[tmp] prototype temporal zoom

.

src/actions/types.js

@@ -61,3 +61,4 @@ export const TOGGLE_MEASUREMENTS_OVERALL_MEAN = "TOGGLE_MEASUREMENTS_OVERALL_MEA
 export const CHANGE_MEASUREMENTS_DISPLAY = "CHANGE_MEASUREMENTS_DISPLAY";
 export const APPLY_MEASUREMENTS_FILTER = "APPLY_MEASUREMENTS_FILTER";
 export const UPDATE_MEASUREMENTS_ERROR = "UPDATE_MEASUREMENTS_ERROR";
+export const TOGGLE_TEMPORAL_ZOOM_FLAG = "TOGGLE_TEMPORAL_ZOOM_FLAG";

src/components/controls/choose-zoom-mode.js

@@ -0,0 +1,32 @@
+import React from "react";
+import { connect } from "react-redux";
+import { withTranslation } from "react-i18next";
+
+import Toggle from "./toggle";
+import { controlsWidth } from "../../util/globals";
+import { TOGGLE_TEMPORAL_ZOOM_FLAG } from "../../actions/types";
+
+@connect((state) => {
+  return {
+    treeZoomsTemporally: state.controls.treeZoomsTemporally
+  };
+})
+class ChooseZoomMode extends React.Component {
+  render() {
+    const { t } = this.props;
+    return (
+      <div style={{marginBottom: 10, width: controlsWidth, fontSize: 14}}>
+        <Toggle
+          display
+          on={this.props.treeZoomsTemporally}
+          callback={() => {
+            this.props.dispatch({ type: TOGGLE_TEMPORAL_ZOOM_FLAG });
+          }}
+          label={t("sidebar:Zoom Temporally")}
+        />
+      </div>
+    );
+  }
+}
+
+export default withTranslation()(ChooseZoomMode);

src/components/controls/controls.js

@@ -25,6 +25,7 @@ import {TreeOptionsInfo, MapOptionsInfo, AnimationOptionsInfo, PanelOptionsInfo,
   ExplodeTreeInfo, FrequencyInfo, MeasurementsOptionsInfo} from "./miscInfoText";
 import { AnnotatedHeader } from "./annotatedHeader";
 import MeasurementsOptions from "./measurementsOptions";
+import ChooseZoomMode from "./choose-zoom-mode";
 
 function Controls({mapOn, frequenciesOn, measurementsOn, mobileDisplay}) {
   const { t } = useTranslation();
@@ -44,6 +45,7 @@ function Controls({mapOn, frequenciesOn, measurementsOn, mobileDisplay}) {
       <FilterData measurementsOn={measurementsOn} />
 
       <AnnotatedHeader title={t("sidebar:Tree Options")} tooltip={TreeOptionsInfo} mobile={mobileDisplay}/>
+      <ChooseZoomMode />
       <ChooseLayout />
       <ChooseMetric />
       <ChooseExplodeAttr tooltip={ExplodeTreeInfo} mobile={mobileDisplay} />

src/components/tree/index.js

@@ -24,7 +24,8 @@ const Tree = connect((state) => ({
   canRenderBranchLabels: state.controls.canRenderBranchLabels,
   tipLabelKey: state.controls.tipLabelKey,
   narrativeMode: state.narrative.display,
-  animationPlayPauseButton: state.controls.animationPlayPauseButton
+  animationPlayPauseButton: state.controls.animationPlayPauseButton,
+  treeZoomsTemporally: state.controls.treeZoomsTemporally
 }))(UnconnectedTree);
 
 export default Tree;

src/components/tree/phyloTree/change.js

@@ -179,7 +179,7 @@ export const modifySVG = function modifySVG(elemsToUpdate, svgPropsToUpdate, tra
   }
 
   /* background temporal time slice */
-  if (extras.timeSliceHasPotentiallyChanged) {
+  if (extras.timeSliceHasPotentiallyChanged || (extras.newZoomMode!==undefined)) {
     this.showTemporalSlice();
   }
 
@@ -258,6 +258,7 @@ export const change = function change({
   /* change these things to provided value (unless undefined) */
   newDistance = undefined,
   newLayout = undefined,
+  newZoomMode = undefined,
   updateLayout = undefined, // todo - this seems identical to `newLayout`
   newBranchLabellingKey = undefined,
   newTipLabelKey = undefined,
@@ -277,6 +278,8 @@ export const change = function change({
   const nodePropsToModify = {}; /* which properties (keys) on the nodes should be updated (before the SVG) */
   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. */
+  const timeSliceHasPotentiallyChanged = changeVisibility || newDistance;
+  if (newZoomMode!==undefined) this.treeZoomsTemporally = newZoomMode;
 
   /* calculate dt */
   const idealTransitionTime = 500;
@@ -312,7 +315,8 @@ export const change = function change({
     svgPropsToUpdate.add("stroke-width");
     nodePropsToModify["stroke-width"] = branchThickness;
   }
-  if (newDistance || newLayout || updateLayout || zoomIntoClade || svgHasChangedDimensions || changeNodeOrder) {
+  if (newDistance || newLayout || updateLayout || zoomIntoClade || (newZoomMode!==undefined) ||
+    svgHasChangedDimensions || changeNodeOrder || timeSliceHasPotentiallyChanged) {
     elemsToUpdate.add(".tip").add(".branch.S").add(".branch.T").add(".branch");
     elemsToUpdate.add(".vaccineCross").add(".vaccineDottedLine").add(".conf");
     elemsToUpdate.add('.branchLabel').add('.tipLabel');
@@ -368,13 +372,15 @@ export const change = function change({
   /* mapToScreen */
   if (
     svgPropsToUpdate.has(["stroke-width"]) ||
-    newDistance ||
+    newDistance || // technically unnecessary as part of timeSliceHas...
     newLayout ||
     changeNodeOrder ||
     updateLayout ||
     zoomIntoClade ||
     svgHasChangedDimensions ||
-    showConfidences
+    showConfidences ||
+    (newZoomMode!==undefined) ||
+    timeSliceHasPotentiallyChanged // TODO could be expensive to run mapToScreen every time here...
   ) {
     this.mapToScreen();
   }
@@ -388,8 +394,7 @@ export const change = function change({
   if (svgHasChangedDimensions) {
     this.setClipMask();
   }
-  const extras = { removeConfidences, showConfidences, newBranchLabellingKey };
-  extras.timeSliceHasPotentiallyChanged = changeVisibility || newDistance;
+  const extras = { removeConfidences, showConfidences, newBranchLabellingKey, timeSliceHasPotentiallyChanged, newZoomMode};
   extras.hideTipLabels = animationInProgress;
   if (useModifySVGInStages) {
     this.modifySVGInStages(elemsToUpdate, svgPropsToUpdate, transitionTime, 1000, extras);

src/components/tree/phyloTree/grid.js

@@ -441,7 +441,7 @@ export const temporalWindowTransition = transition('temporalWindowTransition')
  * add background grey rectangles to demarcate the temporal slice
  */
 export const showTemporalSlice = function showTemporalSlice() {
-  if (this.layout !== "rect" || this.distance !== "num_date") {
+  if (this.layout !== "rect" || this.distance !== "num_date" || this.treeZoomsTemporally===true) {
     this.hideTemporalSlice();
     return;
   }

src/components/tree/phyloTree/layouts.js

@@ -355,6 +355,19 @@ export const mapToScreen = function mapToScreen() {
     nodesInDomain = nodesInDomain.filter((d) => !d.n.hasChildren);
   }
 
+  /* experimental -- restrict the nodesInDomain via the time-slice */
+  if (this.treeZoomsTemporally===true) {
+    // TODO -- this works for the max time (and viz is intuitive) but for the earliest date (LHS of rect tree)
+    // we should be a bit smarter.
+    // Note that branches prior to the date cutoff have no visibility (rendered as thin lines) so it's not just
+    // a case of changing the tree domain like I'm prototyping here...
+    const early_cutoff = this.dateRange[0] - 0.1*(this.dateRange[1]-this.dateRange[0]);
+    nodesInDomain = nodesInDomain.filter((d) => {
+      const num_date = getTraitFromNode(d.n, 'num_date');
+      return (num_date > early_cutoff && num_date < this.dateRange[1]);
+    });
+  }
+
   /* Compute the domains to pass to the d3 scales for the x & y axes */
   let xDomain, yDomain, spanX, spanY;
   if (this.layout!=="scatter" || this.scatterVariables.xContinuous) {

src/components/tree/phyloTree/renderers.js

@@ -21,13 +21,14 @@ import { getEmphasizedColor } from "../../../util/colorHelpers";
  * @param {object} scatterVariables  -- {x, y} properties to map nodes => scatterplot (only used if layout="scatter")
  * @return {null}
  */
-export const render = function render(svg, layout, distance, parameters, callbacks, branchThickness, visibility, drawConfidence, vaccines, branchStroke, tipStroke, tipFill, tipRadii, dateRange, scatterVariables) {
+export const render = function render(svg, layout, distance, parameters, callbacks, branchThickness, visibility, drawConfidence, vaccines, branchStroke, tipStroke, tipFill, tipRadii, dateRange, scatterVariables, treeZoomsTemporally) {
   timerStart("phyloTree render()");
   this.svg = svg;
   this.params = Object.assign(this.params, parameters);
   this.callbacks = callbacks;
   this.vaccines = vaccines ? vaccines.map((d) => d.shell) : undefined;
   this.dateRange = dateRange;
+  this.treeZoomsTemporally = treeZoomsTemporally;
 
   /* set nodes stroke / fill */
   this.nodes.forEach((d, i) => {

src/components/tree/reactD3Interface/change.js

@@ -97,6 +97,11 @@ export const changePhyloTreeViaPropsComparison = (mainTree, phylotree, oldProps,
     }
   }
 
+  if (oldProps.treeZoomsTemporally !== newProps.treeZoomsTemporally) {
+    args.newZoomMode = newProps.treeZoomsTemporally;
+    args.updateLayout = true; // unsure why this' needed
+  }
+
   if (oldProps.width !== newProps.width || oldProps.height !== newProps.height) {
     args.svgHasChangedDimensions = true;
   }

src/components/tree/reactD3Interface/initialRender.js

@@ -47,6 +47,7 @@ export const renderTree = (that, main, phylotree, props) => {
     treeState.nodeColors.map(getBrighterColor),
     treeState.tipRadii, /* might be null */
     [props.dateMinNumeric, props.dateMaxNumeric],
-    props.scatterVariables
+    props.scatterVariables,
+    props.treeZoomsTemporally
   );
 };

src/reducers/controls.js

@@ -85,6 +85,7 @@ export const getDefaultControlsState = () => {
     showTangle: false,
     zoomMin: undefined,
     zoomMax: undefined,
+    treeZoomsTemporally: true,
     branchLengthsToDisplay: "divAndDate",
     sidebarOpen: initialSidebarState.sidebarOpen,
     treeLegendOpen: undefined,
@@ -123,6 +124,9 @@ const Controls = (state = getDefaultControlsState(), action) => {
         explodeAttr: action.explodeAttr,
         colorScale: Object.assign({}, state.colorScale, { visibleLegendValues: action.visibleLegendValues })
       });
+    case types.TOGGLE_TEMPORAL_ZOOM_FLAG: {
+      return Object.assign({}, state, {treeZoomsTemporally: !state.treeZoomsTemporally});
+    }
     case types.CHANGE_BRANCH_LABEL:
       return Object.assign({}, state, { selectedBranchLabel: action.value });
     case types.CHANGE_LAYOUT: