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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,172 @@ | ||
| import "./App.css"; | ||
| import React, { useEffect, useState, useCallback, useMemo } from "react"; | ||
| import Deck from "./Deck"; | ||
| import SearchPanel from "./components/SearchPanel"; | ||
| import axios from "axios"; | ||
|
|
||
| import { | ||
| kn_expand_node, | ||
| kn_reorder, | ||
| kn_parse, | ||
| kn_calxy, | ||
| } from "./helpers/tree.js"; | ||
|
|
||
| var protobuf = require("protobufjs"); | ||
| protobuf.parse.defaults.keepCase = true; | ||
|
|
||
| const searchColors = [ | ||
| [255, 0, 0], | ||
| [183, 0, 255], | ||
| [255, 213, 0], | ||
|
|
||
| [0, 0, 255], | ||
| [0, 255, 255], | ||
| ]; | ||
|
|
||
| function Taxodium() { | ||
| const [zoomToSearch, setZoomToSearch] = useState({ index: null }); | ||
|
|
||
| const [searchItems, setSearchItemsBasic] = useState([ | ||
| { | ||
| id: 0.123, | ||
| category: "lineage", | ||
| value: "", | ||
| enabled: true, | ||
| }, | ||
| ]); | ||
|
|
||
| const setSearchItems = useCallback((x) => { | ||
| setSearchItemsBasic(x); | ||
| }, []); | ||
|
|
||
| const [colourBy, setColourBy] = useState("lineage"); | ||
| const setColourByWithCheck = useCallback((x) => { | ||
| setColourBy(x); | ||
| }, []); | ||
| const [nodeData, setNodeData] = useState({ | ||
| status: "not_attempted", | ||
| data: { node_data: { ids: [] } }, | ||
| }); | ||
|
|
||
| const [selectedNode, setSelectedNode] = useState(null); | ||
|
|
||
| useEffect(() => { | ||
| axios.get("/bac120.tree").then(function (response) { | ||
| // handle success | ||
| console.log(response); | ||
| console.log("start"); | ||
| const tree = kn_parse(response.data); | ||
| console.log("order"); | ||
| kn_reorder(tree, tree.root); | ||
| console.log("expand"); | ||
| tree.node_order = kn_expand_node(tree, tree.root); | ||
| tree.parents[tree.root] = tree.root; | ||
| console.log("xy"); | ||
| kn_calxy(tree, true); | ||
| console.log("done"); | ||
| tree.x = tree.x.map((a) => 15 * (a + 0.1)); | ||
| tree.y = tree.y.map((a) => 30 * (a + 0.1)); | ||
| tree.ids = [...Array(tree.names.length).keys()]; | ||
| setNodeData({ status: "loaded", data: { node_data: tree } }); | ||
| }); | ||
| }, []); | ||
|
|
||
| const data = useMemo( | ||
| () => | ||
| nodeData.status === "loaded" ? nodeData.data : { node_data: { ids: [] } }, | ||
| [nodeData] | ||
| ); | ||
|
|
||
| const scatterIds = useMemo( | ||
| () => data.node_data.ids.filter((x) => data.node_data.names[x] !== ""), | ||
| [data] | ||
| ); | ||
|
|
||
| const [search_configs_initial, numSearchResults, totalSeqs] = useMemo(() => { | ||
| const configs = searchItems.map((item, counter) => { | ||
| let filter_function; | ||
| const lowercase_query = item.value.toLowerCase().trim(); | ||
| if (item.category === "mutation") { | ||
| const the_index = data.mutation_mapping.indexOf(item.value); | ||
| filter_function = (x) => | ||
| data.node_data.mutations[x].mutation && | ||
| data.node_data.mutations[x].mutation.includes(the_index); | ||
| } | ||
|
|
||
| if (item.category === "name") { | ||
| filter_function = (x) => | ||
| data.node_data.names[x].toLowerCase().includes(lowercase_query); //TODO precompute lowercase mapping for perf? | ||
| } | ||
|
|
||
| if (item.category === "country") { | ||
| filter_function = (x) => | ||
| data.country_mapping[data.node_data.countries[x]].toLowerCase() === | ||
| lowercase_query; //TODO precompute lowercase mapping for perf | ||
| } | ||
| if (item.category === "lineage") { | ||
| filter_function = (x) => | ||
| data.lineage_mapping[data.node_data.lineages[x]].toLowerCase() === | ||
| lowercase_query; //TODO precompute lowercase mapping for perf | ||
| } | ||
| const enabled = item.value !== null && item.value !== "" && item.enabled; | ||
| return { | ||
| original_index: counter, | ||
| id: "main-search-" + counter, | ||
| enabled: enabled, | ||
| data: item.value !== "" ? scatterIds.filter(filter_function) : [], | ||
| opacity: 0.7, | ||
| getRadius: 7 + counter * 2, | ||
| filled: false, | ||
| stroked: true, | ||
| radiusUnits: "pixels", | ||
| lineWidthUnits: "pixels", | ||
| lineWidthScale: 1, | ||
|
|
||
| getPosition: (d) => { | ||
| return [data.node_data.x[d], data.node_data.y[d]]; | ||
| }, | ||
| getFillColor: (d) => [0, 0, 0], | ||
| getLineColor: (d) => searchColors[counter % searchColors.length], | ||
| }; | ||
| }); | ||
| const num_results = configs.map((x) => x.data.length); | ||
| const filtered_configs = configs.filter((item) => item.enabled); | ||
| return [filtered_configs, num_results, scatterIds.length]; | ||
| }, [data, searchItems, scatterIds]); | ||
|
|
||
| return ( | ||
| <div className="main_content"> | ||
| <div className="md:grid md:grid-cols-12 h-full"> | ||
| <div className="md:col-span-8 h-3/6 md:h-full w-full"> | ||
| <Deck | ||
| search_configs_initial={search_configs_initial} | ||
| scatterIds={scatterIds} | ||
| searchColors={searchColors} | ||
| setSelectedNode={setSelectedNode} | ||
| searchItems={searchItems} | ||
| data={data} | ||
| progress={nodeData.progress} | ||
| colourBy={colourBy} | ||
| zoomToSearch={zoomToSearch} | ||
| /> | ||
| </div> | ||
| <div className="md:col-span-4 h-full bg-white border-gray-600 pl-5 shadow-xl"> | ||
| <SearchPanel | ||
| setZoomToSearch={setZoomToSearch} | ||
| totalSeqs={totalSeqs} | ||
| numSearchResults={numSearchResults} | ||
| searchColors={searchColors} | ||
| selectedNode={selectedNode} | ||
| searchItems={searchItems} | ||
| data={data} | ||
| setSearchItems={setSearchItems} | ||
| colourBy={colourBy} | ||
| setColourBy={setColourByWithCheck} | ||
| /> | ||
| </div> | ||
| </div> | ||
| </div> | ||
| ); | ||
| } | ||
|
|
||
| export default Taxodium; |