grapholscape/dist/grapholscape.esm.min.js

ontology visualization

/**
 * MIT License
 *
 * Copyright (c) 2018-2024 OBDA Systems
 *
 * Permission is hereby granted, free of charge, to any person obtaining a copy
 * of this software and associated documentation files (the "Software"), to deal
 * in the Software without restriction, including without limitation the rights
 * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the Software is
 * furnished to do so, subject to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included in all
 * copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 * SOFTWARE.
 */

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t=In(e),n=t.dampingFactor,r=t.precision,i=t.iterations,o=t.weight,a=this._private.cy,s=this.byGroup(),l=s.nodes,c=s.edges,u=l.length,h=u*u,d=c.length,p=new Array(h),g=new Array(u),f=(1-n)/u,v=0;v<u;v++){for(var y=0;y<u;y++){p[v*u+y]=0}g[v]=0}for(var m=0;m<d;m++){var b=c[m],E=b.data("source"),w=b.data("target");if(E!==w){var _=l.indexOfId(E),x=l.indexOfId(w),T=o(b);p[x*u+_]+=T,g[_]+=T}}for(var C=1/u+f,N=0;N<u;N++)if(0===g[N])for(var A=0;A<u;A++){p[A*u+N]=C}else for(var I=0;I<u;I++){var O=I*u+N;p[O]=p[O]/g[N]+f}for(var S,L=new Array(u),P=new Array(u),R=0;R<u;R++)L[R]=1;for(var D=0;D<i;D++){for(var M=0;M<u;M++)P[M]=0;for(var k=0;k<u;k++)for(var F=0;F<u;F++){var B=k*u+F;P[k]+=p[B]*L[F]}Yt(P),S=L,L=P,P=S;for(var G=0,$=0;$<u;$++){var V=S[$]-L[$];G+=V*V}if(G<r)break}return{rank:function(e){return e=a.collection(e)[0],L[l.indexOf(e)]}}}},Sn=lt({root:null,weight:function(e){return 1},directed:!1,alpha:0}),Ln={degreeCentralityNormalized:function(e){e=Sn(e);var t=this.cy(),n=this.nodes(),r=n.length;if(e.directed){for(var i={},o={},a=0,s=0,l=0;l<r;l++){var c=n[l],u=c.id();e.root=c;var h=this.degreeCentrality(e);a<h.indegree&&(a=h.indegree),s<h.outdegree&&(s=h.outdegree),i[u]=h.indegree,o[u]=h.outdegree}return{indegree:function(e){return 0==a?0:(Y(e)&&(e=t.filter(e)),i[e.id()]/a)},outdegree:function(e){return 0===s?0:(Y(e)&&(e=t.filter(e)),o[e.id()]/s)}}}for(var d={},p=0,g=0;g<r;g++){var f=n[g];e.root=f;var v=this.degreeCentrality(e);p<v.degree&&(p=v.degree),d[f.id()]=v.degree}return{degree:function(e){return 0===p?0:(Y(e)&&(e=t.filter(e)),d[e.id()]/p)}}},degreeCentrality:function(e){e=Sn(e);var t=this.cy(),n=this,r=e,i=r.root,o=r.weight,a=r.directed,s=r.alpha;if(i=t.collection(i)[0],a){for(var l=i.connectedEdges(),c=l.filter((function(e){return e.target().same(i)&&n.has(e)})),u=l.filter((function(e){return e.source().same(i)&&n.has(e)})),h=c.length,d=u.length,p=0,g=0,f=0;f<c.length;f++)p+=o(c[f]);for(var v=0;v<u.length;v++)g+=o(u[v]);return{indegree:Math.pow(h,1-s)*Math.pow(p,s),outdegree:Math.pow(d,1-s)*Math.pow(g,s)}}for(var y=i.connectedEdges().intersection(n),m=y.length,b=0,E=0;E<y.length;E++)b+=o(y[E]);return{degree:Math.pow(m,1-s)*Math.pow(b,s)}}};Ln.dc=Ln.degreeCentrality,Ln.dcn=Ln.degreeCentralityNormalised=Ln.degreeCentralityNormalized;var Pn=lt({harmonic:!0,weight:function(){return 1},directed:!1,root:null}),Rn={closenessCentralityNormalized:function(e){for(var t=Pn(e),n=t.harmonic,r=t.weight,i=t.directed,o=this.cy(),a={},s=0,l=this.nodes(),c=this.floydWarshall({weight:r,directed:i}),u=0;u<l.length;u++){for(var h=0,d=l[u],p=0;p<l.length;p++)if(u!==p){var g=c.distance(d,l[p]);h+=n?1/g:g}n||(h=1/h),s<h&&(s=h),a[d.id()]=h}return{closeness:function(e){return 0==s?0:(e=Y(e)?o.filter(e)[0].id():e.id(),a[e]/s)}}},closenessCentrality:function(e){var t=Pn(e),n=t.root,r=t.weight,i=t.directed,o=t.harmonic;n=this.filter(n)[0];for(var a=this.dijkstra({root:n,weight:r,directed:i}),s=0,l=this.nodes(),c=0;c<l.length;c++){var u=l[c];if(!u.same(n)){var h=a.distanceTo(u);s+=o?1/h:h}}return o?s:1/s}};Rn.cc=Rn.closenessCentrality,Rn.ccn=Rn.closenessCentralityNormalised=Rn.closenessCentralityNormalized;var Dn=lt({weight:null,directed:!1}),Mn={betweennessCentrality:function(e){for(var t=Dn(e),n=t.directed,r=t.weight,i=null!=r,o=this.cy(),a=this.nodes(),s={},l={},c=0,u=function(e,t){l[e]=t,t>c&&(c=t)},h=function(e){return l[e]},d=0;d<a.length;d++){var p=a[d],g=p.id();s[g]=n?p.outgoers().nodes():p.openNeighborhood().nodes(),u(g,0)}for(var f=function(){for(var e=a[v].id(),t=[],n={},l={},c={},d=new Ct((function(e,t){return c[e]-c[t]})),p=0;p<a.length;p++){var g=a[p].id();n[g]=[],l[g]=0,c[g]=1/0}for(l[e]=1,c[e]=0,d.push(e);!d.empty();){var f=d.pop();if(t.push(f),i)for(var y=0;y<s[f].length;y++){var m=s[f][y],b=o.getElementById(f),E=void 0;E=b.edgesTo(m).length>0?b.edgesTo(m)[0]:m.edgesTo(b)[0];var w=r(E);m=m.id(),c[m]>c[f]+w&&(c[m]=c[f]+w,d.nodes.indexOf(m)<0?d.push(m):d.updateItem(m),l[m]=0,n[m]=[]),c[m]==c[f]+w&&(l[m]=l[m]+l[f],n[m].push(f))}else for(var _=0;_<s[f].length;_++){var x=s[f][_].id();c[x]==1/0&&(d.push(x),c[x]=c[f]+1),c[x]==c[f]+1&&(l[x]=l[x]+l[f],n[x].push(f))}}for(var T={},C=0;C<a.length;C++)T[a[C].id()]=0;for(;t.length>0;){for(var N=t.pop(),A=0;A<n[N].length;A++){var I=n[N][A];T[I]=T[I]+l[I]/l[N]*(1+T[N])}N!=a[v].id()&&u(N,h(N)+T[N])}},v=0;v<a.length;v++)f();var y={betweenness:function(e){var t=o.collection(e).id();return h(t)},betweennessNormalized:function(e){if(0==c)return 0;var t=o.collection(e).id();return h(t)/c}};return y.betweennessNormalised=y.betweennessNormalized,y}};Mn.bc=Mn.betweennessCentrality;var kn=lt({expandFactor:2,inflateFactor:2,multFactor:1,maxIterations:20,attributes:[function(e){return 1}]}),Fn=function(e,t){for(var n=0,r=0;r<t.length;r++)n+=t[r](e);return n},Bn=function(e,t){for(var n,r=0;r<t;r++){n=0;for(var i=0;i<t;i++)n+=e[i*t+r];for(var o=0;o<t;o++)e[o*t+r]=e[o*t+r]/n}},Gn=function(e,t,n){for(var r=new Array(n*n),i=0;i<n;i++){for(var o=0;o<n;o++)r[i*n+o]=0;for(var a=0;a<n;a++)for(var s=0;s<n;s++)r[i*n+s]+=e[i*n+a]*t[a*n+s]}return r},$n=function(e,t,n){for(var r=e.slice(0),i=1;i<n;i++)e=Gn(e,r,t);return e},Vn=function(e,t,n){for(var r=new Array(t*t),i=0;i<t*t;i++)r[i]=Math.pow(e[i],n);return Bn(r,t),r},zn=function(e,t,n,r){for(var i=0;i<n;i++){if(Math.round(e[i]*Math.pow(10,r))/Math.pow(10,r)!==Math.round(t[i]*Math.pow(10,r))/Math.pow(10,r))return!1}return!0},Un=function(e,t){for(var n=0;n<e.length;n++)if(!t[n]||e[n].id()!==t[n].id())return!1;return!0},qn=function(e){for(var t=this.nodes(),n=this.edges(),r=this.cy(),i=function(e){return kn(e)}(e),o={},a=0;a<t.length;a++)o[t[a].id()]=a;for(var s,l=t.length,c=l*l,u=new Array(c),h=0;h<c;h++)u[h]=0;for(var d=0;d<n.length;d++){var p=n[d],g=o[p.source().id()],f=o[p.target().id()],v=Fn(p,i.attributes);u[g*l+f]+=v,u[f*l+g]+=v}!function(e,t,n){for(var r=0;r<t;r++)e[r*t+r]=n}(u,l,i.multFactor),Bn(u,l);for(var y=!0,m=0;y&&m<i.maxIterations;)y=!1,s=$n(u,l,i.expandFactor),u=Vn(s,l,i.inflateFactor),zn(u,s,c,4)||(y=!0),m++;var b=function(e,t,n,r){for(var i=[],o=0;o<t;o++){for(var a=[],s=0;s<t;s++)Math.round(1e3*e[o*t+s])/1e3>0&&a.push(n[s]);0!==a.length&&i.push(r.collection(a))}return i}(u,l,t,r);return b=function(e){for(var t=0;t<e.length;t++)for(var n=0;n<e.length;n++)t!=n&&Un(e[t],e[n])&&e.splice(n,1);return e}(b),b},jn={markovClustering:qn,mcl:qn},Hn=function(e){return e},Yn=function(e,t){return Math.abs(t-e)},Xn=function(e,t,n){return e+Yn(t,n)},Wn=function(e,t,n){return e+Math.pow(n-t,2)},Qn=function(e){return Math.sqrt(e)},Zn=function(e,t,n){return Math.max(e,Yn(t,n))},Jn=function(e,t,n,r,i){for(var o=arguments.length>5&&void 0!==arguments[5]?arguments[5]:Hn,a=r,s=0;s<e;s++)a=i(a,t(s),n(s));return o(a)},Kn={euclidean:function(e,t,n){return e>=2?Jn(e,t,n,0,Wn,Qn):Jn(e,t,n,0,Xn)},squaredEuclidean:function(e,t,n){return Jn(e,t,n,0,Wn)},manhattan:function(e,t,n){return Jn(e,t,n,0,Xn)},max:function(e,t,n){return Jn(e,t,n,-1/0,Zn)}};function er(e,t,n,r,i,o){var a;return a=X(e)?e:Kn[e]||Kn.euclidean,0===t&&X(e)?a(i,o):a(t,n,r,i,o)}Kn["squared-euclidean"]=Kn.squaredEuclidean,Kn.squaredeuclidean=Kn.squaredEuclidean;var tr=lt({k:2,m:2,sensitivityThreshold:1e-4,distance:"euclidean",maxIterations:10,attributes:[],testMode:!1,testCentroids:null}),nr=function(e){return tr(e)},rr=function(e,t,n,r,i){var o="kMedoids"!==i?function(e){return n[e]}:function(e){return r[e](n)},a=n,s=t;return er(e,r.length,o,(function(e){return r[e](t)}),a,s)},ir=function(e,t,n){for(var r=n.length,i=new Array(r),o=new Array(r),a=new Array(t),s=null,l=0;l<r;l++)i[l]=e.min(n[l]).value,o[l]=e.max(n[l]).value;for(var c=0;c<t;c++){s=[];for(var u=0;u<r;u++)s[u]=Math.random()*(o[u]-i[u])+i[u];a[c]=s}return a},or=function(e,t,n,r,i){for(var o=1/0,a=0,s=0;s<t.length;s++){var l=rr(n,e,t[s],r,i);l<o&&(o=l,a=s)}return a},ar=function(e,t,n){for(var r=[],i=null,o=0;o<t.length;o++)n[(i=t[o]).id()]===e&&r.push(i);return r},sr=function(e,t,n){return Math.abs(t-e)<=n},lr=function(e,t,n){for(var r=0;r<e.length;r++)for(var i=0;i<e[r].length;i++){if(Math.abs(e[r][i]-t[r][i])>n)return!1}return!0},cr=function(e,t,n){for(var r=0;r<n;r++)if(e===t[r])return!0;return!1},ur=function(e,t){var n=new Array(t);if(e.length<50)for(var r=0;r<t;r++){for(var i=e[Math.floor(Math.random()*e.length)];cr(i,n,r);)i=e[Math.floor(Math.random()*e.length)];n[r]=i}else for(var o=0;o<t;o++)n[o]=e[Math.floor(Math.random()*e.length)];return n},hr=function(e,t,n){for(var r=0,i=0;i<t.length;i++)r+=rr("manhattan",t[i],e,n,"kMedoids");return r},dr=function(e,t,n,r,i){for(var o,a,s=0;s<t.length;s++)for(var l=0;l<e.length;l++)r[s][l]=Math.pow(n[s][l],i.m);for(var c=0;c<e.length;c++)for(var u=0;u<i.attributes.length;u++){o=0,a=0;for(var h=0;h<t.length;h++)o+=r[h][c]*i.attributes[u](t[h]),a+=r[h][c];e[c][u]=o/a}},pr=function(e,t,n,r,i){for(var o=0;o<e.length;o++)t[o]=e[o].slice();for(var a,s,l,c=2/(i.m-1),u=0;u<n.length;u++)for(var h=0;h<r.length;h++){a=0;for(var d=0;d<n.length;d++)s=rr(i.distance,r[h],n[u],i.attributes,"cmeans"),l=rr(i.distance,r[h],n[d],i.attributes,"cmeans"),a+=Math.pow(s/l,c);e[h][u]=1/a}},gr=function(e){var t,n,r,i,o,a=this.cy(),s=this.nodes(),l=nr(e);i=new Array(s.length);for(var c=0;c<s.length;c++)i[c]=new Array(l.k);r=new Array(s.length);for(var u=0;u<s.length;u++)r[u]=new Array(l.k);for(var h=0;h<s.length;h++){for(var d=0,p=0;p<l.k;p++)r[h][p]=Math.random(),d+=r[h][p];for(var g=0;g<l.k;g++)r[h][g]=r[h][g]/d}n=new Array(l.k);for(var f=0;f<l.k;f++)n[f]=new Array(l.attributes.length);o=new Array(s.length);for(var v=0;v<s.length;v++)o[v]=new Array(l.k);for(var y=!0,m=0;y&&m<l.maxIterations;)y=!1,dr(n,s,r,o,l),pr(r,i,n,s,l),lr(r,i,l.sensitivityThreshold)||(y=!0),m++;return t=function(e,t,n,r){for(var i,o,a=new Array(n.k),s=0;s<a.length;s++)a[s]=[];for(var l=0;l<t.length;l++){i=-1/0,o=-1;for(var c=0;c<t[0].length;c++)t[l][c]>i&&(i=t[l][c],o=c);a[o].push(e[l])}for(var u=0;u<a.length;u++)a[u]=r.collection(a[u]);return a}(s,r,l,a),{clusters:t,degreeOfMembership:r}},fr={kMeans:function(e){var t,n=this.cy()