Merge pull request #1880 from nextstrain/james/improve-tree-perf

Improve tree performance for trees with over 4000 tips

src/components/tree/index.ts

@@ -30,7 +30,8 @@ const Tree = connect((state: RootState) => ({
   tipLabelKey: state.controls.tipLabelKey,
   narrativeMode: state.narrative.display,
   animationPlayPauseButton: state.controls.animationPlayPauseButton,
-  showOnlyPanels: state.controls.showOnlyPanels
+  showOnlyPanels: state.controls.showOnlyPanels,
+  performanceFlags: state.controls.performanceFlags,
 }))(UnconnectedTree);
 
 export default Tree;

src/components/tree/phyloTree/change.js

@@ -99,15 +99,12 @@ const createUpdateCall = (treeElem, properties) => (selection) => {
 
 const genericSelectAndModify = (svg, treeElem, updateCall, transitionTime) => {
   // console.log("general svg update for", treeElem);
-  svg.selectAll(treeElem)
-    .filter((d) => d.update)
-    .transition().duration(transitionTime)
-    .call(updateCall);
-  if (!transitionTime) {
-    /* https://github.com/d3/d3-timer#timerFlush */
-    timerFlush();
-    // console.log("\t\t--FLUSHING TIMER--");
+  let selection = svg.selectAll(treeElem)
+    .filter((d) => d.update);
+  if (transitionTime) {
+    selection = selection.transition().duration(transitionTime);
   }
+  selection.call(updateCall);
 };
 
 /* use D3 to select and modify elements, such that a given element is only ever modified _once_
@@ -271,7 +268,8 @@ export const change = function change({
   branchThickness = undefined,
   /* other data */
   focus = undefined,
-  scatterVariables = undefined
+  scatterVariables = undefined,
+  performanceFlags = {},
 }) {
   // console.log("\n** phylotree.change() (time since last run:", Date.now() - this.timeLastRenderRequested, "ms) **\n\n");
   timerStart("phylotree.change()");
@@ -280,10 +278,11 @@ export const change = function change({
   const svgPropsToUpdate = new Set(); /* which SVG properties shall be changed. E.g. "fill", "stroke" */
   const useModifySVGInStages = newLayout; /* use modifySVGInStages rather than modifySVG. Not used often. */
 
+
   /* calculate dt */
   const idealTransitionTime = 500;
   let transitionTime = idealTransitionTime;
-  if ((Date.now() - this.timeLastRenderRequested) < idealTransitionTime * 2) {
+  if ((Date.now() - this.timeLastRenderRequested) < idealTransitionTime * 2 || performanceFlags.get("skipTreeAnimation")===true) {
     transitionTime = 0;
   }
 

src/components/tree/phyloTree/labels.js

@@ -1,4 +1,3 @@
-import { timerFlush } from "d3-timer";
 import { NODE_VISIBLE } from "../../../util/globals";
 import { numericToDateObject, prettifyDate } from "../../../util/dateHelpers";
 import { getTraitFromNode } from "../../../util/treeMiscHelpers";
@@ -108,16 +107,16 @@ export const updateBranchLabels = function updateBranchLabels(dt) {
   );
   const labelSize = branchLabelSize(this.params.branchLabelKey);
   const fontWeight = branchLabelFontWeight(this.params.branchLabelKey);
-  this.groups.branchLabels
+  let selection = this.groups.branchLabels
     .selectAll(".branchLabel")
-    .transition()
-    .duration(dt)
-    .attr("x", (d) => d.xTip - 5)
+  if (dt) {
+    selection = selection.transition().duration(dt);
+  }
+  selection.attr("x", (d) => d.xTip - 5)
     .attr("y", (d) => d.yTip - this.params.branchLabelPadY)
     .style("visibility", visibility)
     .style("font-weight", fontWeight)
     .style("font-size", labelSize);
-  if (!dt) timerFlush();
 };
 
 export const removeBranchLabels = function removeBranchLabels() {

src/components/tree/reactD3Interface/change.js

@@ -127,6 +127,7 @@ export const changePhyloTreeViaPropsComparison = (mainTree, phylotree, oldProps,
   const change = Object.keys(args).length;
   if (change) {
     args.animationInProgress = newProps.animationPlayPauseButton === "Pause";
+    args.performanceFlags = newProps.performanceFlags;
     // console.log('\n\n** ', phylotree.id, 'changePhyloTreeViaPropsComparison **', args);
     phylotree.change(args);
   }

src/middleware/performanceFlags.js

@@ -0,0 +1,28 @@
+import * as types from "../actions/types";
+
+/**
+ * Performance flags (reduxState.controls.performanceFlags) represent flags
+ * for which we enable/disable certain functionality in Auspice. These flags
+ * shouldn't be depended on, i.e. Auspice should work just fine without them
+ * (but may be a little slow).
+ */
+
+
+export const performanceFlags = (_store) => (next) => (action) => {
+  let modifiedAction;
+  switch (action.type) {
+    case types.URL_QUERY_CHANGE_WITH_COMPUTED_STATE: /* fallthrough */
+    case types.CLEAN_START: {
+      modifiedAction = {...action};
+      modifiedAction.controls.performanceFlags = calculate(action)
+    }
+  }
+  return next(modifiedAction || action); // send action to other middleware / reducers
+};
+
+function calculate({tree}) {
+  const flags = new Map();
+  const totalTipCount = tree?.nodes?.[0]?.fullTipCount;
+  flags.set("skipTreeAnimation", totalTipCount > 4000);
+  return flags;
+}

src/reducers/controls.ts

@@ -137,7 +137,8 @@ export const getDefaultControlsState = () => {
     measurementsDisplay: undefined,
     measurementsShowOverallMean: undefined,
     measurementsShowThreshold: undefined,
-    measurementsFilters: {}
+    measurementsFilters: {},
+    performanceFlags: new Map(),
   };
 };
 

src/store.ts

@@ -3,10 +3,12 @@ import { changeURLMiddleware } from "./middleware/changeURL";
 import rootReducer from "./reducers";
 // import { loggingMiddleware } from "./middleware/logActions";
 import { keepScatterplotStateInSync } from "./middleware/scatterplot";
+import { performanceFlags } from "./middleware/performanceFlags";
 
 const middleware = [
   keepScatterplotStateInSync,
   changeURLMiddleware,
+  performanceFlags,
   // loggingMiddleware
 ];