From 11e711b1485d1cf6d9c9f1dfb06a64dbf69b6010 Mon Sep 17 00:00:00 2001
From: Jean-Daniel Fekete <Jean-Daniel.Fekete@inria.fr>
Date: Fri, 24 Apr 2015 15:47:17 -0400
Subject: [PATCH] added adjacent_exchange pass for barycenter heuristic

---
 examples/matrix.js       |  7 +++-
 reorder.v1.js            | 66 ++++++++++++++----------------
 reorder.v1.min.js        |  5 ++-
 src/adjacent_exchange.js | 87 ++++++++++++++++++++++++++++++++++++++++
 src/barycenter.js        | 19 +++------
 src/count_crossings.js   |  8 ++--
 src/graph.js             |  4 --
 test/barycenter-test.js  | 25 ++++++++----
 8 files changed, 153 insertions(+), 68 deletions(-)
 create mode 100644 src/adjacent_exchange.js

diff --git a/examples/matrix.js b/examples/matrix.js
index 65c6c07..f92ec0f 100644
--- a/examples/matrix.js
+++ b/examples/matrix.js
@@ -72,9 +72,12 @@ function matrix(json) {
     }
     
     function computeBarycenter() {
-	var barycenter = reorder.barycenter(graph);
+	var barycenter = reorder.barycenter(graph),
+	    improved = reorder.adjacent_exchange(graph,
+						 barycenter[0],
+						 barycenter[1]);
 
-	barycenter[0].forEach(function(lo, i) {
+	improved[0].forEach(function(lo, i) {
 	    nodes[i].barycenter = lo;
 	});
 
diff --git a/reorder.v1.js b/reorder.v1.js
index c77fb3f..0e4533f 100644
--- a/reorder.v1.js
+++ b/reorder.v1.js
@@ -469,8 +469,6 @@ reorder.graph = function(nodes, links, directed) {
     graph.sinks = function() {
 	var sinks = [],
 	    i;
-	if (! directed)
-	    return reorder.range(nodes.length);
 
 	for (i = 0; i < nodes.length; i++) {
 	    if (outEdges(i).length == 0)
@@ -482,8 +480,6 @@ reorder.graph = function(nodes, links, directed) {
     graph.sources = function() {
 	var sources = [],
 	    i;
-	if (! directed)
-	    return reorder.range(nodes.length);
 
 	for (i = 0; i < nodes.length; i++) {
 	    if (inEdges(i).length == 0)
@@ -796,13 +792,14 @@ function count_crossings(graph, north, south) {
 	firstIndex, treeSize, tree, index, weightSum,
 	invert = false, crosscount;
 
+    var comp = reorder.permutation(graph.nodes().length);
+
     if (north==undefined) {
-	var comp = reorder.permutation(graph.nodes().length);
 	north = comp.filter(function(n) {
-	    return graph.outEdges(n).length!=0;
+	    return graph.outDegree(n) != 0;
 	}),
 	south = comp.filter(function(n) {
-	    return graph.inEdges(n).length!=0;
+	    return graph.inDegree(n) != 0;
 	});
     }
 
@@ -853,6 +850,7 @@ function count_crossings(graph, north, south) {
     }
     return crosscount;
 }
+
 reorder.count_crossings = count_crossings;
 // Accorging to
 // E. R. Gansner, E. Koutsofios, S. C. North, and K.-P. Vo. 1993. A
@@ -885,36 +883,40 @@ function count_out_crossings(graph, v, w, inv) {
 	iv, iw, p0, cross = 0;
 
     for (iw = 0; iw < w_edges.length; iw++) {
-	p0 = inv[w_edges[iw].target.index];
+	p0 = inv[w_edges[iw].source.index];
 	for (iv = 0; iv < v_edges.length; iv++) {
-	    if (inv[v_edges[iv].target.index] > p0)
+	    if (inv[v_edges[iv].source.index] > p0)
 		cross++;
 	}
     }
     return cross;
 }
 
-function adjacent_exchange(graph, layer1, layer2, crossings) {
+function adjacent_exchange(graph, layer1, layer2) {
+    layer1 = layer1.slice();
+    layer2 = layer2.slice();
     var i, v, w, c0, c1,
 	inv_layer1 = inverse_permutation(layer1),
 	inv_layer2 = inverse_permutation(layer2),
-	swapped = true;
-    
+	swapped = true,
+	improved = 0;
+
     while (swapped) {
 	swapped = false;
 	for (i = 0; i < layer1.length-1; i++) {
 	    v = layer1[i];
 	    w = layer1[i+1];
+	    // should reduce the in crossing and the out crossing
+	    // otherwise what we gain horizontally is lost vertically
 	    c0 = count_out_crossings(graph, v, w, inv_layer2);
 	    c1 = count_out_crossings(graph, w, v, inv_layer2);
-	    if (c1 < c0) {
+	    if (c0 > c1) {
 		layer1[i] = w;
 		layer1[i+1] = v;
-		c0 = inv_layer1[v];
-		inv_layer1[v] = inv_layer1[w];
-		inv_layer1[w] = c0;
+		inv_layer1[w] = i;
+		inv_layer1[v] = i+1;
 		swapped = true;
-		crossings -= c0-c1;
+		improved += c0 - c1;
 	    }
 	}
 	for (i = 0; i < layer2.length-1; i++) {
@@ -922,19 +924,18 @@ function adjacent_exchange(graph, layer1, layer2, crossings) {
 	    w = layer2[i+1];
 	    c0 = count_in_crossings(graph, v, w, inv_layer1);
 	    c1 = count_in_crossings(graph, w, v, inv_layer1);
-	    if (c1 < c0) {
+	    if (c0 > c1) {
 		layer2[i] = w;
 		layer2[i+1] = v;
-		c0 = inv_layer2[v];
-		inv_layer2[v] = inv_layer2[w];
-		inv_layer2[w] = c0;
+		inv_layer2[w] = i;
+		inv_layer2[v] = i+1;
 		swapped = true;
-		crossings -= c0-c1;
+		improved += c0 - c1;
 	    }
 	}
     }
 
-    return [layer1, layer2, crossings];
+    return [layer1, layer2, improved];
 };
 
 reorder.adjacent_exchange = adjacent_exchange;
@@ -984,10 +985,10 @@ reorder.barycenter1 = function(graph, comp, max_iter) {
 	i, v, neighbors;
 
     layer1 = comp.filter(function(n) {
-	return graph.outEdges(n).length!=0;
+	return graph.outDegree(n) != 0;
     });
     layer2 = comp.filter(function(n) {
-	return graph.inEdges(n).length!=0;
+	return graph.inDegree(n) != 0;
     });
     if (comp.length < 3) {
 	return [layer1, layer2,
@@ -999,19 +1000,12 @@ reorder.barycenter1 = function(graph, comp, max_iter) {
     else if ((max_iter%2)==1)
 	max_iter++; // want even number of iterations
 
-    layer1 = comp.filter(function(n) {
-	return graph.outEdges(n).length!=0;
-    });
-    layer2 = comp.filter(function(n) {
-	return graph.inEdges(n).length!=0;
-    });
-
     for (i = 0; i < layer2.length; i++)
 	nodes[layer2[i]].pos = i;
 
     best_crossings = count_crossings(graph, layer1, layer2);
-    best_layer1 = layer1;
-    best_layer2 = layer2;
+    best_layer1 = layer1.slice();
+    best_layer2 = layer2.slice();
     best_iter = 0;
 
     for (layer = layer1, iter = 0;
@@ -1049,8 +1043,8 @@ reorder.barycenter1 = function(graph, comp, max_iter) {
 	crossings = count_crossings(graph, layer1, layer2);
 	if (crossings < best_crossings) {
 	    best_crossings = crossings;
-	    best_layer1 = layer1;
-	    best_layer2 = layer2;
+	    best_layer1 = layer1.slice();
+	    best_layer2 = layer2.slice();
 	    best_iter = iter;
 	    max_iter = Math.max(max_iter, iter + 2); // we improved so go on
 	}
diff --git a/reorder.v1.min.js b/reorder.v1.min.js
index 234b54c..fce0c21 100644
--- a/reorder.v1.min.js
+++ b/reorder.v1.min.js
@@ -1,2 +1,3 @@
-(function(exports){reorder={version:"0.0.5"};reorder.cmp_number_asc=function(a,b){return a-b};reorder.cmp_number=reorder.cmp_number_asc;reorder.cmp_number_desc=function(a,b){return b-a};reorder.flatten=function(a,b){return a.concat(b)};reorder.infinities=function(n){var i=-1,a=[];if(arguments.length===1)while(++i<n)a[i]=Infinity;else while(++i<n)a[i]=reorder.infinities.apply(this,Array.prototype.slice.call(arguments,1));return a};reorder.array1d=function(n,v){var i=-1,a=Array(n);while(++i<n)a[i]=v;return a};reorder.dot=science.lin.dot;reorder.length=science.lin.length;reorder.normalize=science.lin.normalize;reorder.zeroes=science.zeroes;reorder.displaymat=function(mat,rowperm,colperm){var i,j,row,col,str;if(!rowperm){rowperm=reorder.range(mat.length)}if(!colperm){colperm=reorder.range(mat[0].length)}console.log("Matrix:");for(i=0;i<mat.length;i++){row=rowperm?mat[rowperm[i]]:mat[i];str="";for(j=0;j<row.length;j++){col=colperm?row[colperm[j]]:row[j];str+=col?"*":" "}console.log(str)}};reorder.printmat=function(m){var i,j,row,line;for(i=0;i<m.length;i++){row=m[i];line="";for(j=0;j<row.length;j++){if(line.length!=0)line+=", ";line+=row[j].toFixed(4)}console.log(i.toPrecision(3)+": "+line)}};reorder.assert=function(v,msg){if(!v){console.log(msg);throw msg||"Assertion failed"}};reorder.printhcluster=function(cluster,indent){if(cluster.left==null)return Array(indent+1).join(" ")+"id: "+cluster.id;return Array(indent+1).join(" ")+"id: "+cluster.id+", dist: "+cluster.dist+"\n"+reorder.printhcluster(cluster.left,indent+1)+"\n"+reorder.printhcluster(cluster.right,indent+1)};reorder.mean=science.stats.mean;reorder.meantranspose=function(v,j){var n=v.length;if(n==0)return NaN;var o=v[0].length,m=0,i=-1,row;while(++i<n)m+=(v[i][j]-m)/(i+1);return m};reorder.meancolumns=function(v){var n=v.length;if(n==0)return NaN;var o=v[0].length,m=v[0].slice(0),i=0,j,row;while(++i<n){row=v[i];for(j=0;j<o;j++)m[j]+=(row[j]-m[j])/(i+1)}return m};reorder.sum=function(v){var i=v.length,s=v[0];while(i-->1)s+=v[i];return s};function isNum(a,b){return!(isNaN(a)||isNaN(b)||a==Infinity||b==Infinity)}reorder.distance={euclidean:function(a,b){var i=a.length,s=0,x;while(i-->0){if(isNum(a[i],b[i])){x=a[i]-b[i];s+=x*x}}return Math.sqrt(s)},manhattan:function(a,b){var i=a.length,s=0;while(i-->0){if(isNum(a[i],b[i])){s+=Math.abs(a[i]-b[i])}}return s},minkowski:function(p){return function(a,b){var i=a.length,s=0;while(i-->0){if(isNum(a[i],b[i])){s+=Math.pow(Math.abs(a[i]-b[i]),p)}}return Math.pow(s,1/p)}},chebyshev:function(a,b){var i=a.length,max=0,x;while(i-->0){if(isNum(a[i],b[i])){x=Math.abs(a[i]-b[i]);if(x>max)max=x}}return max},hamming:function(a,b){var i=a.length,d=0;while(i-->0){if(isNum(a[i],b[i])){if(a[i]!==b[i])d++}}return d},jaccard:function(a,b){var n=0,i=a.length,s=0;while(i-->0){if(isNum(a[i],b[i])){if(a[i]===b[i])s++;n++}}if(n==0)return 0;return s/n},braycurtis:function(a,b){var i=a.length,s0=0,s1=0,ai,bi;while(i-->0){ai=a[i];bi=b[i];if(isNum(ai,bi)){s0+=Math.abs(ai-bi);s1+=Math.abs(ai+bi)}}if(s1==0)return 0;return s0/s1}};reorder.range=function(start,stop,step){if(arguments.length<3){step=1;if(arguments.length<2){stop=start;start=0}}var range=[],i=start;if(step<0)for(;i>stop;i+=step)range.push(i);else for(;i<stop;i+=step)range.push(i);return range};reorder.transpose=science.lin.transpose;reorder.transposeSlice=function(a,start,end){if(arguments.length<3){end=a[0].length;if(arguments.length<2){start=0}}var m=a.length,n=end,i=start-1,j,b=new Array(end-start);while(++i<n){b[i]=new Array(m);j=-1;while(++j<m)b[i-start][j]=a[j][i]}return b};reorder.correlation={pearson:function(a,b){var ma=science.stats.mean(a),mb=science.stats.mean(b),s1=0,s2=0,s3=0,i,dx,dy,n=Math.min(a.length,b.length);if(n===0)return NaN;for(i=0;i<n;i++){dx=a[i]-ma;dy=b[i]-mb;s1+=dx*dy;s2+=dx*dx;s3+=dy*dy}return s1/Math.sqrt(s2*s3)},pearsonMatrix:function(matrix){var a,ma,i,j,dx,n=matrix.length,ret,mx,sx,sx2;if(n===0)return NaN;mx=Array(n);sx=reorder.zeroes(n);sx2=reorder.zeroes(n);for(i=0;i<n;i++){mx[i]=science.stats.mean(matrix[i])}for(i=0;i<n;i++){a=matrix[i];ma=mx[i];for(j=0;j<n;j++){dx=a[j]-ma;sx[j]+=dx;sx2[j]+=dx*dx}}ret=Array(n);for(i=0;i<n;i++){ret[i]=Array(n);for(j=0;j<n;j++){ret[i][j]=sx[i]*sx[j]/Math.sqrt(sx2[i]*sx2[j])}}return ret}};reorder.bandwidth=function(graph,order){if(!order)order=reorder.range(graph.nodes().length);var inv=inverse_permutation(order),links=graph.links(),i,e,d,max=0;for(i=0;i<links.length;i++){e=links[i];d=Math.abs(inv[e.source.index]-inv[e.target.index]);max=Math.max(max,d)}return max};reorder.permutation=reorder.range;function inverse_permutation(perm){var inv={};for(var i=0;i<perm.length;i++){inv[perm[i]]=i}return inv}reorder.inverse_permutation=inverse_permutation;reorder.graph=function(nodes,links,directed){var graph={},linkDistance=1,edges,inEdges,outEdges,components;graph.nodes=function(x){if(!arguments.length)return nodes;nodes=x;return graph};graph.nodes_indices=function(){return nodes.map(function(n){return n.index})};graph.links=function(x){if(!arguments.length)return links;links=x;return graph};graph.links_indices=function(){return links.map(function(l){return{source:l.source.index,target:l.target.index}})};graph.linkDistance=function(x){if(!arguments.length)return linkDistance;linkDistance=typeof x==="function"?x:+x;return graph};graph.directed=function(x){if(!arguments.length)return directed;directed=x;return graph};function init(){var i,o,n=nodes.length,m=links.length;components=undefined;for(i=0;i<n;++i){(o=nodes[i]).index=i;o.weight=0}for(i=0;i<m;++i){(o=links[i]).index=i;if(typeof o.source=="number")o.source=nodes[o.source];if(typeof o.target=="number")o.target=nodes[o.target];if(!("value"in o))o.value=1;++o.source.weight;++o.target.weight}if(typeof linkDistance==="function")for(i=0;i<m;++i)links[i].distance=+linkDistance.call(this,links[i],i);else for(i=0;i<m;++i)links[i].distance=linkDistance;edges=Array(nodes.length);for(i=0;i<nodes.length;++i){edges[i]=[]}if(directed){inEdges=Array(nodes.length);outEdges=Array(nodes.length);for(i=0;i<nodes.length;++i){inEdges[i]=[];outEdges[i]=[]}}else{inEdges=outEdges=edges}for(i=0;i<links.length;++i){o=links[i];edges[o.source.index].push(o);if(o.source.index!=o.target.index)edges[o.target.index].push(o);if(directed)inEdges[o.source.index].push(o);if(directed)outEdges[o.target.index].push(o)}return graph}graph.init=init;function edges(node){if(typeof node!="number"){node=node.index;console.log("received node %d",node)}return edges[node]}graph.edges=edges;graph.degree=function(node){if(typeof node!="number")node=node.index;return edges[node].length};function inEdges(node){if(typeof node!="number")node=node.index;return inEdges[node]}graph.inEdges=inEdges;graph.inDegree=function(node){if(typeof node!="number")node=node.index;return inEdges[node].length};function outEdges(node){if(typeof node!="number")node=node.index;return outEdges[node]}graph.outEdges=outEdges;graph.outDegree=function(node){if(typeof node!="number")node=node.index;return outEdges[node].length};graph.sinks=function(){var sinks=[],i;if(!directed)return reorder.range(nodes.length);for(i=0;i<nodes.length;i++){if(outEdges(i).length==0)sinks.push(i)}return sinks};graph.sources=function(){var sources=[],i;if(!directed)return reorder.range(nodes.length);for(i=0;i<nodes.length;i++){if(inEdges(i).length==0)sources.push(i)}return sources};function distance(i){return links[i].distance}graph.distance=distance;function neighbors(node){var e=edges[node],ret=[];for(var i=0;i<e.length;++i){var o=e[i];if(o.source.index==node)ret.push(o.target);else ret.push(o.source)}return ret}graph.neighbors=neighbors;graph.other=function(o,node){if(typeof o=="number")o=links[o];if(o.source.index==node)return o.target;else return o.source};function compute_components(){var stack=[],comp=0,comps=[],ccomp,n=nodes.length,i,j,v,l,o,e;for(i=0;i<n;i++)nodes[i].comp=0;for(j=0;j<n;j++){if(nodes[j].comp!=0)continue;comp=comp+1;nodes[j].comp=comp;stack.push(j);ccomp=[j];while(stack.length){v=stack.shift();l=edges[v];for(i=0;i<l.length;i++){e=l[i];o=e.source;if(o.index==v)o=e.target;if(o.index==v)continue;if(o.comp==0){o.comp=comp;ccomp.push(o.index);stack.push(o.index)}}}if(ccomp.length){ccomp.sort(reorder.cmp_number);comps.push(ccomp)}}comps.sort(function(a,b){return b.length-a.length});return comps}graph.components=function(){if(!components)components=compute_components();return components};return graph};reorder.graph_random_erdos_renyi=function(n,p,directed){if(p<=0)return reorder.graph_empty(n,directed);else if(p>=1)return reorder.graph_complete(n,directed);var nodes=graph_empty_nodes(n),links=[],v,w,i,lr,lp;w=-1;lp=Math.log(1-p);if(directed){for(v=0;v<n;){lr=Math.log(1-Math.random());w=w+1+Math.floor(lr/lp);if(v==w)w=w+1;while(w>=n&&v<n){w=w-n;v=v+1;if(v==w)w=w+1}if(v<n)links.push({source:v,target:w})}}else{for(v=1;v<n;){lr=Math.log(1-Math.random());w=w+1+Math.floor(lr/lp);while(w>=v&&v<n){w=w-v;v=v+1}if(v<n)links.push({source:v,target:w})}}return reorder.graph(nodes,links,directed).init()};reorder.graph_random=reorder.graph_random_erdos_renyi;function graph_empty_nodes(n){var nodes=Array(n),i;for(i=0;i<n;i++)nodes[i]={id:i};return nodes}reorder.graph_empty_nodes=graph_empty_nodes;reorder.graph_empty=function(n,directed){return graph(graph_empty_nodes(n),[],directed)};reorder.complete_graph=function(n,directed){var nodes=graph_empty_nodes(n),links=[],i,j;if(directed){for(i=0;i<n;i++){for(j=0;j<n;j++){if(i!=j)links.push({source:i,target:j})}}}else{for(i=0;i<n-1;i++){for(j=i+1;j<n;j++)links.push({source:i,target:j})}}return reorder.graph(nodes,links,directed).init()};reorder.graph_connect=function(graph,comps){var i,j,links=graph.links();if(!comps)comps=graph.components();for(i=0;i<comps.length-1;i++){for(j=i+1;j<comps.length;j++){links.push({source:comps[i][0],target:comps[j][0]})}}graph.links(links);return graph.init()};reorder.bfs=function(graph,v,fn){var q=new Queue,discovered={};q.push(v);discovered[v]=true;fn(v,undefined);while(q.length){v=q.shift();fn(v,v);graph.edges(v).forEach(function(e){var v2=graph.other(e,v).index;if(!discovered[v2]){q.push(v2);discovered[v2]=true;fn(v,v2)}});fn(v,-1)}};reorder.bfs_distances=function(graph,v){var dist={};dist[v]=0;reorder.bfs(graph,v,function(v,c){if(c>=0&&v!=c)dist[c]=dist[v]+1});return dist};reorder.all_pairs_distance_bfs=function(graph,comps){if(!comps)comps=[graph.nodes_indices()];var nodes=comps.reduce(reorder.flatten).sort(reorder.cmp_number),mat=Array(nodes.length),i,j,dist;for(i=0;i<nodes.length;i++)mat[i]=Array(nodes.length);for(i=0;i<nodes.length;i++){dist=reorder.bfs_distances(graph,i);for(j in dist){mat[i][j]=dist[j];mat[j][i]=dist[j]}}return mat};reorder.mat2graph=function(mat,directed){var n=mat.length,nodes=[],links=[],max_value=Number.NEGATIVE_INFINITY,i,j,v,m;for(i=0;i<n;i++)nodes.push({id:i});for(i=0;i<n;i++){v=mat[i];m=directed?0:i;for(j=m;j<v.length;j++){if(j==nodes.length)nodes.push({id:j});if(v[j]!=0){if(v[j]>max_value)max_value=v[j];links.push({source:i,target:j,value:v[j]})}}}return reorder.graph(nodes,links,directed).linkDistance(function(l,i){return 1+max_value-l.value}).init()};reorder.graph2mat=function(graph,directed){var nodes=graph.nodes(),links=graph.links(),n=nodes.length,i,l,mat;if(!directed)directed=graph.directed();if(directed){var rows=n,cols=n;for(i=n-1;i>=0;i--){if(graph.inEdges(i).length!=0)break;else rows--}for(i=n-1;i>=0;i--){if(graph.outEdges(i).length!=0)break;else cols--}mat=reorder.zeroes(rows,cols);for(i=0;i<links.length;i++){l=links[i];mat[l.source.index][l.target.index]=l.value?l.value:1}}else{mat=reorder.zeroes(n,n);for(i=0;i<links.length;i++){l=links[i];mat[l.source.index][l.target.index]=l.value?l.value:1;mat[l.target.index][l.source.index]=l.value?l.value:1}}return mat};function count_crossings(graph,north,south){var i,j,n,firstIndex,treeSize,tree,index,weightSum,invert=false,crosscount;if(north==undefined){var comp=reorder.permutation(graph.nodes().length);north=comp.filter(function(n){return graph.outEdges(n).length!=0}),south=comp.filter(function(n){return graph.inEdges(n).length!=0})}if(north.length<south.length){var tmp=north;north=south;south=tmp;invert=true}var south_inv=inverse_permutation(south),southsequence=[];for(i=0;i<north.length;i++){if(invert){n=graph.inEdges(north[i]).map(function(e){return south_inv[e.target.index]})}else{n=graph.outEdges(north[i]).map(function(e){return south_inv[e.source.index]})}n.sort(reorder.cmp_number);southsequence=southsequence.concat(n)}firstIndex=1;while(firstIndex<south.length)firstIndex<<=1;treeSize=2*firstIndex-1;firstIndex-=1;tree=reorder.zeroes(treeSize);crosscount=0;for(i=0;i<southsequence.length;i++){index=southsequence[i]+firstIndex;tree[index]++;while(index>0){if(index%2)crosscount+=tree[index+1];index=index-1>>1;tree[index]++}}return crosscount}reorder.count_crossings=count_crossings;function count_in_crossings(graph,v,w,inv){var v_edges=graph.inEdges(v),w_edges=graph.inEdges(w),iv,iw,p0,cross=0;for(iw=0;iw<w_edges.length;iw++){p0=inv[w_edges[iw].target.index];for(iv=0;iv<v_edges.length;iv++){if(inv[v_edges[iv].target.index]>p0)cross++}}return cross}function count_out_crossings(graph,v,w,inv){var v_edges=graph.outEdges(v),w_edges=graph.outEdges(w),iv,iw,p0,cross=0;for(iw=0;iw<w_edges.length;iw++){p0=inv[w_edges[iw].target.index];for(iv=0;iv<v_edges.length;iv++){if(inv[v_edges[iv].target.index]>p0)cross++}}return cross}function adjacent_exchange(graph,layer1,layer2,crossings){var i,v,w,c0,c1,inv_layer1=inverse_permutation(layer1),inv_layer2=inverse_permutation(layer2),swapped=true;while(swapped){swapped=false;for(i=0;i<layer1.length-1;i++){v=layer1[i];w=layer1[i+1];c0=count_out_crossings(graph,v,w,inv_layer2);c1=count_out_crossings(graph,w,v,inv_layer2);if(c1<c0){layer1[i]=w;layer1[i+1]=v;c0=inv_layer1[v];inv_layer1[v]=inv_layer1[w];inv_layer1[w]=c0;swapped=true;crossings-=c0-c1}}for(i=0;i<layer2.length-1;i++){v=layer2[i];w=layer2[i+1];c0=count_in_crossings(graph,v,w,inv_layer1);c1=count_in_crossings(graph,w,v,inv_layer1);if(c1<c0){layer2[i]=w;layer2[i+1]=v;c0=inv_layer2[v];inv_layer2[v]=inv_layer2[w];inv_layer2[w]=c0;swapped=true;crossings-=c0-c1}}}return[layer1,layer2,crossings]}reorder.adjacent_exchange=adjacent_exchange;reorder.barycenter=function(graph,iter,comps){var perms=[[],[],0];if(!comps){comps=graph.components()}for(var i=0;i<comps.length;i++){var p=reorder.barycenter1(graph,comps[i],iter);perms=[perms[0].concat(p[0]),perms[1].concat(p[1]),perms[2]+p[2]]}return perms};function median(neighbors){if(neighbors.length==0)return-1;if(neighbors.length==1)return neighbors[0];if(neighbors.length==2)return(neighbors[0]+neighbors[1])/2;neighbors.sort(reorder.cmp_number);if(neighbors.length%2)return neighbors[(neighbors.length-1)/2];var rm=neighbors.length/2,lm=rm-1,rspan=neighbors[neighbors.length-1]-neighbors[rm],lspan=neighbors[lm]-neighbors[0];if(lspan==rspan)return(neighbors[lm]+neighbors[rm])/2;else return(neighbors[lm]*rspan+neighbors[rm]*lspan)/(lspan+rspan)}reorder.barycenter1=function(graph,comp,max_iter){var nodes=graph.nodes(),layer1,layer2,crossings,iter,best_layer1,best_layer2,best_crossings,best_iter,layer,i,v,neighbors;layer1=comp.filter(function(n){return graph.outEdges(n).length!=0});layer2=comp.filter(function(n){return graph.inEdges(n).length!=0});if(comp.length<3){return[layer1,layer2,count_crossings(graph,layer1,layer2)]}if(!max_iter)max_iter=24;else if(max_iter%2==1)max_iter++;layer1=comp.filter(function(n){return graph.outEdges(n).length!=0});layer2=comp.filter(function(n){return graph.inEdges(n).length!=0});for(i=0;i<layer2.length;i++)nodes[layer2[i]].pos=i;best_crossings=count_crossings(graph,layer1,layer2);best_layer1=layer1;best_layer2=layer2;best_iter=0;for(layer=layer1,iter=0;iter<max_iter;iter++,layer=layer==layer1?layer2:layer1){for(i=0;i<layer.length;i++){v=nodes[layer[i]];if(layer==layer1)neighbors=graph.outEdges(v.index);else neighbors=graph.inEdges(v.index);neighbors=neighbors.map(function(e){var n=e.source==v?e.target:e.source;return nodes[n.index].pos});v.median=median(neighbors)}layer.sort(function(a,b){var d=nodes[a].median-nodes[b].median;if(d==0){d=graph.edges(b).length%2-graph.edges(a).length%2}if(d<0)return-1;else if(d>0)return 1;return 0});for(i=0;i<layer.length;i++)nodes[layer[i]].pos=i;crossings=count_crossings(graph,layer1,layer2);if(crossings<best_crossings){best_crossings=crossings;best_layer1=layer1;best_layer2=layer2;best_iter=iter;max_iter=Math.max(max_iter,iter+2)}}return[best_layer1,best_layer2,best_crossings]};reorder.all_pairs_distance=function(graph,comps){var distances=[];if(!comps)comps=graph.components();for(var i=0;i<comps.length;i++)distances.push(reorder.all_pairs_distance1(graph,comps[i]));return distances};function all_pairs_distance_floyd_warshall(graph,comp){var dist=reorder.infinities(comp.length,comp.length),edges,i,j,k,inv;inv=inverse_permutation(comp);for(i=0;i<comp.length;i++)dist[i][i]=0;for(i=0;i<comp.length;i++){edges={};graph.edges(comp[i]).forEach(function(e){if(e.source==e.target)return;if(!(e.source.index in inv)||!(e.target.index in inv))return;var u=inv[e.source.index],v=inv[e.target.index];dist[v][u]=dist[u][v]=graph.distance(e.index)})}for(k=0;k<comp.length;k++){for(i=0;i<comp.length;i++)if(dist[i][k]!=Infinity){for(j=0;j<comp.length;j++)if(dist[k][j]!=Infinity&&dist[i][j]>dist[i][k]+dist[k][j]){dist[i][j]=dist[i][k]+dist[k][j];dist[j][i]=dist[i][j]}}}return dist}reorder.all_pairs_distance1=all_pairs_distance_floyd_warshall;function floyd_warshall_with_path(graph,comp){if(!comp)comp=graph.components()[0];var dist=reorder.infinities(comp.length,comp.length),next=Array(comp.length),directed=graph.directed(),edges,i,j,k,inv;inv=inverse_permutation(comp);for(i=0;i<comp.length;i++){dist[i][i]=0;next[i]=Array(comp.length)}for(i=0;i<comp.length;i++){edges={};graph.edges(comp[i]).forEach(function(e){if(e.source==e.target)return;var u=inv[e.source.index],v=inv[e.target.index];dist[u][v]=graph.distance(e);next[u][v]=v;if(!directed){dist[v][u]=graph.distance(e);next[v][u]=u}})}for(k=0;k<comp.length;k++){for(i=0;i<comp.length;i++){for(j=0;j<comp.length;j++){if(dist[i][j]>dist[i][k]+dist[k][j]){dist[i][j]=dist[i][k]+dist[k][j];next[i][j]=next[i][k];if(!directed){dist[j][i]=dist[i][j];next[j][i]=next[k][j]}}}}}return[dist,next]}reorder.floyd_warshall_with_path=floyd_warshall_with_path;reorder.floyd_warshall_path=function(next,u,v){if(next[u][v]==undefined)return[];var path=[u];while(u!=v){u=next[u][v];path.push(u)}return path};function distmat2valuemat(distmat){var n=distmat.length,valuemat=reorder.zeroes(n,n),max_dist=reorder.distmax(distmat),i,j;for(i=0;i<n;i++){for(j=i;j<n;j++){valuemat[j][i]=valuemat[i][j]=1+max_dist-distmat[i][j]}}return valuemat}reorder.distmat2valuemat=distmat2valuemat;reorder.graph2valuemats=function(graph,comps){if(!comps)comps=graph.components();var dists=reorder.all_pairs_distance(graph,comps);return dists.map(distmat2valuemat)};reorder.valuemats_reorder=function(valuemats,leaforder,comps){var orders=valuemats.map(leaforder);if(comps){orders=orders.map(function(d,i){return reorder.permute(comps[i],d)})}return orders.reduce(reorder.flatten)};reorder.distmax=function(distMatrix){var max=0,n=distMatrix.length,i,j,row;for(i=0;i<n;i++){row=distMatrix[i];for(j=i+1;j<n;j++)if(row[j]>max)max=row[j]}return max};reorder.distmin=function(distMatrix){var min=Infinity,n=distMatrix.length,i,j,row;for(i=0;i<n;i++){row=distMatrix[i];for(j=i+1;j<n;j++)if(row[j]<min)min=row[j]}return min};reorder.dist=function(){var distance=reorder.distance.euclidean;function dist(vectors){var n=vectors.length,distMatrix=[];for(var i=0;i<n;i++){var d=[];distMatrix[i]=d;for(var j=0;j<n;j++){if(j<i){d.push(distMatrix[j][i])}else if(i===j){d.push(0)}else{d.push(distance(vectors[i],vectors[j]))}}}return distMatrix}dist.distance=function(x){if(!arguments.length)return distance;distance=x;return dist};return dist};reorder.dist_remove=function(dist,n,m){if(arguments.length<3)m=n+1;var i;dist.splice(n,m-n);for(i=dist.length;i-->0;)dist[i].splice(n,m-n);return dist};reorder.randomPermute=function(array,i,j){if(arguments.length<3){j=array.length;if(arguments.length<2){i=0}}var m=j-i,t,k;while(m>0){k=i+Math.floor(Math.random()*m--);t=array[i+m];array[i+m]=array[k];array[k]=t}return array};reorder.randomPermutation=function(n){return reorder.randomPermute(reorder.permutation(n))};reorder.random_matrix=function(p,n,m,sym){if(!m)m=n;if(n!=m)sym=false;else if(!sym)sym=true;var mat=reorder.zeroes(n,m),i,j,cnt;if(sym){for(i=0;i<n;i++){cnt=0;for(j=0;j<i+1;j++){if(Math.random()<p){mat[i][j]=mat[j][i]=1;cnt++}}if(cnt==0){j=Math.floor(Math.random()*n/2);mat[i][j]=mat[j][i]=1}}}else{for(i=0;i<n;i++){cnt=0;for(j=0;j<m;j++){if(Math.random()<p){mat[i][j]=1;cnt++}}if(cnt==0)mat[i][Math.floor(Math.random()*m)]=1}}return mat};reorder.permute=function(list,perm){var m=perm.length;var copy=list.slice(0);while(m--)copy[m]=list[perm[m]];return copy};reorder.permutetranspose=function(array,indexes){var m=array.length;while(m-->0)array[m]=reorder.permute(array[m],indexes);return array};reorder.stablepermute=function(list,indexes){var p=reorder.permute(list,indexes);if(p[0]>p[p.length-1])p.reverse();return p};if(typeof science=="undefined"){science={version:"1.9.1"};science.stats={}}science.stats.hcluster=function(){var distance=reorder.distance.euclidean,linkage="single",distMatrix=null;function hcluster(vectors){var n=vectors.length,dMin=[],cSize=[],clusters=[],c1,c2,c1Cluster,c2Cluster,p,root,i,j,id=0;if(distMatrix==null){distMatrix=[];i=-1;while(++i<n){dMin[i]=0;distMatrix[i]=[];j=-1;while(++j<n){distMatrix[i][j]=i===j?Infinity:distance(vectors[i],vectors[j]);if(distMatrix[i][dMin[i]]>distMatrix[i][j])dMin[i]=j}}}else{if(distMatrix.length<n||distMatrix[0].length<n)throw{error:"Provided distance matrix length "+distMatrix.length+" instead of "+n};i=-1;while(++i<n){dMin[i]=0;j=-1;while(++j<n){if(i===j)distMatrix[i][j]=Infinity;if(distMatrix[i][dMin[i]]>distMatrix[i][j])dMin[i]=j}}}i=-1;while(++i<n){clusters[i]=[];clusters[i][0]={left:null,right:null,dist:0,centroid:vectors[i],id:id++,size:1,depth:0};cSize[i]=1}for(p=0;p<n-1;p++){c1=0;for(i=0;i<n;i++){if(distMatrix[i][dMin[i]]<distMatrix[c1][dMin[c1]])c1=i}c2=dMin[c1];c1Cluster=clusters[c1][0];c2Cluster=clusters[c2][0];var newCluster={left:c1Cluster,right:c2Cluster,dist:distMatrix[c1][c2],centroid:calculateCentroid(c1Cluster.size,c1Cluster.centroid,c2Cluster.size,c2Cluster.centroid),id:id++,size:c1Cluster.size+c2Cluster.size,depth:1+Math.max(c1Cluster.depth,c2Cluster.depth)};clusters[c1].splice(0,0,newCluster);cSize[c1]+=cSize[c2];for(j=0;j<n;j++){switch(linkage){case"single":if(distMatrix[c1][j]>distMatrix[c2][j])distMatrix[j][c1]=distMatrix[c1][j]=distMatrix[c2][j];break;case"complete":if(distMatrix[c1][j]<distMatrix[c2][j])distMatrix[j][c1]=distMatrix[c1][j]=distMatrix[c2][j];break;case"average":distMatrix[j][c1]=distMatrix[c1][j]=(cSize[c1]*distMatrix[c1][j]+cSize[c2]*distMatrix[c2][j])/(cSize[c1]+cSize[j]);break}}distMatrix[c1][c1]=Infinity;for(i=0;i<n;i++)distMatrix[i][c2]=distMatrix[c2][i]=Infinity;for(j=0;j<n;j++){if(dMin[j]==c2)dMin[j]=c1;if(distMatrix[c1][j]<distMatrix[c1][dMin[c1]])dMin[c1]=j}root=newCluster}return root}hcluster.linkage=function(x){if(!arguments.length)return linkage;linkage=x;return hcluster};hcluster.distance=function(x){if(!arguments.length)return distance;distance=x;return hcluster};hcluster.distanceMatrix=function(x){if(!arguments.length)return distMatrix;distMatrix=x.map(function(y){return y.slice(0)});return hcluster};return hcluster};function calculateCentroid(c1Size,c1Centroid,c2Size,c2Centroid){var newCentroid=[],newSize=c1Size+c2Size,n=c1Centroid.length,i=-1;while(++i<n){newCentroid[i]=(c1Size*c1Centroid[i]+c2Size*c2Centroid[i])/newSize}return newCentroid}reorder.leafOrder=function(){var distanceMatrix=null,distance=reorder.distance.euclidean,linkage="complete",debug=0,leavesMap={},orderMap={};function isLeaf(n){return n.depth==0}function leaves(n){if(n==null)return[];if(n.id in leavesMap)return leavesMap[n.id];return leavesMap[n.id]=_leaves(n)}function _leaves(n){if(n==null)return[];if(n.depth==0)return[n.id];return leaves(n.left).concat(leaves(n.right))}function order(v,i,j){var key="k"+v.id+"-"+i+"-"+j;if(key in orderMap)return orderMap[key];return orderMap[key]=_order(v,i,j)}function _order(v,i,j){if(v.depth==0)return[0,[v.id]];var l=v.left,r=v.right;var L=leaves(l),R=leaves(r);var w,x;if(L.indexOf(i)!=-1&&R.indexOf(j)!=-1){w=l;x=r}else if(R.indexOf(i)!=-1&&L.indexOf(j)!=-1){w=r;x=l}else throw{error:"Node is not common ancestor of "+i+", "+j};var Wl=leaves(w.left),Wr=leaves(w.right);var Ks=Wr.indexOf(i)!=-1?Wl:Wr;if(Ks.length==0)Ks=[i];var Xl=leaves(x.left),Xr=leaves(x.right);var Ls=Xr.indexOf(j)!=-1?Xl:Xr;if(Ls.length==0)Ls=[j];var max=Infinity,optimal_order=[];for(var k=0;k<Ks.length;k++){var w_max=order(w,i,Ks[k]);for(var m=0;m<Ls.length;m++){var x_max=order(x,Ls[m],j);var sim=w_max[0]+distanceMatrix[Ks[k]][Ls[m]]+x_max[0];if(sim<max){max=sim;optimal_order=w_max[1].concat(x_max[1])}}}return[max,optimal_order]}function orderFull(v){leavesMap={};orderMap={};var max=Infinity,optimal_order=[],left=leaves(v.left),right=leaves(v.right);if(debug)console.log(reorder.printhcluster(v,0));for(var i=0;i<left.length;i++){for(var j=0;j<right.length;j++){var so=order(v,left[i],right[j]);if(so[0]<max){max=so[0];optimal_order=so[1]}}}distanceMatrix=null;return optimal_order}function leafOrder(vector){if(distanceMatrix==null)distanceMatrix=reorder.dist().distance(distance)(vector);var hcluster=science.stats.hcluster().linkage(linkage).distanceMatrix(distanceMatrix);return orderFull(hcluster(vector))}leafOrder.debug=function(x){if(!arguments.length)return debug;debug=x;return leafOrder};leafOrder.distance=function(x){if(!arguments.length)return distance;distance=x;distanceMatrix=null;return leafOrder};leafOrder.linkage=function(x){if(!arguments.length)return linkage;linkage=x;return leafOrder};leafOrder.distanceMatrix=function(x){if(!arguments.length)return distanceMatrix;distanceMatrix=x.map(function(y){return y.slice(0)});return leafOrder};leafOrder.orderFull=orderFull;return leafOrder};reorder.order=function(){var distance=reorder.distance.euclidean,ordering=reorder.leafOrder,linkage="complete",distanceMatrix,vector,except=[],debug=0,i=0,j=Infinity;function _reset(){distance=reorder.distance.euclidean;ordering=reorder.leafOrder;linkage="complete";distanceMatrix=null;vector=null;except=[];debug=0;i=0;j=Infinity}function order(v){vector=v;j=Math.min(j,v.length);var i0=i>0?i-1:0,j0=j<vector.length?j+1:j,k,low,high;for(k=except.length-1;k>0;k-=2){low=except[k-1];high=except[k];if(high>=j0){if(j0>j){j0=Math.min(j0,low+1);except.splice(k-1,2)}else{high=j0}}else if(low<=i0){if(i0<i){i0=Math.max(i0,high-1);except.splice(k-1,2)}else{low=i0}}else if(high-low<3)except.splice(k-1,2)}try{return _order_limits(i0,j0)}finally{_reset()}}function _order_limits(i0,j0){var orig=vector,perm,row,k,l;vector=vector.slice(i0,j0);if(i==0&&j==vector.length)return _order_except();if(debug)console.log("i0="+i0+" j0="+j0);if(distanceMatrix!=null){if(j0!=vector.length)reorder.dist_remove(distanceMatrix,j0,vector.length);if(i0>0)reorder.dist_remove(distanceMatrix,0,i0)}else{_compute_dist()}var max=reorder.distmax(distanceMatrix);if(i0<i){row=distanceMatrix[0];for(k=row.length;k-->1;)row[k]+=max;for(k=distanceMatrix.length;k-->1;)distanceMatrix[k][0]+=max;max+=max;if(i0!=0){for(k=0;k<except.length;k++)except[k]-=i0}}if(j0>j){l=distanceMatrix.length-1;row=distanceMatrix[l];for(k=l;k-->0;){row[k]+=max;distanceMatrix[k][l]+=max}}perm=_order_except();if(i0<i){if(perm[0]!=0)perm.reverse();if(j0>j){reorder.assert(perm[0]==0&&perm[perm.length-1]==perm.length-1,"Invalid constrained permutation endpoints")}else{reorder.assert(perm[0]==0,"Invalid constrained permutation start")}}else if(j0>j){if(perm[perm.length-1]!=perm.length-1)perm=perm.reverse();reorder.assert(perm[perm.length-1]==perm.length-1,"Invalid constrained permutation end")}if(i0!=0){perm=reorder.permutation(i0).concat(perm.map(function(v){return v+i0}))}if(orig.length>j0){perm=perm.concat(reorder.range(j0,orig.length))}return perm}function _order_except(){var perm,k,l,low,high,pos;if(except.length==0)return _order_equiv();_compute_dist();for(k=except.length-1;k>0;k-=2){low=except[k-1];high=except[k];distanceMatrix=reorder.dist_remove(distanceMatrix,low+1,high-1);vector.splice(low+1,high-low-2);if(debug)console.log("Except["+low+", "+high+"]");if(distanceMatrix[low][low+1]!=0){distanceMatrix[low][low+1]=distanceMatrix[low+1][low]=-1}}perm=_order_equiv();for(k=0;k<except.length;k+=2){low=except[k];high=except[k+1];for(l=0;l<perm.length;l++){if(perm[l]>low)perm[l]+=high-low-2;else if(perm[l]==low)pos=l}if(pos>0&&perm[pos-1]==high-1){Array.prototype.splice.apply(perm,[pos,0].concat(reorder.range(high-2,low,-1)))}else if(perm[pos+1]==high-1){Array.prototype.splice.apply(perm,[pos+1,0].concat(reorder.range(low+1,high-1)))}else{throw"Range not respected"}}return perm}function _order_equiv(){var perm,row,e,j,k,l,m,n,has_1=false,equiv=[],fix_except={};_compute_dist();for(k=0;k<distanceMatrix.length-1;k++){row=distanceMatrix[k];e=[];j=row.indexOf(-1);if(j!=-1){fix_except[k]=[k,j];has_1=true}for(l=row.length;--l>k;){if(row[l]==0){j=distanceMatrix[l].indexOf(-1);if(j!=-1){fix_except[k]=[l,j];distanceMatrix[j][k]=row[j]=-1;has_1=true}e.unshift(l);distanceMatrix=reorder.dist_remove(distanceMatrix,l);vector.splice(l,1)}else if(row[l]<0)has_1=true}if(e.length!=0){e.unshift(k);equiv.push(e)}}if(has_1){for(k=0;k<distanceMatrix.length-1;k++){row=distanceMatrix[k];for(l=k+1;l<row.length-1;l++){if(distanceMatrix[l][l+1]==-1){distanceMatrix[l+1][l]=distanceMatrix[l][l+1]=0}}}}perm=_order();for(k=equiv.length;k-->0;){e=equiv[k];l=perm.indexOf(e[0]);m=fix_except[e[0]];if(m&&m[0]==e[0]){l=_fix_exception(perm,l,m[0],m[1],0);m=undefined}for(n=1;n<e.length;n++){perm=_perm_insert(perm,l,e[n]);if(m&&m[0]==e[n]){l=_fix_exception(perm,l,m[0],m[1],n);m=undefined}}}return perm}function _fix_exception(perm,l,m,next,len){var i,j,k;if(l>0&&perm[l-1]==next){_swap(perm,l,perm.indexOf(m));return l+1}else if(perm[l+len+1]==next){_swap(perm,l+len,perm.indexOf(m));return l}else throw"Index not found"}function _swap(perm,a,b){if(a==b)return;var c=perm[a];perm[a]=perm[b];perm[b]=c}function _order(){if(debug>1)reorder.printmat(distanceMatrix);if(debug>2)reorder.printmat(vector);var perm=ordering().debug(debug).linkage(linkage).distanceMatrix(distanceMatrix)(vector);if(debug)console.log("Permutation: "+perm);return perm}function _perm_insert(perm,i,nv){perm=perm.map(function(v){return v<nv?v:v+1});perm.splice(i,0,nv);return perm}order.debug=function(x){if(!arguments.length)return debug;debug=x;return order};function _compute_dist(){if(distanceMatrix==null)distanceMatrix=reorder.dist().distance(distance)(vector);return distanceMatrix}order.distance=function(x){if(!arguments.length)return distance;distance=x;return order};order.linkage=function(x){if(!arguments.length)return linkage;linkage=x;return order};order.limits=function(x,y){if(!arguments.length)return[i,j];i=x;j=y;return order};order.except=function(list){if(!arguments.length)return except.slice(0);except=list.sort(function(a,b){if(a>=b)throw"Invalid list, indices not sorted";return a-b});return order};function _orderExcept(vector,i,j){var distanceMatrix=reorder.dist().distance(distance)(vector);var row,k,l,rev=false,args,pos=-1;distanceMatrix[i][i+1]=0;distanceMatrix[i+1][i]=0;var perm=ordering().distanceMatrix(distanceMatrix)(vector);pos=perm.indexOf(i);for(k=0;k<perm.length;k++){l=perm[k];if(l>i)perm[k]+=j-i-2}if(pos!=0&&perm[pos-1]==j-1)rev=true;if(rev){perm.reverse();pos=perm.length-pos-1}args=[pos+1,0].concat(reorder.range(i+1,j-1));Array.prototype.splice.apply(perm,args);return perm}order.orderrowsexcept=order.orderexcept;return order};reorder.covariance=science.lin.dot;reorder.covariancetranspose=function(v,a,b){var n=v.length,cov=0,i;for(i=0;i<n;i++){cov+=v[i][a]*v[i][b]}return cov};reorder.variancecovariance=function(v){
-var o=v[0].length,cov=Array(o),i,j;for(i=0;i<o;i++){cov[i]=Array(o)}for(i=0;i<o;i++){for(j=i;j<o;j++)cov[i][j]=cov[j][i]=reorder.covariancetranspose(v,i,j)}return cov};function normalize(v){var norm=science.lin.length(v),i=v.length;while(i-->0)v[i]/=norm;return v}reorder.poweriteration=function(v,eps){if(arguments.length<2)eps=1e-4;var n=v.length,b=Array(n),i,j,tmp=Array(n),norm,s=10;reorder.assert(n==v[0].length,"poweriteration needs a square matrix");for(i=0;i<n;i++)b[i]=Math.random();b=normalize(b);while(s-->0){for(i=0;i<n;i++){tmp[i]=0;for(j=0;j<n;j++)tmp[i]+=v[i][j]*b[j]}tmp=normalize(tmp);var t=tmp;tmp=b;b=t}return tmp};reorder.sortorder=function(v){return reorder.range(0,v.length).sort(function(a,b){return v[a]-v[b]})};reorder.center=function(v){var n=v.length;if(n==0)return null;var mean=reorder.meancolumns(v),o=mean.length,v1=Array(n),i,j,row;for(i=0;i<n;i++){row=v[i].slice(0);for(j=0;j<o;j++){row[j]-=mean[j]}v1[i]=row}return v1};reorder.pca1d=function(v,eps){if(arguments.length<2)eps=1e-4;var n=v.length;if(v.length==0)return null;v=reorder.center(v);var cov=reorder.variancecovariance(v);return reorder.poweriteration(cov,eps)};reorder.pca1dorder=function(v,eps){return reorder.sortorder(pca1d(v,eps))};reorder.sumlines=function(v){var n=v.length,o=v[0].length,sumline=Array(n),i,j,row,s;for(i=0;i<n;i++){row=v[i];s=0;for(j=0;j<o;j++)s+=row[j];sumline[i]=s}return sumline};reorder.sumcols=function(v){var n=v.length,o=v[0].length,sumcol=reorder.zeroes(o),i,j,row;for(i=0;i<n;i++){row=v[i];for(j=0;j<o;j++)sumcol[j]+=row[j]}return sumcol};reorder.ca=function(v,eps){if(arguments.length<2)eps=1e-4;var n=v.length,o=v[0].length,sumline=reorder.sumlines(v),sumcol=reorder.sumcols(v),s=reorder.sum(sumcol),i,j,row;for(i=0;i<n;i++){v[i]=v[i].map(function(a){return a/s})}sumline=reorder.sumlines(v);sumcol=reorder.sumcols(v);var v2=Array(n),ep;for(i=0;i<n;i++){v2[i]=Array(o);for(j=0;j<o;j++){ep=sumline[i]*sumcol[j];v2[i][j]=(v[i][j]-ep)/Math.sqrt(ep)}}for(i=0;i<n;i++){for(j=0;j<o;j++){ep=sumline[i]*sumcol[j];v[i][j]=(v[i][j]-ep)/(sumcol[j]*Math.sqrt(sumline[i]))}}var cov=Array(n);for(i=0;i<n;i++)cov[i]=Array(n);for(i=0;i<n;i++)for(j=i;j<n;j++)cov[i][j]=cov[j][i]=reorder.covariance(v2[i],v2[j]);var eigenvector1=reorder.poweriteration(cov,eps),eigenvalue1=0;for(i=0;i<n;i++)eigenvalue1+=eigenvector1[i]*cov[i][0];eigenvalue1/=eigenvector1[0];return eigenvector1};reorder.cuthill_mckee=function(graph,comps){var i,order=[];if(!comps){comps=graph.components()}for(i=0;i<comps.length;i++){order=order.concat(reorder.cuthill_mckee1(graph,comps[i]))}return order};reorder.cuthill_mckee1=function(graph,comp){if(comp.length<2)return comp;var nodes=graph.nodes(),start=comp[0],min_deg=graph.degree(start),i,n,edges,e,visited={},queue=new Queue,order=[];for(i=0;i<comp.length;i++){n=nodes[comp[i]].index;if(graph.degree(n)<min_deg){min_deg=graph.degree(n);start=n;if(min_deg==1)break}}queue.push(start);while(queue.length!=0){n=queue.shift();if(visited[n])continue;visited[n]=true;order.push(n);e=graph.edges(n).map(function(edge){return graph.other(edge,n).index}).filter(function(n){return!visited[n]}).sort(function(a,b){return graph.degree(a)-graph.degree(b)});e.forEach(queue.push,queue)}return order};reorder.reverse_cuthill_mckee=function(graph,comps){return reorder.cuthill_mckee(graph,comps).reverse()}})(this);
\ No newline at end of file
+(function(exports){reorder={version:"0.0.5"};reorder.cmp_number_asc=function(a,b){return a-b};reorder.cmp_number=reorder.cmp_number_asc;reorder.cmp_number_desc=function(a,b){return b-a};reorder.flatten=function(a,b){return a.concat(b)};reorder.infinities=function(n){var i=-1,a=[];if(arguments.length===1)while(++i<n)a[i]=Infinity;else while(++i<n)a[i]=reorder.infinities.apply(this,Array.prototype.slice.call(arguments,1));return a};reorder.array1d=function(n,v){var i=-1,a=Array(n);while(++i<n)a[i]=v;return a};reorder.dot=science.lin.dot;reorder.length=science.lin.length;reorder.normalize=science.lin.normalize;reorder.zeroes=science.zeroes;reorder.displaymat=function(mat,rowperm,colperm){var i,j,row,col,str;if(!rowperm){rowperm=reorder.range(mat.length)}if(!colperm){colperm=reorder.range(mat[0].length)}console.log("Matrix:");for(i=0;i<mat.length;i++){row=rowperm?mat[rowperm[i]]:mat[i];str="";for(j=0;j<row.length;j++){col=colperm?row[colperm[j]]:row[j];str+=col?"*":" "}console.log(str)}};reorder.printmat=function(m){var i,j,row,line;for(i=0;i<m.length;i++){row=m[i];line="";for(j=0;j<row.length;j++){if(line.length!=0)line+=", ";line+=row[j].toFixed(4)}console.log(i.toPrecision(3)+": "+line)}};reorder.assert=function(v,msg){if(!v){console.log(msg);throw msg||"Assertion failed"}};reorder.printhcluster=function(cluster,indent){if(cluster.left==null)return Array(indent+1).join(" ")+"id: "+cluster.id;return Array(indent+1).join(" ")+"id: "+cluster.id+", dist: "+cluster.dist+"\n"+reorder.printhcluster(cluster.left,indent+1)+"\n"+reorder.printhcluster(cluster.right,indent+1)};reorder.mean=science.stats.mean;reorder.meantranspose=function(v,j){var n=v.length;if(n==0)return NaN;var o=v[0].length,m=0,i=-1,row;while(++i<n)m+=(v[i][j]-m)/(i+1);return m};reorder.meancolumns=function(v){var n=v.length;if(n==0)return NaN;var o=v[0].length,m=v[0].slice(0),i=0,j,row;while(++i<n){row=v[i];for(j=0;j<o;j++)m[j]+=(row[j]-m[j])/(i+1)}return m};reorder.sum=function(v){var i=v.length,s=v[0];while(i-->1)s+=v[i];return s};function isNum(a,b){return!(isNaN(a)||isNaN(b)||a==Infinity||b==Infinity)}reorder.distance={euclidean:function(a,b){var i=a.length,s=0,x;while(i-->0){if(isNum(a[i],b[i])){x=a[i]-b[i];s+=x*x}}return Math.sqrt(s)},manhattan:function(a,b){var i=a.length,s=0;while(i-->0){if(isNum(a[i],b[i])){s+=Math.abs(a[i]-b[i])}}return s},minkowski:function(p){return function(a,b){var i=a.length,s=0;while(i-->0){if(isNum(a[i],b[i])){s+=Math.pow(Math.abs(a[i]-b[i]),p)}}return Math.pow(s,1/p)}},chebyshev:function(a,b){var i=a.length,max=0,x;while(i-->0){if(isNum(a[i],b[i])){x=Math.abs(a[i]-b[i]);if(x>max)max=x}}return max},hamming:function(a,b){var i=a.length,d=0;while(i-->0){if(isNum(a[i],b[i])){if(a[i]!==b[i])d++}}return d},jaccard:function(a,b){var n=0,i=a.length,s=0;while(i-->0){if(isNum(a[i],b[i])){if(a[i]===b[i])s++;n++}}if(n==0)return 0;return s/n},braycurtis:function(a,b){var i=a.length,s0=0,s1=0,ai,bi;while(i-->0){ai=a[i];bi=b[i];if(isNum(ai,bi)){s0+=Math.abs(ai-bi);s1+=Math.abs(ai+bi)}}if(s1==0)return 0;return s0/s1}};reorder.range=function(start,stop,step){if(arguments.length<3){step=1;if(arguments.length<2){stop=start;start=0}}var range=[],i=start;if(step<0)for(;i>stop;i+=step)range.push(i);else for(;i<stop;i+=step)range.push(i);return range};reorder.transpose=science.lin.transpose;reorder.transposeSlice=function(a,start,end){if(arguments.length<3){end=a[0].length;if(arguments.length<2){start=0}}var m=a.length,n=end,i=start-1,j,b=new Array(end-start);while(++i<n){b[i]=new Array(m);j=-1;while(++j<m)b[i-start][j]=a[j][i]}return b};reorder.correlation={pearson:function(a,b){var ma=science.stats.mean(a),mb=science.stats.mean(b),s1=0,s2=0,s3=0,i,dx,dy,n=Math.min(a.length,b.length);if(n===0)return NaN;for(i=0;i<n;i++){dx=a[i]-ma;dy=b[i]-mb;s1+=dx*dy;s2+=dx*dx;s3+=dy*dy}return s1/Math.sqrt(s2*s3)},pearsonMatrix:function(matrix){var a,ma,i,j,dx,n=matrix.length,ret,mx,sx,sx2;if(n===0)return NaN;mx=Array(n);sx=reorder.zeroes(n);sx2=reorder.zeroes(n);for(i=0;i<n;i++){mx[i]=science.stats.mean(matrix[i])}for(i=0;i<n;i++){a=matrix[i];ma=mx[i];for(j=0;j<n;j++){dx=a[j]-ma;sx[j]+=dx;sx2[j]+=dx*dx}}ret=Array(n);for(i=0;i<n;i++){ret[i]=Array(n);for(j=0;j<n;j++){ret[i][j]=sx[i]*sx[j]/Math.sqrt(sx2[i]*sx2[j])}}return ret}};reorder.bandwidth=function(graph,order){if(!order)order=reorder.range(graph.nodes().length);var inv=inverse_permutation(order),links=graph.links(),i,e,d,max=0;for(i=0;i<links.length;i++){e=links[i];d=Math.abs(inv[e.source.index]-inv[e.target.index]);max=Math.max(max,d)}return max};reorder.permutation=reorder.range;function inverse_permutation(perm){var inv={};for(var i=0;i<perm.length;i++){inv[perm[i]]=i}return inv}reorder.inverse_permutation=inverse_permutation;reorder.graph=function(nodes,links,directed){var graph={},linkDistance=1,edges,inEdges,outEdges,components;graph.nodes=function(x){if(!arguments.length)return nodes;nodes=x;return graph};graph.nodes_indices=function(){return nodes.map(function(n){return n.index})};graph.links=function(x){if(!arguments.length)return links;links=x;return graph};graph.links_indices=function(){return links.map(function(l){return{source:l.source.index,target:l.target.index}})};graph.linkDistance=function(x){if(!arguments.length)return linkDistance;linkDistance=typeof x==="function"?x:+x;return graph};graph.directed=function(x){if(!arguments.length)return directed;directed=x;return graph};function init(){var i,o,n=nodes.length,m=links.length;components=undefined;for(i=0;i<n;++i){(o=nodes[i]).index=i;o.weight=0}for(i=0;i<m;++i){(o=links[i]).index=i;if(typeof o.source=="number")o.source=nodes[o.source];if(typeof o.target=="number")o.target=nodes[o.target];if(!("value"in o))o.value=1;++o.source.weight;++o.target.weight}if(typeof linkDistance==="function")for(i=0;i<m;++i)links[i].distance=+linkDistance.call(this,links[i],i);else for(i=0;i<m;++i)links[i].distance=linkDistance;edges=Array(nodes.length);for(i=0;i<nodes.length;++i){edges[i]=[]}if(directed){inEdges=Array(nodes.length);outEdges=Array(nodes.length);for(i=0;i<nodes.length;++i){inEdges[i]=[];outEdges[i]=[]}}else{inEdges=outEdges=edges}for(i=0;i<links.length;++i){o=links[i];edges[o.source.index].push(o);if(o.source.index!=o.target.index)edges[o.target.index].push(o);if(directed)inEdges[o.source.index].push(o);if(directed)outEdges[o.target.index].push(o)}return graph}graph.init=init;function edges(node){if(typeof node!="number"){node=node.index;console.log("received node %d",node)}return edges[node]}graph.edges=edges;graph.degree=function(node){if(typeof node!="number")node=node.index;return edges[node].length};function inEdges(node){if(typeof node!="number")node=node.index;return inEdges[node]}graph.inEdges=inEdges;graph.inDegree=function(node){if(typeof node!="number")node=node.index;return inEdges[node].length};function outEdges(node){if(typeof node!="number")node=node.index;return outEdges[node]}graph.outEdges=outEdges;graph.outDegree=function(node){if(typeof node!="number")node=node.index;return outEdges[node].length};graph.sinks=function(){var sinks=[],i;for(i=0;i<nodes.length;i++){if(outEdges(i).length==0)sinks.push(i)}return sinks};graph.sources=function(){var sources=[],i;for(i=0;i<nodes.length;i++){if(inEdges(i).length==0)sources.push(i)}return sources};function distance(i){return links[i].distance}graph.distance=distance;function neighbors(node){var e=edges[node],ret=[];for(var i=0;i<e.length;++i){var o=e[i];if(o.source.index==node)ret.push(o.target);else ret.push(o.source)}return ret}graph.neighbors=neighbors;graph.other=function(o,node){if(typeof o=="number")o=links[o];if(o.source.index==node)return o.target;else return o.source};function compute_components(){var stack=[],comp=0,comps=[],ccomp,n=nodes.length,i,j,v,l,o,e;for(i=0;i<n;i++)nodes[i].comp=0;for(j=0;j<n;j++){if(nodes[j].comp!=0)continue;comp=comp+1;nodes[j].comp=comp;stack.push(j);ccomp=[j];while(stack.length){v=stack.shift();l=edges[v];for(i=0;i<l.length;i++){e=l[i];o=e.source;if(o.index==v)o=e.target;if(o.index==v)continue;if(o.comp==0){o.comp=comp;ccomp.push(o.index);stack.push(o.index)}}}if(ccomp.length){ccomp.sort(reorder.cmp_number);comps.push(ccomp)}}comps.sort(function(a,b){return b.length-a.length});return comps}graph.components=function(){if(!components)components=compute_components();return components};return graph};reorder.graph_random_erdos_renyi=function(n,p,directed){if(p<=0)return reorder.graph_empty(n,directed);else if(p>=1)return reorder.graph_complete(n,directed);var nodes=graph_empty_nodes(n),links=[],v,w,i,lr,lp;w=-1;lp=Math.log(1-p);if(directed){for(v=0;v<n;){lr=Math.log(1-Math.random());w=w+1+Math.floor(lr/lp);if(v==w)w=w+1;while(w>=n&&v<n){w=w-n;v=v+1;if(v==w)w=w+1}if(v<n)links.push({source:v,target:w})}}else{for(v=1;v<n;){lr=Math.log(1-Math.random());w=w+1+Math.floor(lr/lp);while(w>=v&&v<n){w=w-v;v=v+1}if(v<n)links.push({source:v,target:w})}}return reorder.graph(nodes,links,directed).init()};reorder.graph_random=reorder.graph_random_erdos_renyi;function graph_empty_nodes(n){var nodes=Array(n),i;for(i=0;i<n;i++)nodes[i]={id:i};return nodes}reorder.graph_empty_nodes=graph_empty_nodes;reorder.graph_empty=function(n,directed){return graph(graph_empty_nodes(n),[],directed)};reorder.complete_graph=function(n,directed){var nodes=graph_empty_nodes(n),links=[],i,j;if(directed){for(i=0;i<n;i++){for(j=0;j<n;j++){if(i!=j)links.push({source:i,target:j})}}}else{for(i=0;i<n-1;i++){for(j=i+1;j<n;j++)links.push({source:i,target:j})}}return reorder.graph(nodes,links,directed).init()};reorder.graph_connect=function(graph,comps){var i,j,links=graph.links();if(!comps)comps=graph.components();for(i=0;i<comps.length-1;i++){for(j=i+1;j<comps.length;j++){links.push({source:comps[i][0],target:comps[j][0]})}}graph.links(links);return graph.init()};reorder.bfs=function(graph,v,fn){var q=new Queue,discovered={};q.push(v);discovered[v]=true;fn(v,undefined);while(q.length){v=q.shift();fn(v,v);graph.edges(v).forEach(function(e){var v2=graph.other(e,v).index;if(!discovered[v2]){q.push(v2);discovered[v2]=true;fn(v,v2)}});fn(v,-1)}};reorder.bfs_distances=function(graph,v){var dist={};dist[v]=0;reorder.bfs(graph,v,function(v,c){if(c>=0&&v!=c)dist[c]=dist[v]+1});return dist};reorder.all_pairs_distance_bfs=function(graph,comps){if(!comps)comps=[graph.nodes_indices()];var nodes=comps.reduce(reorder.flatten).sort(reorder.cmp_number),mat=Array(nodes.length),i,j,dist;for(i=0;i<nodes.length;i++)mat[i]=Array(nodes.length);for(i=0;i<nodes.length;i++){dist=reorder.bfs_distances(graph,i);for(j in dist){mat[i][j]=dist[j];mat[j][i]=dist[j]}}return mat};reorder.mat2graph=function(mat,directed){var n=mat.length,nodes=[],links=[],max_value=Number.NEGATIVE_INFINITY,i,j,v,m;for(i=0;i<n;i++)nodes.push({id:i});for(i=0;i<n;i++){v=mat[i];m=directed?0:i;for(j=m;j<v.length;j++){if(j==nodes.length)nodes.push({id:j});if(v[j]!=0){if(v[j]>max_value)max_value=v[j];links.push({source:i,target:j,value:v[j]})}}}return reorder.graph(nodes,links,directed).linkDistance(function(l,i){return 1+max_value-l.value}).init()};reorder.graph2mat=function(graph,directed){var nodes=graph.nodes(),links=graph.links(),n=nodes.length,i,l,mat;if(!directed)directed=graph.directed();if(directed){var rows=n,cols=n;for(i=n-1;i>=0;i--){if(graph.inEdges(i).length!=0)break;else rows--}for(i=n-1;i>=0;i--){if(graph.outEdges(i).length!=0)break;else cols--}mat=reorder.zeroes(rows,cols);for(i=0;i<links.length;i++){l=links[i];mat[l.source.index][l.target.index]=l.value?l.value:1}}else{mat=reorder.zeroes(n,n);for(i=0;i<links.length;i++){l=links[i];mat[l.source.index][l.target.index]=l.value?l.value:1;mat[l.target.index][l.source.index]=l.value?l.value:1}}return mat};function count_crossings(graph,north,south){var i,j,n,firstIndex,treeSize,tree,index,weightSum,invert=false,crosscount;var comp=reorder.permutation(graph.nodes().length);if(north==undefined){north=comp.filter(function(n){return graph.outDegree(n)!=0}),south=comp.filter(function(n){return graph.inDegree(n)!=0})}if(north.length<south.length){var tmp=north;north=south;south=tmp;invert=true}var south_inv=inverse_permutation(south),southsequence=[];for(i=0;i<north.length;i++){if(invert){n=graph.inEdges(north[i]).map(function(e){return south_inv[e.target.index]})}else{n=graph.outEdges(north[i]).map(function(e){return south_inv[e.source.index]})}n.sort(reorder.cmp_number);southsequence=southsequence.concat(n)}firstIndex=1;while(firstIndex<south.length)firstIndex<<=1;treeSize=2*firstIndex-1;firstIndex-=1;tree=reorder.zeroes(treeSize);crosscount=0;for(i=0;i<southsequence.length;i++){index=southsequence[i]+firstIndex;tree[index]++;while(index>0){if(index%2)crosscount+=tree[index+1];index=index-1>>1;tree[index]++}}return crosscount}reorder.count_crossings=count_crossings;function count_in_crossings(graph,v,w,inv){var v_edges=graph.inEdges(v),w_edges=graph.inEdges(w),iv,iw,p0,cross=0;for(iw=0;iw<w_edges.length;iw++){p0=inv[w_edges[iw].target.index];for(iv=0;iv<v_edges.length;iv++){if(inv[v_edges[iv].target.index]>p0)cross++}}return cross}function count_out_crossings(graph,v,w,inv){var v_edges=graph.outEdges(v),w_edges=graph.outEdges(w),iv,iw,p0,cross=0;for(iw=0;iw<w_edges.length;iw++){p0=inv[w_edges[iw].source.index];for(iv=0;iv<v_edges.length;iv++){if(inv[v_edges[iv].source.index]>p0)cross++}}return cross}function adjacent_exchange(graph,layer1,layer2){layer1=layer1.slice();layer2=layer2.slice();var i,v,w,c0,c1,inv_layer1=inverse_permutation(layer1),inv_layer2=inverse_permutation(layer2),swapped=true,improved=0;while(swapped){swapped=false;for(i=0;i<layer1.length-1;i++){v=layer1[i];w=layer1[i+1];c0=count_out_crossings(graph,v,w,inv_layer2);c1=count_out_crossings(graph,w,v,inv_layer2);if(c0>c1){layer1[i]=w;layer1[i+1]=v;inv_layer1[w]=i;inv_layer1[v]=i+1;swapped=true;improved+=c0-c1}}for(i=0;i<layer2.length-1;i++){v=layer2[i];w=layer2[i+1];c0=count_in_crossings(graph,v,w,inv_layer1);c1=count_in_crossings(graph,w,v,inv_layer1);if(c0>c1){layer2[i]=w;layer2[i+1]=v;inv_layer2[w]=i;inv_layer2[v]=i+1;swapped=true;improved+=c0-c1}}}return[layer1,layer2,improved]}reorder.adjacent_exchange=adjacent_exchange;reorder.barycenter=function(graph,iter,comps){var perms=[[],[],0];if(!comps){comps=graph.components()}for(var i=0;i<comps.length;i++){var p=reorder.barycenter1(graph,comps[i],iter);perms=[perms[0].concat(p[0]),perms[1].concat(p[1]),perms[2]+p[2]]}return perms};function median(neighbors){if(neighbors.length==0)return-1;if(neighbors.length==1)return neighbors[0];if(neighbors.length==2)return(neighbors[0]+neighbors[1])/2;neighbors.sort(reorder.cmp_number);if(neighbors.length%2)return neighbors[(neighbors.length-1)/2];var rm=neighbors.length/2,lm=rm-1,rspan=neighbors[neighbors.length-1]-neighbors[rm],lspan=neighbors[lm]-neighbors[0];if(lspan==rspan)return(neighbors[lm]+neighbors[rm])/2;else return(neighbors[lm]*rspan+neighbors[rm]*lspan)/(lspan+rspan)}reorder.barycenter1=function(graph,comp,max_iter){var nodes=graph.nodes(),layer1,layer2,crossings,iter,best_layer1,best_layer2,best_crossings,best_iter,layer,i,v,neighbors;layer1=comp.filter(function(n){return graph.outDegree(n)!=0});layer2=comp.filter(function(n){return graph.inDegree(n)!=0});if(comp.length<3){return[layer1,layer2,count_crossings(graph,layer1,layer2)]}if(!max_iter)max_iter=24;else if(max_iter%2==1)max_iter++;for(i=0;i<layer2.length;i++)nodes[layer2[i]].pos=i;best_crossings=count_crossings(graph,layer1,layer2);best_layer1=layer1.slice();best_layer2=layer2.slice();best_iter=0;for(layer=layer1,iter=0;iter<max_iter;iter++,layer=layer==layer1?layer2:layer1){for(i=0;i<layer.length;i++){v=nodes[layer[i]];if(layer==layer1)neighbors=graph.outEdges(v.index);else neighbors=graph.inEdges(v.index);neighbors=neighbors.map(function(e){var n=e.source==v?e.target:e.source;return nodes[n.index].pos});v.median=median(neighbors)}layer.sort(function(a,b){var d=nodes[a].median-nodes[b].median;if(d==0){d=graph.edges(b).length%2-graph.edges(a).length%2}if(d<0)return-1;else if(d>0)return 1;return 0});for(i=0;i<layer.length;i++)nodes[layer[i]].pos=i;crossings=count_crossings(graph,layer1,layer2);if(crossings<best_crossings){best_crossings=crossings;best_layer1=layer1.slice();best_layer2=layer2.slice();best_iter=iter;max_iter=Math.max(max_iter,iter+2)}}return[best_layer1,best_layer2,best_crossings]};reorder.all_pairs_distance=function(graph,comps){var distances=[];if(!comps)comps=graph.components();for(var i=0;i<comps.length;i++)distances.push(reorder.all_pairs_distance1(graph,comps[i]));return distances};function all_pairs_distance_floyd_warshall(graph,comp){var dist=reorder.infinities(comp.length,comp.length),edges,i,j,k,inv;inv=inverse_permutation(comp);for(i=0;i<comp.length;i++)dist[i][i]=0;for(i=0;i<comp.length;i++){edges={};graph.edges(comp[i]).forEach(function(e){if(e.source==e.target)return;if(!(e.source.index in inv)||!(e.target.index in inv))return;var u=inv[e.source.index],v=inv[e.target.index];dist[v][u]=dist[u][v]=graph.distance(e.index)})}for(k=0;k<comp.length;k++){for(i=0;i<comp.length;i++)if(dist[i][k]!=Infinity){for(j=0;j<comp.length;j++)if(dist[k][j]!=Infinity&&dist[i][j]>dist[i][k]+dist[k][j]){dist[i][j]=dist[i][k]+dist[k][j];dist[j][i]=dist[i][j]}}}return dist}reorder.all_pairs_distance1=all_pairs_distance_floyd_warshall;function floyd_warshall_with_path(graph,comp){if(!comp)comp=graph.components()[0];var dist=reorder.infinities(comp.length,comp.length),next=Array(comp.length),directed=graph.directed(),edges,i,j,k,inv;inv=inverse_permutation(comp);for(i=0;i<comp.length;i++){dist[i][i]=0;next[i]=Array(comp.length)}for(i=0;i<comp.length;i++){edges={};graph.edges(comp[i]).forEach(function(e){if(e.source==e.target)return;var u=inv[e.source.index],v=inv[e.target.index];dist[u][v]=graph.distance(e);next[u][v]=v;if(!directed){dist[v][u]=graph.distance(e);next[v][u]=u}})}for(k=0;k<comp.length;k++){for(i=0;i<comp.length;i++){for(j=0;j<comp.length;j++){if(dist[i][j]>dist[i][k]+dist[k][j]){dist[i][j]=dist[i][k]+dist[k][j];next[i][j]=next[i][k];if(!directed){dist[j][i]=dist[i][j];next[j][i]=next[k][j]}}}}}return[dist,next]}reorder.floyd_warshall_with_path=floyd_warshall_with_path;reorder.floyd_warshall_path=function(next,u,v){if(next[u][v]==undefined)return[];var path=[u];while(u!=v){u=next[u][v];path.push(u)}return path};function distmat2valuemat(distmat){var n=distmat.length,valuemat=reorder.zeroes(n,n),max_dist=reorder.distmax(distmat),i,j;for(i=0;i<n;i++){for(j=i;j<n;j++){valuemat[j][i]=valuemat[i][j]=1+max_dist-distmat[i][j]}}return valuemat}reorder.distmat2valuemat=distmat2valuemat;reorder.graph2valuemats=function(graph,comps){if(!comps)comps=graph.components();var dists=reorder.all_pairs_distance(graph,comps);return dists.map(distmat2valuemat)};reorder.valuemats_reorder=function(valuemats,leaforder,comps){var orders=valuemats.map(leaforder);if(comps){orders=orders.map(function(d,i){return reorder.permute(comps[i],d)})}return orders.reduce(reorder.flatten)};reorder.distmax=function(distMatrix){var max=0,n=distMatrix.length,i,j,row;for(i=0;i<n;i++){row=distMatrix[i];for(j=i+1;j<n;j++)if(row[j]>max)max=row[j]}return max};reorder.distmin=function(distMatrix){var min=Infinity,n=distMatrix.length,i,j,row;for(i=0;i<n;i++){row=distMatrix[i];for(j=i+1;j<n;j++)if(row[j]<min)min=row[j]}return min};reorder.dist=function(){var distance=reorder.distance.euclidean;function dist(vectors){var n=vectors.length,distMatrix=[];for(var i=0;i<n;i++){var d=[];distMatrix[i]=d;for(var j=0;j<n;j++){if(j<i){d.push(distMatrix[j][i])}else if(i===j){d.push(0)}else{d.push(distance(vectors[i],vectors[j]))}}}return distMatrix}dist.distance=function(x){if(!arguments.length)return distance;distance=x;return dist};return dist};reorder.dist_remove=function(dist,n,m){if(arguments.length<3)m=n+1;var i;dist.splice(n,m-n);for(i=dist.length;i-->0;)dist[i].splice(n,m-n);return dist};reorder.randomPermute=function(array,i,j){if(arguments.length<3){j=array.length;if(arguments.length<2){i=0}}var m=j-i,t,k;while(m>0){k=i+Math.floor(Math.random()*m--);t=array[i+m];array[i+m]=array[k];array[k]=t}return array};reorder.randomPermutation=function(n){return reorder.randomPermute(reorder.permutation(n))};reorder.random_matrix=function(p,n,m,sym){if(!m)m=n;if(n!=m)sym=false;else if(!sym)sym=true;var mat=reorder.zeroes(n,m),i,j,cnt;if(sym){for(i=0;i<n;i++){cnt=0;for(j=0;j<i+1;j++){if(Math.random()<p){mat[i][j]=mat[j][i]=1;cnt++}}if(cnt==0){j=Math.floor(Math.random()*n/2);mat[i][j]=mat[j][i]=1}}}else{for(i=0;i<n;i++){cnt=0;for(j=0;j<m;j++){if(Math.random()<p){mat[i][j]=1;cnt++}}if(cnt==0)mat[i][Math.floor(Math.random()*m)]=1}}return mat};reorder.permute=function(list,perm){var m=perm.length;var copy=list.slice(0);while(m--)copy[m]=list[perm[m]];return copy};reorder.permutetranspose=function(array,indexes){var m=array.length;while(m-->0)array[m]=reorder.permute(array[m],indexes);return array};reorder.stablepermute=function(list,indexes){var p=reorder.permute(list,indexes);if(p[0]>p[p.length-1])p.reverse();return p};if(typeof science=="undefined"){science={version:"1.9.1"};science.stats={}}science.stats.hcluster=function(){var distance=reorder.distance.euclidean,linkage="single",distMatrix=null;function hcluster(vectors){var n=vectors.length,dMin=[],cSize=[],clusters=[],c1,c2,c1Cluster,c2Cluster,p,root,i,j,id=0;if(distMatrix==null){distMatrix=[];i=-1;while(++i<n){dMin[i]=0;distMatrix[i]=[];j=-1;while(++j<n){distMatrix[i][j]=i===j?Infinity:distance(vectors[i],vectors[j]);if(distMatrix[i][dMin[i]]>distMatrix[i][j])dMin[i]=j}}}else{if(distMatrix.length<n||distMatrix[0].length<n)throw{error:"Provided distance matrix length "+distMatrix.length+" instead of "+n};i=-1;while(++i<n){dMin[i]=0;j=-1;while(++j<n){if(i===j)distMatrix[i][j]=Infinity;if(distMatrix[i][dMin[i]]>distMatrix[i][j])dMin[i]=j}}}i=-1;while(++i<n){clusters[i]=[];clusters[i][0]={left:null,right:null,dist:0,centroid:vectors[i],id:id++,size:1,depth:0};cSize[i]=1}for(p=0;p<n-1;p++){c1=0;for(i=0;i<n;i++){if(distMatrix[i][dMin[i]]<distMatrix[c1][dMin[c1]])c1=i}c2=dMin[c1];c1Cluster=clusters[c1][0];c2Cluster=clusters[c2][0];var newCluster={left:c1Cluster,right:c2Cluster,dist:distMatrix[c1][c2],centroid:calculateCentroid(c1Cluster.size,c1Cluster.centroid,c2Cluster.size,c2Cluster.centroid),id:id++,size:c1Cluster.size+c2Cluster.size,depth:1+Math.max(c1Cluster.depth,c2Cluster.depth)};clusters[c1].splice(0,0,newCluster);cSize[c1]+=cSize[c2];for(j=0;j<n;j++){switch(linkage){case"single":if(distMatrix[c1][j]>distMatrix[c2][j])distMatrix[j][c1]=distMatrix[c1][j]=distMatrix[c2][j];break;case"complete":if(distMatrix[c1][j]<distMatrix[c2][j])distMatrix[j][c1]=distMatrix[c1][j]=distMatrix[c2][j];break;case"average":distMatrix[j][c1]=distMatrix[c1][j]=(cSize[c1]*distMatrix[c1][j]+cSize[c2]*distMatrix[c2][j])/(cSize[c1]+cSize[j]);break}}distMatrix[c1][c1]=Infinity;for(i=0;i<n;i++)distMatrix[i][c2]=distMatrix[c2][i]=Infinity;for(j=0;j<n;j++){if(dMin[j]==c2)dMin[j]=c1;if(distMatrix[c1][j]<distMatrix[c1][dMin[c1]])dMin[c1]=j}root=newCluster}return root}hcluster.linkage=function(x){if(!arguments.length)return linkage;linkage=x;return hcluster};hcluster.distance=function(x){if(!arguments.length)return distance;distance=x;return hcluster};hcluster.distanceMatrix=function(x){if(!arguments.length)return distMatrix;distMatrix=x.map(function(y){return y.slice(0)});return hcluster};return hcluster};function calculateCentroid(c1Size,c1Centroid,c2Size,c2Centroid){var newCentroid=[],newSize=c1Size+c2Size,n=c1Centroid.length,i=-1;while(++i<n){newCentroid[i]=(c1Size*c1Centroid[i]+c2Size*c2Centroid[i])/newSize}return newCentroid}reorder.leafOrder=function(){var distanceMatrix=null,distance=reorder.distance.euclidean,linkage="complete",debug=0,leavesMap={},orderMap={};function isLeaf(n){return n.depth==0}function leaves(n){if(n==null)return[];if(n.id in leavesMap)return leavesMap[n.id];return leavesMap[n.id]=_leaves(n)}function _leaves(n){if(n==null)return[];if(n.depth==0)return[n.id];return leaves(n.left).concat(leaves(n.right))}function order(v,i,j){var key="k"+v.id+"-"+i+"-"+j;if(key in orderMap)return orderMap[key];return orderMap[key]=_order(v,i,j)}function _order(v,i,j){if(v.depth==0)return[0,[v.id]];var l=v.left,r=v.right;var L=leaves(l),R=leaves(r);var w,x;if(L.indexOf(i)!=-1&&R.indexOf(j)!=-1){w=l;x=r}else if(R.indexOf(i)!=-1&&L.indexOf(j)!=-1){w=r;x=l}else throw{error:"Node is not common ancestor of "+i+", "+j};var Wl=leaves(w.left),Wr=leaves(w.right);var Ks=Wr.indexOf(i)!=-1?Wl:Wr;if(Ks.length==0)Ks=[i];var Xl=leaves(x.left),Xr=leaves(x.right);var Ls=Xr.indexOf(j)!=-1?Xl:Xr;if(Ls.length==0)Ls=[j];var max=Infinity,optimal_order=[];for(var k=0;k<Ks.length;k++){var w_max=order(w,i,Ks[k]);for(var m=0;m<Ls.length;m++){var x_max=order(x,Ls[m],j);var sim=w_max[0]+distanceMatrix[Ks[k]][Ls[m]]+x_max[0];if(sim<max){max=sim;optimal_order=w_max[1].concat(x_max[1])}}}return[max,optimal_order]}function orderFull(v){leavesMap={};orderMap={};var max=Infinity,optimal_order=[],left=leaves(v.left),right=leaves(v.right);if(debug)console.log(reorder.printhcluster(v,0));for(var i=0;i<left.length;i++){for(var j=0;j<right.length;j++){var so=order(v,left[i],right[j]);if(so[0]<max){max=so[0];optimal_order=so[1]}}}distanceMatrix=null;return optimal_order}function leafOrder(vector){if(distanceMatrix==null)distanceMatrix=reorder.dist().distance(distance)(vector);var hcluster=science.stats.hcluster().linkage(linkage).distanceMatrix(distanceMatrix);return orderFull(hcluster(vector))}leafOrder.debug=function(x){if(!arguments.length)return debug;debug=x;return leafOrder};leafOrder.distance=function(x){if(!arguments.length)return distance;distance=x;distanceMatrix=null;return leafOrder};leafOrder.linkage=function(x){if(!arguments.length)return linkage;linkage=x;return leafOrder};leafOrder.distanceMatrix=function(x){if(!arguments.length)return distanceMatrix;distanceMatrix=x.map(function(y){return y.slice(0)});return leafOrder};leafOrder.orderFull=orderFull;return leafOrder};reorder.order=function(){var distance=reorder.distance.euclidean,ordering=reorder.leafOrder,linkage="complete",distanceMatrix,vector,except=[],debug=0,i=0,j=Infinity;function _reset(){distance=reorder.distance.euclidean;ordering=reorder.leafOrder;linkage="complete";distanceMatrix=null;vector=null;except=[];debug=0;i=0;j=Infinity}function order(v){vector=v;j=Math.min(j,v.length);var i0=i>0?i-1:0,j0=j<vector.length?j+1:j,k,low,high;for(k=except.length-1;k>0;k-=2){low=except[k-1];high=except[k];if(high>=j0){if(j0>j){j0=Math.min(j0,low+1);except.splice(k-1,2)}else{high=j0}}else if(low<=i0){if(i0<i){i0=Math.max(i0,high-1);except.splice(k-1,2)}else{low=i0}}else if(high-low<3)except.splice(k-1,2)}try{return _order_limits(i0,j0)}finally{_reset()}}function _order_limits(i0,j0){var orig=vector,perm,row,k,l;vector=vector.slice(i0,j0);if(i==0&&j==vector.length)return _order_except();if(debug)console.log("i0="+i0+" j0="+j0);if(distanceMatrix!=null){if(j0!=vector.length)reorder.dist_remove(distanceMatrix,j0,vector.length);if(i0>0)reorder.dist_remove(distanceMatrix,0,i0)}else{_compute_dist()}var max=reorder.distmax(distanceMatrix);if(i0<i){row=distanceMatrix[0];for(k=row.length;k-->1;)row[k]+=max;for(k=distanceMatrix.length;k-->1;)distanceMatrix[k][0]+=max;max+=max;if(i0!=0){for(k=0;k<except.length;k++)except[k]-=i0}}if(j0>j){l=distanceMatrix.length-1;row=distanceMatrix[l];for(k=l;k-->0;){row[k]+=max;distanceMatrix[k][l]+=max}}perm=_order_except();if(i0<i){if(perm[0]!=0)perm.reverse();if(j0>j){reorder.assert(perm[0]==0&&perm[perm.length-1]==perm.length-1,"Invalid constrained permutation endpoints")}else{reorder.assert(perm[0]==0,"Invalid constrained permutation start")}}else if(j0>j){if(perm[perm.length-1]!=perm.length-1)perm=perm.reverse();reorder.assert(perm[perm.length-1]==perm.length-1,"Invalid constrained permutation end")}if(i0!=0){perm=reorder.permutation(i0).concat(perm.map(function(v){return v+i0}))}if(orig.length>j0){perm=perm.concat(reorder.range(j0,orig.length))}return perm}function _order_except(){var perm,k,l,low,high,pos;if(except.length==0)return _order_equiv();_compute_dist();for(k=except.length-1;k>0;k-=2){low=except[k-1];high=except[k];distanceMatrix=reorder.dist_remove(distanceMatrix,low+1,high-1);vector.splice(low+1,high-low-2);if(debug)console.log("Except["+low+", "+high+"]");if(distanceMatrix[low][low+1]!=0){distanceMatrix[low][low+1]=distanceMatrix[low+1][low]=-1}}perm=_order_equiv();for(k=0;k<except.length;k+=2){low=except[k];high=except[k+1];for(l=0;l<perm.length;l++){if(perm[l]>low)perm[l]+=high-low-2;else if(perm[l]==low)pos=l}if(pos>0&&perm[pos-1]==high-1){Array.prototype.splice.apply(perm,[pos,0].concat(reorder.range(high-2,low,-1)))}else if(perm[pos+1]==high-1){Array.prototype.splice.apply(perm,[pos+1,0].concat(reorder.range(low+1,high-1)))}else{throw"Range not respected"}}return perm}function _order_equiv(){var perm,row,e,j,k,l,m,n,has_1=false,equiv=[],fix_except={};_compute_dist();for(k=0;k<distanceMatrix.length-1;k++){row=distanceMatrix[k];e=[];j=row.indexOf(-1);if(j!=-1){fix_except[k]=[k,j];has_1=true}for(l=row.length;--l>k;){if(row[l]==0){j=distanceMatrix[l].indexOf(-1);if(j!=-1){fix_except[k]=[l,j];distanceMatrix[j][k]=row[j]=-1;has_1=true}e.unshift(l);distanceMatrix=reorder.dist_remove(distanceMatrix,l);vector.splice(l,1)}else if(row[l]<0)has_1=true}if(e.length!=0){e.unshift(k);equiv.push(e)}}if(has_1){for(k=0;k<distanceMatrix.length-1;k++){row=distanceMatrix[k];for(l=k+1;l<row.length-1;l++){if(distanceMatrix[l][l+1]==-1){distanceMatrix[l+1][l]=distanceMatrix[l][l+1]=0}}}}perm=_order();for(k=equiv.length;k-->0;){e=equiv[k];l=perm.indexOf(e[0]);m=fix_except[e[0]];if(m&&m[0]==e[0]){l=_fix_exception(perm,l,m[0],m[1],0);m=undefined}for(n=1;n<e.length;n++){perm=_perm_insert(perm,l,e[n]);if(m&&m[0]==e[n]){l=_fix_exception(perm,l,m[0],m[1],n);m=undefined}}}return perm}function _fix_exception(perm,l,m,next,len){var i,j,k;if(l>0&&perm[l-1]==next){_swap(perm,l,perm.indexOf(m));return l+1}else if(perm[l+len+1]==next){_swap(perm,l+len,perm.indexOf(m));return l}else throw"Index not found"}function _swap(perm,a,b){if(a==b)return;var c=perm[a];perm[a]=perm[b];perm[b]=c}function _order(){if(debug>1)reorder.printmat(distanceMatrix);if(debug>2)reorder.printmat(vector);var perm=ordering().debug(debug).linkage(linkage).distanceMatrix(distanceMatrix)(vector);if(debug)console.log("Permutation: "+perm);return perm}function _perm_insert(perm,i,nv){perm=perm.map(function(v){return v<nv?v:v+1});perm.splice(i,0,nv);return perm}order.debug=function(x){if(!arguments.length)return debug;debug=x;return order};function _compute_dist(){if(distanceMatrix==null)distanceMatrix=reorder.dist().distance(distance)(vector);return distanceMatrix}order.distance=function(x){if(!arguments.length)return distance;distance=x;return order};order.linkage=function(x){if(!arguments.length)return linkage;linkage=x;return order};order.limits=function(x,y){if(!arguments.length)return[i,j];i=x;j=y;return order};order.except=function(list){if(!arguments.length)return except.slice(0);except=list.sort(function(a,b){if(a>=b)throw"Invalid list, indices not sorted";return a-b});return order};function _orderExcept(vector,i,j){var distanceMatrix=reorder.dist().distance(distance)(vector);var row,k,l,rev=false,args,pos=-1;distanceMatrix[i][i+1]=0;distanceMatrix[i+1][i]=0;var perm=ordering().distanceMatrix(distanceMatrix)(vector);pos=perm.indexOf(i);for(k=0;k<perm.length;k++){l=perm[k];if(l>i)perm[k]+=j-i-2}if(pos!=0&&perm[pos-1]==j-1)rev=true;if(rev){perm.reverse();pos=perm.length-pos-1}args=[pos+1,0].concat(reorder.range(i+1,j-1));Array.prototype.splice.apply(perm,args);return perm}order.orderrowsexcept=order.orderexcept;return order};reorder.covariance=science.lin.dot;reorder.covariancetranspose=function(v,a,b){var n=v.length,cov=0,i;for(i=0;i<n;i++){cov+=v[i][a]*v[i][b]}return cov};reorder.variancecovariance=function(v){var o=v[0].length,cov=Array(o),i,j;for(i=0;i<o;i++){cov[i]=Array(o)}for(i=0;i<o;i++){for(j=i;j<o;j++)cov[i][j]=cov[j][i]=reorder.covariancetranspose(v,i,j)}return cov};function normalize(v){var norm=science.lin.length(v),i=v.length;while(i-->0)v[i]/=norm;
+
+return v}reorder.poweriteration=function(v,eps){if(arguments.length<2)eps=1e-4;var n=v.length,b=Array(n),i,j,tmp=Array(n),norm,s=10;reorder.assert(n==v[0].length,"poweriteration needs a square matrix");for(i=0;i<n;i++)b[i]=Math.random();b=normalize(b);while(s-->0){for(i=0;i<n;i++){tmp[i]=0;for(j=0;j<n;j++)tmp[i]+=v[i][j]*b[j]}tmp=normalize(tmp);var t=tmp;tmp=b;b=t}return tmp};reorder.sortorder=function(v){return reorder.range(0,v.length).sort(function(a,b){return v[a]-v[b]})};reorder.center=function(v){var n=v.length;if(n==0)return null;var mean=reorder.meancolumns(v),o=mean.length,v1=Array(n),i,j,row;for(i=0;i<n;i++){row=v[i].slice(0);for(j=0;j<o;j++){row[j]-=mean[j]}v1[i]=row}return v1};reorder.pca1d=function(v,eps){if(arguments.length<2)eps=1e-4;var n=v.length;if(v.length==0)return null;v=reorder.center(v);var cov=reorder.variancecovariance(v);return reorder.poweriteration(cov,eps)};reorder.pca1dorder=function(v,eps){return reorder.sortorder(pca1d(v,eps))};reorder.sumlines=function(v){var n=v.length,o=v[0].length,sumline=Array(n),i,j,row,s;for(i=0;i<n;i++){row=v[i];s=0;for(j=0;j<o;j++)s+=row[j];sumline[i]=s}return sumline};reorder.sumcols=function(v){var n=v.length,o=v[0].length,sumcol=reorder.zeroes(o),i,j,row;for(i=0;i<n;i++){row=v[i];for(j=0;j<o;j++)sumcol[j]+=row[j]}return sumcol};reorder.ca=function(v,eps){if(arguments.length<2)eps=1e-4;var n=v.length,o=v[0].length,sumline=reorder.sumlines(v),sumcol=reorder.sumcols(v),s=reorder.sum(sumcol),i,j,row;for(i=0;i<n;i++){v[i]=v[i].map(function(a){return a/s})}sumline=reorder.sumlines(v);sumcol=reorder.sumcols(v);var v2=Array(n),ep;for(i=0;i<n;i++){v2[i]=Array(o);for(j=0;j<o;j++){ep=sumline[i]*sumcol[j];v2[i][j]=(v[i][j]-ep)/Math.sqrt(ep)}}for(i=0;i<n;i++){for(j=0;j<o;j++){ep=sumline[i]*sumcol[j];v[i][j]=(v[i][j]-ep)/(sumcol[j]*Math.sqrt(sumline[i]))}}var cov=Array(n);for(i=0;i<n;i++)cov[i]=Array(n);for(i=0;i<n;i++)for(j=i;j<n;j++)cov[i][j]=cov[j][i]=reorder.covariance(v2[i],v2[j]);var eigenvector1=reorder.poweriteration(cov,eps),eigenvalue1=0;for(i=0;i<n;i++)eigenvalue1+=eigenvector1[i]*cov[i][0];eigenvalue1/=eigenvector1[0];return eigenvector1};reorder.cuthill_mckee=function(graph,comps){var i,order=[];if(!comps){comps=graph.components()}for(i=0;i<comps.length;i++){order=order.concat(reorder.cuthill_mckee1(graph,comps[i]))}return order};reorder.cuthill_mckee1=function(graph,comp){if(comp.length<2)return comp;var nodes=graph.nodes(),start=comp[0],min_deg=graph.degree(start),i,n,edges,e,visited={},queue=new Queue,order=[];for(i=0;i<comp.length;i++){n=nodes[comp[i]].index;if(graph.degree(n)<min_deg){min_deg=graph.degree(n);start=n;if(min_deg==1)break}}queue.push(start);while(queue.length!=0){n=queue.shift();if(visited[n])continue;visited[n]=true;order.push(n);e=graph.edges(n).map(function(edge){return graph.other(edge,n).index}).filter(function(n){return!visited[n]}).sort(function(a,b){return graph.degree(a)-graph.degree(b)});e.forEach(queue.push,queue)}return order};reorder.reverse_cuthill_mckee=function(graph,comps){return reorder.cuthill_mckee(graph,comps).reverse()}})(this);
\ No newline at end of file
diff --git a/src/adjacent_exchange.js b/src/adjacent_exchange.js
new file mode 100644
index 0000000..834cd87
--- /dev/null
+++ b/src/adjacent_exchange.js
@@ -0,0 +1,87 @@
+// Accorging to
+// E. R. Gansner, E. Koutsofios, S. C. North, and K.-P. Vo. 1993. A
+// Technique for Drawing Directed Graphs. IEEE Trans. Softw. Eng. 19, 3
+// (March 1993), 214-230. DOI=10.1109/32.221135
+// http://dx.doi.org/10.1109/32.221135 
+// page 14: "[...] reduce obvious crossings after the vertices have
+// been sorted, transforming a given ordering to one that is locally
+// optimal with respect to transposition of adjacent vertices. It
+// typically provides an additional 20-50% reduction in edge crossings.
+
+function count_in_crossings(graph, v, w, inv) {
+    var v_edges = graph.inEdges(v),
+	w_edges = graph.inEdges(w),
+	iv, iw, p0, cross = 0;
+
+    for (iw = 0; iw < w_edges.length; iw++) {
+	p0 = inv[w_edges[iw].target.index];
+	for (iv = 0; iv < v_edges.length; iv++) {
+	    if (inv[v_edges[iv].target.index] > p0)
+		cross++;
+	}
+    }
+    return cross;
+}
+
+function count_out_crossings(graph, v, w, inv) {
+    var v_edges = graph.outEdges(v),
+	w_edges = graph.outEdges(w),
+	iv, iw, p0, cross = 0;
+
+    for (iw = 0; iw < w_edges.length; iw++) {
+	p0 = inv[w_edges[iw].source.index];
+	for (iv = 0; iv < v_edges.length; iv++) {
+	    if (inv[v_edges[iv].source.index] > p0)
+		cross++;
+	}
+    }
+    return cross;
+}
+
+function adjacent_exchange(graph, layer1, layer2) {
+    layer1 = layer1.slice();
+    layer2 = layer2.slice();
+    var i, v, w, c0, c1,
+	inv_layer1 = inverse_permutation(layer1),
+	inv_layer2 = inverse_permutation(layer2),
+	swapped = true,
+	improved = 0;
+
+    while (swapped) {
+	swapped = false;
+	for (i = 0; i < layer1.length-1; i++) {
+	    v = layer1[i];
+	    w = layer1[i+1];
+	    // should reduce the in crossing and the out crossing
+	    // otherwise what we gain horizontally is lost vertically
+	    c0 = count_out_crossings(graph, v, w, inv_layer2);
+	    c1 = count_out_crossings(graph, w, v, inv_layer2);
+	    if (c0 > c1) {
+		layer1[i] = w;
+		layer1[i+1] = v;
+		inv_layer1[w] = i;
+		inv_layer1[v] = i+1;
+		swapped = true;
+		improved += c0 - c1;
+	    }
+	}
+	for (i = 0; i < layer2.length-1; i++) {
+	    v = layer2[i];
+	    w = layer2[i+1];
+	    c0 = count_in_crossings(graph, v, w, inv_layer1);
+	    c1 = count_in_crossings(graph, w, v, inv_layer1);
+	    if (c0 > c1) {
+		layer2[i] = w;
+		layer2[i+1] = v;
+		inv_layer2[w] = i;
+		inv_layer2[v] = i+1;
+		swapped = true;
+		improved += c0 - c1;
+	    }
+	}
+    }
+
+    return [layer1, layer2, improved];
+};
+
+reorder.adjacent_exchange = adjacent_exchange;
diff --git a/src/barycenter.js b/src/barycenter.js
index 7e21519..828eacd 100644
--- a/src/barycenter.js
+++ b/src/barycenter.js
@@ -44,10 +44,10 @@ reorder.barycenter1 = function(graph, comp, max_iter) {
 	i, v, neighbors;
 
     layer1 = comp.filter(function(n) {
-	return graph.outEdges(n).length!=0;
+	return graph.outDegree(n) != 0;
     });
     layer2 = comp.filter(function(n) {
-	return graph.inEdges(n).length!=0;
+	return graph.inDegree(n) != 0;
     });
     if (comp.length < 3) {
 	return [layer1, layer2,
@@ -59,19 +59,12 @@ reorder.barycenter1 = function(graph, comp, max_iter) {
     else if ((max_iter%2)==1)
 	max_iter++; // want even number of iterations
 
-    layer1 = comp.filter(function(n) {
-	return graph.outEdges(n).length!=0;
-    });
-    layer2 = comp.filter(function(n) {
-	return graph.inEdges(n).length!=0;
-    });
-
     for (i = 0; i < layer2.length; i++)
 	nodes[layer2[i]].pos = i;
 
     best_crossings = count_crossings(graph, layer1, layer2);
-    best_layer1 = layer1;
-    best_layer2 = layer2;
+    best_layer1 = layer1.slice();
+    best_layer2 = layer2.slice();
     best_iter = 0;
 
     for (layer = layer1, iter = 0;
@@ -109,8 +102,8 @@ reorder.barycenter1 = function(graph, comp, max_iter) {
 	crossings = count_crossings(graph, layer1, layer2);
 	if (crossings < best_crossings) {
 	    best_crossings = crossings;
-	    best_layer1 = layer1;
-	    best_layer2 = layer2;
+	    best_layer1 = layer1.slice();
+	    best_layer2 = layer2.slice();
 	    best_iter = iter;
 	    max_iter = Math.max(max_iter, iter + 2); // we improved so go on
 	}
diff --git a/src/count_crossings.js b/src/count_crossings.js
index 0297597..1cfa302 100644
--- a/src/count_crossings.js
+++ b/src/count_crossings.js
@@ -6,13 +6,14 @@ function count_crossings(graph, north, south) {
 	firstIndex, treeSize, tree, index, weightSum,
 	invert = false, crosscount;
 
+    var comp = reorder.permutation(graph.nodes().length);
+
     if (north==undefined) {
-	var comp = reorder.permutation(graph.nodes().length);
 	north = comp.filter(function(n) {
-	    return graph.outEdges(n).length!=0;
+	    return graph.outDegree(n) != 0;
 	}),
 	south = comp.filter(function(n) {
-	    return graph.inEdges(n).length!=0;
+	    return graph.inDegree(n) != 0;
 	});
     }
 
@@ -63,4 +64,5 @@ function count_crossings(graph, north, south) {
     }
     return crosscount;
 }
+
 reorder.count_crossings = count_crossings;
diff --git a/src/graph.js b/src/graph.js
index 8434d32..692fc2c 100644
--- a/src/graph.js
+++ b/src/graph.js
@@ -139,8 +139,6 @@ reorder.graph = function(nodes, links, directed) {
     graph.sinks = function() {
 	var sinks = [],
 	    i;
-	if (! directed)
-	    return reorder.range(nodes.length);
 
 	for (i = 0; i < nodes.length; i++) {
 	    if (outEdges(i).length == 0)
@@ -152,8 +150,6 @@ reorder.graph = function(nodes, links, directed) {
     graph.sources = function() {
 	var sources = [],
 	    i;
-	if (! directed)
-	    return reorder.range(nodes.length);
 
 	for (i = 0; i < nodes.length; i++) {
 	    if (inEdges(i).length == 0)
diff --git a/test/barycenter-test.js b/test/barycenter-test.js
index d35ce97..f7fe30f 100644
--- a/test/barycenter-test.js
+++ b/test/barycenter-test.js
@@ -9,17 +9,26 @@ var suite = vows.describe("reorder.barycenter");
 
 function dotest(mat) {
     var graph = reorder.mat2graph(mat, true);
-    //reorder.printmat(mat);
+    //reorder.displaymat(mat);
     var initial_crossings = reorder.count_crossings(graph);
     var perms = reorder.barycenter(graph);
-    //console.log('VOrder: %j, HOrder: %j, Crossings: %d',
-    //perms[1], perms[0], perms[2]);
-    //reorder.printmat(mat, perms[1], perms[0]);
+    // console.log('VOrder: %j, HOrder: %j, Crossings: %d',
+    // 		perms[1], perms[0], perms[2]);
+    // reorder.displaymat(mat, perms[1], perms[0]);
     assert.isTrue(initial_crossings > perms[2]);
-    var perm2 = reorder.adjacent_exchange(graph,
-					  perms[0], perms[1], perms[2]);
-    assert.isTrue(perm2[2] >= perms[2]);
-    console.log('Improved by: %d', perm2[2]-perms[2]);
+    var perms2 = reorder.adjacent_exchange(graph, perms[0], perms[1]);
+    if (perms2[2]) {
+	//reorder.displaymat(mat, perms2[1], perms2[0]);
+	var crossings = reorder.count_crossings(
+	    graph, perms2[0], perms2[1]);
+	assert.equal(crossings, perms[2]-perms2[2]);
+	// console.log('final crossings: %d, improved by %d (%d%) %d',
+	// 	    crossings, perms[2]-crossings,
+	// 	    Math.round((perms[2]-crossings)*100.0/perms[2]),
+	// 	   perms2[2]);
+	// console.log('VOrder: %j, HOrder: %j', perms2[1], perms2[0]);
+	assert.isTrue(crossings < perms[2]);
+    }
 }
 
 suite.addBatch({