@weng-lab/visualization 2.5.1 → 2.6.0-beta.1

package/dist/visualization.es101.js.map

@@ -1 +1 @@
-{"version":3,"file":"visualization.es101.js","sources":["../src/components/Graph/ScaleLegend.tsx"],"sourcesContent":["import React, { CSSProperties } from 'react';\nimport Typography from '@mui/material/Typography';\nimport InfoIcon from '@mui/icons-material/Info';\nimport Tooltip from '@mui/material/Tooltip';\n\ninterface ScaleProps {\n  scales: number[];\n  width: (n: number) => number;\n  scaleLabel?: string;\n}\n\nconst ScaleLegend: React.FC<ScaleProps> = ({ scales, width, scaleLabel }) => {\n  if (scales.length === 0) return null;\n\n  const sorted = [...scales].sort((a, b) => a - b);\n  const min = sorted[0];\n  const max = sorted[sorted.length - 1];\n  const mid1 = sorted[Math.floor(sorted.length / 4)];\n  const mid2 = sorted[Math.floor((sorted.length * 3) / 4)];\n\n  const scaleFunctionStr = width.toString();\n  let scaleFormula =\n    scaleFunctionStr\n      .match(/=>\\s*(.*)/)?.[1]\n      ?.trim()\n      .replace('Math.', '') || scaleFunctionStr;\n  if (scaleLabel) {\n    scaleFormula = scaleLabel;\n  }\n\n  const divStyle: CSSProperties = {\n    top: '20vh',\n    zIndex: 1000,\n    backgroundColor: 'white',\n    padding: '10px',\n    borderRadius: '5px',\n    fontSize: '13px',\n    width: '225px',\n    textAlign: 'left',\n  };\n\n  const scaleItemStyle: CSSProperties = {\n    display: 'flex',\n    alignItems: 'center',\n    justifyContent: 'left',\n    marginBottom: '5px',\n  };\n\n  return (\n    <div style={divStyle}>\n      <>\n        <Typography\n          variant=\"body2\"\n          component=\"h4\"\n          style={{\n            margin: '3px 0',\n            fontSize: '16px',\n            fontFamily: 'Arial',\n          }}\n        >\n          Edge Weight Scale:\n          <Tooltip\n            title={scaleFormula}\n            color=\"primary\"\n            sx={{ ml: 0.5 }}\n            placement=\"bottom\"\n          >\n            <InfoIcon\n              fontSize=\"small\"\n              style={{ marginBottom: '-4.5px', marginTop: '-7px' }}\n            />\n          </Tooltip>\n        </Typography>\n\n        <div\n          style={{\n            display: 'flex',\n            flexDirection: 'column',\n            alignItems: 'left',\n            marginTop: '10px',\n          }}\n        >\n          <div style={scaleItemStyle}>\n            <div\n              style={{\n                width: width(min),\n                height: '10px',\n                backgroundColor: 'black',\n                display: 'inline-block',\n              }}\n            ></div>\n            <Typography\n              variant=\"body2\"\n              style={{\n                marginLeft: '10px',\n                fontSize: '14px',\n                fontFamily: 'Arial',\n              }}\n            >\n              {min.toFixed(2)}\n            </Typography>\n          </div>\n          <div style={scaleItemStyle}>\n            <div\n              style={{\n                width: width(mid1),\n                height: '10px',\n                backgroundColor: 'black',\n                display: 'inline-block',\n              }}\n            ></div>\n            <Typography\n              variant=\"body2\"\n              style={{\n                marginLeft: '10px',\n                fontSize: '14px',\n                fontFamily: 'Arial',\n              }}\n            >\n              {mid1.toFixed(2)}\n            </Typography>\n          </div>\n          <div style={scaleItemStyle}>\n            <div\n              style={{\n                width: width(mid2),\n                height: '10px',\n                backgroundColor: 'black',\n                display: 'inline-block',\n              }}\n            ></div>\n            <Typography\n              variant=\"body2\"\n              style={{\n                marginLeft: '10px',\n                fontSize: '14px',\n                fontFamily: 'Arial',\n              }}\n            >\n              {mid2.toFixed(2)}\n            </Typography>\n          </div>\n        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package/dist/visualization.es102.js

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-import { __require as r } from "./visualization.es243.js";
-var t = r();
-const d = /* @__PURE__ */ o(t);
+import { jsx as l, jsxs as R, Fragment as y } from "react/jsx-runtime";
+import { c as f } from "react/compiler-runtime";
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+    boundedWidth: e,
+    boundedHeight: o
+  } = h, {
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+    y: n
+  } = x;
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+  let i;
+  t[4] !== o || t[5] !== e || t[6] !== s ? (i = s >= 0 && s <= e && /* @__PURE__ */ l("line", { x1: s, x2: s, y1: 0, y2: o, stroke: c, strokeWidth: d, strokeDasharray: S.join(","), pointerEvents: "none" }), t[4] = o, t[5] = e, t[6] = s, t[7] = i) : i = t[7];
+  let a;
+  return t[8] !== r || t[9] !== i ? (a = /* @__PURE__ */ R(y, { children: [
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+    i
+  ] }), t[8] = r, t[9] = i, t[10] = a) : a = t[10], a;
+};
 export {
-  d as default
+  S as CROSSHAIR_DASH,
+  c as CROSSHAIR_STROKE,
+  d as CROSSHAIR_STROKE_WIDTH,
+  H as default
 };
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package/dist/visualization.es102.js.map

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package/dist/visualization.es103.js

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-import { getDefaultExportFromCjs as o } from "./visualization.es135.js";
-import { __require as r } from "./visualization.es245.js";
-var e = r();
-const a = /* @__PURE__ */ o(e);
+import { c as q } from "react/compiler-runtime";
+import { useState as w } from "react";
+import { rescaleX as A, rescaleY as B, isPointInLasso as F } from "./visualization.es18.js";
+import G from "./visualization.es248.js";
+const Q = (k) => {
+  const t = q(27), {
+    pointData: S,
+    margin: s,
+    xScale: v,
+    yScale: g,
+    onSelectionChange: M
+  } = k;
+  let r;
+  t[0] === /* @__PURE__ */ Symbol.for("react.memo_cache_sentinel") ? (r = [], t[0] = r) : r = t[0];
+  const [n, c] = w(r);
+  let f;
+  t[1] !== s.left || t[2] !== s.top ? (f = (e) => {
+    if (e?.x === void 0 || e?.y === void 0)
+      return;
+    const o = e.x, l = e.y;
+    c((i) => [...i, [{
+      x: o - s.left,
+      y: l - s.top
+    }]]);
+  }, t[1] = s.left, t[2] = s.top, t[3] = f) : f = t[3];
+  const X = f;
+  let d;
+  t[4] !== s.left || t[5] !== s.top ? (d = (e) => {
+    if (e?.x === void 0 || e?.y === void 0)
+      return;
+    const o = e.x - s.left, l = e.y - s.top;
+    c((i) => {
+      const a = [...i], p = {
+        x: o + e.dx,
+        y: l + e.dy
+      }, $ = a.length - 1;
+      return a[$] = [...a[$] || [], p], a;
+    });
+  }, t[4] = s.left, t[5] = s.top, t[6] = d) : d = t[6];
+  const Y = d;
+  let x;
+  t[7] !== n || t[8] !== M || t[9] !== S || t[10] !== v || t[11] !== g ? (x = (e) => {
+    const o = n[n.length - 1];
+    if (!o) {
+      c([]);
+      return;
+    }
+    const l = A(v, e.transformMatrix.translateX, e.transformMatrix.scaleX), i = B(g, e.transformMatrix.translateY, e.transformMatrix.scaleY), a = S.filter((p) => F({
+      x: l(p.x),
+      y: i(p.y)
+    }, o));
+    M?.(a), c([]);
+  }, t[7] = n, t[8] = M, t[9] = S, t[10] = v, t[11] = g, t[12] = x) : x = t[12];
+  const h = x;
+  let m;
+  t[13] !== Y || t[14] !== X ? (m = {
+    onDragStart: X,
+    onDragMove: Y,
+    resetOnStart: !0
+  }, t[13] = Y, t[14] = X, t[15] = m) : m = t[15];
+  const {
+    x: E,
+    y: O,
+    dx: L,
+    dy: u,
+    isDragging: I,
+    dragStart: j,
+    dragEnd: P,
+    dragMove: T
+  } = G(m), b = E === void 0 ? 0 : E, C = O === void 0 ? 0 : O;
+  let y;
+  return t[16] !== h || t[17] !== P || t[18] !== T || t[19] !== j || t[20] !== L || t[21] !== u || t[22] !== I || t[23] !== n || t[24] !== b || t[25] !== C ? (y = {
+    lines: n,
+    isDragging: I,
+    x: b,
+    y: C,
+    dx: L,
+    dy: u,
+    dragStart: j,
+    dragMove: T,
+    dragEnd: P,
+    completeSelection: h
+  }, t[16] = h, t[17] = P, t[18] = T, t[19] = j, t[20] = L, t[21] = u, t[22] = I, t[23] = n, t[24] = b, t[25] = C, t[26] = y) : y = t[26], y;
+};
 export {
-  a as default
+  Q as useDragSelection
 };
 //# sourceMappingURL=visualization.es103.js.map

package/dist/visualization.es103.js.map

@@ -1 +1 @@
-{"version":3,"file":"visualization.es103.js","sources":[],"sourcesContent":[],"names":[],"mappings":";;;;"}
+{"version":3,"file":"visualization.es103.js","sources":["../src/components/ScatterPlot/hooks/useDragSelection.ts"],"sourcesContent":["import { useCallback, useState } from \"react\";\nimport { useDrag, HandlerArgs } from \"@visx/drag\";\nimport { ScaleLinear } from \"@visx/vendor/d3-scale\";\nimport { Line, Lines, Point, ZoomType } from \"../types\";\nimport { isPointInLasso, rescaleX, rescaleY } from \"../helpers\";\n\ntype UseDragSelectionProps<T extends object> = {\n    pointData: Point<T>[];\n    margin: { top: number; left: number };\n    xScale: ScaleLinear<number, number, never>;\n    yScale: ScaleLinear<number, number, never>;\n    onSelectionChange?: (selectedPoints: Point<T>[]) => void;\n};\n\nexport const useDragSelection = <T extends object>({\n    pointData,\n    margin,\n    xScale,\n    yScale,\n    onSelectionChange,\n}: UseDragSelectionProps<T>) => {\n    const [lines, setLines] = useState<Lines>([]);\n\n    const onDragStart = useCallback((currDrag: HandlerArgs) => {\n        if (currDrag?.x === undefined || currDrag?.y === undefined) return;\n        const startX = currDrag.x;\n        const startY = currDrag.y;\n\n        setLines((currLines) => [\n            ...currLines,\n            [{ x: startX - margin.left, y: startY - margin.top }],\n        ]);\n    }, [margin.left, margin.top]);\n\n    const onDragMove = useCallback((currDrag: HandlerArgs) => {\n        if (currDrag?.x === undefined || currDrag?.y === undefined) return;\n\n        const adjustedX = currDrag.x - margin.left;\n        const adjustedY = currDrag.y - margin.top;\n        setLines((currLines) => {\n            const nextLines = [...currLines];\n            const nextPoint = { x: adjustedX + currDrag.dx, y: adjustedY + currDrag.dy };\n            const lastIndex = nextLines.length - 1;\n            nextLines[lastIndex] = [...(nextLines[lastIndex] || []), nextPoint];\n            return nextLines;\n        });\n    }, [margin.left, margin.top]);\n\n    const 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 export {
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+import { __require as q } from "./visualization.es107.js";
+var j = O.exports, x;
+function W() {
+  return x ? O.exports : (x = 1, (function(b, Q) {
+    (function(c, d) {
+      b.exports = d(q());
+    })(j, function(F) {
+      return (
+        /******/
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+              return d[i].exports;
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+              /******/
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+          }
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+            return i;
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+          }, o.o = function(i, n) {
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+          }, o.p = "", o(o.s = 1);
+        })([
+          /* 0 */
+          /***/
+          (function(c, d) {
+            c.exports = F;
+          }),
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+            var i = o(0).layoutBase.LayoutConstants, n = o(0).layoutBase.FDLayoutConstants, s = o(0).CoSEConstants, H = o(0).CoSELayout, G = o(0).CoSENode, B = o(0).layoutBase.PointD, V = o(0).layoutBase.DimensionD, Y = {
+              // 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: !1,
+              // number of ticks per frame; higher is faster but more jerky
+              refresh: 30,
+              // Whether to fit the network view after when done
+              fit: !0,
+              // Padding on fit
+              padding: 10,
+              // Whether to enable incremental mode
+              randomize: !0,
+              // 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: !0,
+              // 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,
+              // Gravity range (constant)
+              gravityRange: 3.8,
+              // Initial cooling factor for incremental layout
+              initialEnergyOnIncremental: 0.5
+            };
+            function h(u, t) {
+              var l = {};
+              for (var r in u)
+                l[r] = u[r];
+              for (var r in t)
+                l[r] = t[r];
+              return l;
+            }
+            function p(u) {
+              this.options = h(Y, u), w(this.options);
+            }
+            var w = function(t) {
+              t.nodeRepulsion != null && (s.DEFAULT_REPULSION_STRENGTH = n.DEFAULT_REPULSION_STRENGTH = t.nodeRepulsion), t.idealEdgeLength != null && (s.DEFAULT_EDGE_LENGTH = n.DEFAULT_EDGE_LENGTH = t.idealEdgeLength), t.edgeElasticity != null && (s.DEFAULT_SPRING_STRENGTH = n.DEFAULT_SPRING_STRENGTH = t.edgeElasticity), t.nestingFactor != null && (s.PER_LEVEL_IDEAL_EDGE_LENGTH_FACTOR = n.PER_LEVEL_IDEAL_EDGE_LENGTH_FACTOR = t.nestingFactor), t.gravity != null && (s.DEFAULT_GRAVITY_STRENGTH = n.DEFAULT_GRAVITY_STRENGTH = t.gravity), t.numIter != null && (s.MAX_ITERATIONS = n.MAX_ITERATIONS = t.numIter), t.gravityRange != null && (s.DEFAULT_GRAVITY_RANGE_FACTOR = n.DEFAULT_GRAVITY_RANGE_FACTOR = t.gravityRange), t.gravityCompound != null && (s.DEFAULT_COMPOUND_GRAVITY_STRENGTH = n.DEFAULT_COMPOUND_GRAVITY_STRENGTH = t.gravityCompound), t.gravityRangeCompound != null && (s.DEFAULT_COMPOUND_GRAVITY_RANGE_FACTOR = n.DEFAULT_COMPOUND_GRAVITY_RANGE_FACTOR = t.gravityRangeCompound), t.initialEnergyOnIncremental != null && (s.DEFAULT_COOLING_FACTOR_INCREMENTAL = n.DEFAULT_COOLING_FACTOR_INCREMENTAL = t.initialEnergyOnIncremental), t.quality == "draft" ? i.QUALITY = 0 : t.quality == "proof" ? i.QUALITY = 2 : i.QUALITY = 1, s.NODE_DIMENSIONS_INCLUDE_LABELS = n.NODE_DIMENSIONS_INCLUDE_LABELS = i.NODE_DIMENSIONS_INCLUDE_LABELS = t.nodeDimensionsIncludeLabels, s.DEFAULT_INCREMENTAL = n.DEFAULT_INCREMENTAL = i.DEFAULT_INCREMENTAL = !t.randomize, s.ANIMATE = n.ANIMATE = i.ANIMATE = t.animate, s.TILE = t.tile, s.TILING_PADDING_VERTICAL = typeof t.tilingPaddingVertical == "function" ? t.tilingPaddingVertical.call() : t.tilingPaddingVertical, s.TILING_PADDING_HORIZONTAL = typeof t.tilingPaddingHorizontal == "function" ? t.tilingPaddingHorizontal.call() : t.tilingPaddingHorizontal;
+            };
+            p.prototype.run = function() {
+              var u, t, l = this.options;
+              this.idToLNode = {};
+              var r = this.layout = new H(), a = this;
+              a.stopped = !1, this.cy = this.options.cy, this.cy.trigger({ type: "layoutstart", layout: this });
+              var e = r.newGraphManager();
+              this.gm = e;
+              var g = this.options.eles.nodes(), f = this.options.eles.edges();
+              this.root = e.addRoot(), this.processChildrenList(this.root, this.getTopMostNodes(g), r);
+              for (var E = 0; E < f.length; E++) {
+                var A = f[E], v = this.idToLNode[A.data("source")], D = this.idToLNode[A.data("target")];
+                if (v !== D && v.getEdgesBetween(D).length == 0) {
+                  var N = e.add(r.newEdge(), v, D);
+                  N.id = A.id();
+                }
+              }
+              var U = function(L, m) {
+                typeof L == "number" && (L = m);
+                var I = L.data("id"), R = a.idToLNode[I];
+                return {
+                  x: R.getRect().getCenterX(),
+                  y: R.getRect().getCenterY()
+                };
+              }, z = function S() {
+                for (var L = function() {
+                  l.fit && l.cy.fit(l.eles, l.padding), u || (u = !0, a.cy.one("layoutready", l.ready), a.cy.trigger({ type: "layoutready", layout: a }));
+                }, m = a.options.refresh, I, R = 0; R < m && !I; R++)
+                  I = a.stopped || a.layout.tick();
+                if (I) {
+                  r.checkLayoutSuccess() && !r.isSubLayout && r.doPostLayout(), r.tilingPostLayout && r.tilingPostLayout(), r.isLayoutFinished = !0, a.options.eles.nodes().positions(U), L(), a.cy.one("layoutstop", a.options.stop), a.cy.trigger({ type: "layoutstop", layout: a }), t && cancelAnimationFrame(t), u = !1;
+                  return;
+                }
+                var C = a.layout.getPositionsData();
+                l.eles.nodes().positions(function(y, k) {
+                  if (typeof y == "number" && (y = k), !y.isParent()) {
+                    for (var M = y.id(), T = C[M], _ = y; T == null && (T = C[_.data("parent")] || C["DummyCompound_" + _.data("parent")], C[M] = T, _ = _.parent()[0], _ != null); )
+                      ;
+                    return T != null ? {
+                      x: T.x,
+                      y: T.y
+                    } : {
+                      x: y.position("x"),
+                      y: y.position("y")
+                    };
+                  }
+                }), L(), t = requestAnimationFrame(S);
+              };
+              return r.addListener("layoutstarted", function() {
+                a.options.animate === "during" && (t = requestAnimationFrame(z));
+              }), r.runLayout(), this.options.animate !== "during" && (a.options.eles.nodes().not(":parent").layoutPositions(a, a.options, U), u = !1), this;
+            }, p.prototype.getTopMostNodes = function(u) {
+              for (var t = {}, l = 0; l < u.length; l++)
+                t[u[l].id()] = !0;
+              var r = u.filter(function(a, e) {
+                typeof a == "number" && (a = e);
+                for (var g = a.parent()[0]; g != null; ) {
+                  if (t[g.id()])
+                    return !1;
+                  g = g.parent()[0];
+                }
+                return !0;
+              });
+              return r;
+            }, p.prototype.processChildrenList = function(u, t, l) {
+              for (var r = t.length, a = 0; a < r; a++) {
+                var e = t[a], g = e.children(), f, E = e.layoutDimensions({
+                  nodeDimensionsIncludeLabels: this.options.nodeDimensionsIncludeLabels
+                });
+                if (e.outerWidth() != null && e.outerHeight() != null ? f = u.add(new G(l.graphManager, new B(e.position("x") - E.w / 2, e.position("y") - E.h / 2), new V(parseFloat(E.w), parseFloat(E.h)))) : f = u.add(new G(this.graphManager)), f.id = e.data("id"), f.paddingLeft = parseInt(e.css("padding")), f.paddingTop = parseInt(e.css("padding")), f.paddingRight = parseInt(e.css("padding")), f.paddingBottom = parseInt(e.css("padding")), this.options.nodeDimensionsIncludeLabels && e.isParent()) {
+                  var A = e.boundingBox({ includeLabels: !0, includeNodes: !1 }).w, v = e.boundingBox({ includeLabels: !0, includeNodes: !1 }).h, D = e.css("text-halign");
+                  f.labelWidth = A, f.labelHeight = v, f.labelPos = D;
+                }
+                if (this.idToLNode[e.data("id")] = f, isNaN(f.rect.x) && (f.rect.x = 0), isNaN(f.rect.y) && (f.rect.y = 0), g != null && g.length > 0) {
+                  var N;
+                  N = l.getGraphManager().add(l.newGraph(), f), this.processChildrenList(N, g, l);
+                }
+              }
+            }, p.prototype.stop = function() {
+              return this.stopped = !0, this;
+            };
+            var P = function(t) {
+              t("layout", "cose-bilkent", p);
+            };
+            typeof cytoscape < "u" && P(cytoscape), c.exports = P;
+          })
+          /******/
+        ])
+      );
+    });
+  })(O), O.exports);
+}
 export {
-  H as default
+  W as __require
 };
 //# sourceMappingURL=visualization.es105.js.map

package/dist/visualization.es105.js.map

@@ -1 +1 @@
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higher is faster but more jerky\n  refresh: 30,\n  // Whether to fit the network view after when done\n  fit: true,\n  // Padding on fit\n  padding: 10,\n  // Whether to enable incremental mode\n  randomize: true,\n  // Node repulsion (non overlapping) multiplier\n  nodeRepulsion: 4500,\n  // Ideal edge (non nested) length\n  idealEdgeLength: 50,\n  // Divisor to compute edge forces\n  edgeElasticity: 0.45,\n  // Nesting factor (multiplier) to compute ideal edge length for nested edges\n  nestingFactor: 0.1,\n  // Gravity force (constant)\n  gravity: 0.25,\n  // Maximum number of iterations to perform\n  numIter: 2500,\n  // For enabling tiling\n  tile: true,\n  // Type of layout animation. The option set is {'during', 'end', false}\n  animate: 'end',\n  // Duration for animate:end\n  animationDuration: 500,\n  // Represents the amount of the vertical space to put between the zero degree members during the tiling operation(can also be a function)\n  tilingPaddingVertical: 10,\n  // Represents the amount of the horizontal space to put between the zero degree members during the tiling operation(can also be a function)\n  tilingPaddingHorizontal: 10,\n  // Gravity range (constant) for compounds\n  gravityRangeCompound: 1.5,\n  // Gravity force (constant) for compounds\n  gravityCompound: 1.0,\n  // Gravity range (constant)\n  gravityRange: 3.8,\n  // Initial cooling factor for incremental layout\n  initialEnergyOnIncremental: 0.5\n};\n\nfunction extend(defaults, options) {\n  var obj = {};\n\n  for (var i in defaults) {\n    obj[i] = defaults[i];\n  }\n\n  for (var i in options) {\n    obj[i] = options[i];\n  }\n\n  return obj;\n};\n\nfunction _CoSELayout(_options) {\n  this.options = extend(defaults, _options);\n  getUserOptions(this.options);\n}\n\nvar getUserOptions = function getUserOptions(options) {\n  if (options.nodeRepulsion != null) CoSEConstants.DEFAULT_REPULSION_STRENGTH = FDLayoutConstants.DEFAULT_REPULSION_STRENGTH = options.nodeRepulsion;\n  if (options.idealEdgeLength != null) CoSEConstants.DEFAULT_EDGE_LENGTH = FDLayoutConstants.DEFAULT_EDGE_LENGTH = options.idealEdgeLength;\n  if (options.edgeElasticity != null) CoSEConstants.DEFAULT_SPRING_STRENGTH = FDLayoutConstants.DEFAULT_SPRING_STRENGTH = options.edgeElasticity;\n  if (options.nestingFactor != null) CoSEConstants.PER_LEVEL_IDEAL_EDGE_LENGTH_FACTOR = FDLayoutConstants.PER_LEVEL_IDEAL_EDGE_LENGTH_FACTOR = options.nestingFactor;\n  if (options.gravity != null) CoSEConstants.DEFAULT_GRAVITY_STRENGTH = FDLayoutConstants.DEFAULT_GRAVITY_STRENGTH = options.gravity;\n  if (options.numIter != null) CoSEConstants.MAX_ITERATIONS = FDLayoutConstants.MAX_ITERATIONS = options.numIter;\n  if (options.gravityRange != null) CoSEConstants.DEFAULT_GRAVITY_RANGE_FACTOR = FDLayoutConstants.DEFAULT_GRAVITY_RANGE_FACTOR = options.gravityRange;\n  if (options.gravityCompound != null) CoSEConstants.DEFAULT_COMPOUND_GRAVITY_STRENGTH = FDLayoutConstants.DEFAULT_COMPOUND_GRAVITY_STRENGTH = options.gravityCompound;\n  if (options.gravityRangeCompound != null) CoSEConstants.DEFAULT_COMPOUND_GRAVITY_RANGE_FACTOR = FDLayoutConstants.DEFAULT_COMPOUND_GRAVITY_RANGE_FACTOR = options.gravityRangeCompound;\n  if (options.initialEnergyOnIncremental != null) CoSEConstants.DEFAULT_COOLING_FACTOR_INCREMENTAL = FDLayoutConstants.DEFAULT_COOLING_FACTOR_INCREMENTAL = options.initialEnergyOnIncremental;\n\n  if (options.quality == 'draft') LayoutConstants.QUALITY = 0;else if (options.quality == 'proof') LayoutConstants.QUALITY = 2;else LayoutConstants.QUALITY = 1;\n\n  CoSEConstants.NODE_DIMENSIONS_INCLUDE_LABELS = FDLayoutConstants.NODE_DIMENSIONS_INCLUDE_LABELS = LayoutConstants.NODE_DIMENSIONS_INCLUDE_LABELS = options.nodeDimensionsIncludeLabels;\n  CoSEConstants.DEFAULT_INCREMENTAL = FDLayoutConstants.DEFAULT_INCREMENTAL = LayoutConstants.DEFAULT_INCREMENTAL = !options.randomize;\n  CoSEConstants.ANIMATE = FDLayoutConstants.ANIMATE = LayoutConstants.ANIMATE = options.animate;\n  CoSEConstants.TILE = options.tile;\n  CoSEConstants.TILING_PADDING_VERTICAL = typeof options.tilingPaddingVertical === 'function' ? options.tilingPaddingVertical.call() : options.tilingPaddingVertical;\n  CoSEConstants.TILING_PADDING_HORIZONTAL = typeof options.tilingPaddingHorizontal === 'function' ? options.tilingPaddingHorizontal.call() : options.tilingPaddingHorizontal;\n};\n\n_CoSELayout.prototype.run = function () {\n  var ready;\n  var frameId;\n  var options = this.options;\n  var idToLNode = this.idToLNode = {};\n  var layout = this.layout = new CoSELayout();\n  var self = this;\n\n  self.stopped = false;\n\n  this.cy = this.options.cy;\n\n  this.cy.trigger({ type: 'layoutstart', layout: this });\n\n  var gm = layout.newGraphManager();\n  this.gm = gm;\n\n  var nodes = this.options.eles.nodes();\n  var edges = this.options.eles.edges();\n\n  this.root = gm.addRoot();\n  this.processChildrenList(this.root, this.getTopMostNodes(nodes), layout);\n\n  for (var i = 0; i < edges.length; i++) {\n    var edge = edges[i];\n    var sourceNode = this.idToLNode[edge.data(\"source\")];\n    var targetNode = this.idToLNode[edge.data(\"target\")];\n    if (sourceNode !== targetNode && sourceNode.getEdgesBetween(targetNode).length == 0) {\n      var e1 = gm.add(layout.newEdge(), sourceNode, targetNode);\n      e1.id = edge.id();\n    }\n  }\n\n  var getPositions = function getPositions(ele, i) {\n    if (typeof ele === \"number\") {\n      ele = i;\n    }\n    var theId = ele.data('id');\n    var lNode = self.idToLNode[theId];\n\n    return {\n      x: lNode.getRect().getCenterX(),\n      y: lNode.getRect().getCenterY()\n    };\n  };\n\n  /*\n   * Reposition nodes in iterations animatedly\n   */\n  var iterateAnimated = function iterateAnimated() {\n    // Thigs to perform after nodes are repositioned on screen\n    var afterReposition = function afterReposition() {\n      if (options.fit) {\n        options.cy.fit(options.eles, options.padding);\n      }\n\n      if (!ready) {\n        ready = true;\n        self.cy.one('layoutready', options.ready);\n        self.cy.trigger({ type: 'layoutready', layout: self });\n      }\n    };\n\n    var ticksPerFrame = self.options.refresh;\n    var isDone;\n\n    for (var i = 0; i < ticksPerFrame && !isDone; i++) {\n      isDone = self.stopped || self.layout.tick();\n    }\n\n    // If layout is done\n    if (isDone) {\n      // If the layout is not a sublayout and it is successful perform post layout.\n      if (layout.checkLayoutSuccess() && !layout.isSubLayout) {\n        layout.doPostLayout();\n      }\n\n      // If layout has a tilingPostLayout function property call it.\n      if (layout.tilingPostLayout) {\n        layout.tilingPostLayout();\n      }\n\n      layout.isLayoutFinished = true;\n\n      self.options.eles.nodes().positions(getPositions);\n\n      afterReposition();\n\n      // trigger layoutstop when the layout stops (e.g. finishes)\n      self.cy.one('layoutstop', self.options.stop);\n      self.cy.trigger({ type: 'layoutstop', layout: self });\n\n      if (frameId) {\n        cancelAnimationFrame(frameId);\n      }\n\n      ready = false;\n      return;\n    }\n\n    var animationData = self.layout.getPositionsData(); // Get positions of layout nodes note that all nodes may not be layout nodes because of tiling\n\n    // Position nodes, for the nodes whose id does not included in data (because they are removed from their parents and included in dummy compounds)\n    // use position of their ancestors or dummy ancestors\n    options.eles.nodes().positions(function (ele, i) {\n      if (typeof ele === \"number\") {\n        ele = i;\n      }\n      // If ele is a compound node, then its position will be defined by its children\n      if (!ele.isParent()) {\n        var theId = ele.id();\n        var pNode = animationData[theId];\n        var temp = ele;\n        // If pNode is undefined search until finding position data of its first ancestor (It may be dummy as well)\n        while (pNode == null) {\n          pNode = animationData[temp.data('parent')] || animationData['DummyCompound_' + temp.data('parent')];\n          animationData[theId] = pNode;\n          temp = temp.parent()[0];\n          if (temp == undefined) {\n            break;\n          }\n        }\n        if (pNode != null) {\n          return {\n            x: pNode.x,\n            y: pNode.y\n          };\n        } else {\n          return {\n            x: ele.position('x'),\n            y: ele.position('y')\n          };\n        }\n      }\n    });\n\n    afterReposition();\n\n    frameId = requestAnimationFrame(iterateAnimated);\n  };\n\n  /*\n  * Listen 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