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V1: Dynamic tree do not merge #41

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V1: Dynamic tree do not merge #41

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f9ad063
parsing working
theosanderson Jul 10, 2021
b9db7d1
working
theosanderson Jul 10, 2021
b01bff1
updates
theosanderson Jul 10, 2021
0db3dbb
updates
theosanderson Jul 10, 2021
793ecb5
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theosanderson Jul 10, 2021
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1 change: 1 addition & 0 deletions public/bac120.tree
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1 change: 1 addition & 0 deletions public/cog_global_tree.newick.REMOVED.git-id
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Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
dfec1fcd21f6ba8420045894f854363de63746f3
198 changes: 5 additions & 193 deletions src/App.jsx
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Original file line number Diff line number Diff line change
@@ -1,171 +1,13 @@
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 React, { useState, Suspense } from "react";
import AboutOverlay from "./components/AboutOverlay";
import { BrowserRouter as Router } from "react-router-dom";
import { CgListTree } from "react-icons/cg";
//import {FaGithub} from "react-icons/fa";
import { BsInfoSquare } from "react-icons/bs";


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],
];



const Taxodium = React.lazy(() => import("./Taxodium"));
function App() {

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);

const [aboutEnabled, setAboutEnabled] = useState(false);

useEffect(() => {
if (nodeData.status === "not_attempted") {
console.log("starting dl");
setNodeData({
status: "loading",
progress: 0,
data: { node_data: { ids: [] } },
});

protobuf.load("./tree.proto").then(function (root) {
axios
.get("/nodelist.pb", {
responseType: "arraybuffer",
onDownloadProgress: (progressEvent) => {
let percentCompleted = Math.floor(
1 * (progressEvent.loaded / 100000000) * 100
);
setNodeData({
status: "loading",
progress: percentCompleted,
data: { node_data: { ids: [] } },
});
},
})
.then(function (response) {
return response.data;
})
.then(function (buffer) {
console.log("buffer loaded");
var NodeList = root.lookupType("AllData");

var message = NodeList.decode(new Uint8Array(buffer));
var result = NodeList.toObject(message);
result.node_data.ids = [...Array(result.node_data.x.length).keys()];
setNodeData({ status: "loaded", data: result });
});
});
}
}, [nodeData.status]);

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 (
<Router>
<AboutOverlay enabled={aboutEnabled} setEnabled={setAboutEnabled} />
Expand Down Expand Up @@ -194,41 +36,11 @@ const scatterIds = useMemo(
</div>
</div>
</div>
<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>
<Suspense fallback={<div>Loading...</div>}>
<Taxodium />
</Suspense>
</div>
</Router>
);
}

export default App;
11 changes: 6 additions & 5 deletions src/Deck.jsx
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Expand Up @@ -131,10 +131,10 @@ function toRGB(string) {
}
return rgb;
}
function toRGBCSS(string) {
/*function toRGBCSS(string) {
const output = toRGB(string);
return `rgb(${output[0]},${output[1]},${output[2]})`;
}
}*/

let getMMatrix = (zoom) => [
1 / 2 ** (zoom - 5.6),
Expand Down Expand Up @@ -564,7 +564,8 @@ function Deck({ data, colourBy, progress, setSelectedNode,scatterIds,search_conf

const hoverStuff = useMemo(() => {
if (hoverInfo && hoverInfo.object) {
const lineage =
return <>{hoverInfo.object}</>
/*const lineage =
data.lineage_mapping[node_data.lineages[hoverInfo.object]];
const country =
data.country_mapping[node_data.countries[hoverInfo.object]];
Expand Down Expand Up @@ -604,8 +605,8 @@ function Deck({ data, colourBy, progress, setSelectedNode,scatterIds,search_conf
</div>
</div>
);
}
}, [data, node_data, hoverInfo]);
*/}
}, [hoverInfo]);
const spinnerShown = useMemo(() => node_data.ids.length === 0, [node_data]);


Expand Down
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