Upload folder using huggingface_hub (part 28)

tools/ui/node_modules/cytoscape-cose-bilkent/.babelrc

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+{
+  "presets": ["env"]
+}

tools/ui/node_modules/cytoscape-cose-bilkent/.eslintignore

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+node_modules/**/*

tools/ui/node_modules/cytoscape-cose-bilkent/.eslintrc

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+{
+    "env": {
+        "browser": true,
+        "commonjs": true,
+        "node": true,
+        "amd": true,
+        "es6": true
+    },
+    "extends": "eslint:recommended",
+    "rules": {
+      "semi": "error"
+    }
+}

tools/ui/node_modules/cytoscape-cose-bilkent/LICENSE

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+
+
+Copyright (c) 2016-2018, The Cytoscape Consortium.
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of
+this software and associated documentation files (the “Software”), to deal in
+the Software without restriction, including without limitation the rights to
+use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies
+of the Software, and to permit persons to whom the Software is furnished to do
+so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

tools/ui/node_modules/cytoscape-cose-bilkent/README.md

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+cytoscape-cose-bilkent
+================================================================================
+
+[![DOI](https://zenodo.org/badge/42200589.svg)](https://zenodo.org/badge/latestdoi/42200589)
+
+## Description
+
+The CoSE (Compound Spring Embedder) layout for Cytoscape.js developed by [i-Vis Lab](http://cs.bilkent.edu.tr/~ivis/) in Bilkent University is a spring embedder layout with support for compound graphs (nested structures) and varying (non-uniform) node dimensions.
+([demo](https://raw.githack.com/cytoscape/cytoscape.js-cose-bilkent/master/demo.html), [compound demo](https://raw.githack.com/cytoscape/cytoscape.js-cose-bilkent/master/demo-compound.html))
+
+Please cite the following when using this layout:
+
+U. Dogrusoz, E. Giral, A. Cetintas, A. Civril, and E. Demir, "[A Layout Algorithm For Undirected Compound Graphs](http://www.sciencedirect.com/science/article/pii/S0020025508004799)", Information Sciences, 179, pp. 980-994, 2009.
+
+## Dependencies
+
+ * Cytoscape.js ^3.2.0
+ * cose-base ^1.0.0
+
+
+## Usage instructions
+
+Download the library:
+ * via npm: `npm install cytoscape-cose-bilkent`,
+ * via bower: `bower install cytoscape-cose-bilkent`, or
+ * via direct download in the repository (probably from a tag).
+
+Import the library as appropriate for your project:
+
+ES import:
+
+```js
+import cytoscape from 'cytoscape';
+import coseBilkent from 'cytoscape-cose-bilkent';
+
+cytoscape.use( coseBilkent );
+```
+
+CommonJS require:
+
+```js
+let cytoscape = require('cytoscape');
+let coseBilkent = require('cytoscape-cose-bilkent');
+
+cytoscape.use( coseBilkent ); // register extension
+```
+
+AMD:
+
+```js
+require(['cytoscape', 'cytoscape-cose-bilkent'], function( cytoscape, coseBilkent ){
+  coseBilkent( cytoscape ); // register extension
+});
+```
+
+Plain HTML/JS has the extension registered for you automatically, because no `require()` is needed.
+
+
+## API
+
+When calling the layout, e.g. `cy.layout({ name: 'cose-bilkent', ... })`, the following options are supported:
+
+```js
+var defaultOptions = {
+  // Called on `layoutready`
+  ready: function () {
+  },
+  // Called on `layoutstop`
+  stop: function () {
+  },
+  // 'draft', 'default' or 'proof" 
+  // - 'draft' fast cooling rate 
+  // - 'default' moderate cooling rate 
+  // - "proof" slow cooling rate
+  quality: 'default',
+  // Whether to include labels in node dimensions. Useful for avoiding label overlap
+  nodeDimensionsIncludeLabels: false,
+  // number of ticks per frame; higher is faster but more jerky
+  refresh: 30,
+  // Whether to fit the network view after when done
+  fit: true,
+  // Padding on fit
+  padding: 10,
+  // Whether to enable incremental mode
+  randomize: true,
+  // Node repulsion (non overlapping) multiplier
+  nodeRepulsion: 4500,
+  // Ideal (intra-graph) edge length
+  idealEdgeLength: 50,
+  // Divisor to compute edge forces
+  edgeElasticity: 0.45,
+  // Nesting factor (multiplier) to compute ideal edge length for inter-graph edges
+  nestingFactor: 0.1,
+  // Gravity force (constant)
+  gravity: 0.25,
+  // Maximum number of iterations to perform
+  numIter: 2500,
+  // Whether to tile disconnected nodes
+  tile: true,
+  // Type of layout animation. The option set is {'during', 'end', false}
+  animate: 'end',
+  // Duration for animate:end
+  animationDuration: 500,
+  // Amount of vertical space to put between degree zero nodes during tiling (can also be a function)
+  tilingPaddingVertical: 10,
+  // Amount of horizontal space to put between degree zero nodes during tiling (can also be a function)
+  tilingPaddingHorizontal: 10,
+  // Gravity range (constant) for compounds
+  gravityRangeCompound: 1.5,
+  // Gravity force (constant) for compounds
+  gravityCompound: 1.0,
+  // Gravity range (constant)
+  gravityRange: 3.8,
+  // Initial cooling factor for incremental layout
+  initialEnergyOnIncremental: 0.5
+};
+```
+
+*Note that this extension supports only relatively modern browsers.  Browsers like IE require significant shimming, for example with [core-js](https://www.npmjs.com/package/core-js).*
+
+*Note that while running Cytoscape.js in headless mode, stylingEnabled option of Cytoscape.js should be set as true because this extension considers node dimensions and some other styling properties.*
+
+
+## Build targets
+
+* `npm run test` : Run Mocha tests in `./test`
+* `npm run build` : Build `./src/**` into `cytoscape-cose-bilkent.js`
+* `npm run watch` : Automatically build on changes with live reloading (N.b. you must already have an HTTP server running)
+* `npm run dev` : Automatically build on changes with live reloading with webpack dev server
+* `npm run lint` : Run eslint on the source
+
+N.b. all builds use babel, so modern ES features can be used in the `src`.
+
+
+## Publishing instructions
+
+This project is set up to automatically be published to npm and bower.  To publish:
+
+1. Build the extension : `npm run build:release`
+1. Commit the build : `git commit -am "Build for release"`
+1. Bump the version number and tag: `npm version major|minor|patch`
+1. Push to origin: `git push && git push --tags`
+1. Publish to npm: `npm publish .`
+1. If publishing to bower for the first time, you'll need to run `bower register cytoscape-cose-bilkent https://github.com/cytoscape/cytoscape.js-cose-bilkent.git`
+1. [Make a new release](https://github.com/cytoscape/cytoscape.js-cose-bilkent/releases/new) for Zenodo.

tools/ui/node_modules/cytoscape-cose-bilkent/bower.json

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+{
+  "name": "cytoscape-cose-bilkent",
+  "description": "The CoSE layout for Cytoscape.js by Bilkent with enhanced compound node placement",
+  "main": "cytoscape-cose-bilkent.js",
+  "dependencies": {
+    "cytoscape": "^3.2.0",
+    "cose-base": "^1.0.0"
+  },
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/cytoscape/cytoscape.js-cose-bilkent.git"
+  },
+  "ignore": [
+    "**/.*",
+    "node_modules",
+    "bower_components",
+    "test",
+    "tests"
+  ],
+  "keywords": [
+    "cytoscape",
+    "cytoscape-extension"
+  ],
+  "license": "MIT"
+}

tools/ui/node_modules/cytoscape-cose-bilkent/cytoscape-cose-bilkent.js

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+(function webpackUniversalModuleDefinition(root, factory) {
+	if(typeof exports === 'object' && typeof module === 'object')
+		module.exports = factory(require("cose-base"));
+	else if(typeof define === 'function' && define.amd)
+		define(["cose-base"], factory);
+	else if(typeof exports === 'object')
+		exports["cytoscapeCoseBilkent"] = factory(require("cose-base"));
+	else
+		root["cytoscapeCoseBilkent"] = factory(root["coseBase"]);
+})(this, function(__WEBPACK_EXTERNAL_MODULE_0__) {
+return /******/ (function(modules) { // webpackBootstrap
+/******/ 	// The module cache
+/******/ 	var installedModules = {};
+/******/
+/******/ 	// The require function
+/******/ 	function __webpack_require__(moduleId) {
+/******/
+/******/ 		// Check if module is in cache
+/******/ 		if(installedModules[moduleId]) {
+/******/ 			return installedModules[moduleId].exports;
+/******/ 		}
+/******/ 		// Create a new module (and put it into the cache)
+/******/ 		var module = installedModules[moduleId] = {
+/******/ 			i: moduleId,
+/******/ 			l: false,
+/******/ 			exports: {}
+/******/ 		};
+/******/
+/******/ 		// Execute the module function
+/******/ 		modules[moduleId].call(module.exports, module, module.exports, __webpack_require__);
+/******/
+/******/ 		// Flag the module as loaded
+/******/ 		module.l = true;
+/******/
+/******/ 		// Return the exports of the module
+/******/ 		return module.exports;
+/******/ 	}
+/******/
+/******/
+/******/ 	// expose the modules object (__webpack_modules__)
+/******/ 	__webpack_require__.m = modules;
+/******/
+/******/ 	// expose the module cache
+/******/ 	__webpack_require__.c = installedModules;
+/******/
+/******/ 	// identity function for calling harmony imports with the correct context
+/******/ 	__webpack_require__.i = function(value) { return value; };
+/******/
+/******/ 	// define getter function for harmony exports
+/******/ 	__webpack_require__.d = function(exports, name, getter) {
+/******/ 		if(!__webpack_require__.o(exports, name)) {
+/******/ 			Object.defineProperty(exports, name, {
+/******/ 				configurable: false,
+/******/ 				enumerable: true,
+/******/ 				get: getter
+/******/ 			});
+/******/ 		}
+/******/ 	};
+/******/
+/******/ 	// getDefaultExport function for compatibility with non-harmony modules
+/******/ 	__webpack_require__.n = function(module) {
+/******/ 		var getter = module && module.__esModule ?
+/******/ 			function getDefault() { return module['default']; } :
+/******/ 			function getModuleExports() { return module; };
+/******/ 		__webpack_require__.d(getter, 'a', getter);
+/******/ 		return getter;
+/******/ 	};
+/******/
+/******/ 	// Object.prototype.hasOwnProperty.call
+/******/ 	__webpack_require__.o = function(object, property) { return Object.prototype.hasOwnProperty.call(object, property); };
+/******/
+/******/ 	// __webpack_public_path__
+/******/ 	__webpack_require__.p = "";
+/******/
+/******/ 	// Load entry module and return exports
+/******/ 	return __webpack_require__(__webpack_require__.s = 1);
+/******/ })
+/************************************************************************/
+/******/ ([
+/* 0 */
+/***/ (function(module, exports) {
+
+module.exports = __WEBPACK_EXTERNAL_MODULE_0__;
+
+/***/ }),
+/* 1 */
+/***/ (function(module, exports, __webpack_require__) {
+
+"use strict";
+
+
+var LayoutConstants = __webpack_require__(0).layoutBase.LayoutConstants;
+var FDLayoutConstants = __webpack_require__(0).layoutBase.FDLayoutConstants;
+var CoSEConstants = __webpack_require__(0).CoSEConstants;
+var CoSELayout = __webpack_require__(0).CoSELayout;
+var CoSENode = __webpack_require__(0).CoSENode;
+var PointD = __webpack_require__(0).layoutBase.PointD;
+var DimensionD = __webpack_require__(0).layoutBase.DimensionD;
+
+var defaults = {
+  // Called on `layoutready`
+  ready: function ready() {},
+  // Called on `layoutstop`
+  stop: function stop() {},
+  // 'draft', 'default' or 'proof" 
+  // - 'draft' fast cooling rate 
+  // - 'default' moderate cooling rate 
+  // - "proof" slow cooling rate
+  quality: 'default',
+  // include labels in node dimensions
+  nodeDimensionsIncludeLabels: false,
+  // number of ticks per frame; higher is faster but more jerky
+  refresh: 30,
+  // Whether to fit the network view after when done
+  fit: true,
+  // Padding on fit
+  padding: 10,
+  // Whether to enable incremental mode
+  randomize: true,
+  // Node repulsion (non overlapping) multiplier
+  nodeRepulsion: 4500,
+  // Ideal edge (non nested) length
+  idealEdgeLength: 50,
+  // Divisor to compute edge forces
+  edgeElasticity: 0.45,
+  // Nesting factor (multiplier) to compute ideal edge length for nested edges
+  nestingFactor: 0.1,
+  // Gravity force (constant)
+  gravity: 0.25,
+  // Maximum number of iterations to perform
+  numIter: 2500,
+  // For enabling tiling
+  tile: true,
+  // Type of layout animation. The option set is {'during', 'end', false}
+  animate: 'end',
+  // Duration for animate:end
+  animationDuration: 500,
+  // Represents the amount of the vertical space to put between the zero degree members during the tiling operation(can also be a function)
+  tilingPaddingVertical: 10,
+  // Represents the amount of the horizontal space to put between the zero degree members during the tiling operation(can also be a function)
+  tilingPaddingHorizontal: 10,
+  // Gravity range (constant) for compounds
+  gravityRangeCompound: 1.5,
+  // Gravity force (constant) for compounds
+  gravityCompound: 1.0,
+  // Gravity range (constant)
+  gravityRange: 3.8,
+  // Initial cooling factor for incremental layout
+  initialEnergyOnIncremental: 0.5
+};
+
+function extend(defaults, options) {
+  var obj = {};
+
+  for (var i in defaults) {
+    obj[i] = defaults[i];
+  }
+
+  for (var i in options) {
+    obj[i] = options[i];
+  }
+
+  return obj;
+};
+
+function _CoSELayout(_options) {
+  this.options = extend(defaults, _options);
+  getUserOptions(this.options);
+}
+
+var getUserOptions = function getUserOptions(options) {
+  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) CoSEConstants.PER_LEVEL_IDEAL_EDGE_LENGTH_FACTOR = FDLayoutConstants.PER_LEVEL_IDEAL_EDGE_LENGTH_FACTOR = options.nestingFactor;
+  if (options.gravity != null) CoSEConstants.DEFAULT_GRAVITY_STRENGTH = FDLayoutConstants.DEFAULT_GRAVITY_STRENGTH = options.gravity;
+  if (options.numIter != null) CoSEConstants.MAX_ITERATIONS = FDLayoutConstants.MAX_ITERATIONS = options.numIter;
+  if (options.gravityRange != null) CoSEConstants.DEFAULT_GRAVITY_RANGE_FACTOR = FDLayoutConstants.DEFAULT_GRAVITY_RANGE_FACTOR = options.gravityRange;
+  if (options.gravityCompound != null) CoSEConstants.DEFAULT_COMPOUND_GRAVITY_STRENGTH = FDLayoutConstants.DEFAULT_COMPOUND_GRAVITY_STRENGTH = options.gravityCompound;
+  if (options.gravityRangeCompound != null) CoSEConstants.DEFAULT_COMPOUND_GRAVITY_RANGE_FACTOR = FDLayoutConstants.DEFAULT_COMPOUND_GRAVITY_RANGE_FACTOR = options.gravityRangeCompound;
+  if (options.initialEnergyOnIncremental != null) CoSEConstants.DEFAULT_COOLING_FACTOR_INCREMENTAL = FDLayoutConstants.DEFAULT_COOLING_FACTOR_INCREMENTAL = options.initialEnergyOnIncremental;
+
+  if (options.quality == 'draft') LayoutConstants.QUALITY = 0;else if (options.quality == 'proof') LayoutConstants.QUALITY = 2;else LayoutConstants.QUALITY = 1;
+
+  CoSEConstants.NODE_DIMENSIONS_INCLUDE_LABELS = FDLayoutConstants.NODE_DIMENSIONS_INCLUDE_LABELS = LayoutConstants.NODE_DIMENSIONS_INCLUDE_LABELS = options.nodeDimensionsIncludeLabels;
+  CoSEConstants.DEFAULT_INCREMENTAL = FDLayoutConstants.DEFAULT_INCREMENTAL = LayoutConstants.DEFAULT_INCREMENTAL = !options.randomize;
+  CoSEConstants.ANIMATE = FDLayoutConstants.ANIMATE = LayoutConstants.ANIMATE = options.animate;
+  CoSEConstants.TILE = options.tile;
+  CoSEConstants.TILING_PADDING_VERTICAL = typeof options.tilingPaddingVertical === 'function' ? options.tilingPaddingVertical.call() : options.tilingPaddingVertical;
+  CoSEConstants.TILING_PADDING_HORIZONTAL = typeof options.tilingPaddingHorizontal === 'function' ? options.tilingPaddingHorizontal.call() : options.tilingPaddingHorizontal;
+};
+
+_CoSELayout.prototype.run = function () {
+  var ready;
+  var frameId;
+  var options = this.options;
+  var idToLNode = this.idToLNode = {};
+  var layout = this.layout = new CoSELayout();
+  var self = this;
+
+  self.stopped = false;
+
+  this.cy = this.options.cy;
+
+  this.cy.trigger({ type: 'layoutstart', layout: this });
+
+  var gm = layout.newGraphManager();
+  this.gm = gm;
+
+  var nodes = this.options.eles.nodes();
+  var edges = this.options.eles.edges();
+
+  this.root = gm.addRoot();
+  this.processChildrenList(this.root, this.getTopMostNodes(nodes), layout);
+
+  for (var i = 0; i < edges.length; i++) {
+    var edge = edges[i];
+    var sourceNode = this.idToLNode[edge.data("source")];
+    var targetNode = this.idToLNode[edge.data("target")];
+    if (sourceNode !== targetNode && sourceNode.getEdgesBetween(targetNode).length == 0) {
+      var e1 = gm.add(layout.newEdge(), sourceNode, targetNode);
+      e1.id = edge.id();
+    }
+  }
+
+  var getPositions = function getPositions(ele, i) {
+    if (typeof ele === "number") {
+      ele = i;
+    }
+    var theId = ele.data('id');
+    var lNode = self.idToLNode[theId];
+
+    return {
+      x: lNode.getRect().getCenterX(),
+      y: lNode.getRect().getCenterY()
+    };
+  };
+
+  /*
+   * Reposition nodes in iterations animatedly
+   */
+  var iterateAnimated = function iterateAnimated() {
+    // Thigs to perform after nodes are repositioned on screen
+    var afterReposition = function afterReposition() {
+      if (options.fit) {
+        options.cy.fit(options.eles, options.padding);
+      }
+
+      if (!ready) {
+        ready = true;
+        self.cy.one('layoutready', options.ready);
+        self.cy.trigger({ type: 'layoutready', layout: self });
+      }
+    };
+
+    var ticksPerFrame = self.options.refresh;
+    var isDone;
+
+    for (var i = 0; i < ticksPerFrame && !isDone; i++) {
+      isDone = self.stopped || self.layout.tick();
+    }
+
+    // If layout is done
+    if (isDone) {
+      // If the layout is not a sublayout and it is successful perform post layout.
+      if (layout.checkLayoutSuccess() && !layout.isSubLayout) {
+        layout.doPostLayout();
+      }
+
+      // If layout has a tilingPostLayout function property call it.
+      if (layout.tilingPostLayout) {
+        layout.tilingPostLayout();
+      }
+
+      layout.isLayoutFinished = true;
+
+      self.options.eles.nodes().positions(getPositions);
+
+      afterReposition();
+
+      // trigger layoutstop when the layout stops (e.g. finishes)
+      self.cy.one('layoutstop', self.options.stop);
+      self.cy.trigger({ type: 'layoutstop', layout: self });
+
+      if (frameId) {
+        cancelAnimationFrame(frameId);
+      }
+
+      ready = false;
+      return;
+    }
+
+    var animationData = self.layout.getPositionsData(); // Get positions of layout nodes note that all nodes may not be layout nodes because of tiling
+
+    // Position nodes, for the nodes whose id does not included in data (because they are removed from their parents and included in dummy compounds)
+    // use position of their ancestors or dummy ancestors
+    options.eles.nodes().positions(function (ele, i) {
+      if (typeof ele === "number") {
+        ele = i;
+      }
+      // If ele is a compound node, then its position will be defined by its children
+      if (!ele.isParent()) {
+        var theId = ele.id();
+        var pNode = animationData[theId];
+        var temp = ele;
+        // If pNode is undefined search until finding position data of its first ancestor (It may be dummy as well)
+        while (pNode == null) {
+          pNode = animationData[temp.data('parent')] || animationData['DummyCompound_' + temp.data('parent')];
+          animationData[theId] = pNode;
+          temp = temp.parent()[0];
+          if (temp == undefined) {
+            break;
+          }
+        }
+        if (pNode != null) {
+          return {
+            x: pNode.x,
+            y: pNode.y
+          };
+        } else {
+          return {
+            x: ele.position('x'),
+            y: ele.position('y')
+          };
+        }
+      }
+    });
+
+    afterReposition();
+
+    frameId = requestAnimationFrame(iterateAnimated);
+  };
+
+  /*
+  * Listen 'layoutstarted' event and start animated iteration if animate option is 'during'
+  */
+  layout.addListener('layoutstarted', function () {
+    if (self.options.animate === 'during') {
+      frameId = requestAnimationFrame(iterateAnimated);
+    }
+  });
+
+  layout.runLayout(); // Run cose layout
+
+  /*
+   * If animate option is not 'during' ('end' or false) perform these here (If it is 'during' similar things are already performed)
+   */
+  if (this.options.animate !== "during") {
+    self.options.eles.nodes().not(":parent").layoutPositions(self, self.options, getPositions); // Use layout positions to reposition the nodes it considers the options parameter
+    ready = false;
+  }
+
+  return this; // chaining
+};
+
+//Get the top most ones of a list of nodes
+_CoSELayout.prototype.getTopMostNodes = function (nodes) {
+  var nodesMap = {};
+  for (var i = 0; i < nodes.length; i++) {
+    nodesMap[nodes[i].id()] = true;
+  }
+  var roots = nodes.filter(function (ele, i) {
+    if (typeof ele === "number") {
+      ele = i;
+    }
+    var parent = ele.parent()[0];
+    while (parent != null) {
+      if (nodesMap[parent.id()]) {
+        return false;
+      }
+      parent = parent.parent()[0];
+    }
+    return true;
+  });
+
+  return roots;
+};
+
+_CoSELayout.prototype.processChildrenList = function (parent, children, layout) {
+  var size = children.length;
+  for (var i = 0; i < size; i++) {
+    var theChild = children[i];
+    var children_of_children = theChild.children();
+    var theNode;
+
+    var dimensions = theChild.layoutDimensions({
+      nodeDimensionsIncludeLabels: this.options.nodeDimensionsIncludeLabels
+    });
+
+    if (theChild.outerWidth() != null && theChild.outerHeight() != null) {
+      theNode = parent.add(new CoSENode(layout.graphManager, new PointD(theChild.position('x') - dimensions.w / 2, theChild.position('y') - dimensions.h / 2), new DimensionD(parseFloat(dimensions.w), parseFloat(dimensions.h))));
+    } else {
+      theNode = parent.add(new CoSENode(this.graphManager));
+    }
+    // Attach id to the layout node
+    theNode.id = theChild.data("id");
+    // Attach the paddings of cy node to layout node
+    theNode.paddingLeft = parseInt(theChild.css('padding'));
+    theNode.paddingTop = parseInt(theChild.css('padding'));
+    theNode.paddingRight = parseInt(theChild.css('padding'));
+    theNode.paddingBottom = parseInt(theChild.css('padding'));
+
+    //Attach the label properties to compound if labels will be included in node dimensions  
+    if (this.options.nodeDimensionsIncludeLabels) {
+      if (theChild.isParent()) {
+        var labelWidth = theChild.boundingBox({ includeLabels: true, includeNodes: false }).w;
+        var labelHeight = theChild.boundingBox({ includeLabels: true, includeNodes: false }).h;
+        var labelPos = theChild.css("text-halign");
+        theNode.labelWidth = labelWidth;
+        theNode.labelHeight = labelHeight;
+        theNode.labelPos = labelPos;
+      }
+    }
+
+    // Map the layout node
+    this.idToLNode[theChild.data("id")] = theNode;
+
+    if (isNaN(theNode.rect.x)) {
+      theNode.rect.x = 0;
+    }
+
+    if (isNaN(theNode.rect.y)) {
+      theNode.rect.y = 0;
+    }
+
+    if (children_of_children != null && children_of_children.length > 0) {
+      var theNewGraph;
+      theNewGraph = layout.getGraphManager().add(layout.newGraph(), theNode);
+      this.processChildrenList(theNewGraph, children_of_children, layout);
+    }
+  }
+};
+
+/**
+ * @brief : called on continuous layouts to stop them before they finish
+ */
+_CoSELayout.prototype.stop = function () {
+  this.stopped = true;
+
+  return this; // chaining
+};
+
+var register = function register(cytoscape) {
+  //  var Layout = getLayout( cytoscape );
+
+  cytoscape('layout', 'cose-bilkent', _CoSELayout);
+};
+
+// auto reg for globals
+if (typeof cytoscape !== 'undefined') {
+  register(cytoscape);
+}
+
+module.exports = register;
+
+/***/ })
+/******/ ]);
+});

tools/ui/node_modules/cytoscape-cose-bilkent/demo-compound.html

@@ -0,0 +1,199 @@
+<!DOCTYPE>
+
+<html>
+
+  <head>
+    <title>cytoscape-cose-bilkent.js demo (compound)</title>
+
+    <meta name="viewport" content="width=device-width, user-scalable=no, initial-scale=1, maximum-scale=1">
+
+    <script src="https://unpkg.com/cytoscape/dist/cytoscape.min.js"></script>
+
+    <!-- for testing with local version of cytoscape.js -->
+    <!--<script src="../cytoscape.js/build/cytoscape.js"></script>-->
+
+    <!--polyfills are needed for this extension for old browsers like IE -->
+    <script src="https://cdnjs.cloudflare.com/ajax/libs/core-js/2.5.7/shim.min.js"></script>
+    <script src="https://unpkg.com/layout-base/layout-base.js"></script>
+    <script src="https://unpkg.com/cose-base/cose-base.js"></script>
+    <script src="cytoscape-cose-bilkent.js"></script>
+
+    <style>
+      body {
+        font-family: helvetica;
+        font-size: 14px;
+      }
+
+      #cy {
+        width: 100%;
+        height: 90%;
+        z-index: 999;
+      }
+
+      h1 {
+        opacity: 0.5;
+        font-size: 1em;
+      }
+
+      button {
+        margin-right: 10px;
+      }
+    </style>
+
+    <script>
+      document.addEventListener('DOMContentLoaded', function(){
+
+        var cy = window.cy = cytoscape({
+          container: document.getElementById('cy'),
+
+          ready: function(){
+            this.nodes().forEach(function(node){
+              let width = [30, 70, 110];
+              let size = width[Math.floor(Math.random()*3)];
+              node.css("width", size);
+              node.css("height", size);
+            });
+            this.layout({name: 'cose-bilkent', animationDuration: 1000}).run();
+          },
+            
+          style: [
+            {
+              selector: 'node',
+              style: {
+                'background-color': '#ad1a66'
+              }
+            },
+
+            {
+              selector: ':parent',
+              style: {
+                'background-opacity': 0.333
+              }
+            },
+
+            {
+              selector: 'edge',
+              style: {
+                'width': 3,
+                'line-color': '#ad1a66'
+              }
+            }
+          ],
+
+            elements: [{ group:'nodes', data:{ id: 'n0'}},
+                    { group:'nodes', data:{ id: 'n1'}},
+                    { group:'nodes', data:{ id: 'n2'}},
+                    { group:'nodes', data:{ id: 'n3'}},
+                    { group:'nodes', data:{ id: 'n4', parent: 'n37'}},
+                    { group:'nodes', data:{ id: 'n5'}},
+                    { group:'nodes', data:{ id: 'n6'}},
+                    { group:'nodes', data:{ id: 'n7', parent: 'n37'}},
+                    { group:'nodes', data:{ id: 'n8', parent: 'n37'}},
+                    { group:'nodes', data:{ id: 'n9', parent: 'n37'}},
+                    { group:'nodes', data:{ id: 'n10', parent: 'n38'}},
+                    { group:'nodes', data:{ id: 'n12'}},
+                    { group:'nodes', data:{ id: 'n13'}},
+                    { group:'nodes', data:{ id: 'n14'}},
+                    { group:'nodes', data:{ id: 'n15'}},
+                    { group:'nodes', data:{ id: 'n16'}},
+                    { group:'nodes', data:{ id: 'n17'}},
+                    { group:'nodes', data:{ id: 'n18'}},
+                    { group:'nodes', data:{ id: 'n19'}},
+                    { group:'nodes', data:{ id: 'n20'}},
+                    { group:'nodes', data:{ id: 'n21'}},
+                    { group:'nodes', data:{ id: 'n22'}},
+                    { group:'nodes', data:{ id: 'n23'}},
+                    { group:'nodes', data:{ id: 'n24', parent: 'n39'}},
+                    { group:'nodes', data:{ id: 'n25', parent: 'n39'}},
+                    { group:'nodes', data:{ id: 'n26', parent: 'n42'}},
+                    { group:'nodes', data:{ id: 'n27', parent: 'n42'}},
+                    { group:'nodes', data:{ id: 'n28', parent: 'n42'}},
+                    { group:'nodes', data:{ id: 'n29', parent: 'n40'}},
+                    { group:'nodes', data:{ id: 'n31', parent: 'n41'}},
+                    { group:'nodes', data:{ id: 'n32', parent: 'n41'}},
+                    { group:'nodes', data:{ id: 'n33', parent: 'n41'}},
+                    { group:'nodes', data:{ id: 'n34', parent: 'n41'}},
+                    { group:'nodes', data:{ id: 'n35', parent: 'n41'}},
+                    { group:'nodes', data:{ id: 'n36', parent: 'n41'}},
+                    { group:'nodes', data:{ id: 'n37'}},
+                    { group:'nodes', data:{ id: 'n38'}},
+                    { group:'nodes', data:{ id: 'n39', parent: 'n43'}},
+                    { group:'nodes', data:{ id: 'n40', parent: 'n42'}},
+                    { group:'nodes', data:{ id: 'n41', parent: 'n42'}},
+                    { group:'nodes', data:{ id: 'n42', parent: 'n43'}},
+                    { group:'nodes', data:{ id: 'n43'}},
+                    { group:'edges', data:{ id: 'e0', source: 'n0', target: 'n1'} },
+                    { group:'edges', data:{ id: 'e1', source: 'n1', target: 'n2'} },
+                    { group:'edges', data:{ id: 'e2', source: 'n2', target: 'n3'} },
+                    { group:'edges', data:{ id: 'e3', source: 'n0', target: 'n3'} },
+                    { group:'edges', data:{ id: 'e4', source: 'n1', target: 'n4'} },
+                    { group:'edges', data:{ id: 'e5', source: 'n2', target: 'n4'} },
+                    { group:'edges', data:{ id: 'e6', source: 'n4', target: 'n5'} },
+                    { group:'edges', data:{ id: 'e7', source: 'n5', target: 'n6'} },
+                    { group:'edges', data:{ id: 'e8', source: 'n4', target: 'n6'} },
+                    { group:'edges', data:{ id: 'e9', source: 'n4', target: 'n7'} },
+                    { group:'edges', data:{ id: 'e10', source: 'n7', target: 'n8'} },
+                    { group:'edges', data:{ id: 'e11', source: 'n8', target: 'n9'} },
+                    { group:'edges', data:{ id: 'e12', source: 'n7', target: 'n9'} },
+                    { group:'edges', data:{ id: 'e13', source: 'n13', target: 'n14'} },
+                    { group:'edges', data:{ id: 'e14', source: 'n12', target: 'n14'} },
+                    { group:'edges', data:{ id: 'e15', source: 'n14', target: 'n15'} },
+                    { group:'edges', data:{ id: 'e16', source: 'n14', target: 'n16'} },
+                    { group:'edges', data:{ id: 'e17', source: 'n15', target: 'n17'} },
+                    { group:'edges', data:{ id: 'e18', source: 'n17', target: 'n18'} },
+                    { group:'edges', data:{ id: 'e19', source: 'n18', target: 'n19'} },
+                    { group:'edges', data:{ id: 'e20', source: 'n17', target: 'n20'} },
+                    { group:'edges', data:{ id: 'e21', source: 'n19', target: 'n20'} },
+                    { group:'edges', data:{ id: 'e22', source: 'n16', target: 'n20'} },
+                    { group:'edges', data:{ id: 'e23', source: 'n20', target: 'n21'} },
+                    { group:'edges', data:{ id: 'e25', source: 'n23', target: 'n24'} },
+                    { group:'edges', data:{ id: 'e26', source: 'n24', target: 'n25'} },
+                    { group:'edges', data:{ id: 'e27', source: 'n26', target: 'n38'} },
+                    { group:'edges', data:{ id: 'e29', source: 'n26', target: 'n39'} },
+                    { group:'edges', data:{ id: 'e30', source: 'n26', target: 'n27'} },
+                    { group:'edges', data:{ id: 'e31', source: 'n26', target: 'n28'} },
+                    { group:'edges', data:{ id: 'e33', source: 'n21', target: 'n31'} },
+                    { group:'edges', data:{ id: 'e35', source: 'n31', target: 'n33'} },
+                    { group:'edges', data:{ id: 'e36', source: 'n31', target: 'n34'} },
+                    { group:'edges', data:{ id: 'e37', source: 'n33', target: 'n34'} },
+                    { group:'edges', data:{ id: 'e38', source: 'n32', target: 'n35'} },
+                    { group:'edges', data:{ id: 'e39', source: 'n32', target: 'n36'} },
+                    { group:'edges', data:{ id: 'e40', source: 'n16', target: 'n40'} }
+                   ]
+        });
+        document.getElementById("layoutButton").addEventListener("click", function(){
+          var layout = cy.layout({
+            name: 'cose-bilkent',
+            animate: 'end',
+            animationEasing: 'ease-out',
+            animationDuration: 1000,
+            randomize: true
+          });
+
+          layout.run();
+        });
+        document.getElementById("randomize").addEventListener("click", function(){
+          var layout = cy.layout({
+            name: 'random',
+            animate: true,
+            animationDuration: 1000,
+            animationEasing: 'ease-out'
+          });
+
+          layout.run();
+        });
+      });
+    </script>
+  </head>
+
+  <body>
+    <h1>cytoscape-cose-bilkent demo (compound)</h1>
+
+    <button id="randomize" type="button">Randomize</button>
+    <button id="layoutButton" type="button">CoSE-Bilkent</button>
+
+    <div id="cy"></div>
+
+  </body>
+
+</html>

tools/ui/node_modules/cytoscape-cose-bilkent/demo.html

@@ -0,0 +1,117 @@
+<!DOCTYPE>
+
+<html>
+
+  <head>
+    <title>cytoscape-cose-bilkent.js demo</title>
+
+    <meta name="viewport" content="width=device-width, user-scalable=no, initial-scale=1, maximum-scale=1">
+
+    <script src="https://unpkg.com/cytoscape/dist/cytoscape.min.js"></script>
+
+    <!-- for testing with local version of cytoscape.js -->
+    <!--<script src="../cytoscape.js/build/cytoscape.js"></script>-->
+
+    <!--polyfills are needed for this extension for old browsers like IE -->
+    <script src="https://cdnjs.cloudflare.com/ajax/libs/core-js/2.5.7/shim.min.js"></script>
+    <script src="https://unpkg.com/layout-base/layout-base.js"></script>
+    <script src="https://unpkg.com/cose-base/cose-base.js"></script>
+    <script src="cytoscape-cose-bilkent.js"></script>
+
+    <style>
+      body {
+        font-family: helvetica;
+        font-size: 14px;
+      }
+
+      #cy {
+        width: 100%;
+        height: 90%;
+        z-index: 999;
+      }
+
+      h1 {
+        opacity: 0.5;
+        font-size: 1em;
+      }
+
+      button {
+        margin-right: 10px;
+      }
+    </style>
+
+    <script>
+      document.addEventListener('DOMContentLoaded',function(){
+
+        var cy = window.cy = cytoscape({
+          container: document.getElementById('cy'),
+
+          ready: function(){
+            this.nodes().forEach(function(node){
+              let width = [30, 70, 110];
+              let size = width[Math.floor(Math.random()*3)];
+              node.css("width", size);
+              node.css("height", size);
+            });
+            this.layout({name: 'cose-bilkent', animationDuration: 1000}).run();
+          },
+
+          style: [
+            {
+              selector: 'node',
+              style: {
+                'background-color': '#ad1a66'
+              }
+            },
+
+            {
+              selector: 'edge',
+              style: {
+                'width': 3,
+                'line-color': '#ad1a66'
+              }
+            }
+          ],
+
+          elements: [{"data":{"id":"glyph9","sbgnbbox":{"x":1452.639173965406,"y":609.3619416544145,"w":"120.0","h":"60.0"},"sbgnclass":"macromolecule","sbgnlabel":"hexokinase","sbgnstatesandinfos":[],"ports":[]},"position":{"x":1452.639173965406,"y":609.3619416544145},"group":"nodes","removed":false,"selected":false,"selectable":true,"locked":false,"grabbed":false,"grabbable":true,"classes":""},{"data":{"id":"glyph0","sbgnbbox":{"x":1351.3490293961959,"y":518.9529901384763,"w":"60.0","h":"60.0"},"sbgnclass":"simple chemical","sbgnlabel":"glucose","sbgnstatesandinfos":[],"ports":[]},"position":{"x":1351.3490293961959,"y":518.9529901384763},"group":"nodes","removed":false,"selected":false,"selectable":true,"locked":false,"grabbed":false,"grabbable":true,"classes":""},{"data":{"id":"glyph6","sbgnbbox":{"x":1358.2854747390154,"y":707.9866590968695,"w":"60.0","h":"60.0"},"sbgnclass":"simple 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+        document.getElementById("layoutButton").addEventListener("click", function(){
+          var layout = cy.layout({
+            name: 'cose-bilkent',
+            animate: 'end',
+            animationEasing: 'ease-out',
+            animationDuration: 1000,
+            randomize: true
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+          layout.run();
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+        document.getElementById("randomize").addEventListener("click", function(){
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+            name: 'random',
+            animate: true,
+            animationDuration: 1000,
+            animationEasing: 'ease-out'
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+          layout.run();
+        });
+      });
+    </script>
+  </head>
+
+  <body>
+    <h1>cytoscape-cose-bilkent demo</h1>
+
+    <button id="randomize" type="button">Randomize</button>
+    <button id="layoutButton" type="button">CoSE-Bilkent</button>
+
+    <div id="cy"></div>
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+  </body>
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tools/ui/node_modules/cytoscape-cose-bilkent/nbproject/private/private.properties

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+browser=Chrome.INTEGRATED

tools/ui/node_modules/cytoscape-cose-bilkent/nbproject/project.properties

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+files.encoding=UTF-8
+site.root.folder=
+source.folder=

tools/ui/node_modules/cytoscape-cose-bilkent/nbproject/project.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://www.netbeans.org/ns/project/1">
+    <type>org.netbeans.modules.web.clientproject</type>
+    <configuration>
+        <data xmlns="http://www.netbeans.org/ns/clientside-project/1">
+            <name>cytoscape-cose-bilkent</name>
+        </data>
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tools/ui/node_modules/cytoscape-cose-bilkent/package.json

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+{
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+  "version": "4.1.0",
+  "description": "The CoSE layout for Cytoscape.js by Bilkent with enhanced compound node placement",
+  "main": "cytoscape-cose-bilkent.js",
+  "scripts": {
+    "postpublish": "run-s gh-pages",
+    "gh-pages": "gh-pages -d pages",
+    "copyright": "update license",
+    "lint": "eslint src",
+    "build": "cross-env NODE_ENV=production webpack",
+    "build:min": "cross-env NODE_ENV=production MIN=true webpack",
+    "build:release": "run-s build copyright",
+    "watch": "webpack --progress --watch",
+    "dev": "webpack-dev-server --open",
+    "test": "mocha"
+  },
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/cytoscape/cytoscape.js-cose-bilkent.git"
+  },
+  "keywords": [
+    "cytoscape",
+    "cytoscape-extension"
+  ],
+  "license": "MIT",
+  "bugs": {
+    "url": "https://github.com/cytoscape/cytoscape.js-cose-bilkent/issues"
+  },
+  "homepage": "https://github.com/cytoscape/cytoscape.js-cose-bilkent",
+  "devDependencies": {
+    "babel-core": "^6.24.1",
+    "babel-loader": "^7.0.0",
+    "babel-preset-env": "^1.5.1",
+    "camelcase": "^4.1.0",
+    "chai": "4.0.2",
+    "cpy-cli": "^1.0.1",
+    "cross-env": "^5.0.0",
+    "eslint": "^3.9.1",
+    "gh-pages": "^1.0.0",
+    "mocha": "3.4.2",
+    "npm-run-all": "^4.1.2",
+    "rimraf": "^2.6.2",
+    "update": "^0.7.4",
+    "updater-license": "^1.0.0",
+    "webpack": "^2.6.1",
+    "webpack-dev-server": "^2.4.5"
+  },
+  "peerDependencies": {
+    "cytoscape": "^3.2.0"
+  },
+  "dependencies": {
+    "cose-base": "^1.0.0"
+  }
+}

tools/ui/node_modules/cytoscape-cose-bilkent/src/index.js

@@ -0,0 +1,390 @@
+'use strict';
+
+var LayoutConstants = require('cose-base').layoutBase.LayoutConstants;
+var FDLayoutConstants = require('cose-base').layoutBase.FDLayoutConstants;
+var CoSEConstants = require('cose-base').CoSEConstants;
+var CoSELayout = require('cose-base').CoSELayout;
+var CoSENode = require('cose-base').CoSENode;
+var PointD = require('cose-base').layoutBase.PointD;
+var DimensionD = require('cose-base').layoutBase.DimensionD;
+
+var defaults = {
+  // Called on `layoutready`
+  ready: function () {
+  },
+  // Called on `layoutstop`
+  stop: function () {
+  },
+  // 'draft', 'default' or 'proof" 
+  // - 'draft' fast cooling rate 
+  // - 'default' moderate cooling rate 
+  // - "proof" slow cooling rate
+  quality: 'default',
+  // include labels in node dimensions
+  nodeDimensionsIncludeLabels: false,
+  // number of ticks per frame; higher is faster but more jerky
+  refresh: 30,
+  // Whether to fit the network view after when done
+  fit: true,
+  // Padding on fit
+  padding: 10,
+  // Whether to enable incremental mode
+  randomize: true,
+  // Node repulsion (non overlapping) multiplier
+  nodeRepulsion: 4500,
+  // Ideal edge (non nested) length
+  idealEdgeLength: 50,
+  // Divisor to compute edge forces
+  edgeElasticity: 0.45,
+  // Nesting factor (multiplier) to compute ideal edge length for nested edges
+  nestingFactor: 0.1,
+  // Gravity force (constant)
+  gravity: 0.25,
+  // Maximum number of iterations to perform
+  numIter: 2500,
+  // For enabling tiling
+  tile: true,
+  // Type of layout animation. The option set is {'during', 'end', false}
+  animate: 'end',
+  // Duration for animate:end
+  animationDuration: 500,
+  // Represents the amount of the vertical space to put between the zero degree members during the tiling operation(can also be a function)
+  tilingPaddingVertical: 10,
+  // Represents the amount of the horizontal space to put between the zero degree members during the tiling operation(can also be a function)
+  tilingPaddingHorizontal: 10,
+  // Gravity range (constant) for compounds
+  gravityRangeCompound: 1.5,
+  // Gravity force (constant) for compounds
+  gravityCompound: 1.0,
+  // Gravity range (constant)
+  gravityRange: 3.8,
+  // Initial cooling factor for incremental layout
+  initialEnergyOnIncremental: 0.5
+};
+
+function extend(defaults, options) {
+  var obj = {};
+
+  for (var i in defaults) {
+    obj[i] = defaults[i];
+  }
+
+  for (var i in options) {
+    obj[i] = options[i];
+  }
+
+  return obj;
+};
+
+function _CoSELayout(_options) {
+  this.options = extend(defaults, _options);
+  getUserOptions(this.options);
+}
+
+var getUserOptions = function (options) {
+  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)
+    CoSEConstants.PER_LEVEL_IDEAL_EDGE_LENGTH_FACTOR = FDLayoutConstants.PER_LEVEL_IDEAL_EDGE_LENGTH_FACTOR = options.nestingFactor;
+  if (options.gravity != null)
+    CoSEConstants.DEFAULT_GRAVITY_STRENGTH = FDLayoutConstants.DEFAULT_GRAVITY_STRENGTH = options.gravity;
+  if (options.numIter != null)
+    CoSEConstants.MAX_ITERATIONS = FDLayoutConstants.MAX_ITERATIONS = options.numIter;
+  if (options.gravityRange != null)
+    CoSEConstants.DEFAULT_GRAVITY_RANGE_FACTOR = FDLayoutConstants.DEFAULT_GRAVITY_RANGE_FACTOR = options.gravityRange;
+  if(options.gravityCompound != null)
+    CoSEConstants.DEFAULT_COMPOUND_GRAVITY_STRENGTH = FDLayoutConstants.DEFAULT_COMPOUND_GRAVITY_STRENGTH = options.gravityCompound;
+  if(options.gravityRangeCompound != null)
+    CoSEConstants.DEFAULT_COMPOUND_GRAVITY_RANGE_FACTOR = FDLayoutConstants.DEFAULT_COMPOUND_GRAVITY_RANGE_FACTOR = options.gravityRangeCompound;
+  if (options.initialEnergyOnIncremental != null)
+    CoSEConstants.DEFAULT_COOLING_FACTOR_INCREMENTAL = FDLayoutConstants.DEFAULT_COOLING_FACTOR_INCREMENTAL = options.initialEnergyOnIncremental;
+  
+  if (options.quality == 'draft')
+    LayoutConstants.QUALITY = 0;
+  else if(options.quality == 'proof')
+    LayoutConstants.QUALITY = 2;
+  else
+    LayoutConstants.QUALITY = 1;
+
+  CoSEConstants.NODE_DIMENSIONS_INCLUDE_LABELS = FDLayoutConstants.NODE_DIMENSIONS_INCLUDE_LABELS = LayoutConstants.NODE_DIMENSIONS_INCLUDE_LABELS = options.nodeDimensionsIncludeLabels;
+  CoSEConstants.DEFAULT_INCREMENTAL = FDLayoutConstants.DEFAULT_INCREMENTAL = LayoutConstants.DEFAULT_INCREMENTAL =
+          !(options.randomize);
+  CoSEConstants.ANIMATE = FDLayoutConstants.ANIMATE = LayoutConstants.ANIMATE = options.animate;
+  CoSEConstants.TILE = options.tile;
+  CoSEConstants.TILING_PADDING_VERTICAL = 
+          typeof options.tilingPaddingVertical === 'function' ? options.tilingPaddingVertical.call() : options.tilingPaddingVertical;
+  CoSEConstants.TILING_PADDING_HORIZONTAL = 
+          typeof options.tilingPaddingHorizontal === 'function' ? options.tilingPaddingHorizontal.call() : options.tilingPaddingHorizontal;
+};
+
+_CoSELayout.prototype.run = function () {
+  var ready;
+  var frameId;
+  var options = this.options;
+  var idToLNode = this.idToLNode = {};
+  var layout = this.layout = new CoSELayout();
+  var self = this;
+  
+  self.stopped = false;
+
+  this.cy = this.options.cy;
+
+  this.cy.trigger({ type: 'layoutstart', layout: this });
+
+  var gm = layout.newGraphManager();
+  this.gm = gm;
+
+  var nodes = this.options.eles.nodes();
+  var edges = this.options.eles.edges();
+
+  this.root = gm.addRoot();
+  this.processChildrenList(this.root, this.getTopMostNodes(nodes), layout);
+
+
+  for (var i = 0; i < edges.length; i++) {
+    var edge = edges[i];
+    var sourceNode = this.idToLNode[edge.data("source")];
+    var targetNode = this.idToLNode[edge.data("target")];
+    if(sourceNode !== targetNode && sourceNode.getEdgesBetween(targetNode).length == 0){
+      var e1 = gm.add(layout.newEdge(), sourceNode, targetNode);
+      e1.id = edge.id();
+    }
+  }
+  
+   var getPositions = function(ele, i){
+    if(typeof ele === "number") {
+      ele = i;
+    }
+    var theId = ele.data('id');
+    var lNode = self.idToLNode[theId];
+
+    return {
+      x: lNode.getRect().getCenterX(),
+      y: lNode.getRect().getCenterY()
+    };
+  };
+  
+  /*
+   * Reposition nodes in iterations animatedly
+   */
+  var iterateAnimated = function () {
+    // Thigs to perform after nodes are repositioned on screen
+    var afterReposition = function() {
+      if (options.fit) {
+        options.cy.fit(options.eles, options.padding);
+      }
+
+      if (!ready) {
+        ready = true;
+        self.cy.one('layoutready', options.ready);
+        self.cy.trigger({type: 'layoutready', layout: self});
+      }
+    };
+    
+    var ticksPerFrame = self.options.refresh;
+    var isDone;
+
+    for( var i = 0; i < ticksPerFrame && !isDone; i++ ){
+      isDone = self.stopped || self.layout.tick();
+    }
+    
+    // If layout is done
+    if (isDone) {
+      // If the layout is not a sublayout and it is successful perform post layout.
+      if (layout.checkLayoutSuccess() && !layout.isSubLayout) {
+        layout.doPostLayout();
+      }
+      
+      // If layout has a tilingPostLayout function property call it.
+      if (layout.tilingPostLayout) {
+        layout.tilingPostLayout();
+      }
+      
+      layout.isLayoutFinished = true;
+      
+      self.options.eles.nodes().positions(getPositions);
+      
+      afterReposition();
+      
+      // trigger layoutstop when the layout stops (e.g. finishes)
+      self.cy.one('layoutstop', self.options.stop);
+      self.cy.trigger({ type: 'layoutstop', layout: self });
+
+      if (frameId) {
+        cancelAnimationFrame(frameId);
+      }
+      
+      ready = false;
+      return;
+    }
+    
+    var animationData = self.layout.getPositionsData(); // Get positions of layout nodes note that all nodes may not be layout nodes because of tiling
+    
+    // Position nodes, for the nodes whose id does not included in data (because they are removed from their parents and included in dummy compounds)
+    // use position of their ancestors or dummy ancestors
+    options.eles.nodes().positions(function (ele, i) {
+      if (typeof ele === "number") {
+        ele = i;
+      }
+      // If ele is a compound node, then its position will be defined by its children
+      if(!ele.isParent()){
+        var theId = ele.id();
+        var pNode = animationData[theId];
+        var temp = ele;
+        // If pNode is undefined search until finding position data of its first ancestor (It may be dummy as well)
+        while (pNode == null) {
+          pNode = animationData[temp.data('parent')] || animationData['DummyCompound_' + temp.data('parent')];
+          animationData[theId] = pNode;
+          temp = temp.parent()[0];
+          if(temp == undefined){
+            break;
+          }
+        }
+        if(pNode != null){
+          return {
+            x: pNode.x,
+            y: pNode.y
+          };
+        } else{
+          return {
+            x: ele.position('x'),
+            y: ele.position('y')
+          };
+        }
+      }
+    });
+
+    afterReposition();
+
+    frameId = requestAnimationFrame(iterateAnimated);
+  };
+  
+  /*
+  * Listen 'layoutstarted' event and start animated iteration if animate option is 'during'
+  */
+  layout.addListener('layoutstarted', function () {
+    if (self.options.animate === 'during') {
+      frameId = requestAnimationFrame(iterateAnimated);
+    }
+  });
+  
+  layout.runLayout(); // Run cose layout
+  
+  /*
+   * If animate option is not 'during' ('end' or false) perform these here (If it is 'during' similar things are already performed)
+   */
+  if(this.options.animate !== "during"){
+    self.options.eles.nodes().not(":parent").layoutPositions(self, self.options, getPositions); // Use layout positions to reposition the nodes it considers the options parameter
+    ready = false;
+  }
+
+  return this; // chaining
+};
+
+//Get the top most ones of a list of nodes
+_CoSELayout.prototype.getTopMostNodes = function(nodes) {
+  var nodesMap = {};
+  for (var i = 0; i < nodes.length; i++) {
+      nodesMap[nodes[i].id()] = true;
+  }
+  var roots = nodes.filter(function (ele, i) {
+      if(typeof ele === "number") {
+        ele = i;
+      }
+      var parent = ele.parent()[0];
+      while(parent != null){
+        if(nodesMap[parent.id()]){
+          return false;
+        }
+        parent = parent.parent()[0];
+      }
+      return true;
+  });
+
+  return roots;
+};
+
+_CoSELayout.prototype.processChildrenList = function (parent, children, layout) {
+  var size = children.length;
+  for (var i = 0; i < size; i++) {
+    var theChild = children[i];
+    var children_of_children = theChild.children();
+    var theNode;    
+
+    var dimensions = theChild.layoutDimensions({
+      nodeDimensionsIncludeLabels: this.options.nodeDimensionsIncludeLabels
+    });
+
+    if (theChild.outerWidth() != null
+            && theChild.outerHeight() != null) {
+      theNode = parent.add(new CoSENode(layout.graphManager,
+              new PointD(theChild.position('x') - dimensions.w / 2, theChild.position('y') - dimensions.h / 2),
+              new DimensionD(parseFloat(dimensions.w), parseFloat(dimensions.h))));
+    }
+    else {
+      theNode = parent.add(new CoSENode(this.graphManager));
+    }
+    // Attach id to the layout node
+    theNode.id = theChild.data("id");
+    // Attach the paddings of cy node to layout node
+    theNode.paddingLeft = parseInt( theChild.css('padding') );
+    theNode.paddingTop = parseInt( theChild.css('padding') );
+    theNode.paddingRight = parseInt( theChild.css('padding') );
+    theNode.paddingBottom = parseInt( theChild.css('padding') );
+    
+    //Attach the label properties to compound if labels will be included in node dimensions  
+    if(this.options.nodeDimensionsIncludeLabels){
+      if(theChild.isParent()){
+          var labelWidth = theChild.boundingBox({ includeLabels: true, includeNodes: false }).w;          
+          var labelHeight = theChild.boundingBox({ includeLabels: true, includeNodes: false }).h;
+          var labelPos = theChild.css("text-halign");
+          theNode.labelWidth = labelWidth;
+          theNode.labelHeight = labelHeight;
+          theNode.labelPos = labelPos;
+      }
+    }
+    
+    // Map the layout node
+    this.idToLNode[theChild.data("id")] = theNode;
+
+    if (isNaN(theNode.rect.x)) {
+      theNode.rect.x = 0;
+    }
+
+    if (isNaN(theNode.rect.y)) {
+      theNode.rect.y = 0;
+    }
+
+    if (children_of_children != null && children_of_children.length > 0) {
+      var theNewGraph;
+      theNewGraph = layout.getGraphManager().add(layout.newGraph(), theNode);
+      this.processChildrenList(theNewGraph, children_of_children, layout);
+    }
+  }
+};
+
+/**
+ * @brief : called on continuous layouts to stop them before they finish
+ */
+_CoSELayout.prototype.stop = function () {
+  this.stopped = true;
+
+  return this; // chaining
+};
+
+var register = function( cytoscape ){
+//  var Layout = getLayout( cytoscape );
+
+  cytoscape('layout', 'cose-bilkent', _CoSELayout);
+};
+
+// auto reg for globals
+if( typeof cytoscape !== 'undefined' ){
+  register( cytoscape );
+}
+
+module.exports = register;

tools/ui/node_modules/cytoscape-cose-bilkent/test/example.js

@@ -0,0 +1,7 @@
+const chai = require('chai');
+
+describe('This', function(){
+  it('does that', function(){
+    expect( true ).to.be.true;
+  });
+});

tools/ui/node_modules/cytoscape-cose-bilkent/webpack.config.js

@@ -0,0 +1,43 @@
+const path = require('path');
+const pkg = require('./package.json');
+const camelcase = require('camelcase');
+const process = require('process');
+const webpack = require('webpack');
+const env = process.env;
+const NODE_ENV = env.NODE_ENV;
+const MIN = env.MIN;
+const PROD = NODE_ENV === 'production';
+
+let config = {
+  devtool: PROD ? false : 'inline-source-map',
+  entry: './src/index.js',
+  output: {
+    path: path.join( __dirname ),
+    filename: pkg.name + '.js',
+    library: camelcase( pkg.name ),
+    libraryTarget: 'umd'
+  },
+  module: {
+    rules: [
+      { test: /\.js$/, exclude: /node_modules/, use: 'babel-loader' }
+    ]
+  },
+  externals: PROD ? {
+    'cose-base': {
+      commonjs2: 'cose-base',
+      commonjs: 'cose-base',
+      amd: 'cose-base',
+      root: 'coseBase'
+    }
+  } : {},
+  plugins: MIN ? [
+    new webpack.optimize.UglifyJsPlugin({
+      compress: {
+        warnings: false,
+        drop_console: false,
+      }
+    })
+  ] : []
+};
+
+module.exports = config;

tools/ui/node_modules/cytoscape-fcose/.babelrc

@@ -0,0 +1,3 @@
+{
+  "presets": ["env"]
+}

tools/ui/node_modules/cytoscape-fcose/.eslintignore

@@ -0,0 +1 @@
+node_modules/**/*

tools/ui/node_modules/cytoscape-fcose/.eslintrc

@@ -0,0 +1,13 @@
+{
+    "env": {
+        "browser": true,
+        "commonjs": true,
+        "node": true,
+        "amd": true,
+        "es6": true
+    },
+    "extends": "eslint:recommended",
+    "rules": {
+      "semi": "error"
+    }
+}

tools/ui/node_modules/cytoscape-fcose/CITATION.cff

@@ -0,0 +1,31 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+authors:
+- family-names: "Balci"
+  given-names: "Hasan"
+  orcid: "https://orcid.org/0000-0001-8319-7758"
+- family-names: "Dogrusoz"
+  given-names: "Ugur"
+  orcid: "https://orcid.org/0000-0002-7153-0784"
+title: "cytoscape.js-fcose"
+version: 2.1.0
+date-released: 2021-06-25
+url: "https://github.com/iVis-at-Bilkent/cytoscape.js-fcose"
+preferred-citation:
+  type: article
+  authors:
+  - family-names: "Balci"
+    given-names: "Hasan"
+    orcid: "https://orcid.org/0000-0001-8319-7758"
+  - family-names: "Dogrusoz"
+    given-names: "Ugur"
+    orcid: "https://orcid.org/0000-0002-7153-0784"
+  doi: "10.1109/TVCG.2021.3095303"
+  journal: "IEEE Transactions on Visualization and Computer Graphics"
+  title: "fCoSE: A Fast Compound Graph Layout Algorithm with Constraint Support"
+  issue: 12
+  volume: 28  
+  start: 4582 # First page number
+  end: 4593 # Last page number
+  month: 12
+  year: 2022

tools/ui/node_modules/cytoscape-fcose/LICENSE

@@ -0,0 +1,19 @@
+Copyright (c) 2018 - present, iVis-at-Bilkent.
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of
+this software and associated documentation files (the “Software”), to deal in
+the Software without restriction, including without limitation the rights to
+use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies
+of the Software, and to permit persons to whom the Software is furnished to do
+so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

tools/ui/node_modules/cytoscape-fcose/README.md

@@ -0,0 +1,236 @@
+cytoscape-fcose
+================================================================================
+
+
+## Description
+
+
+fCoSE (pron. "f-cosay", **f**ast **Co**mpound **S**pring **E**mbedder), 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.
+
+Here are some demos: **simple**, **compound**, and **constraints**, respectively:
+<p align="center">
+<a href="https://ivis-at-bilkent.github.io/cytoscape.js-fcose/demo/demo.html" title="Simple"><img src="https://www.cs.bilkent.edu.tr/~ivis/images/demo1.png" height=42px></a> &emsp;
+<a href="https://ivis-at-bilkent.github.io/cytoscape.js-fcose/demo/demo-compound.html" title="Compound"><img src="https://www.cs.bilkent.edu.tr/~ivis/images/demo2.png" height=42px></a> &emsp;
+<a href="https://ivis-at-bilkent.github.io/cytoscape.js-fcose/demo/demo-constraint.html" title="Constraints"><img src="https://www.cs.bilkent.edu.tr/~ivis/images/demo3.png" height=42px></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/vRZVlwntzGY), [alignment](https://youtu.be/O5rddJ7DteU), [relative placement](https://youtu.be/Xcm87bT50RA), [hybrid](https://youtu.be/KRAQHmnTvUA), [real life graphs](https://youtu.be/vTPy9G2ALcI). Constraints can also be added [incrementally](https://youtu.be/DTm2WmzwP4k) on a given layout. 
+
+Please cite the following when you use this layout:
+
+H. Balci and U. Dogrusoz, "[fCoSE: A Fast Compound Graph Layout Algorithm with Constraint Support](https://doi.org/10.1109/TVCG.2021.3095303)," in IEEE Transactions on Visualization and Computer Graphics, 28(12), pp. 4582-4593, 2022.
+
+U. Dogrusoz, E. Giral, A. Cetintas, A. Civril and E. Demir, "[A Layout Algorithm For Undirected Compound Graphs](http://www.sciencedirect.com/science/article/pii/S0020025508004799)", Information Sciences, 179, pp. 980-994, 2009.
+
+## Dependencies
+
+ * Cytoscape.js ^3.2.0
+ * 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']]},
+  ```
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;***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}],
+  ```
+  The `gap` property is optional. If it is omitted, average `idealEdgeLength` is used as the gap value.
+
+## Usage instructions
+
+Download the library:
+ * via npm: `npm install cytoscape-fcose`,
+ * via bower: `bower install cytoscape-fcose`, or
+ * via direct download in the repository (probably from a tag).
+
+Import the library as appropriate for your project:
+
+ES import:
+
+```js
+import cytoscape from 'cytoscape';
+import fcose from 'cytoscape-fcose';
+
+cytoscape.use( fcose );
+```
+
+CommonJS require:
+
+```js
+let cytoscape = require('cytoscape');
+let fcose = require('cytoscape-fcose');
+
+cytoscape.use( fcose ); // register extension
+```
+
+AMD:
+
+```js
+require(['cytoscape', 'cytoscape-fcose'], function( cytoscape, fcose ){
+  fcose( cytoscape ); // register extension
+});
+```
+
+Plain HTML/JS has the extension registered for you automatically, because no `require()` is needed. Just add the following files:
+
+```
+<script src="https://unpkg.com/layout-base/layout-base.js"></script>
+<script src="https://unpkg.com/cose-base/cose-base.js"></script>
+<script src="https://unpkg.com/cytoscape-fcose/cytoscape-fcose.js"></script>
+```
+
+
+## API
+
+When calling the layout, e.g. `cy.layout({ name: 'fcose', ... })`, the following options are supported:
+
+```js
+var defaultOptions = {
+
+  // 'draft', 'default' or 'proof' 
+  // - "draft" only applies spectral layout 
+  // - "default" improves the quality with incremental layout (fast cooling rate)
+  // - "proof" improves the quality with incremental layout (slow cooling rate) 
+  quality: "default",
+  // Use random node positions at beginning of layout
+  // if this is set to false, then quality option must be "proof"
+  randomize: true, 
+  // Whether or not to animate the layout
+  animate: true, 
+  // Duration of animation in ms, if enabled
+  animationDuration: 1000, 
+  // Easing of animation, if enabled
+  animationEasing: undefined, 
+  // Fit the viewport to the repositioned nodes
+  fit: true, 
+  // Padding around layout
+  padding: 30,
+  // Whether to include labels in node dimensions. Valid in "proof" quality
+  nodeDimensionsIncludeLabels: false,
+  // Whether or not simple nodes (non-compound nodes) are of uniform dimensions
+  uniformNodeDimensions: false,
+  // Whether to pack disconnected components - cytoscape-layout-utilities extension should be registered and initialized
+  packComponents: true,
+  // Layout step - all, transformed, enforced, cose - for debug purpose only
+  step: "all",
+  
+  /* spectral layout options */
+  
+  // False for random, true for greedy sampling
+  samplingType: true,
+  // Sample size to construct distance matrix
+  sampleSize: 25,
+  // Separation amount between nodes
+  nodeSeparation: 75,
+  // Power iteration tolerance
+  piTol: 0.0000001,
+  
+  /* incremental layout options */
+  
+  // Node repulsion (non overlapping) multiplier
+  nodeRepulsion: node => 4500,
+  // Ideal edge (non nested) length
+  idealEdgeLength: edge => 50,
+  // Divisor to compute edge forces
+  edgeElasticity: edge => 0.45,
+  // Nesting factor (multiplier) to compute ideal edge length for nested edges
+  nestingFactor: 0.1,
+  // Maximum number of iterations to perform - this is a suggested value and might be adjusted by the algorithm as required
+  numIter: 2500,
+  // For enabling tiling
+  tile: true,
+  // The comparison function to be used while sorting nodes during tiling operation.
+  // Takes the ids of 2 nodes that will be compared as a parameter and the default tiling operation is performed when this option is not set.
+  // It works similar to ``compareFunction`` parameter of ``Array.prototype.sort()``
+  // If node1 is less then node2 by some ordering criterion ``tilingCompareBy(nodeId1, nodeId2)`` must return a negative value
+  // If node1 is greater then node2 by some ordering criterion ``tilingCompareBy(nodeId1, nodeId2)`` must return a positive value
+  // If node1 is equal to node2 by some ordering criterion ``tilingCompareBy(nodeId1, nodeId2)`` must return 0
+  tilingCompareBy: undefined, 
+  // Represents the amount of the vertical space to put between the zero degree members during the tiling operation(can also be a function)
+  tilingPaddingVertical: 10,
+  // Represents the amount of the horizontal space to put between the zero degree members during the tiling operation(can also be a function)
+  tilingPaddingHorizontal: 10,
+  // Gravity force (constant)
+  gravity: 0.25,
+  // Gravity range (constant) for compounds
+  gravityRangeCompound: 1.5,
+  // Gravity force (constant) for compounds
+  gravityCompound: 1.0,
+  // Gravity range (constant)
+  gravityRange: 3.8, 
+  // Initial cooling factor for incremental layout  
+  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 */
+  ready: () => {}, // on layoutready
+  stop: () => {} // on layoutstop
+};
+```
+To be able to use `packComponents` option, `cytoscape-layout-utilities` extension should also be registered in the application.
+Packing related [options](https://github.com/iVis-at-Bilkent/cytoscape.js-layout-utilities#default-options) should be set via `cytoscape-layout-utilities` extension.
+If they are not set, fCoSE uses default options.
+
+
+## Build targets
+
+* `npm run test` : Run Mocha tests in `./test`
+* `npm run build` : Build `./src/**` into `cytoscape-fcose.js`
+* `npm run watch` : Automatically build on changes with live reloading (N.b. you must already have an HTTP server running)
+* `npm run dev` : Automatically build on changes with live reloading with webpack dev server
+* `npm run lint` : Run eslint on the source
+
+N.b. all builds use babel, so modern ES features can be used in the `src`.
+
+
+## Publishing instructions
+
+This project is set up to automatically be published to npm and bower.  To publish:
+
+1. Build the extension : `npm run build:release`
+1. Commit the build : `git commit -am "Build for release"`
+1. Bump the version number and tag: `npm version major|minor|patch`
+1. Push to origin: `git push && git push --tags`
+1. Publish to npm: `npm publish .`
+1. If publishing to bower for the first time, you'll need to run `bower register cytoscape-fcose https://github.com/iVis-at-Bilkent/cytoscape.js-fcose.git`
+1. [Make a new release](https://github.com/iVis-at-Bilkent/cytoscape.js-fcose/releases/new) for Zenodo.
+
+## Team
+
+  * [Hasan Balcı](https://github.com/hasanbalci) and [Ugur Dogrusoz](https://github.com/ugurdogrusoz) of [i-Vis at Bilkent University](http://www.cs.bilkent.edu.tr/~ivis)

tools/ui/node_modules/cytoscape-fcose/bower.json

@@ -0,0 +1,25 @@
+{
+  "name": "cytoscape-fcose",
+  "description": "The fCoSE layout for Cytoscape.js by Bilkent with fast compound node placement",
+  "main": "cytoscape-fcose.js",
+  "dependencies": {
+    "cytoscape": "^3.2.0",
+    "cose-base": "^1.0.0"
+  },
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/iVis-at-Bilkent/cytoscape.js-fcose.git"
+  },
+  "ignore": [
+    "**/.*",
+    "node_modules",
+    "bower_components",
+    "test",
+    "tests"
+  ],
+  "keywords": [
+    "cytoscape",
+    "cytoscape-extension"
+  ],
+  "license": "MIT"
+}

tools/ui/node_modules/cytoscape-fcose/cytoscape-fcose.js

@@ -0,0 +1,1549 @@
+(function webpackUniversalModuleDefinition(root, factory) {
+	if(typeof exports === 'object' && typeof module === 'object')
+		module.exports = factory(require("cose-base"));
+	else if(typeof define === 'function' && define.amd)
+		define(["cose-base"], factory);
+	else if(typeof exports === 'object')
+		exports["cytoscapeFcose"] = factory(require("cose-base"));
+	else
+		root["cytoscapeFcose"] = factory(root["coseBase"]);
+})(this, function(__WEBPACK_EXTERNAL_MODULE__140__) {
+return /******/ (() => { // webpackBootstrap
+/******/ 	"use strict";
+/******/ 	var __webpack_modules__ = ({
+
+/***/ 658:
+/***/ ((module) => {
+
+
+
+// Simple, internal Object.assign() polyfill for options objects etc.
+
+module.exports = Object.assign != null ? Object.assign.bind(Object) : function (tgt) {
+  for (var _len = arguments.length, srcs = Array(_len > 1 ? _len - 1 : 0), _key = 1; _key < _len; _key++) {
+    srcs[_key - 1] = arguments[_key];
+  }
+
+  srcs.forEach(function (src) {
+    Object.keys(src).forEach(function (k) {
+      return tgt[k] = src[k];
+    });
+  });
+
+  return tgt;
+};
+
+/***/ }),
+
+/***/ 548:
+/***/ ((module, __unused_webpack_exports, __webpack_require__) => {
+
+
+
+var _slicedToArray = function () { function sliceIterator(arr, i) { var _arr = []; var _n = true; var _d = false; var _e = undefined; try { for (var _i = arr[Symbol.iterator](), _s; !(_n = (_s = _i.next()).done); _n = true) { _arr.push(_s.value); if (i && _arr.length === i) break; } } catch (err) { _d = true; _e = err; } finally { try { if (!_n && _i["return"]) _i["return"](); } finally { if (_d) throw _e; } } return _arr; } return function (arr, i) { if (Array.isArray(arr)) { return arr; } else if (Symbol.iterator in Object(arr)) { return sliceIterator(arr, i); } else { throw new TypeError("Invalid attempt to destructure non-iterable instance"); } }; }();
+
+/*
+ * Auxiliary functions
+ */
+
+var LinkedList = __webpack_require__(140).layoutBase.LinkedList;
+
+var auxiliary = {};
+
+// get the top most nodes
+auxiliary.getTopMostNodes = function (nodes) {
+  var nodesMap = {};
+  for (var i = 0; i < nodes.length; i++) {
+    nodesMap[nodes[i].id()] = true;
+  }
+  var roots = nodes.filter(function (ele, i) {
+    if (typeof ele === "number") {
+      ele = i;
+    }
+    var parent = ele.parent()[0];
+    while (parent != null) {
+      if (nodesMap[parent.id()]) {
+        return false;
+      }
+      parent = parent.parent()[0];
+    }
+    return true;
+  });
+
+  return roots;
+};
+
+// find disconnected components and create dummy nodes that connect them
+auxiliary.connectComponents = function (cy, eles, topMostNodes, dummyNodes) {
+  var queue = new LinkedList();
+  var visited = new Set();
+  var visitedTopMostNodes = [];
+  var currentNeighbor = void 0;
+  var minDegreeNode = void 0;
+  var minDegree = void 0;
+
+  var isConnected = false;
+  var count = 1;
+  var nodesConnectedToDummy = [];
+  var components = [];
+
+  var _loop = function _loop() {
+    var cmpt = cy.collection();
+    components.push(cmpt);
+
+    var currentNode = topMostNodes[0];
+    var childrenOfCurrentNode = cy.collection();
+    childrenOfCurrentNode.merge(currentNode).merge(currentNode.descendants().intersection(eles));
+    visitedTopMostNodes.push(currentNode);
+
+    childrenOfCurrentNode.forEach(function (node) {
+      queue.push(node);
+      visited.add(node);
+      cmpt.merge(node);
+    });
+
+    var _loop2 = function _loop2() {
+      currentNode = queue.shift();
+
+      // Traverse all neighbors of this node
+      var neighborNodes = cy.collection();
+      currentNode.neighborhood().nodes().forEach(function (node) {
+        if (eles.intersection(currentNode.edgesWith(node)).length > 0) {
+          neighborNodes.merge(node);
+        }
+      });
+
+      for (var i = 0; i < neighborNodes.length; i++) {
+        var neighborNode = neighborNodes[i];
+        currentNeighbor = topMostNodes.intersection(neighborNode.union(neighborNode.ancestors()));
+        if (currentNeighbor != null && !visited.has(currentNeighbor[0])) {
+          var childrenOfNeighbor = currentNeighbor.union(currentNeighbor.descendants());
+
+          childrenOfNeighbor.forEach(function (node) {
+            queue.push(node);
+            visited.add(node);
+            cmpt.merge(node);
+            if (topMostNodes.has(node)) {
+              visitedTopMostNodes.push(node);
+            }
+          });
+        }
+      }
+    };
+
+    while (queue.length != 0) {
+      _loop2();
+    }
+
+    cmpt.forEach(function (node) {
+      eles.intersection(node.connectedEdges()).forEach(function (e) {
+        // connectedEdges() usually cached
+        if (cmpt.has(e.source()) && cmpt.has(e.target())) {
+          // has() is cheap
+          cmpt.merge(e);
+        }
+      });
+    });
+
+    if (visitedTopMostNodes.length == topMostNodes.length) {
+      isConnected = true;
+    }
+
+    if (!isConnected || isConnected && count > 1) {
+      minDegreeNode = visitedTopMostNodes[0];
+      minDegree = minDegreeNode.connectedEdges().length;
+      visitedTopMostNodes.forEach(function (node) {
+        if (node.connectedEdges().length < minDegree) {
+          minDegree = node.connectedEdges().length;
+          minDegreeNode = node;
+        }
+      });
+      nodesConnectedToDummy.push(minDegreeNode.id());
+      // TO DO: Check efficiency of this part
+      var temp = cy.collection();
+      temp.merge(visitedTopMostNodes[0]);
+      visitedTopMostNodes.forEach(function (node) {
+        temp.merge(node);
+      });
+      visitedTopMostNodes = [];
+      topMostNodes = topMostNodes.difference(temp);
+      count++;
+    }
+  };
+
+  do {
+    _loop();
+  } while (!isConnected);
+
+  if (dummyNodes) {
+    if (nodesConnectedToDummy.length > 0) {
+      dummyNodes.set('dummy' + (dummyNodes.size + 1), nodesConnectedToDummy);
+    }
+  }
+  return components;
+};
+
+// relocates componentResult to originalCenter if there is no fixedNodeConstraint
+auxiliary.relocateComponent = function (originalCenter, componentResult, options) {
+  if (!options.fixedNodeConstraint) {
+    var minXCoord = Number.POSITIVE_INFINITY;
+    var maxXCoord = Number.NEGATIVE_INFINITY;
+    var minYCoord = Number.POSITIVE_INFINITY;
+    var maxYCoord = Number.NEGATIVE_INFINITY;
+    if (options.quality == "draft") {
+      // calculate current bounding box
+      var _iteratorNormalCompletion = true;
+      var _didIteratorError = false;
+      var _iteratorError = undefined;
+
+      try {
+        for (var _iterator = componentResult.nodeIndexes[Symbol.iterator](), _step; !(_iteratorNormalCompletion = (_step = _iterator.next()).done); _iteratorNormalCompletion = true) {
+          var _ref = _step.value;
+
+          var _ref2 = _slicedToArray(_ref, 2);
+
+          var key = _ref2[0];
+          var value = _ref2[1];
+
+          var cyNode = options.cy.getElementById(key);
+          if (cyNode) {
+            var nodeBB = cyNode.boundingBox();
+            var leftX = componentResult.xCoords[value] - nodeBB.w / 2;
+            var rightX = componentResult.xCoords[value] + nodeBB.w / 2;
+            var topY = componentResult.yCoords[value] - nodeBB.h / 2;
+            var bottomY = componentResult.yCoords[value] + nodeBB.h / 2;
+
+            if (leftX < minXCoord) minXCoord = leftX;
+            if (rightX > maxXCoord) maxXCoord = rightX;
+            if (topY < minYCoord) minYCoord = topY;
+            if (bottomY > maxYCoord) maxYCoord = bottomY;
+          }
+        }
+        // find difference between current and original center
+      } catch (err) {
+        _didIteratorError = true;
+        _iteratorError = err;
+      } finally {
+        try {
+          if (!_iteratorNormalCompletion && _iterator.return) {
+            _iterator.return();
+          }
+        } finally {
+          if (_didIteratorError) {
+            throw _iteratorError;
+          }
+        }
+      }
+
+      var diffOnX = originalCenter.x - (maxXCoord + minXCoord) / 2;
+      var diffOnY = originalCenter.y - (maxYCoord + minYCoord) / 2;
+      // move component to original center
+      componentResult.xCoords = componentResult.xCoords.map(function (x) {
+        return x + diffOnX;
+      });
+      componentResult.yCoords = componentResult.yCoords.map(function (y) {
+        return y + diffOnY;
+      });
+    } else {
+      // calculate current bounding box
+      Object.keys(componentResult).forEach(function (item) {
+        var node = componentResult[item];
+        var leftX = node.getRect().x;
+        var rightX = node.getRect().x + node.getRect().width;
+        var topY = node.getRect().y;
+        var bottomY = node.getRect().y + node.getRect().height;
+
+        if (leftX < minXCoord) minXCoord = leftX;
+        if (rightX > maxXCoord) maxXCoord = rightX;
+        if (topY < minYCoord) minYCoord = topY;
+        if (bottomY > maxYCoord) maxYCoord = bottomY;
+      });
+      // find difference between current and original center
+      var _diffOnX = originalCenter.x - (maxXCoord + minXCoord) / 2;
+      var _diffOnY = originalCenter.y - (maxYCoord + minYCoord) / 2;
+      // move component to original center
+      Object.keys(componentResult).forEach(function (item) {
+        var node = componentResult[item];
+        node.setCenter(node.getCenterX() + _diffOnX, node.getCenterY() + _diffOnY);
+      });
+    }
+  }
+};
+
+auxiliary.calcBoundingBox = function (parentNode, xCoords, yCoords, nodeIndexes) {
+  // calculate bounds
+  var left = Number.MAX_SAFE_INTEGER;
+  var right = Number.MIN_SAFE_INTEGER;
+  var top = Number.MAX_SAFE_INTEGER;
+  var bottom = Number.MIN_SAFE_INTEGER;
+  var nodeLeft = void 0;
+  var nodeRight = void 0;
+  var nodeTop = void 0;
+  var nodeBottom = void 0;
+
+  var nodes = parentNode.descendants().not(":parent");
+  var s = nodes.length;
+  for (var i = 0; i < s; i++) {
+    var node = nodes[i];
+
+    nodeLeft = xCoords[nodeIndexes.get(node.id())] - node.width() / 2;
+    nodeRight = xCoords[nodeIndexes.get(node.id())] + node.width() / 2;
+    nodeTop = yCoords[nodeIndexes.get(node.id())] - node.height() / 2;
+    nodeBottom = yCoords[nodeIndexes.get(node.id())] + node.height() / 2;
+
+    if (left > nodeLeft) {
+      left = nodeLeft;
+    }
+
+    if (right < nodeRight) {
+      right = nodeRight;
+    }
+
+    if (top > nodeTop) {
+      top = nodeTop;
+    }
+
+    if (bottom < nodeBottom) {
+      bottom = nodeBottom;
+    }
+  }
+
+  var boundingBox = {};
+  boundingBox.topLeftX = left;
+  boundingBox.topLeftY = top;
+  boundingBox.width = right - left;
+  boundingBox.height = bottom - top;
+  return boundingBox;
+};
+
+// This function finds and returns parent nodes whose all children are hidden
+auxiliary.calcParentsWithoutChildren = function (cy, eles) {
+  var parentsWithoutChildren = cy.collection();
+  eles.nodes(':parent').forEach(function (parent) {
+    var check = false;
+    parent.children().forEach(function (child) {
+      if (child.css('display') != 'none') {
+        check = true;
+      }
+    });
+    if (!check) {
+      parentsWithoutChildren.merge(parent);
+    }
+  });
+
+  return parentsWithoutChildren;
+};
+
+module.exports = auxiliary;
+
+/***/ }),
+
+/***/ 816:
+/***/ ((module, __unused_webpack_exports, __webpack_require__) => {
+
+
+
+/**
+  The implementation of the postprocessing part that applies CoSE layout over the spectral layout
+*/
+
+var aux = __webpack_require__(548);
+var CoSELayout = __webpack_require__(140).CoSELayout;
+var CoSENode = __webpack_require__(140).CoSENode;
+var PointD = __webpack_require__(140).layoutBase.PointD;
+var DimensionD = __webpack_require__(140).layoutBase.DimensionD;
+var LayoutConstants = __webpack_require__(140).layoutBase.LayoutConstants;
+var FDLayoutConstants = __webpack_require__(140).layoutBase.FDLayoutConstants;
+var CoSEConstants = __webpack_require__(140).CoSEConstants;
+
+// main function that cose layout is processed
+var coseLayout = function coseLayout(options, spectralResult) {
+
+  var cy = options.cy;
+  var eles = options.eles;
+  var nodes = eles.nodes();
+  var edges = eles.edges();
+
+  var nodeIndexes = void 0;
+  var xCoords = void 0;
+  var yCoords = void 0;
+  var idToLNode = {};
+
+  if (options.randomize) {
+    nodeIndexes = spectralResult["nodeIndexes"];
+    xCoords = spectralResult["xCoords"];
+    yCoords = spectralResult["yCoords"];
+  }
+
+  var isFn = function isFn(fn) {
+    return typeof fn === 'function';
+  };
+
+  var optFn = function optFn(opt, ele) {
+    if (isFn(opt)) {
+      return opt(ele);
+    } else {
+      return opt;
+    }
+  };
+
+  /**** Postprocessing functions ****/
+
+  var parentsWithoutChildren = aux.calcParentsWithoutChildren(cy, eles);
+
+  // transfer cytoscape nodes to cose nodes
+  var processChildrenList = function processChildrenList(parent, children, layout, options) {
+    var size = children.length;
+    for (var i = 0; i < size; i++) {
+      var theChild = children[i];
+      var children_of_children = null;
+      if (theChild.intersection(parentsWithoutChildren).length == 0) {
+        children_of_children = theChild.children();
+      }
+      var theNode = void 0;
+
+      var dimensions = theChild.layoutDimensions({
+        nodeDimensionsIncludeLabels: options.nodeDimensionsIncludeLabels
+      });
+
+      if (theChild.outerWidth() != null && theChild.outerHeight() != null) {
+        if (options.randomize) {
+          if (!theChild.isParent()) {
+            theNode = parent.add(new CoSENode(layout.graphManager, new PointD(xCoords[nodeIndexes.get(theChild.id())] - dimensions.w / 2, yCoords[nodeIndexes.get(theChild.id())] - dimensions.h / 2), new DimensionD(parseFloat(dimensions.w), parseFloat(dimensions.h))));
+          } else {
+            var parentInfo = aux.calcBoundingBox(theChild, xCoords, yCoords, nodeIndexes);
+            if (theChild.intersection(parentsWithoutChildren).length == 0) {
+              theNode = parent.add(new CoSENode(layout.graphManager, new PointD(parentInfo.topLeftX, parentInfo.topLeftY), new DimensionD(parentInfo.width, parentInfo.height)));
+            } else {
+              // for the parentsWithoutChildren
+              theNode = parent.add(new CoSENode(layout.graphManager, new PointD(parentInfo.topLeftX, parentInfo.topLeftY), new DimensionD(parseFloat(dimensions.w), parseFloat(dimensions.h))));
+            }
+          }
+        } else {
+          theNode = parent.add(new CoSENode(layout.graphManager, new PointD(theChild.position('x') - dimensions.w / 2, theChild.position('y') - dimensions.h / 2), new DimensionD(parseFloat(dimensions.w), parseFloat(dimensions.h))));
+        }
+      } else {
+        theNode = parent.add(new CoSENode(this.graphManager));
+      }
+      // 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
+      theNode.paddingLeft = parseInt(theChild.css('padding'));
+      theNode.paddingTop = parseInt(theChild.css('padding'));
+      theNode.paddingRight = parseInt(theChild.css('padding'));
+      theNode.paddingBottom = parseInt(theChild.css('padding'));
+
+      //Attach the label properties to both compound and simple nodes if labels will be included in node dimensions
+      //These properties will be used while updating bounds of compounds during iterations or tiling
+      //and will be used for simple nodes while transferring final positions to cytoscape
+      if (options.nodeDimensionsIncludeLabels) {
+        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");
+      }
+
+      // Map the layout node
+      idToLNode[theChild.data("id")] = theNode;
+
+      if (isNaN(theNode.rect.x)) {
+        theNode.rect.x = 0;
+      }
+
+      if (isNaN(theNode.rect.y)) {
+        theNode.rect.y = 0;
+      }
+
+      if (children_of_children != null && children_of_children.length > 0) {
+        var theNewGraph = void 0;
+        theNewGraph = layout.getGraphManager().add(layout.newGraph(), theNode);
+        processChildrenList(theNewGraph, children_of_children, layout, options);
+      }
+    }
+  };
+
+  // transfer cytoscape edges to cose edges
+  var processEdges = function processEdges(layout, gm, edges) {
+    var idealLengthTotal = 0;
+    var edgeCount = 0;
+    for (var i = 0; i < edges.length; i++) {
+      var edge = edges[i];
+      var sourceNode = idToLNode[edge.data("source")];
+      var targetNode = idToLNode[edge.data("target")];
+      if (sourceNode && targetNode && sourceNode !== targetNode && sourceNode.getEdgesBetween(targetNode).length == 0) {
+        var e1 = gm.add(layout.newEdge(), sourceNode, targetNode);
+        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 (edgeCount > 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
+  var processConstraints = function processConstraints(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.nestingFactor != null) CoSEConstants.PER_LEVEL_IDEAL_EDGE_LENGTH_FACTOR = FDLayoutConstants.PER_LEVEL_IDEAL_EDGE_LENGTH_FACTOR = options.nestingFactor;
+  if (options.gravity != null) CoSEConstants.DEFAULT_GRAVITY_STRENGTH = FDLayoutConstants.DEFAULT_GRAVITY_STRENGTH = options.gravity;
+  if (options.numIter != null) CoSEConstants.MAX_ITERATIONS = FDLayoutConstants.MAX_ITERATIONS = options.numIter;
+  if (options.gravityRange != null) CoSEConstants.DEFAULT_GRAVITY_RANGE_FACTOR = FDLayoutConstants.DEFAULT_GRAVITY_RANGE_FACTOR = options.gravityRange;
+  if (options.gravityCompound != null) CoSEConstants.DEFAULT_COMPOUND_GRAVITY_STRENGTH = FDLayoutConstants.DEFAULT_COMPOUND_GRAVITY_STRENGTH = options.gravityCompound;
+  if (options.gravityRangeCompound != null) CoSEConstants.DEFAULT_COMPOUND_GRAVITY_RANGE_FACTOR = FDLayoutConstants.DEFAULT_COMPOUND_GRAVITY_RANGE_FACTOR = options.gravityRangeCompound;
+  if (options.initialEnergyOnIncremental != null) CoSEConstants.DEFAULT_COOLING_FACTOR_INCREMENTAL = FDLayoutConstants.DEFAULT_COOLING_FACTOR_INCREMENTAL = options.initialEnergyOnIncremental;
+
+  if (options.tilingCompareBy != null) CoSEConstants.TILING_COMPARE_BY = options.tilingCompareBy;
+
+  if (options.quality == 'proof') LayoutConstants.QUALITY = 2;else LayoutConstants.QUALITY = 0;
+
+  CoSEConstants.NODE_DIMENSIONS_INCLUDE_LABELS = FDLayoutConstants.NODE_DIMENSIONS_INCLUDE_LABELS = LayoutConstants.NODE_DIMENSIONS_INCLUDE_LABELS = options.nodeDimensionsIncludeLabels;
+  CoSEConstants.DEFAULT_INCREMENTAL = FDLayoutConstants.DEFAULT_INCREMENTAL = LayoutConstants.DEFAULT_INCREMENTAL = !options.randomize;
+  CoSEConstants.ANIMATE = FDLayoutConstants.ANIMATE = LayoutConstants.ANIMATE = options.animate;
+  CoSEConstants.TILE = options.tile;
+  CoSEConstants.TILING_PADDING_VERTICAL = typeof options.tilingPaddingVertical === 'function' ? options.tilingPaddingVertical.call() : options.tilingPaddingVertical;
+  CoSEConstants.TILING_PADDING_HORIZONTAL = typeof options.tilingPaddingHorizontal === 'function' ? options.tilingPaddingHorizontal.call() : options.tilingPaddingHorizontal;
+
+  CoSEConstants.DEFAULT_INCREMENTAL = FDLayoutConstants.DEFAULT_INCREMENTAL = LayoutConstants.DEFAULT_INCREMENTAL = true;
+  CoSEConstants.PURE_INCREMENTAL = !options.randomize;
+  LayoutConstants.DEFAULT_UNIFORM_LEAF_NODE_SIZES = options.uniformNodeDimensions;
+
+  // 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.fixedNodeConstraint || options.alignmentConstraint || options.relativePlacementConstraint) {
+    CoSEConstants.TREE_REDUCTION_ON_INCREMENTAL = false;
+  } else {
+    CoSEConstants.TREE_REDUCTION_ON_INCREMENTAL = true;
+  }
+
+  var coseLayout = new CoSELayout();
+  var gm = coseLayout.newGraphManager();
+
+  processChildrenList(gm.addRoot(), aux.getTopMostNodes(nodes), coseLayout, options);
+  processEdges(coseLayout, gm, edges);
+  processConstraints(coseLayout, options);
+
+  coseLayout.runLayout();
+
+  return idToLNode;
+};
+
+module.exports = { coseLayout: coseLayout };
+
+/***/ }),
+
+/***/ 212:
+/***/ ((module, __unused_webpack_exports, __webpack_require__) => {
+
+
+
+var _createClass = function () { function defineProperties(target, props) { for (var i = 0; i < props.length; i++) { var descriptor = props[i]; descriptor.enumerable = descriptor.enumerable || false; descriptor.configurable = true; if ("value" in descriptor) descriptor.writable = true; Object.defineProperty(target, descriptor.key, descriptor); } } return function (Constructor, protoProps, staticProps) { if (protoProps) defineProperties(Constructor.prototype, protoProps); if (staticProps) defineProperties(Constructor, staticProps); return Constructor; }; }();
+
+function _classCallCheck(instance, Constructor) { if (!(instance instanceof Constructor)) { throw new TypeError("Cannot call a class as a function"); } }
+
+/**
+  The implementation of the fcose layout algorithm
+*/
+
+var assign = __webpack_require__(658);
+var aux = __webpack_require__(548);
+
+var _require = __webpack_require__(657),
+    spectralLayout = _require.spectralLayout;
+
+var _require2 = __webpack_require__(816),
+    coseLayout = _require2.coseLayout;
+
+var defaults = Object.freeze({
+
+  // 'draft', 'default' or 'proof' 
+  // - 'draft' only applies spectral layout 
+  // - 'default' improves the quality with subsequent CoSE layout (fast cooling rate)
+  // - 'proof' improves the quality with subsequent CoSE layout (slow cooling rate) 
+  quality: "default",
+  // Use random node positions at beginning of layout
+  // if this is set to false, then quality option must be "proof"
+  randomize: true,
+  // Whether or not to animate the layout
+  animate: true,
+  // Duration of animation in ms, if enabled
+  animationDuration: 1000,
+  // Easing of animation, if enabled
+  animationEasing: undefined,
+  // Fit the viewport to the repositioned nodes
+  fit: true,
+  // Padding around layout
+  padding: 30,
+  // Whether to include labels in node dimensions. Valid in "proof" quality
+  nodeDimensionsIncludeLabels: false,
+  // Whether or not simple nodes (non-compound nodes) are of uniform dimensions
+  uniformNodeDimensions: false,
+  // Whether to pack disconnected components - valid only if randomize: true
+  packComponents: true,
+  // Layout step - all, transformed, enforced, cose - for debug purpose only
+  step: "all",
+
+  /* spectral layout options */
+
+  // False for random, true for greedy
+  samplingType: true,
+  // Sample size to construct distance matrix
+  sampleSize: 25,
+  // Separation amount between nodes
+  nodeSeparation: 75,
+  // Power iteration tolerance
+  piTol: 0.0000001,
+
+  /* CoSE layout options */
+
+  // Node repulsion (non overlapping) multiplier
+  nodeRepulsion: function nodeRepulsion(node) {
+    return 4500;
+  },
+  // Ideal edge (non nested) length
+  idealEdgeLength: function idealEdgeLength(edge) {
+    return 50;
+  },
+  // Divisor to compute edge forces
+  edgeElasticity: function edgeElasticity(edge) {
+    return 0.45;
+  },
+  // Nesting factor (multiplier) to compute ideal edge length for nested edges
+  nestingFactor: 0.1,
+  // Gravity force (constant)
+  gravity: 0.25,
+  // Maximum number of iterations to perform
+  numIter: 2500,
+  // For enabling tiling
+  tile: true,
+  // The function that specifies the criteria for comparing nodes while sorting them during tiling operation.
+  // Takes the node id as a parameter and the default tiling operation is perfomed when this option is not set.
+  tilingCompareBy: undefined,
+  // Represents the amount of the vertical space to put between the zero degree members during the tiling operation(can also be a function)
+  tilingPaddingVertical: 10,
+  // Represents the amount of the horizontal space to put between the zero degree members during the tiling operation(can also be a function)
+  tilingPaddingHorizontal: 10,
+  // Gravity range (constant) for compounds
+  gravityRangeCompound: 1.5,
+  // Gravity force (constant) for compounds
+  gravityCompound: 1.0,
+  // Gravity range (constant)
+  gravityRange: 3.8,
+  // Initial cooling factor for incremental layout  
+  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 */
+  ready: function ready() {}, // on layoutready
+  stop: function stop() {} // on layoutstop
+});
+
+var Layout = function () {
+  function Layout(options) {
+    _classCallCheck(this, Layout);
+
+    this.options = assign({}, defaults, options);
+  }
+
+  _createClass(Layout, [{
+    key: 'run',
+    value: function run() {
+      var layout = this;
+      var options = this.options;
+      var cy = options.cy;
+      var eles = options.eles;
+
+      var spectralResult = [];
+      var xCoords = void 0;
+      var yCoords = void 0;
+      var coseResult = [];
+      var components = void 0;
+      var componentCenters = [];
+
+      // basic validity check for constraint inputs 
+      if (options.fixedNodeConstraint && (!Array.isArray(options.fixedNodeConstraint) || options.fixedNodeConstraint.length == 0)) {
+        options.fixedNodeConstraint = undefined;
+      }
+
+      if (options.alignmentConstraint) {
+        if (options.alignmentConstraint.vertical && (!Array.isArray(options.alignmentConstraint.vertical) || options.alignmentConstraint.vertical.length == 0)) {
+          options.alignmentConstraint.vertical = undefined;
+        }
+        if (options.alignmentConstraint.horizontal && (!Array.isArray(options.alignmentConstraint.horizontal) || options.alignmentConstraint.horizontal.length == 0)) {
+          options.alignmentConstraint.horizontal = undefined;
+        }
+      }
+
+      if (options.relativePlacementConstraint && (!Array.isArray(options.relativePlacementConstraint) || options.relativePlacementConstraint.length == 0)) {
+        options.relativePlacementConstraint = undefined;
+      }
+
+      // if any constraint exists, set some options
+      var constraintExist = options.fixedNodeConstraint || options.alignmentConstraint || options.relativePlacementConstraint;
+      if (constraintExist) {
+        // constraints work with these options
+        options.tile = false;
+        options.packComponents = false;
+      }
+
+      // decide component packing is enabled or not
+      var layUtil = void 0;
+      var packingEnabled = false;
+      if (cy.layoutUtilities && options.packComponents) {
+        layUtil = cy.layoutUtilities("get");
+        if (!layUtil) layUtil = cy.layoutUtilities();
+        packingEnabled = true;
+      }
+
+      if (eles.nodes().length > 0) {
+        // if packing is not enabled, perform layout on the whole graph
+        if (!packingEnabled) {
+          // store component center
+          var boundingBox = options.eles.boundingBox();
+          componentCenters.push({ x: boundingBox.x1 + boundingBox.w / 2, y: boundingBox.y1 + boundingBox.h / 2 });
+          // apply spectral layout
+          if (options.randomize) {
+            var result = spectralLayout(options);
+            spectralResult.push(result);
+          }
+          // apply cose layout as postprocessing
+          if (options.quality == "default" || options.quality == "proof") {
+            coseResult.push(coseLayout(options, spectralResult[0]));
+            aux.relocateComponent(componentCenters[0], coseResult[0], options); // relocate center to original position
+          } else {
+            aux.relocateComponent(componentCenters[0], spectralResult[0], options); // relocate center to original position
+          }
+        } else {
+          // packing is enabled
+          var topMostNodes = aux.getTopMostNodes(options.eles.nodes());
+          components = aux.connectComponents(cy, options.eles, topMostNodes);
+          // store component centers
+          components.forEach(function (component) {
+            var boundingBox = component.boundingBox();
+            componentCenters.push({ x: boundingBox.x1 + boundingBox.w / 2, y: boundingBox.y1 + boundingBox.h / 2 });
+          });
+
+          //send each component to spectral layout if randomized
+          if (options.randomize) {
+            components.forEach(function (component) {
+              options.eles = component;
+              spectralResult.push(spectralLayout(options));
+            });
+          }
+
+          if (options.quality == "default" || options.quality == "proof") {
+            var toBeTiledNodes = cy.collection();
+            if (options.tile) {
+              // behave nodes to be tiled as one component
+              var nodeIndexes = new Map();
+              var _xCoords = [];
+              var _yCoords = [];
+              var count = 0;
+              var tempSpectralResult = { nodeIndexes: nodeIndexes, xCoords: _xCoords, yCoords: _yCoords };
+              var indexesToBeDeleted = [];
+              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 (toBeTiledNodes.length > 1) {
+                var _boundingBox = toBeTiledNodes.boundingBox();
+                componentCenters.push({ x: _boundingBox.x1 + _boundingBox.w / 2, y: _boundingBox.y1 + _boundingBox.h / 2 });
+                components.push(toBeTiledNodes);
+                spectralResult.push(tempSpectralResult);
+                for (var i = indexesToBeDeleted.length - 1; i >= 0; i--) {
+                  components.splice(indexesToBeDeleted[i], 1);
+                  spectralResult.splice(indexesToBeDeleted[i], 1);
+                  componentCenters.splice(indexesToBeDeleted[i], 1);
+                };
+              }
+            }
+            components.forEach(function (component, index) {
+              // send each component to cose layout
+              options.eles = component;
+              coseResult.push(coseLayout(options, spectralResult[index]));
+              aux.relocateComponent(componentCenters[index], coseResult[index], options); // relocate center to original position
+            });
+          } else {
+            components.forEach(function (component, index) {
+              aux.relocateComponent(componentCenters[index], spectralResult[index], options); // relocate center to original position
+            });
+          }
+
+          // packing
+          var componentsEvaluated = new Set();
+          if (components.length > 1) {
+            var subgraphs = [];
+            var hiddenEles = eles.filter(function (ele) {
+              return ele.css('display') == 'none';
+            });
+            components.forEach(function (component, index) {
+              var nodeIndexes = void 0;
+              if (options.quality == "draft") {
+                nodeIndexes = spectralResult[index].nodeIndexes;
+              }
+
+              if (component.nodes().not(hiddenEles).length > 0) {
+                var subgraph = {};
+                subgraph.edges = [];
+                subgraph.nodes = [];
+                var nodeIndex = void 0;
+                component.nodes().not(hiddenEles).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 {
+                      var 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 {
+                    if (coseResult[index][node.id()]) {
+                      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) {
+                  var source = edge.source();
+                  var target = edge.target();
+                  if (source.css("display") != "none" && target.css("display") != "none") {
+                    if (options.quality == "draft") {
+                      var sourceNodeIndex = nodeIndexes.get(source.id());
+                      var targetNodeIndex = nodeIndexes.get(target.id());
+                      var sourceCenter = [];
+                      var targetCenter = [];
+                      if (source.isParent()) {
+                        var 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()) {
+                        var _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 {
+                      if (coseResult[index][source.id()] && coseResult[index][target.id()]) {
+                        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() });
+                      }
+                    }
+                  }
+                });
+                if (subgraph.nodes.length > 0) {
+                  subgraphs.push(subgraph);
+                  componentsEvaluated.add(index);
+                }
+              }
+            });
+            var shiftResult = layUtil.packComponents(subgraphs, options.randomize).shifts;
+            if (options.quality == "draft") {
+              spectralResult.forEach(function (result, index) {
+                var newXCoords = result.xCoords.map(function (x) {
+                  return x + shiftResult[index].dx;
+                });
+                var newYCoords = result.yCoords.map(function (y) {
+                  return y + shiftResult[index].dy;
+                });
+                result.xCoords = newXCoords;
+                result.yCoords = newYCoords;
+              });
+            } else {
+              var _count = 0;
+              componentsEvaluated.forEach(function (index) {
+                Object.keys(coseResult[index]).forEach(function (item) {
+                  var nodeRectangle = coseResult[index][item];
+                  nodeRectangle.setCenter(nodeRectangle.getCenterX() + shiftResult[_count].dx, nodeRectangle.getCenterY() + shiftResult[_count].dy);
+                });
+                _count++;
+              });
+            }
+          }
+        }
+      }
+
+      // get each element's calculated position
+      var getPositions = function getPositions(ele, i) {
+        if (options.quality == "default" || options.quality == "proof") {
+          if (typeof ele === "number") {
+            ele = i;
+          }
+          var pos = void 0;
+          var node = void 0;
+          var theId = ele.data('id');
+          coseResult.forEach(function (result) {
+            if (theId in result) {
+              pos = { x: result[theId].getRect().getCenterX(), y: result[theId].getRect().getCenterY() };
+              node = result[theId];
+            }
+          });
+          if (options.nodeDimensionsIncludeLabels) {
+            if (node.labelWidth) {
+              if (node.labelPosHorizontal == "left") {
+                pos.x += node.labelWidth / 2;
+              } else if (node.labelPosHorizontal == "right") {
+                pos.x -= node.labelWidth / 2;
+              }
+            }
+            if (node.labelHeight) {
+              if (node.labelPosVertical == "top") {
+                pos.y += node.labelHeight / 2;
+              } else if (node.labelPosVertical == "bottom") {
+                pos.y -= node.labelHeight / 2;
+              }
+            }
+          }
+          if (pos == undefined) pos = { x: ele.position("x"), y: ele.position("y") };
+          return {
+            x: pos.x,
+            y: pos.y
+          };
+        } else {
+          var _pos = void 0;
+          spectralResult.forEach(function (result) {
+            var index = result.nodeIndexes.get(ele.id());
+            if (index != undefined) {
+              _pos = { x: result.xCoords[index], y: result.yCoords[index] };
+            }
+          });
+          if (_pos == undefined) _pos = { x: ele.position("x"), y: ele.position("y") };
+          return {
+            x: _pos.x,
+            y: _pos.y
+          };
+        }
+      };
+
+      // quality = "draft" and randomize = false are contradictive so in that case positions don't change
+      if (options.quality == "default" || options.quality == "proof" || options.randomize) {
+        // transfer calculated positions to nodes (positions of only simple nodes are evaluated, compounds are positioned automatically)
+        var parentsWithoutChildren = aux.calcParentsWithoutChildren(cy, eles);
+        var _hiddenEles = eles.filter(function (ele) {
+          return ele.css('display') == 'none';
+        });
+        options.eles = eles.not(_hiddenEles);
+
+        eles.nodes().not(":parent").not(_hiddenEles).layoutPositions(layout, options, getPositions);
+
+        if (parentsWithoutChildren.length > 0) {
+          parentsWithoutChildren.forEach(function (ele) {
+            ele.position(getPositions(ele));
+          });
+        }
+      } else {
+        console.log("If randomize option is set to false, then quality option must be 'default' or 'proof'.");
+      }
+    }
+  }]);
+
+  return Layout;
+}();
+
+module.exports = Layout;
+
+/***/ }),
+
+/***/ 657:
+/***/ ((module, __unused_webpack_exports, __webpack_require__) => {
+
+
+
+/**
+  The implementation of the spectral layout that is the first part of the fcose layout algorithm
+*/
+
+var aux = __webpack_require__(548);
+var Matrix = __webpack_require__(140).layoutBase.Matrix;
+var SVD = __webpack_require__(140).layoutBase.SVD;
+
+// main function that spectral layout is processed
+var spectralLayout = function spectralLayout(options) {
+
+  var cy = options.cy;
+  var eles = options.eles;
+  var nodes = eles.nodes();
+  var parentNodes = eles.nodes(":parent");
+
+  var dummyNodes = new Map(); // map to keep dummy nodes and their neighbors
+  var nodeIndexes = new Map(); // map to keep indexes to nodes
+  var parentChildMap = new Map(); // mapping btw. compound and its representative node 
+  var allNodesNeighborhood = []; // array to keep neighborhood of all nodes
+  var xCoords = [];
+  var yCoords = [];
+
+  var samplesColumn = []; // sampled vertices
+  var minDistancesColumn = [];
+  var C = []; // column sampling matrix
+  var PHI = []; // intersection of column and row sampling matrices 
+  var INV = []; // inverse of PHI 
+
+  var firstSample = void 0; // the first sampled node
+  var nodeSize = void 0;
+
+  var infinity = 100000000;
+  var small = 0.000000001;
+
+  var piTol = options.piTol;
+  var samplingType = options.samplingType; // false for random, true for greedy
+  var nodeSeparation = options.nodeSeparation;
+  var sampleSize = void 0;
+
+  /**** Spectral-preprocessing functions ****/
+
+  /**** Spectral layout functions ****/
+
+  // determine which columns to be sampled
+  var randomSampleCR = function randomSampleCR() {
+    var sample = 0;
+    var count = 0;
+    var flag = false;
+
+    while (count < sampleSize) {
+      sample = Math.floor(Math.random() * nodeSize);
+
+      flag = false;
+      for (var i = 0; i < count; i++) {
+        if (samplesColumn[i] == sample) {
+          flag = true;
+          break;
+        }
+      }
+
+      if (!flag) {
+        samplesColumn[count] = sample;
+        count++;
+      } else {
+        continue;
+      }
+    }
+  };
+
+  // takes the index of the node(pivot) to initiate BFS as a parameter
+  var BFS = function BFS(pivot, index, samplingMethod) {
+    var path = []; // the front of the path
+    var front = 0; // the back of the path
+    var back = 0;
+    var current = 0;
+    var temp = void 0;
+    var distance = [];
+
+    var max_dist = 0; // the furthest node to be returned
+    var max_ind = 1;
+
+    for (var i = 0; i < nodeSize; i++) {
+      distance[i] = infinity;
+    }
+
+    path[back] = pivot;
+    distance[pivot] = 0;
+
+    while (back >= front) {
+      current = path[front++];
+      var neighbors = allNodesNeighborhood[current];
+      for (var _i = 0; _i < neighbors.length; _i++) {
+        temp = nodeIndexes.get(neighbors[_i]);
+        if (distance[temp] == infinity) {
+          distance[temp] = distance[current] + 1;
+          path[++back] = temp;
+        }
+      }
+      C[current][index] = distance[current] * nodeSeparation;
+    }
+
+    if (samplingMethod) {
+      for (var _i2 = 0; _i2 < nodeSize; _i2++) {
+        if (C[_i2][index] < minDistancesColumn[_i2]) minDistancesColumn[_i2] = C[_i2][index];
+      }
+
+      for (var _i3 = 0; _i3 < nodeSize; _i3++) {
+        if (minDistancesColumn[_i3] > max_dist) {
+          max_dist = minDistancesColumn[_i3];
+          max_ind = _i3;
+        }
+      }
+    }
+    return max_ind;
+  };
+
+  // apply BFS to all nodes or selected samples
+  var allBFS = function allBFS(samplingMethod) {
+
+    var sample = void 0;
+
+    if (!samplingMethod) {
+      randomSampleCR();
+
+      // call BFS
+      for (var i = 0; i < sampleSize; i++) {
+        BFS(samplesColumn[i], i, samplingMethod, false);
+      }
+    } else {
+      sample = Math.floor(Math.random() * nodeSize);
+      firstSample = sample;
+
+      for (var _i4 = 0; _i4 < nodeSize; _i4++) {
+        minDistancesColumn[_i4] = infinity;
+      }
+
+      for (var _i5 = 0; _i5 < sampleSize; _i5++) {
+        samplesColumn[_i5] = sample;
+        sample = BFS(sample, _i5, samplingMethod);
+      }
+    }
+
+    // form the squared distances for C
+    for (var _i6 = 0; _i6 < nodeSize; _i6++) {
+      for (var j = 0; j < sampleSize; j++) {
+        C[_i6][j] *= C[_i6][j];
+      }
+    }
+
+    // form PHI
+    for (var _i7 = 0; _i7 < sampleSize; _i7++) {
+      PHI[_i7] = [];
+    }
+
+    for (var _i8 = 0; _i8 < sampleSize; _i8++) {
+      for (var _j = 0; _j < sampleSize; _j++) {
+        PHI[_i8][_j] = C[samplesColumn[_j]][_i8];
+      }
+    }
+  };
+
+  // perform the SVD algorithm and apply a regularization step
+  var sample = function sample() {
+
+    var SVDResult = SVD.svd(PHI);
+
+    var a_q = SVDResult.S;
+    var a_u = SVDResult.U;
+    var a_v = SVDResult.V;
+
+    var max_s = a_q[0] * a_q[0] * a_q[0];
+
+    var a_Sig = [];
+
+    //  regularization
+    for (var i = 0; i < sampleSize; i++) {
+      a_Sig[i] = [];
+      for (var j = 0; j < sampleSize; j++) {
+        a_Sig[i][j] = 0;
+        if (i == j) {
+          a_Sig[i][j] = a_q[i] / (a_q[i] * a_q[i] + max_s / (a_q[i] * a_q[i]));
+        }
+      }
+    }
+
+    INV = Matrix.multMat(Matrix.multMat(a_v, a_Sig), Matrix.transpose(a_u));
+  };
+
+  // calculate final coordinates 
+  var powerIteration = function powerIteration() {
+    // two largest eigenvalues
+    var theta1 = void 0;
+    var theta2 = void 0;
+
+    // initial guesses for eigenvectors
+    var Y1 = [];
+    var Y2 = [];
+
+    var V1 = [];
+    var V2 = [];
+
+    for (var i = 0; i < nodeSize; i++) {
+      Y1[i] = Math.random();
+      Y2[i] = Math.random();
+    }
+
+    Y1 = Matrix.normalize(Y1);
+    Y2 = Matrix.normalize(Y2);
+
+    var count = 0;
+    // to keep track of the improvement ratio in power iteration
+    var current = small;
+    var previous = small;
+
+    var temp = void 0;
+
+    while (true) {
+      count++;
+
+      for (var _i9 = 0; _i9 < nodeSize; _i9++) {
+        V1[_i9] = Y1[_i9];
+      }
+
+      Y1 = Matrix.multGamma(Matrix.multL(Matrix.multGamma(V1), C, INV));
+      theta1 = Matrix.dotProduct(V1, Y1);
+      Y1 = Matrix.normalize(Y1);
+
+      current = Matrix.dotProduct(V1, Y1);
+
+      temp = Math.abs(current / previous);
+
+      if (temp <= 1 + piTol && temp >= 1) {
+        break;
+      }
+
+      previous = current;
+    }
+
+    for (var _i10 = 0; _i10 < nodeSize; _i10++) {
+      V1[_i10] = Y1[_i10];
+    }
+
+    count = 0;
+    previous = small;
+    while (true) {
+      count++;
+
+      for (var _i11 = 0; _i11 < nodeSize; _i11++) {
+        V2[_i11] = Y2[_i11];
+      }
+
+      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 = Matrix.dotProduct(V2, Y2);
+
+      temp = Math.abs(current / previous);
+
+      if (temp <= 1 + piTol && temp >= 1) {
+        break;
+      }
+
+      previous = current;
+    }
+
+    for (var _i12 = 0; _i12 < nodeSize; _i12++) {
+      V2[_i12] = Y2[_i12];
+    }
+
+    // theta1 now contains dominant eigenvalue
+    // theta2 now contains the second-largest eigenvalue
+    // V1 now contains theta1's eigenvector
+    // V2 now contains theta2's eigenvector
+
+    //populate the two vectors
+    xCoords = Matrix.multCons(V1, Math.sqrt(Math.abs(theta1)));
+    yCoords = Matrix.multCons(V2, Math.sqrt(Math.abs(theta2)));
+  };
+
+  /**** Preparation for spectral layout (Preprocessing) ****/
+
+  // connect disconnected components (first top level, then inside of each compound node)
+  aux.connectComponents(cy, eles, aux.getTopMostNodes(nodes), dummyNodes);
+
+  parentNodes.forEach(function (ele) {
+    aux.connectComponents(cy, eles, aux.getTopMostNodes(ele.descendants().intersection(eles)), dummyNodes);
+  });
+
+  // assign indexes to nodes (first real, then dummy nodes)
+  var index = 0;
+  for (var i = 0; i < nodes.length; i++) {
+    if (!nodes[i].isParent()) {
+      nodeIndexes.set(nodes[i].id(), index++);
+    }
+  }
+
+  var _iteratorNormalCompletion = true;
+  var _didIteratorError = false;
+  var _iteratorError = undefined;
+
+  try {
+    for (var _iterator = dummyNodes.keys()[Symbol.iterator](), _step; !(_iteratorNormalCompletion = (_step = _iterator.next()).done); _iteratorNormalCompletion = true) {
+      var key = _step.value;
+
+      nodeIndexes.set(key, index++);
+    }
+
+    // instantiate the neighborhood matrix
+  } catch (err) {
+    _didIteratorError = true;
+    _iteratorError = err;
+  } finally {
+    try {
+      if (!_iteratorNormalCompletion && _iterator.return) {
+        _iterator.return();
+      }
+    } finally {
+      if (_didIteratorError) {
+        throw _iteratorError;
+      }
+    }
+  }
+
+  for (var _i13 = 0; _i13 < nodeIndexes.size; _i13++) {
+    allNodesNeighborhood[_i13] = [];
+  }
+
+  // form a parent-child map to keep representative node of each compound node  
+  parentNodes.forEach(function (ele) {
+    var children = ele.children().intersection(eles);
+
+    //      let random = 0;
+    while (children.nodes(":childless").length == 0) {
+      //        random = Math.floor(Math.random() * children.nodes().length); // if all children are compound then proceed randomly
+      children = children.nodes()[0].children().intersection(eles);
+    }
+    //  select the representative node - we can apply different methods here
+    //      random = Math.floor(Math.random() * children.nodes(":childless").length);
+    var index = 0;
+    var min = children.nodes(":childless")[0].connectedEdges().length;
+    children.nodes(":childless").forEach(function (ele2, i) {
+      if (ele2.connectedEdges().length < min) {
+        min = ele2.connectedEdges().length;
+        index = i;
+      }
+    });
+    parentChildMap.set(ele.id(), children.nodes(":childless")[index].id());
+  });
+
+  // add neighborhood relations (first real, then dummy nodes)
+  nodes.forEach(function (ele) {
+    var eleIndex = void 0;
+
+    if (ele.isParent()) eleIndex = nodeIndexes.get(parentChildMap.get(ele.id()));else eleIndex = nodeIndexes.get(ele.id());
+
+    ele.neighborhood().nodes().forEach(function (node) {
+      if (eles.intersection(ele.edgesWith(node)).length > 0) {
+        if (node.isParent()) allNodesNeighborhood[eleIndex].push(parentChildMap.get(node.id()));else allNodesNeighborhood[eleIndex].push(node.id());
+      }
+    });
+  });
+
+  var _loop = function _loop(_key) {
+    var eleIndex = nodeIndexes.get(_key);
+    var disconnectedId = void 0;
+    dummyNodes.get(_key).forEach(function (id) {
+      if (cy.getElementById(id).isParent()) disconnectedId = parentChildMap.get(id);else disconnectedId = id;
+
+      allNodesNeighborhood[eleIndex].push(disconnectedId);
+      allNodesNeighborhood[nodeIndexes.get(disconnectedId)].push(_key);
+    });
+  };
+
+  var _iteratorNormalCompletion2 = true;
+  var _didIteratorError2 = false;
+  var _iteratorError2 = undefined;
+
+  try {
+    for (var _iterator2 = dummyNodes.keys()[Symbol.iterator](), _step2; !(_iteratorNormalCompletion2 = (_step2 = _iterator2.next()).done); _iteratorNormalCompletion2 = true) {
+      var _key = _step2.value;
+
+      _loop(_key);
+    }
+
+    // nodeSize now only considers the size of transformed graph
+  } catch (err) {
+    _didIteratorError2 = true;
+    _iteratorError2 = err;
+  } finally {
+    try {
+      if (!_iteratorNormalCompletion2 && _iterator2.return) {
+        _iterator2.return();
+      }
+    } finally {
+      if (_didIteratorError2) {
+        throw _iteratorError2;
+      }
+    }
+  }
+
+  nodeSize = nodeIndexes.size;
+
+  var spectralResult = void 0;
+
+  // If number of nodes in transformed graph is 1 or 2, either SVD or powerIteration causes problem
+  // So skip spectral and layout the graph with cose
+  if (nodeSize > 2) {
+    // if # of nodes in transformed graph is smaller than sample size,
+    // then use # of nodes as sample size
+    sampleSize = nodeSize < options.sampleSize ? nodeSize : options.sampleSize;
+
+    // instantiates the partial matrices that will be used in spectral layout
+    for (var _i14 = 0; _i14 < nodeSize; _i14++) {
+      C[_i14] = [];
+    }
+    for (var _i15 = 0; _i15 < sampleSize; _i15++) {
+      INV[_i15] = [];
+    }
+
+    /**** Apply spectral layout ****/
+
+    if (options.quality == "draft" || options.step == "all") {
+      allBFS(samplingType);
+      sample();
+      powerIteration();
+
+      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;
+  } else {
+    var iterator = nodeIndexes.keys();
+    var firstNode = cy.getElementById(iterator.next().value);
+    var firstNodePos = firstNode.position();
+    var firstNodeWidth = firstNode.outerWidth();
+    xCoords.push(firstNodePos.x);
+    yCoords.push(firstNodePos.y);
+    if (nodeSize == 2) {
+      var secondNode = cy.getElementById(iterator.next().value);
+      var secondNodeWidth = secondNode.outerWidth();
+      xCoords.push(firstNodePos.x + firstNodeWidth / 2 + secondNodeWidth / 2 + options.idealEdgeLength);
+      yCoords.push(firstNodePos.y);
+    }
+
+    spectralResult = { nodeIndexes: nodeIndexes, xCoords: xCoords, yCoords: yCoords };
+    return spectralResult;
+  }
+};
+
+module.exports = { spectralLayout: spectralLayout };
+
+/***/ }),
+
+/***/ 579:
+/***/ ((module, __unused_webpack_exports, __webpack_require__) => {
+
+
+
+var impl = __webpack_require__(212);
+
+// registers the extension on a cytoscape lib ref
+var register = function register(cytoscape) {
+  if (!cytoscape) {
+    return;
+  } // can't register if cytoscape unspecified
+
+  cytoscape('layout', 'fcose', impl); // register with cytoscape.js
+};
+
+if (typeof cytoscape !== 'undefined') {
+  // expose to global cytoscape (i.e. window.cytoscape)
+  register(cytoscape);
+}
+
+module.exports = register;
+
+/***/ }),
+
+/***/ 140:
+/***/ ((module) => {
+
+module.exports = __WEBPACK_EXTERNAL_MODULE__140__;
+
+/***/ })
+
+/******/ 	});
+/************************************************************************/
+/******/ 	// The module cache
+/******/ 	var __webpack_module_cache__ = {};
+/******/ 	
+/******/ 	// The require function
+/******/ 	function __webpack_require__(moduleId) {
+/******/ 		// Check if module is in cache
+/******/ 		var cachedModule = __webpack_module_cache__[moduleId];
+/******/ 		if (cachedModule !== undefined) {
+/******/ 			return cachedModule.exports;
+/******/ 		}
+/******/ 		// Create a new module (and put it into the cache)
+/******/ 		var module = __webpack_module_cache__[moduleId] = {
+/******/ 			// no module.id needed
+/******/ 			// no module.loaded needed
+/******/ 			exports: {}
+/******/ 		};
+/******/ 	
+/******/ 		// Execute the module function
+/******/ 		__webpack_modules__[moduleId](module, module.exports, __webpack_require__);
+/******/ 	
+/******/ 		// Return the exports of the module
+/******/ 		return module.exports;
+/******/ 	}
+/******/ 	
+/************************************************************************/
+/******/ 	
+/******/ 	// startup
+/******/ 	// Load entry module and return exports
+/******/ 	// This entry module is referenced by other modules so it can't be inlined
+/******/ 	var __webpack_exports__ = __webpack_require__(579);
+/******/ 	
+/******/ 	return __webpack_exports__;
+/******/ })()
+;
+});

tools/ui/node_modules/cytoscape-fcose/demo/demo-compound.html

@@ -0,0 +1,465 @@
+<!DOCTYPE>
+
+<html>
+
+  <head>
+    <title>cytoscape-fcose.js demo</title>
+
+      <meta name="viewport" content="width=device-width, user-scalable=no, initial-scale=1, maximum-scale=1">
+      
+      <!-- Bootstrap, popper, jQuery and filesaver - for demo purpose only -->
+      <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.4.1/jquery.min.js"></script>
+      <script src="https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.11.0/umd/popper.min.js"></script>
+      <script src="https://stackpath.bootstrapcdn.com/bootstrap/4.3.1/js/bootstrap.min.js"></script>      
+      <link href="https://stackpath.bootstrapcdn.com/bootstrap/4.3.1/css/bootstrap.min.css" rel="stylesheet">       
+
+      <script src="https://unpkg.com/cytoscape/dist/cytoscape.min.js"></script>
+      <script src="https://unpkg.com/layout-base/layout-base.js"></script>
+      <script src="https://unpkg.com/cose-base/cose-base.js"></script>
+      <script src="https://unpkg.com/cytoscape-layout-utilities/cytoscape-layout-utilities.js"></script>
+
+      <!-- for testing with local version of cytoscape.js -->
+      <!--<script src="../cytoscape.js/build/cytoscape.js"></script>-->
+
+      <script src="../cytoscape-fcose.js"></script>
+
+      <style>
+        body {
+          font-family: helvetica neue, helvetica, liberation sans, arial, sans-serif;
+          font-size: 14px;
+        }
+
+        #cy {
+          position: relative;
+          width: auto;
+          height: 90%;
+          z-index: 999;
+          margin-left: 290px;
+          right: 0px;
+        }
+
+        h1 {
+          opacity: 1;
+          color: #555;
+          font-size: 15px;
+          font-weight: bold;
+          padding-top: 5px;
+        }
+                
+        /* The sidepanel menu */
+        .sidepanel {
+          height: auto; /* Specify a height */
+          width: 290px; /* 0 width - change this with JavaScript */
+          position: absolute; /* Stay in place */
+          z-index: 1000; /* Stay on top */
+          float: left;
+          top: auto;
+          left: 0;
+          background-color: #b7ffff; /* Black*/
+          overflow-x: hidden; /* Disable horizontal scroll */
+          padding-top: 10px; /* Place content 10px from the top */
+          padding-bottom: 10px; /* Place content 10px from the bottom */
+          transition: 0s; /* 0.5 second transition effect to slide in the sidepanel */
+        }
+
+        table{
+          margin-left: 4px;
+          margin-right: auto;
+          table-layout: fixed;
+        }        
+        
+        /* The sidepanel links */
+        table td {
+          padding: 0px 8px 8px 8px;
+          text-decoration: none;
+          font-size: 13px;
+          color: #555;
+          transition: 0.3s;
+          vertical-align: middle;          
+        }
+
+        /* Style the button that is used to open the sidepanel */
+        .button {
+          font-size: 15px;
+          color: #555;
+          cursor: pointer;
+          background-color: #b7ffff;
+          padding: 5px 10px;
+          border: none;
+          margin-bottom: 5px;
+        }
+        
+        .textField {
+          padding-left: 5px;
+        }
+        
+        .checkbox {
+          margin-left: 0px;
+        }        
+
+        .button:hover {
+          background-color: #0f0;
+        }
+        
+        .btn-group-sm>.btn, .btn-sm { 
+          font-size: 13px;
+          background-color: #7d8991;
+          border-color: #7d8991;
+        }
+        
+        .btn-primary:hover, .btn-primary:focus, .btn-primary:active, .btn-primary.active, .open>.dropdown-toggle.btn-primary {
+            color: #fff;
+            background-color: #60717d;
+            border-color: #60717d; /*set the color you want here*/
+        }  
+        
+        .btn-outline-primary:hover, .btn-outline-primary:focus, .btn-outline-primary:active, .btn-outline-primary.active, .open>.dropdown-toggle.btn-primary {
+            color: #fff;
+            background-color: #60717d;
+            border-color: #60717d; /*set the color you want here*/
+        }         
+        
+        .form-control-sm { 
+          font-size: 13px
+        }
+
+        .custom-select-sm {
+          font-size: 13px
+        } 
+        
+        .custom-control-label {
+          padding-top: 2px;
+        }
+        
+        .custom-control-input:checked~.custom-control-label::before {
+            color: #fff;
+            border-color: #7d8991;
+            background-color: #7d8991;
+        }   
+      </style>
+
+      <script>
+        document.addEventListener('DOMContentLoaded', function(){
+
+          var cy = window.cy = cytoscape({
+            container: document.getElementById('cy'),
+            
+            ready: function(){
+              let layoutUtilities = this.layoutUtilities({
+                desiredAspectRatio: this.width()/this.height()
+              });              
+              this.nodes().forEach(function(node){
+                let size = Math.random()*120+30;
+                node.css("width", size);
+                node.css("height", size);
+              });
+              this.layout({name: 'fcose', animationEasing: 'ease-out'}).run();
+            },
+            
+            // demo your layout
+            layout: {
+              name: 'grid'
+            },
+
+            style: [
+              {
+                selector: 'node',
+                style: {
+                  'background-color': '#2B65EC'                 
+                }
+              },
+              
+              {
+              selector: ':parent',
+                style: {
+                  'background-opacity': 0.333,
+                  'border-color': '#2B65EC'
+                }
+              },
+
+              {
+                selector: 'edge',
+                style: {
+                  'line-color': '#2B65EC'
+                }
+              },
+              
+              {
+                selector: 'node:selected',
+                style: {
+                  'background-color': '#F08080',
+                  'border-color': 'red'
+                }
+              },
+              
+              {
+                selector: 'edge:selected',
+                style: {
+                  'line-color': '#F08080'
+                }
+              }                 
+            ],  
+            
+            elements: [{ group:'nodes', data:{ id: 'n0'}},
+                    { group:'nodes', data:{ id: 'n1'}},
+                    { group:'nodes', data:{ id: 'n2'}},
+                    { group:'nodes', data:{ id: 'n3'}},
+                    { group:'nodes', data:{ id: 'n4', parent: 'n37'}},
+                    { group:'nodes', data:{ id: 'n5'}},
+                    { group:'nodes', data:{ id: 'n6'}},
+                    { group:'nodes', data:{ id: 'n7', parent: 'n37'}},
+                    { group:'nodes', data:{ id: 'n8', parent: 'n37'}},
+                    { group:'nodes', data:{ id: 'n9', parent: 'n37'}},
+                    { group:'nodes', data:{ id: 'n10', parent: 'n38'}},
+                    { group:'nodes', data:{ id: 'n12'}},
+                    { group:'nodes', data:{ id: 'n13'}},
+                    { group:'nodes', data:{ id: 'n14'}},
+                    { group:'nodes', data:{ id: 'n15'}},
+                    { group:'nodes', data:{ id: 'n16'}},
+                    { group:'nodes', data:{ id: 'n17'}},
+                    { group:'nodes', data:{ id: 'n18'}},
+                    { group:'nodes', data:{ id: 'n19'}},
+                    { group:'nodes', data:{ id: 'n20'}},
+                    { group:'nodes', data:{ id: 'n21'}},
+                    { group:'nodes', data:{ id: 'n22'}},
+                    { group:'nodes', data:{ id: 'n23'}},
+                    { group:'nodes', data:{ id: 'n24', parent: 'n39'}},
+                    { group:'nodes', data:{ id: 'n25', parent: 'n39'}},
+                    { group:'nodes', data:{ id: 'n26', parent: 'n42'}},
+                    { group:'nodes', data:{ id: 'n27', parent: 'n42'}},
+                    { group:'nodes', data:{ id: 'n28', parent: 'n42'}},
+                    { group:'nodes', data:{ id: 'n29', parent: 'n40'}},
+                    { group:'nodes', data:{ id: 'n31', parent: 'n41'}},
+                    { group:'nodes', data:{ id: 'n32', parent: 'n41'}},
+                    { group:'nodes', data:{ id: 'n33', parent: 'n41'}},
+                    { group:'nodes', data:{ id: 'n34', parent: 'n41'}},
+                    { group:'nodes', data:{ id: 'n35', parent: 'n41'}},
+                    { group:'nodes', data:{ id: 'n36', parent: 'n41'}},
+                    { group:'nodes', data:{ id: 'n37'}},
+                    { group:'nodes', data:{ id: 'n38'}},
+                    { group:'nodes', data:{ id: 'n39', parent: 'n43'}},
+                    { group:'nodes', data:{ id: 'n40', parent: 'n42'}},
+                    { group:'nodes', data:{ id: 'n41', parent: 'n42'}},
+                    { group:'nodes', data:{ id: 'n42', parent: 'n43'}},
+                    { group:'nodes', data:{ id: 'n43'}},
+                    { group:'nodes', data:{ id: 'n44'}},
+                    { group:'nodes', data:{ id: 'n45'}},
+                    { group:'nodes', data:{ id: 'n46'}},
+                    { group:'nodes', data:{ id: 'n47'}},
+                    { group:'edges', data:{ id: 'e0', source: 'n0', target: 'n1'} },
+                    { group:'edges', data:{ id: 'e1', source: 'n1', target: 'n2'} },
+                    { group:'edges', data:{ id: 'e2', source: 'n2', target: 'n3'} },
+                    { group:'edges', data:{ id: 'e3', source: 'n0', target: 'n3'} },
+                    { group:'edges', data:{ id: 'e4', source: 'n1', target: 'n4'} },
+                    { group:'edges', data:{ id: 'e5', source: 'n2', target: 'n4'} },
+                    { group:'edges', data:{ id: 'e6', source: 'n4', target: 'n5'} },
+                    { group:'edges', data:{ id: 'e7', source: 'n5', target: 'n6'} },
+                    { group:'edges', data:{ id: 'e8', source: 'n4', target: 'n6'} },
+                    { group:'edges', data:{ id: 'e9', source: 'n4', target: 'n7'} },
+                    { group:'edges', data:{ id: 'e10', source: 'n7', target: 'n8'} },
+                    { group:'edges', data:{ id: 'e11', source: 'n8', target: 'n9'} },
+                    { group:'edges', data:{ id: 'e12', source: 'n7', target: 'n9'} },
+                    { group:'edges', data:{ id: 'e13', source: 'n13', target: 'n14'} },
+                    //{ group:'edges', data:{ id: 'e14', source: 'n12', target: 'n14'} },
+                    { group:'edges', data:{ id: 'e15', source: 'n14', target: 'n15'} },
+                    { group:'edges', data:{ id: 'e16', source: 'n14', target: 'n16'} },
+                    { group:'edges', data:{ id: 'e17', source: 'n15', target: 'n17'} },
+                    { group:'edges', data:{ id: 'e18', source: 'n17', target: 'n18'} },
+                    { group:'edges', data:{ id: 'e19', source: 'n18', target: 'n19'} },
+                    { group:'edges', data:{ id: 'e20', source: 'n17', target: 'n20'} },
+                    { group:'edges', data:{ id: 'e21', source: 'n19', target: 'n20'} },
+                    { group:'edges', data:{ id: 'e22', source: 'n16', target: 'n20'} },
+                    { group:'edges', data:{ id: 'e23', source: 'n20', target: 'n21'} },
+                    { group:'edges', data:{ id: 'e25', source: 'n23', target: 'n24'} },
+                    { group:'edges', data:{ id: 'e26', source: 'n24', target: 'n25'} },
+                    { group:'edges', data:{ id: 'e27', source: 'n26', target: 'n38'} },
+                    { group:'edges', data:{ id: 'e29', source: 'n26', target: 'n39'} },
+                    { group:'edges', data:{ id: 'e30', source: 'n26', target: 'n27'} },
+                    { group:'edges', data:{ id: 'e31', source: 'n26', target: 'n28'} },
+                    { group:'edges', data:{ id: 'e33', source: 'n21', target: 'n31'} },
+                    { group:'edges', data:{ id: 'e35', source: 'n31', target: 'n33'} },
+                    { group:'edges', data:{ id: 'e36', source: 'n31', target: 'n34'} },
+                    { group:'edges', data:{ id: 'e37', source: 'n33', target: 'n34'} },
+                    { group:'edges', data:{ id: 'e38', source: 'n32', target: 'n35'} },
+                    { group:'edges', data:{ id: 'e39', source: 'n32', target: 'n36'} },
+                    { group:'edges', data:{ id: 'e40', source: 'n16', target: 'n40'} },
+                    { group:'edges', data:{ id: 'e41', source: 'n44', target: 'n45'} },
+                    { group:'edges', data:{ id: 'e42', source: 'n44', target: 'n46'} },
+                    { group:'edges', data:{ id: 'e43', source: 'n45', target: 'n46'} }                 
+                   ]
+            
+          });          
+          
+          document.getElementById("randomizeButton").addEventListener("click", function(){
+            var layout = cy.layout({
+              name: 'random',
+              animate: true,
+              animationDuration: 1000
+            });
+            
+            layout.run();        
+          });          
+          
+          document.getElementById("fcoseButton").addEventListener("click", function(){
+            let qualityItem = document.getElementById("quality");
+            var layout = cy.layout({
+              name: 'fcose',
+              quality: qualityItem.options[qualityItem.selectedIndex].value,
+              randomize: !(document.getElementById("randomize").checked),
+              animate: document.getElementById("animate").checked,
+              animationEasing: 'ease-out',
+              fit: document.getElementById("fit").checked,
+              uniformNodeDimensions: document.getElementById("uniformNodeDimensions").checked,
+              packComponents: document.getElementById("packComponents").checked,
+              tile: document.getElementById("tile").checked,
+              nodeRepulsion: parseFloat(document.getElementById("nodeRepulsion").value),
+              idealEdgeLength: parseFloat(document.getElementById("idealEdgeLength").value),
+              edgeElasticity: parseFloat(document.getElementById("edgeElasticity").value),
+              nestingFactor: parseFloat(document.getElementById("nestingFactor").value),
+              gravity: parseFloat(document.getElementById("gravity").value),
+              gravityRange: parseFloat(document.getElementById("gravityRange").value),
+              gravityCompound: parseFloat(document.getElementById("gravityCompound").value),
+              gravityRangeCompound: parseFloat(document.getElementById("gravityRangeCompound").value),
+              numIter: parseFloat(document.getElementById("numIter").value),
+              tilingPaddingVertical: parseFloat(document.getElementById("tilingPaddingVertical").value),
+              tilingPaddingHorizontal: parseFloat(document.getElementById("tilingPaddingHorizontal").value),
+              initialEnergyOnIncremental: document.getElementById("initialEnergyOnIncremental").value,
+              step:"all"
+            });
+            
+            layout.run();        
+          });
+          
+        });
+      </script>
+  </head>
+
+  <body>
+          <h1 class="ml-2">cytoscape-fcose demo (compound)</h1>
+          <div style='width: 300px; position: absolute;'>
+            <button id="randomizeButton" class="btn btn-primary btn-sm mb-2 ml-2">Randomize</button>&nbsp &nbsp
+            <button id="fcoseButton" class="btn btn-primary btn-sm mb-2 ml-2">fCoSE</button>
+          
+            <div id="mySidepanel" class="sidepanel">
+              <table>
+                <tr>
+                  <td><span class="add-on layout-text" title="Quality of the layout"> Quality </span></td>
+                  <td>            
+                    <select id="quality" class='custom-select custom-select-sm'>
+                      <option value="draft">draft</option>
+                      <option value="default" selected="">default</option>
+                      <option value="proof">proof</option>
+                    </select>
+                  </td>
+                </tr>
+                <tr>
+                  <td><span class="add-on layout-text" title="Whether to enable incremental mode"> Incremental </span></td>
+                  <td>        
+                    <div class="custom-control custom-control-inline custom-checkbox">
+                      <input type="checkbox" class="custom-control-input" id="randomize" name="incremental">
+                      <label class="custom-control-label" for="randomize"></label>
+                    </div>
+                  </td>
+                </tr>
+                <tr>
+                  <td><span class="add-on layout-text" title="Whether to perform animation after layout"> Animate </span></td>
+                  <td>
+                    <div class="custom-control custom-control-inline custom-checkbox">
+                      <input type="checkbox" class="custom-control-input" id="animate" name="animate" checked>
+                      <label class="custom-control-label" for="animate"></label>
+                    </div>                  
+                  </td>
+                </tr>
+                <tr>
+                  <td><span class="add-on layout-text" title="Whether to fit the viewport to the repositioned nodes"> Fit </span></td>
+                  <td>
+                    <div class="custom-control custom-control-inline custom-checkbox">
+                      <input type="checkbox" class="custom-control-input" id="fit" name="fit" checked>
+                      <label class="custom-control-label" for="fit"></label>
+                    </div>
+                  </td>
+                </tr>
+                <tr>
+                  <td><span class="add-on layout-text" title="Whether nodes are of uniform dimensions"> Uniform Node Dimensions </span></td>
+                  <td>
+                    <div class="custom-control custom-control-inline custom-checkbox">
+                      <input type="checkbox" class="custom-control-input" id="uniformNodeDimensions" name="uniformNodeDimensions">
+                      <label class="custom-control-label" for="uniformNodeDimensions"></label>
+                    </div> 
+                  </td>
+                </tr>
+                <tr>
+                  <td><span class="add-on layout-text" title="Whether to pack components"> Pack Components to Window </span></td>
+                  <td>
+                    <div class="custom-control custom-control-inline custom-checkbox">
+                      <input type="checkbox" class="custom-control-input" id="packComponents" name="packComponents" checked>
+                      <label class="custom-control-label" for="packComponents"></label>
+                    </div>                     
+                  </td>
+                </tr>
+                <tr>
+                  <td><span class="add-on layout-text" title="Whether to tile disconnected nodes"> Tile Disconnected </span></td>
+                  <td>
+                    <div class="custom-control custom-control-inline custom-checkbox">
+                      <input type="checkbox" class="custom-control-input" id="tile" name="tile" checked>
+                      <label class="custom-control-label" for="tile"></label>
+                    </div>                     
+                  </td>
+                </tr>              
+                <tr>
+                  <td><span class="add-on layout-text" title="Node repulsion (non overlapping) multiplier"> Node Repulsion </span></td>
+                  <td><input id="nodeRepulsion" class="textField form-control form-control-sm" type="text" value="4500" maxlength=5 size="5"></td>
+                </tr>
+                <tr>
+                  <td><span class="add-on layout-text" title="Ideal (intra-graph) edge length"> Ideal Edge Length </span></td>
+                  <td><input id="idealEdgeLength" class="textField form-control form-control-sm" type="text" value="50" maxlength=5 size="5"></td>
+                </tr>
+                <tr>
+                  <td><span class="add-on layout-text" title="Divisor to compute edge forces"> Edge Elasticity </span></td>
+                  <td><input id="edgeElasticity" class="textField form-control form-control-sm" type="text" value="0.45" maxlength=5 size="5"></td>
+                </tr>
+                <tr>
+                  <td><span class="add-on layout-text" title="Nesting factor (multiplier) to compute ideal edge length for inter-graph edges"> Nesting Factor </span></td>
+                  <td><input id="nestingFactor" class="textField form-control form-control-sm" type="text" value="0.1" maxlength=5 size="5"></td>
+                </tr>
+                <tr>
+                  <td><span class="add-on layout-text" title="Gravity force (constant)"> Gravity </span></td>
+                  <td><input id="gravity" class="textField form-control form-control-sm" type="text" value="0.25" maxlength=5 size="5"></td>
+                </tr>
+                <tr>
+                  <td><span class="add-on layout-text" title="Gravity range (constant)"> Gravity Range </span></td>
+                  <td><input id="gravityRange" class="textField form-control form-control-sm" type="text" value="3.8" maxlength=5 size="5"></td>
+                </tr>
+                <tr>
+                  <td><span class="add-on layout-text" title="Gravity force (constant) for compounds"> Compound Gravity </span></td>
+                  <td><input id="gravityCompound" class="textField form-control form-control-sm" type="text" value="1" maxlength=5 size="5"></td>
+                </tr>
+                <tr>
+                  <td><span class="add-on layout-text" title="Gravity range (constant) for compounds"> Compound Gravity Range </span></td>
+                  <td><input id="gravityRangeCompound" class="textField form-control form-control-sm" type="text" value="1.5" maxlength=5 size="5"></td>
+                </tr>
+                <tr>
+                  <td><span class="add-on layout-text" title="Maximum number of iterations to perform"> Number of Iterations </span></td>
+                  <td><input id="numIter" class="textField form-control form-control-sm" type="text" value="2500" size="5"></td>
+                </tr>
+                <tr>
+                  <td><span class="add-on layout-text" title="Amount of vertical space to put between degree zero nodes during tiling"> Tiling Vertical Padding </span></td>
+                  <td><input id="tilingPaddingVertical" class="textField form-control form-control-sm" type="text" value="10" maxlength=5 size="5"></td>
+                </tr>
+                <tr>
+                  <td><span class="add-on layout-text" title="Amount of horizontal space to put between degree zero nodes during tiling"> Tiling Horizontal Padding </span></td>
+                  <td><input id="tilingPaddingHorizontal" class="textField form-control form-control-sm" type="text" value="10" maxlength=5 size="5"></td>
+                </tr>
+                <tr>
+                  <td><span class="add-on layout-text" title="Initial cooling factor for incremental layout"> Incremental Cooling Factor </span></td>
+                  <td><input id="initialEnergyOnIncremental" class="textField form-control form-control-sm" type="text" value="0.3" maxlength=5 size="5"></td>
+                </tr>               
+              </table>
+
+            </div>
+          </div>
+          <div id="cy"></div>
+
+  </body>
+
+</html>

tools/ui/node_modules/cytoscape-fcose/demo/demo-constraint-control.js

@@ -0,0 +1,1482 @@
+// define default stylesheet
+let defaultStylesheet =  [
+  {
+    selector: 'node',
+    style: {
+      'background-color': '#bdd3d4',
+      'label': 'data(id)',
+      'text-valign': 'center',
+      'background-opacity': 0.7
+    }
+  },         
+
+  {
+  selector: ':parent',
+    style: {
+//      'background-opacity': 0.333,
+      'background-color': '#e8e8e8',
+      'border-color': '#DADADA',
+//      'border-width': 3,
+      'text-valign': 'bottom'
+    }
+  },
+
+  {
+    selector: 'edge',
+    style: {
+      'curve-style': 'straight',
+      'line-color': '#bdd3d4'
+    }
+  },
+
+  {
+    selector: 'node:selected',
+    style: {
+      'background-color': '#33ff00',
+      'border-color': '#22ee00'
+    }
+  },
+  
+  {
+    selector: 'node.fixed',
+    style: {
+      'shape': 'diamond',
+      'background-color': '#9D9696',
+    }
+  }, 
+  
+  {
+    selector: 'node.fixed:selected',
+    style: {
+      'background-color': '#33ff00',
+    }
+  },
+  
+  {
+    selector: 'node.alignment',
+    style: {
+      'shape': 'round-heptagon',
+      'background-color': '#fef2d1',
+    }
+  }, 
+  
+  {
+    selector: 'node.alignment:selected',
+    style: {
+      'background-color': '#33ff00',
+    }
+  },  
+
+  {
+    selector: 'node.relative',
+    style: {
+      'shape': 'rectangle',
+      'background-color': '#fed3d1',
+    }
+  }, 
+  
+  {
+    selector: 'node.relative:selected',
+    style: {
+      'background-color': '#33ff00',
+    }
+  },
+
+  {
+    selector: 'edge:selected',
+    style: {
+      'line-color': '#33ff00'
+    }
+  }                 
+];
+
+let cy = window.cy = cytoscape({
+  container: document.getElementById('cy'),
+  ready: function(){              
+    let layoutUtilities = this.layoutUtilities({
+      desiredAspectRatio: this.width()/this.height()
+    });
+
+    this.nodes().forEach(function(node){
+      let size = Math.random()*40+30;
+      node.css("width", size);
+      node.css("height", size);
+    });
+
+    let initialLayout = this.layout({name: 'fcose', step: 'all', animationEasing: 'ease-out'});
+    initialLayout.pon('layoutstart').then(function( event ){
+      constraints.fixedNodeConstraint = JSON.parse(JSON.stringify(sample1_constraints.fixedNodeConstraint));
+      clearConstraintListTable();
+      fillConstraintListTableFromConstraints(); 
+    });
+    initialLayout.run();     
+  },
+  layout: {name: 'preset'},
+  style: defaultStylesheet,
+  elements: {
+        nodes: [
+      {data: {id: 'n1'}},
+      {data: {id: 'n2'}},
+      {data: {id: 'n3', parent: 'n8'}},
+      {data: {id: 'n5'}},
+      {data: {id: 'n6', parent: 'n8'}},
+      {data: {id: 'n7', parent: 'n8'}},
+      {data: {id: 'n8'}},
+      {data: {id: 'f1'}, classes: ['fixed']},
+      {data: {id: 'f2'}, classes: ['fixed']},
+      {data: {id: 'f3', parent: 'n8'}, classes: ['fixed']}, 
+    ],
+    edges: [
+      {data: {source: 'n1', target: 'f1'}},
+      {data: {source: 'n1', target: 'n3'}},
+      {data: {source: 'f1', target: 'n2'}},
+      {data: {source: 'f1', target: 'n3'}},
+      {data: {source: 'n3', target: 'f2'}},
+      {data: {source: 'f2', target: 'n5'}},
+      {data: {source: 'n5', target: 'n8'}},
+      {data: {source: 'n6', target: 'n3'}},
+      {data: {source: 'n6', target: 'n7'}},
+      {data: {source: 'n6', target: 'f3'}}
+    ]
+  },
+  wheelSensitivity: 0.3
+});
+
+let constraints = {
+  fixedNodeConstraint: undefined,
+  alignmentConstraint: undefined,
+  relativePlacementConstraint: undefined
+};
+
+// Handle Menu ------------------------------------------
+
+// Graph file input
+document.getElementById("openFile").addEventListener("click", function () {
+  document.getElementById("inputFile").click();
+});
+
+$("body").on("change", "#inputFile", function (e, fileObject) {
+  var inputFile = this.files[0] || fileObject;
+
+  if (inputFile) {
+    var fileExtension = inputFile.name.split('.').pop();
+    var r = new FileReader();
+    r.onload = function (e) {
+      cy.remove(cy.elements());
+      var content = e.target.result;
+      if (fileExtension == "graphml" || fileExtension == "xml") {
+        cy.graphml({layoutBy: 'null'});
+        cy.graphml(content);
+//        updateGraphStyle();
+      } else if (fileExtension == "json") {
+        cy.json({elements: JSON.parse(content)});
+//        updateGraphStyle();
+      } else {
+        var tsv = cy.tsv();
+        tsv.importTo(content);
+      }
+    };
+    r.addEventListener('loadend', function () {      
+      onLoad();
+      clearConstraintListTable();      
+      constraints.fixedNodeConstraint = undefined;
+      constraints.alignmentConstraint = undefined;
+      constraints.relativePlacementConstraint = undefined;
+      
+      document.getElementById("nodeList").addEventListener("change", function(){
+        document.getElementById("fixedNodeX").value = Math.round(cy.getElementById(document.getElementById("nodeList").value).position("x"));
+        document.getElementById("fixedNodeY").value = Math.round(cy.getElementById(document.getElementById("nodeList").value).position("y"));
+      });
+      
+//      if (inputFile.name == "samples/sample1.graphml") {
+//        cy.nodes().forEach(function (node, i) {
+//          let width = [30, 70, 110];
+//          let size = width[i % 3];
+//          node.css("width", size);
+//          node.css("height", size);
+//        });
+//      }
+       
+    });
+    r.readAsText(inputFile);
+  } else {
+    alert("Failed to load file");
+  }
+  $("#inputFile").val(null);
+});
+
+let updateGraphStyle = function () {
+  cy.nodes().forEach(function (node) {
+    node.style({
+      'background-image': node.data('background-image'),
+      'width': node.data('bbox').w,
+      'height': node.data('bbox').h,
+      "border-width": node.data('border-width'),
+      "border-color": node.data('border-color'),
+      "background-color": node.data('background-color'),
+      "background-opacity": node.data('background-opacity'),
+      "background-fit": "cover",
+      "background-position-x": "50%",
+      "background-position-y": "50%",
+      "text-wrap": "wrap",
+      "font-size": node.data('font-size'),
+      "color": node.data('color')
+    });
+
+    if (node.data('label')) {
+      node.style({
+        'label': node.data('label')
+      });
+    }
+  });
+
+  cy.edges().forEach(function (edge) {
+    edge.style({
+      'width': edge.data('width'),
+      "line-color": edge.data('line-color')
+    });
+  });
+};
+
+$("body").on("change", "#inputConstraint", function (e, fileObject) {
+  var inputFile = this.files[0] || fileObject;
+
+  if (inputFile) {
+    var fileExtension = inputFile.name.split('.').pop();
+    var r = new FileReader();
+    r.onload = function (e) {
+      var content = e.target.result;
+      if (fileExtension == "json") {
+        constraints.fixedNodeConstraint = undefined;
+        constraints.alignmentConstraint = undefined;
+        constraints.relativePlacementConstraint = undefined;        
+        let constraintObject = JSON.parse( content );
+        if(constraintObject.fixedNodeConstraint)
+          constraints.fixedNodeConstraint = constraintObject.fixedNodeConstraint;
+        if(constraintObject.alignmentConstraint)
+          constraints.alignmentConstraint = constraintObject.alignmentConstraint;
+        if(constraintObject.relativePlacementConstraint)
+          constraints.relativePlacementConstraint = constraintObject.relativePlacementConstraint;
+        clearConstraintListTable();
+        fillConstraintListTableFromConstraints();
+      }
+    };
+    r.addEventListener('loadend', function () {          
+    });
+    r.readAsText(inputFile);
+  } else {
+    alert("Failed to load file");
+  }
+  $("#inputFile").val(null);
+});
+
+document.getElementById("exportConstraint").addEventListener("click", function(){
+  let constraintString = JSON.stringify(constraints, null, 2);
+  download('constraint.json', constraintString);
+});
+
+let download = function(filename, text) {
+    var pom = document.createElement('a');
+    pom.setAttribute('href', 'data:text/plain;charset=utf-8,' + encodeURIComponent(text));
+    pom.setAttribute('download', filename);
+
+    if (document.createEvent) {
+        var event = document.createEvent('MouseEvents');
+        event.initEvent('click', true, true);
+        pom.dispatchEvent(event);
+    }
+    else {
+        pom.click();
+    }
+};
+
+/*
+// SVG
+document.getElementById("saveAsSVG").addEventListener("click", function(){
+    let svgContent = cy.svg({scale: 1, full: true});
+    let blob = new Blob([svgContent], {type:"image/svg+xml;charset=utf-8"});
+    saveAs(blob, "graph.svg");
+});
+
+// see http://stackoverflow.com/questions/16245767/creating-a-blob-from-a-base64-string-in-javascript
+let b64toBlob = function(b64Data, contentType, sliceSize) {
+  contentType = contentType || '';
+  sliceSize = sliceSize || 512;
+
+  var byteCharacters = atob(b64Data);
+  var byteArrays = [];
+
+  for (var offset = 0; offset < byteCharacters.length; offset += sliceSize) {
+    var slice = byteCharacters.slice(offset, offset + sliceSize);
+
+    var byteNumbers = new Array(slice.length);
+    for (var i = 0; i < slice.length; i++) {
+      byteNumbers[i] = slice.charCodeAt(i);
+    }
+
+    var byteArray = new Uint8Array(byteNumbers);
+
+    byteArrays.push(byteArray);
+  }
+
+  var blob = new Blob(byteArrays, {type: contentType});
+  return blob;
+}
+*/
+
+// Sample File Changer
+let sampleFileNames = {
+    "sample5" : unix,
+    "sample5_constraints" : unix_constraints,
+    "sample6" : chalk,
+    "sample6_constraints" : chalk_constraints,    
+    "sample7" : uwsn,
+    "sample7_constraints" : uwsn_constraints,
+    "sample8" : call_graph,
+    "sample8_constraints" : callGraph_constraints,
+    "sample9" : wsn,
+    "sample9_constraints" : wsn_constraints,
+};
+
+document.getElementById("sample").addEventListener("change", function(){
+  cy.startBatch();
+  cy.elements().remove();
+  cy.style().clear();
+  
+  var selectionObject = document.getElementById("sample");
+  
+  var selected = selectionObject.options[selectionObject.selectedIndex].index;
+  if(selected == 0){
+    cy.add(elements1);
+    applyPostLoadOperations(selected);
+  }
+  else if(selected == 1){
+    cy.add(elements2);
+    applyPostLoadOperations(selected);
+  }
+  else if(selected == 2){
+    cy.add(elements3);
+    applyPostLoadOperations(selected);
+  }
+  else if(selected == 3){
+    cy.add(elements4);
+    applyPostLoadOperations(selected);
+  }
+  else if(selected == 4){
+    cy.add(elements5);
+    applyPostLoadOperations(selected);
+  }    
+
+  function applyPostLoadOperations(selected){
+    cy.nodes().forEach(function(node){
+      let size = Math.random()*40+30;
+      node.css("width", size);
+      node.css("height", size);   
+    });
+    cy.style(defaultStylesheet);
+    
+    clearConstraintListTable();
+    constraints.fixedNodeConstraint = undefined;
+    constraints.alignmentConstraint = undefined;
+    constraints.relativePlacementConstraint = undefined;
+    
+    if(selected == 0){
+      if(sample1_constraints.fixedNodeConstraint)
+        constraints.fixedNodeConstraint = JSON.parse(JSON.stringify(sample1_constraints.fixedNodeConstraint));
+      clearConstraintListTable();
+      fillConstraintListTableFromConstraints(); 
+    }    
+    if(selected == 1){
+      if(sample2_constraints.alignmentConstraint)
+        constraints.alignmentConstraint = JSON.parse(JSON.stringify(sample2_constraints.alignmentConstraint));
+      clearConstraintListTable();
+      fillConstraintListTableFromConstraints(); 
+    }
+    if(selected == 2){
+      if(sample3_constraints.relativePlacementConstraint)
+        constraints.relativePlacementConstraint = JSON.parse(JSON.stringify(sample3_constraints.relativePlacementConstraint));
+      clearConstraintListTable();
+      fillConstraintListTableFromConstraints(); 
+    }    
+    if(selected == 3){
+      if(sample4_constraints.fixedNodeConstraint)
+        constraints.fixedNodeConstraint = JSON.parse(JSON.stringify(sample4_constraints.fixedNodeConstraint));
+      if(sample4_constraints.alignmentConstraint)
+        constraints.alignmentConstraint = JSON.parse(JSON.stringify(sample4_constraints.alignmentConstraint));
+      if(sample4_constraints.relativePlacementConstraint)
+        constraints.relativePlacementConstraint = JSON.parse(JSON.stringify(sample4_constraints.relativePlacementConstraint));
+      clearConstraintListTable();
+      fillConstraintListTableFromConstraints(); 
+    }     
+  }
+  
+  if (sampleFileNames[selectionObject.value]) {
+    //$.getJSON("samples/" + sampleFileNames[selectionObject.value] + ".json", function(json) {
+        let json = sampleFileNames[selectionObject.value];
+        cy.json(json);
+        cy.nodes().forEach(function (node) {
+          node.style({
+            'width': node.data('bbox').w,
+            'height': node.data('bbox').h,
+            "border-width": node.data('border-width'),
+//            "border-color": node.data('border-color'),
+          });
+
+          if (node.data('class') === 'process' || node.data('class') === 'association' || node.data('class') === "dissociation") {
+            node.style({
+              'background-color': node.data('background-color'),
+              'background-opacity': 0.3
+            });
+          } else {
+            node.style({
+              'background-image': node.data('background-image'),
+//              'background-color': node.data('background-color'),
+              'background-opacity': node.data('background-opacity'),
+              'background-fit': 'contain',
+              'background-position-x': '50%',
+              'background-position-y': '50%',
+            });
+          }
+
+          if (node.data('label')) {
+            node.style({
+              'label': node.data('label'),
+              'text-wrap': 'wrap',
+              'font-size': node.data('font-size'),
+              'color': node.data('color')
+            });
+          }
+        });
+        
+        constraints.fixedNodeConstraint = undefined;
+        constraints.alignmentConstraint = undefined;
+        constraints.relativePlacementConstraint = undefined; 
+        
+        let constraintObject = sampleFileNames[selectionObject.value + "_constraints"];
+        if(constraintObject.fixedNodeConstraint)
+          constraints.fixedNodeConstraint = JSON.parse(JSON.stringify(constraintObject.fixedNodeConstraint));
+        if(constraintObject.alignmentConstraint)
+          constraints.alignmentConstraint = JSON.parse(JSON.stringify(constraintObject.alignmentConstraint));
+        if(constraintObject.relativePlacementConstraint)
+          constraints.relativePlacementConstraint = JSON.parse(JSON.stringify(constraintObject.relativePlacementConstraint));
+        clearConstraintListTable();
+        fillConstraintListTableFromConstraints(); 
+     // });
+
+  }
+  cy.endBatch();
+
+  if(selected == 4){  
+    cy.nodes().not(":parent").positions(function(node, i){
+      return {
+        x: elements5_positions[i].x,
+        y: elements5_positions[i].y
+      };    
+    });
+    cy.layout({name: "preset", fit:true, animate:true, animationDuration: 1000, animationEasing: undefined}).run();
+  }
+  else {
+    let finalOptions = Object.assign({}, options);
+    finalOptions.step = "all";
+    cy.layout(finalOptions).run();
+  }
+//  cy.layout({name: 'random', padding: 100}).run();
+  onLoad();  
+
+  document.getElementById("nodeList").addEventListener("change", function(){
+    document.getElementById("fixedNodeX").value = Math.round(cy.getElementById(document.getElementById("nodeList").value).position("x"));
+    document.getElementById("fixedNodeY").value = Math.round(cy.getElementById(document.getElementById("nodeList").value).position("y"));
+  });
+});
+
+// Layout buttons
+
+let options = {
+  name: 'fcose',
+  quality: "default",
+  randomize: true,
+  animate: true,
+  animationDuration: 1000,
+  animationEasing: undefined,
+  fit: true,
+  padding: 30,
+  nestingFactor: 0.1,
+  gravityRangeCompound: 1.5,
+  gravityCompound: 1.0
+};
+
+// Randomize
+document.getElementById("randomizeButton").addEventListener("click", function () {
+  var layout = cy.layout({
+    name: 'random',
+    animate: true
+  });
+
+  layout.run();
+});
+
+// Fcose
+document.getElementById("fcoseButton").addEventListener("click", function(){
+  let finalOptions = Object.assign({}, options);
+  finalOptions.step = "all";
+  finalOptions.randomize = !(document.getElementById("incremental").checked);
+  
+  if(document.getElementById("sample").value == "sample6"){
+    finalOptions.nestingFactor = 0.4;
+    finalOptions.gravityRangeCompound = 0;
+    finalOptions.gravityCompound = 3.0;
+  }
+  
+  if(document.getElementById("sample").value == "sample8"){
+    finalOptions.idealEdgeLength = 70; 
+  }  
+  
+  finalOptions.fixedNodeConstraint = constraints.fixedNodeConstraint ? constraints.fixedNodeConstraint : undefined;
+  finalOptions.alignmentConstraint = constraints.alignmentConstraint ? constraints.alignmentConstraint : undefined;
+  finalOptions.relativePlacementConstraint = constraints.relativePlacementConstraint ? constraints.relativePlacementConstraint : undefined;
+  let layout = cy.layout(finalOptions);
+  layout.one("layoutstop", function( event ){
+    document.getElementById("fixedNodeX").value = Math.round(cy.getElementById(document.getElementById("nodeList").value).position("x"));
+    document.getElementById("fixedNodeY").value = Math.round(cy.getElementById(document.getElementById("nodeList").value).position("y"));
+  });
+  cy.layoutUtilities("get").setOption("randomize", finalOptions.randomize);
+//  let start = performance.now();
+  layout.run();
+//  console.log((performance.now() - start) + " ms" );
+});
+
+/*
+// CoLa
+document.getElementById("colaButton").addEventListener("click", function(){
+  
+  if(constraints.fixedNodeConstraint) {
+    constraints.fixedNodeConstraint.forEach(function(constraint){
+      cy.getElementById(constraint.nodeId).position({x: constraint.position.x, y: constraint.position.y});
+      cy.getElementById(constraint.nodeId).lock();
+    });
+  }
+  
+  let gapInequalities = [];
+  if(constraints.relativePlacementConstraint) {
+    constraints.relativePlacementConstraint.forEach(function(constraint){
+      if(constraint.left) {
+        gapInequalities.push({"axis": "x", "left": cy.getElementById(constraint.left), "right": cy.getElementById(constraint.right), "gap": constraint.gap});
+      }
+      else {
+        gapInequalities.push({"axis": "y", "left": cy.getElementById(constraint.top), "right": cy.getElementById(constraint.bottom), "gap": constraint.gap});
+      }
+    });
+  }
+  
+  let options = {
+    name: 'cola',
+    animate: false,
+    maxSimulationTime: 20000,
+    randomize: true,
+    unconstrIter: 10, 
+    userConstIter: 15, 
+    allConstIter: 20,
+    handleDisconnected: false,
+    edgeLength: 50,
+    alignment: constraints.alignmentConstraint ? constraints.alignmentConstraint : undefined,
+    gapInequalities: gapInequalities
+  };
+  
+  let layout = cy.layout(options);
+  layout.one("layoutstop", function( event ){
+    document.getElementById("fixedNodeX").value = Math.round(cy.getElementById(document.getElementById("nodeList").value).position("x"));
+    document.getElementById("fixedNodeY").value = Math.round(cy.getElementById(document.getElementById("nodeList").value).position("y"));
+  });
+
+  let start = performance.now();
+  layout.run();
+  console.log((performance.now() - start) + " ms" );
+  
+  cy.nodes().unlock();
+});
+*/
+
+// Draft
+document.getElementById("draftButton").addEventListener("click", function(){
+  let finalOptions = Object.assign({}, options);
+  finalOptions.quality = "draft";
+  finalOptions.fixedNodeConstraint = constraints.fixedNodeConstraint ? constraints.fixedNodeConstraint : undefined;
+  finalOptions.alignmentConstraint = constraints.alignmentConstraint ? constraints.alignmentConstraint : undefined;
+  finalOptions.relativePlacementConstraint = constraints.relativePlacementConstraint ? constraints.relativePlacementConstraint : undefined;  
+  let layout = cy.layout(finalOptions);
+  layout.one("layoutstop", function( event ){
+    document.getElementById("fixedNodeX").value = Math.round(cy.getElementById(document.getElementById("nodeList").value).position("x"));
+    document.getElementById("fixedNodeY").value = Math.round(cy.getElementById(document.getElementById("nodeList").value).position("y"));
+  });
+  cy.layoutUtilities("get").setOption("randomize", true);
+  layout.run();
+});
+
+// Transform
+document.getElementById("transformButton").addEventListener("click", function(){
+  let finalOptions = Object.assign({}, options);
+  finalOptions.step = "transformed";
+  finalOptions.fixedNodeConstraint = constraints.fixedNodeConstraint ? constraints.fixedNodeConstraint : undefined;
+  finalOptions.alignmentConstraint = constraints.alignmentConstraint ? constraints.alignmentConstraint : undefined;
+  finalOptions.relativePlacementConstraint = constraints.relativePlacementConstraint ? constraints.relativePlacementConstraint : undefined;
+  
+  let layout = cy.layout(finalOptions);
+  layout.one("layoutstop", function( event ){
+    document.getElementById("fixedNodeX").value = Math.round(cy.getElementById(document.getElementById("nodeList").value).position("x"));
+    document.getElementById("fixedNodeY").value = Math.round(cy.getElementById(document.getElementById("nodeList").value).position("y"));
+  });            
+  layout.run();
+});
+
+// Enforce
+document.getElementById("enforceButton").addEventListener("click", function(){
+  let finalOptions = Object.assign({}, options);
+  finalOptions.step = "enforced";
+  
+  finalOptions.fixedNodeConstraint = constraints.fixedNodeConstraint ? constraints.fixedNodeConstraint : undefined;
+  finalOptions.alignmentConstraint = constraints.alignmentConstraint ? constraints.alignmentConstraint : undefined;
+  finalOptions.relativePlacementConstraint = constraints.relativePlacementConstraint ? constraints.relativePlacementConstraint : undefined;
+
+  let layout = cy.layout(finalOptions);
+  layout.one("layoutstop", function( event ){
+    document.getElementById("fixedNodeX").value = Math.round(cy.getElementById(document.getElementById("nodeList").value).position("x"));
+    document.getElementById("fixedNodeY").value = Math.round(cy.getElementById(document.getElementById("nodeList").value).position("y"));
+  });            
+  layout.run();
+});
+
+document.getElementById("coseButton").addEventListener("click", function(){
+  let finalOptions = Object.assign({}, options);
+  
+  if(document.getElementById("sample").value == "sample6"){
+    finalOptions.nestingFactor = 0.4;
+    finalOptions.gravityRangeCompound = 0;
+    finalOptions.gravityCompound = 3.0;
+  }
+  
+  if(document.getElementById("sample").value == "sample8"){
+    finalOptions.idealEdgeLength = 70; 
+  }   
+
+  finalOptions.fixedNodeConstraint = constraints.fixedNodeConstraint ? constraints.fixedNodeConstraint : undefined;
+  finalOptions.alignmentConstraint = constraints.alignmentConstraint ? constraints.alignmentConstraint : undefined;
+  finalOptions.relativePlacementConstraint = constraints.relativePlacementConstraint ? constraints.relativePlacementConstraint : undefined;
+  
+  finalOptions.randomize = false;
+  finalOptions.step = "cose";  
+  let layout = cy.layout(finalOptions);
+  layout.one("layoutstop", function( event ){
+    document.getElementById("fixedNodeX").value = Math.round(cy.getElementById(document.getElementById("nodeList").value).position("x"));
+    document.getElementById("fixedNodeY").value = Math.round(cy.getElementById(document.getElementById("nodeList").value).position("y"));
+  });
+  cy.layoutUtilities("get").setOption("randomize", finalOptions.randomize);
+  layout.run();
+});
+
+// Handle Constraints ----------------------------
+
+let onLoad = function(){
+  let nodeList = "<select id='nodeList' class='custom-select custom-select-sm' style='width:auto;' onchange='onSelect()'>";
+  let simpleNodes = cy.nodes().not(":parent");
+  for(let i = 0; i < simpleNodes.length; i++){
+    let node = simpleNodes[i];
+    let label = (node.data('label'))?(node.data('label')):(node.id());
+    if(label.length > 15)
+      label = label.substring(0, 12).concat("...");
+    nodeList += "<option value='" + cy.nodes().not(":parent")[i].id() + "'>" + label + "</option>";
+  }
+  let listComponentForFixed = document.getElementById("nodeListColumn");
+  listComponentForFixed.innerHTML = nodeList;
+  document.getElementById("fixedNodeX").value = Math.round(cy.nodes().not(":parent")[0].position("x"));
+  document.getElementById("fixedNodeY").value = Math.round(cy.nodes().not(":parent")[0].position("y"));
+
+  let nodeListRP1 = "<select id='nodeListRP1' class='custom-select custom-select-sm' style='width:auto;' onchange='onSelectRP1()'>";
+  for(let i = 0; i < simpleNodes.length; i++){
+    let node = simpleNodes[i];
+    let label = (node.data('label'))?(node.data('label')):(node.id()); 
+    if(label.length > 15)
+      label = label.substring(0, 12).concat("...");    
+    nodeListRP1 += "<option value=" + cy.nodes().not(":parent")[i].id() + ">" + label + "</option>";
+  }
+
+  let nodeListRP2 = "<select id='nodeListRP2' class='custom-select custom-select-sm' style='width:auto;' onchange='onSelectRP2()'>";
+  for(let i = 0; i < simpleNodes.length; i++){
+    let node = simpleNodes[i];
+    let label = (node.data('label'))?(node.data('label')):(node.id());
+    if(label.length > 15)
+      label = label.substring(0, 12).concat("...");    
+    nodeListRP2 += "<option value=" + cy.nodes().not(":parent")[i].id() + ">" + label + "</option>";
+  }            
+
+  let listComponentForRP1 = document.getElementById("nodeListColumnRP1");
+  listComponentForRP1.innerHTML = nodeListRP1;
+
+  let listComponentForRP2 = document.getElementById("nodeListColumnRP2");
+  listComponentForRP2.innerHTML = nodeListRP2;            
+};
+
+let onSelect = function(){
+  let id = document.getElementById("nodeList").value;
+  cy.elements().unselect();
+  cy.getElementById(id).select();
+};
+
+let onSelectRP1 = function(){
+  let id = document.getElementById("nodeListRP1").value;
+  cy.elements().unselect();
+  cy.getElementById(id).select();
+};
+
+let onSelectRP2 = function(){
+  let id = document.getElementById("nodeListRP2").value;
+  cy.elements().unselect();
+  cy.getElementById(id).select();
+};
+
+document.addEventListener('DOMContentLoaded', function(){
+  document.getElementById("nodeList").addEventListener("change", function(){
+    document.getElementById("fixedNodeX").value = Math.round(cy.getElementById(document.getElementById("nodeList").value).position("x"));
+    document.getElementById("fixedNodeY").value = Math.round(cy.getElementById(document.getElementById("nodeList").value).position("y"));
+  });
+});
+
+cy.ready( function(event){
+  onLoad();
+});
+
+document.getElementById("nodeList").addEventListener("change", function(){
+  document.getElementById("fixedNodeX").value = Math.round(cy.getElementById(document.getElementById("nodeList").value).position("x"));
+  document.getElementById("fixedNodeY").value = Math.round(cy.getElementById(document.getElementById("nodeList").value).position("y"));
+});
+
+cy.on("position", "node", function(event) {
+  if(event.target.id() == document.getElementById("nodeList").value){
+    document.getElementById("fixedNodeX").value = Math.round(cy.getElementById(document.getElementById("nodeList").value).position("x"));
+    document.getElementById("fixedNodeY").value = Math.round(cy.getElementById(document.getElementById("nodeList").value).position("y"));
+  }
+});
+
+// Adding Constraints
+let constraintListTable = document.getElementById("constraintListTable");
+
+document.getElementById("fixedNode").addEventListener("click",function(){
+  let nodeId = document.getElementById("nodeList").value;
+  let exist = false;
+  if(constraints.fixedNodeConstraint){
+    constraints.fixedNodeConstraint.forEach(function(constraintObject){
+      if(constraintObject.nodeId == nodeId){
+        exist = true;
+      }
+    }); 
+  }
+  if(!exist){
+    let fixedNode = {nodeId: nodeId, position: Object.assign({}, {x: parseInt(document.getElementById("fixedNodeX").value), y: parseInt(document.getElementById("fixedNodeY").value)})};
+    if(constraints.fixedNodeConstraint){
+      constraints.fixedNodeConstraint.push(fixedNode);
+    }
+    else{
+      constraints.fixedNodeConstraint = [fixedNode];
+    }
+      
+    addToHistory("Fixed", [nodeId], fixedNode.position);
+  }
+});
+
+document.getElementById("verticalAlignment").addEventListener("click", function(){
+  if(cy.nodes(":selected").not(":parent").length > 0){
+    let valignArray = [];
+    cy.nodes(":selected").not(":parent").forEach(function(node){
+      valignArray.push(node.id());
+    });
+    if(constraints.alignmentConstraint){
+      if(constraints.alignmentConstraint.vertical){
+        constraints.alignmentConstraint.vertical.push(valignArray);
+      }
+      else{
+        constraints.alignmentConstraint.vertical = [valignArray];
+      }
+    }
+    else{
+      constraints.alignmentConstraint = {};
+      constraints.alignmentConstraint.vertical = [valignArray];
+    }
+    addToHistory("Alignment", valignArray, 'vertical'); 
+  }
+});
+
+document.getElementById("horizontalAlignment").addEventListener("click", function(){
+  if(cy.nodes(":selected").not(":parent").length > 0){
+    let halignArray = [];
+    cy.nodes(":selected").not(":parent").forEach(function(node){
+      halignArray.push(node.id());
+    });
+    if(constraints.alignmentConstraint){
+      if(constraints.alignmentConstraint.horizontal){
+        constraints.alignmentConstraint.horizontal.push(halignArray);
+      }
+      else{
+        constraints.alignmentConstraint.horizontal = [halignArray];
+      }
+    }
+    else{
+      constraints.alignmentConstraint = {};
+      constraints.alignmentConstraint.horizontal = [halignArray];
+    }
+    addToHistory("Alignment", halignArray, 'horizontal'); 
+  }
+});
+
+document.getElementById("relativePlacement").addEventListener("click", function(){
+  let nodeId1 = document.getElementById("nodeListRP1").value;
+  let nodeId2 = document.getElementById("nodeListRP2").value;
+  let isExist = false;
+  if(constraints.relativePlacementConstraint){
+    constraints.relativePlacementConstraint.forEach(function(constraint){
+      if(constraint["left"]){
+        if((constraint["left"] == nodeId1 && constraint["right"] == nodeId2 || constraint["left"] == nodeId2 && constraint["right"] == nodeId1) && document.getElementById("directionList").value == "left-right"){
+          isExist = true;
+        }
+      }
+      else {
+        if((constraint["top"] == nodeId1 && constraint["bottom"] == nodeId2 || constraint["top"] == nodeId2 && constraint["bottom"] == nodeId1) && document.getElementById("directionList").value == "top-bottom"){
+          isExist = true;
+        }
+      }
+    });
+  }
+  if((nodeId1 != nodeId2) && !isExist){
+    let relativePlacementConstraint;
+    if(document.getElementById("directionList").value == "left-right"){
+      relativePlacementConstraint = {left: nodeId1, right: nodeId2, gap: (document.getElementById("gap").value) ? (parseInt(document.getElementById("gap").value)) : undefined};
+    }
+    else{
+      relativePlacementConstraint = {top: nodeId1, bottom: nodeId2, gap: (document.getElementById("gap").value) ? (parseInt(document.getElementById("gap").value)) : undefined};
+    }            
+    if(constraints.relativePlacementConstraint){
+      constraints.relativePlacementConstraint.push(relativePlacementConstraint);
+    }
+    else{
+      constraints.relativePlacementConstraint = [];
+      constraints.relativePlacementConstraint.push(relativePlacementConstraint);
+    }
+    
+    if(document.getElementById("directionList").value == "left-right")
+      addToHistory("Relative", [nodeId1, nodeId2], 'l-r - ' + ((document.getElementById("gap").value) ? (parseInt(document.getElementById("gap").value)) : parseInt(cy.getElementById(nodeId1).width()/2 + cy.getElementById(nodeId2).width()/2 + 50)));
+    else{
+      addToHistory("Relative", [nodeId1, nodeId2], 't-b - ' + ((document.getElementById("gap").value) ? (parseInt(document.getElementById("gap").value)) : parseInt(cy.getElementById(nodeId1).height()/2 + cy.getElementById(nodeId2).height()/2 + 50)));
+    }
+  }
+});
+
+let addToHistory = function( constraintType, nodeIds, constraintInfo) {
+  
+  let row = constraintListTable.insertRow();
+  let cell4 = row.insertCell(0);
+  let cell3 = row.insertCell(0);
+  let cell2 = row.insertCell(0);
+  let cell1 = row.insertCell(0);
+  cell1.innerHTML = constraintType;
+  
+  if(constraintType == 'Fixed'){
+    let label = (cy.getElementById(nodeIds[0]).css('label') ? cy.getElementById(nodeIds[0]).css('label') : nodeIds);
+    if(label.length > 15)
+      label = label.substring(0, 12).concat("...");
+    cell2.innerHTML = label;
+    cell3.innerHTML = "x: "+constraintInfo.x+" y: "+constraintInfo.y;
+  }
+  else if(constraintType == 'Alignment'){
+    let nodeList = "";
+    nodeIds.forEach(function(nodeId, index){
+      let label = (cy.getElementById(nodeId).css('label') ? cy.getElementById(nodeId).css('label') : nodeId);
+      if(label.length > 15)
+        label = label.substring(0, 12).concat("...");      
+      if(index == 0)
+        nodeList += label;
+      else
+        nodeList += ' - ' + label;
+    });
+    cell2.innerHTML = nodeList;
+    cell3.innerHTML = constraintInfo;
+  }
+  else{
+    let nodeList = "";
+    nodeIds.forEach(function(nodeId, index){
+      let label = (cy.getElementById(nodeId).css('label') ? cy.getElementById(nodeId).css('label') : nodeId);
+      if(label.length > 15)
+        label = label.substring(0, 12).concat("...");       
+      if(index == 0)
+        nodeList += label;
+      else
+        nodeList += ' - ' + label;
+    });
+    cell2.innerHTML = nodeList;
+    cell3.innerHTML = constraintInfo;
+  }
+  
+  // needed for highlighting constrained nodes
+  let instance = cy.viewUtilities({
+    highlightStyles: [
+      { node: { 'background-color': '#da14ff', 'border-color': '#980eb2'}, edge: {} }
+    ]
+  });
+
+  let rowToHighlight = $('#constraintListTable').find('tr').eq(row.rowIndex);
+
+  let collectionToHighlight = cy.collection();
+  nodeIds.forEach(function(id){
+    collectionToHighlight = collectionToHighlight.union(cy.getElementById(id));
+  });
+
+  // 'Delete' symbol
+  let button = document.createElement('button');
+  button.setAttribute('class','close');
+  button.setAttribute('aria-label', 'Close');
+  if(constraintType == 'Fixed')
+    button.onclick = function(event){
+      deleteRowElements(row, nodeIds);
+      instance.removeHighlights(collectionToHighlight.nodes());
+    };
+  else if(constraintType == 'Alignment')
+    button.onclick = function(event){
+      deleteRowElements(row, nodeIds, constraintInfo);
+      instance.removeHighlights(collectionToHighlight.nodes());
+    };
+  else
+    button.onclick = function(event){
+      deleteRowElements(row, nodeIds, constraintInfo);
+      instance.removeHighlights(collectionToHighlight.nodes());
+    };
+  let xSymbol = document.createElement('span');
+  xSymbol.setAttribute('aria-hidden', 'true');
+  xSymbol.style.color = "red";
+  xSymbol.innerHTML = '&times';
+  button.appendChild(xSymbol);
+  cell4.appendChild(button);
+  
+  rowToHighlight.hover(function() {
+    instance.highlight(collectionToHighlight.nodes(), 0);
+  }, function() {
+    instance.removeHighlights(collectionToHighlight.nodes());
+  });
+};
+
+// Delete Row Elements
+let deleteRowElements = function (row, nodeIds, info) {
+  let constraintType = row.cells[0].innerHTML;
+  if (constraintType == 'Fixed') {
+    constraints.fixedNodeConstraint.forEach(function (item, index) {
+      if (item.nodeId == nodeIds[0]) {
+        constraints.fixedNodeConstraint.splice(index, 1);
+      }
+    });
+    if (constraints.fixedNodeConstraint.length == 0) {
+      constraints.fixedNodeConstraint = undefined;
+    }
+  } else if (constraintType == 'Alignment') {
+    if (info == 'vertical') {
+      constraints.alignmentConstraint.vertical.forEach(function (item, index) {
+        if (item.length == nodeIds.length) {
+          let equal = true;
+          item.forEach(function (nodeId, i) {
+            if (nodeId != nodeIds[i]) {
+              equal = false;
+            }
+          });
+          if (equal) {
+            constraints.alignmentConstraint.vertical.splice(index, 1);
+            if (constraints.alignmentConstraint.vertical.length == 0) {
+              delete constraints.alignmentConstraint.vertical;
+              if (!constraints.alignmentConstraint.horizontal) {
+                constraints.alignmentConstraint = undefined;
+              }
+            }
+          }
+        }
+      });
+    } else {
+      constraints.alignmentConstraint.horizontal.forEach(function (item, index) {
+        if (item.length == nodeIds.length) {
+          let equal = true;
+          item.forEach(function (nodeId, i) {
+            if (nodeId != nodeIds[i]) {
+              equal = false;
+            }
+          });
+          if (equal) {
+            constraints.alignmentConstraint.horizontal.splice(index, 1);
+            if (constraints.alignmentConstraint.horizontal.length == 0) {
+              delete constraints.alignmentConstraint.horizontal;
+              if (!constraints.alignmentConstraint.vertical) {
+                constraints.alignmentConstraint = undefined;
+              }
+            }
+          }
+        }
+      });
+    }
+  }
+  else{
+    constraints.relativePlacementConstraint.forEach(function(item, index){
+      if(info.substring(0,1) == 'l'){
+        if(item.left && item.left == nodeIds[0] && item.right == nodeIds[1]){
+          constraints.relativePlacementConstraint.splice(index, 1);
+          if(constraints.relativePlacementConstraint.length == 0){
+            constraints.relativePlacementConstraint = undefined;
+          }
+        }
+      }
+      else{
+        if(item.top && item.top == nodeIds[0] && item.bottom == nodeIds[1]){
+          constraints.relativePlacementConstraint.splice(index, 1);
+          if(constraints.relativePlacementConstraint.length == 0){
+            constraints.relativePlacementConstraint = undefined;
+          }          
+        }        
+      }
+    });
+  }
+  constraintListTable.deleteRow(row.rowIndex);
+};
+
+// Clear logs table
+let clearConstraintListTable = function() {
+  if (constraintListTable.rows.length > 1) {
+    let length = constraintListTable.rows.length;
+    for (let i = 0; i < length - 1; i++) {
+      constraintListTable.deleteRow(1);
+    }
+  }
+};
+
+let fillConstraintListTableFromConstraints = function () {
+  if(constraints.fixedNodeConstraint){
+    constraints.fixedNodeConstraint.forEach(function(constraint){
+      addToHistory("Fixed", [constraint.nodeId], constraint.position);
+    });    
+  }
+  if(constraints.alignmentConstraint){
+    if(constraints.alignmentConstraint.vertical){
+      constraints.alignmentConstraint.vertical.forEach(function(item){
+        addToHistory("Alignment", item, 'vertical');
+      });
+    }
+    if(constraints.alignmentConstraint.horizontal){
+      constraints.alignmentConstraint.horizontal.forEach(function(item){
+        addToHistory("Alignment", item, 'horizontal');
+      });
+    }    
+  }
+  if(constraints.relativePlacementConstraint){
+    constraints.relativePlacementConstraint.forEach(function(constraint){
+      if(constraint.left)
+        addToHistory("Relative", [constraint.left, constraint.right], 'l-r - ' + (constraint.gap ? parseInt(constraint.gap) : parseInt(cy.getElementById(constraint.left).width()/2 + cy.getElementById(constraint.right).width()/2 + 50)));
+      else
+        addToHistory("Relative", [constraint.top, constraint.bottom], 't-b - ' + (constraint.gap ? parseInt(constraint.gap) : parseInt(cy.getElementById(constraint.top).height()/2 + cy.getElementById(constraint.bottom).height()/2 + 50)));
+    });
+    
+  }
+};
+
+//// Samples
+let elements1 = {
+  nodes: [
+    {data: {id: 'n1'}},    
+    {data: {id: 'n2'}},
+    {data: {id: 'n3', parent: 'n8'}},
+    {data: {id: 'n5'}},
+    {data: {id: 'n6', parent: 'n8'}},
+    {data: {id: 'n7', parent: 'n8'}},
+    {data: {id: 'n8'}},
+    {data: {id: 'f1'}, classes: ['fixed']},
+    {data: {id: 'f2'}, classes: ['fixed']},
+    {data: {id: 'f3', parent: 'n8'}, classes: ['fixed']}, 
+  ],
+  edges: [
+    {data: {source: 'n1', target: 'f1'}},
+    {data: {source: 'n1', target: 'n3'}},
+    {data: {source: 'f1', target: 'n2'}},
+    {data: {source: 'f1', target: 'n3'}},
+    {data: {source: 'n3', target: 'f2'}},
+    {data: {source: 'f2', target: 'n5'}},
+    {data: {source: 'n5', target: 'n8'}},
+    {data: {source: 'n6', target: 'n3'}},
+    {data: {source: 'n6', target: 'n7'}},
+    {data: {source: 'n6', target: 'f3'}}
+  ]
+};
+
+let elements2 = {
+  nodes: [
+    {data: {id: 'n1', parent: 'n6'}},    
+    {data: {id: 'n2', parent: 'n6'}},    
+    {data: {id: 'n3'}},    
+    {data: {id: 'n4'}},
+    {data: {id: 'n5', parent: 'n8'}},     
+    {data: {id: 'n6'}},
+    {data: {id: 'n7'}},
+    {data: {id: 'n8'}},    
+    {data: {id: 'v1', parent: 'n6'}, classes: ['alignment']},
+    {data: {id: 'v2'}, classes: ['alignment']},    
+    {data: {id: 'v3', parent: 'n8'}, classes: ['alignment']},
+    {data: {id: 'v4', parent: 'n8'}, classes: ['alignment']},
+    {data: {id: 'v5', parent: 'n5'}, classes: ['alignment']},
+    {data: {id: 'h1'}, classes: ['alignment']},
+    {data: {id: 'h2'}, classes: ['alignment']},
+    {data: {id: 'h3'}, classes: ['alignment']},     
+    {data: {id: 'h4', parent: 'n7'}, classes: ['alignment']},
+    {data: {id: 'h5', parent: 'n7'}, classes: ['alignment']},     
+    {data: {id: 'vh1', parent: 'n6'}, classes: ['alignment']},
+    {data: {id: 'vh2', parent: 'n5'}, classes: ['alignment']}
+  ],
+  edges: [
+    {data: {source: 'v1', target: 'vh1'}},
+    {data: {source: 'v1', target: 'n1'}}, 
+    {data: {source: 'n1', target: 'n2'}},    
+    {data: {source: 'n2', target: 'vh1'}},
+    {data: {source: 'n6', target: 'h1'}},
+    {data: {source: 'h1', target: 'h2'}},
+    {data: {source: 'n6', target: 'n3'}},
+    {data: {source: 'n3', target: 'v2'}},
+    {data: {source: 'n3', target: 'h4'}},    
+    {data: {source: 'h4', target: 'h5'}},
+    {data: {source: 'h4', target: 'v3'}},
+    {data: {source: 'v3', target: 'v4'}},
+    {data: {source: 'v3', target: 'n5'}},
+    {data: {source: 'v5', target: 'vh2'}},    
+    {data: {source: 'v3', target: 'n4'}},
+    {data: {source: 'h3', target: 'n8'}},    
+    {data: {source: 'n4', target: 'h3'}}
+  ]
+};
+
+let elements3 = {
+  nodes: [
+    {data: {id: 'r1', parent: 'n8'}, classes: ['relative']},
+    {data: {id: 'r2', parent: 'n8'}, classes: ['relative']},
+    {data: {id: 'r3', parent: 'n8'}, classes: ['relative']},
+    {data: {id: 'r4'}, classes: ['relative']},
+    {data: {id: 'r5'}, classes: ['relative']},
+    {data: {id: 'r6', parent: 'n7'}, classes: ['relative']},
+    {data: {id: 'r7', parent: 'n10'}, classes: ['relative']},    
+    {data: {id: 'r8', parent: 'n10'}, classes: ['relative']},    
+    {data: {id: 'n1', parent: 'n7'}},
+    {data: {id: 'n2'}},
+    {data: {id: 'n3'}},
+    {data: {id: 'n4'}},
+    {data: {id: 'n5'}},
+    {data: {id: 'n6'}},
+    {data: {id: 'n7', parent: 'n10'}},
+    {data: {id: 'n8'}},
+    {data: {id: 'n9'}},
+    {data: {id: 'n10'}}
+  ],
+  edges: [
+    {data: {source: 'r6', target: 'n1'}},
+    {data: {source: 'r6', target: 'n3'}},
+    {data: {source: 'n1', target: 'r8'}},
+    {data: {source: 'n1', target: 'r5'}},
+    {data: {source: 'n1', target: 'r7'}},
+    {data: {source: 'n2', target: 'n3'}},
+    {data: {source: 'n2', target: 'r2'}},
+    {data: {source: 'n2', target: 'n4'}},
+    {data: {source: 'r5', target: 'n5'}},
+    {data: {source: 'r5', target: 'n6'}},
+    {data: {source: 'r2', target: 'r1'}},
+    {data: {source: 'r2', target: 'r3'}},
+    {data: {source: 'n7', target: 'n9'}},
+    {data: {source: 'n5', target: 'n6'}},
+    {data: {source: 'n5', target: 'r4'}}
+  ]
+};
+
+let elements4 = [
+  {group: 'nodes', data: {id: 'n1'}},
+  {group: 'nodes', data: {id: 'n2'}},
+  {group: 'nodes', data: {id: 'n3'}},
+  {group: 'nodes', data: {id: 'n4'}},
+  {group: 'nodes', data: {id: 'n5'}},  
+  {group: 'nodes', data: {id: 'n6', parent: 'n24'}},
+  {group: 'nodes', data: {id: 'n7', parent: 'n24'}},
+  {group: 'nodes', data: {id: 'n8', parent: 'n24'}},
+  {group: 'nodes', data: {id: 'n9'}},
+  {group: 'nodes', data: {id: 'n10', parent: 'n28'}},
+  {group: 'nodes', data: {id: 'n11', parent: 'n28'}},
+  {group: 'nodes', data: {id: 'n12', parent: 'n28'}},
+  {group: 'nodes', data: {id: 'n13', parent: 'n28'}},
+  {group: 'nodes', data: {id: 'n14', parent: 'n28'}},
+  {group: 'nodes', data: {id: 'n15'}},
+  {group: 'nodes', data: {id: 'n16'}},
+  {group: 'nodes', data: {id: 'n17'}},
+  {group: 'nodes', data: {id: 'n18'}},
+  {group: 'nodes', data: {id: 'n19'}},
+  {group: 'nodes', data: {id: 'n20', parent: 'n26'}},
+  {group: 'nodes', data: {id: 'n21', parent: 'n26'}},
+  {group: 'nodes', data: {id: 'n22', parent: 'n27'}},    
+  {group: 'nodes', data: {id: 'n23', parent: 'n25'}},
+  {group: 'nodes', data: {id: 'n24'}},
+  {group: 'nodes', data: {id: 'n25'}},
+  {group: 'nodes', data: {id: 'n26', parent: 'n30'}},
+  {group: 'nodes', data: {id: 'n27', parent: 'n29'}},
+  {group: 'nodes', data: {id: 'n28', parent: 'n29'}},
+  {group: 'nodes', data: {id: 'n29', parent: 'n30'}},
+  {group: 'nodes', data: {id: 'n30'}},
+  {group: 'nodes', data: {id: 'f1', parent: 'n29'}, classes: ['fixed']},
+  {group: 'nodes', data: {id: 'f2', parent: 'n28'}, classes: ['fixed']},  
+  {group: 'nodes', data: {id: 'h1'}, classes: ['alignment']},
+  {group: 'nodes', data: {id: 'h2'}, classes: ['alignment']},
+  {group: 'nodes', data: {id: 'h3'}, classes: ['alignment']},
+  {group: 'nodes', data: {id: 'v1', parent: 'n24'}, classes: ['alignment']},  
+  {group: 'nodes', data: {id: 'v2', parent: 'n25'}, classes: ['alignment']},  
+  {group: 'nodes', data: {id: 'v3'}, classes: ['alignment']},
+  {group: 'nodes', data: {id: 'v4'}, classes: ['alignment']},
+  {group: 'nodes', data: {id: 'h4r'}, classes: ['alignment']},
+  {group: 'nodes', data: {id: 'r1', parent: 'n29'}, classes: ['relative']},  
+  {group: 'nodes', data: {id: 'r2', parent: 'n29'}, classes: ['relative']},
+  {group: 'nodes', data: {id: 'r3'}, classes: ['relative']},
+  {group: 'edges', data: {id: 'e2', source: 'n2', target: 'n3'}},
+  {group: 'edges', data: {id: 'e3', source: 'n1', target: 'n2'}},
+  {group: 'edges', data: {id: 'e4', source: 'n3', target: 'v1'}},
+  {group: 'edges', data: {id: 'e5', source: 'n2', target: 'v1'}},
+  {group: 'edges', data: {id: 'e6', source: 'v1', target: 'n4'}},
+//  {group: 'edges', data: {id: 'e7', source: 'n5', target: 'n6'}},
+  {group: 'edges', data: {id: 'e8', source: 'v1', target: 'n5'}},
+  {group: 'edges', data: {id: 'e9', source: 'v1', target: 'n6'}},
+  {group: 'edges', data: {id: 'e10', source: 'v1', target: 'n7'}},
+//  {group: 'edges', data: {id: 'e11', source: 'n3', target: 'n9'}},
+  {group: 'edges', data: {id: 'e12', source: 'n6', target: 'n8'}},
+  {group: 'edges', data: {id: 'e13', source: 'h1', target: 'n16'}},
+  { group:'edges', data:{ id: 'e14', source: 'v2', target: 'n23'} },
+  {group: 'edges', data: {id: 'e15', source: 'n16', target: 'n15'}},
+  {group: 'edges', data: {id: 'e16', source: 'n16', target: 'h2'}},
+  {group: 'edges', data: {id: 'e17', source: 'n15', target: 'n17'}},
+  {group: 'edges', data: {id: 'e18', source: 'h3', target: 'v3'}},
+  {group: 'edges', data: {id: 'e19', source: 'v3', target: 'n18'}},
+  {group: 'edges', data: {id: 'e20', source: 'n17', target: 'n19'}},
+  {group: 'edges', data: {id: 'e21', source: 'n18', target: 'n19'}},
+  {group: 'edges', data: {id: 'e22', source: 'h2', target: 'n19'}},
+  {group: 'edges', data: {id: 'e23', source: 'n19', target: 'h3'}},
+  {group: 'edges', data: {id: 'e25', source: 'v4', target: 'n20'}},
+  {group: 'edges', data: {id: 'e26', source: 'n20', target: 'n21'}},
+  {group: 'edges', data: {id: 'e27', source: 'n25', target: 'f1'}},
+  {group: 'edges', data: {id: 'e29', source: 'f1', target: 'n26'}},
+  {group: 'edges', data: {id: 'e30', source: 'f1', target: 'r2'}},
+  {group: 'edges', data: {id: 'e31', source: 'f1', target: 'r1'}},
+  {group: 'edges', data: {id: 'e33', source: 'h3', target: 'v2'}},
+  {group: 'edges', data: {id: 'e35', source: 'f2', target: 'n11'}},
+  {group: 'edges', data: {id: 'e36', source: 'f2', target: 'n10'}},
+  {group: 'edges', data: {id: 'e37', source: 'n11', target: 'n10'}},
+  {group: 'edges', data: {id: 'e38', source: 'n12', target: 'n13'}},
+  {group: 'edges', data: {id: 'e39', source: 'n12', target: 'n14'}},
+  {group: 'edges', data: {id: 'e40', source: 'h2', target: 'n27'}},
+  {group: 'edges', data: {id: 'e41', source: 'n9', target: 'r3'}},
+  {group: 'edges', data: {id: 'e42', source: 'n9', target: 'h4r'}},
+  {group: 'edges', data: {id: 'e43', source: 'r3', target: 'h4r'}},
+  {group: 'edges', data: {id: 'e44', source: 'n11', target: 'r3'}},
+  {group: 'edges', data: {id: 'e45', source: 'n14', target: 'r3'}}
+];
+
+let elements5 = {
+  nodes: [
+    {data: {id: 'r1'}, classes: ['relative'], position:{x:318, y:150}},
+    {data: {id: 'r2'}, classes: ['relative'], position:{x:413, y:148}},
+    {data: {id: 'r3'}, classes: ['relative'], position:{x:128, y:-151}},
+    {data: {id: 'r4'}, classes: ['relative'], position:{x:132, y:-38}},   
+    {data: {id: 'f1v', parent: 'n8'}, classes: ['fixed'], position:{x:-79, y:276}},    
+    {data: {id: 'f2h', parent: 'n6'}, classes: ['fixed'], position:{x:96, y:82}},
+    {data: {id: 'v1', parent: 'n5'}, classes: ['alignment'], position:{x:-290, y:153}},
+    {data: {id: 'v2', parent: 'n5'}, classes: ['alignment'], position:{x:-197, y:152}},
+    {data: {id: 'v3', parent: 'n8'}, classes: ['alignment'], position:{x:-85, y:177}},
+    {data: {id: 'h1', parent: 'n7'}, classes: ['alignment'], position:{x:1, y:-9}},
+    {data: {id: 'h2', parent: 'n7'}, classes: ['alignment'], position:{x:0, y:-104}},
+    {data: {id: 'n0', parent: 'n6'}, position:{x:186, y:219}},
+    {data: {id: 'n1', parent: 'n6'}, position:{x:197, y:122}},
+    {data: {id: 'n2', parent: 'n6'}, position:{x:93, y:186}},
+    {data: {id: 'n3'}, position:{x:-267, y:20}},
+    {data: {id: 'n4'}, position:{x:-167, y:-10}},
+    {data: {id: 'n5', parent: 'n8'}},
+    {data: {id: 'n6'}},
+    {data: {id: 'n7'}},
+    {data: {id: 'n8'}}    
+  ],
+  edges: [
+    {data: {source: 'n0', target: 'n1'}},
+    {data: {source: 'n0', target: 'n2'}},
+    {data: {source: 'n6', target: 'r1'}},
+    {data: {source: 'n1', target: 'f2h'}},
+    {data: {source: 'r1', target: 'r2'}},
+    {data: {source: 'n2', target: 'f2h'}},
+    {data: {source: 'n6', target: 'r4'}},
+    {data: {source: 'n3', target: 'n4'}},
+    {data: {source: 'n3', target: 'n8'}},
+    {data: {source: 'n4', target: 'v3'}},
+    {data: {source: 'r4', target: 'h1'}},
+    {data: {source: 'r4', target: 'r3'}},
+    {data: {source: 'h1', target: 'h2'}},
+    {data: {source: 'v1', target: 'v2'}},
+    {data: {source: 'v3', target: 'n5'}},
+    {data: {source: 'h1', target: 'v3'}},
+    {data: {source: 'v3', target: 'f1v'}}
+  ]
+};
+
+let elements5_positions = [
+  {x:318, y:150}, 
+  {x:413, y:148},
+  {x:128, y:-151},
+  {x:132, y:-38},
+  {x:-79, y:276},
+  {x:96, y:82},
+  {x:-290, y:153},
+  {x:-197, y:152},
+  {x:-85, y:177},
+  {x:1, y:-9},
+  {x:0, y:-104},
+  {x:186, y:219},
+  {x:197, y:122},
+  {x:93, y:186},
+  {x:-267, y:20},
+  {x:-167, y:-10},
+  {x:318, y:150},
+  {x:318, y:150}
+];
+
+let sample1_constraints = {
+  "fixedNodeConstraint": [
+    {
+      "nodeId": "f1",
+      "position": {
+        "x": -150,
+        "y": -100
+      }
+    },
+    {
+      "nodeId": "f2",
+      "position": {
+        "x": -50,
+        "y": -150
+      }
+    },
+    {
+      "nodeId": "f3",
+      "position": {
+        "x": 100,
+        "y": 150
+      }
+    }
+  ]
+};
+
+let sample2_constraints = {
+  "alignmentConstraint": {
+    "vertical": [
+      [
+        "v1",
+        "v2",
+        "vh1"
+      ],
+      [
+        "v3",
+        "v4",
+        "v5",
+        "vh2"
+      ]
+    ],
+    "horizontal": [
+      [
+        "h1",
+        "h2",
+        "h3"
+      ],
+      [
+        "h4",
+        "h5",
+        "vh1",
+        "vh2"
+      ]
+    ]
+  }
+};
+
+let sample3_constraints = {
+  "relativePlacementConstraint": [
+    {
+      "left": "r1",
+      "right": "r2",
+      "gap": 100
+    },
+    {
+      "top": "r1",
+      "bottom": "r2",
+      "gap": 100
+    },
+    {
+      "left": "r2",
+      "right": "r3",
+      "gap": 200
+    },
+    {
+      "top": "r4",
+      "bottom": "r5",
+      "gap": 150
+    },
+    {
+      "left": "r6",
+      "right": "r7",
+      "gap": 150
+    },
+    {
+      "top": "r8",
+      "bottom": "r7",
+      "gap": 100
+    }
+  ]
+};
+
+let sample4_constraints = {
+  "fixedNodeConstraint": [
+    {
+      "nodeId": "f1",
+      "position": {
+        "x": -100,
+        "y": 0
+      }
+    },
+    {
+      "nodeId": "f2",
+      "position": {
+        "x": 300,
+        "y": 0
+      }
+    }
+  ],
+  "alignmentConstraint": {
+    "horizontal": [
+      [
+        "h1",
+        "h2",
+        "h3",
+        "h4r"
+      ]
+    ],
+    "vertical": [
+      [
+        "v1",
+        "v2",
+        "v3",
+        "v4"        
+      ]
+    ]
+  },
+  "relativePlacementConstraint": [
+    {
+      "top": "r1",
+      "bottom": "r2",
+      "gap": 150
+    },    
+    {
+      "left": "r3",
+      "right": "h4r",
+      "gap": 150
+    }
+  ]
+}; 

tools/ui/node_modules/cytoscape-fcose/demo/demo-constraint.html

@@ -0,0 +1,345 @@
+<!DOCTYPE>
+
+<html>
+
+  <head>
+    <title>cytoscape-fcose.js demo</title>
+
+      <meta name="viewport" content="width=device-width, user-scalable=no, initial-scale=1, maximum-scale=1">
+      
+      <!-- Bootstrap, popper, jQuery and filesaver - for demo purpose only -->
+      <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.4.1/jquery.min.js"></script>
+      <script src="https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.11.0/umd/popper.min.js"></script>
+      <script src="https://stackpath.bootstrapcdn.com/bootstrap/4.3.1/js/bootstrap.min.js"></script>
+      <script src="https://raw.githack.com/eligrey/FileSaver.js/master/dist/FileSaver.min.js"></script>      
+      <link href="https://stackpath.bootstrapcdn.com/bootstrap/4.3.1/css/bootstrap.min.css" rel="stylesheet">
+      
+      <!-- Cytoscape and fcose -->
+      <script src="https://unpkg.com/cytoscape/dist/cytoscape.min.js"></script>
+      <script src="https://unpkg.com/layout-base/layout-base.js"></script> 
+      <script src="https://unpkg.com/cose-base/cose-base.js"></script>
+      <script src="../cytoscape-fcose.js"></script>
+      
+      <script src="demo-constraint-control.js" defer></script>
+      
+      <!-- CoLa for local comparison only -->
+      <!-- <script src="https://unpkg.com/webcola/WebCola/cola.min.js"></script> -->
+      <!-- <script src="cytoscape-cola.js"></script> -->      
+      
+      <script src="https://unpkg.com/cytoscape-layout-utilities/cytoscape-layout-utilities.js"></script>
+      <script src="https://unpkg.com/cytoscape-view-utilities/cytoscape-view-utilities.js"></script>
+      <script src="https://unpkg.com/cytoscape-graphml/cytoscape-graphml.js"></script>  <!-- graphml - for demo purpose only--> 	
+      <!-- <script src="https://raw.githack.com/iVis-at-Bilkent/cytoscape.js-layvo/unstable/cytoscape-layvo.js"></script> -->  <!-- For quality metrics -->
+      <!-- <script src="https://raw.githack.com/kinimesi/cytoscape-svg/master/cytoscape-svg.js"></script> --> <!-- For svg export -->
+      
+      <!-- We use a workaround here to be able to debug real world files in local by keeping json content as js variable. -->
+      <script type="text/javascript" src="samples/unix.js"></script>
+      <script type="text/javascript" src="samples/unix_constraints.js"></script>
+      <script type="text/javascript" src="samples/chalk.js"></script>
+      <script type="text/javascript" src="samples/chalk_constraints.js"></script>      
+      <script type="text/javascript" src="samples/uwsn.js"></script>
+      <script type="text/javascript" src="samples/uwsn_constraints.js"></script>
+      <script type="text/javascript" src="samples/callGraph.js"></script>
+      <script type="text/javascript" src="samples/callGraph_constraints.js"></script>
+      <script type="text/javascript" src="samples/wsn.js"></script>
+      <script type="text/javascript" src="samples/wsn_constraints.js"></script>
+
+      <style>
+        body {
+          font-family: helvetica neue, helvetica, liberation sans, arial, sans-serif;
+          font-size: 13px;
+        }
+
+        #cy {
+          position: relative;
+          width: auto;
+          height: 95%;
+          z-index: 999;
+          margin-left: 375px;
+          right: 0px;
+        }
+
+        h1 {
+          opacity: 1;
+          color: #555;
+          font-size: 15px;
+          font-weight: bold;
+          padding-top: 5px;
+        }
+        
+        hr.line {
+            margin-top: 9px;
+            margin-bottom: 9px
+        }        
+                
+        /* The sidepanel menu */
+        .sidepanel {
+          height: auto; /* Specify a height */
+          width: 375px; /* 0 width - change this with JavaScript */
+          position: absolute; /* Stay in place */
+          z-index: 1000; /* Stay on top */
+          float: left;
+          top: auto;
+          left: 0;
+          background-color: #d9fbff;
+          overflow-x: hidden; /* Disable horizontal scroll */
+          padding-top: 10px; /* Place content 10px from the top */
+          padding-bottom: 10px; /* Place content 10px from the bottom */
+          transition: 0s; /* 0.5 second transition effect to slide in the sidepanel */
+        }
+
+        table{
+          margin-left: 8;
+          margin-right: 10;
+          width: 360px;
+        }       
+        
+        /* The sidepanel links */
+        table td {
+          padding: 4px 4px 4px 0px;
+          text-decoration: none;
+          font-size: 14px;
+          color: #555;
+          transition: 0.3s;
+          text-align: left;
+        }
+
+        .layoutButton {
+          color: #555;
+          cursor: pointer;
+          background-color: #b7ffff;
+          padding: 5px 10px;
+          border: none;
+          margin-bottom: 5px;
+        }
+
+        .constraintButton {
+          cursor: pointer;
+          padding: 2px 5px;
+          background-color: #64ffee;
+          border-radius: 3px;
+          border-width: 1px;
+        }
+        
+        .constraintButtonLarge {
+          cursor: pointer;
+          padding: 5px;
+          background-color: #64ffee;
+          border-radius: 3px;
+          border-width: 1px;         
+        }
+        
+        .btn-group-sm>.btn, .btn-sm { 
+          font-size: 13px;
+          background-color: #7d8991;
+          border-color: #7d8991;
+        }
+        
+        .btn-primary:hover, .btn-primary:focus, .btn-primary:active, .btn-primary.active, .open>.dropdown-toggle.btn-primary {
+            color: #fff;
+            background-color: #60717d;
+            border-color: #60717d; /*set the color you want here*/
+        }  
+        
+        .btn-outline-primary:hover, .btn-outline-primary:focus, .btn-outline-primary:active, .btn-outline-primary.active, .open>.dropdown-toggle.btn-primary {
+            color: #fff;
+            background-color: #60717d;
+            border-color: #60717d; /*set the color you want here*/
+        }        
+        
+        .btn-outline-primary{ 
+          font-size: 13px;
+          background-color: #ffffff;
+          color: #7d8991;
+        }        
+        
+        .form-control-sm { 
+          font-size: 13px
+        } 
+
+        .custom-select-sm {
+          font-size: 13px
+        }        
+        
+        .textField {
+          padding-left: 5px;
+        }
+        
+        .checkbox {
+          margin-left: 0px;
+        }        
+
+        .button:hover {
+          background-color: #0f0;
+        }
+        
+        .custom-control-label {
+          padding-top: 2px;
+        }
+        
+        .custom-control-input:checked~.custom-control-label::before {
+            color: #fff;
+            border-color: #7d8991;
+            background-color: #7d8991;
+        }        
+        
+      </style>
+  </head>
+  <body>
+    <h1 class="ml-2">cytoscape-fcose demo (constraint)</h1>
+      <div style='width: 375px; position: absolute;'>          
+        <!-- File menu-->
+        <input id="inputFile" type='file' style="display: none" />
+        <input type="button" id="openFile" type="button" class="btn btn-primary btn-sm ml-2" data-toggle="tooltip" title="Load graphml file" value="Load Graph"/>&nbsp
+        <select id="sample" class="custom-select custom-select-sm ml-2" style="width:auto;">
+          <option value="sample1" selected="">sample1 - fixed</option>
+          <option value="sample2">sample2 - alignment</option>
+          <option value="sample3">sample3 - relative</option>
+          <option value="sample4">sample4 - hybrid</option>
+          <option value="sample4">sample5</option>
+          <option value="sample5">unix-family-tree</option>
+          <option value="sample6">chalk-dependency</option>              
+          <option value="sample7">UW-sensor-network</option>
+          <option value="sample8">python-call-graph</option>
+          <option value="sample9">wireless-sensor-network</option>          
+        </select>
+        <!-- File Menu End -->
+
+        <hr class="line">
+
+        <!-- Layout Menu-->
+        <button id="randomizeButton" class="btn btn-primary btn-sm mb-2 ml-2">Randomize</button>&nbsp
+        <button id="fcoseButton" class="btn btn-primary btn-sm mb-2">fCoSE</button>&nbsp
+    <!--    <button id="colaButton" class="btn btn-primary btn-sm mb-2">CoLa</button>&nbsp -->
+        <div class="custom-control custom-control-inline custom-checkbox">
+          <input type="checkbox" class="custom-control-input" id="incremental" name="incremental">
+          <label class="custom-control-label" for="incremental">Incremental</label>
+        </div><br>
+        <button id="draftButton" class="btn btn-outline-primary btn-sm ml-2">Draft</button>&nbsp
+        <button id="transformButton" class="btn btn-outline-primary btn-sm">Transform</button>&nbsp
+        <button id="enforceButton" class="btn btn-outline-primary btn-sm">Enforce</button>&nbsp
+        <button id="coseButton" class="btn btn-outline-primary btn-sm">CoSE</button><br>
+        <!-- Layout Menu End-->
+
+        <hr class="line">
+        <div id="mySidepanel" class="sidepanel">
+        <!-- Constraints Menu -->
+        <table id="ConstraintIOTable">
+          <tr>
+            <td style = "width: 25%"><h7 class="card-subtitle mt-1 text-muted"><b>Constraints</b></h7></td>
+            <td><button id="importConstraint" type="button" class="btn btn-primary btn-sm ml-1" onclick="document.getElementById('inputConstraint').click();" data-toggle="tooltip" title="Import constraint file">Import</button>
+              <input id="inputConstraint" type='file' style="display: none" /></td> 
+            <td><button id="exportConstraint" type="button" class="btn btn-primary btn-sm" data-toggle="tooltip" title="Export constraint file">Export</button></td> 
+            <td style = "width: 35%"></td>
+          </tr>
+        </table>
+        
+        <hr class="line">
+        
+        <!-- <button id="saveAsSVG" type="button" class="layoutButton" data-toggle="tooltip" title="Save graph as SVG file">Save as SVG</button> -->                      
+          <!-- Fixed Node Constraints -->
+          <form>
+            <div class="form-row">
+              <div class="form-group col-md-12 mb-2">
+                <h7 class="card-subtitle ml-2 mt-1 text-muted"><b>Fixed Node Constraint</b></h7>
+              </div>
+            </div>
+            <div class="form-row form-inline">
+              <div id="nodeListColumn" class="form-group col-md-4 ml-2 mr-3">
+              </div>
+              <div class="form-group col-md-5">
+                <label>x : </label>
+                <input type="text" class="form-control form-control-sm w-25 ml-1 mr-1" style="display:flex; flex-grow:1" id="fixedNodeX" value="">
+                <label>y : </label>
+                <input type="text" class="form-control form-control-sm w-25 ml-1 mr-1" style="display:flex; flex-grow:1" id="fixedNodeY" value=""> 
+              </div>
+              <div class="form-group col-md-2">
+                <input type="button" id="fixedNode" class="btn btn-primary btn-sm" value="Add"/>
+              </div>
+            </div>                
+          </form>
+
+          <hr class="line">
+
+          <!-- Alignment Constraints -->
+          <form>
+            <div class="form-row">
+              <div class="form-group col-md-12 mb-2">
+                <h7 class="card-subtitle ml-2 mt-1 text-muted"><b>Alignment Constraint</b></h7>
+              </div>
+            </div>
+            <div class="form-row form-inline mb-2">
+              <div class="form-group col-md-8">
+                <h7 class="card-subtitle ml-2 mt-1 text-muted">Selected Nodes Vertically</h7>
+              </div>
+              <div class="form-group col-md-3">
+                <input type="button" id="verticalAlignment" class="btn btn-primary btn-sm" value="Add"/>
+              </div>
+            </div>
+            <div class="form-row form-inline">
+              <div class="form-group col-md-8">
+                <h7 class="card-subtitle ml-2 mt-1 text-muted">Selected Nodes Horizontally</h7>
+              </div>
+              <div class="form-group col-md-3">
+                <input type="button" id="horizontalAlignment" class="btn btn-primary btn-sm" value="Add"/>
+              </div>
+            </div>
+            <div class="form-row">
+              <div class="form-group col-md-12 mt-2 mb-0">
+                <span style="margin-left: 9px; font-size: 12px">Click on a node for selecting. Shift + click for extending selection.</span>
+              </div>
+            </div>            
+          </form>
+
+          <hr class="line">
+
+          <!-- Relative Placement Constraints -->
+          <form>
+            <div class="form-row">
+              <div class="form-group col-md-12 mb-2">
+                <h7 class="card-subtitle ml-2 mt-1 text-muted"><b>Relative Placement Constraint</b></h7>
+              </div>
+            </div>
+            <div class="form-row form-inline">
+              <div id="nodeListColumnRP1" class="form-group col-md-12 ml-2 mb-2"></div>
+            </div>
+            <div class="form-row form-inline mb-2">
+              <div class="form-group col-md-4">
+                <select id="directionList" class='custom-select custom-select-sm ml-2' style='width:auto;'>
+                  <option value="left-right">left-right</option>
+                  <option value="top-bottom">top-bottom</option>
+                </select>
+              </div>
+              <div class="form-group col-md-4">
+                <label>Gap: </label>
+                <input type="text" class="form-control form-control-sm w-50 ml-1" id="gap" value="">
+              </div>
+              <div class="form-group col-md-2">
+                <input type="button" id="relativePlacement" class="btn btn-primary btn-sm" value="Add"/>
+              </div>
+            </div>
+            <div class="form-row form-inline mb-2">
+              <div id="nodeListColumnRP2" class="form-group col-md-12 ml-2"></div>
+            </div>
+          </form>              
+
+          <hr class="line">
+
+          <table id="constraintListTable" class="table-striped">
+            <div class="form-group col-md-12 mt-1 mb-1" style="padding-left: 9px">
+              <span style="font-size: 12px">Hover a constraint row to see involved nodes.</span>
+            </div>            
+            <tr>
+              <th style="font-size: 0.9em; text-align: left; width:25%">Type</th>
+              <th style="font-size: 0.9em; text-align: left; width:40%">Nodes</th>
+              <th style="font-size: 0.9em; text-align: left;">Info</th>
+              <th style="font-size: 0.9em; text-align: left;"></th>
+            </tr>
+          </table>              
+        </div>
+        <!-- Constraints Menu End-->
+      </div>
+      <div id="cy"></div>
+  </body>
+
+</html>

tools/ui/node_modules/cytoscape-fcose/demo/demo.html

@@ -0,0 +1,457 @@
+<!DOCTYPE>
+
+<html>
+
+  <head>
+    <title>cytoscape-fcose.js demo</title>
+
+      <meta name="viewport" content="width=device-width, user-scalable=no, initial-scale=1, maximum-scale=1">
+      
+      <!-- Bootstrap, popper, jQuery and filesaver - for demo purpose only -->
+      <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.4.1/jquery.min.js"></script>
+      <script src="https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.11.0/umd/popper.min.js"></script>
+      <script src="https://stackpath.bootstrapcdn.com/bootstrap/4.3.1/js/bootstrap.min.js"></script>      
+      <link href="https://stackpath.bootstrapcdn.com/bootstrap/4.3.1/css/bootstrap.min.css" rel="stylesheet">      
+
+      <script src="https://unpkg.com/cytoscape/dist/cytoscape.min.js"></script>
+      <script src="https://unpkg.com/layout-base/layout-base.js"></script>
+      <script src="https://unpkg.com/cose-base/cose-base.js"></script>
+      <script src="https://unpkg.com/cytoscape-layout-utilities/cytoscape-layout-utilities.js"></script>
+
+      <!-- for testing with local version of cytoscape.js -->
+      <!--<script src="../cytoscape.js/build/cytoscape.js"></script>-->
+
+      <script src="../cytoscape-fcose.js"></script>
+
+      <style>
+        body {
+          font-family: helvetica neue, helvetica, liberation sans, arial, sans-serif;
+          font-size: 14px;
+        }
+
+        #cy {
+          position: relative;
+          width: auto;
+          height: 90%;
+          z-index: 999;
+          margin-left: 290px;
+          right: 0px;
+        }
+
+        h1 {
+          opacity: 1;
+          color: #555;
+          font-size: 15px;
+          font-weight: bold;
+          padding-top: 5px;
+        }        
+        
+        /* The sidepanel menu */
+        .sidepanel {
+          height: auto; /* Specify a height */
+          width: 290px; /* 0 width - change this with JavaScript */
+          position: absolute; /* Stay in place */
+          z-index: 1000; /* Stay on top */
+          float: left;
+          top: auto;
+          left: 0;
+          background-color: #b7ffff; /* Black*/
+          overflow-x: hidden; /* Disable horizontal scroll */
+          padding-top: 10px; /* Place content 10px from the top */
+          padding-bottom: 10px; /* Place content 10px from the bottom */
+          transition: 0s; /* 0.5 second transition effect to slide in the sidepanel */
+        }
+
+        table{
+          margin-left: 4px;
+          margin-right: auto;
+          table-layout: fixed;
+        }       
+        
+        /* The sidepanel links */
+        table td {
+          padding: 0px 8px 8px 8px;
+          text-decoration: none;
+          font-size: 13px;
+          color: #555;
+          transition: 0.3s;
+          vertical-align: middle;
+        }
+        
+        /* Style the button that is used to open the sidepanel */
+        .button {
+          font-size: 15px;
+          color: #555;
+          cursor: pointer;
+          background-color: #b7ffff;
+          padding: 5px 10px;
+          border: none;
+          margin-bottom: 5px;
+        }
+        
+        .textField {
+          padding-left: 5px;
+        }
+        
+        .checkbox {
+          margin-left: 0px;
+        }        
+
+        .button:hover {
+          background-color: #0f0;
+        }
+        
+        .btn-group-sm>.btn, .btn-sm { 
+          font-size: 13px;
+          background-color: #7d8991;
+          border-color: #7d8991;
+        }
+        
+        .btn-primary:hover, .btn-primary:focus, .btn-primary:active, .btn-primary.active, .open>.dropdown-toggle.btn-primary {
+            color: #fff;
+            background-color: #60717d;
+            border-color: #60717d; /*set the color you want here*/
+        }  
+        
+        .btn-outline-primary:hover, .btn-outline-primary:focus, .btn-outline-primary:active, .btn-outline-primary.active, .open>.dropdown-toggle.btn-primary {
+            color: #fff;
+            background-color: #60717d;
+            border-color: #60717d; /*set the color you want here*/
+        }        
+        
+        .form-control-sm { 
+          font-size: 13px
+        }
+
+        .custom-select-sm {
+          font-size: 13px
+        }
+
+        .custom-control-label {
+          padding-top: 2px;
+        }
+        
+        .custom-control-input:checked~.custom-control-label::before {
+            color: #fff;
+            border-color: #7d8991;
+            background-color: #7d8991;
+        }         
+      </style>
+
+      <script>
+        document.addEventListener('DOMContentLoaded', function(){
+
+          var cy = window.cy = cytoscape({
+            container: document.getElementById('cy'),
+            
+            ready: function(){
+              let layoutUtilities = this.layoutUtilities({
+                desiredAspectRatio: this.width()/this.height()
+              });
+              this.nodes().forEach(function(node){
+                let size = Math.random()*120+30;
+                node.css("width", size);
+                node.css("height", size);
+              });
+              this.layout({name: 'fcose'}).run();
+            },          
+
+            style: [
+              {
+                selector: 'node',
+                style: {
+                  'background-color': '#2B65EC'
+                }
+              },
+
+              {
+                selector: 'edge',
+                style: {
+                  'width': 3,
+                  'line-color': '#2B65EC'
+                }
+              },
+                            
+              {
+                selector: 'node:selected',
+                style: {
+                  'background-color': '#F08080',
+                  'border-color': 'red'
+                }
+              },
+              
+              {
+                selector: 'edge:selected',
+                style: {
+                  'line-color': '#F08080'
+                }
+              }                 
+            ], 
+
+          elements: [{"data":{"id":"glyph9","position":{"x":1452.639173965406,"y":609.3619416544145},"group":"nodes"}},
+            {"data":{"id":"glyph0","position":{"x":1351.3490293961959,"y":518.9529901384763},"group":"nodes"}},
+            {"data":{"id":"glyph6","position":{"x":1358.2854747390154,"y":707.9866590968695},"group":"nodes"}},
+            {"data":{"id":"glyph8","position":{"x":1322.9939787691299,"y":614.6878118623499},"group":"nodes"}},
+            {"data":{"id":"glyph7","position":{"x":1239.4852011317887,"y":543.2369849876238},"group":"nodes"}},
+            {"data":{"id":"glyph12","position":{"x":841.6855140740067,"y":765.0152660242113},"group":"nodes"}},
+            {"data":{"id":"glyph13","position":{"x":1019.5908382748769,"y":841.6087025848726},"group":"nodes"}},
+            {"data":{"id":"glyph1","position":{"x":1231.2768042260652,"y":673.2683218469676},"group":"nodes"}},
+            {"data":{"id":"glyph2","position":{"x":1039.8995038336504,"y":730.180116446269},"group":"nodes"}},
+            {"data":{"id":"glyph15","position":{"x":569.5498472077387,"y":506.89980858075364},"group":"nodes"}},
+            {"data":{"id":"glyph3","position":{"x":903.0347368937041,"y":654.3308627056822},"group":"nodes"}},
+            {"data":{"id":"glyph17","position":{"x":1195.6310733031135,"y":820.9504141631944},"group":"nodes"}},
+            {"data":{"id":"glyph10","position":{"x":1141.2404374322139,"y":732.3190922346248},"group":"nodes"}},
+            {"data":{"id":"glyph19","position":{"x":893.1427762830865,"y":856.2695126662625},"group":"nodes"}},
+            {"data":{"id":"glyph11","position":{"x":939.3335184518824,"y":758.3699048922733},"group":"nodes"}},
+            {"data":{"id":"glyph18","position":{"x":770.4114528170364,"y":659.2220219290564},"group":"nodes"}},
+            {"data":{"id":"glyph16","position":{"x":818.0111009023315,"y":564.8072603606723},"group":"nodes"}},
+            {"data":{"id":"glyph22","position":{"x":651.1292498357636,"y":314.1387423188818},"group":"nodes"}},
+            {"data":{"id":"glyph4","position":{"x":792.0076145303351,"y":454.0225025614517},"group":"nodes"}},
+            {"data":{"id":"glyph23","position":{"x":704.0937009722281,"y":398.0421081673902},"group":"nodes"}},
+            {"data":{"id":"glyph24","position":{"x":809.2974819306742,"y":231.7141323534711},"group":"nodes"}},
+            {"data":{"id":"glyph25","position":{"x":890.826951363933,"y":299.74915938409947},"group":"nodes"}},
+            {"data":{"id":"glyph20","position":{"x":786.2625869125006,"y":331.67766378118495},"group":"nodes"}},
+            {"data":{"id":"glyph26","position":{"x":879.2981049664311,"y":389.27232563593486},"group":"nodes"}},
+            {"data":{"id":"glyph35","position":{"x":627.088268638501,"y":40.089848876876886},"group":"nodes"}},
+            {"data":{"id":"glyph36","position":{"x":329.6761506918384,"y":187.20503497360494},"group":"nodes"}},
+            {"data":{"id":"glyph37","position":{"x":155.12947729633356,"y":379.5263531900425},"group":"nodes"}},
+            {"data":{"id":"glyph38","position":{"x":70.13952165372024,"y":581.2691021233562},"group":"nodes"}},
+            {"data":{"id":"glyph21","position":{"x":713.4639263718316,"y":229.06355211274115},"group":"nodes"}},
+            {"data":{"id":"glyph42","position":{"x":523.848994074475,"y":108.47701882803744},"group":"nodes"}},
+            {"data":{"id":"glyph41","position":{"x":718.966532806447,"y":116.46683749236911},"group":"nodes"}},
+            {"data":{"id":"glyph31","position":{"x":621.3138039842713,"y":145.7168752444793},"group":"nodes"}},
+            {"data":{"id":"glyph27","position":{"x":525.2099120385327,"y":210.92542274858295},"group":"nodes"}},
+            {"data":{"id":"glyph32","position":{"x":426.3492127437995,"y":257.85665030680025},"group":"nodes"}},
+            {"data":{"id":"glyph28","position":{"x":346.30926488002945,"y":344.4562152937847},"group":"nodes"}},
+            {"data":{"id":"glyph43","position":{"x":363.54724181648487,"y":486.5705174517715},"group":"nodes"}},
+            {"data":{"id":"glyph33","position":{"x":269.87972487503066,"y":430.2423722580144},"group":"nodes"}},
+            {"data":{"id":"glyph29","position":{"x":227.86139816113416,"y":531.824141876398},"group":"nodes"}},
+            {"data":{"id":"glyph39","position":{"x":104.77693104995387,"y":691.8382969303054},"group":"nodes"}},
+            {"data":{"id":"glyph40","position":{"x":292.039416141131,"y":643.4009391289965},"group":"nodes"}},
+            {"data":{"id":"glyph34","position":{"x":193.8304385062596,"y":632.9540034207419},"group":"nodes"}},
+            {"data":{"id":"glyph30","position":{"x":205.4745704273754,"y":733.5181650652648},"group":"nodes"}},
+            {"data":{"id":"glyph14","position":{"x":695.1248473196924,"y":482.8828321494848},"group":"nodes"}},
+            {"data":{"id":"glyph5","position":{"x":721.6687687330186,"y":570.3868893775194},"group":"nodes"}},
+            {"data":{"id":"e22","source":"glyph9","target":"glyph8","group":"edges"}},
+            {"data":{"id":"e23","source":"glyph0","target":"glyph8","group":"edges"}},
+            {"data":{"id":"e24","source":"glyph8","target":"glyph1","group":"edges"}},
+            {"data":{"id":"e25","source":"glyph6","target":"glyph8","group":"edges"}},
+            {"data":{"id":"e26","source":"glyph8","target":"glyph7","group":"edges"}},
+            {"data":{"id":"e27","source":"glyph11","target":"glyph12","group":"edges"}},
+            {"data":{"id":"e28","source":"glyph13","target":"glyph11","group":"edges"}},
+            {"data":{"id":"e29","source":"glyph1","target":"glyph10","group":"edges"}},
+            {"data":{"id":"e30","source":"glyph10","target":"glyph2","group":"edges"}},
+            {"data":{"id":"e31","source":"glyph2","target":"glyph11","group":"edges"}},
+            //{"data":{"id":"e32","source":"glyph11","target":"glyph3","group":"edges"}},
+            {"data":{"id":"e33","source":"glyph14","target":"glyph4","group":"edges"}},
+            {"data":{"id":"e34","source":"glyph15","target":"glyph14","group":"edges"}},
+            {"data":{"id":"e35","source":"glyph3","target":"glyph16","group":"edges"}},
+            {"data":{"id":"e36","source":"glyph16","target":"glyph5","group":"edges"}},
+            {"data":{"id":"e37","source":"glyph16","target":"glyph4","group":"edges"}},
+            {"data":{"id":"e38","source":"glyph17","target":"glyph10","group":"edges"}},
+            {"data":{"id":"e39","source":"glyph19","target":"glyph11","group":"edges"}},
+            {"data":{"id":"e40","source":"glyph18","target":"glyph16","group":"edges"}},
+            //{"data":{"id":"e41","source":"glyph22","target":"glyph20","group":"edges"}},
+            {"data":{"id":"e42","source":"glyph4","target":"glyph20","group":"edges"}},
+            {"data":{"id":"e43","source":"glyph20","target":"glyph21","group":"edges"}},
+            {"data":{"id":"e44","source":"glyph23","target":"glyph20","group":"edges"}},
+            {"data":{"id":"e45","source":"glyph24","target":"glyph20","group":"edges"}},
+            {"data":{"id":"e46","source":"glyph20","target":"glyph25","group":"edges"}},
+            {"data":{"id":"e47","source":"glyph20","target":"glyph26","group":"edges"}},
+            {"data":{"id":"e48","source":"glyph35","target":"glyph31","group":"edges"}},
+            {"data":{"id":"e49","source":"glyph36","target":"glyph32","group":"edges"}},
+            //{"data":{"id":"e50","source":"glyph37","target":"glyph33","group":"edges"}},
+            {"data":{"id":"e51","source":"glyph38","target":"glyph34","group":"edges"}},
+            {"data":{"id":"e52","source":"glyph21","target":"glyph31","group":"edges"}},
+            {"data":{"id":"e53","source":"glyph42","target":"glyph31","group":"edges"}},
+            {"data":{"id":"e54","source":"glyph31","target":"glyph41","group":"edges"}},
+            {"data":{"id":"e55","source":"glyph31","target":"glyph27","group":"edges"}},
+            {"data":{"id":"e56","source":"glyph27","target":"glyph32","group":"edges"}},
+            {"data":{"id":"e57","source":"glyph32","target":"glyph28","group":"edges"}},
+            {"data":{"id":"e58","source":"glyph28","target":"glyph33","group":"edges"}},
+            //{"data":{"id":"e59","source":"glyph33","target":"glyph43","group":"edges"}},
+            //{"data":{"id":"e60","source":"glyph33","target":"glyph29","group":"edges"}},
+            {"data":{"id":"e61","source":"glyph29","target":"glyph34","group":"edges"}},
+            //{"data":{"id":"e62","source":"glyph39","target":"glyph34","group":"edges"}},
+            {"data":{"id":"e63","source":"glyph34","target":"glyph40","group":"edges"}},
+            {"data":{"id":"e64","source":"glyph34","target":"glyph30","group":"edges"}},
+            {"data":{"id":"e65","source":"glyph14","target":"glyph5","group":"edges"}},
+            {"data":{"id":"e66","source":"glyph33","target":"glyph35","group":"edges"}},
+            {"data":{"id":"e67","source":"glyph13","target":"glyph22","group":"edges"}},
+            {"data":{"id":"e68","source":"glyph17","target":"glyph6","group":"edges"}},
+            {"data":{"id":"e69","source":"glyph25","target":"glyph27","group":"edges"}}]
+          });          
+          
+          document.getElementById("randomizeButton").addEventListener("click", function(){
+            var layout = cy.layout({
+              name: 'random',
+              animate: true,
+              animationDuration: 1000
+            });
+            
+            layout.run();        
+          });          
+          
+          document.getElementById("fcoseButton").addEventListener("click", function(){
+            let qualityItem = document.getElementById("quality");
+            var layout = cy.layout({
+              name: 'fcose',
+              quality: qualityItem.options[qualityItem.selectedIndex].value,
+              randomize: !(document.getElementById("randomize").checked),
+              animate: document.getElementById("animate").checked,
+              animationEasing: 'ease-out',
+              fit: document.getElementById("fit").checked,
+              uniformNodeDimensions: document.getElementById("uniformNodeDimensions").checked,
+              packComponents: document.getElementById("packComponents").checked,
+              tile: document.getElementById("tile").checked,
+              nodeRepulsion: parseFloat(document.getElementById("nodeRepulsion").value),
+              idealEdgeLength: parseFloat(document.getElementById("idealEdgeLength").value),
+              edgeElasticity: parseFloat(document.getElementById("edgeElasticity").value),
+              nestingFactor: parseFloat(document.getElementById("nestingFactor").value),
+              gravity: parseFloat(document.getElementById("gravity").value),
+              gravityRange: parseFloat(document.getElementById("gravityRange").value),
+              gravityCompound: parseFloat(document.getElementById("gravityCompound").value),
+              gravityRangeCompound: parseFloat(document.getElementById("gravityRangeCompound").value),
+              numIter: parseFloat(document.getElementById("numIter").value),
+              tilingPaddingVertical: parseFloat(document.getElementById("tilingPaddingVertical").value),
+              tilingPaddingHorizontal: parseFloat(document.getElementById("tilingPaddingHorizontal").value),
+              initialEnergyOnIncremental: document.getElementById("initialEnergyOnIncremental").value,
+              step:"all"
+            });
+            
+            layout.run();        
+          });
+
+        });
+      </script>
+  </head>
+
+  <body>
+          <h1 class="ml-2">cytoscape-fcose demo</h1>
+          <div style='width: 300px; position: absolute;'>
+            <button id="randomizeButton" class="btn btn-primary btn-sm mb-2 ml-2">Randomize</button>&nbsp
+            <button id="fcoseButton" class="btn btn-primary btn-sm mb-2">fCoSE</button>&nbsp
+          
+            <div id="mySidepanel" class="sidepanel">
+              <table>
+                <tr>
+                  <td><span class="add-on layout-text" title="Quality of the layout"> Quality </span></td>
+                  <td>            
+                    <select id="quality" class='custom-select custom-select-sm'>
+                      <option value="draft">draft</option>
+                      <option value="default" selected="">default</option>
+                      <option value="proof">proof</option>
+                    </select>
+                  </td>
+                </tr>
+                <tr>
+                  <td><span class="add-on layout-text" title="Whether to enable incremental mode"> Incremental </span></td>
+                  <td>        
+                    <div class="custom-control custom-control-inline custom-checkbox">
+                      <input type="checkbox" class="custom-control-input" id="randomize" name="incremental">
+                      <label class="custom-control-label" for="randomize"></label>
+                    </div>
+                  </td>
+                </tr>
+                <tr>
+                  <td><span class="add-on layout-text" title="Whether to perform animation after layout"> Animate </span></td>
+                  <td>
+                    <div class="custom-control custom-control-inline custom-checkbox">
+                      <input type="checkbox" class="custom-control-input" id="animate" name="animate" checked>
+                      <label class="custom-control-label" for="animate"></label>
+                    </div>                  
+                  </td>
+                </tr>
+                <tr>
+                  <td><span class="add-on layout-text" title="Whether to fit the viewport to the repositioned nodes"> Fit </span></td>
+                  <td>
+                    <div class="custom-control custom-control-inline custom-checkbox">
+                      <input type="checkbox" class="custom-control-input" id="fit" name="fit" checked>
+                      <label class="custom-control-label" for="fit"></label>
+                    </div>
+                  </td>
+                </tr>
+                <tr>
+                  <td><span class="add-on layout-text" title="Whether nodes are of uniform dimensions"> Uniform Node Dimensions </span></td>
+                  <td>
+                    <div class="custom-control custom-control-inline custom-checkbox">
+                      <input type="checkbox" class="custom-control-input" id="uniformNodeDimensions" name="uniformNodeDimensions">
+                      <label class="custom-control-label" for="uniformNodeDimensions"></label>
+                    </div> 
+                  </td>
+                </tr>
+                <tr>
+                  <td><span class="add-on layout-text" title="Whether to pack components"> Pack Components to Window</span></td>
+                  <td>
+                    <div class="custom-control custom-control-inline custom-checkbox">
+                      <input type="checkbox" class="custom-control-input" id="packComponents" name="packComponents" checked>
+                      <label class="custom-control-label" for="packComponents"></label>
+                    </div>                     
+                  </td>
+                </tr>
+                <tr>
+                  <td><span class="add-on layout-text" title="Whether to tile disconnected nodes"> Tile Disconnected </span></td>
+                  <td>
+                    <div class="custom-control custom-control-inline custom-checkbox">
+                      <input type="checkbox" class="custom-control-input" id="tile" name="tile" checked>
+                      <label class="custom-control-label" for="tile"></label>
+                    </div>                     
+                  </td>
+                </tr>              
+                <tr>
+                  <td><span class="add-on layout-text" title="Node repulsion (non overlapping) multiplier"> Node Repulsion </span></td>
+                  <td><input id="nodeRepulsion" class="textField form-control form-control-sm" type="text" value="4500" maxlength=5 size="5"></td>
+                </tr>
+                <tr>
+                  <td><span class="add-on layout-text" title="Ideal (intra-graph) edge length"> Ideal Edge Length </span></td>
+                  <td><input id="idealEdgeLength" class="textField form-control form-control-sm" type="text" value="50" maxlength=5 size="5"></td>
+                </tr>
+                <tr>
+                  <td><span class="add-on layout-text" title="Divisor to compute edge forces"> Edge Elasticity </span></td>
+                  <td><input id="edgeElasticity" class="textField form-control form-control-sm" type="text" value="0.45" maxlength=5 size="5"></td>
+                </tr>
+                <tr>
+                  <td><span class="add-on layout-text" title="Nesting factor (multiplier) to compute ideal edge length for inter-graph edges"> Nesting Factor </span></td>
+                  <td><input id="nestingFactor" class="textField form-control form-control-sm" type="text" value="0.1" maxlength=5 size="5"></td>
+                </tr>
+                <tr>
+                  <td><span class="add-on layout-text" title="Gravity force (constant)"> Gravity </span></td>
+                  <td><input id="gravity" class="textField form-control form-control-sm" type="text" value="0.25" maxlength=5 size="5"></td>
+                </tr>
+                <tr>
+                  <td><span class="add-on layout-text" title="Gravity range (constant)"> Gravity Range </span></td>
+                  <td><input id="gravityRange" class="textField form-control form-control-sm" type="text" value="3.8" maxlength=5 size="5"></td>
+                </tr>
+                <tr>
+                  <td><span class="add-on layout-text" title="Gravity force (constant) for compounds"> Compound Gravity </span></td>
+                  <td><input id="gravityCompound" class="textField form-control form-control-sm" type="text" value="1" maxlength=5 size="5"></td>
+                </tr>
+                <tr>
+                  <td><span class="add-on layout-text" title="Gravity range (constant) for compounds"> Compound Gravity Range </span></td>
+                  <td><input id="gravityRangeCompound" class="textField form-control form-control-sm" type="text" value="1.5" maxlength=5 size="5"></td>
+                </tr>
+                <tr>
+                  <td><span class="add-on layout-text" title="Maximum number of iterations to perform"> Number of Iterations </span></td>
+                  <td><input id="numIter" class="textField form-control form-control-sm" type="text" value="2500" size="5"></td>
+                </tr>
+                <tr>
+                  <td><span class="add-on layout-text" title="Amount of vertical space to put between degree zero nodes during tiling"> Tiling Vertical Padding </span></td>
+                  <td><input id="tilingPaddingVertical" class="textField form-control form-control-sm" type="text" value="10" maxlength=5 size="5"></td>
+                </tr>
+                <tr>
+                  <td><span class="add-on layout-text" title="Amount of horizontal space to put between degree zero nodes during tiling"> Tiling Horizontal Padding </span></td>
+                  <td><input id="tilingPaddingHorizontal" class="textField form-control form-control-sm" type="text" value="10" maxlength=5 size="5"></td>
+                </tr>
+                <tr>
+                  <td><span class="add-on layout-text" title="Initial cooling factor for incremental layout"> Incremental Cooling Factor </span></td>
+                  <td><input id="initialEnergyOnIncremental" class="textField form-control form-control-sm" type="text" value="0.3" maxlength=5 size="5"></td>
+                </tr>               
+              </table>
+
+            </div>
+          </div>
+          <div id="cy"></div>      
+
+  </body>
+
+</html>

tools/ui/node_modules/cytoscape-fcose/demo/samples/callGraph.js

@@ -0,0 +1,1616 @@
+call_graph = {
+	"elements": {
+		"nodes": [
+			{
+				"data": {
+					"id": "nwtN_6edbfba5-6884-4f26-868f-18bc2481616e",
+					"bbox": {
+						"x": 1048.6375489786594,
+						"y": 153.7561581259744,
+						"w": 91.52294921875,
+						"h": 50.25
+					},
+					"minWidth": 91.52294921875,
+					"minWidthBiasLeft": 0.00005,
+					"minWidthBiasRight": 0.00005,
+					"minHeight": 50.25,
+					"minHeightBiasTop": 0.00005,
+					"minHeightBiasBottom": 0.00005,
+					"originalW": 119.52294921875,
+					"originalH": 78.25,
+					"class": "compartment",
+					"label": "__main__",
+					"statesandinfos": [],
+					"language": "PD",
+					"border-width": 3.25,
+					"border-color": "#555555",
+					"background-color": "#ffffff",
+					"background-opacity": 0.5,
+					"background-image-opacity": 1,
+					"text-wrap": "wrap",
+					"font-size": 14,
+					"font-family": "Helvetica",
+					"font-style": "normal",
+					"font-weight": "normal",
+					"color": "#000",
+					"background-image": "",
+					"ports": [],
+					"infoboxCalculated": true,
+					"auxunitlayouts": {}
+				},
+				"position": {
+					"x": 1048.6375489786594,
+					"y": 153.7561581259744
+				},
+				"group": "nodes",
+				"removed": false,
+				"selected": false,
+				"selectable": true,
+				"locked": false,
+				"grabbable": true,
+				"classes": ""
+			},
+			{
+				"data": {
+					"id": "nwtN_6e27959a-ae83-4cb0-898f-9a1e6c5cafae",
+					"bbox": {
+						"x": 1048.6375489786594,
+						"y": 153.7561581259744,
+						"w": 88.27294921875,
+						"h": 47
+					},
+					"class": "macromolecule",
+					"label": "main\ncalls: 1\ntime: 0.000000s",
+					"statesandinfos": [],
+					"parent": "nwtN_6edbfba5-6884-4f26-868f-18bc2481616e",
+					"language": "PD",
+					"border-width": 1.25,
+					"border-color": "#555555",
+					"background-color": "#9999e5",
+					"background-opacity": 1,
+					"background-image-opacity": 1,
+					"text-wrap": "wrap",
+					"font-size": 11,
+					"font-family": "Helvetica",
+					"font-style": "normal",
+					"font-weight": "normal",
+					"color": "#000",
+					"background-image": "",
+					"ports": [],
+					"infoboxCalculated": true,
+					"auxunitlayouts": {}
+				},
+				"position": {
+					"x": 1048.6375489786594,
+					"y": 153.7561581259744
+				},
+				"group": "nodes",
+				"removed": false,
+				"selected": false,
+				"selectable": true,
+				"locked": false,
+				"grabbable": true,
+				"classes": ""
+			},
+			{
+				"data": {
+					"id": "nwtN_e872ccff-fb1a-4264-a66a-cbc72d1e9711",
+					"bbox": {
+						"x": 832.2602245209991,
+						"y": 267.2349457952003,
+						"w": 203.3974609375,
+						"h": 50.25
+					},
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+			{
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+					"class": "production",
+					"bendPointPositions": [],
+					"language": "PD",
+					"line-color": "#555555",
+					"width": 1.25,
+					"background-image": "",
+					"background-color": "#ffffff",
+					"label": 1,
+					"source": "2f560d5b-bb1b-cc3f-d5b5-a69e6fab8d47",
+					"target": "1f64237f-dd15-2d5f-18f0-02a0d0338f44",
+					"portsource": "2f560d5b-bb1b-cc3f-d5b5-a69e6fab8d47",
+					"porttarget": "1f64237f-dd15-2d5f-18f0-02a0d0338f44"
+				},
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+				"group": "edges",
+				"removed": false,
+				"selected": false,
+				"selectable": true,
+				"locked": false,
+				"grabbable": true,
+				"classes": ""
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+					"porttarget": "63edffef-16cf-a216-5ace-a27a4290e3d8"
+				},
+				"position": {},
+				"group": "edges",
+				"removed": false,
+				"selected": false,
+				"selectable": true,
+				"locked": false,
+				"grabbable": true,
+				"classes": ""
+			},
+			{
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+					"id": "nwtE_d748d6aa-f386-4ced-bac6-d2587064d47b",
+					"class": "production",
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+					"line-color": "#555555",
+					"width": 1.25,
+					"background-image": "",
+					"background-color": "#ffffff",
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+					"source": "d07ee031-2818-7c9c-5589-e8a161b9946c",
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+					"portsource": "d07ee031-2818-7c9c-5589-e8a161b9946c",
+					"porttarget": "d6768356-8772-a49a-c2f7-c3b9802c954b"
+				},
+				"position": {},
+				"group": "edges",
+				"removed": false,
+				"selected": false,
+				"selectable": true,
+				"locked": false,
+				"grabbable": true,
+				"classes": ""
+			},
+			{
+				"data": {
+					"id": "nwtE_c71d9e10-11c4-4e9a-baf7-fa043282103c",
+					"class": "production",
+					"bendPointPositions": [],
+					"language": "PD",
+					"line-color": "#555555",
+					"width": 1.25,
+					"background-image": "",
+					"background-color": "#ffffff",
+					"label": 1,
+					"source": "d07ee031-2818-7c9c-5589-e8a161b9946c",
+					"target": "05b42313-71a4-e1a9-383b-6b4be641e69d",
+					"portsource": "d07ee031-2818-7c9c-5589-e8a161b9946c",
+					"porttarget": "05b42313-71a4-e1a9-383b-6b4be641e69d"
+				},
+				"position": {},
+				"group": "edges",
+				"removed": false,
+				"selected": false,
+				"selectable": true,
+				"locked": false,
+				"grabbable": true,
+				"classes": ""
+			},
+			{
+				"data": {
+					"id": "nwtE_55f140c5-f99c-4bc5-b8ef-e7c808ae8d66",
+					"class": "production",
+					"bendPointPositions": [],
+					"language": "PD",
+					"line-color": "#555555",
+					"width": 1.25,
+					"background-image": "",
+					"background-color": "#ffffff",
+					"label": 1,
+					"source": "63edffef-16cf-a216-5ace-a27a4290e3d8",
+					"target": "3c161178-1fca-ec7e-3fc7-425ce940fe1a",
+					"portsource": "63edffef-16cf-a216-5ace-a27a4290e3d8",
+					"porttarget": "3c161178-1fca-ec7e-3fc7-425ce940fe1a"
+				},
+				"position": {},
+				"group": "edges",
+				"removed": false,
+				"selected": false,
+				"selectable": true,
+				"locked": false,
+				"grabbable": true,
+				"classes": ""
+			},
+			{
+				"data": {
+					"id": "nwtE_741a21e2-6999-4d7f-8f01-bc7fecbbc41b",
+					"class": "production",
+					"bendPointPositions": [],
+					"language": "PD",
+					"line-color": "#555555",
+					"width": 1.25,
+					"background-image": "",
+					"background-color": "#ffffff",
+					"label": 1,
+					"source": "63edffef-16cf-a216-5ace-a27a4290e3d8",
+					"target": "bab5c8a0-0f39-66d4-eaca-7f9160ef25fa",
+					"portsource": "63edffef-16cf-a216-5ace-a27a4290e3d8",
+					"porttarget": "bab5c8a0-0f39-66d4-eaca-7f9160ef25fa"
+				},
+				"position": {},
+				"group": "edges",
+				"removed": false,
+				"selected": false,
+				"selectable": true,
+				"locked": false,
+				"grabbable": true,
+				"classes": ""
+			},
+			{
+				"data": {
+					"id": "nwtE_790b1a2d-2b2c-481a-967f-e696d23e6824",
+					"class": "production",
+					"bendPointPositions": [],
+					"language": "PD",
+					"line-color": "#555555",
+					"width": 1.25,
+					"background-image": "",
+					"background-color": "#ffffff",
+					"label": 1,
+					"source": "63edffef-16cf-a216-5ace-a27a4290e3d8",
+					"target": "a0d92978-e6e9-6d87-9a06-567d139d15af",
+					"portsource": "63edffef-16cf-a216-5ace-a27a4290e3d8",
+					"porttarget": "a0d92978-e6e9-6d87-9a06-567d139d15af"
+				},
+				"position": {},
+				"group": "edges",
+				"removed": false,
+				"selected": false,
+				"selectable": true,
+				"locked": false,
+				"grabbable": true,
+				"classes": ""
+			},
+			{
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+					"id": "nwtE_664a54ae-b07a-4c85-a503-349ca4edf006",
+					"class": "production",
+					"bendPointPositions": [],
+					"language": "PD",
+					"line-color": "#555555",
+					"width": 1.25,
+					"background-image": "",
+					"background-color": "#ffffff",
+					"label": 1,
+					"source": "nwtN_6e27959a-ae83-4cb0-898f-9a1e6c5cafae",
+					"target": "nwtN_a44ad134-4c47-4cf5-b244-9d9fc0804e93",
+					"portsource": "nwtN_6e27959a-ae83-4cb0-898f-9a1e6c5cafae",
+					"porttarget": "nwtN_a44ad134-4c47-4cf5-b244-9d9fc0804e93"
+				},
+				"position": {},
+				"group": "edges",
+				"removed": false,
+				"selected": false,
+				"selectable": true,
+				"locked": false,
+				"grabbable": true,
+				"classes": ""
+			}
+		]
+	},
+	"style": [
+	    {
+	      "selector": "node",
+	      "style": {
+	        "shape": "rectangle",
+	        "text-halign": "center",
+	        "text-valign": "center",
+	        "font-weight" : "normal",
+	        "background-color": "#ffffff",
+	        "opacity": "1",
+	        "border-color": "#555555"
+	      }
+	    },
+	    {
+	      "selector": "node[class = 'simple chemical']",
+	      "style": {
+	        "shape": "ellipse",
+	        "font-size": 14,
+	        "background-color": "#fddbc7"
+	      }
+	    },
+	    {
+	      "selector": "node[class = 'macromolecule']",
+	      "style": {
+	        "shape": "roundrectangle",
+	        "background-color": "#9999e5"	        
+	      }
+	    },
+	    {
+	      "selector": "node[class = 'unspecified entity']",
+	      "style": {
+	        "shape": "ellipse",
+	        "background-color": "#f7f7f7"
+	      }
+	    },
+	    {
+	      "selector": "node[class = 'nucleic acid feature']",
+	      "style": {
+	        "shape": "rectangle",
+	        "background-color": "#f4a582",	        
+	      }
+	    },	    	    	   
+	    {
+	      "selector": ":parent",
+	      "style": {
+	        "background-opacity": "0.333",
+	        "text-valign": "bottom",
+	        "shape": "barrel",
+	        "text-margin-y": "2px",
+	        "font-weight" : "normal",
+	        "border-color": "#555555"
+	      }
+	    },
+	    {
+	      "selector": "node:selected",
+	      "style": {
+	        "background-color": "#33ff00",
+	        "border-color": "#22ee00"
+	      }
+	    },
+	    {
+	      "selector": "edge",
+	      "style": {
+	        "curve-style": "bezier",
+	        "width": "2px",
+	        "line-color": "rgb(58,126,207)",
+	        "opacity": "1"
+	      }
+	    },
+	    {
+	      "selector": "edge:selected",
+	      "style": {
+	        "line-color": "#33ff00",
+	        "font-size": "13px",
+	        "text-opacity": "1",
+	        "text-rotation": "autorotate",
+	        "color": "#33ff00",
+	        "font-weight": "bold",
+	        "text-background-shape": "roundrectangle",
+	        "text-background-opacity": "1",
+	        "text-background-padding": "2px"
+	      }
+	    },
+	    {
+	      "selector": "edge[class = 'production']",
+	      "style": {
+	        "target-arrow-shape": "triangle",
+	        "target-arrow-color": "rgb(58,126,207)"
+	      }
+	    },
+	    {
+	      "selector": "edge:selected[class = 'production']",
+	      "style": {
+	        "target-arrow-shape": "triangle",
+	        "target-arrow-color": "#33ff00"
+	      }
+	    },	    
+	  ],
+	"zoomingEnabled": true,
+	"userZoomingEnabled": true,
+	"zoom": 0.9387299878673792,
+	"minZoom": 0.125,
+	"maxZoom": 16,
+	"panningEnabled": true,
+	"userPanningEnabled": true,
+	"pan": {
+		"x": -275.1308697557213,
+		"y": -85.14353945866765
+	},
+	"boxSelectionEnabled": true,
+	"renderer": {
+		"name": "canvas"
+	},
+	"wheelSensitivity": 0.1,
+	"motionBlur": true
+}

tools/ui/node_modules/cytoscape-fcose/demo/samples/callGraph_constraints.js

@@ -0,0 +1,123 @@
+callGraph_constraints = {
+  "alignmentConstraint": {
+    "horizontal": [
+      [
+        "288a2f9b-2930-701e-c68e-400307fbffd4",
+        "nwtN_a44ad134-4c47-4cf5-b244-9d9fc0804e93",
+        "nwtN_ac02fa71-2428-47ad-8c3c-80bb5659a066"
+      ],
+      [
+        "nwtN_550a66a2-1061-45cc-9f78-14570daaff94",
+        "82181180-e275-b004-243e-eb4383e1e72f",
+        "359e920c-52a4-459e-2262-4ec90824f21e",
+        "5a34dca5-646c-cae7-affe-ef4142c5ad73",
+        "2f560d5b-bb1b-cc3f-d5b5-a69e6fab8d47",
+        "d07ee031-2818-7c9c-5589-e8a161b9946c",
+        "912c0f08-87fb-c746-18cb-19909a2b41c8"
+      ],
+      [
+        "1f64237f-dd15-2d5f-18f0-02a0d0338f44",
+        "63edffef-16cf-a216-5ace-a27a4290e3d8",
+        "d6768356-8772-a49a-c2f7-c3b9802c954b",
+        "05b42313-71a4-e1a9-383b-6b4be641e69d"
+      ],
+      [
+        "3c161178-1fca-ec7e-3fc7-425ce940fe1a",
+        "bab5c8a0-0f39-66d4-eaca-7f9160ef25fa",
+        "a0d92978-e6e9-6d87-9a06-567d139d15af"
+      ]
+    ]
+  },
+  "relativePlacementConstraint": [
+    {
+      "top": "nwtN_6e27959a-ae83-4cb0-898f-9a1e6c5cafae",
+      "bottom": "d2f78da5-fbd3-fe91-4046-3b5aea0648f6",
+      "gap": 98.25
+    },
+    {
+      "top": "nwtN_6e27959a-ae83-4cb0-898f-9a1e6c5cafae",
+      "bottom": "nwtN_a44ad134-4c47-4cf5-b244-9d9fc0804e93",
+      "gap": 98.25
+    },
+    {
+      "top": "d2f78da5-fbd3-fe91-4046-3b5aea0648f6",
+      "bottom": "288a2f9b-2930-701e-c68e-400307fbffd4",
+      "gap": 98.25
+    },
+    {
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+      "bottom": "nwtN_ac02fa71-2428-47ad-8c3c-80bb5659a066",
+      "gap": 98.25
+    },
+    {
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+      "bottom": "912c0f08-87fb-c746-18cb-19909a2b41c8",
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+    },
+    {
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+      "bottom": "82181180-e275-b004-243e-eb4383e1e72f",
+      "gap": 98.25
+    },
+    {
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+      "bottom": "359e920c-52a4-459e-2262-4ec90824f21e",
+      "gap": 98.25
+    },
+    {
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+      "bottom": "5a34dca5-646c-cae7-affe-ef4142c5ad73",
+      "gap": 98.25
+    },
+    {
+      "top": "nwtN_ac02fa71-2428-47ad-8c3c-80bb5659a066",
+      "bottom": "2f560d5b-bb1b-cc3f-d5b5-a69e6fab8d47",
+      "gap": 98.25
+    },
+    {
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+      "bottom": "nwtN_550a66a2-1061-45cc-9f78-14570daaff94",
+      "gap": 98.25
+    },
+    {
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+      "bottom": "d07ee031-2818-7c9c-5589-e8a161b9946c",
+      "gap": 98.25
+    },
+    {
+      "top": "2f560d5b-bb1b-cc3f-d5b5-a69e6fab8d47",
+      "bottom": "1f64237f-dd15-2d5f-18f0-02a0d0338f44",
+      "gap": 98.25
+    },
+    {
+      "top": "d07ee031-2818-7c9c-5589-e8a161b9946c",
+      "bottom": "63edffef-16cf-a216-5ace-a27a4290e3d8",
+      "gap": 98.25
+    },
+    {
+      "top": "d07ee031-2818-7c9c-5589-e8a161b9946c",
+      "bottom": "d6768356-8772-a49a-c2f7-c3b9802c954b",
+      "gap": 98.25
+    },
+    {
+      "top": "d07ee031-2818-7c9c-5589-e8a161b9946c",
+      "bottom": "05b42313-71a4-e1a9-383b-6b4be641e69d",
+      "gap": 98.25
+    },
+    {
+      "top": "63edffef-16cf-a216-5ace-a27a4290e3d8",
+      "bottom": "3c161178-1fca-ec7e-3fc7-425ce940fe1a",
+      "gap": 98.25
+    },
+    {
+      "top": "63edffef-16cf-a216-5ace-a27a4290e3d8",
+      "bottom": "bab5c8a0-0f39-66d4-eaca-7f9160ef25fa",
+      "gap": 98.25
+    },
+    {
+      "top": "63edffef-16cf-a216-5ace-a27a4290e3d8",
+      "bottom": "a0d92978-e6e9-6d87-9a06-567d139d15af",
+      "gap": 98.25
+    }
+  ]
+}

tools/ui/node_modules/cytoscape-fcose/demo/samples/chalk.js

@@ -0,0 +1,1305 @@
+chalk = {
+	"elements": {
+		"nodes": [
+			{
+				"data": {
+					"id": "nwtN_00dcd31b-2631-4af1-980b-4493dc7d43f7",
+					"bbox": {
+						"x": 506.4608860015869,
+						"y": 105.05675506591797,
+						"w": 60.3330078125,
+						"h": 28.25
+					},
+					"originalW": 88.3330078125,
+					"originalH": 56.25,
+					"class": "compartment",
+					"label": "types",
+					"statesandinfos": [],
+					"parent": "nwtN_80eb137f-5cd7-4584-9acc-87cc5698d255",
+					"language": "PD",
+					"border-width": 2.25,
+					"border-color": "#555555",
+					"background-color": "#f5f5f5",
+					"background-opacity": 0.5,
+					"background-image-opacity": "",
+					"text-wrap": "wrap",
+					"font-size": 11,
+					"font-family": "Helvetica",
+					"font-style": "normal",
+					"font-weight": "bold",
+					"color": "#000000",
+					"ports": [],
+					"background-image": "",
+					"background-fit": "",
+					"background-position-x": "",
+					"background-position-y": "",
+					"background-width": "",
+					"background-height": "",
+					"infoboxCalculated": true,
+					"auxunitlayouts": {}
+				},
+				"position": {
+					"x": 506.4608860015869,
+					"y": 105.05675506591797
+				},
+				"group": "nodes",
+				"removed": false,
+				"selected": false,
+				"selectable": true,
+				"locked": false,
+				"grabbable": true,
+				"classes": ""
+			},		
+			{
+				"data": {
+					"id": "nwtN_80eb137f-5cd7-4584-9acc-87cc5698d255",
+					"bbox": {
+						"x": 503.796484757312,
+						"y": 149.75074733690965,
+						"w": 141.2687438947998,
+						"h": 150.88798454198337
+					},
+					"originalW": 169.2687438947998,
+					"originalH": 178.88798454198337,
+					"class": "compartment",
+					"label": "chalk",
+					"statesandinfos": [],
+					"language": "PD",
+					"border-width": 2.25,
+					"border-color": "#555555",
+					"background-color": "#f5f5f5",
+					"background-opacity": 0.5,
+					"background-image-opacity": "",
+					"text-wrap": "wrap",
+					"font-size": 11,
+					"font-family": "Helvetica",
+					"font-style": "normal",
+					"font-weight": "bold",
+					"color": "#000000",
+					"ports": [],
+					"background-image": "",
+					"background-fit": "",
+					"background-position-x": "",
+					"background-position-y": "",
+					"background-width": "",
+					"background-height": "",
+					"infoboxCalculated": true,
+					"auxunitlayouts": {}
+				},
+				"position": {
+					"x": 503.796484757312,
+					"y": 149.75074733690965
+				},
+				"group": "nodes",
+				"removed": false,
+				"selected": false,
+				"selectable": true,
+				"locked": false,
+				"grabbable": true,
+				"classes": ""
+			},
+			{
+				"data": {
+					"id": "nwtN_23452b85-7855-413f-a03d-26412ed87bfc",
+					"bbox": {
+						"x": 506.4608860015869,
+						"y": 105.05675506591797,
+						"w": 57.0830078125,
+						"h": 25
+					},
+					"class": "simple chemical",
+					"label": "index.d.ts",
+					"statesandinfos": [],
+					"parent": "nwtN_00dcd31b-2631-4af1-980b-4493dc7d43f7",
+					"language": "PD",
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+	        "text-halign": "center",
+	        "text-valign": "center",
+	        "background-color": "#ffffff",
+	        "opacity": "1",
+	        "border-color": "#555555"
+	      }
+	    },
+	    {
+	      "selector": "node[class = 'simple chemical']",
+	      "style": {
+	        "shape": "ellipse",
+	        "background-color": "#c7eae5"
+	      }
+	    },
+	    {
+	      "selector": "node[class = 'macromolecule']",
+	      "style": {
+	        "shape": "roundrectangle",
+	        "background-color": "#dfc27d"
+	      }
+	    },
+	    {
+	      "selector": "node[class = 'unspecified entity']",
+	      "style": {
+	        "shape": "ellipse",
+	        "background-color": "#f5f5f5"
+	      }
+	    },	    
+	    {
+	      "selector": ":parent",
+	      "style": {
+	        "background-opacity": "0.333",
+	        "text-valign": "bottom",
+	        "shape": "barrel",
+	        "text-margin-y": "2px",
+	        "font-weight" : "bold",
+	        "border-color": "#555555"
+	      }
+	    },
+	    {
+	      "selector": "node:selected",
+	      "style": {
+	        "background-color": "#33ff00",
+	        "border-color": "#22ee00"
+	      }
+	    },
+	    {
+	      "selector": "edge",
+	      "style": {
+	        "curve-style": "bezier",
+	        "width": "2px",
+	        "line-color": "rgb(58,126,207)",
+	        "opacity": "1",
+        	"target-arrow-shape": "triangle",
+        	"target-arrow-color": "rgb(58,126,207)",
+	      }
+	    },
+	    {
+	      "selector": "edge:selected",
+	      "style": {
+	        "line-color": "#33ff00",
+	        "font-size": "13px",
+	        "text-opacity": "1",
+	        "text-rotation": "autorotate",
+	        "color": "#33ff00",
+	        "font-weight": "bold",
+	        "text-background-shape": "roundrectangle",
+	        "text-background-opacity": "1",
+	        "text-background-padding": "2px",
+	        "target-arrow-color": "#33ff00",
+	        "target-arrow-shape": "triangle",
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+	    }
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+}

tools/ui/node_modules/cytoscape-fcose/demo/samples/chalk_constraints.js

@@ -0,0 +1,78 @@
+chalk_constraints = {
+  "alignmentConstraint": {
+    "vertical": [
+      [
+        "nwtN_c152aeef-01df-49fc-9539-9e022e8d4c64",
+        "nwtN_fa99aac7-9500-4ead-82c3-90c72e9837f3",
+        "nwtN_6442ea6c-8a74-4948-ab60-2a2fc6b904f7",
+        "nwtN_395e3fed-fcd4-427a-909a-c01a7fc94607"
+      ],
+      [
+        "nwtN_fc4a5aa8-171f-41bd-8ab3-5eee343c4f9f",
+        "nwtN_10cd6cfc-6d2a-48b1-82e1-29d16dadd069",
+        "nwtN_88c73829-9d76-4b03-ab27-335fd9581531"
+      ],
+      [
+        "nwtN_23452b85-7855-413f-a03d-26412ed87bfc",
+        "nwtN_6ffc1fdf-602f-4395-89b5-666b383a5059"
+      ]
+    ]
+  },
+  "relativePlacementConstraint": [
+    {
+      "left": "nwtN_6ffc1fdf-602f-4395-89b5-666b383a5059",
+      "right": "nwtN_c152aeef-01df-49fc-9539-9e022e8d4c64",
+      "gap": 180
+    },
+    {
+      "left": "nwtN_6ffc1fdf-602f-4395-89b5-666b383a5059",
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tools/ui/node_modules/cytoscape-fcose/demo/samples/unix.js

@@ -0,0 +1,2868 @@
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+		]
+	},
+	"style": [
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+	      "style": {
+	        "shape": "rectangle",
+	        "text-halign": "center",
+	        "text-valign": "center",
+	        "background-color": "#b2dfee",
+	        "opacity": "1",
+	        "border-color": "#555555"
+	      }
+	    },
+	    {
+	      "selector": "node[class = 'simple chemical']",
+	      "style": {
+	        "shape": "ellipse"
+	      }
+	    },
+	    {
+	      "selector": "node[class = 'macromolecule']",
+	      "style": {
+	        "shape": "roundrectangle"
+	      }
+	    },
+	    {
+	      "selector": "node[class = 'unspecified entity']",
+	      "style": {
+	        "shape": "ellipse"
+	      }
+	    },	    
+	    {
+	      "selector": ":parent",
+	      "style": {
+	        "background-opacity": "0.333",
+	        "text-valign": "bottom",
+	        "shape": "barrel",
+	        "text-margin-y": "2px",
+	        "font-weight" : "bold",
+	        "border-color": "#555555"
+	      }
+	    },
+	    {
+	      "selector": "node:selected",
+	      "style": {
+	        "background-color": "#33ff00",
+	        "border-color": "#22ee00"
+	      }
+	    },
+	    {
+	      "selector": "edge",
+	      "style": {
+	        "curve-style": "bezier",
+	        "width": "2px",
+	        "line-color": "rgb(58,126,207)",
+	        "opacity": "1",
+	        "target-arrow-shape": "triangle",
+	        "target-arrow-color": "rgb(58,126,207)"
+	      }
+	    },
+	    {
+	      "selector": "edge:selected",
+	      "style": {
+	        "line-color": "#33ff00",
+	        "font-size": "13px",
+	        "text-opacity": "1",
+	        "text-rotation": "autorotate",
+	        "color": "#33ff00",
+	        "font-weight": "bold",
+	        "text-background-shape": "roundrectangle",
+	        "text-background-opacity": "1",
+	        "text-background-padding": "2px",
+	        "target-arrow-shape": "triangle",
+	        "target-arrow-color": "#33ff00"	        
+	      }
+	    }
+	  ],
+	"zoomingEnabled": true,
+	"userZoomingEnabled": true,
+	"zoom": 0.8336504719979256,
+	"minZoom": 0.125,
+	"maxZoom": 16,
+	"panningEnabled": true,
+	"userPanningEnabled": true,
+	"pan": {
+		"x": -17.245693955834554,
+		"y": -155.00970669805537
+	},
+	"boxSelectionEnabled": true,
+	"renderer": {
+		"name": "canvas"
+	},
+	"wheelSensitivity": 0.1,
+	"motionBlur": true
+}

tools/ui/node_modules/cytoscape-fcose/demo/samples/unix_constraints.js

@@ -0,0 +1,249 @@
+unix_constraints = {
+  "relativePlacementConstraint": [
+    {
+      "top": "nwtN_4451c335-4668-4f8d-9f71-274aa2e6ab06",
+      "bottom": "nwtN_8d99e7af-1b2f-4605-a381-ce3127b6199a",
+      "gap": 76.25
+    },
+    {
+      "top": "nwtN_4451c335-4668-4f8d-9f71-274aa2e6ab06",
+      "bottom": "nwtN_37220ed2-0cbe-4d1f-9cac-07dfb11d6eda",
+      "gap": 76.25
+    },
+    {
+      "top": "nwtN_8d99e7af-1b2f-4605-a381-ce3127b6199a",
+      "bottom": "nwtN_020b84b2-717f-4465-b716-7520e5c9c470",
+      "gap": 76.25
+    },
+    {
+      "top": "nwtN_8d99e7af-1b2f-4605-a381-ce3127b6199a",
+      "bottom": "nwtN_c1880331-8411-443e-9218-87e78c057b22",
+      "gap": 76.25
+    },
+    {
+      "top": "nwtN_8d99e7af-1b2f-4605-a381-ce3127b6199a",
+      "bottom": "nwtN_3f3b6234-e449-44bb-9ba8-059d1f843c98",
+      "gap": 76.25
+    },
+    {
+      "top": "nwtN_8d99e7af-1b2f-4605-a381-ce3127b6199a",
+      "bottom": "nwtN_d7bbe746-9028-4268-a642-70544788d687",
+      "gap": 76.25
+    },
+    {
+      "top": "nwtN_8d99e7af-1b2f-4605-a381-ce3127b6199a",
+      "bottom": "nwtN_5bb0a938-c7ee-42d8-85c8-17bdc1ff0ade",
+      "gap": 76.25
+    },
+    {
+      "top": "nwtN_37220ed2-0cbe-4d1f-9cac-07dfb11d6eda",
+      "bottom": "nwtN_8227939a-5dc0-433e-8c4d-987ec44a1f8f",
+      "gap": 76.25
+    },
+    {
+      "top": "nwtN_37220ed2-0cbe-4d1f-9cac-07dfb11d6eda",
+      "bottom": "nwtN_3f7d61be-a016-4383-9b8d-8c1db26192f2",
+      "gap": 76.25
+    },
+    {
+      "top": "nwtN_020b84b2-717f-4465-b716-7520e5c9c470",
+      "bottom": "nwtN_166d8364-fd55-499e-9098-0a48db6615c1",
+      "gap": 76.25
+    },
+    {
+      "top": "nwtN_c1880331-8411-443e-9218-87e78c057b22",
+      "bottom": "nwtN_167a075d-9d93-49d0-b5be-446efebec06c",
+      "gap": 76.25
+    },
+    {
+      "top": "nwtN_c1880331-8411-443e-9218-87e78c057b22",
+      "bottom": "nwtN_db35fc70-2b89-4857-acb2-9dd545e61447",
+      "gap": 76.25
+    },
+    {
+      "top": "nwtN_c1880331-8411-443e-9218-87e78c057b22",
+      "bottom": "nwtN_9dfde51e-a410-4e3b-a472-9061ae4fae7a",
+      "gap": 76.25
+    },
+    {
+      "top": "nwtN_8227939a-5dc0-433e-8c4d-987ec44a1f8f",
+      "bottom": "nwtN_9dfde51e-a410-4e3b-a472-9061ae4fae7a",
+      "gap": 76.25
+    },
+    {
+      "top": "nwtN_3f7d61be-a016-4383-9b8d-8c1db26192f2",
+      "bottom": "nwtN_a186f2a4-524e-4a84-95c0-66d41dbda586",
+      "gap": 76.25
+    },
+    {
+      "top": "nwtN_3f7d61be-a016-4383-9b8d-8c1db26192f2",
+      "bottom": "nwtN_26c73172-708d-45cc-8ba5-f29671089767",
+      "gap": 76.25
+    },
+    {
+      "top": "nwtN_167a075d-9d93-49d0-b5be-446efebec06c",
+      "bottom": "nwtN_a2bfb9bd-8b13-43a5-87a5-d88b0137bd78",
+      "gap": 76.25
+    },
+    {
+      "top": "nwtN_167a075d-9d93-49d0-b5be-446efebec06c",
+      "bottom": "nwtN_2d9c1f24-1482-46fb-a0f4-f963ba454710",
+      "gap": 76.25
+    },
+    {
+      "top": "nwtN_167a075d-9d93-49d0-b5be-446efebec06c",
+      "bottom": "nwtN_15fb1e74-6b08-4914-95ac-ee4ecb1b7f17",
+      "gap": 76.25
+    },
+    {
+      "top": "nwtN_167a075d-9d93-49d0-b5be-446efebec06c",
+      "bottom": "nwtN_485d980b-dc42-48ca-9ada-3c1b754cc2ef",
+      "gap": 76.25
+    },
+    {
+      "top": "nwtN_167a075d-9d93-49d0-b5be-446efebec06c",
+      "bottom": "nwtN_bce869d1-7c58-4489-81aa-e87e9418ab70",
+      "gap": 76.25
+    },
+    {
+      "top": "nwtN_9dfde51e-a410-4e3b-a472-9061ae4fae7a",
+      "bottom": "nwtN_db35fc70-2b89-4857-acb2-9dd545e61447",
+      "gap": 76.25
+    },
+    {
+      "top": "nwtN_a186f2a4-524e-4a84-95c0-66d41dbda586",
+      "bottom": "nwtN_2cf0c5aa-67eb-4394-85e3-dc84f4b1cd52",
+      "gap": 76.25
+    },
+    {
+      "top": "nwtN_26c73172-708d-45cc-8ba5-f29671089767",
+      "bottom": "nwtN_2b6ef682-26c7-48d7-9fd8-09fa76c7b718",
+      "gap": 76.25
+    },
+    {
+      "top": "nwtN_a2bfb9bd-8b13-43a5-87a5-d88b0137bd78",
+      "bottom": "nwtN_be8097dc-4a84-4d3f-ade9-e80221f86dd6",
+      "gap": 76.25
+    },
+    {
+      "top": "nwtN_d53ea35c-4609-4051-917a-8a183e5976cf",
+      "bottom": "nwtN_c261ca93-6060-49c1-8286-2a98900c3b9e",
+      "gap": 76.25
+    },
+    {
+      "top": "nwtN_db35fc70-2b89-4857-acb2-9dd545e61447",
+      "bottom": "nwtN_a68571c0-2669-4894-aa53-332555f625a2",
+      "gap": 76.25
+    },
+    {
+      "top": "nwtN_eed8fc62-a21d-4677-85f2-f1244e3abf00",
+      "bottom": "nwtN_2f175f07-154a-4873-98cc-bc4e4d6d13a1",
+      "gap": 76.25
+    },
+    {
+      "top": "nwtN_eed8fc62-a21d-4677-85f2-f1244e3abf00",
+      "bottom": "nwtN_a68571c0-2669-4894-aa53-332555f625a2",
+      "gap": 76.25
+    },
+    {
+      "top": "nwtN_eed8fc62-a21d-4677-85f2-f1244e3abf00",
+      "bottom": "nwtN_e55d29c7-89bc-4aa0-b599-3637e141f17f",
+      "gap": 76.25
+    },
+    {
+      "top": "nwtN_c261ca93-6060-49c1-8286-2a98900c3b9e",
+      "bottom": "nwtN_02a50d8b-3939-492a-ac5b-1f356cd514f6",
+      "gap": 76.25
+    },
+    {
+      "top": "nwtN_2f175f07-154a-4873-98cc-bc4e4d6d13a1",
+      "bottom": "nwtN_a68571c0-2669-4894-aa53-332555f625a2",
+      "gap": 76.25
+    },
+    {
+      "top": "nwtN_166d8364-fd55-499e-9098-0a48db6615c1",
+      "bottom": "nwtN_205680d2-dc98-4faf-baf4-21e27e8585e4",
+      "gap": 76.25
+    },
+    {
+      "top": "nwtN_02a50d8b-3939-492a-ac5b-1f356cd514f6",
+      "bottom": "nwtN_205680d2-dc98-4faf-baf4-21e27e8585e4",
+      "gap": 76.25
+    },
+    {
+      "top": "nwtN_02a50d8b-3939-492a-ac5b-1f356cd514f6",
+      "bottom": "nwtN_75318a95-e179-40fc-b6e1-e01fcd66cd8c",
+      "gap": 76.25
+    },
+    {
+      "top": "nwtN_02a50d8b-3939-492a-ac5b-1f356cd514f6",
+      "bottom": "nwtN_bce869d1-7c58-4489-81aa-e87e9418ab70",
+      "gap": 76.25
+    },
+    {
+      "top": "nwtN_a68571c0-2669-4894-aa53-332555f625a2",
+      "bottom": "nwtN_8ed84db0-02da-43c6-847c-6b33f657f52c",
+      "gap": 76.25
+    },
+    {
+      "top": "nwtN_205680d2-dc98-4faf-baf4-21e27e8585e4",
+      "bottom": "nwtN_be8097dc-4a84-4d3f-ade9-e80221f86dd6",
+      "gap": 76.25
+    },
+    {
+      "top": "nwtN_205680d2-dc98-4faf-baf4-21e27e8585e4",
+      "bottom": "nwtN_8489a816-b7af-452f-a722-04d06226341c",
+      "gap": 76.25
+    },
+    {
+      "top": "nwtN_75318a95-e179-40fc-b6e1-e01fcd66cd8c",
+      "bottom": "nwtN_d4bf8470-416d-4387-a563-3c9cccf55079",
+      "gap": 76.25
+    },
+    {
+      "top": "nwtN_75318a95-e179-40fc-b6e1-e01fcd66cd8c",
+      "bottom": "nwtN_e48d9732-8ee0-4714-8b62-8de8238ec9c2",
+      "gap": 76.25
+    },
+    {
+      "top": "nwtN_bce869d1-7c58-4489-81aa-e87e9418ab70",
+      "bottom": "nwtN_103a9105-ef50-47a4-b501-840a431fcbdd",
+      "gap": 76.25
+    },
+    {
+      "top": "nwtN_8ed84db0-02da-43c6-847c-6b33f657f52c",
+      "bottom": "nwtN_6385f491-0d09-4d53-a34c-781a861e8b42",
+      "gap": 76.25
+    },
+    {
+      "top": "nwtN_6385f491-0d09-4d53-a34c-781a861e8b42",
+      "bottom": "nwtN_88e20782-9221-4b12-9b62-6a6c7116a70f",
+      "gap": 76.25
+    },
+    {
+      "top": "nwtN_167a075d-9d93-49d0-b5be-446efebec06c",
+      "bottom": "nwtN_be8097dc-4a84-4d3f-ade9-e80221f86dd6",
+      "gap": 76.25
+    },
+    {
+      "top": "nwtN_485d980b-dc42-48ca-9ada-3c1b754cc2ef",
+      "bottom": "nwtN_d53ea35c-4609-4051-917a-8a183e5976cf",
+      "gap": 76.25
+    },
+    {
+      "top": "nwtN_2cf0c5aa-67eb-4394-85e3-dc84f4b1cd52",
+      "bottom": "nwtN_db35fc70-2b89-4857-acb2-9dd545e61447",
+      "gap": 76.25
+    },
+    {
+      "top": "nwtN_cc15f875-f4dd-4df8-a09e-a4f2e6c8a3f5",
+      "bottom": "nwtN_db35fc70-2b89-4857-acb2-9dd545e61447",
+      "gap": 76.25
+    },
+    {
+      "top": "nwtN_2b6ef682-26c7-48d7-9fd8-09fa76c7b718",
+      "bottom": "nwtN_eed8fc62-a21d-4677-85f2-f1244e3abf00",
+      "gap": 76.25
+    }
+  ]
+}

tools/ui/node_modules/cytoscape-fcose/demo/samples/uwsn.js

@@ -0,0 +1,2303 @@
+uwsn = {
+	"elements": {
+		"nodes": [
+			{
+				"data": {
+					"id": "nwtN_91cff953-5f55-4626-96fa-e2f675e13e54",
+					"bbox": {
+						"x": 155.38677910343796,
+						"y": 230.06625595029607,
+						"w": 140,
+						"h": 75
+					},
+					"class": "nucleic acid feature",
+					"label": "Surface\nBuoy 1",
+					"statesandinfos": [],
+					"language": "PD",
+					"border-width": 1.25,
+					"border-color": "#555555",
+					"background-color": "#f4a582",
+					"background-opacity": 1,
+					"background-image-opacity": 1,
+					"text-wrap": "wrap",
+					"font-size": 26,
+					"font-family": "Helvetica",
+					"font-style": "normal",
+					"font-weight": "normal",
+					"color": "#000000",
+					"background-image": "",
+					"ports": [],
+					"infoboxCalculated": true,
+					"auxunitlayouts": {}
+				},
+				"position": {
+					"x": 155.38677910343796,
+					"y": 230.06625595029607
+				},
+				"group": "nodes",
+				"removed": false,
+				"selected": false,
+				"selectable": true,
+				"locked": false,
+				"grabbable": true,
+				"classes": ""
+			},
+			{
+				"data": {
+					"id": "nwtN_b20cc3f4-dc9c-4031-ac79-df665d4c53cd",
+					"bbox": {
+						"x": 584.0229153054016,
+						"y": 223.74407633970037,
+						"w": 140,
+						"h": 75
+					},
+					"class": "nucleic acid feature",
+					"label": "Surface\nBuoy 2",
+					"statesandinfos": [],
+					"language": "PD",
+					"border-width": 1.25,
+					"border-color": "#555555",
+					"background-color": "#f4a582",
+					"background-opacity": 1,
+					"background-image-opacity": 1,
+					"text-wrap": "wrap",
+					"font-size": 26,
+					"font-family": "Helvetica",
+					"font-style": "normal",
+					"font-weight": "normal",
+					"color": "#000000",
+					"background-image": "",
+					"ports": [],
+					"infoboxCalculated": true,
+					"auxunitlayouts": {}
+				},
+				"position": {
+					"x": 584.0229153054016,
+					"y": 223.74407633970037
+				},
+				"group": "nodes",
+				"removed": false,
+				"selected": false,
+				"selectable": true,
+				"locked": false,
+				"grabbable": true,
+				"classes": ""
+			},
+			{
+				"data": {
+					"id": "nwtN_5d6f7198-03e4-48e5-9004-919221f87e66",
+					"bbox": {
+						"x": 964.8261492755391,
+						"y": 225.00851226181948,
+						"w": 140,
+						"h": 75
+					},
+					"class": "nucleic acid feature",
+					"label": "Surface\nBuoy 3",
+					"statesandinfos": [],
+					"language": "PD",
+					"border-width": 1.25,
+					"border-color": "#555555",
+					"background-color": "#f4a582",
+					"background-opacity": 1,
+					"background-image-opacity": 1,
+					"text-wrap": "wrap",
+					"font-size": 26,
+					"font-family": "Helvetica",
+					"font-style": "normal",
+					"font-weight": "normal",
+					"color": "#000000",
+					"background-image": "",
+					"ports": [],
+					"infoboxCalculated": true,
+					"auxunitlayouts": {}
+				},
+				"position": {
+					"x": 964.8261492755391,
+					"y": 225.00851226181948
+				},
+				"group": "nodes",
+				"removed": false,
+				"selected": false,
+				"selectable": true,
+				"locked": false,
+				"grabbable": true,
+				"classes": ""
+			},
+			{
+				"data": {
+					"id": "nwtN_7e09bf9e-a4da-4618-baba-60a2b3a0b134",
+					"bbox": {
+						"x": 149.1895292305374,
+						"y": 445.5622580973788,
+						"w": 140,
+						"h": 75
+					},
+					"class": "unspecified entity",
+					"label": "UW Sink 1",
+					"statesandinfos": [],
+					"language": "PD",
+					"border-width": 1.25,
+					"border-color": "#555555",
+					"background-color": "#f7f7f7",
+					"background-opacity": 1,
+					"background-image-opacity": 1,
+					"text-wrap": "wrap",
+					"font-size": 26,
+					"font-family": "Helvetica",
+					"font-style": "normal",
+					"font-weight": "normal",
+					"color": "#000000",
+					"background-image": "",
+					"ports": [],
+					"infoboxCalculated": true,
+					"auxunitlayouts": {}
+				},
+				"position": {
+					"x": 149.1895292305374,
+					"y": 445.5622580973788
+				},
+				"group": "nodes",
+				"removed": false,
+				"selected": false,
+				"selectable": true,
+				"locked": false,
+				"grabbable": true,
+				"classes": ""
+			},
+			{
+				"data": {
+					"id": "661498c7-ace9-bd34-0289-7c9931d3e1ba",
+					"bbox": {
+						"x": 586.7621909195482,
+						"y": 383.25228042246914,
+						"w": 140,
+						"h": 75
+					},
+					"class": "unspecified entity",
+					"label": "UW Sink 2",
+					"statesandinfos": [],
+					"language": "PD",
+					"border-width": 1.25,
+					"border-color": "#555555",
+					"background-color": "#f7f7f7",
+					"background-opacity": 1,
+					"background-image-opacity": 1,
+					"text-wrap": "wrap",
+					"font-size": 26,
+					"font-family": "Helvetica",
+					"font-style": "normal",
+					"font-weight": "normal",
+					"color": "#000000",
+					"background-image": "",
+					"ports": [],
+					"infoboxCalculated": true,
+					"auxunitlayouts": {}
+				},
+				"position": {
+					"x": 586.7621909195482,
+					"y": 383.25228042246914
+				},
+				"group": "nodes",
+				"removed": false,
+				"selected": false,
+				"selectable": true,
+				"locked": false,
+				"grabbable": true,
+				"classes": ""
+			},
+			{
+				"data": {
+					"id": "aeee80bf-8280-f4ec-c1f3-26f3a7a0651c",
+					"bbox": {
+						"x": 966.963391645274,
+						"y": 484.473671607378,
+						"w": 140,
+						"h": 75
+					},
+					"class": "unspecified entity",
+					"label": "UW Sink 3",
+					"statesandinfos": [],
+					"language": "PD",
+					"border-width": 1.25,
+					"border-color": "#555555",
+					"background-color": "#f7f7f7",
+					"background-opacity": 1,
+					"background-image-opacity": 1,
+					"text-wrap": "wrap",
+					"font-size": 26,
+					"font-family": "Helvetica",
+					"font-style": "normal",
+					"font-weight": "normal",
+					"color": "#000000",
+					"background-image": "",
+					"ports": [],
+					"infoboxCalculated": true,
+					"auxunitlayouts": {}
+				},
+				"position": {
+					"x": 966.963391645274,
+					"y": 484.473671607378
+				},
+				"group": "nodes",
+				"removed": false,
+				"selected": false,
+				"selectable": true,
+				"locked": false,
+				"grabbable": true,
+				"classes": ""
+			},
+			{
+				"data": {
+					"id": "nwtN_9ad406e1-da86-489d-84aa-627c8f5898e6",
+					"bbox": {
+						"x": -18.820589676794867,
+						"y": 580.4283573759083,
+						"w": 172.45719865368562,
+						"h": 192.7296338070105
+					},
+					"originalW": 200.45719865368562,
+					"originalH": 220.7296338070105,
+					"class": "submap",
+					"statesandinfos": [],
+					"language": "PD",
+					"border-width": 2.25,
+					"border-color": "#555555",
+					"background-color": "#f7f7f7",
+					"background-opacity": 0.5,
+					"background-image-opacity": 1,
+					"text-wrap": "wrap",
+					"font-size": 14,
+					"font-family": "Helvetica",
+					"font-style": "normal",
+					"font-weight": "normal",
+					"color": "#000",
+					"background-image": "",
+					"ports": [],
+					"infoboxCalculated": true,
+					"auxunitlayouts": {}
+				},
+				"position": {
+					"x": -18.82058967679486,
+					"y": 580.4283573759083
+				},
+				"group": "nodes",
+				"removed": false,
+				"selected": false,
+				"selectable": true,
+				"locked": false,
+				"grabbable": true,
+				"classes": ""
+			},
+			{
+				"data": {
+					"id": "nwtN_cbc5909d-c0a3-4be5-9c36-988ca48a9d30",
+					"bbox": {
+						"x": -65.92418900363768,
+						"y": 613.8182505696195,
+						"w": 75,
+						"h": 75
+					},
+					"class": "simple chemical",
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+				"classes": ""
+			},
+			{
+				"data": {
+					"id": "cba4c2db-9aa8-2429-37b7-ef58e51ccef5",
+					"class": "production",
+					"bendPointPositions": [],
+					"language": "PD",
+					"line-color": "#555555",
+					"width": 1.25,
+					"background-image": "",
+					"background-color": "#ffffff",
+					"cardinality": 0,
+					"source": "212adf44-8401-5b11-c49a-b43b67369698",
+					"target": "5c108d5c-88e4-7b97-95a8-67238c33d283",
+					"portsource": "212adf44-8401-5b11-c49a-b43b67369698",
+					"porttarget": "5c108d5c-88e4-7b97-95a8-67238c33d283"
+				},
+				"position": {},
+				"group": "edges",
+				"removed": false,
+				"selected": false,
+				"selectable": true,
+				"locked": false,
+				"grabbable": true,
+				"classes": ""
+			},
+			{
+				"data": {
+					"id": "75e10cd7-b168-147e-9842-dd6859a94e61",
+					"class": "production",
+					"bendPointPositions": [],
+					"language": "PD",
+					"line-color": "#555555",
+					"width": 1.25,
+					"background-image": "",
+					"background-color": "#ffffff",
+					"cardinality": 0,
+					"source": "4f9485a2-a66f-2cf1-cc4e-126f7889fcd0",
+					"target": "5c108d5c-88e4-7b97-95a8-67238c33d283",
+					"portsource": "4f9485a2-a66f-2cf1-cc4e-126f7889fcd0",
+					"porttarget": "5c108d5c-88e4-7b97-95a8-67238c33d283"
+				},
+				"position": {},
+				"group": "edges",
+				"removed": false,
+				"selected": false,
+				"selectable": true,
+				"locked": false,
+				"grabbable": true,
+				"classes": ""
+			},
+			{
+				"data": {
+					"id": "20b1d70b-c88f-acaf-0ced-07374db84055",
+					"class": "production",
+					"bendPointPositions": [],
+					"language": "PD",
+					"line-color": "#555555",
+					"width": 1.25,
+					"background-image": "",
+					"background-color": "#ffffff",
+					"cardinality": 0,
+					"source": "f1bf3c87-1357-3ce2-4645-8cb4ed59ac9b",
+					"target": "3ea6020e-8918-8abf-a8e5-62427070f84f",
+					"portsource": "f1bf3c87-1357-3ce2-4645-8cb4ed59ac9b",
+					"porttarget": "3ea6020e-8918-8abf-a8e5-62427070f84f"
+				},
+				"position": {},
+				"group": "edges",
+				"removed": false,
+				"selected": false,
+				"selectable": true,
+				"locked": false,
+				"grabbable": true,
+				"classes": ""
+			},
+			{
+				"data": {
+					"id": "1fefa878-d380-55e4-4d18-ec760fc294f4",
+					"class": "production",
+					"bendPointPositions": [],
+					"language": "PD",
+					"line-color": "#555555",
+					"width": 1.25,
+					"background-image": "",
+					"background-color": "#ffffff",
+					"cardinality": 0,
+					"source": "2f96a4e1-9767-4df9-6ad7-a4010baa376b",
+					"target": "3ea6020e-8918-8abf-a8e5-62427070f84f",
+					"portsource": "2f96a4e1-9767-4df9-6ad7-a4010baa376b",
+					"porttarget": "3ea6020e-8918-8abf-a8e5-62427070f84f"
+				},
+				"position": {},
+				"group": "edges",
+				"removed": false,
+				"selected": false,
+				"selectable": true,
+				"locked": false,
+				"grabbable": true,
+				"classes": ""
+			}
+		]
+	},
+	"style": [
+	    {
+	      "selector": "node",
+	      "style": {
+	        "shape": "rectangle",
+	        "text-halign": "center",
+	        "text-valign": "center",
+	        "font-weight" : "normal",
+	        "background-color": "#ffffff",
+	        "opacity": "1",
+	        "border-color": "#555555"
+	      }
+	    },
+	    {
+	      "selector": "node[class = 'simple chemical']",
+	      "style": {
+	        "shape": "ellipse",
+	        "font-size": 14,
+	        "background-color": "#fddbc7"
+	      }
+	    },
+	    {
+	      "selector": "node[class = 'macromolecule']",
+	      "style": {
+	        "shape": "roundrectangle"
+	      }
+	    },
+	    {
+	      "selector": "node[class = 'unspecified entity']",
+	      "style": {
+	        "shape": "ellipse",
+	        "background-color": "#f7f7f7"
+	      }
+	    },
+	    {
+	      "selector": "node[class = 'nucleic acid feature']",
+	      "style": {
+	        "shape": "rectangle",
+	        "background-color": "#f4a582",	        
+	      }
+	    },	    	    	   
+	    {
+	      "selector": ":parent",
+	      "style": {
+	        "background-opacity": "0.333",
+	        "text-valign": "bottom",
+	        "shape": "barrel",
+	        "text-margin-y": "2px",
+	        "font-weight" : "normal",
+	        "border-color": "#555555"
+	      }
+	    },
+	    {
+	      "selector": "node:selected",
+	      "style": {
+	        "background-color": "#33ff00",
+	        "border-color": "#22ee00"
+	      }
+	    },
+	    {
+	      "selector": "edge",
+	      "style": {
+	        "curve-style": "bezier",
+	        "width": "2px",
+	        "line-color": "rgb(58,126,207)",
+	        "opacity": "1"
+	      }
+	    },
+	    {
+	      "selector": "edge:selected",
+	      "style": {
+	        "line-color": "#33ff00",
+	        "font-size": "13px",
+	        "text-opacity": "1",
+	        "text-rotation": "autorotate",
+	        "color": "#33ff00",
+	        "font-weight": "bold",
+	        "text-background-shape": "roundrectangle",
+	        "text-background-opacity": "1",
+	        "text-background-padding": "2px"
+	      }
+	    },
+	    {
+	      "selector": "edge[class = 'production']",
+	      "style": {
+	        "target-arrow-shape": "triangle",
+	        "target-arrow-color": "rgb(58,126,207)"
+	      }
+	    },
+	    {
+	      "selector": "edge:selected[class = 'production']",
+	      "style": {
+	        "target-arrow-shape": "triangle",
+	        "target-arrow-color": "#33ff00"
+	      }
+	    },	    
+	  ],
+	"zoomingEnabled": true,
+	"userZoomingEnabled": true,
+	"zoom": 0.8925320450269244,
+	"minZoom": 0.125,
+	"maxZoom": 16,
+	"panningEnabled": true,
+	"userPanningEnabled": true,
+	"pan": {
+		"x": 128.15184671589566,
+		"y": -93.65929006599106
+	},
+	"boxSelectionEnabled": true,
+	"renderer": {
+		"name": "canvas"
+	},
+	"wheelSensitivity": 0.1,
+	"motionBlur": true
+}

tools/ui/node_modules/cytoscape-fcose/demo/samples/uwsn_constraints.js

@@ -0,0 +1,88 @@
+uwsn_constraints = {
+  "fixedNodeConstraint": [
+    {
+      "nodeId": "nwtN_91cff953-5f55-4626-96fa-e2f675e13e54",
+      "position": {
+        "x": -650,
+        "y": -230
+      }
+    },
+    {
+      "nodeId": "nwtN_b20cc3f4-dc9c-4031-ac79-df665d4c53cd",
+      "position": {
+        "x": 0,
+        "y": -230
+      }
+    },
+    {
+      "nodeId": "nwtN_5d6f7198-03e4-48e5-9004-919221f87e66",
+      "position": {
+        "x": 650,
+        "y": -230
+      }
+    }
+  ],
+  "alignmentConstraint": {
+    "vertical": [
+      [
+        "nwtN_91cff953-5f55-4626-96fa-e2f675e13e54",
+        "nwtN_7e09bf9e-a4da-4618-baba-60a2b3a0b134"
+      ],
+      [
+        "nwtN_b20cc3f4-dc9c-4031-ac79-df665d4c53cd",
+        "661498c7-ace9-bd34-0289-7c9931d3e1ba"
+      ],
+      [
+        "nwtN_5d6f7198-03e4-48e5-9004-919221f87e66",
+        "aeee80bf-8280-f4ec-c1f3-26f3a7a0651c"
+      ]
+    ]
+  },
+  "relativePlacementConstraint": [
+    {
+      "top": "nwtN_7e09bf9e-a4da-4618-baba-60a2b3a0b134",
+      "bottom": "nwtN_be627c29-b885-460c-bf92-8f9bb7b8c8c5",
+      "gap": 100
+    },
+    {
+      "top": "nwtN_7e09bf9e-a4da-4618-baba-60a2b3a0b134",
+      "bottom": "nwtN_64abed47-d1b1-474c-b944-b9ad6354c086",
+      "gap": 100
+    },
+    {
+      "top": "661498c7-ace9-bd34-0289-7c9931d3e1ba",
+      "bottom": "nwtN_0185dada-235a-4b51-bce7-e8bd3b8ee661",
+      "gap": 100
+    },
+    {
+      "top": "661498c7-ace9-bd34-0289-7c9931d3e1ba",
+      "bottom": "nwtN_273f6927-f05a-425b-aa2b-92de2be06bd9",
+      "gap": 100
+    },
+    {
+      "top": "aeee80bf-8280-f4ec-c1f3-26f3a7a0651c",
+      "bottom": "5c108d5c-88e4-7b97-95a8-67238c33d283",
+      "gap": 100
+    },
+    {
+      "top": "aeee80bf-8280-f4ec-c1f3-26f3a7a0651c",
+      "bottom": "3ea6020e-8918-8abf-a8e5-62427070f84f",
+      "gap": 100
+    },
+    {
+      "top": "nwtN_5d6f7198-03e4-48e5-9004-919221f87e66",
+      "bottom": "aeee80bf-8280-f4ec-c1f3-26f3a7a0651c",
+      "gap": 250
+    },
+    {
+      "top": "nwtN_b20cc3f4-dc9c-4031-ac79-df665d4c53cd",
+      "bottom": "661498c7-ace9-bd34-0289-7c9931d3e1ba",
+      "gap": 250
+    },
+    {
+      "top": "nwtN_91cff953-5f55-4626-96fa-e2f675e13e54",
+      "bottom": "nwtN_7e09bf9e-a4da-4618-baba-60a2b3a0b134",
+      "gap": 250
+    }
+  ]
+}

tools/ui/node_modules/cytoscape-fcose/demo/samples/wsn_constraints.js

@@ -0,0 +1,102 @@
+wsn_constraints = {
+  "fixedNodeConstraint": [
+    {
+      "nodeId": "86f48f58-145d-92cc-0d33-aaf639984733",
+      "position": {
+        "x": 399,
+        "y": 139
+      }
+    },
+    {
+      "nodeId": "f91d914e-6ab7-92cf-b16d-b9a7661e0044",
+      "position": {
+        "x": 857,
+        "y": 340
+      }
+    },
+    {
+      "nodeId": "33f80abd-028e-ad1c-068b-33d5b40d9a93",
+      "position": {
+        "x": 1068,
+        "y": 288
+      }
+    },
+    {
+      "nodeId": "2b855d36-0c89-996d-9281-ea54f711cc8e",
+      "position": {
+        "x": 520,
+        "y": 518
+      }
+    },
+    {
+      "nodeId": "0ddcc98c-7b7c-ac2e-2207-081c5ffc9921",
+      "position": {
+        "x": 533,
+        "y": -37
+      }
+    },
+    {
+      "nodeId": "e53126c9-70fe-ca8a-3b85-bab123a93d70",
+      "position": {
+        "x": 816,
+        "y": 280
+      }
+    },
+    {
+      "nodeId": "4ca3044f-9b82-020b-e1cb-bbb45e4b0088",
+      "position": {
+        "x": 630,
+        "y": 205
+      }
+    },
+    {
+      "nodeId": "bc0420e3-9b6e-4c97-74c6-61278dbc18d4",
+      "position": {
+        "x": 507,
+        "y": 407
+      }
+    },
+    {
+      "nodeId": "a97f8f48-6652-7e09-8eda-2d87eae7d20b",
+      "position": {
+        "x": 323,
+        "y": 330
+      }
+    },
+    {
+      "nodeId": "889eedb3-8cb8-b906-8beb-904cd499c4f6",
+      "position": {
+        "x": 892,
+        "y": -55
+      }
+    },
+    {
+      "nodeId": "bd77a77c-4627-ad77-1c5a-2c390ba21959",
+      "position": {
+        "x": 1114,
+        "y": 570
+      }
+    },
+    {
+      "nodeId": "ffbd69bf-481f-faa8-73db-1489f3175b75",
+      "position": {
+        "x": 666,
+        "y": 533
+      }
+    },
+    {
+      "nodeId": "5fdc6150-63bb-18e8-1f03-33bb8d6b7529",
+      "position": {
+        "x": 726,
+        "y": 670
+      }
+    },
+    {
+      "nodeId": "b386ca2b-81a7-e365-4706-f955f13db03f",
+      "position": {
+        "x": 721,
+        "y": -36
+      }
+    }
+  ]
+}

tools/ui/node_modules/cytoscape-fcose/node_modules/cose-base/.babelrc

@@ -0,0 +1,3 @@
+{
+  "presets": ["env"]
+}

tools/ui/node_modules/cytoscape-fcose/node_modules/cose-base/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2019 - present, iVis@Bilkent.
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

tools/ui/node_modules/cytoscape-fcose/node_modules/cose-base/README.md

@@ -0,0 +1,26 @@
+cose-base
+================================================================================
+
+## Description
+
+This is a core module for compound spring embedder based layout styles such as CoSE-Bilkent, fCoSE, and CiSE.
+
+## Dependencies
+
+ * layout-base ^2.0.0
+
+## Usage instructions
+
+Add `cose-base` as a dependecy to your layout extension.
+
+`require()` in the extension to reach functionality:
+
+ * `var CoSEConstants = require('cose-base').CoSEConstants`,
+ * `var CoSELayout = require('cose-base').CoSELayout`,
+ * `...`
+
+To reach functionality of `layout-base`:
+
+ * `var Integer = require('cose-base').layoutBase.Integer`,
+ * `var Layout = require('cose-base').layoutBase.Layout`,
+ * `...`

tools/ui/node_modules/cytoscape-fcose/node_modules/cose-base/bower.json

@@ -0,0 +1,23 @@
+{
+  "name": "cose-base",
+  "description": "Core module for compound spring embedder based layout styles",
+  "main": "cose-base.js",
+  "dependencies": {
+    "layout-base": "^1.0.0"
+  },
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/iVis-at-Bilkent/cose-base.git"
+  },
+  "ignore": [
+    "**/.*",
+    "node_modules",
+    "bower_components",
+    "test",
+    "tests"
+  ],
+  "keywords": [
+    "layout"
+  ],
+  "license": "MIT"
+}

tools/ui/node_modules/cytoscape-fcose/node_modules/cose-base/index.js

@@ -0,0 +1,16 @@
+'use strict';
+
+let coseBase = {};
+
+coseBase.layoutBase = require('layout-base');
+coseBase.CoSEConstants = require('./src/CoSEConstants');
+coseBase.CoSEEdge = require('./src/CoSEEdge');
+coseBase.CoSEGraph = require('./src/CoSEGraph');
+coseBase.CoSEGraphManager = require('./src/CoSEGraphManager');
+coseBase.CoSELayout = require('./src/CoSELayout');
+coseBase.CoSENode = require('./src/CoSENode');
+coseBase.ConstraintHandler = require('./src/ConstraintHandler');
+
+module.exports = coseBase;
+
+

tools/ui/node_modules/cytoscape-fcose/node_modules/cose-base/package.json

@@ -0,0 +1,40 @@
+{
+  "name": "cose-base",
+  "version": "2.2.0",
+  "description": "Core module for compound spring embedder based layout styles",
+  "main": "cose-base.js",
+  "scripts": {
+    "test": "echo \"Error: no test specified\" && exit 1",
+    "build": "cross-env NODE_ENV=production webpack",
+    "build:min": "cross-env NODE_ENV=production MIN=true webpack"
+  },
+  "repository": {
+    "type": "git",
+    "url": "git+https://github.com/iVis-at-Bilkent/cose-base.git"
+  },
+  "author": "",
+  "license": "MIT",
+  "bugs": {
+    "url": "https://github.com/iVis-at-Bilkent/cose-base/issues"
+  },
+  "homepage": "https://github.com/iVis-at-Bilkent/cose-base#readme",
+  "devDependencies": {
+    "babel-core": "^6.24.1",
+    "babel-loader": "^7.0.0",
+    "babel-preset-env": "^1.5.1",
+    "camelcase": "^4.1.0",
+    "cross-env": "^5.1.6",
+    "eslint": "^3.19.0",
+    "gh-pages": "^1.1.0",
+    "npm-run-all": "^4.1.2",
+    "rimraf": "^2.6.2",
+    "update": "^0.7.4",
+    "updater-license": "^1.0.0",
+    "webpack": "^5.36.1",
+    "webpack-cli": "^4.6.0",
+    "webpack-dev-server": "^3.11.2"
+  },
+  "dependencies": {
+    "layout-base": "^2.0.0"
+  }
+}

tools/ui/node_modules/cytoscape-fcose/node_modules/cose-base/src/CoSEConstants.js

@@ -0,0 +1,26 @@
+var FDLayoutConstants = require('layout-base').FDLayoutConstants;
+
+function CoSEConstants() {
+}
+
+//CoSEConstants inherits static props in FDLayoutConstants
+for (var prop in FDLayoutConstants) {
+  CoSEConstants[prop] = FDLayoutConstants[prop];
+}
+
+CoSEConstants.DEFAULT_USE_MULTI_LEVEL_SCALING = false;
+CoSEConstants.DEFAULT_RADIAL_SEPARATION = FDLayoutConstants.DEFAULT_EDGE_LENGTH;
+CoSEConstants.DEFAULT_COMPONENT_SEPERATION = 60;
+CoSEConstants.TILE = true;
+CoSEConstants.TILING_PADDING_VERTICAL = 10;
+CoSEConstants.TILING_PADDING_HORIZONTAL = 10;
+CoSEConstants.TRANSFORM_ON_CONSTRAINT_HANDLING = true;
+CoSEConstants.ENFORCE_CONSTRAINTS = true;
+CoSEConstants.APPLY_LAYOUT = true;
+CoSEConstants.RELAX_MOVEMENT_ON_CONSTRAINTS = true;
+CoSEConstants.TREE_REDUCTION_ON_INCREMENTAL = true;  // this should be set to false if there will be a constraint
+// This constant is for differentiating whether actual layout algorithm that uses cose-base wants to apply only incremental layout or 
+// an incremental layout on top of a randomized layout. If it is only incremental layout, then this constant should be true.
+CoSEConstants.PURE_INCREMENTAL = CoSEConstants.DEFAULT_INCREMENTAL;
+
+module.exports = CoSEConstants;

tools/ui/node_modules/cytoscape-fcose/node_modules/cose-base/src/CoSEEdge.js

@@ -0,0 +1,12 @@
+var FDLayoutEdge = require('layout-base').FDLayoutEdge;
+
+function CoSEEdge(source, target, vEdge) {
+  FDLayoutEdge.call(this, source, target, vEdge);
+}
+
+CoSEEdge.prototype = Object.create(FDLayoutEdge.prototype);
+for (var prop in FDLayoutEdge) {
+  CoSEEdge[prop] = FDLayoutEdge[prop];
+}
+
+module.exports = CoSEEdge

tools/ui/node_modules/cytoscape-fcose/node_modules/cose-base/src/CoSEGraph.js

@@ -0,0 +1,12 @@
+var LGraph = require('layout-base').LGraph;
+
+function CoSEGraph(parent, graphMgr, vGraph) {
+  LGraph.call(this, parent, graphMgr, vGraph);
+}
+
+CoSEGraph.prototype = Object.create(LGraph.prototype);
+for (var prop in LGraph) {
+  CoSEGraph[prop] = LGraph[prop];
+}
+
+module.exports = CoSEGraph;