		{
		"name": "cytoscape-fcose",
		"version": "1.2.3",
		"version": "2.0.0",
		"description": "The fCoSE layout for Cytoscape.js by Bilkent with fast compound node placement",
		@@ -54,4 +54,4 @@ "main": "cytoscape-fcose.js",
		"dependencies": {
		"cose-base": "^1.0.0"
		"cose-base": "^2.0.0"
		}
		}

README.md

		@@ -7,6 +7,21 @@ cytoscape-fcose

		fCoSE (fast Compound Spring Embedder) is a faster version of our earlier compound spring embedder algorithm named [CoSE](https://github.com/cytoscape/cytoscape.js-cose-bilkent), implemented as a Cytoscape.js extension by [i-Vis Lab](http://cs.bilkent.edu.tr/~ivis/) in Bilkent University ([demo](https://ivis-at-bilkent.github.io/cytoscape.js-fcose/demo.html), [compound demo](https://ivis-at-bilkent.github.io/cytoscape.js-fcose/demo-compound.html))
		fCoSE (fast Compound Spring Embedder) is a faster version of our earlier compound spring embedder algorithm named [CoSE](https://github.com/cytoscape/cytoscape.js-cose-bilkent), implemented as a Cytoscape.js extension by [i-Vis Lab](http://cs.bilkent.edu.tr/~ivis/) in Bilkent University.

		fCoSE layout algorithm combines the speed of spectral layout with the aesthetics of force-directed layout. fCoSE runs up to 10 times as fast as CoSE while achieving similar aesthetics. In addition, fCoSE supports varying (non-uniform) node dimensions similar to its predecessor CoSE.
		<p align="center"> <a href="https://ivis-at-bilkent.github.io/cytoscape.js-fcose/demo/demo.html" title="Simple Demo">DEMO (simple)</a>

		<a href="https://ivis-at-bilkent.github.io/cytoscape.js-fcose/demo/demo-compound.html" title="Compound Demo">DEMO (compound)</a>

		<a href="https://ivis-at-bilkent.github.io/cytoscape.js-fcose/demo/demo-constraint.html" title="Constraint Demo">DEMO (constraint)</a>
		</p>

		fCoSE layout algorithm combines the speed of spectral layout with the aesthetics of force-directed layout. fCoSE runs up to 2 times as fast as CoSE while achieving similar aesthetics.

		<p align="center"><img src="demo/demo.gif" width="440"></p>

		Furthermore, fCoSE also supports a fairly rich set of constraint types (i.e., fixed position, vertical/horizontal alignment and relative placement).

		<p align="center"><img src="demo/incrementalConstraints.gif" width="800"></p>

		You can see constraint support in action in the following videos: [fixed node](https://youtu.be/OTke5XQXzQA), [alignment](https://youtu.be/XCj_-_cTuRc), [relative placement](https://youtu.be/k0PmRliwdmo), [hybrid](https://youtu.be/cS3rkTyIMqU), [real life graphs](https://youtu.be/S7aIr9cNKbI). Constraints can also be added [incrementally](https://youtu.be/mxRKGvzM900) on a given layout.

		Please cite the following when you use this layout until an fCoSE publication is available:
		@@ -18,11 +33,32 @@

		<p align="center"><img src="demo.gif" width="480"></p>

		## Dependencies

		* Cytoscape.js ^3.2.0
		* cose-base ^1.0.0
		* cose-base ^2.0.0
		* cytoscape-layout-utilities.js (optional for packing disconnected components) ^1.0.0

		## Documentation

		fCoSE supports user-defined placement constraints as well as its full support for compound graphs. These constraints may be defined for simple nodes. Supported constraint types are:

		* Fixed node constraint: The user may provide exact desired positions for a set of nodes called fixed nodes. For example, in order to position node n1 to (x: 100, y: 200) and node n2 to (x: 200, y: -300) as a result of the layout, ```fixedNodeConstraint``` option should be set as follows:

		```js
		fixedNodeConstraint: [{nodeId: 'n1', position: {x: 100, y: 200}},
		{nodeId: 'n2', position: {x: 200, y: -300}}],
		```

		* Alignment constraint: This constraint aims to align two or more nodes (with respect to their centers) vertically or horizontally. For example, for the vertical alignment of nodes {n1, n2, n3} and {n4, n5}, and horizontal alignment of nodes {n2, n4} as a result of the layout, ```alignmentConstraint``` option should be set as follows:
		```js
		alignmentConstraint: {vertical: [['n1', 'n2', 'n3'], ['n4', 'n5']], horizontal: [['n2', 'n4']]},
		```
		*Note: Alignment constraints in a direction must be given in most compact form. Example: ```['n1', 'n2', 'n3']``` instead of ```['n1', 'n2'], ['n1', 'n3']```.*

		* Relative placement constraint: The user may constrain the position of a node relative to another node in either vertical or horizontal direction. For example, in order to position node n1 to be above of node n2 by at least 100 pixels and position node n3 to be on the left of node n4 by at least 75 pixels as a result of the layout, ```relativePlacementConstraint``` option should be set as follows:

		```js
		relativePlacementConstraint: [{top: 'n1', bottom: 'n2', gap: 100},
		{left: 'n3', right: 'n4', gap: 75}],
		```

		## Usage instructions
		@@ -103,2 +139,4 @@
		packComponents: true,
		// Layout step - all, transformed, enforced, cose - for debug purpose only
		step: "all",

		@@ -119,7 +157,7 @@ /* spectral layout options */
		// Node repulsion (non overlapping) multiplier
		nodeRepulsion: 4500,
		nodeRepulsion: node => 4500,
		// Ideal edge (non nested) length
		idealEdgeLength: 50,
		idealEdgeLength: edge => 50,
		// Divisor to compute edge forces
		edgeElasticity: 0.45,
		edgeElasticity: edge => 0.45,
		// Nesting factor (multiplier) to compute ideal edge length for nested edges
		@@ -144,4 +182,16 @@ nestingFactor: 0.1,
		// Initial cooling factor for incremental layout
		initialEnergyOnIncremental: 0.3,
		initialEnergyOnIncremental: 0.3,

		/* constraint options */

		// Fix desired nodes to predefined positions
		// [{nodeId: 'n1', position: {x: 100, y: 200}}, {...}]
		fixedNodeConstraint: undefined,
		// Align desired nodes in vertical/horizontal direction
		// {vertical: [['n1', 'n2'], [...]], horizontal: [['n2', 'n4'], [...]]}
		alignmentConstraint: undefined,
		// Place two nodes relatively in vertical/horizontal direction
		// [{top: 'n1', bottom: 'n2', gap: 100}, {left: 'n3', right: 'n4', gap: 75}, {...}]
		relativePlacementConstraint: undefined,

		/* layout event callbacks */
		@@ -148,0 +198,0 @@ ready: () => {}, // on layoutready

759

src/fcose/auxiliary.js

		@@ -9,126 +9,2 @@ /*

		auxiliary.multMat = function(array1, array2){
		let result = [];

		for(let i = 0; i < array1.length; i++){
		result[i] = [];
		for(let j = 0; j < array2[0].length; j++){
		result[i][j] = 0;
		for(let k = 0; k < array1[0].length; k++){
		result[i][j] += array1[i][k] * array2[k][j];
		}
		}
		}
		return result;
		};

		auxiliary.multGamma = function(array){
		let result = [];
		let sum = 0;

		for(let i = 0; i < array.length; i++){
		sum += array[i];
		}

		sum *= (-1)/array.length;

		for(let i = 0; i < array.length; i++){
		result[i] = sum + array[i];
		}
		return result;
		};

		auxiliary.multL = function(array, C, INV){
		let result = [];
		let temp1 = [];
		let temp2 = [];

		// multiply by C^T
		for(let i = 0; i < C[0].length; i++){
		let sum = 0;
		for(let j = 0; j < C.length; j++){
		sum += -0.5 * C[j][i] * array[j];
		}
		temp1[i] = sum;
		}
		// multiply the result by INV
		for(let i = 0; i < INV.length; i++){
		let sum = 0;
		for(let j = 0; j < INV.length; j++){
		sum += INV[i][j] * temp1[j];
		}
		temp2[i] = sum;
		}
		// multiply the result by C
		for(let i = 0; i < C.length; i++){
		let sum = 0;
		for(let j = 0; j < C[0].length; j++){
		sum += C[i][j] * temp2[j];
		}
		result[i] = sum;
		}

		return result;
		};

		auxiliary.multCons = function(array, constant){
		let result = [];

		for(let i = 0; i < array.length; i++){
		result[i] = array[i] * constant;
		}

		return result;
		};

		// assumes arrays have same size
		auxiliary.minusOp = function(array1, array2){
		let result = [];

		for(let i = 0; i < array1.length; i++){
		result[i] = array1[i] - array2[i];
		}

		return result;
		};

		// assumes arrays have same size
		auxiliary.dotProduct = function(array1, array2){
		let product = 0;

		for(let i = 0; i < array1.length; i++){
		product += array1[i] * array2[i];
		}

		return product;
		};

		auxiliary.mag = function(array){
		return Math.sqrt(this.dotProduct(array, array));
		};

		auxiliary.normalize = function(array){
		let result = [];
		let magnitude = this.mag(array);

		for(let i = 0; i < array.length; i++){
		result[i] = array[i] / magnitude;
		}

		return result;
		};

		auxiliary.transpose = function(array){
		let result = [];

		for(let i = 0; i < array[0].length; i++){
		result[i] = [];
		for(let j = 0; j < array.length; j++){
		result[i][j] = array[j][i];
		}
		}

		return result;
		};

		// get the top most nodes
		@@ -192,3 +68,3 @@ auxiliary.getTopMostNodes = function(nodes) {
		currentNode.neighborhood().nodes().forEach(function(node){
		if(eles.intersection(currentNode.edgesWith(node))){
		if(eles.intersection(currentNode.edgesWith(node)).length > 0){
		neighborNodes.merge(node);
		@@ -312,635 +188,2 @@ }

		/* Below singular value decomposition (svd) code including hypot function is adopted from https://github.com/dragonfly-ai/JamaJS
		Some changes are applied to make the code compatible with the fcose code and to make it independent from Jama.
		Input matrix is changed to a 2D array instead of Jama matrix. Matrix dimensions are taken according to 2D array instead of using Jama functions.
		An object that includes singular value components is created for return.
		The types of input parameters of the hypot function are removed.
		let is used instead of var for the variable initialization.
		*/
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		auxiliary.svd = function (A) {
		this.U = null;
		this.V = null;
		this.s = null;
		this.m = 0;
		this.n = 0;
		this.m = A.length;
		this.n = A[0].length;
		let nu = Math.min(this.m, this.n);
		this.s = (function (s) {
		let a = [];
		while (s-- > 0)
		a.push(0);
		return a;
		})(Math.min(this.m + 1, this.n));
		this.U = (function (dims) {
		let allocate = function (dims) {
		if (dims.length == 0) {
		return 0;
		} else {
		let array = [];
		for (let i = 0; i < dims[0]; i++) {
		array.push(allocate(dims.slice(1)));
		}
		return array;
		}
		};
		return allocate(dims);
		})([this.m, nu]);
		this.V = (function (dims) {
		let allocate = function (dims) {
		if (dims.length == 0) {
		return 0;
		} else {
		let array = [];
		for (let i = 0; i < dims[0]; i++) {
		array.push(allocate(dims.slice(1)));
		}
		return array;
		}
		};
		return allocate(dims);
		})([this.n, this.n]);
		let e = (function (s) {
		let a = [];
		while (s-- > 0)
		a.push(0);
		return a;
		})(this.n);
		let work = (function (s) {
		let a = [];
		while (s-- > 0)
		a.push(0);
		return a;
		})(this.m);
		let wantu = true;
		let wantv = true;
		let nct = Math.min(this.m - 1, this.n);
		let nrt = Math.max(0, Math.min(this.n - 2, this.m));
		for (let k = 0; k < Math.max(nct, nrt); k++) {
		if (k < nct) {
		this.s[k] = 0;
		for (let i = k; i < this.m; i++) {
		this.s[k] = auxiliary.hypot(this.s[k], A[i][k]);
		}
		;
		if (this.s[k] !== 0.0) {
		if (A[k][k] < 0.0) {
		this.s[k] = -this.s[k];
		}
		for (let i = k; i < this.m; i++) {
		A[i][k] /= this.s[k];
		}
		;
		A[k][k] += 1.0;
		}
		this.s[k] = -this.s[k];
		}
		for (let j = k + 1; j < this.n; j++) {
		if ((function (lhs, rhs) {
		return lhs && rhs;
		})((k < nct), (this.s[k] !== 0.0))) {
		let t = 0;
		for (let i = k; i < this.m; i++) {
		t += A[i][k] * A[i][j];
		}
		;
		t = -t / A[k][k];
		for (let i = k; i < this.m; i++) {
		A[i][j] += t * A[i][k];
		}
		;
		}
		e[j] = A[k][j];
		}
		;
		if ((function (lhs, rhs) {
		return lhs && rhs;
		})(wantu, (k < nct))) {
		for (let i = k; i < this.m; i++) {
		this.U[i][k] = A[i][k];
		}
		;
		}
		if (k < nrt) {
		e[k] = 0;
		for (let i = k + 1; i < this.n; i++) {
		e[k] = auxiliary.hypot(e[k], e[i]);
		}
		;
		if (e[k] !== 0.0) {
		if (e[k + 1] < 0.0) {
		e[k] = -e[k];
		}
		for (let i = k + 1; i < this.n; i++) {
		e[i] /= e[k];
		}
		;
		e[k + 1] += 1.0;
		}
		e[k] = -e[k];
		if ((function (lhs, rhs) {
		return lhs && rhs;
		})((k + 1 < this.m), (e[k] !== 0.0))) {
		for (let i = k + 1; i < this.m; i++) {
		work[i] = 0.0;
		}
		;
		for (let j = k + 1; j < this.n; j++) {
		for (let i = k + 1; i < this.m; i++) {
		work[i] += e[j] * A[i][j];
		}
		;
		}
		;
		for (let j = k + 1; j < this.n; j++) {
		let t = -e[j] / e[k + 1];
		for (let i = k + 1; i < this.m; i++) {
		A[i][j] += t * work[i];
		}
		;
		}
		;
		}
		if (wantv) {
		for (let i = k + 1; i < this.n; i++) {
		this.V[i][k] = e[i];
		};
		}
		}
		};
		let p = Math.min(this.n, this.m + 1);
		if (nct < this.n) {
		this.s[nct] = A[nct][nct];
		}
		if (this.m < p) {
		this.s[p - 1] = 0.0;
		}
		if (nrt + 1 < p) {
		e[nrt] = A[nrt][p - 1];
		}
		e[p - 1] = 0.0;
		if (wantu) {
		for (let j = nct; j < nu; j++) {
		for (let i = 0; i < this.m; i++) {
		this.U[i][j] = 0.0;
		}
		;
		this.U[j][j] = 1.0;
		};
		for (let k = nct - 1; k >= 0; k--) {
		if (this.s[k] !== 0.0) {
		for (let j = k + 1; j < nu; j++) {
		let t = 0;
		for (let i = k; i < this.m; i++) {
		t += this.U[i][k] * this.U[i][j];
		};
		t = -t / this.U[k][k];
		for (let i = k; i < this.m; i++) {
		this.U[i][j] += t * this.U[i][k];
		};
		};
		for (let i = k; i < this.m; i++) {
		this.U[i][k] = -this.U[i][k];
		};
		this.U[k][k] = 1.0 + this.U[k][k];
		for (let i = 0; i < k - 1; i++) {
		this.U[i][k] = 0.0;
		};
		} else {
		for (let i = 0; i < this.m; i++) {
		this.U[i][k] = 0.0;
		};
		this.U[k][k] = 1.0;
		}
		};
		}
		if (wantv) {
		for (let k = this.n - 1; k >= 0; k--) {
		if ((function (lhs, rhs) {
		return lhs && rhs;
		})((k < nrt), (e[k] !== 0.0))) {
		for (let j = k + 1; j < nu; j++) {
		let t = 0;
		for (let i = k + 1; i < this.n; i++) {
		t += this.V[i][k] * this.V[i][j];
		};
		t = -t / this.V[k + 1][k];
		for (let i = k + 1; i < this.n; i++) {
		this.V[i][j] += t * this.V[i][k];
		};
		};
		}
		for (let i = 0; i < this.n; i++) {
		this.V[i][k] = 0.0;
		};
		this.V[k][k] = 1.0;
		};
		}
		let pp = p - 1;
		let iter = 0;
		let eps = Math.pow(2.0, -52.0);
		let tiny = Math.pow(2.0, -966.0);
		while ((p > 0)) {
		let k = void 0;
		let kase = void 0;
		for (k = p - 2; k >= -1; k--) {
		if (k === -1) {
		break;
		}
		if (Math.abs(e[k]) <= tiny + eps * (Math.abs(this.s[k]) + Math.abs(this.s[k + 1]))) {
		e[k] = 0.0;
		break;
		}
		};
		if (k === p - 2) {
		kase = 4;
		} else {
		let ks = void 0;
		for (ks = p - 1; ks >= k; ks--) {
		if (ks === k) {
		break;
		}
		let t = (ks !== p ? Math.abs(e[ks]) : 0.0) + (ks !== k + 1 ? Math.abs(e[ks - 1]) : 0.0);
		if (Math.abs(this.s[ks]) <= tiny + eps * t) {
		this.s[ks] = 0.0;
		break;
		}
		};
		if (ks === k) {
		kase = 3;
		} else if (ks === p - 1) {
		kase = 1;
		} else {
		kase = 2;
		k = ks;
		}
		}
		k++;
		switch ((kase)) {
		case 1:
		{
		let f = e[p - 2];
		e[p - 2] = 0.0;
		for (let j = p - 2; j >= k; j--) {
		let t = auxiliary.hypot(this.s[j], f);
		let cs = this.s[j] / t;
		let sn = f / t;
		this.s[j] = t;
		if (j !== k) {
		f = -sn * e[j - 1];
		e[j - 1] = cs * e[j - 1];
		}
		if (wantv) {
		for (let i = 0; i < this.n; i++) {
		t = cs * this.V[i][j] + sn * this.V[i][p - 1];
		this.V[i][p - 1] = -sn * this.V[i][j] + cs * this.V[i][p - 1];
		this.V[i][j] = t;
		};
		}
		};
		};
		break;
		case 2:
		{
		let f = e[k - 1];
		e[k - 1] = 0.0;
		for (let j = k; j < p; j++) {
		let t = auxiliary.hypot(this.s[j], f);
		let cs = this.s[j] / t;
		let sn = f / t;
		this.s[j] = t;
		f = -sn * e[j];
		e[j] = cs * e[j];
		if (wantu) {
		for (let i = 0; i < this.m; i++) {
		t = cs * this.U[i][j] + sn * this.U[i][k - 1];
		this.U[i][k - 1] = -sn * this.U[i][j] + cs * this.U[i][k - 1];
		this.U[i][j] = t;
		};
		}
		};
		};
		break;
		case 3:
		{
		let scale = Math.max(Math.max(Math.max(Math.max(Math.abs(this.s[p - 1]), Math.abs(this.s[p - 2])), Math.abs(e[p - 2])), Math.abs(this.s[k])), Math.abs(e[k]));
		let sp = this.s[p - 1] / scale;
		let spm1 = this.s[p - 2] / scale;
		let epm1 = e[p - 2] / scale;
		let sk = this.s[k] / scale;
		let ek = e[k] / scale;
		let b = ((spm1 + sp) * (spm1 - sp) + epm1 * epm1) / 2.0;
		let c = (sp * epm1) * (sp * epm1);
		let shift = 0.0;
		if ((function (lhs, rhs) {
		return lhs \|\| rhs;
		})((b !== 0.0), (c !== 0.0))) {
		shift = Math.sqrt(b * b + c);
		if (b < 0.0) {
		shift = -shift;
		}
		shift = c / (b + shift);
		}
		let f = (sk + sp) * (sk - sp) + shift;
		let g = sk * ek;
		for (let j = k; j < p - 1; j++) {
		let t = auxiliary.hypot(f, g);
		let cs = f / t;
		let sn = g / t;
		if (j !== k) {
		e[j - 1] = t;
		}
		f = cs * this.s[j] + sn * e[j];
		e[j] = cs * e[j] - sn * this.s[j];
		g = sn * this.s[j + 1];
		this.s[j + 1] = cs * this.s[j + 1];
		if (wantv) {
		for (let i = 0; i < this.n; i++) {
		t = cs * this.V[i][j] + sn * this.V[i][j + 1];
		this.V[i][j + 1] = -sn * this.V[i][j] + cs * this.V[i][j + 1];
		this.V[i][j] = t;
		};
		}
		t = auxiliary.hypot(f, g);
		cs = f / t;
		sn = g / t;
		this.s[j] = t;
		f = cs * e[j] + sn * this.s[j + 1];
		this.s[j + 1] = -sn * e[j] + cs * this.s[j + 1];
		g = sn * e[j + 1];
		e[j + 1] = cs * e[j + 1];
		if (wantu && (j < this.m - 1)) {
		for (let i = 0; i < this.m; i++) {
		t = cs * this.U[i][j] + sn * this.U[i][j + 1];
		this.U[i][j + 1] = -sn * this.U[i][j] + cs * this.U[i][j + 1];
		this.U[i][j] = t;
		};
		}
		};
		e[p - 2] = f;
		iter = iter + 1;
		};
		break;
		case 4:
		{
		if (this.s[k] <= 0.0) {
		this.s[k] = (this.s[k] < 0.0 ? -this.s[k] : 0.0);
		if (wantv) {
		for (let i = 0; i <= pp; i++) {
		this.V[i][k] = -this.V[i][k];
		};
		}
		}
		while ((k < pp)) {
		if (this.s[k] >= this.s[k + 1]) {
		break;
		}
		let t = this.s[k];
		this.s[k] = this.s[k + 1];
		this.s[k + 1] = t;
		if (wantv && (k < this.n - 1)) {
		for (let i = 0; i < this.n; i++) {
		t = this.V[i][k + 1];
		this.V[i][k + 1] = this.V[i][k];
		this.V[i][k] = t;
		};
		}
		if (wantu && (k < this.m - 1)) {
		for (let i = 0; i < this.m; i++) {
		t = this.U[i][k + 1];
		this.U[i][k + 1] = this.U[i][k];
		this.U[i][k] = t;
		};
		}
		k++;
		};
		iter = 0;
		p--;
		};
		break;
		}
		};
		let result = {U: this.U, V: this.V, S: this.s};
		return result;
		};

		// sqrt(a^2 + b^2) without under/overflow.
		auxiliary.hypot = function(a, b) {
		let r;
		if (Math.abs(a) > Math.abs(b)) {
		r = b/a;
		r = Math.abs(a)Math.sqrt(1+rr);
		} else if (b != 0) {
		r = a/b;
		r = Math.abs(b)Math.sqrt(1+rr);
		} else {
		r = 0.0;
		}
		return r;
		};

		module.exports = auxiliary;

102

src/fcose/cose.js

		@@ -32,2 +32,12 @@ /**

		const isFn = fn => typeof fn === 'function';

		const optFn = ( opt, ele ) => {
		if( isFn( opt ) ){
		return opt( ele );
		} else {
		return opt;
		}
		};

		/** Postprocessing functions **/
		@@ -71,4 +81,5 @@
		}
		// Attach id to the layout node
		// Attach id to the layout node and repulsion value
		theNode.id = theChild.data("id");
		theNode.nodeRepulsion = optFn( options.nodeRepulsion, theChild );
		// Attach the paddings of cy node to layout node
		@@ -83,8 +94,6 @@ theNode.paddingLeft = parseInt( theChild.css('padding') );
		if(theChild.isParent()){
		let labelWidth = theChild.boundingBox({ includeLabels: true, includeNodes: false }).w;
		let labelHeight = theChild.boundingBox({ includeLabels: true, includeNodes: false }).h;
		let labelPos = theChild.css("text-halign");
		theNode.labelWidth = labelWidth;
		theNode.labelHeight = labelHeight;
		theNode.labelPos = labelPos;
		theNode.labelWidth = theChild.boundingBox({ includeLabels: true, includeNodes: false, includeOverlays: false }).w;
		theNode.labelHeight = theChild.boundingBox({ includeLabels: true, includeNodes: false, includeOverlays: false }).h;
		theNode.labelPosVertical = theChild.css("text-valign");
		theNode.labelPosHorizontal = theChild.css("text-halign");
		}
		@@ -114,2 +123,4 @@ }
		let processEdges = function(layout, gm, edges){
		let idealLengthTotal = 0;
		let edgeCount = 0;
		for (let i = 0; i < edges.length; i++) {
		@@ -122,14 +133,40 @@ let edge = edges[i];
		e1.id = edge.id();
		e1.idealLength = optFn( options.idealEdgeLength, edge );
		e1.edgeElasticity = optFn( options.edgeElasticity, edge );
		idealLengthTotal += e1.idealLength;
		edgeCount++;
		}
		}
		};
		// we need to update the ideal edge length constant with the avg. ideal length value after processing edges
		// in case there is no edge, use other options
		if (options.idealEdgeLength != null){
		if (edges.length > 0)
		CoSEConstants.DEFAULT_EDGE_LENGTH = FDLayoutConstants.DEFAULT_EDGE_LENGTH = idealLengthTotal / edgeCount;
		else if(!isFn(options.idealEdgeLength)) // in case there is no edge, but option gives a value to use
		CoSEConstants.DEFAULT_EDGE_LENGTH = FDLayoutConstants.DEFAULT_EDGE_LENGTH = options.idealEdgeLength;
		else // in case there is no edge and we cannot get a value from option (because it's a function)
		CoSEConstants.DEFAULT_EDGE_LENGTH = FDLayoutConstants.DEFAULT_EDGE_LENGTH = 50;
		// we need to update these constant values based on the ideal edge length constant
		CoSEConstants.MIN_REPULSION_DIST = FDLayoutConstants.MIN_REPULSION_DIST = FDLayoutConstants.DEFAULT_EDGE_LENGTH / 10.0;
		CoSEConstants.DEFAULT_RADIAL_SEPARATION = FDLayoutConstants.DEFAULT_EDGE_LENGTH;
		}
		};

		// transfer cytoscape constraints to cose layout
		let processConstraints = function(layout, options){
		// get nodes to be fixed
		if(options.fixedNodeConstraint){
		layout.constraints["fixedNodeConstraint"] = options.fixedNodeConstraint;
		}
		// get nodes to be aligned
		if(options.alignmentConstraint){
		layout.constraints["alignmentConstraint"] = options.alignmentConstraint;
		}
		// get nodes to be relatively placed
		if(options.relativePlacementConstraint){
		layout.constraints["relativePlacementConstraint"] = options.relativePlacementConstraint;
		}
		};

		/** Apply postprocessing **/

		if (options.nodeRepulsion != null)
		CoSEConstants.DEFAULT_REPULSION_STRENGTH = FDLayoutConstants.DEFAULT_REPULSION_STRENGTH = options.nodeRepulsion;
		if (options.idealEdgeLength != null)
		CoSEConstants.DEFAULT_EDGE_LENGTH = FDLayoutConstants.DEFAULT_EDGE_LENGTH = options.idealEdgeLength;
		if (options.edgeElasticity != null)
		CoSEConstants.DEFAULT_SPRING_STRENGTH = FDLayoutConstants.DEFAULT_SPRING_STRENGTH = options.edgeElasticity;
		if (options.nestingFactor != null)
		@@ -167,4 +204,35 @@ CoSEConstants.PER_LEVEL_IDEAL_EDGE_LENGTH_FACTOR = FDLayoutConstants.PER_LEVEL_IDEAL_EDGE_LENGTH_FACTOR = options.nestingFactor;
		LayoutConstants.DEFAULT_UNIFORM_LEAF_NODE_SIZES = options.uniformNodeDimensions;
		CoSEConstants.TREE_REDUCTION_ON_INCREMENTAL = options.randomize ? true : false;

		// This part is for debug/demo purpose
		if(options.step == "transformed"){
		CoSEConstants.TRANSFORM_ON_CONSTRAINT_HANDLING = true;
		CoSEConstants.ENFORCE_CONSTRAINTS = false;
		CoSEConstants.APPLY_LAYOUT = false;
		}
		if(options.step == "enforced"){
		CoSEConstants.TRANSFORM_ON_CONSTRAINT_HANDLING = false;
		CoSEConstants.ENFORCE_CONSTRAINTS = true;
		CoSEConstants.APPLY_LAYOUT = false;
		}
		if(options.step == "cose"){
		CoSEConstants.TRANSFORM_ON_CONSTRAINT_HANDLING = false;
		CoSEConstants.ENFORCE_CONSTRAINTS = false;
		CoSEConstants.APPLY_LAYOUT = true;
		}
		if(options.step == "all"){
		if(options.randomize)
		CoSEConstants.TRANSFORM_ON_CONSTRAINT_HANDLING = true;
		else
		CoSEConstants.TRANSFORM_ON_CONSTRAINT_HANDLING = false;
		CoSEConstants.ENFORCE_CONSTRAINTS = true;
		CoSEConstants.APPLY_LAYOUT = true;
		}

		if(options.randomize && !(options.fixedNodeConstraint \|\| options.alignmentConstraint \|\| options.relativePlacementConstraint)){
		CoSEConstants.TREE_REDUCTION_ON_INCREMENTAL = true;
		}
		else{
		CoSEConstants.TREE_REDUCTION_ON_INCREMENTAL = false;
		}

		let coseLayout = new CoSELayout();
		@@ -174,4 +242,4 @@ let gm = coseLayout.newGraphManager();
		processChildrenList(gm.addRoot(), aux.getTopMostNodes(nodes), coseLayout, options);

		processEdges(coseLayout, gm, edges);
		processConstraints(coseLayout, options);

		@@ -178,0 +246,0 @@ coseLayout.runLayout();

306

src/fcose/index.js

		@@ -36,2 +36,4 @@ /**
		packComponents: true,
		// Layout step - all, transformed, enforced, cose - for debug purpose only
		step: "all",

		@@ -52,7 +54,7 @@ /* spectral layout options */
		// Node repulsion (non overlapping) multiplier
		nodeRepulsion: 4500,
		nodeRepulsion: node => 4500,
		// Ideal edge (non nested) length
		idealEdgeLength: 50,
		idealEdgeLength: edge => 50,
		// Divisor to compute edge forces
		edgeElasticity: 0.45,
		edgeElasticity: edge => 0.45,
		// Nesting factor (multiplier) to compute ideal edge length for nested edges
		@@ -77,4 +79,16 @@ nestingFactor: 0.1,
		// Initial cooling factor for incremental layout
		initialEnergyOnIncremental: 0.3,

		initialEnergyOnIncremental: 0.3,

		/* constraint options */

		// Fix required nodes to predefined positions
		// [{nodeId: 'n1', position: {x: 100, y: 200}, {...}]
		fixedNodeConstraint: undefined,
		// Align required nodes in vertical/horizontal direction
		// {vertical: [['n1', 'n2')], ['n3', 'n4']], horizontal: ['n2', 'n4']}
		alignmentConstraint: undefined,
		// Place two nodes relatively in vertical/horizontal direction
		// [{top: 'n1', bottom: 'n2', gap: 100}, {left: 'n3', right: 'n4', gap: 75}]
		relativePlacementConstraint: undefined,

		/* layout event callbacks */
		@@ -102,2 +116,11 @@ ready: () => {}, // on layoutready

		let constraintExist = options.fixedNodeConstraint \|\| options.alignmentConstraint \|\| options.relativePlacementConstraint;

		// if any constraint exists, set some options
		if(constraintExist){
		// constraints work with these options
		options.tile = false;
		options.packComponents = false;
		}

		// decide component packing is enabled or not
		@@ -113,29 +136,27 @@ let layUtil;

		// if packing is not enabled, perform layout on the whole graph
		if(!packingEnabled){
		if(options.randomize){
		// Apply spectral layout
		spectralResult.push(spectralLayout(options));
		xCoords = spectralResult[0]["xCoords"];
		yCoords = spectralResult[0]["yCoords"];
		if(eles.nodes().length > 0) {
		// if packing is not enabled, perform layout on the whole graph
		if(!packingEnabled){
		if(options.randomize){
		let result = spectralLayout(options); // apply spectral layout
		spectralResult.push(result);
		}
		// apply cose layout as postprocessing
		if(options.quality == "default" \|\| options.quality == "proof"){
		coseResult.push(coseLayout(options, spectralResult[0]));
		}
		}
		else{ // packing is enabled
		let topMostNodes = aux.getTopMostNodes(options.eles.nodes());
		components = aux.connectComponents(cy, options.eles, topMostNodes);

		//send each component to spectral layout
		if(options.randomize){
		components.forEach(function(component){
		options.eles = component;
		spectralResult.push(spectralLayout(options));
		});
		}

		// Apply cose layout as postprocessing
		if(options.quality == "default" \|\| options.quality == "proof"){
		coseResult.push(coseLayout(options, spectralResult[0]));
		}
		}
		else{ // packing is enabled
		let topMostNodes = aux.getTopMostNodes(options.eles.nodes());
		components = aux.connectComponents(cy, options.eles, topMostNodes);

		//send each component to spectral layout
		if(options.randomize){
		components.forEach(function(component){
		options.eles = component;
		spectralResult.push(spectralLayout(options));
		});
		}

		if(options.quality == "default" \|\| options.quality == "proof"){
		if(options.quality == "default" \|\| options.quality == "proof"){
		let toBeTiledNodes = cy.collection();
		@@ -150,13 +171,13 @@ if(options.tile){ // behave nodes to be tiled as one component
		components.forEach(function(component, index){
		if(component.edges().length == 0){
		component.nodes().forEach(function(node, i){
		toBeTiledNodes.merge(component.nodes()[i]);
		if(!node.isParent()){
		tempSpectralResult.nodeIndexes.set(component.nodes()[i].id(), count++);
		tempSpectralResult.xCoords.push(component.nodes()[0].position().x);
		tempSpectralResult.yCoords.push(component.nodes()[0].position().y);
		}
		});
		indexesToBeDeleted.push(index);
		}
		if(component.edges().length == 0){
		component.nodes().forEach(function(node, i){
		toBeTiledNodes.merge(component.nodes()[i]);
		if(!node.isParent()){
		tempSpectralResult.nodeIndexes.set(component.nodes()[i].id(), count++);
		tempSpectralResult.xCoords.push(component.nodes()[0].position().x);
		tempSpectralResult.yCoords.push(component.nodes()[0].position().y);
		}
		});
		indexesToBeDeleted.push(index);
		}
		});
		@@ -176,82 +197,139 @@ if(toBeTiledNodes.length > 1){
		});
		}

		// packing
		let subgraphs = [];
		components.forEach(function(component, index){
		let nodeIndexes;
		if(options.quality == "draft"){
		nodeIndexes = spectralResult[index].nodeIndexes;
		}
		let subgraph = {};
		subgraph.nodes = [];
		subgraph.edges = [];
		let nodeIndex;
		component.nodes().forEach(function (node) {
		if(options.quality == "draft"){
		if(!node.isParent()){
		nodeIndex = nodeIndexes.get(node.id());
		subgraph.nodes.push({x: spectralResult[index].xCoords[nodeIndex] - node.boundingbox().w/2, y: spectralResult[index].yCoords[nodeIndex] - node.boundingbox().h/2, width: node.boundingbox().w, height: node.boundingbox().h});
		}

		// packing
		if(components.length > 1){
		let subgraphs = [];
		components.forEach(function(component, index){
		let nodeIndexes;
		if(options.quality == "draft"){
		nodeIndexes = spectralResult[index].nodeIndexes;
		}
		else{
		let parentInfo = aux.calcBoundingBox(node, spectralResult[index].xCoords, spectralResult[index].yCoords, nodeIndexes);
		subgraph.nodes.push({x: parentInfo.topLeftX, y: parentInfo.topLeftY, width: parentInfo.width, height: parentInfo.height});
		}
		}
		else{
		subgraph.nodes.push({x: coseResult[index][node.id()].getLeft(), y: coseResult[index][node.id()].getTop(), width: coseResult[index][node.id()].getWidth(), height: coseResult[index][node.id()].getHeight()});
		}
		});
		component.edges().forEach(function (edge) {
		let source = edge.source();
		let target = edge.target();
		let subgraph = {};
		subgraph.nodes = [];
		subgraph.edges = [];
		let nodeIndex;
		component.nodes().forEach(function (node) {
		if(options.quality == "draft"){
		if(!node.isParent()){
		nodeIndex = nodeIndexes.get(node.id());
		subgraph.nodes.push({x: spectralResult[index].xCoords[nodeIndex] - node.boundingbox().w/2, y: spectralResult[index].yCoords[nodeIndex] - node.boundingbox().h/2, width: node.boundingbox().w, height: node.boundingbox().h});
		}
		else{
		let parentInfo = aux.calcBoundingBox(node, spectralResult[index].xCoords, spectralResult[index].yCoords, nodeIndexes);
		subgraph.nodes.push({x: parentInfo.topLeftX, y: parentInfo.topLeftY, width: parentInfo.width, height: parentInfo.height});
		}
		}
		else{
		subgraph.nodes.push({x: coseResult[index][node.id()].getLeft(), y: coseResult[index][node.id()].getTop(), width: coseResult[index][node.id()].getWidth(), height: coseResult[index][node.id()].getHeight()});
		}
		});
		component.edges().forEach(function (edge) {
		let source = edge.source();
		let target = edge.target();
		if(options.quality == "draft"){
		let sourceNodeIndex = nodeIndexes.get(source.id());
		let targetNodeIndex = nodeIndexes.get(target.id());
		let sourceCenter = [];
		let targetCenter = [];
		if(source.isParent()){
		let parentInfo = aux.calcBoundingBox(source, spectralResult[index].xCoords, spectralResult[index].yCoords, nodeIndexes);
		sourceCenter.push(parentInfo.topLeftX + parentInfo.width / 2);
		sourceCenter.push(parentInfo.topLeftY + parentInfo.height / 2);
		}
		else{
		sourceCenter.push(spectralResult[index].xCoords[sourceNodeIndex]);
		sourceCenter.push(spectralResult[index].yCoords[sourceNodeIndex]);
		}
		if(target.isParent()){
		let parentInfo = aux.calcBoundingBox(target, spectralResult[index].xCoords, spectralResult[index].yCoords, nodeIndexes);
		targetCenter.push(parentInfo.topLeftX + parentInfo.width / 2);
		targetCenter.push(parentInfo.topLeftY + parentInfo.height / 2);
		}
		else{
		targetCenter.push(spectralResult[index].xCoords[targetNodeIndex]);
		targetCenter.push(spectralResult[index].yCoords[targetNodeIndex]);
		}
		subgraph.edges.push({startX: sourceCenter[0], startY: sourceCenter[1], endX: targetCenter[0], endY: targetCenter[1]});
		}
		else{
		subgraph.edges.push({startX: coseResult[index][source.id()].getCenterX(), startY: coseResult[index][source.id()].getCenterY(), endX: coseResult[index][target.id()].getCenterX(), endY: coseResult[index][target.id()].getCenterY()});
		}
		});
		subgraphs.push(subgraph);
		});
		let shiftResult = layUtil.packComponents(subgraphs).shifts;
		if(options.quality == "draft"){
		let sourceNodeIndex = nodeIndexes.get(source.id());
		let targetNodeIndex = nodeIndexes.get(target.id());
		let sourceCenter = [];
		let targetCenter = [];
		if(source.isParent()){
		let parentInfo = aux.calcBoundingBox(source, spectralResult[index].xCoords, spectralResult[index].yCoords, nodeIndexes);
		sourceCenter.push(parentInfo.topLeftX + parentInfo.width / 2);
		sourceCenter.push(parentInfo.topLeftY + parentInfo.height / 2);
		}
		else{
		sourceCenter.push(spectralResult[index].xCoords[sourceNodeIndex]);
		sourceCenter.push(spectralResult[index].yCoords[sourceNodeIndex]);
		}
		if(target.isParent()){
		let parentInfo = aux.calcBoundingBox(target, spectralResult[index].xCoords, spectralResult[index].yCoords, nodeIndexes);
		targetCenter.push(parentInfo.topLeftX + parentInfo.width / 2);
		targetCenter.push(parentInfo.topLeftY + parentInfo.height / 2);
		}
		else{
		targetCenter.push(spectralResult[index].xCoords[targetNodeIndex]);
		targetCenter.push(spectralResult[index].yCoords[targetNodeIndex]);
		}
		subgraph.edges.push({startX: sourceCenter[0], startY: sourceCenter[1], endX: targetCenter[0], endY: targetCenter[1]});
		spectralResult.forEach(function(result, index){
		let newXCoords = result.xCoords.map(x => x + shiftResult[index].dx);
		let newYCoords = result.yCoords.map(y => y + shiftResult[index].dy);
		result.xCoords = newXCoords;
		result.yCoords = newYCoords;
		});
		}
		else{
		subgraph.edges.push({startX: coseResult[index][source.id()].getCenterX(), startY: coseResult[index][source.id()].getCenterY(), endX: coseResult[index][target.id()].getCenterX(), endY: coseResult[index][target.id()].getCenterY()});
		coseResult.forEach(function(result, index){
		Object.keys(result).forEach(function (item) {
		let nodeRectangle = result[item];
		nodeRectangle.setCenter(nodeRectangle.getCenterX() + shiftResult[index].dx, nodeRectangle.getCenterY() + shiftResult[index].dy);
		});
		});
		}
		});
		subgraphs.push(subgraph);
		});
		let shiftResult = layUtil.packComponents(subgraphs).shifts;
		if(options.quality == "draft"){
		spectralResult.forEach(function(result, index){
		let newXCoords = result.xCoords.map(x => x + shiftResult[index].dx);
		let newYCoords = result.yCoords.map(y => y + shiftResult[index].dy);
		result.xCoords = newXCoords;
		result.yCoords = newYCoords;
		});
		}
		}
		else{
		coseResult.forEach(function(result, index){
		Object.keys(result).forEach(function (item) {
		let nodeRectangle = result[item];
		nodeRectangle.setCenter(nodeRectangle.getCenterX() + shiftResult[index].dx, nodeRectangle.getCenterY() + shiftResult[index].dy);

		// move graph to its original position because spectral moves it to origin
		if(!options.fixedNodeConstraint) {
		let minXCoord = Number.POSITIVE_INFINITY;
		let maxXCoord = Number.NEGATIVE_INFINITY;
		let minYCoord = Number.POSITIVE_INFINITY;
		let maxYCoord = Number.NEGATIVE_INFINITY;
		if(options.quality == "draft") {
		spectralResult.forEach(function(result){
		result.xCoords.forEach(function (value) {
		if (value < minXCoord)
		minXCoord = value;
		if (value > maxXCoord)
		maxXCoord = value;
		});
		result.yCoords.forEach(function (value) {
		if (value < minYCoord)
		minYCoord = value;
		if (value > maxYCoord)
		maxYCoord = value;
		});
		});
		});
		let boundingBox = options.eles.boundingBox();
		let diffOnX = (boundingBox.x1 + boundingBox.w / 2) - (maxXCoord + minXCoord) / 2;
		let diffOnY = (boundingBox.y1 + boundingBox.h / 2) - (maxYCoord + minYCoord) / 2;
		spectralResult.forEach(function(result){
		result.xCoords = result.xCoords.map(x => x + diffOnX);
		result.yCoords = result.yCoords.map(y => y + diffOnY);
		});
		}
		else {
		coseResult.forEach(function(result){
		Object.keys(result).forEach(function (item) {
		let node = result[item];
		if (node.getCenterX() < minXCoord)
		minXCoord = node.getCenterX();
		if (node.getCenterX() > maxXCoord)
		maxXCoord = node.getCenterX();
		if (node.getCenterY() < minYCoord)
		minYCoord = node.getCenterY();
		if (node.getCenterY() > maxYCoord)
		maxYCoord = node.getCenterY();
		});
		});
		let boundingBox = options.eles.boundingBox();
		let diffOnX = (boundingBox.x1 + boundingBox.w / 2) - (maxXCoord + minXCoord) / 2;
		let diffOnY = (boundingBox.y1 + boundingBox.h / 2) - (maxYCoord + minYCoord) / 2;
		coseResult.forEach(function(result, index){
		Object.keys(result).forEach(function (item) {
		let node = result[item];
		node.setCenter(node.getCenterX() + diffOnX, node.getCenterY() + diffOnY);
		});
		});
		}
		}

		}
		@@ -302,3 +380,3 @@
		console.log("If randomize option is set to false, then quality option must be 'default' or 'proof'.");
		}
		}

		@@ -305,0 +383,0 @@ }

src/fcose/spectral.js

		@@ -6,2 +6,4 @@ /**
		const aux = require('./auxiliary');
		const Matrix = require('cose-base').layoutBase.Matrix;
		const SVD = require('cose-base').layoutBase.SVD;

		@@ -170,3 +172,3 @@ // main function that spectral layout is processed

		let SVDResult = aux.svd(PHI);
		let SVDResult = SVD.svd(PHI);

		@@ -192,3 +194,3 @@ let a_q = SVDResult.S;

		INV = aux.multMat(aux.multMat(a_v, a_Sig), aux.transpose(a_u));
		INV = Matrix.multMat(Matrix.multMat(a_v, a_Sig), Matrix.transpose(a_u));

		@@ -215,4 +217,4 @@ };

		Y1 = aux.normalize(Y1);
		Y2 = aux.normalize(Y2);
		Y1 = Matrix.normalize(Y1);
		Y2 = Matrix.normalize(Y2);

		@@ -233,7 +235,7 @@ let count = 0;

		Y1 = aux.multGamma(aux.multL(aux.multGamma(V1), C, INV));
		theta1 = aux.dotProduct(V1, Y1);
		Y1 = aux.normalize(Y1);
		Y1 = Matrix.multGamma(Matrix.multL(Matrix.multGamma(V1), C, INV));
		theta1 = Matrix.dotProduct(V1, Y1);
		Y1 = Matrix.normalize(Y1);

		current = aux.dotProduct(V1, Y1);
		current = Matrix.dotProduct(V1, Y1);

		@@ -262,8 +264,8 @@ temp = Math.abs(current/previous);

		V2 = aux.minusOp(V2, aux.multCons(V1, (aux.dotProduct(V1, V2))));
		Y2 = aux.multGamma(aux.multL(aux.multGamma(V2), C, INV));
		theta2 = aux.dotProduct(V2, Y2);
		Y2 = aux.normalize(Y2);
		V2 = Matrix.minusOp(V2, Matrix.multCons(V1, (Matrix.dotProduct(V1, V2))));
		Y2 = Matrix.multGamma(Matrix.multL(Matrix.multGamma(V2), C, INV));
		theta2 = Matrix.dotProduct(V2, Y2);
		Y2 = Matrix.normalize(Y2);

		current = aux.dotProduct(V2, Y2);
		current = Matrix.dotProduct(V2, Y2);

		@@ -289,4 +291,4 @@ temp = Math.abs(current/previous);
		//populate the two vectors
		xCoords = aux.multCons(V1, Math.sqrt(Math.abs(theta1)));
		yCoords = aux.multCons(V2, Math.sqrt(Math.abs(theta2)));
		xCoords = Matrix.multCons(V1, Math.sqrt(Math.abs(theta1)));
		yCoords = Matrix.multCons(V2, Math.sqrt(Math.abs(theta2)));

		@@ -353,3 +355,3 @@ };
		ele.neighborhood().nodes().forEach(function(node){
		if(eles.intersection(ele.edgesWith(node))){
		if(eles.intersection(ele.edgesWith(node)).length > 0){
		if(node.isParent())
		@@ -399,7 +401,16 @@ allNodesNeighborhood[eleIndex].push(parentChildMap.get(node.id()));

		allBFS(samplingType);
		sample();
		powerIteration();
		if(options.quality == "draft" \|\| options.step == "all"){
		allBFS(samplingType);
		sample();
		powerIteration();

		spectralResult = { nodeIndexes: nodeIndexes, xCoords: xCoords, yCoords: yCoords };
		spectralResult = { nodeIndexes: nodeIndexes, xCoords: xCoords, yCoords: yCoords };
		}
		else{
		nodeIndexes.forEach(function(value, key){
		xCoords.push(cy.getElementById(key).position("x"));
		yCoords.push(cy.getElementById(key).position("y"));
		});
		spectralResult = { nodeIndexes: nodeIndexes, xCoords: xCoords, yCoords: yCoords };
		}
		return spectralResult;
		@@ -406,0 +417,0 @@ }

demo-compound.html

demo.gif

demo.html

cytoscape-fcose.js

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