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cytoscape-fcose.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["cytoscapeFcose"] = factory(require("cose-base"));
else
root["cytoscapeFcose"] = 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 = 6);
/******/ })
/************************************************************************/
/******/ ([
/* 0 */
/***/ (function(module, exports) {
module.exports = __WEBPACK_EXTERNAL_MODULE_0__;
/***/ }),
/* 1 */
/***/ (function(module, exports, __webpack_require__) {
"use strict";
/*
* Auxiliary functions
*/
var LinkedList = __webpack_require__(0).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); // forEach() only considers nodes -- sets N at call time
}
});
});
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;
};
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;
};
module.exports = auxiliary;
/***/ }),
/* 2 */
/***/ (function(module, exports, __webpack_require__) {
"use strict";
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__(3);
var aux = __webpack_require__(1);
var _require = __webpack_require__(5),
spectralLayout = _require.spectralLayout;
var _require2 = __webpack_require__(4),
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: 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,
// 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 constraintExist = options.fixedNodeConstraint || options.alignmentConstraint || options.relativePlacementConstraint;
// if any constraint exists, set some options
if (constraintExist) {
// constraints work with these options
options.tile = false;
options.packComponents = false;
}
// decide component packing is enabled or not
var layUtil = void 0;
var packingEnabled = false;
if (cy.layoutUtilities && options.packComponents && options.randomize) {
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) {
if (options.randomize) {
var result = spectralLayout(options); // apply spectral layout
spectralResult.push(result);
}
// apply cose layout as postprocessing
if (options.quality == "default" || options.quality == "proof") {
coseResult.push(coseLayout(options, spectralResult[0]));
}
} else {
// packing is enabled
var topMostNodes = aux.getTopMostNodes(options.eles.nodes());
components = aux.connectComponents(cy, options.eles, topMostNodes);
//send each component to spectral layout
if (options.randomize) {
components.forEach(function (component) {
options.eles = component;
spectralResult.push(spectralLayout(options));
});
}
if (options.quality == "default" || options.quality == "proof") {
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) {
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);
};
}
}
components.forEach(function (component, index) {
// send each component to cose layout
options.eles = component;
coseResult.push(coseLayout(options, spectralResult[index]));
});
}
// packing
if (components.length > 1) {
var subgraphs = [];
components.forEach(function (component, index) {
var nodeIndexes = void 0;
if (options.quality == "draft") {
nodeIndexes = spectralResult[index].nodeIndexes;
}
var subgraph = {};
subgraph.nodes = [];
subgraph.edges = [];
var nodeIndex = void 0;
component.nodes().forEach(function (node) {
if (options.quality == "draft") {
if (!node.isParent()) {
nodeIndex = nodeIndexes.get(node.id());
subgraph.nodes.push({ x: spectralResult[index].xCoords[nodeIndex] - node.boundingbox().w / 2, y: spectralResult[index].yCoords[nodeIndex] - node.boundingbox().h / 2, width: node.boundingbox().w, height: node.boundingbox().h });
} else {
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 {
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 (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 {
subgraph.edges.push({ startX: coseResult[index][source.id()].getCenterX(), startY: coseResult[index][source.id()].getCenterY(), endX: coseResult[index][target.id()].getCenterX(), endY: coseResult[index][target.id()].getCenterY() });
}
});
subgraphs.push(subgraph);
});
var shiftResult = layUtil.packComponents(subgraphs).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 {
coseResult.forEach(function (result, index) {
Object.keys(result).forEach(function (item) {
var nodeRectangle = result[item];
nodeRectangle.setCenter(nodeRectangle.getCenterX() + shiftResult[index].dx, nodeRectangle.getCenterY() + shiftResult[index].dy);
});
});
}
}
}
// move graph to its original position because spectral moves it to origin
if (!options.fixedNodeConstraint) {
var minXCoord = Number.POSITIVE_INFINITY;
var maxXCoord = Number.NEGATIVE_INFINITY;
var minYCoord = Number.POSITIVE_INFINITY;
var maxYCoord = Number.NEGATIVE_INFINITY;
if (options.quality == "draft") {
spectralResult.forEach(function (result) {
result.xCoords.forEach(function (value) {
if (value < minXCoord) minXCoord = value;
if (value > maxXCoord) maxXCoord = value;
});
result.yCoords.forEach(function (value) {
if (value < minYCoord) minYCoord = value;
if (value > maxYCoord) maxYCoord = value;
});
});
var boundingBox = options.eles.boundingBox();
var diffOnX = boundingBox.x1 + boundingBox.w / 2 - (maxXCoord + minXCoord) / 2;
var diffOnY = boundingBox.y1 + boundingBox.h / 2 - (maxYCoord + minYCoord) / 2;
spectralResult.forEach(function (result) {
result.xCoords = result.xCoords.map(function (x) {
return x + diffOnX;
});
result.yCoords = result.yCoords.map(function (y) {
return y + diffOnY;
});
});
} else {
coseResult.forEach(function (result) {
Object.keys(result).forEach(function (item) {
var node = result[item];
if (node.getCenterX() < minXCoord) minXCoord = node.getCenterX();
if (node.getCenterX() > maxXCoord) maxXCoord = node.getCenterX();
if (node.getCenterY() < minYCoord) minYCoord = node.getCenterY();
if (node.getCenterY() > maxYCoord) maxYCoord = node.getCenterY();
});
});
var _boundingBox = options.eles.boundingBox();
var _diffOnX = _boundingBox.x1 + _boundingBox.w / 2 - (maxXCoord + minXCoord) / 2;
var _diffOnY = _boundingBox.y1 + _boundingBox.h / 2 - (maxYCoord + minYCoord) / 2;
coseResult.forEach(function (result, index) {
Object.keys(result).forEach(function (item) {
var node = result[item];
node.setCenter(node.getCenterX() + _diffOnX, node.getCenterY() + _diffOnY);
});
});
}
}
}
// 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 theId = ele.data('id');
coseResult.forEach(function (result) {
if (theId in result) {
pos = { x: result[theId].getRect().getCenterX(), y: result[theId].getRect().getCenterY() };
}
});
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)
options.eles = eles;
eles.nodes().not(":parent").layoutPositions(layout, options, getPositions);
} else {
console.log("If randomize option is set to false, then quality option must be 'default' or 'proof'.");
}
}
}]);
return Layout;
}();
module.exports = Layout;
/***/ }),
/* 3 */
/***/ (function(module, exports, __webpack_require__) {
"use strict";
// 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;
};
/***/ }),
/* 4 */
/***/ (function(module, exports, __webpack_require__) {
"use strict";
/**
The implementation of the postprocessing part that applies CoSE layout over the spectral layout
*/
var aux = __webpack_require__(1);
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 LayoutConstants = __webpack_require__(0).layoutBase.LayoutConstants;
var FDLayoutConstants = __webpack_require__(0).layoutBase.FDLayoutConstants;
var CoSEConstants = __webpack_require__(0).CoSEConstants;
// main function that cose layout is processed
var coseLayout = function coseLayout(options, spectralResult) {
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"];
}
/**** Postprocessing functions ****/
// 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 = 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);
theNode = parent.add(new CoSENode(layout.graphManager, new PointD(parentInfo.topLeftX, parentInfo.topLeftY), new DimensionD(parentInfo.width, parentInfo.height)));
}
} 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
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 (options.nodeDimensionsIncludeLabels) {
if (theChild.isParent()) {
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) {
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.getEdgesBetween(targetNode).length == 0) {
var e1 = gm.add(layout.newEdge(), sourceNode, targetNode);
e1.id = edge.id();
}
}
};
// 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.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 == '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;
LayoutConstants.DEFAULT_UNIFORM_LEAF_NODE_SIZES = options.uniformNodeDimensions;
// This part is for demo purpose and will change during release
if (options.step == "transformed") {
CoSEConstants.TRANSFORM_ON_CONSTRAINT_HANDLING = true;
CoSEConstants.ENFORCE_CONSTRAINTS = false;
CoSEConstants.APPLY_LAYOUT = false;
}
if (options.step == "enforced") {
CoSEConstants.TRANSFORM_ON_CONSTRAINT_HANDLING = false;
CoSEConstants.ENFORCE_CONSTRAINTS = true;
CoSEConstants.APPLY_LAYOUT = false;
}
if (options.step == "cose") {
CoSEConstants.TRANSFORM_ON_CONSTRAINT_HANDLING = false;
CoSEConstants.ENFORCE_CONSTRAINTS = false;
CoSEConstants.APPLY_LAYOUT = true;
}
if (options.step == "all") {
if (options.randomize) CoSEConstants.TRANSFORM_ON_CONSTRAINT_HANDLING = true;else CoSEConstants.TRANSFORM_ON_CONSTRAINT_HANDLING = false;
CoSEConstants.ENFORCE_CONSTRAINTS = true;
CoSEConstants.APPLY_LAYOUT = true;
}
if (options.randomize && !(options.fixedNodeConstraint || options.alignmentConstraint || options.relativePlacementConstraint)) {
CoSEConstants.TREE_REDUCTION_ON_INCREMENTAL = true;
} else {
CoSEConstants.TREE_REDUCTION_ON_INCREMENTAL = false;
}
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 };
/***/ }),
/* 5 */
/***/ (function(module, exports, __webpack_require__) {
"use strict";
/**
The implementation of the spectral layout that is the first part of the fcose layout algorithm
*/
var aux = __webpack_require__(1);
var Matrix = __webpack_require__(0).layoutBase.Matrix;
var SVD = __webpack_require__(0).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;