l[f]=c[f]);e.add(new o(-1-a,new u,new u,this.initModulesFromGroup(c),l))}return e},t.prototype.merge=function(t,e,n){void 0===n&&(n=0);var r=t.incoming.intersection(e.incoming),i=t.outgoing.intersection(e.outgoing),a=new s;a.add(t),a.add(e);var u=new o(this.modules.length,i,r,a);this.modules.push(u);var c=function(n,r,i){n.forAll((function(n,o){n.forAll((function(n){var a=n[r];a.add(o,u),a.remove(o,t),a.remove(o,e),t[i].remove(o,n),e[i].remove(o,n)}))}))};return c(i,"incoming","outgoing"),c(r,"outgoing","incoming"),this.R-=r.count()+i.count(),this.roots[n].remove(t),this.roots[n].remove(e),this.roots[n].add(u),u},t.prototype.rootMerges=function(t){void 0===t&&(t=0);for(var e=this.roots[t].modules(),n=e.length,r=new Array(n*(n-1)),i=0,o=0,a=n-1;o<a;++o)for(var s=o+1;s<n;++s){var u=e[o],c=e[s];r[i]={id:i,nEdges:this.nEdges(u,c),a:u,b:c},i++}return r},t.prototype.greedyMerge=function(){for(var t=0;t<this.roots.length;++t)if(!(this.roots[t].modules().length<2)){var e=this.rootMerges(t).sort((function(t,e){return t.nEdges==e.nEdges?t.id-e.id:t.nEdges-e.nEdges}))[0];if(!(e.nEdges>=this.R))return this.merge(e.a,e.b,t),!0}},t.prototype.nEdges=function(t,e){var n=t.incoming.intersection(e.incoming),r=t.outgoing.intersection(e.outgoing);return this.R-n.count()-r.count()},t.prototype.getGroupHierarchy=function(t){var e=this,n=[];return function t(e,n,r){e.forAll((function(e){if(e.isLeaf())n.leaves||(n.leaves=[]),n.leaves.push(e.id);else{var i=n;if(e.gid=r.length,!e.isIsland()||e.isPredefined()){if(i={id:e.gid},e.isPredefined())for(var o in e.definition)i[o]=e.definition[o];n.groups||(n.groups=[]),n.groups.push(e.gid),r.push(i)}t(e.children,i,r)}}))}(this.roots[0],{},n),this.allEdges().forEach((function(i){var o=e.modules[i.source],a=e.modules[i.target];t.push(new r(void 0===o.gid?i.source:n[o.gid],void 0===a.gid?i.target:n[a.gid],i.type))})),n},t.prototype.allEdges=function(){var e=[];return t.getEdges(this.roots[0],e),e},t.getEdges=function(e,n){e.forAll((function(e){e.getEdges(n),t.getEdges(e.children,n)}))},t}();n.Configuration=i;var o=function(){function t(t,e,n,r,i){void 0===e&&(e=new u),void 0===n&&(n=new u),void 0===r&&(r=new s),this.id=t,this.outgoing=e,this.incoming=n,this.children=r,this.definition=i}return t.prototype.getEdges=function(t){var e=this;this.outgoing.forAll((function(n,i){n.forAll((function(n){t.push(new r(e.id,n.id,i))}))}))},t.prototype.isLeaf=function(){return 0===this.children.count()},t.prototype.isIsland=function(){return 0===this.outgoing.count()&&0===this.incoming.count()},t.prototype.isPredefined=function(){return void 0!==this.definition},t}();function a(t,e){var n={};for(var r in t)r in e&&(n[r]=t[r]);return n}n.Module=o;var s=function(){function t(){this.table={}}return t.prototype.count=function(){return Object.keys(this.table).length},t.prototype.intersection=function(e){var n=new t;return n.table=a(this.table,e.table),n},t.prototype.intersectionCount=function(t){return this.intersection(t).count()},t.prototype.contains=function(t){return t in this.table},t.prototype.add=function(t){this.table[t.id]=t},t.prototype.remove=function(t){delete this.table[t.id]},t.prototype.forAll=function(t){for(var e in this.table)t(this.table[e])},t.prototype.modules=function(){var t=[];return 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null;for(;null!==t.left;)t=t.left;return t.data},t.prototype.max=function(){var t=this._root;if(null===t)return null;for(;null!==t.right;)t=t.right;return t.data},t.prototype.iterator=function(){return new a(this)},t.prototype.each=function(t){for(var e,n=this.iterator();null!==(e=n.next());)t(e)},t.prototype.reach=function(t){for(var e,n=this.iterator();null!==(e=n.prev());)t(e)},t.prototype._bound=function(t,e){for(var n=this._root,r=this.iterator();null!==n;){var i=this._comparator(t,n.data);if(0===i)return r._cursor=n,r;r._ancestors.push(n),n=n.get_child(i>0)}for(var o=r._ancestors.length-1;o>=0;--o)if(e(t,(n=r._ancestors[o]).data)>0)return r._cursor=n,r._ancestors.length=o,r;return r._ancestors.length=0,r},t}();n.TreeBase=o;var a=function(){function t(t){this._tree=t,this._ancestors=[],this._cursor=null}return t.prototype.data=function(){return null!==this._cursor?this._cursor.data:null},t.prototype.next=function(){if(null===this._cursor){var 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r=t("./pqueue"),i=function(t,e){this.id=t,this.distance=e},o=function(t){this.id=t,this.neighbours=[]},a=function(t,e,n){this.node=t,this.prev=e,this.d=n},s=function(){function t(t,e,n,r,a){this.n=t,this.es=e,this.neighbours=new Array(this.n);for(var s=this.n;s--;)this.neighbours[s]=new o(s);for(s=this.es.length;s--;){var u=this.es[s],c=n(u),l=r(u),f=a(u);this.neighbours[c].neighbours.push(new i(l,f)),this.neighbours[l].neighbours.push(new i(c,f))}}return t.prototype.DistanceMatrix=function(){for(var t=new Array(this.n),e=0;e<this.n;++e)t[e]=this.dijkstraNeighbours(e);return t},t.prototype.DistancesFromNode=function(t){return this.dijkstraNeighbours(t)},t.prototype.PathFromNodeToNode=function(t,e){return this.dijkstraNeighbours(t,e)},t.prototype.PathFromNodeToNodeWithPrevCost=function(t,e,n){var i=new r.PriorityQueue((function(t,e){return t.d<=e.d})),o=this.neighbours[t],s=new a(o,null,0),u={};for(i.push(s);!i.empty()&&(o=(s=i.pop()).node).id!==e;)for(var 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2*this.weight*(this.position()-this.desiredPosition)},t.prototype.position=function(){return(this.block.ps.scale*this.block.posn+this.offset)/this.scale},t.prototype.visitNeighbours=function(t,e){var n=function(n,r){return n.active&&t!==r&&e(n,r)};this.cOut.forEach((function(t){return n(t,t.right)})),this.cIn.forEach((function(t){return n(t,t.left)}))},t}();n.Variable=o;var a=function(){function t(t){this.vars=[],t.offset=0,this.ps=new r(t.scale),this.addVariable(t)}return t.prototype.addVariable=function(t){t.block=this,this.vars.push(t),this.ps.addVariable(t),this.posn=this.ps.getPosn()},t.prototype.updateWeightedPosition=function(){this.ps.AB=this.ps.AD=this.ps.A2=0;for(var t=0,e=this.vars.length;t<e;++t)this.ps.addVariable(this.vars[t]);this.posn=this.ps.getPosn()},t.prototype.compute_lm=function(t,e,n){var r=this,i=t.dfdv();return t.visitNeighbours(e,(function(e,o){var a=r.compute_lm(o,t,n);o===e.right?(i+=a*e.left.scale,e.lm=a):(i+=a*e.right.scale,e.lm=-a),n(e)})),i/t.scale},t.prototype.populateSplitBlock=function(t,e){var n=this;t.visitNeighbours(e,(function(e,r){r.offset=t.offset+(r===e.right?e.gap:-e.gap),n.addVariable(r),n.populateSplitBlock(r,t)}))},t.prototype.traverse=function(t,e,n,r){var i=this;void 0===n&&(n=this.vars[0]),void 0===r&&(r=null),n.visitNeighbours(r,(function(r,o){e.push(t(r)),i.traverse(t,e,o,n)}))},t.prototype.findMinLM=function(){var t=null;return this.compute_lm(this.vars[0],null,(function(e){!e.equality&&(null===t||e.lm<t.lm)&&(t=e)})),t},t.prototype.findMinLMBetween=function(t,e){this.compute_lm(t,null,(function(){}));var n=null;return this.findPath(t,null,e,(function(t,e){!t.equality&&t.right===e&&(null===n||t.lm<n.lm)&&(n=t)})),n},t.prototype.findPath=function(t,e,n,r){var i=this,o=!1;return t.visitNeighbours(e,(function(e,a){o||a!==n&&!i.findPath(a,t,n,r)||(o=!0,r(e,a))})),o},t.prototype.isActiveDirectedPathBetween=function(t,e){if(t===e)return!0;for(var n=t.cOut.length;n--;){var r=t.cOut[n];if(r.active&&this.isActiveDirectedPathBetween(r.right,e))return!0}return!1},t.split=function(e){return e.active=!1,[t.createSplitBlock(e.left),t.createSplitBlock(e.right)]},t.createSplitBlock=function(e){var n=new t(e);return n.populateSplitBlock(e,null),n},t.prototype.splitBetween=function(e,n){var r=this.findMinLMBetween(e,n);if(null!==r){var i=t.split(r);return{constraint:r,lb:i[0],rb:i[1]}}return null},t.prototype.mergeAcross=function(t,e,n){e.active=!0;for(var r=0,i=t.vars.length;r<i;++r){var o=t.vars[r];o.offset+=n,this.addVariable(o)}this.posn=this.ps.getPosn()},t.prototype.cost=function(){for(var t=0,e=this.vars.length;e--;){var n=this.vars[e],r=n.position()-n.desiredPosition;t+=r*r*n.weight}return t},t}();n.Block=a;var s=function(){function t(t){this.vs=t;var e=t.length;for(this.list=new Array(e);e--;){var n=new a(t[e]);this.list[e]=n,n.blockInd=e}}return t.prototype.cost=function(){for(var t=0,e=this.list.length;e--;)t+=this.list[e].cost();return t},t.prototype.insert=function(t){t.blockInd=this.list.length,this.list.push(t)},t.prototype.remove=function(t){var e=this.list.length-1,n=this.list[e];this.list.length=e,t!==n&&(this.list[t.blockInd]=n,n.blockInd=t.blockInd)},t.prototype.merge=function(t){var e=t.left.block,n=t.right.block,r=t.right.offset-t.left.offset-t.gap;e.vars.length<n.vars.length?(n.mergeAcross(e,t,r),this.remove(e)):(e.mergeAcross(n,t,-r),this.remove(n))},t.prototype.forEach=function(t){this.list.forEach(t)},t.prototype.updateBlockPositions=function(){this.list.forEach((function(t){return t.updateWeightedPosition()}))},t.prototype.split=function(t){var e=this;this.updateBlockPositions(),this.list.forEach((function(n){var r=n.findMinLM();null!==r&&r.lm<u.LAGRANGIAN_TOLERANCE&&(n=r.left.block,a.split(r).forEach((function(t){return e.insert(t)})),e.remove(n),t.push(r))}))},t}();n.Blocks=s;var u=function(){function t(t,e){this.vs=t,this.cs=e,this.vs=t,t.forEach((function(t){t.cIn=[],t.cOut=[]})),this.cs=e,e.forEach((function(t){t.left.cOut.push(t),t.right.cIn.push(t)})),this.inactive=e.map((function(t){return t.active=!1,t})),this.bs=null}return t.prototype.cost=function(){return this.bs.cost()},t.prototype.setStartingPositions=function(t){this.inactive=this.cs.map((function(t){return t.active=!1,t})),this.bs=new s(this.vs),this.bs.forEach((function(e,n){return e.posn=t[n]}))},t.prototype.setDesiredPositions=function(t){this.vs.forEach((function(e,n){return e.desiredPosition=t[n]}))},t.prototype.mostViolated=function(){for(var e=Number.MAX_VALUE,n=null,r=this.inactive,i=r.length,o=i,a=0;a<i;++a){var s=r[a];if(!s.unsatisfiable){var u=s.slack();if((s.equality||u<e)&&(e=u,n=s,o=a,s.equality))break}}return 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d=this;i.select(this.ticks).transition().attr("opacity",0).duration(s/4).each("end",(function(){i.select(this).selectAll("*").remove()}));var y=this.stickZoom,g=this.rotation,v=i.ease("cubic-in-out");if(t){var x,m=k(this.annotationSets);try{for(m.s();!(x=m.n()).done;){var b=w(x.value,2),S=b[0],_=b[1];if(!0===this.app.annotationSetsShown.get(S)){var M,E=k(_);try{for(E.s();!(M=E.n()).done;){var A=M.value;if(A.fuzzyStart){var C=A.fuzzyStart;i.select(C).transition().attr("d",this.getAnnotationPieSlicePath(A.seqDatum.uncertainBegin,A.seqDatum.begin,A,!1)).duration(s)}if(A.certain){var L=A.certain;i.select(L).transition().attr("d",this.getAnnotationPieSlicePath(A.seqDatum.begin,A.seqDatum.end,A,!1)).duration(s)}if(A.fuzzyEnd){var N=A.fuzzyEnd;i.select(N).transition().attr("d",this.getAnnotationPieSlicePath(A.seqDatum.end,A.seqDatum.uncertainEnd,A,!1)).duration(s)}}}catch(t){E.e(t)}finally{E.f()}}}}catch(t){m.e(t)}finally{m.f()}i.timer((function(t){return T(t/s)}))}else T(1);function T(t){var e=i.transform(d.labelSVG.getAttribute("transform")),n=d.app.svgElement.createSVGMatrix().rotate(e.rotate).translate(h(v(t)),d.labelY);if(d.labelSVG.transform.baseVal.initialize(d.app.svgElement.createSVGTransformFromMatrix(n)),null!==p&&d.setPosition(p(v(t)),d.iy),d.stickZoom=c(v(t)),d.setAllLinkCoordinates(),1===t){d.expanded=!1,d.checkLinks();var r,o=k(d.annotationSets);try{for(o.s();!(r=o.n()).done;){var a=w(r.value,2),s=a[0],u=a[1];if(!0===d.app.annotationSetsShown.get(s)){var l,f=k(u);try{for(f.s();!(l=f.n()).done;){var x=l.value;if(x.fuzzyStart){var m=x.fuzzyStart;i.select(m).attr("d",d.getAnnotationPieSlicePath(x.seqDatum.uncertainBegin,x.seqDatum.begin,x))}if(x.certain){var b=x.certain;i.select(b).attr("d",d.getAnnotationPieSlicePath(x.seqDatum.begin,x.seqDatum.end,x))}if(x.fuzzyEnd){var S=x.fuzzyEnd;i.select(S).attr("d",d.getAnnotationPieSlicePath(x.seqDatum.end,x.seqDatum.uncertainEnd,x))}}}catch(t){f.e(t)}finally{f.f()}}}}catch(t){o.e(t)}finally{o.f()}return d.stickZoom=y,d.rotation=g,d.busy=!1,!0}return!!(t>1||isNaN(t))&&T(1)}}},{key:"toStick",value:function(){var t=!(arguments.length>0&&void 0!==arguments[0])||arguments[0],e=t?a.transitionTime:0;this.busy=!0,this.expanded=!0,this.postAnimExpanded=!0;var n=this.size*this.stickZoom,r=this.getSymbolRadius(),o=i.interpolate(2*r,n),s=i.interpolate(0,this.stickZoom),u=i.interpolate(-(r+5),-(this.size/2*this.stickZoom+(this.nTermFeatures.length>0?25:10))),c=this.stickZoom;this.stickZoom=0,this.checkLinks(),this.stickZoom=c,i.select(this.background).transition().attr("height",a.STICKHEIGHT).attr("y",-a.STICKHEIGHT/2).attr("rx",0).attr("ry",0).duration(e),i.select(this.outline).transition().attr("height",a.STICKHEIGHT).attr("y",-a.STICKHEIGHT/2).attr("rx",0).attr("ry",0).duration(e),i.select(this.highlight).transition().attr("width",n+5).attr("height",a.STICKHEIGHT+5).attr("x",this.getResXWithStickZoom(.5)-2.5).attr("y",-a.STICKHEIGHT/2-2.5).attr("rx",0).attr("ry",0).duration(e);var l=this,f=i.ease("cubic-in-out");if(t){var h,p=k(this.annotationSets);try{for(p.s();!(h=p.n()).done;){var d=w(h.value,2),y=d[0],g=d[1];if(!0===this.app.annotationSetsShown.get(y)){var v,x=k(g);try{for(x.s();!(v=x.n()).done;){var m=v.value;if(m.fuzzyStart){var b=m.fuzzyStart;b.setAttribute("d",this.getAnnotationPieSlicePath(m.seqDatum.uncertainBegin,m.seqDatum.begin,m,!1)),i.select(b).transition().attr("d",this.getAnnotationRectPath(m.seqDatum.uncertainBegin,m.seqDatum.begin,m)).duration(a.transitionTime)}if(m.certain){var S=m.certain,_=m.seqDatum.begin,M=m.seqDatum.end;m.seqDatum.uncertainBegin&&(_+=1),m.seqDatum.uncertainEnd&&(M-=1),S.setAttribute("d",this.getAnnotationPieSlicePath(_,M,m,!1)),i.select(S).transition().attr("d",this.getAnnotationRectPath(_,M,m)).duration(a.transitionTime)}if(m.fuzzyEnd){var E=m.fuzzyEnd;E.setAttribute("d",this.getAnnotationPieSlicePath(m.seqDatum.end,m.seqDatum.uncertainEnd,m,!1)),i.select(E).transition().attr("d",this.getAnnotationRectPath(m.seqDatum.end,m.seqDatum.uncertainEnd,m)).duration(a.transitionTime)}}}catch(t){x.e(t)}finally{x.f()}}}}catch(t){p.e(t)}finally{p.f()}i.timer((function(t){return A(t/e)}))}else A(1);function A(t){var e=i.transform(l.labelSVG.getAttribute("transform")),n=l.app.svgElement.createSVGMatrix().rotate(e.rotate).translate(u(f(t)),l.labelY);l.labelSVG.transform.baseVal.initialize(l.app.svgElement.createSVGTransformFromMatrix(n));var r=o(f(t));return i.select(l.highlight).attr("width",r).attr("x",-r/2+.5*l.stickZoom),i.select(l.outline).attr("width",r).attr("x",-r/2+.5*l.stickZoom),i.select(l.background).attr("width",r).attr("x",-r/2+.5*l.stickZoom),l.stickZoom=s(f(t)),l.setAllLinkCoordinates(),1===t?(l.updateAnnotationRectanglesNoTransition(),l.busy=!1,!0):!!(t>1||isNaN(t))&&A(1)}i.select(this.ticks).attr("opacity",0),this.setScaleGroup(),i.select(this.ticks).transition().attr("opacity",1).delay(.8*e).duration(e/2)}},{key:"updateAnnotationRectanglesNoTransition",value:function(){var t,e=k(this.annotationSets);try{for(e.s();!(t=e.n()).done;){var n=w(t.value,2),r=n[0],o=n[1];if(!0===this.app.annotationSetsShown.get(r)){var a,s=k(o);try{for(s.s();!(a=s.n()).done;){var u=a.value;if(u.fuzzyStart){var c=u.fuzzyStart;i.select(c).attr("d",this.getAnnotationRectPath(u.seqDatum.uncertainBegin,u.seqDatum.begin,u))}if(u.certain){var l=u.seqDatum.begin,f=u.seqDatum.end;u.seqDatum.uncertainBegin&&(l+=1),u.seqDatum.uncertainEnd&&(f-=1),u.certain.setAttribute("d",this.getAnnotationRectPath(l,f,u))}if(u.fuzzyEnd){var h=u.fuzzyEnd;i.select(h).attr("d",this.getAnnotationRectPath(u.seqDatum.end,u.seqDatum.uncertainEnd,u))}}}catch(t){s.e(t)}finally{s.f()}}}}catch(t){e.e(t)}finally{e.f()}}},{key:"getResXWithStickZoom",value:function(t){return"n-n"===t?-this.size/2*this.stickZoom-20:"c-c"===t?this.size/2*this.stickZoom+20:(t-this.size/2)*this.stickZoom}},{key:"getResidueCoordinates",value:function(t,e){void 0===t&&console.error("ERROR: residue number is undefined");var n,r=this.getResXWithStickZoom(1*t);if(0!==r){var i=Math.abs(r),o=Math.acos(r/i),a=this.rotation/360*Math.PI*2;r=i*Math.cos(a+o),n=i*Math.sin(a+o),void 0!==e&&(r+=e*Math.cos(a+Math.PI/2),n+=e*Math.sin(a+Math.PI/2))}else n=e;return[r+=this.ix,n+=this.iy]}},{key:"clearPositionalFeatures",value:function(){this.annotations=[],this.annotationTypes=[],this.annotationsSvgGroup.textContent="",this.nTermFeatures=[],this.cTermFeatures=[]}},{key:"updatePositionalFeatures",value:function(){var t=this,e=function(e){var n=e.target.correspondingUseElement?e.target.correspondingUseElement:e.target;t.app.preventDefaultsAndStopPropagation(e),t.app.setTooltip(n.name,n.getAttribute("fill")),t.showHighlight(!0)},n=-1,r=[];function i(t,e){var n,r=k(t);try{for(r.s();!(n=r.n()).done;)if(n.value.seqDatum.overlaps(e.seqDatum))return!0}catch(t){r.e(t)}finally{r.f()}return!1}var o,a=k(this.annotationSets);try{for(a.s();!(o=a.n()).done;){var s=w(o.value,2),u=s[0],c=s[1];if(!0===this.app.annotationSetsShown.get(u)){c&&c.length>0&&(r[++n]=[]);var l,f=new Set,h=k(Array.from(c.values()).sort((function(t,e){var n=t.description,r=e.description;return n<r?-1:n>r?1:0})));try{for(h.s();!(l=h.n()).done;){var p=l.value;if(!f.has(p.toString()))if(f.add(p.toString()),"n-n"===p.seqDatum.sequenceDatumString||"c-c"===p.seqDatum.sequenceDatumString)"n-n"===p.seqDatum.sequenceDatumString?(p.rung=this.nTermFeatures.length,this.nTermFeatures.push(p)):(p.rung=this.cTermFeatures.length,this.cTermFeatures.push(p));else{var y=r[n];i(y,p)&&(r[++n]=[],y=r[n]),p.rung=n,y.push(p)}}}catch(t){h.e(t)}finally{h.f()}}}}catch(t){a.e(t)}finally{a.f()}this.rungCount=n+1;var g,v=k(this.annotationSets);try{for(v.s();!(g=v.n()).done;){var x=w(g.value,2),m=x[0],b=x[1];if(!0===this.app.annotationSetsShown.get(m)){var S,_=new Set,M=k(b.values());try{for(M.s();!(S=M.n()).done;){var E=S.value;if(!_.has(E.toString())){_.add(E.toString());var A=E.toString();if(E.seqDatum.uncertainBegin&&(E.fuzzyStart=document.createElementNS(d,"path"),this.expanded?E.fuzzyStart.setAttribute("d",this.getAnnotationRectPath(E.seqDatum.uncertainBegin,E.seqDatum.begin,E)):E.fuzzyStart.setAttribute("d",this.getAnnotationPieSlicePath(E.seqDatum.uncertainBegin,E.seqDatum.begin,E)),E.fuzzyStart.setAttribute("stroke-width","1"),E.fuzzyStart.name=A,E.fuzzyStart.onmouseover=e,this.annotationsSvgGroup.appendChild(E.fuzzyStart)),E.seqDatum.begin&&E.seqDatum.end){E.certain=document.createElementNS(d,"path");var C=E.seqDatum.begin,L=E.seqDatum.end;E.seqDatum.uncertainBegin&&(C+=1),E.seqDatum.uncertainEnd&&(L-=1),this.expanded?E.certain.setAttribute("d",this.getAnnotationRectPath(C,L,E)):E.certain.setAttribute("d",this.getAnnotationPieSlicePath(C,L,E)),E.certain.setAttribute("stroke-width","1"),E.certain.name=A,E.certain.onmouseover=e,this.annotationsSvgGroup.appendChild(E.certain)}E.seqDatum.uncertainEnd&&(E.fuzzyEnd=document.createElementNS(d,"path"),this.expanded?E.fuzzyEnd.setAttribute("d",this.getAnnotationRectPath(E.seqDatum.end,E.seqDatum.uncertainEnd,E)):E.fuzzyEnd.setAttribute("d",this.getAnnotationPieSlicePath(E.seqDatum.end,E.seqDatum.uncertainEnd,E)),E.fuzzyEnd.setAttribute("stroke-width","1"),E.fuzzyEnd.name=A,E.fuzzyEnd.onmouseover=e,this.annotationsSvgGroup.appendChild(E.fuzzyEnd))}}}catch(t){M.e(t)}finally{M.f()}}}}catch(t){v.e(t)}finally{v.f()}this.scale()}},{key:"getAnnotationPieSlicePath",value:function(t,e,n){var r,i,o,s,u,c=!(arguments.length>3&&void 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m,b=[(v[0]+x[0])/2,(v[1]+x[1])/2],w=this.fromSequenceData.length,k=this.toSequenceData.length,S="M"+b[0]+","+b[1],_="M"+b[0]+","+b[1],M=0;M<w;M++)(t((m=this.fromSequenceData[M]).begin)&&t(m.end)||"protein"!==o.type)&&(S+=e(b,v,m.begin,m.end,o,p,u)),t(m.uncertainBegin)&&(_+=e(b,v,m.uncertainBegin,m.begin,o,p,u)),t(m.uncertainEnd)&&(_+=e(b,v,m.end,m.uncertainEnd,o,p,u));for(var E=0;E<k;E++)(t((m=this.toSequenceData[E]).begin)&&t(m.end)||"protein"!==a.type)&&(S+=e(b,x,m.begin,m.end,a,y,s)),t(m.uncertainBegin)&&(_+=e(b,x,m.uncertainBegin,m.begin,a,y,s)),t(m.uncertainEnd)&&(_+=e(b,x,m.end,m.uncertainEnd,a,y,s));this.glyph||this.initSVG(),this.glyph.setAttribute("d",S),this.uncertainGlyph.setAttribute("d",_)}}])&&Yt(e.prototype,n),r&&Yt(e,r),o}(zt);function te(t){return(te="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 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function(t){if(Array.isArray(t))return t}(t)||function(t,e){var n=null==t?null:"undefined"!=typeof Symbol&&t[Symbol.iterator]||t["@@iterator"];if(null==n)return;var r,i,o=[],a=!0,s=!1;try{for(n=n.call(t);!(a=(r=n.next()).done)&&(o.push(r.value),!e||o.length!==e);a=!0);}catch(t){s=!0,i=t}finally{try{a||null==n.return||n.return()}finally{if(s)throw i}}return o}(t,e)||Pe(t,e)||function(){throw new TypeError("Invalid attempt to destructure non-iterable instance.\nIn order to be iterable, non-array objects must have a [Symbol.iterator]() method.")}()}function Te(t,e){var n="undefined"!=typeof Symbol&&t[Symbol.iterator]||t["@@iterator"];if(!n){if(Array.isArray(t)||(n=Pe(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]() 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0!==arguments[1]?arguments[1]:4;De(this,t),this.el=e,this.el.textContent="",this.maxCountInitiallyExpanded=n,this.d3cola=u.d3adaptor().groupCompactness(Number.MIN_VALUE).avoidOverlaps(!0);var o=i.select(this.el).append("div").classed("custom-menu-margin",!0).append("div").classed("custom-menu",!0).append("ul"),a=this,s=o.append("li").classed("collapse",!0);s.text("Collapse"),s[0][0].onclick=function(t){a.collapseProtein(t)};var c=o.append("li").text("Scale: "),l=c.selectAll("ul.custom-menu").data(t.barScales).enter().append("div").attr("class","bar-scale").append("label");l.append("span").text((function(t){return 8===t?"AA":t})),l.append("input").attr("class",(function(t){return"scaleButton scaleButton_"+100*t})).attr("name","scaleButtons").attr("type","radio").on("change",(function(t){a.preventDefaultsAndStopPropagation(t),a.contextMenuProt.setStickScale(t,a.contextMenuPoint)}));var f=i.select(".custom-menu-margin").node();f.onmouseout=function(t){var e=t.relatedTarget;do{if(e===this)return;e=e.parentNode}while(e);a.contextMenuProt=null,i.select(this).style("display","none")},this.svgElement=document.createElementNS(d,"svg"),this.svgElement.classList.add("complexViewerSVG"),this.svgElement.onmousedown=function(t){a.mouseDown(t)},this.svgElement.onmousemove=function(t){a.move(t)},this.svgElement.onmouseup=function(t){a.mouseUp(t)},this.svgElement.onmouseout=function(t){a.mouseOut(t)},this.svgElement.ontouchstart=function(t){a.touchStart(t)},this.svgElement.ontouchmove=function(t){a.move(t)},this.svgElement.ontouchend=function(t){a.mouseUp(t)},this.lastMouseUp=(new Date).getTime(),this.el.oncontextmenu=function(t){return t.preventDefault&&t.preventDefault(),t.returnValue=!1,!1};var h=/Firefox/i.test(navigator.userAgent)?"DOMMouseScroll":"mousewheel";document.attachEvent?this.svgElement.attachEvent("on"+h,(function(t){a.mouseWheel(t)})):document.addEventListener&&this.svgElement.addEventListener(h,(function(t){a.mouseWheel(t)}),!1),this.hoverListeners=new Set,this.expandListeners=new Set,this.el.appendChild(this.svgElement),this.container=document.createElementNS(d,"g"),this.container.setAttribute("id","container");var p=i.select(this.svgElement);this.defs=p.append("defs"),this.acknowledgement=document.createElementNS(d,"g");var y=document.createElementNS(d,"text");y.innerHTML="<a href='https://academic.oup.com/bioinformatics/article/33/22/3673/4061280' target='_blank'><tspan x='0' dy='1.2em' style='text-decoration: underline'>ComplexViewer "+r.version+"</tspan></a><tspan x='0' dy='1.2em'>by <a href='https://rappsilberlab.org/' target='_blank'>Rappsilber 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g=document.createTextNode("tooltip");this.tooltip.classList.add("label","tooltip"),this.tooltip.appendChild(g),this.tooltip_bg=document.createElementNS(d,"rect"),this.tooltip_bg.classList.add("tooltip-background"),this.tooltip_subBg=document.createElementNS(d,"rect"),this.tooltip_subBg.classList.add("tooltip-sub-background"),this.svgElement.appendChild(this.tooltip_subBg),this.svgElement.appendChild(this.tooltip_bg),this.svgElement.appendChild(this.tooltip),this.annotationSetsShown=new Map,this.annotationSetsShown.set("Interactor",!1),this.annotationSetsShown.set("UniprotKB",!1),this.annotationSetsShown.set("Superfamily",!1),this.annotationSetsShown.set("MI Features",!0),this.clear()}var e,n,o;return e=t,(n=[{key:"clear",value:function(){this.d3cola.stop(),this.naryLinks.textContent="",this.p_pLinksWide.textContent="",this.highlights.textContent="",this.p_pLinks.textContent="",this.res_resLinks.textContent="",this.proteinUpper.textContent="",this.selfRes_resLinks.textContent="",this.dragElement=null,this.dragStart=null,this.participants=new Map,this.allNaryLinks=new Map,this.allBinaryLinks=new Map,this.allUnaryLinks=new Map,this.allSequenceLinks=new Map,this.complexes=[];var e,n=[],r=Te(a);try{for(r.s();!(e=r.n()).done;){var o=e.value,s=i.hsl(o);s.l=.9,n.push(s+"")}}catch(t){r.e(t)}finally{r.f()}Xt.naryColors=i.scale.ordinal().range(n),this.z=1,this.hideTooltip(),this.state=t.STATES.MOUSE_UP}},{key:"collapseProtein",value:function(){i.select(".custom-menu-margin").style("display","none"),this.contextMenuProt.setExpanded(!1,this.contextMenuPoint),this.contextMenuProt=null,this.notifyExpandListeners()}},{key:"init",value:function(){this.d3cola.stop();var e,n=0,r=Te(this.participants.values());try{for(r.s();!(e=r.n()).done;){var o=e.value;o.size>n&&(n=o.size)}}catch(t){r.e(t)}finally{r.f()}var a,s,u,c=.8*this.svgElement.parentNode.clientWidth/n;this.defaultBarScale=(a=t.barScales,s=c,0===(u=(0,i.bisector((function(t){return t})).left)(a,s))||1===u?a[1]:u===a.length?a[a.length-1]:a[u-1]);var l,f=Te(this.participants.values());try{for(f.s();!(l=f.n()).done;){var h=l.value;"complex"!==h.type&&(h.setPosition(-500,-500),this.proteinUpper.appendChild(h.upperGroup))}}catch(t){f.e(t)}finally{f.f()}var p,d=Te(this.participants.values());try{for(d.s();!(p=d.n()).done;){var y=p.value;"protein"===y.type&&(y.stickZoom=this.defaultBarScale,this.participants.size<this.maxCountInitiallyExpanded&&y.toStick(!1))}}catch(t){d.e(t)}finally{d.f()}this.updateAnnotations();var g=this;!function(t,e){var n,r=Array.from(t.participants.values()).filter((function(t){return"protein"===t.type})),i=0,o=r.length,a=Me(r);try{for(a.s();!(n=a.n()).done;){var s=n.value,u=new RegExp("[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}![-]","i").exec(s.json.identifier.id);u&&u[0]===s.json.identifier.id.trim()&&(Ce(s,(function(){++i===o&&e()})),Ae(s,(function(){++i===o&&e()})))}}catch(t){a.e(t)}finally{a.f()}}(this,(function(){g.updateAnnotations()})),this.checkLinks(),this.autoLayout()}},{key:"zoomToExtent",value:function(){var t=this.svgElement.parentNode.clientWidth,e=this.svgElement.parentNode.clientHeight,n=this.container.getBBox(),r=(t/n.width).toFixed(4),i=(e/n.height).toFixed(4);if((i<r?i:r)<1){var o;r=(t-40)/n.width,(o=(i=(e-40)/n.height)<r?i:r)>this.z&&(o=this.z);var a=-n.x+20/o,s=-n.y+20/o;this.container.setAttribute("transform","scale("+o+") translate("+a+" "+s+") "),this.z=this.container.getCTM().inverse().a}else{var u=t-n.width,c=e-n.height,l=u/2-n.x,f=c/2-n.y;this.container.setAttribute("transform","scale(1) translate("+l+" "+f+")"),this.z=1}this.acknowledgement.setAttribute("transform","translate("+(t-150)+", 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t,e=Te(r.d3cola.nodes());try{for(e.s();!(t=e.n()).done;){var n=t.value;n.setPositionFromCola(n.x,n.y)}}catch(t){e.e(t)}finally{e.f()}r.setAllLinkCoordinates(),r.zoomToExtent(),r.debug&&o.attr({x:function(t){return t.bounds.x},y:function(t){return t.bounds.y},width:function(t){return t.bounds.width()},height:function(t){return t.bounds.height()}})}))}}h(n,f,!0),h(n,f,!1)}},{key:"getSVG",value:function(){var t=[i.select(this.el).selectAll("svg").node()],e=l.capture(t);return l.makeXMLStr(new XMLSerializer,e[0])}},{key:"readMIJSON",value:function(t){var e=!(arguments.length>1&&void 0!==arguments[1])||arguments[1];_e(t,this,e),this.init()}},{key:"checkLinks",value:function(){var t,e=Te(this.allNaryLinks.values());try{for(e.s();!(t=e.n()).done;)t.value.check()}catch(t){e.e(t)}finally{e.f()}var n,r=Te(this.allBinaryLinks.values());try{for(r.s();!(n=r.n()).done;)n.value.check()}catch(t){r.e(t)}finally{r.f()}var i,o=Te(this.allUnaryLinks.values());try{for(o.s();!(i=o.n()).done;)i.value.check()}catch(t){o.e(t)}finally{o.f()}var a,s=Te(this.allSequenceLinks.values());try{for(s.s();!(a=s.n()).done;)a.value.check()}catch(t){s.e(t)}finally{s.f()}}},{key:"setAllLinkCoordinates",value:function(){var t,e=Te(this.allNaryLinks.values());try{for(e.s();!(t=e.n()).done;)t.value.setLinkCoordinates()}catch(t){e.e(t)}finally{e.f()}var n,r=Te(this.allBinaryLinks.values());try{for(r.s();!(n=r.n()).done;)n.value.setLinkCoordinates()}catch(t){r.e(t)}finally{r.f()}var i,o=Te(this.allUnaryLinks.values());try{for(o.s();!(i=o.n()).done;)i.value.setLinkCoordinates()}catch(t){o.e(t)}finally{o.f()}var a,s=Te(this.allSequenceLinks.values());try{for(s.s();!(a=s.n()).done;)a.value.setLinkCoordinates()}catch(t){s.e(t)}finally{s.f()}}},{key:"showTooltip",value:function(t){var e,n,r=this.tooltip.getComputedTextLength()+16,i=this.svgElement.parentNode.clientWidth,o=this.svgElement.parentNode.clientHeight;e=t.x+20+r<i?t.x:i-r-20,n=t.y+60<o?t.y:o-60,this.tooltip.setAttribute("x",e+22),this.tooltip.setAttribute("y",n+47),this.tooltip_bg.setAttribute("x",e+16),this.tooltip_bg.setAttribute("y",n+28),this.tooltip_subBg.setAttribute("x",e+16),this.tooltip_subBg.setAttribute("y",n+28)}},{key:"setTooltip",value:function(t,e){if(t){this.tooltip.firstChild.data=t.toString().replace(/&(quot);/g,'"'),this.tooltip.setAttribute("display","block");var n=this.tooltip.getComputedTextLength();this.tooltip_bg.setAttribute("width",n+16),this.tooltip_subBg.setAttribute("width",n+16),void 0!==e&&null!=e?(this.tooltip_bg.setAttribute("fill",e),this.tooltip_bg.setAttribute("stroke",e),this.tooltip_bg.setAttribute("fill-opacity","0.0")):(this.tooltip_bg.setAttribute("fill","white"),this.tooltip_bg.setAttribute("stroke","grey")),this.tooltip_bg.setAttribute("height","28"),this.tooltip_subBg.setAttribute("height","28"),this.tooltip_bg.setAttribute("display","block"),this.tooltip_subBg.setAttribute("display","block")}else this.hideTooltip()}},{key:"hideTooltip",value:function(){this.tooltip.setAttribute("display","none"),this.tooltip_bg.setAttribute("display","none"),this.tooltip_subBg.setAttribute("display","none")}},{key:"setAnnotations",value:function(t){t=t.toUpperCase();var e,n=Te(this.annotationSetsShown.keys());try{for(n.s();!(e=n.n()).done;){var r=e.value;this.annotationSetsShown.set(r,t===r)}}catch(t){n.e(t)}finally{n.f()}return this.updateAnnotations(),this.getColorKeyJson()}},{key:"showAnnotations",value:function(t,e){return this.annotationSetsShown.set(t,e),this.updateAnnotations(),this.getColorKeyJson()}},{key:"updateAnnotations",value:function(){this.defs.textContent="",this.uncertainCategories=new Set,this.certainCategories=new Set,delete this.featureColors;var t,e,n=new Set,r=Te(this.participants.values());try{for(r.s();!(t=r.n()).done;){var o,a=Te(t.value.annotationSets);try{for(a.s();!(o=a.n()).done;){var u=Ne(o.value,2),l=u[0],f=u[1];if(!0===this.annotationSetsShown.get(l)){var h,p=Te(f.values());try{for(p.s();!(h=p.n()).done;){var d=h.value;n.add(d.description)}}catch(t){p.e(t)}finally{p.f()}}}}catch(t){a.e(t)}finally{a.f()}}}catch(t){r.e(t)}finally{r.f()}e=n.size<11?i.scale.ordinal().range(s):i.scale.category20();var y=this;function g(t,e){var n=y.defs.append("pattern").attr("id",t).attr("patternUnits","userSpaceOnUse").attr("x",0).attr("y",0).attr("width",12).attr("height",12).attr("patternTransform","rotate(45)");n.append("rect").attr("x",0).attr("y",2).attr("width",12).attr("height",4).attr("fill",e),n.append("rect").attr("x",0).attr("y",8).attr("width",12).attr("height",4).attr("fill",e)}var v,x=Te(this.participants.values());try{for(x.s();!(v=x.n()).done;){var m=v.value;if("protein"===m.type){m.clearPositionalFeatures(),m.updatePositionalFeatures();var b,w=Te(m.annotationSets);try{for(w.s();!(b=w.n()).done;){var k=Ne(b.value,2),S=k[0],_=k[1];if(!0===this.annotationSetsShown.get(S)){var M,E=Te(_);try{for(E.s();!(M=E.n()).done;){var A=M.value,C=void 0;if(C="No annotations"===A.description?"#eeeeee":e(A.description),A.certain&&(A.certain.setAttribute("fill",C),A.certain.setAttribute("stroke",C),this.certainCategories.add(A.description)),A.fuzzyStart||A.fuzzyEnd){if(!this.uncertainCategories.has(name)){var L=new c(C),N="rgba("+L.r+","+L.g+","+L.b+", 0.6)";g("hatched_"+A.description+"_"+C.toString(),N),this.uncertainCategories.add(A.description)}var T="url('#hatched_"+A.description+"_"+C.toString()+"')";A.fuzzyStart&&(A.fuzzyStart.setAttribute("fill",T),A.fuzzyStart.setAttribute("stroke",C)),A.fuzzyEnd&&(A.fuzzyEnd.setAttribute("fill",T),A.fuzzyEnd.setAttribute("stroke",C))}}}catch(t){E.e(t)}finally{E.f()}}}}catch(t){w.e(t)}finally{w.f()}}}}catch(t){x.e(t)}finally{x.f()}this.featureColors=e}},{key:"getColorKeyJson",value:function(){var t,e={Complex:[]},n=Te(Xt.naryColors.domain());try{for(n.s();!(t=n.n()).done;){var r=t.value;e.Complex.push({name:r,certain:{color:Xt.naryColors(r)}})}}catch(t){n.e(t)}finally{n.f()}if(this.featureColors){var i,o=Te(this.annotationSetsShown);try{for(o.s();!(i=o.n()).done;){var a=Ne(i.value,2),s=a[0];if(a[1]){var u,l=[],f=new Set,h=Te(this.participants.values());try{for(h.s();!(u=h.n()).done;){var p=u.value;if("protein"===p.type){var d=p.annotationSets.get(s);if(d){var y,g=Te(d);try{for(g.s();!(y=g.n()).done;){var v=y.value.description;if(!f.has(v)){f.add(v);var x={name:v};if(this.certainCategories.has(v)&&(x.certain={color:this.featureColors(v)}),this.uncertainCategories.has(v)){var m=new c(this.featureColors(v)),b="rgba("+m.r+","+m.g+","+m.b+", 0.6)";x.uncertain={color:b}}l.push(x)}}}catch(t){g.e(t)}finally{g.f()}}}}}catch(t){h.e(t)}finally{h.f()}e[s]=l}}}catch(t){o.e(t)}finally{o.f()}}return e}},{key:"collapseAll",value:function(){var t,e=Te(this.participants.values());try{for(e.s();!(t=e.n()).done;){var n=t.value;n.expanded&&n.toCircle(!1)}}catch(t){e.e(t)}finally{e.f()}this.autoLayout(),this.notifyExpandListeners()}},{key:"expandAll",value:function(){var t,e=Te(this.participants.values());try{for(e.s();!(t=e.n()).done;){var n=t.value;"protein"!==n.type||n.expanded||n.toStick(!1)}}catch(t){e.e(t)}finally{e.f()}this.autoLayout(),this.notifyExpandListeners()}},{key:"expandAndCollapseSelection",value:function(t){var e,n=Te(this.participants.values());try{for(n.s();!(e=n.n()).done;){var r=e.value,i=r.json.identifier.id;t.includes(i)?r.expanded||r.setExpanded(!0):r.expanded&&r.setExpanded(!1)}}catch(t){n.e(t)}finally{n.f()}this.notifyExpandListeners()}},{key:"addHoverListener",value:function(t){this.hoverListeners.add(t)}},{key:"removeHoverListener",value:function(t){this.hoverListeners.remove(t)}},{key:"notifyHoverListeners",value:function(t){var e,n=Te(this.hoverListeners);try{for(n.s();!(e=n.n()).done;)(0,e.value)(t)}catch(t){n.e(t)}finally{n.f()}}},{key:"addExpandListener",value:function(t){this.expandListeners.add(t)}},{key:"removeExpandListener",value:function(t){this.expandListeners.remove(t)}},{key:"notifyExpandListeners",value:function(){var t,e=this.getExpandedParticipants(),n=Te(this.expandListeners);try{for(n.s();!(t=n.n()).done;)(0,t.value)(e)}catch(t){n.e(t)}finally{n.f()}}},{key:"getExpandedParticipants",value:function(){var t,e=[],n=Te(this.participants.values());try{for(n.s();!(t=n.n()).done;){var r=t.value;r.postAnimExpanded&&e.push(r.json)}}catch(t){n.e(t)}finally{n.f()}return e}},{key:"setCTM",value:function(t,e){var n="matrix("+e.a+","+e.b+","+e.c+","+e.d+","+e.e+","+e.f+")";t.setAttribute("transform",n)}},{key:"mouseDown",value:function(e){e.preventDefault(),this.d3cola.stop(),this.dragStart=e,this.state=t.STATES.SELECT_PAN,i.select(".custom-menu-margin").style("display","none")}},{key:"touchStart",value:function(e){e.preventDefault(),this.d3cola.stop(),this.dragStart=e,this.state=t.STATES.SELECT_PAN,i.select(".custom-menu-margin").style("display","none")}},{key:"move",value:function(e){var n=this.getEventPoint(e),r=n.matrixTransform(this.container.getCTM().inverse());if(r.x)if(this.dragStart){this.hideTooltip();var i=this.getEventPoint(this.dragStart).matrixTransform(this.container.getCTM().inverse());if(null!=this.dragElement){var o=i.x-r.x,a=i.y-r.y;if(this.state===t.STATES.DRAGGING){if(this.dragElement.ix)this.dragElement.changePosition(o,a),this.dragElement.setAllLinkCoordinates();else{var s,u=Te(this.dragElement.participants);try{for(u.s();!(s=u.n()).done;)s.value.changePosition(o,a)}catch(t){u.e(t)}finally{u.f()}this.setAllLinkCoordinates()}this.dragStart=e}else Math.sqrt(o*o+a*a)>5*this.z&&(this.state=t.STATES.DRAGGING)}else this.state===t.STATES.SELECT_PAN&&(this.setCTM(this.container,this.container.getCTM().translate(r.x-i.x,r.y-i.y)),this.dragStart=e)}else this.showTooltip(n)}},{key:"mouseUp",value:function(e){this.preventDefaultsAndStopPropagation(e);var n=(new Date).getTime();if(n-this.lastMouseUp>150&&this.dragElement&&"protein"===this.dragElement.type&&this.state!==t.STATES.DRAGGING&&!this.dragElement.busy)if(this.dragElement.expanded){this.contextMenuProt=this.dragElement;var r=this.getEventPoint(e);this.contextMenuPoint=r.matrixTransform(this.container.getCTM().inverse());var o,a,s=i.select(".custom-menu-margin");e.pageX?(o=e.pageX,a=e.pageY):(o=this.dragStart.touches[0].pageX,a=this.dragStart.touches[0].pageY),s.style("top",a-20+"px").style("left",o-20+"px").style("display","block"),i.select(".scaleButton_"+100*this.dragElement.stickZoom).property("checked",!0)}else this.dragElement.setExpanded(!0),this.notifyExpandListeners();return this.dragElement=null,this.dragStart=null,this.state=t.STATES.MOUSE_UP,this.lastMouseUp=n,!1}},{key:"mouseWheel",value:function(t){this.preventDefaultsAndStopPropagation(t),this.d3cola.stop();var e=1+(t.wheelDelta?t.wheelDelta/3600:t.detail/-90),n=this.container,r=this.getEventPoint(t).matrixTransform(n.getCTM().inverse()),i=this.svgElement.createSVGMatrix().translate(r.x,r.y).scale(e).translate(-r.x,-r.y);return this.setCTM(n,n.getCTM().multiply(i)),!1}},{key:"mouseOut",value:function(){this.hideTooltip()}},{key:"getEventPoint",value:function(t){var e=this.svgElement.createSVGPoint();return e.x=t.pageX-Le(this.el).offset().left,e.y=t.pageY-Le(this.el).offset().top,e}},{key:"preventDefaultsAndStopPropagation",value:function(t){t.stopPropagation&&t.stopPropagation(),null!=t.cancelBubble&&(t.cancelBubble=!0),t.preventDefault&&t.preventDefault()}},{key:"downloadSVG",value:function(t){t||(t="complexViewer");var e=this.getSVG(),n=function(t){var e,n=[];try{e=new TextEncoder("utf-8")}catch(t){e=void 0}if(e)n=e.encode(t);else for(var r=0;r<t.length;r++){var i=t.charCodeAt(r);i<128?n.push(i):i<2048?n.push(192|i>>6,128|63&i):i<55296||i>=57344?n.push(224|i>>12,128|i>>6&63,128|63&i):(r++,i=65536+((1023&i)<<10|1023&t.charCodeAt(r)),n.push(240|i>>18,128|i>>12&63,128|i>>6&63,128|63&i))}return new Blob([new Uint8Array(n)],{type:"image/svg+xml;charset=utf-8"})}(e);if(navigator.msSaveOrOpenBlob)navigator.msSaveOrOpenBlob(n,t);else{var r=document.createElement("a");r.href=window.URL.createObjectURL(n),r.download=t,r.style.display="none",document.body.appendChild(r),r.click(),document.body.removeChild(r),window.URL.revokeObjectURL(r.href)}n=null}}])&&je(e.prototype,n),o&&je(e,o),t}();Ie.STATES={MOUSE_UP:0,SELECT_PAN:1,DRAGGING:2},Ie.barScales=[.01,.2,1,2,4,8]}])}));
\ No newline at end of file
diff --git a/src/js/app.js b/src/js/app.js
index 2eda614..92ede1b 100644
--- a/src/js/app.js
+++ b/src/js/app.js
@@ -239,7 +239,7 @@ export class App {
 
     collapseProtein() {
         d3.select(".custom-menu-margin").style("display", "none");
-        this.contextMenuProt.setExpanded(false);//, this.contextMenuPoint);
+        this.contextMenuProt.setExpanded(false, this.contextMenuPoint);
         this.contextMenuProt = null;
         this.notifyExpandListeners();
     }