@weng-lab/visualization 2.5.0 → 2.5.1-beta.0

package/dist/visualization.es103.js.map

@@ -1 +1 @@
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};\n/******/\n/******/ \t// __webpack_public_path__\n/******/ \t__webpack_require__.p = \"\";\n/******/\n/******/ \t// Load entry module and return exports\n/******/ \treturn __webpack_require__(__webpack_require__.s = 1);\n/******/ })\n/************************************************************************/\n/******/ ([\n/* 0 */\n/***/ (function(module, exports) {\n\nmodule.exports = __WEBPACK_EXTERNAL_MODULE_0__;\n\n/***/ }),\n/* 1 */\n/***/ (function(module, exports, __webpack_require__) {\n\n\"use strict\";\n\n\nvar LayoutConstants = __webpack_require__(0).layoutBase.LayoutConstants;\nvar FDLayoutConstants = __webpack_require__(0).layoutBase.FDLayoutConstants;\nvar CoSEConstants = __webpack_require__(0).CoSEConstants;\nvar CoSELayout = __webpack_require__(0).CoSELayout;\nvar CoSENode = __webpack_require__(0).CoSENode;\nvar PointD = __webpack_require__(0).layoutBase.PointD;\nvar DimensionD = __webpack_require__(0).layoutBase.DimensionD;\n\nvar defaults = {\n  // Called on `layoutready`\n  ready: function ready() {},\n  // Called on `layoutstop`\n  stop: function stop() {},\n  // 'draft', 'default' or 'proof\" \n  // - 'draft' fast cooling rate \n  // - 'default' moderate cooling rate \n  // - \"proof\" slow cooling rate\n  quality: 'default',\n  // include labels in node dimensions\n  nodeDimensionsIncludeLabels: false,\n  // number of ticks per frame; 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 'layoutstarted' event and start animated iteration if animate option is 'during'\n  */\n  layout.addListener('layoutstarted', function () {\n    if (self.options.animate === 'during') {\n      frameId = requestAnimationFrame(iterateAnimated);\n    }\n  });\n\n  layout.runLayout(); // Run cose layout\n\n  /*\n   * If animate option is not 'during' ('end' or false) perform these here (If it is 'during' similar things are already performed)\n   */\n  if (this.options.animate !== \"during\") {\n    self.options.eles.nodes().not(\":parent\").layoutPositions(self, self.options, getPositions); // Use layout positions to reposition the nodes it considers the options parameter\n    ready = false;\n  }\n\n  return this; // chaining\n};\n\n//Get the top most ones of a list of nodes\n_CoSELayout.prototype.getTopMostNodes = function (nodes) {\n  var nodesMap = {};\n  for (var i = 0; i < nodes.length; i++) {\n    nodesMap[nodes[i].id()] = true;\n  }\n  var roots = nodes.filter(function (ele, i) {\n    if (typeof ele === \"number\") {\n      ele = i;\n    }\n    var parent = ele.parent()[0];\n    while (parent != null) {\n      if (nodesMap[parent.id()]) {\n        return false;\n      }\n      parent = parent.parent()[0];\n    }\n    return true;\n  });\n\n  return roots;\n};\n\n_CoSELayout.prototype.processChildrenList = function (parent, children, layout) {\n  var size = children.length;\n  for (var i = 0; i < size; i++) {\n    var theChild = children[i];\n    var children_of_children = theChild.children();\n    var theNode;\n\n    var dimensions = theChild.layoutDimensions({\n      nodeDimensionsIncludeLabels: this.options.nodeDimensionsIncludeLabels\n    });\n\n    if (theChild.outerWidth() != null && theChild.outerHeight() != null) {\n      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))));\n    } else {\n      theNode = parent.add(new CoSENode(this.graphManager));\n    }\n    // Attach id to the layout node\n    theNode.id = theChild.data(\"id\");\n    // Attach the paddings of cy node to layout node\n    theNode.paddingLeft = parseInt(theChild.css('padding'));\n    theNode.paddingTop = parseInt(theChild.css('padding'));\n    theNode.paddingRight = parseInt(theChild.css('padding'));\n    theNode.paddingBottom = parseInt(theChild.css('padding'));\n\n    //Attach the label properties to compound if labels will be included in node dimensions  \n    if (this.options.nodeDimensionsIncludeLabels) {\n      if (theChild.isParent()) {\n        var labelWidth = theChild.boundingBox({ includeLabels: true, includeNodes: false }).w;\n        var labelHeight = theChild.boundingBox({ includeLabels: true, includeNodes: false }).h;\n        var labelPos = theChild.css(\"text-halign\");\n        theNode.labelWidth = labelWidth;\n        theNode.labelHeight = labelHeight;\n        theNode.labelPos = 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package/dist/visualization.es104.js

@@ -1,17 +1,5 @@
-import { jsx as e } from "react/jsx-runtime";
-import { useBranchLengthTransition as m } from "./visualization.es7.js";
-import { memo as s } from "react";
-import { motion as a } from "./visualization.es55.js";
-const k = s(function({
-  useBranchLengths: n,
-  color: i,
-  baseLeafLinkExtension: o,
-  scaledLeafLinkExtension: t,
-  strokeWidth: r
-}) {
-  return /* @__PURE__ */ e(a.line, { strokeWidth: r, initial: !1, animate: n ? t : o, stroke: i, transition: m });
-});
+var e = { exports: {} };
 export {
-  k as LeafLinkExtension
+  e as __module
 };
 //# sourceMappingURL=visualization.es104.js.map

package/dist/visualization.es104.js.map

@@ -1 +1 @@
-{"version":3,"file":"visualization.es104.js","sources":["../src/components/PhyloTree/LeafLinkExtension.tsx"],"sourcesContent":["import { motion } from \"framer-motion\";\nimport { useBranchLengthTransition } from \"./PhyloTree\";\nimport { memo } from \"react\";\nimport { TreeNode } from \"./types\";\n\n\nexport type LeafLinkExtensionProps = {\n  baseLeafLinkExtension: TreeNode[\"baseLeafLinkExtension\"]\n  scaledLeafLinkExtension: TreeNode[\"scaledLeafLinkExtension\"]\n  color: TreeNode[\"color\"];\n  strokeWidth: TreeNode[\"linkStrokeWidth\"]\n  useBranchLengths: boolean\n};\n\nexport const LeafLinkExtension = memo(function LinkExtension({\n  useBranchLengths,\n  color,\n  baseLeafLinkExtension,\n  scaledLeafLinkExtension,\n  strokeWidth\n}: LeafLinkExtensionProps) {\n\n  return (\n    <motion.line\n      strokeWidth={strokeWidth}\n      initial={false}\n      animate={useBranchLengths ? scaledLeafLinkExtension : baseLeafLinkExtension}\n      stroke={color}\n      transition={useBranchLengthTransition}\n    />\n  );\n});\n"],"names":["LeafLinkExtension","memo","useBranchLengths","color","baseLeafLinkExtension","scaledLeafLinkExtension","strokeWidth","jsx","motion","useBranchLengthTransition"],"mappings":";;;;AAcO,MAAMA,IAAoBC,EAAK,SAAuB;AAAA,EAC3DC,kBAAAA;AAAAA,EACAC,OAAAA;AAAAA,EACAC,uBAAAA;AAAAA,EACAC,yBAAAA;AAAAA,EACAC,aAAAA;AACsB,GAAG;AAEzB,SACE,gBAAAC,EAACC,EAAO,MAAP,EACC,aAAAF,GACA,SAAS,IACT,SAASJ,IAAmBG,IAA0BD,GACtD,QAAQD,GACR,YAAYM,GAA0B;AAG5C,CAAC;"}
+{"version":3,"file":"visualization.es104.js","sources":[],"sourcesContent":[],"names":[],"mappings":";"}