From f9ad063505d95e69666520f5ca4b7263a60128fb Mon Sep 17 00:00:00 2001 From: theosanderson Date: Sat, 10 Jul 2021 01:51:19 +0100 Subject: [PATCH 1/5] parsing working Former-commit-id: f1f3880a5113db65268045a674f6eb0195513434 --- src/App.jsx | 46 ++++++------------------------ src/helpers/tree.js.REMOVED.git-id | 1 + 2 files changed, 9 insertions(+), 38 deletions(-) create mode 100644 src/helpers/tree.js.REMOVED.git-id diff --git a/src/App.jsx b/src/App.jsx index 28933ff4..61249098 100644 --- a/src/App.jsx +++ b/src/App.jsx @@ -8,7 +8,7 @@ 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"; - +import "./helpers/tree.js" var protobuf = require("protobufjs"); protobuf.parse.defaults.keepCase = true; @@ -58,43 +58,13 @@ function App() { 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 }); - }); - }); - } + const tree = window.kn_parse(window.newick) + window.kn_calxy(tree,true) + tree.ids = [...Array(tree.x.length).keys()]; + tree.x=tree.x.map(x=>10*(x+0.1)) + tree.y=tree.y.map(x=>10*(x+0.1)) + window.tree=tree + setNodeData({ status: "loaded", data: {node_data:tree} }); }, [nodeData.status]); const data = useMemo( ()=>nodeData.status === "loaded" diff --git a/src/helpers/tree.js.REMOVED.git-id b/src/helpers/tree.js.REMOVED.git-id new file mode 100644 index 00000000..2fb47a07 --- /dev/null +++ b/src/helpers/tree.js.REMOVED.git-id @@ -0,0 +1 @@ +6dbfc5bcf3223b030bc229590bdbbbef06e05a58 \ No newline at end of file From b9db7d1ebf2d4eae89f13410ac9e774519ede9fe Mon Sep 17 00:00:00 2001 From: theosanderson Date: Sat, 10 Jul 2021 03:20:49 +0100 Subject: [PATCH 2/5] working Former-commit-id: d52006409d81f55e59dae470681251ed0ba8a41c --- src/App.jsx | 14 ++++++++++---- src/Deck.jsx | 11 ++++++----- src/helpers/tree.js.REMOVED.git-id | 2 +- 3 files changed, 17 insertions(+), 10 deletions(-) diff --git a/src/App.jsx b/src/App.jsx index 61249098..dff681a5 100644 --- a/src/App.jsx +++ b/src/App.jsx @@ -2,7 +2,7 @@ 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 axios from "axios"; import AboutOverlay from "./components/AboutOverlay"; import { BrowserRouter as Router } from "react-router-dom"; import { CgListTree } from "react-icons/cg"; @@ -59,11 +59,17 @@ function App() { useEffect(() => { const tree = window.kn_parse(window.newick) + + window.kn_reorder(tree,tree.root) + tree.node_order = window.kn_expand_node(tree,tree.root) window.kn_calxy(tree,true) - tree.ids = [...Array(tree.x.length).keys()]; - tree.x=tree.x.map(x=>10*(x+0.1)) - tree.y=tree.y.map(x=>10*(x+0.1)) window.tree=tree + + tree.x=tree.x.map(a=>15*(a+0.1)) + tree.y=tree.y.map(a=>30*(a+0.1)) + //tree.names=tree.node.map(a=>a.name) + tree.ids = [...Array(tree.names.length).keys()]; + //tree.parents=tree.node.map(a=>tree.node.findIndex(x=>x===a)) setNodeData({ status: "loaded", data: {node_data:tree} }); }, [nodeData.status]); diff --git a/src/Deck.jsx b/src/Deck.jsx index b88b21e1..2c11fadc 100644 --- a/src/Deck.jsx +++ b/src/Deck.jsx @@ -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), @@ -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]]; @@ -604,8 +605,8 @@ function Deck({ data, colourBy, progress, setSelectedNode,scatterIds,search_conf ); - } - }, [data, node_data, hoverInfo]); + */} + }, [hoverInfo]); const spinnerShown = useMemo(() => node_data.ids.length === 0, [node_data]); diff --git a/src/helpers/tree.js.REMOVED.git-id b/src/helpers/tree.js.REMOVED.git-id index 2fb47a07..040fcb37 100644 --- a/src/helpers/tree.js.REMOVED.git-id +++ b/src/helpers/tree.js.REMOVED.git-id @@ -1 +1 @@ -6dbfc5bcf3223b030bc229590bdbbbef06e05a58 \ No newline at end of file +7b99ffc1eb80e2f3e76b17d8ff33535e9aa5b461 \ No newline at end of file From b01bff101ffd212bc369105f542f09650f2e3846 Mon Sep 17 00:00:00 2001 From: theosanderson Date: Sat, 10 Jul 2021 14:44:47 +0100 Subject: [PATCH 3/5] updates Former-commit-id: 82e7472ab8dc0e84c1d5b43aff03af67f33e799f --- src/helpers/tree.js | 195 +++++++++++++++++++++++++++++ src/helpers/tree.js.REMOVED.git-id | 1 - 2 files changed, 195 insertions(+), 1 deletion(-) create mode 100644 src/helpers/tree.js delete mode 100644 src/helpers/tree.js.REMOVED.git-id diff --git a/src/helpers/tree.js b/src/helpers/tree.js new file mode 100644 index 00000000..890d6343 --- /dev/null +++ b/src/helpers/tree.js @@ -0,0 +1,195 @@ +/* eslint-disable */ +window.newick="((A:1,EE:5):3,B:2,(C:5,D:2):3)" +function kn_parse(str) { + var stack = new Array(); + var tree = new Object(); + tree.error = tree.n_tips = 0; + tree.names = new Array(); + tree.distances = new Array(); + tree.parents = new Array(); + tree.children = new Array(); + tree.x = new Array(); + tree.y = new Array(); + tree.miny = new Array(); + tree.maxy = new Array(); + tree.hidden = new Array(); + for (var l = 0; l < str.length;) { + while (l < str.length && (str.charAt(l) < '!' || str.charAt(l) > '~')) ++l; + if (l == str.length) break; + var c = str.charAt(l); + if (c == ',') ++l; + else if (c == '(') { + stack.push(-1); ++l; + } else if (c == ')') { + var x, m, i; + x = tree.names.length; + for (i = stack.length - 1; i >= 0; --i) + if (stack[i] < 0) break; + if (i < 0) { + tree.error |= 1; break; + } + m = stack.length - 1 - i; + l = kn_add_node(str, l + 1, tree, m); + for (i = stack.length - 1, m = m - 1; m >= 0; --m, --i) { + tree.children[x][m] = stack[i]; + tree.parents[stack[i]] = x; + } + stack.length = i; + stack.push(x); + } else { + ++tree.n_tips; + stack.push(tree.names.length); + l = kn_add_node(str, l, tree, 0); + } + } + if (stack.length > 1) tree.error |= 2; + tree.root = tree.names.length - 1 + return tree; +} + +function kn_add_node(str, l, tree, x) // private method +{ + var r, beg, end = 0, z; + + for (var i = l, beg = l; i < str.length && str.charAt(i) != ',' && str.charAt(i) != ')'; ++i) { + var c = str.charAt(i); + if (c == '[') { + var meta_beg = i; + if (end == 0) end = i; + do ++i; while (i < str.length && str.charAt(i) != ']'); + if (i == str.length) { + tree.error |= 4; + break; + } + meta = str.substr(meta_beg, i - meta_beg + 1); //TODO use this + } else if (c == ':') { + if (end == 0) end = i; + for (var j = ++i; i < str.length; ++i) { + var cc = str.charAt(i); + if ((cc < '0' || cc > '9') && cc != 'e' && cc != 'E' && cc != '+' && cc != '-' && cc != '.') + break; + } + var distance = parseFloat(str.substr(j, i - j)); + --i; + } else if (c < '!' && c > '~' && end == 0) end = i; + } + if (end == 0) end = i; + var node_name = "" + if (end > beg) node_name = str.substr(beg, end - beg); + tree.names.push(node_name); + tree.distances.push(distance) + tree.parents.push(null) + tree.children.push([]) + tree.x.push(0) + tree.y.push(0) + tree.miny.push(0) + tree.maxy.push(0) + tree.hidden.push(false) + + + return i; +} + + +function kn_calxy(tree, is_real) { + var i, j, scale; + // calculate y + scale = tree.n_tips - 1; + for (i = j = 0; i < tree.names.length; ++i) { + + tree.y[tree.node_order[i]] = (tree.children[tree.node_order[i]].length && !tree.hidden[tree.node_order[i]]) ? (tree.y[tree.children[tree.node_order[i]][0]] + tree.y[tree.children[tree.node_order[i]][tree.children[tree.node_order[i]].length - 1]]) / 2.0 : (j++) / scale; + if (tree.children[tree.node_order[i]].length == 0) tree.miny[tree.node_order[i]] = tree.maxy[tree.node_order[i]] = tree.y[tree.node_order[i]]; + else tree.miny[tree.node_order[i]] = tree.miny[tree.children[tree.node_order[i]][0]], tree.maxy[tree.node_order[i]] = tree.maxy[tree.children[tree.node_order[i]][tree.children[tree.node_order[i]].length - 1]]; + } + // calculate x + if (is_real) { // use branch length + var root = tree.names.length - 1; + scale = tree.x[root] = (tree.distances[root] >= 0.0) ? tree.distances[root] : 0.0; + for (i = tree.names.length - 2; i >= 0; --i) { + tree.x[i] = tree.x[tree.parents[i]] + (tree.distances[i] >= 0.0 ? tree.distances[i] : 0.0); + if (tree.x[i] > scale) scale = tree.x[i]; + } + if (scale == 0.0) is_real = false; + } + if (!is_real) { // no branch length + scale = tree.x[tree.names.length - 1] = 1.0; + for (i = tree.names.length - 2; i >= 0; --i) { + tree.x[i] = tree.x[tree.parents[i]] + 1.0; + if (tree.x[i] > scale) scale = tree.x[i]; + } + for (i = 0; i < tree.names.length - 1; ++i) + if (tree.children[i].length == 0) + tree.x[i] = scale; + } + // rescale x + for (i = 0; i < tree.names.length; ++i) + tree.x[i] /= scale; + return is_real; +} + +function kn_expand_node(tree, root) { + var node, stack; + node = new Array(); + stack = new Array(); + stack.push({ p: root, i: 0 }); + for (; ;) { + while (stack[stack.length - 1].i != tree.children[stack[stack.length - 1].p].length && !tree.hidden[stack[stack.length - 1].p]) { + var q = stack[stack.length - 1]; + stack.push({ p: tree.children[q.p][q.i], i: 0 }); + } + node.push(stack.pop().p); + if (stack.length > 0) ++stack[stack.length - 1].i; + else break; + } + return node; +} + + +function kn_reorder(tree, root) { + var depths = {} + var tip_numbers = {} + var weights = {} + + var sort_leaf = function (a, b) { + if (depths[a] < depths[b]) return 1; + if (depths[a] > depths[b]) return -1; + return String(tree.names[a]) < String(tree.names[b]) ? -1 : String(tree.names[a]) > String(tree.names[b]) ? 1 : 0; + }; + var sort_weight = function (a, b) { return weights[a] / tip_numbers[a] - weights[b] / tip_numbers[b]; }; + //console.log("yp") + var x = new Array(); + var i, node = kn_expand_node(tree,root); + window.node= node + // get depth + depths[node.length - 1] = 0; + for (i = node.length - 2; i >= 0; --i) { + var q = node[i]; + depths[q] = depths[tree.parents[q]] + 1; + if (tree.children[q].length == 0) x.push(q); + } + // set weight for leaves + x.sort(sort_leaf); + for (i = 0; i < x.length; ++i) weights[x[i]] = i, tip_numbers[x[i]] = 1; + // set weight for internal nodes + for (i = 0; i < node.length; ++i) { + var q = node[i]; + if (tree.children[q].length) { // internal + var j, n = 0, w = 0; + for (j = 0; j < tree.children[q].length; ++j) { + n += tip_numbers[tree.children[q][j]]; + w += weights[tree.children[q][j]]; + } + tip_numbers[q] = n; weights[q] = w; + } + } + // swap children + for (i = 0; i < node.length; ++i) + if (tree.children[node[i]].length >= 2) + tree.children[node[i]].sort(sort_weight); + //console.log("node",node) + // console.log("weight",weights) +} + + + +export {kn_expand_node,kn_reorder,kn_parse,kn_calxy} diff --git a/src/helpers/tree.js.REMOVED.git-id b/src/helpers/tree.js.REMOVED.git-id deleted file mode 100644 index 040fcb37..00000000 --- a/src/helpers/tree.js.REMOVED.git-id +++ /dev/null @@ -1 +0,0 @@ -7b99ffc1eb80e2f3e76b17d8ff33535e9aa5b461 \ No newline at end of file From 0db3dbb47b1041fe98cfae1fe5e1ca6de4a0113b Mon Sep 17 00:00:00 2001 From: theosanderson Date: Sat, 10 Jul 2021 14:44:55 +0100 Subject: [PATCH 4/5] updates Former-commit-id: ec35c5d593f54df0da48ce0769624037575c606d --- public/cog_global_tree.newick.REMOVED.git-id | 1 + src/App.jsx | 40 +++++++++++++------- 2 files changed, 27 insertions(+), 14 deletions(-) create mode 100644 public/cog_global_tree.newick.REMOVED.git-id diff --git a/public/cog_global_tree.newick.REMOVED.git-id b/public/cog_global_tree.newick.REMOVED.git-id new file mode 100644 index 00000000..d36bf178 --- /dev/null +++ b/public/cog_global_tree.newick.REMOVED.git-id @@ -0,0 +1 @@ +dfec1fcd21f6ba8420045894f854363de63746f3 \ No newline at end of file diff --git a/src/App.jsx b/src/App.jsx index dff681a5..c41105cc 100644 --- a/src/App.jsx +++ b/src/App.jsx @@ -2,13 +2,13 @@ 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 axios from "axios"; 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"; -import "./helpers/tree.js" +import {kn_expand_node,kn_reorder,kn_parse,kn_calxy} from "./helpers/tree.js"; var protobuf = require("protobufjs"); protobuf.parse.defaults.keepCase = true; @@ -57,21 +57,33 @@ function App() { const [aboutEnabled, setAboutEnabled] = useState(false); - useEffect(() => { - const tree = window.kn_parse(window.newick) - - window.kn_reorder(tree,tree.root) - tree.node_order = window.kn_expand_node(tree,tree.root) - window.kn_calxy(tree,true) - window.tree=tree - +useEffect(() => { + axios.get('/cog_global_tree.newick') + .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.names=tree.node.map(a=>a.name) tree.ids = [...Array(tree.names.length).keys()]; - //tree.parents=tree.node.map(a=>tree.node.findIndex(x=>x===a)) - setNodeData({ status: "loaded", data: {node_data:tree} }); - }, [nodeData.status]); + setNodeData( { status: "loaded", data: {node_data:tree}}) + }) + + + },[]) + + + + const data = useMemo( ()=>nodeData.status === "loaded" ? nodeData.data From 793ecb58d5cf93054c99f1e8ca4beeac626d8f40 Mon Sep 17 00:00:00 2001 From: theosanderson Date: Sat, 10 Jul 2021 20:54:32 +0100 Subject: [PATCH 5/5] updates Former-commit-id: 780b4595a111b6838c5e0670adeaebc2ae674e9c --- public/bac120.tree | 1 + src/App.jsx | 186 ++------------------------------------------- src/Taxodium.jsx | 172 +++++++++++++++++++++++++++++++++++++++++ 3 files changed, 178 insertions(+), 181 deletions(-) create mode 100644 public/bac120.tree create mode 100644 src/Taxodium.jsx diff --git a/public/bac120.tree b/public/bac120.tree new file mode 100644 index 00000000..9fc237a1 --- /dev/null +++ b/public/bac120.tree @@ -0,0 +1 @@ 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f__UBA5177':0.37517)22.0:0.03873)99.0:0.04941,((((((((((((((GB_GCA_001795245.1:0.05049,GB_GCA_004297395.1:0.04391)100.0:0.03031,GB_GCA_013822395.1:0.06723)97.0:0.02645,GB_GCA_004298915.1:0.12299)100.0:0.04954,((GB_GCA_002413045.1:0.0803,GB_GCA_005889475.1:0.07158)100.0:0.05159,(GB_GCA_003250155.1:0.05508,GB_GCA_012026785.1:0.0408)100.0:0.06447)100.0:0.05518)'100.0:g__UBA5189':0.04589,GB_GCA_903822495.1:0.16082)67.0:0.01972,((GB_GCA_903924005.1:0.025,GB_GCA_903925955.1:0.02727)100.0:0.07442,GB_GCA_903930745.1:0.10415)'100.0:g__CAIXZV01':0.14054)27.0:0.01671,((((GB_GCA_013695505.1:0.04589,GB_GCA_013698095.1:0.06171)100.0:0.03808,GB_GCA_005882635.1:0.07667)'100.0:g__CF-46':0.07261,(GB_GCA_004525275.1:0.12182,GB_GCA_013698385.1:0.10343)'100.0:g__SPCO01':0.05062)31.0:0.02076,GB_GCA_013695255.1:0.12692)72.0:0.01895)88.0:0.03102,(((GB_GCA_005880805.1:0.08244,GB_GCA_005883615.1:0.0773)'100.0:g__CF-16':0.05603,GB_GCA_005881055.1:0.14313)100.0:0.03181,(GB_GCA_003152165.1:0.04296,GB_GCA_003169655.1:0.04305)'100.0:g__Palsa-1033':0.14945)63.0:0.01864)99.0:0.03704,((((((((GB_GCA_003158875.1:0.06737,GB_GCA_003171035.1:0.04735)95.0:0.01638,GB_GCA_003156975.1:0.06052)99.0:0.01942,GB_GCA_003157875.1:0.06457)51.0:0.00846,(GB_GCA_003153755.1:0.10106,GB_GCA_003158495.1:0.06663)71.0:0.01976)34.0:0.00804,(GB_GCA_003142755.1:0.04002,GB_GCA_003171255.1:0.0271)100.0:0.04097)23.0:0.01355,GB_GCA_003165675.1:0.05512)95.0:0.02406,(((((GB_GCA_003141955.1:0.02033,GB_GCA_003171065.1:0.02602)100.0:0.01441,GB_GCA_003157175.1:0.03191)98.0:0.01488,GB_GCA_003152995.1:0.05077)60.0:0.01028,GB_GCA_003158675.1:0.06765)83.0:0.01737,GB_GCA_003141245.1:0.05745)100.0:0.03555)55.0:0.01683,(GB_GCA_003141455.1:0.02199,GB_GCA_003158295.1:0.02126)100.0:0.05342)'100.0:g__Fen-1039':0.15705)62.0:0.02816,GB_GCA_903928275.1:0.21307)100.0:0.04542,(((((((GB_GCA_013696275.1:0.14291,GB_GCA_013813905.1:0.11519)32.0:0.01768,GB_GCA_013696945.1:0.10695)74.0:0.02481,GB_GCA_003169735.1:0.1406)'100.0:g__Palsa-1032':0.06982,GB_GCA_013694835.1:0.16121)90.0:0.02936,GB_GCA_013815585.1:0.17653)52.0:0.02467,GB_GCA_001443375.1:0.15452)100.0:0.05493,GB_GCA_001794945.1:0.21698)86.0:0.02956)'100.0:f__CSP1-4':0.08032,((((((((((GB_GCA_009692905.1:0.01163,GB_GCA_903820655.1:0.0065)94.0:0.00433,GB_GCA_003670455.1:0.00678)54.0:0.0024,GB_GCA_903938075.1:0.01404)88.0:0.00624,GB_GCA_009919365.1:0.01741)97.0:0.00842,GB_GCA_009925905.1:0.01157)55.0:0.00652,GB_GCA_903851225.1:0.04022)97.0:0.01882,GB_GCA_009919005.1:0.05823)100.0:0.08849,GB_GCA_903864185.1:0.12376)50.0:0.02933,(((GB_GCA_003476885.1:0.0086,GB_GCA_903937225.1:0.00614)100.0:0.01974,GB_GCA_903847005.1:0.04047)100.0:0.02702,(GB_GCA_003670475.1:0.01091,GB_GCA_903944295.1:0.00949)100.0:0.04297)100.0:0.06838)50.0:0.03067,GB_GCA_003670745.1:0.0897)'100.0:f__UBA10416; g__UBA10416':0.39391)'100.0:o__CSP1-4':0.13117,(((((GB_GCA_005879815.1:0.01611,GB_GCA_005880165.1:0.01838)100.0:0.0293,GB_GCA_005882055.1:0.05703)'100.0:g__CF-82':0.09987,GB_GCA_003243965.1:0.13309)84.0:0.02649,(GB_GCA_005879775.1:0.10418,GB_GCA_013816405.1:0.10154)'100.0:g__CF-167':0.049)83.0:0.03217,((GB_GCA_013694645.1:0.0665,GB_GCA_013697395.1:0.07991)96.0:0.02669,(GB_GCA_013694795.1:0.06708,GB_GCA_013820865.1:0.07404)99.0:0.02554)'100.0:g__JACDBZ01':0.07722)'100.0:o__QHBO01; f__QHBO01':0.24396)100.0:0.14948,((((((((((((GB_GCA_005880575.1:0.03251,GB_GCA_005882765.1:0.02503)50.0:0.00599,GB_GCA_005883775.1:0.02146)72.0:0.00942,GB_GCA_005881085.1:0.03871)83.0:0.00927,GB_GCA_005889295.1:0.03226)100.0:0.05938,((GB_GCA_005879975.1:0.02895,GB_GCA_005881885.1:0.02854)90.0:0.01669,GB_GCA_001917735.1:0.04874)100.0:0.03777)94.0:0.02111,(GB_GCA_005889275.1:0.05474,GB_GCA_005889445.1:0.05628)100.0:0.03774)71.0:0.01743,GB_GCA_005889075.1:0.09228)100.0:0.03224,(GB_GCA_001919195.1:0.00776,GB_GCA_001920645.1:0.00426)100.0:0.09128)'100.0:g__3-1-20CM-2-70-9':0.06961,((GB_GCA_005882255.1:0.02474,GB_GCA_005889405.1:0.01928)100.0:0.08387,GB_GCA_005887995.1:0.12318)'100.0:g__CF-39':0.05313)100.0:0.03809,((GB_GCA_009692785.1:0.19135,GB_GCA_013695575.1:0.16784)63.0:0.0257,GB_GCA_002404155.1:0.16047)87.0:0.03663)80.0:0.03067,GB_GCA_001795345.1:0.20371)'100.0:f__P2-11E':0.10774,GB_GCA_005881435.1:0.25988)'100.0:o__P2-11E':0.26828)'100.0:c__Ellin6529':0.09364)'65.0:p__Chloroflexota':0.02545)d__Bacteria; diff --git a/src/App.jsx b/src/App.jsx index c41105cc..82f1bf3a 100644 --- a/src/App.jsx +++ b/src/App.jsx @@ -1,159 +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"; -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], -]; - - - +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(() => { - axios.get('/cog_global_tree.newick') - .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 ( @@ -182,41 +36,11 @@ const scatterIds = useMemo( -
-
-
- -
-
- -
-
-
+ Loading...}> + + ); } - export default App; diff --git a/src/Taxodium.jsx b/src/Taxodium.jsx new file mode 100644 index 00000000..5c7a64cc --- /dev/null +++ b/src/Taxodium.jsx @@ -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 ( +
+
+
+ +
+
+ +
+
+
+ ); +} + +export default Taxodium;