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yeroslavizyeroslaviz
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rendering pages for PTM
1 parent 0a2212e commit 26dd096

9 files changed

Lines changed: 1159 additions & 198 deletions

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‎docs/Download_Installation.html‎

Lines changed: 144 additions & 24 deletions
Original file line numberDiff line numberDiff line change
@@ -2,7 +2,7 @@
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
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<meta charset="utf-8">
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<meta name="generator" content="quarto-1.3.433">
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<meta name="generator" content="quarto-1.4.315">
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<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
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@@ -101,6 +101,11 @@
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"panel-placement": "end",
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"type": "overlay",
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"limit": 20,
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"keyboard-shortcut": [
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"f",
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"/",
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"s"
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],
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"language": {
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"search-no-results-text": "No results",
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"search-matching-documents-text": "matching documents",
@@ -127,7 +132,7 @@
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<header id="quarto-header" class="headroom fixed-top">
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<nav class="navbar navbar-expand-lg navbar-dark ">
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<div class="navbar-container container-fluid">
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<div class="navbar-brand-container">
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<div class="navbar-brand-container mx-auto">
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<a href="./index.html" class="navbar-brand navbar-brand-logo">
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<img src="./Figures/coxlab_logo2.png" alt="" class="navbar-logo">
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</a>
@@ -139,47 +144,47 @@
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<div class="collapse navbar-collapse" id="navbarCollapse">
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<ul class="navbar-nav navbar-nav-scroll me-auto">
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<li class="nav-item">
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<a class="nav-link" href="./index.html" rel="" target="">
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<span class="menu-text">HOME</span></a>
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<a class="nav-link" href="./index.html">
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<span class="menu-text">HOME</span></a>
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</li>
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<li class="nav-item">
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<a class="nav-link" href="./maxquant_instructions.html" rel="" target="">
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<span class="menu-text">MaxQuant</span></a>
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<a class="nav-link" href="./maxquant_instructions.html">
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<span class="menu-text">MaxQuant</span></a>
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</li>
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<li class="nav-item">
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<a class="nav-link" href="./perseus_instructions.html" rel="" target="">
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<span class="menu-text">Perseus</span></a>
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<a class="nav-link" href="./perseus_instructions.html">
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<span class="menu-text">Perseus</span></a>
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</li>
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<li class="nav-item">
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<a class="nav-link" href="./andromeda_instructions.html" rel="" target="">
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<span class="menu-text">Andromeda</span></a>
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<a class="nav-link" href="./andromeda_instructions.html">
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<span class="menu-text">Andromeda</span></a>
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</li>
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</ul>
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<ul class="navbar-nav navbar-nav-scroll ms-auto">
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<li class="nav-item compact">
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<a class="nav-link" href="./contact.html" rel="" target=""><i class="bi bi-envelope" role="img">
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<a class="nav-link" href="./contact.html"> <i class="bi bi-envelope" role="img">
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</i>
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<span class="menu-text"></span></a>
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<span class="menu-text"></span></a>
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</li>
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<li class="nav-item compact">
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<a class="nav-link" href="https://github.com/cox-labs/CoxLab_Bug_Reporting" rel="" target=""><i class="bi bi-github" role="img">
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<a class="nav-link" href="https://github.com/cox-labs/CoxLab_Bug_Reporting"> <i class="bi bi-github" role="img">
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</i>
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<span class="menu-text"></span></a>
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<span class="menu-text"></span></a>
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</li>
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<li class="nav-item compact">
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<a class="nav-link" href="https://twitter.com/TheCoxLab" rel="" target=""><i class="bi bi-twitter" role="img">
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<a class="nav-link" href="https://twitter.com/TheCoxLab"> <i class="bi bi-twitter" role="img">
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</i>
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<span class="menu-text"></span></a>
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<span class="menu-text"></span></a>
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</li>
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<li class="nav-item compact">
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<a class="nav-link" href="https://www.linkedin.com/in/juergen-cox-2437ba17/" rel="" target=""><i class="bi bi-fa-linkedin fa-lg" role="img">
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<a class="nav-link" href="https://www.linkedin.com/in/juergen-cox-2437ba17/"> <i class="bi bi-fa-linkedin fa-lg" role="img">
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</i>
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<span class="menu-text"></span></a>
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<span class="menu-text"></span></a>
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</li>
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</ul>
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<div class="quarto-navbar-tools">
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</div>
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</div> <!-- /navcollapse -->
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<div class="quarto-navbar-tools">
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</div>
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</div> <!-- /container-fluid -->
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</nav>
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</header>
@@ -244,6 +249,7 @@ <h1 class="title">Download &amp; Installation</h1>
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</div>
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</header>
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<section id="download" class="level1" data-number="1">
@@ -505,10 +511,9 @@ <h3 data-number="3.0.3" class="anchored" data-anchor-id="monster-pc"><span class
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// clear code selection
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e.clearSelection();
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});
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function tippyHover(el, contentFn) {
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function tippyHover(el, contentFn, onTriggerFn, onUntriggerFn) {
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const config = {
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allowHTML: true,
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content: contentFn,
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maxWidth: 500,
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delay: 100,
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arrow: false,
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interactive: true,
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interactiveBorder: 10,
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theme: 'quarto',
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placement: 'bottom-start'
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placement: 'bottom-start',
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};
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if (contentFn) {
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config.content = contentFn;
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}
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if (onTriggerFn) {
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config.onTrigger = onTriggerFn;
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}
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if (onUntriggerFn) {
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config.onUntrigger = onUntriggerFn;
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}
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window.tippy(el, config);
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}
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const noterefs = window.document.querySelectorAll('a[role="doc-noteref"]');
@@ -533,6 +547,81 @@ <h3 data-number="3.0.3" class="anchored" data-anchor-id="monster-pc"><span class
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const note = window.document.getElementById(id);
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return note.innerHTML;
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});
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}
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const xrefs = window.document.querySelectorAll('a.quarto-xref');
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const processXRef = (id, note) => {
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// Strip column container classes
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const stripColumnClz = (el) => {
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el.classList.remove("page-full", "page-columns");
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if (el.children) {
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for (const child of el.children) {
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stripColumnClz(child);
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}
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}
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}
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stripColumnClz(note)
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if (id.startsWith('sec-')) {
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// Special case sections, only their first couple elements
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const container = document.createElement("div");
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if (note.children && note.children.length > 2) {
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for (let i = 0; i < 2; i++) {
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container.appendChild(note.children[i].cloneNode(true));
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}
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return container.innerHTML
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} else {
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return note.innerHTML;
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}
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} else {
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// Remove any anchor links if they are present
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const anchorLink = note.querySelector('a.anchorjs-link');
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if (anchorLink) {
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anchorLink.remove();
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}
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return note.innerHTML;
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}
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}
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for (var i=0; i<xrefs.length; i++) {
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const xref = xrefs[i];
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tippyHover(xref, undefined, function(instance) {
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instance.disable();
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let url = xref.getAttribute('href');
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let hash = undefined;
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if (url.startsWith('#')) {
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hash = url;
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} else {
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try { hash = new URL(url).hash; } catch {}
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}
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if (hash) {
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const id = hash.replace(/^#\/?/, "");
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const note = window.document.getElementById(id);
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if (note !== null) {
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try {
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const html = processXRef(id, note.cloneNode(true));
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instance.setContent(html);
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} finally {
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instance.enable();
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instance.show();
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}
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} else {
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// See if we can fetch this
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fetch(url.split('#')[0])
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.then(res => res.text())
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.then(html => {
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const parser = new DOMParser();
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const htmlDoc = parser.parseFromString(html, "text/html");
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const note = htmlDoc.getElementById(id);
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if (note !== null) {
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const html = processXRef(id, note);
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instance.setContent(html);
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}
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}).finally(() => {
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instance.enable();
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instance.show();
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});
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}
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}
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}, function(instance) {
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});
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}
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let selectedAnnoteEl;
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const selectorForAnnotation = ( cell, annotation) => {
@@ -575,6 +664,7 @@ <h3 data-number="3.0.3" class="anchored" data-anchor-id="monster-pc"><span class
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}
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div.style.top = top - 2 + "px";
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div.style.height = height + 4 + "px";
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div.style.left = 0;
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let gutterDiv = window.document.getElementById("code-annotation-line-highlight-gutter");
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if (gutterDiv === null) {
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gutterDiv = window.document.createElement("div");
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});
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selectedAnnoteEl = undefined;
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};
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// Handle positioning of the toggle
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window.addEventListener(
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"resize",
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throttle(() => {
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console.log("RESIZE");
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elRect = undefined;
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if (selectedAnnoteEl) {
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selectCodeLines(selectedAnnoteEl);
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}
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}, 10)
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);
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function throttle(fn, ms) {
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let throttle = false;
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let timer;
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return (...args) => {
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if(!throttle) { // first call gets through
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fn.apply(this, args);
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throttle = true;
711+
} else { // all the others get throttled
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if(timer) clearTimeout(timer); // cancel #2
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timer = setTimeout(() => {
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fn.apply(this, args);
715+
timer = throttle = false;
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}, ms);
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}
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};
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}
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// Attach click handler to the DT
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const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
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for (const annoteDlNode of annoteDls) {
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<div class="nav-footer-left">
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&nbsp;
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</div>
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<div class="nav-footer-center">© 2023, created by and maintained by Cox lab</div>
785+
<div class="nav-footer-center">
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<p>© 2023, created by and maintained by Cox lab</p>
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</div>
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<div class="nav-footer-right">
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&nbsp;
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</div>
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</body></html>

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