Tree render order

.eslintrc

@@ -46,6 +46,7 @@ rules:
   no-unneeded-ternary: ["error", { "defaultAssignment": true }]
   quote-props: ["error", "as-needed"]
   prefer-const: ["error", {"destructuring": "all"}]
+  indent: ["error", 2, {"MemberExpression": "off"}]
 parserOptions:
   ecmaVersion: 6
   sourceType: module

src/components/tree/phyloTree/change.js

@@ -40,9 +40,6 @@ const svgSetters = {
     ".vaccineCross": {
       d: (d) => d.vaccineCross
     },
-    ".vaccineDottedLine": {
-      d: (d) => d.vaccineLine
-    },
     ".conf": {
       d: (d) => d.confLine
     }
@@ -53,9 +50,6 @@ const svgSetters = {
       "stroke": (d) => d.tipStroke,
       "visibility": (d) => d["visibility"]
     },
-    ".vaccineDottedLine": {
-      opacity: (d) => d.that.distance === "num_date" ? 1 : 0
-    },
     ".conf": {
       "stroke": (d) => d.branchStroke,
       "stroke-width": calcConfidenceWidth
@@ -159,7 +153,7 @@ export const modifySVG = function modifySVG(elemsToUpdate, svgPropsToUpdate, tra
     else this.hideGrid();
   }
   if (elemsToUpdate.has('.regression')) {
-    this.svg.selectAll(".regression").remove();
+    this.removeRegression();
     if (this.layout === "clock" && this.distance === "num_date") this.drawRegression();
   }
 
@@ -179,7 +173,7 @@ export const modifySVG = function modifySVG(elemsToUpdate, svgPropsToUpdate, tra
 
   /* branch labels */
   if (extras.newBranchLabellingKey) {
-    this.svg.selectAll('.branchLabel').remove();
+    this.removeBranchLabels();
     if (extras.newBranchLabellingKey !== "none") {
       this.drawBranchLabels(extras.newBranchLabellingKey);
     }

src/components/tree/phyloTree/confidence.js

@@ -1,31 +1,39 @@
 
 export const removeConfidence = function removeConfidence(dt) {
   this.confidencesInSVG = false;
+  if (!("confidenceIntervals" in this.groups)) return;
+
   if (dt) {
-    this.svg.selectAll(".conf")
+    this.groups.confidenceIntervals
+      .selectAll("*")
       .transition().duration(dt)
-      .style("opacity", 0)
-      .remove();
+        .style("opacity", 0)
+        .remove();
   } else {
-    this.svg.selectAll(".conf").remove();
+    this.groups.confidenceIntervals.selectAll("*").remove();
   }
 };
 
 export const drawConfidence = function drawConfidence(dt) {
   this.confidencesInSVG = true;
+  if (!("confidenceIntervals" in this.groups)) {
+    this.groups.confidenceIntervals = this.svg.append("g").attr("id", "confidenceIntervals");
+  }
   if (dt) {
-    this.confidence = this.svg.append("g").selectAll(".conf")
+    this.groups.confidenceIntervals
+      .selectAll(".conf")
       .data(this.nodes)
       .enter()
       .call((sel) => this.drawSingleCI(sel, 0));
-    this.svg.selectAll(".conf")
+    this.groups.confidenceIntervals
       .transition().duration(dt)
-      .style("opacity", 0.5);
+        .style("opacity", 0.5);
   } else {
-    this.confidence = this.svg.append("g").selectAll(".conf")
+    this.groups.confidenceIntervals
+      .selectAll(".conf")
       .data(this.nodes)
       .enter()
-      .call((sel) => this.drawSingleCI(sel, 0.5));
+        .call((sel) => this.drawSingleCI(sel, 0.5));
   }
 };
 

src/components/tree/phyloTree/grid.js

@@ -3,9 +3,15 @@ import { min, max } from "d3-array";
 import { timerStart, timerEnd } from "../../../util/perf";
 
 export const hideGrid = function hideGrid() {
-  this.svg.selectAll(".majorGrid").style('visibility', 'hidden');
-  this.svg.selectAll(".minorGrid").style('visibility', 'hidden');
-  this.svg.selectAll(".gridTick").style('visibility', 'hidden');
+  if ("majorGrid" in this.groups) {
+    this.groups.majorGrid.selectAll("*").style('visibility', 'hidden');
+  }
+  if ("minorGrid" in this.groups) {
+    this.groups.minorGrid.selectAll("*").style('visibility', 'hidden');
+  }
+  if ("gridText" in this.groups) {
+    this.groups.gridText.selectAll("*").style('visibility', 'hidden');
+  }
 };
 
 const calculateMajorGridSeperation = (range) => {
@@ -144,46 +150,63 @@ export const addGrid = function addGrid(layout) {
   /* D3 commands to add grid + text to the DOM */
 
   // add major grid to svg
-  const majorGrid = this.svg.selectAll('.majorGrid').data(majorGridPoints);
-  majorGrid.exit().remove(); // EXIT
-  majorGrid.enter().append("path") // ENTER
-    .merge(majorGrid) // ENTER + UPDATE
-    .attr("d", gridline(this.xScale, this.yScale, layout))
-    .attr("class", "majorGrid")
-    .style("fill", "none")
-    .style("visibility", (d) => d[1])
-    .style("stroke", this.params.majorGridStroke)
-    .style("stroke-width", this.params.majorGridWidth);
+  if (!("majorGrid" in this.groups)) {
+    this.groups.majorGrid = this.svg.append("g").attr("id", "majorGrid");
+  }
+  this.groups.majorGrid.selectAll("*").remove();
+  this.groups.majorGrid
+    .selectAll('.majorGrid')
+    .data(majorGridPoints)
+    .enter()
+      .append("path")
+        .attr("d", gridline(this.xScale, this.yScale, layout))
+        .attr("class", "majorGrid")
+        .style("fill", "none")
+        .style("visibility", (d) => d[1])
+        .style("stroke", this.params.majorGridStroke)
+        .style("stroke-width", this.params.majorGridWidth);
 
   // add minor grid to SVG
-  const minorGrid = this.svg.selectAll('.minorGrid').data(minorGridPoints);
-  minorGrid.exit().remove(); // EXIT
-  minorGrid.enter().append("path") // ENTER
-    .merge(minorGrid) // ENTER + UPDATE
-    .attr("d", gridline(this.xScale, this.yScale, layout))
-    .attr("class", "minorGrid")
-    .style("fill", "none")
-    .style("visibility", (d) => d[1])
-    .style("stroke", this.params.minorGridStroke)
-    .style("stroke-width", this.params.minorGridWidth);
+  if (!("minorGrid" in this.groups)) {
+    this.groups.minorGrid = this.svg.append("g").attr("id", "minorGrid");
+  }
+  this.groups.minorGrid.selectAll("*").remove();
+  this.svg.selectAll(".minorGrid").remove();
+  this.groups.minorGrid
+    .selectAll('.minorGrid')
+    .data(minorGridPoints)
+    .enter()
+      .append("path")
+        .attr("d", gridline(this.xScale, this.yScale, layout))
+        .attr("class", "minorGrid")
+        .style("fill", "none")
+        .style("visibility", (d) => d[1])
+        .style("stroke", this.params.minorGridStroke)
+        .style("stroke-width", this.params.minorGridWidth);
 
 
   /* draw the text labels for majorGridPoints */
-  const gridLabels = this.svg.selectAll('.gridTick').data(majorGridPoints);
   const precisionX = Math.max(0, -Math.floor(Math.log10(step)));
   const precisionY = Math.max(0, -Math.floor(Math.log10(yStep)));
-  gridLabels.exit().remove(); // EXIT
-  gridLabels.enter().append("text") // ENTER
-    .merge(gridLabels) // ENTER + UPDATE
-    .text((d) => d[0].toFixed(d[2]==='y' ? precisionY : precisionX))
-    .attr("class", "gridTick")
-    .style("font-size", this.params.tickLabelSize)
-    .style("font-family", this.params.fontFamily)
-    .style("fill", this.params.tickLabelFill)
-    .style("text-anchor", textAnchor(layout))
-    .style("visibility", (d) => d[1])
-    .attr("x", xTextPos(this.xScale, layout))
-    .attr("y", yTextPos(this.yScale, layout));
+  if (!("gridText" in this.groups)) {
+    this.groups.gridText = this.svg.append("g").attr("id", "gridText");
+  }
+  this.groups.gridText.selectAll("*").remove();
+  this.svg.selectAll(".gridText").remove();
+  this.groups.gridText
+    .selectAll('.gridText')
+    .data(majorGridPoints)
+    .enter()
+      .append("text")
+        .text((d) => d[0].toFixed(d[2]==='y' ? precisionY : precisionX))
+        .attr("class", "gridText")
+        .style("font-size", this.params.tickLabelSize)
+        .style("font-family", this.params.fontFamily)
+        .style("fill", this.params.tickLabelFill)
+        .style("text-anchor", textAnchor(layout))
+        .style("visibility", (d) => d[1])
+        .attr("x", xTextPos(this.xScale, layout))
+        .attr("y", yTextPos(this.yScale, layout));
 
   this.grid=true;
   timerEnd("addGrid");

src/components/tree/phyloTree/labels.js

@@ -1,7 +1,12 @@
 import { timerFlush } from "d3-timer";
 
 export const updateTipLabels = function updateTipLabels(dt) {
-  this.svg.selectAll('.tipLabel').remove();
+  if ("tipLabels" in this.groups) {
+    this.groups.tipLabels.selectAll("*").remove();
+  } else {
+    this.groups.tipLabels = this.svg.append("g").attr("id", "tipLabels");
+  }
+
   const tLFunc = this.callbacks.tipLabel;
   const xPad = this.params.tipLabelPadX;
   const yPad = this.params.tipLabelPadY;
@@ -20,7 +25,8 @@ export const updateTipLabels = function updateTipLabels(dt) {
     }
 
     window.setTimeout(() => {
-      this.tipLabels = this.svg.append("g").selectAll('.tipLabel')
+      this.groups.tipLabels
+        .selectAll('.tipLabel')
         .data(inViewTerminalNodes)
         .enter()
         .append("text")
@@ -79,7 +85,8 @@ export const updateBranchLabels = function updateBranchLabels(dt) {
   const visibility = createBranchLabelVisibility(this.params.branchLabelKey, this.layout, this.zoomNode.n.tipCount);
   const labelSize = branchLabelSize(this.params.branchLabelKey);
   const fontWeight = branchLabelFontWeight(this.params.branchLabelKey);
-  this.svg.selectAll('.branchLabel')
+  this.groups.branchLabels
+    .selectAll('.branchLabel')
     .transition().duration(dt)
     .attr("x", (d) => d.xTip - 5)
     .attr("y", (d) => d.yTip - this.params.branchLabelPadY)
@@ -89,18 +96,29 @@ export const updateBranchLabels = function updateBranchLabels(dt) {
   if (!dt) timerFlush();
 };
 
+export const removeBranchLabels = function removeBranchLabels() {
+  if ("branchLabels" in this.groups) {
+    this.groups.branchLabels.selectAll("*").remove();
+  }
+};
+
 export const drawBranchLabels = function drawBranchLabels(key) {
   /* salient props: this.zoomNode.n.tipCount, this.zoomNode.n.fullTipCount */
   this.params.branchLabelKey = key;
   const labelSize = branchLabelSize(key);
   const fontWeight = branchLabelFontWeight(key);
   const visibility = createBranchLabelVisibility(key, this.layout, this.zoomNode.n.tipCount);
-  this.svg.append("g").selectAll('.branchLabel')
+
+  if (!("branchLabels" in this.groups)) {
+    this.groups.branchLabels = this.svg.append("g").attr("id", "branchLabels");
+  }
+  this.groups.branchLabels
+    .selectAll('.branchLabel')
     .data(this.nodes.filter((d) => d.n.attr.labels && d.n.attr.labels[key]))
     .enter()
     .append("text")
     .attr("class", "branchLabel")
-    .attr("x", (d) => d.xTip + ((this.params.orientation[0]>0)?-5:5) )
+    .attr("x", (d) => d.xTip + ((this.params.orientation[0]>0)?-5:5))
     .attr("y", (d) => d.yTip - this.params.branchLabelPadY)
     .style("text-anchor", (this.params.orientation[0]>0)?"end":"start")
     .style("visibility", visibility)

src/components/tree/phyloTree/layouts.js

@@ -354,7 +354,6 @@ export const mapToScreen = function mapToScreen() {
       const xTipCross = this.xScale(d.xCross); /* x position of the center of the cross */
       const yTipCross = this.yScale(d.yCross); /* x position of the center of the cross */
       d.vaccineCross = ` M ${xTipCross-n},${yTipCross-n} L ${xTipCross+n},${yTipCross+n} M ${xTipCross-n},${yTipCross+n} L ${xTipCross+n},${yTipCross-n}`;
-      d.vaccineLine = ` M ${d.xTip},${d.yTip} L ${xTipCross},${yTipCross}`;
     });
   }
 

src/components/tree/phyloTree/phyloTree.js

@@ -15,6 +15,9 @@ const PhyloTree = function PhyloTree(reduxNodes, debugId) {
   this.grid = false;
   this.attributes = ['r', 'cx', 'cy', 'id', 'class', 'd'];
   this.params = createDefaultParams();
+  this.groups = {};
+  /* by storing DOM <g> elements, we can quickly refer to groups here rather than scanning the DOM.
+  It also helps preserve the initial order of groups in the DOM as we are not creating new ones upon updates */
   this.debugId = debugId; /* super useful when one is trying to debug multiple trees! */
   /* create this.nodes, which is an array of nodes with properties used by phylotree for drawing.
    this.nodes is the same length as reduxNodes such that this.nodes[i] is related to reduxNodes[i]
@@ -61,6 +64,7 @@ PhyloTree.prototype.drawTips = renderers.drawTips;
 PhyloTree.prototype.drawBranches = renderers.drawBranches;
 PhyloTree.prototype.drawVaccines = renderers.drawVaccines;
 PhyloTree.prototype.drawRegression = renderers.drawRegression;
+PhyloTree.prototype.removeRegression = renderers.removeRegression;
 
 /* C A L C U L A T E    G E O M E T R I E S  E T C   ( M O D I F I E S    N O D E S ,    N O T    S V G ) */
 PhyloTree.prototype.setDistance = layouts.setDistance;
@@ -80,6 +84,7 @@ PhyloTree.prototype.updateConfidence = confidence.updateConfidence;
 
 /* L A B E L S    ( T I P ,    B R A N C H ,   C O N F I D E N C E ) */
 PhyloTree.prototype.drawBranchLabels = labels.drawBranchLabels;
+PhyloTree.prototype.removeBranchLabels = labels.removeBranchLabels;
 PhyloTree.prototype.updateBranchLabels = labels.updateBranchLabels;
 PhyloTree.prototype.updateTipLabels = labels.updateTipLabels;