fixup! Add tree-related types

src/actions/tree.ts

@@ -12,7 +12,7 @@ import { getTraitFromNode } from "../util/treeMiscHelpers";
 import { warningNotification } from "./notifications";
 import { calcFullTipCounts, calcTipCounts } from "../util/treeCountingHelpers";
 import { TreeState } from "../components/tree/tree";
-import { PhyloNode, ReduxNode, Root } from "../components/tree/phyloTree/types";
+import { Metadata, PhyloNode, ReduxNode, Root } from "../components/tree/phyloTree/types";
 import { AppDispatch, RootState } from "../store";
 
 
@@ -405,7 +405,11 @@ const _traverseAndCreateSubtrees = (
 /**
  * sort the subtrees by the order the trait would appear in the legend
  */
-const _orderSubtrees = (metadata: any, nodes: ReduxNode[], attr: string) => {
+const _orderSubtrees = (
+  metadata: Metadata,
+  nodes: ReduxNode[],
+  attr: string,
+) => {
   const attrValueOrder = getLegendOrder(attr, metadata.colorings[attr], nodes, undefined);
   nodes[0].children.sort((childA, childB) => {
     const [attrA, attrB] = [getTraitFromNode(childA, attr), getTraitFromNode(childB, attr)];

src/components/tree/index.ts

@@ -1,9 +1,10 @@
 import { connect, MapStateToProps } from "react-redux";
 import UnconnectedTree from "./tree";
 import { RootState } from "../../store";
-import { TreeComponentPropsFromState } from "./tree";
+import { TreeComponentStateProps } from "./tree";
+import { TreeComponentOwnProps } from "./tree";
 
-const mapStateToProps: MapStateToProps<TreeComponentPropsFromState, Record<string, never>, RootState> = (state: RootState) => ({
+const mapStateToProps: MapStateToProps<TreeComponentStateProps, TreeComponentOwnProps, RootState> = (state: RootState) => ({
   tree: state.tree,
   treeToo: state.treeToo,
   selectedNode: state.controls.selectedNode,

src/components/tree/phyloTree/change.ts

@@ -6,8 +6,7 @@ import { NODE_VISIBLE } from "../../../util/globals";
 import { getBranchVisibility, strokeForBranch } from "./renderers";
 import { shouldDisplayTemporalConfidence } from "../../../reducers/controls";
 import { makeTipLabelFunc } from "./labels";
-import { PhyloTree } from "./phyloTree";
-import { Distance, Layout, PhyloNode, PropsForPhyloNodes, SVGProperty, TreeElement, Visibility } from "./types";
+import { Distance, Layout, PhyloNode, PhyloTree, PropsForPhyloNodes, SVGProperty, TreeElement, Visibility } from "./types";
 import { Selection, Transition } from "d3";
 
 /* loop through the nodes and update each provided prop with the new value

src/components/tree/phyloTree/helpers.ts

@@ -21,7 +21,7 @@ export const getDomId = (type: string, strain: string): string => {
 export const applyToChildren = (
   phyloNode: PhyloNode,
 
-  /** function to apply to each children. Is passed a single argument, the <PhyloNode> of the children. */
+  /** function to apply to each child. Is passed a single argument, the <PhyloNode> of the children. */
   func: (node: PhyloNode) => void,
 ) => {
   func(phyloNode);

src/components/tree/phyloTree/layouts.ts

@@ -6,8 +6,7 @@ import { timerStart, timerEnd } from "../../../util/perf";
 import { getTraitFromNode, getDivFromNode } from "../../../util/treeMiscHelpers";
 import { stemParent, nodeOrdering } from "./helpers";
 import { numDate } from "../../../util/colorHelpers";
-import { PhyloTree } from "./phyloTree";
-import { Distance, Layout, Params, PhyloNode, ReduxNode, ScatterVariables } from "./types";
+import { Distance, Layout, Params, PhyloNode, PhyloTree, ReduxNode, ScatterVariables } from "./types";
 
 /**
  * assigns the attribute this.layout and calls the function that

src/components/tree/phyloTree/phyloTree.ts

@@ -8,89 +8,10 @@ import * as grid from "./grid";
 import * as confidence from "./confidence";
 import * as labels from "./labels";
 import * as regression from "./regression";
-import { Callbacks, Layout, Params, PhyloNode, ReduxNode, ScatterVariables, Visibility } from "./types";
-import { Selection } from "d3";
-
-export interface PhyloTree {
-  grid: boolean
-  attributes: string[]
-  params: Params
-  groups: {
-    branchGradientDefs?: Selection<SVGDefsElement, unknown, null, any>
-    branchStem?: Selection<SVGDefsElement, unknown, null, any>
-    branchTee?: Selection<SVGDefsElement, unknown, null, any>
-    clipPath?: Selection<SVGDefsElement, unknown, null, any>
-    confidenceIntervals?: Selection<SVGDefsElement, unknown, null, any>
-    regression?: Selection<SVGDefsElement, unknown, null, any>
-    tips?: Selection<SVGDefsElement, unknown, null, any>
-    vaccines?: Selection<SVGDefsElement, unknown, null, any>
-  }
-  id: string
-  nodes: PhyloNode[]
-  zoomNode: PhyloNode
-  dateRange: [number, number]
-  strainToNode: Record<string, PhyloNode>
-  change: typeof change
-  modifySVG: typeof modifySVG
-  modifySVGInStages: typeof modifySVGInStages
-  render: typeof renderers.render
-  clearSVG: typeof renderers.clearSVG
-  setClipMask: typeof renderers.setClipMask
-  drawTips: typeof renderers.drawTips
-  drawBranches: typeof renderers.drawBranches
-  drawVaccines: typeof renderers.drawVaccines
-  drawRegression: typeof renderers.drawRegression
-  removeRegression: typeof renderers.removeRegression
-  updateColorBy: typeof renderers.updateColorBy
-  setDistance: typeof layouts.setDistance
-  setLayout: typeof layouts.setLayout
-  rectangularLayout: typeof layouts.rectangularLayout
-  scatterplotLayout: typeof layouts.scatterplotLayout
-  unrootedLayout: typeof layouts.unrootedLayout
-  radialLayout: typeof layouts.radialLayout
-  setScales: typeof layouts.setScales
-  mapToScreen: typeof layouts.mapToScreen
-  calculateRegression: typeof regression.calculateRegression
-  removeConfidence: typeof confidence.removeConfidence
-  drawConfidence: typeof confidence.drawConfidence
-  drawSingleCI: typeof confidence.drawSingleCI
-  drawBranchLabels: typeof labels.drawBranchLabels
-  removeBranchLabels: typeof labels.removeBranchLabels
-  updateBranchLabels: typeof labels.updateBranchLabels
-  updateTipLabels: typeof labels.updateTipLabels
-  removeTipLabels: typeof labels.removeTipLabels
-  hideGrid: typeof grid.hideGrid
-  addGrid: typeof grid.addGrid
-  showTemporalSlice: typeof grid.showTemporalSlice
-  hideTemporalSlice: typeof grid.hideTemporalSlice
-
-  confidencesInSVG: boolean
-  regression?: regression.Regression
-  layout: Layout
-  svg: Selection<SVGSVGElement | null, unknown, null, any>
-  distance: "num_date" | "div"
-  vaccines?: PhyloNode[]
-  timeLastRenderRequested?: number
-  callbacks: Callbacks
-  visibility: Visibility[]
-
-  scatterVariables?: ScatterVariables
-  margins: {
-    right: number
-    left: number
-    top: number
-    bottom: number
-  }
-
-  // TODO: This should be `d3.ScalePoint<string> | d3.ScaleContinuousNumeric<number, number>`, conditional on layout
-  xScale: any
-
-  // TODO: This should be `d3.ScalePoint<string> | d3.ScaleContinuousNumeric<number, number>`, conditional on layout
-  yScale: any
-}
+import { PhyloNode, PhyloTree as PhyloTreeType, ReduxNode } from "./types";
 
 /* phylogenetic tree drawing function - the actual tree is rendered by the render prototype */
-const PhyloTree = function PhyloTree(this: PhyloTree, reduxNodes: ReduxNode[], id: string, idxOfInViewRootNode: number) {
+const PhyloTree = function PhyloTree(this: PhyloTreeType, reduxNodes: ReduxNode[], id: string, idxOfInViewRootNode: number) {
   this.grid = false;
   this.attributes = ['r', 'cx', 'cy', 'id', 'class', 'd'];
   this.params = createDefaultParams();

src/components/tree/phyloTree/regression.ts

@@ -1,8 +1,7 @@
 import { sum } from "d3-array";
 import { formatDivergence, guessAreMutationsPerSite} from "./helpers";
 import { NODE_VISIBLE } from "../../../util/globals";
-import { PhyloTree } from "./phyloTree";
-import { PhyloNode } from "./types";
+import { PhyloNode, PhyloTree } from "./types";
 
 export interface Regression {
   slope?: number

src/components/tree/phyloTree/renderers.ts

@@ -3,8 +3,7 @@ import { NODE_VISIBLE } from "../../../util/globals";
 import { getDomId, setDisplayOrder } from "./helpers";
 import { makeRegressionText } from "./regression";
 import { getEmphasizedColor } from "../../../util/colorHelpers";
-import { PhyloTree } from "./phyloTree";
-import { Callbacks, Distance, Layout, Params, PhyloNode, ReduxNode, ScatterVariables, Visibility } from "./types";
+import { Callbacks, Distance, Layout, Params, PhyloNode, PhyloTree, ReduxNode, ScatterVariables, Visibility } from "./types";
 import { Selection } from "d3";
 
 export const render = function render(

src/components/tree/phyloTree/types.ts

@@ -1,5 +1,13 @@
 import { NODE_NOT_VISIBLE, NODE_VISIBLE_TO_MAP_ONLY, NODE_VISIBLE } from "../../../util/globals";
-import { PhyloTree } from "./phyloTree";
+import { Selection } from "d3";
+import { change, modifySVG, modifySVGInStages } from "./change";
+
+import * as renderers from "./renderers";
+import * as layouts from "./layouts";
+import * as grid from "./grid";
+import * as confidence from "./confidence";
+import * as labels from "./labels";
+import * as regression from "./regression";
 
 export type Layout = "rect" | "radial" | "unrooted" | "clock" | "scatter"
 
@@ -20,12 +28,6 @@ export type TreeElement =
 
 export type Visibility = typeof NODE_NOT_VISIBLE | typeof NODE_VISIBLE_TO_MAP_ONLY | typeof NODE_VISIBLE
 
-export interface Colorings {
-  [key: string]: {
-    type: string
-  }
-}
-
 export interface Genotype {
   gene: string
   positions: number[]
@@ -206,6 +208,84 @@ export interface PhyloNode extends Partial<Omit<CSSStyleDeclarationWithHyphens,
   yTip?: number
 }
 
+export interface PhyloTree {
+  grid: boolean
+  attributes: string[]
+  params: Params
+  groups: {
+    branchGradientDefs?: Selection<SVGDefsElement, unknown, null, any>
+    branchStem?: Selection<SVGDefsElement, unknown, null, any>
+    branchTee?: Selection<SVGDefsElement, unknown, null, any>
+    clipPath?: Selection<SVGDefsElement, unknown, null, any>
+    confidenceIntervals?: Selection<SVGDefsElement, unknown, null, any>
+    regression?: Selection<SVGDefsElement, unknown, null, any>
+    tips?: Selection<SVGDefsElement, unknown, null, any>
+    vaccines?: Selection<SVGDefsElement, unknown, null, any>
+  }
+  id: string
+  nodes: PhyloNode[]
+  zoomNode: PhyloNode
+  dateRange: [number, number]
+  strainToNode: Record<string, PhyloNode>
+  change: typeof change
+  modifySVG: typeof modifySVG
+  modifySVGInStages: typeof modifySVGInStages
+  render: typeof renderers.render
+  clearSVG: typeof renderers.clearSVG
+  setClipMask: typeof renderers.setClipMask
+  drawTips: typeof renderers.drawTips
+  drawBranches: typeof renderers.drawBranches
+  drawVaccines: typeof renderers.drawVaccines
+  drawRegression: typeof renderers.drawRegression
+  removeRegression: typeof renderers.removeRegression
+  updateColorBy: typeof renderers.updateColorBy
+  setDistance: typeof layouts.setDistance
+  setLayout: typeof layouts.setLayout
+  rectangularLayout: typeof layouts.rectangularLayout
+  scatterplotLayout: typeof layouts.scatterplotLayout
+  unrootedLayout: typeof layouts.unrootedLayout
+  radialLayout: typeof layouts.radialLayout
+  setScales: typeof layouts.setScales
+  mapToScreen: typeof layouts.mapToScreen
+  calculateRegression: typeof regression.calculateRegression
+  removeConfidence: typeof confidence.removeConfidence
+  drawConfidence: typeof confidence.drawConfidence
+  drawSingleCI: typeof confidence.drawSingleCI
+  drawBranchLabels: typeof labels.drawBranchLabels
+  removeBranchLabels: typeof labels.removeBranchLabels
+  updateBranchLabels: typeof labels.updateBranchLabels
+  updateTipLabels: typeof labels.updateTipLabels
+  removeTipLabels: typeof labels.removeTipLabels
+  hideGrid: typeof grid.hideGrid
+  addGrid: typeof grid.addGrid
+  showTemporalSlice: typeof grid.showTemporalSlice
+  hideTemporalSlice: typeof grid.hideTemporalSlice
+
+  confidencesInSVG: boolean
+  regression?: regression.Regression
+  layout: Layout
+  svg: Selection<SVGSVGElement | null, unknown, null, any>
+  distance: Distance
+  vaccines?: PhyloNode[]
+  timeLastRenderRequested?: number
+  callbacks: Callbacks
+  visibility: Visibility[]
+
+  scatterVariables?: ScatterVariables
+  margins: {
+    right: number
+    left: number
+    top: number
+    bottom: number
+  }
+
+  // TODO: This should be `d3.ScalePoint<string> | d3.ScaleContinuousNumeric<number, number>`, conditional on layout
+  xScale: any
+
+  // TODO: This should be `d3.ScalePoint<string> | d3.ScaleContinuousNumeric<number, number>`, conditional on layout
+  yScale: any
+}
+
 export interface ScatterVariables {
   showBranches?: boolean
   showRegression?: boolean
@@ -273,3 +353,19 @@ export interface Callbacks {
   onBranchClick: (d: PhyloNode) => void
   tipLabel: (d: PhyloNode) => void
 }
+
+export type Metadata = {
+  colorings: Colorings
+}
+
+export type Colorings = {
+  [key: string]: ColoringInfo
+}
+
+export type ColoringInfo = {
+  title: string
+  type: ScaleType
+
+  /** scale set via JSON */
+  scale: [string, string][]
+}

src/components/tree/reactD3Interface/change.ts

@@ -1,6 +1,6 @@
 import { calculateStrokeColors, getBrighterColor } from "../../../util/colorHelpers";
 import { ChangeParams } from "../phyloTree/change";
-import { PhyloTree } from "../phyloTree/phyloTree";
+import { PhyloTree } from "../phyloTree/types";
 import { TreeComponentProps, TreeComponentState } from "../tree";
 
 export const changePhyloTreeViaPropsComparison = (

src/components/tree/reactD3Interface/initialRender.ts

@@ -3,7 +3,7 @@ import 'd3-transition';
 import { calculateStrokeColors, getBrighterColor } from "../../../util/colorHelpers";
 import * as callbacks from "./callbacks";
 import { makeTipLabelFunc } from "../phyloTree/labels";
-import { PhyloTree } from "../phyloTree/phyloTree";
+import { PhyloTree } from "../phyloTree/types";
 import { TreeComponent, TreeComponentProps } from "../tree";
 
 export const renderTree = (

src/components/tree/tree.tsx

@@ -4,8 +4,8 @@ import { FaSearchMinus } from "react-icons/fa";
 import { updateVisibleTipsAndBranchThicknesses } from "../../actions/tree";
 import Card from "../framework/card";
 import Legend from "./legend/legend";
-import PhyloTreeConstructor, { PhyloTree } from "./phyloTree/phyloTree";
-import { ColorScale, Layout, Mutations, ReactTreeNode, ReduxNode, Root, ScatterVariables, TemporalConfidence, TraitCounts, Visibility } from "./phyloTree/types";
+import PhyloTreeConstructor from "./phyloTree/phyloTree";
+import { ColorScale, Layout, Mutations, PhyloTree, ReactTreeNode, ReduxNode, Root, ScatterVariables, TemporalConfidence, TraitCounts, Visibility } from "./phyloTree/types";
 import { getParentBeyondPolytomy } from "./phyloTree/helpers";
 import HoverInfoPanel from "./infoPanels/hover";
 import NodeClickedPanel from "./infoPanels/click";
@@ -53,15 +53,17 @@ interface TreeTooState extends TreeState {
   tangleTipLookup: any[][]
 }
 
-export interface TreeComponentProps extends WithTranslation, TreeComponentPropsFromState {
+export interface TreeComponentOwnProps {
   dispatch: AppDispatch
   height: number
   width: number
 }
 
+export interface TreeComponentProps extends WithTranslation, TreeComponentStateProps, TreeComponentOwnProps {}
+
 // This is duplicated from RootState, but good to be explicit about what's
 // expected here.
-export interface TreeComponentPropsFromState {
+export interface TreeComponentStateProps {
   animationPlayPauseButton: "Play" | "Pause"
   canRenderBranchLabels: boolean
   colorBy: string

src/util/colorScale.ts

@@ -9,7 +9,7 @@ import { isColorByGenotype, decodeColorByGenotype } from "./getGenotype";
 import { setGenotype, orderOfGenotypeAppearance } from "./setGenotype";
 import { getTraitFromNode } from "./treeMiscHelpers";
 import { sortedDomain } from "./sortedDomain";
-import { ColorScale, Genotype, LegendBounds, LegendLabels, LegendValues, ReduxNode, ScaleType, Visibility } from "../components/tree/phyloTree/types";
+import { ColoringInfo, ColorScale, Genotype, LegendBounds, LegendLabels, LegendValues, ReduxNode, ScaleType, Visibility } from "../components/tree/phyloTree/types";
 import { TreeState } from "../components/tree/tree";
 import { ControlsState } from "../reducers/controls";
 
@@ -402,12 +402,7 @@ function getDiscreteValuesFromTree(
  */
 export function getLegendOrder(
   attr: string,
-  coloringInfo: {
-    type: ScaleType
-
-    /** scale set via JSON */
-    scale: [string, string][]
-  },
+  coloringInfo: ColoringInfo,
   nodesA: ReduxNode[],
   nodesB: ReduxNode[] | undefined,
 ) {