sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
764e2a6d847a5901e615e3d07cc017119bbafd817cc23fadb8b65fded09a6e34 | JavaScript | 379 | 15 | ////////////////////////////////////////////////
// Call all deferred plotting functions
////////////////////////////////////////////////
$(function () {
decompressPlotData(mqc_compressed_plotdata, (mqc_plotdata, err) => {
if (err) {
console.error(err);
return;
}
callAfterDecompressed.forEach... |
207a8c21335a0e00a3ce8914fc09ecff460d97ba860114ba4b0b77b2902ced7e | JavaScript | 386 | 15 | ////////////////////////////////////////////////
// Call all deferred plotting functions
////////////////////////////////////////////////
$(function () {
decompressPlotData(mqc_compressed_plotdata, (mqc_plotdata, err) => {
if (err) {
console.error(err);
return;
}
window.callAfterDecompressed.... |
85c062426f1dba637175c53a9021c047fb86735bc62badfb67c3d821f39dd578 | JavaScript | 396 | 18 | /*
##
## This file is part of the Omics Playground project.
## Copyright (c) 2018-2026 BigOmics Analytics Sagl. All rights reserved.
##
*/
$(document).on('shiny:idle', function() {
console.log("shiny:idle")
Shiny.onInputChange("continue_test", true);
});
$(document).on('shiny:busy', function() {
Shin... |
a19b8c0a0ff9ee9a8d184c0bde94fdd94de0c894af4f71f9e427b5cb118f2693 | JavaScript | 411 | 14 | var DOCUMENTATION_OPTIONS = {
URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
VERSION: '',
LANGUAGE: 'en',
COLLAPSE_INDEX: false,
BUILDER: 'html',
FILE_SUFFIX: '.html',
LINK_SUFFIX: '.html',
HAS_SOURCE: true,
SOURCELINK_SUFFIX: '',
NAVIGA... |
f9ae7f8d8a2c553e17884f92b1a09ba15c412dcecee10c225b636b9b77721b8d | JavaScript | 496 | 14 | function addTick(buttonId) {
var button = document.getElementById(buttonId);
var originalText = button.innerHTML;
if (!originalText.includes('✓')) {
button.innerHTML = originalText + '<span class="tick">✓</span>';
button.classList.add('show-tick');
setTimeout(function() {
button.classList.remove... |
d824ba2443ca4f08cefa8cb4aabe349173fbef492420edcbcc1b65e40ff19673 | JavaScript | 531 | 14 | var shouldWarnOnExit = false;
Shiny.addCustomMessageHandler('warnOnExit', function(message) {
shouldWarnOnExit = message;
});
// Before the user closes the tab
window.addEventListener('beforeunload', function (e) {
if (shouldWarnOnExit) {
var confirmationMessage = 'Dataset computation is running. Are you ... |
295c78a0f3ca011c2113f6519113a058ce1bb749d015434a1955c474c18dafa7 | JavaScript | 559 | 26 | import { resolve } from "path";
export default {
root: resolve(__dirname, "src"),
build: {
outDir: "../compiled",
rollupOptions: {
input: {
main: resolve(__dirname, "src/js/main.js"),
},
output: {
entryFileNames: "js/multiqc.min.js",
assetFileNames: "css/multiqc.mi... |
1c547d78051422f3cf82fed821be0b570239b0305a736ac15aaecebfde046d88 | JavaScript | 569 | 15 | function copyPlotModuleInfo() {
var elements = document.getElementsByClassName('popover-body')[0].children[0].children;
var textToCopy = '';
for (var i = 0; i < elements.length; i++) {
if (elements[i].className === "plotmodule-info") {
textToCopy += elements[i].innerText + '\n';
... |
00a9989c6d54254f32a37e50c7bbc5dab737674231aa2553421f4939624b23e3 | JavaScript | 770 | 27 | var sd_labels_by_text = {};
function ready() {
const li = document.getElementsByClassName("sd-tab-label");
for (const label of li) {
syncId = label.getAttribute("data-sync-id");
if (syncId) {
label.onclick = onLabelClick;
if (!sd_labels_by_text[syncId]) {
sd_labels_by_text[syncId] = [];... |
d968b860e8dc1e6533e76c0d68cd5dc13b07d1c61b13d2ac6e9e56ef2c2ead01 | JavaScript | 816 | 25 | // JS function to make the popovers
// dismissable when clcking outside the
// popover itself.
// Called from ui-DropdownMenu.R
function makePopoverDismissible(id) {
$(document).click(function (e) {
var popover = $('#' + id);
//popover.addClass("btn-active");
if (!popover.is(e.target) && popover.has(e.ta... |
b0a01dad6fd180157778d878b0c27ac46be70f628e9cf5a00fdae1fe7e9dc09d | JavaScript | 878 | 26 | /*
* Copyright 2022 Google LLC.
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* https://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in... |
4aa8f5f6d3646531777c9d4d4ef1a61ab9b8d2f1cc95544e5f6b775e875d27b0 | JavaScript | 949 | 23 | document.addEventListener("DOMContentLoaded", function(){
const toggleDarkMode = document.querySelector('.js-toggle-dark-mode')
const cssFile = document.querySelector('[rel="stylesheet"]')
const originalCssRef = cssFile.getAttribute('href')
const darkModeCssRef = originalCssRef.replace('just-the-docs.css', 'da... |
40309186ba5d967aae61b9f937783aaeeaacc1493b6bc7880702399c82d68f32 | JavaScript | 1,018 | 27 | // Update the "pending received datasets" indicators in the navbar:
// - numeric badge on the "Sharing" sub-item
// - small red dot on the parent "Datasets" dropdown toggle
// Called from loading_module_received.R via shinyjs::runjs("updateSharedBadges(n)").
function updateSharedBadges(n) {
var sub = document.query... |
3956d192870250e97d584be1f68b2c0519b6f4c379fd6c0272076b23167d332e | JavaScript | 1,064 | 41 | /*
* Copyright 2022 Google LLC.
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* https://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in... |
fa31a22fe950aecc309fdf7eef46d97cc76017bbbc1ecca99c9a62cb9b60c977 | JavaScript | 1,205 | 48 | // Import Bootstrap 5 JavaScript
// Tree-shaking should remove unused JS
import * as bootstrap from "bootstrap";
// Make Bootstrap available globally for compatibility
window.bootstrap = bootstrap;
// Import MultiQC JavaScript modules in the correct order
// Core functionality first
import "./decompress.js";
import "... |
e1e49882c71bc3abf5900d2167f9a3327722e48c37a8ab63c9fa31f8a6566352 | JavaScript | 1,485 | 42 | ////////////////////////////////////////////////
// Flat plots controls
////////////////////////////////////////////////
// On page load
$(function () {
function switchPlot(button) {
let plotGroup = $(button).closest(".mqc_mplplot_plotgroup");
let plotAnchor = plotGroup.data("plot-anchor");
let activeDs ... |
84544a55cf3a4f7fd959db201582ce3f2b60fbf03d058f837f33ccc718bee44f | JavaScript | 1,509 | 60 | ////////////////////////////////////////////////
// MultiQC Report Toolbox Constants
////////////////////////////////////////////////
// Make constants available globally
window.mqc_colours = [
"#e41a1c",
"#377eb8",
"#4daf4a",
"#984ea3",
"#ff7f00",
"#a9a904",
"#a65628",
"#f781bf",
"#999999",
];
windo... |
0ed8e08f7412d8a81473bb6ab7c775ead373e6dcb377210a8477ed71fc1fc40e | JavaScript | 1,584 | 47 | function decompressPlotData(base64Str, callback) {
// Decode the Base64 string to bytes.
const binaryString = atob(base64Str);
const bytes = Uint8Array.from(binaryString, (m) => m.codePointAt(0));
// Check if DecompressionStream is supported
if ("DecompressionStream" in window) {
// Passing a callback to... |
c54b2f4bb05823736e010d967e4f0c1ed8f867cc56a83b9df7479449b311dfe5 | JavaScript | 1,591 | 46 | ////////////////////////////////////////////////
// MultiQC Report Help Modal Functionality
////////////////////////////////////////////////
// Make function available globally
window.initHelp = function () {
/////////////////////////
// REGEX HELP MODAL
/////////////////////////
$(".regex_example_buttons butt... |
4e39511ade942ec23f0f831ed667ce31268725cb914f346d7085a1da9fc7086d | JavaScript | 1,679 | 50 | function decompressPlotData(base64Str, callback) {
// Decode the Base64 string to bytes.
const binaryString = atob(base64Str);
const bytes = Uint8Array.from(binaryString, (m) => m.codePointAt(0));
// Check if DecompressionStream is supported
if ("DecompressionStream" in window) {
// Passing a callback to... |
c2e12dbf5782efc0bb6ad4ba72c404c4dc5afb4c42c17b6dc7c8d41404226e68 | JavaScript | 1,858 | 56 | ////////////////////////////////////////////////
// MultiQC Report Citations and DOI Management
////////////////////////////////////////////////
// Make function available globally
window.initCitations = function () {
// Find DOIs and modules
var doi_list = { "10.1093/bioinformatics/btw354": "MultiQC" };
$(".mod... |
9d1c08b685d541edbbc0185a5d2338a1ee6cd92ae92788df2c75ea5c813f4396 | JavaScript | 1,865 | 66 | /*
* Copyright 2022 Google LLC.
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* https://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in... |
220a75ef8016ec03c572fc182db32b90bafad709dde10981ebfebc741a7a05bd | JavaScript | 1,925 | 54 | $('#mysidebar').height($(".nav").height());
$( document ).ready(function() {
//this script says, if the height of the viewport is greater than 800px, then insert affix class, which makes the nav bar float in a fixed
// position as your scroll. if you have a lot of nav items, this height may not work for you.... |
f813a3a8c9291a33508b4f1d9a92a4ddead7960644774a34cd1dd134fd4186da | JavaScript | 2,039 | 38 | //To pick up changes to this you may need to clear cached files in the browser
function do_locuszoom_stuff(input_snp, input_chr, input_bp, input_formatsnp,population)
{
var apiBase = "https://portaldev.sph.umich.edu/api/v1/";
//console.log(document.getElementById("interactive_ref_link").href);
... |
a3720a8b1bcc8fdf4918607ae2d771a937a9028ae3fe4999f6e65cb4412cce20 | JavaScript | 2,404 | 93 | /*
* Copyright 2022 Google LLC.
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* https://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in... |
14f249b7c9c0fb12f8454ebf82cae203ca7cc4078b19ab68c938e576f40a19d1 | JavaScript | 2,446 | 2 | /*! @source http://purl.eligrey.com/github/FileSaver.js/blob/master/FileSaver.js */
var saveAs=saveAs||function(e){"use strict";if(typeof e==="undefined"||typeof navigator!=="undefined"&&/MSIE [1-9]\./.test(navigator.userAgent)){return}var t=e.document,n=function(){return e.URL||e.webkitURL||e},r=t.createElementNS("htt... |
88164c7c15abfe6d284616cc666a4f6d8018c2ee13d0e5ee03b4499f49a5e31f | JavaScript | 2,903 | 69 | /*
* Copyright 2022 Google LLC.
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* https://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in... |
51b48682782adec689a97212450db773c91765e8b58343322b2f0cba9c626b22 | JavaScript | 2,926 | 72 | ////////////////////////////////////////////////
// MultiQC Report Common Filter Handling
//
// This file contains common code for handling filter rows across different
// toolbox sections (highlights, rename samples, hide samples). The filter
// functionality includes adding/removing filter rows, handling input events... |
254a02ae8eded9af40cd9dad42ea930013fc52018d55d36fb303a933f660d645 | JavaScript | 2,998 | 96 | /*
* Copyright 2022 Google LLC.
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* https://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in... |
256b8b071260a5ac20cad7bcf0537201ad71b8b7ea4f5d89546c7015fec1138f | JavaScript | 3,075 | 2 | !function(e){var t={};function n(r){if(t[r])return t[r].exports;var o=t[r]={i:r,l:!1,exports:{}};return e[r].call(o.exports,o,o.exports,n),o.l=!0,o.exports}n.m=e,n.c=t,n.d=function(e,t,r){n.o(e,t)||Object.defineProperty(e,t,{enumerable:!0,get:r})},n.r=function(e){"undefined"!=typeof Symbol&&Symbol.toStringTag&&Object.d... |
27cb4509daa5cdf65394c33a24eb267681952697a9024c008f7cf54e1996a747 | JavaScript | 3,110 | 82 | // https://github.com/ghiculescu/jekyll-table-of-contents
(function($){
$.fn.toc = function(options) {
var defaults = {
noBackToTopLinks: false,
title: '',
minimumHeaders: 3,
headers: 'h1, h2, h3, h4',
listType: 'ol', // values: [ol|ul]
showEffect: 'show', // values: [show|slid... |
7159212cab2c9b26ebfee25a0da82ce186c0af89918ccf71b45b177a42d6cb93 | JavaScript | 3,116 | 103 | ////////////////////////////////////////////////
// Base JS for MultiQC Reports
////////////////////////////////////////////////
// Collect functions to be called after plot data is decompressed.
// Includes functions in plotting.js, and any module-specific JS like multiqc_fastqc.js
let callAfterDecompressed = [];
//... |
1e1a6a5cb258742efc2871e48337bd3db65eee7b7a0587d848849a4ad276aebd | JavaScript | 3,448 | 107 | ////////////////////////////////////////////////
// MultiQC Report Toolbox Code - Main Coordinator
////////////////////////////////////////////////
//////////////////////////////////////////////////////
// TOOLBOX LISTENERS
//////////////////////////////////////////////////////
// Helper function to open/close toolbox... |
a4f1475c0e9223489732f073c2ab651617670f18b2d0b11c45c3e2ffafded0a8 | JavaScript | 3,475 | 112 | /*!
* Color mode toggler for MultiQC based on Bootstrap's implementation
* Licensed under the Apache License, Version 2.0
*/
(() => {
"use strict";
// Check if dark mode is enabled via config
if (window.mqc_config && window.mqc_config.template_dark_mode === false) {
return;
}
const getStoredTheme = ... |
d4c4e9f93523b19beba3b11975d0d2810897b2f956940838c9bff385dd806beb | JavaScript | 3,709 | 114 | ////////////////////////////////////////////////
// Base JS for MultiQC Reports
////////////////////////////////////////////////
// Collect functions to be called after plot data is decompressed.
// Includes functions in plotting.js, and any module-specific JS like multiqc_fastqc.js
window.callAfterDecompressed = [];
... |
ae9aab39b9a105ad71bfe095540766d4fcd14ed5d20627694ca6c2e121639f90 | JavaScript | 3,986 | 126 | /**
* Add attributes to Thebe blocks to initialize thebe properly
*/
var configureThebe = () => {
// Load thebe config in case we want to update it as some point
console.log("[sphinx-thebe]: Loading thebe config...");
thebe_config = $('script[type="text/x-thebe-config"]')[0];
// If we already detect a Thebe ... |
cc4653b8e1b933d56bf943ee4b824fc546b57ba9b051d3332d09c461e6a4f3f1 | JavaScript | 4,065 | 134 | // Initialise module DOI popovers
$(function () {
const HOVER_DELAY = 500;
const HIDE_DELAY = 1000;
const POPOVER_MOUNT_DELAY = 100;
const MOUSELEAVE_CHECK_DELAY = 50;
let doiHoverTimeout = null;
let doiHideTimeout = null;
// Helper functions
const clearTimer = (timer) => timer && clearTimeout(timer);... |
56b6685c31ee02dc3c805de143b5f7d8280eb47166430af966a4766a00ba059c | JavaScript | 4,143 | 177 | /*
* Copyright 2022 Google LLC.
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* https://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in... |
ab411fa710d0934def09ed2150dc84c47ec3f3e9f9dc991a146062ac851f38e4 | JavaScript | 4,251 | 116 | ////////////////////////////////////////////////
// MultiQC Report Toolbox - Highlight Samples
////////////////////////////////////////////////
// Make functions available globally
window.apply_mqc_highlights = function () {
// Collect the filters into an array
var f_texts = [];
var f_cols = [];
var regex_mode... |
2f1e30341b31300bdc3af29ee4a64e0f40ed15492345387bb47542d9b9b4813c | JavaScript | 4,418 | 134 | /*
* _sphinx_javascript_frameworks_compat.js
* ~~~~~~~~~~
*
* Compatability shim for jQuery and underscores.js.
*
* WILL BE REMOVED IN Sphinx 6.0
* xref RemovedInSphinx60Warning
*
*/
/**
* select a different prefix for underscore
*/
$u = _.noConflict();
/**
* small helper function to urldecode strings
*... |
1a3c9f99a6aac2dd522231e1eb63d31d6afbe2b89fd028532c6d609e3b503f21 | JavaScript | 4,456 | 2 | (()=>{"use strict";function e(e){"loading"!=document.readyState?e():document.addEventListener("DOMContentLoaded",e)}var t=window.matchMedia("(prefers-color-scheme: dark)");function o(e){document.documentElement.dataset.theme=t.matches?"dark":"light"}function n(e){"light"!==e&&"dark"!==e&&"auto"!==e&&(console.error(`Got... |
ff6c791dd78e0478f27ec9c873767e04da3c4199305a1bf2e6e207abef5b675b | JavaScript | 4,474 | 141 | ////////////////////////////////////////////////
// MultiQC Report Toolbox Utility Functions
////////////////////////////////////////////////
// Escape HTML meta-characters before interpolating text into markup
window.escapeHtml = function (str) {
return String(str)
.replace(/&/g, "&")
.replace(/</g, "&l... |
5b80cc4165a661a3f2060d6bdb5ccff591f04c4f8e39a06c12d3c2544587cb17 | JavaScript | 4,570 | 7 | /*!
* headroom.js v0.12.0 - Give your page some headroom. Hide your header until you need it
* Copyright (c) 2020 Nick Williams - http://wicky.nillia.ms/headroom.js
* License: MIT
*/
!function(t,n){"object"==typeof exports&&"undefined"!=typeof module?module.exports=n():"function"==typeof define&&define.amd?define(... |
7a8990fb38f6f7be3282a1beee86b7280113517f906d343ccbd16e7810bb4845 | JavaScript | 4,609 | 149 | //To pick up changes to this you may need to clear cached files in the browser
$(document).ready(function(){
// Attach the jquery.ui draggable.
//var containmentTop = $(".content-wrapper").position().top;
$(".draggable").draggable({
cursor: "move",
handle: ".box-header",
cancel: ".box-body",
... |
d35fde9e52ed4840ec7ed105ddb3302a26eb0f53aa151a9491a2dcce0f5d2534 | JavaScript | 4,758 | 199 | /*
* language_data.js
* ~~~~~~~~~~~~~~~~
*
* This script contains the language-specific data used by searchtools.js,
* namely the list of stopwords, stemmer, scorer and splitter.
*
* :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
var stopwords ... |
ecdabaa2d73e9c20361c47fb15c9312ce3a9235a572cb3f91dd8fbcec9e790d4 | JavaScript | 4,863 | 141 | class ScatterPlot extends Plot {
activeDatasetSize() {
if (this.datasets.length === 0) return 0; // no datasets
return this.datasets[this.activeDatasetIdx].points; // no data points in a dataset
}
prepData(dataset) {
// Prepare data to either build Plotly traces or export as a file
dataset = data... |
a09cf4f5502bd93f469e02a99628febe2ce8e28e34dc8cd6821db4cd1e8df6e7 | JavaScript | 4,900 | 172 | class LinePlot extends Plot {
activeDatasetSize() {
if (this.datasets.length === 0) return 0; // no datasets
return this.datasets[this.activeDatasetIdx].lines.length; // no samples in a dataset
}
prepData(dataset) {
// Prepare data to either build Plotly traces or export as a file
dataset = datas... |
5fde64f8d15dd9e000f2280ecc603c9b95de18f54157c593f04bc7f3f63e91b7 | JavaScript | 4,903 | 174 | class LinePlot extends Plot {
activeDatasetSize() {
if (this.datasets.length === 0) return 0; // no datasets
return this.datasets[this.activeDatasetIdx].lines.length; // no samples in a dataset
}
prepData(dataset) {
// Prepare data to either build Plotly traces or export as a file
dataset = datas... |
e53030dea60de716a03f26f0d4e81bb4ecfeb1971d9013b4697d70615d8b5269 | JavaScript | 4,937 | 144 | class ScatterPlot extends Plot {
activeDatasetSize() {
if (this.datasets.length === 0) return 0; // no datasets
return this.datasets[this.activeDatasetIdx].points; // no data points in a dataset
}
prepData(dataset) {
// Prepare data to either build Plotly traces or export as a file
dataset = data... |
9a09ccaa11a372c54aa591d471a5bef89a009ad8b0b5eea89d9057b214f28c9f | JavaScript | 5,385 | 155 | ////////////////////////////////////////////////
// MultiQC Report Toolbox - Hide Samples
////////////////////////////////////////////////
// Make functions available globally
window.apply_mqc_hidesamples = function (mode) {
// Collect the filters into an array
if (mode === undefined) {
mode = $(".mqc_hidesamp... |
0db5b003c2a7f28a73a6262de7d347e0db7d73521074d6f0fbb4c5df00becce0 | JavaScript | 5,507 | 208 | #!/usr/bin/env node
/**
* Tool Metrics Fetcher
*
* Fetches popularity and usage metrics for bioinformatics tools from various sources:
* - GitHub: stars, forks, last commit date
* - PyPI: monthly downloads
* - Conda: total downloads (via anaconda.org)
*
* Usage:
* node fetch-tool-metrics.js github owner/rep... |
4bcf18537481bef7e8076cc9bb7aafb61ea741066dc27f640f767558d6276c99 | JavaScript | 5,887 | 168 | ////////////////////////////////////////////////
// MultiQC Report Toolbox - Rename Samples
////////////////////////////////////////////////
// Make functions available globally
window.apply_mqc_renamesamples = function () {
let valid_from_texts = [];
let valid_to_texts = [];
let regex_mode = $("#mqc_renamesampl... |
2afa6abfe7482985c45569855c8ed94978d2aa26a60f32373a20fb42ffd28aa2 | JavaScript | 6,100 | 190 | /**
* @author Chris Rorden
* See https://github.com/neurolabusc/surf-ice/tree/master/mz3 for more information about this file format
*/
( function ( THREE ) {
'use strict';
function decodeMZ3( buffer ) {
if (buffer.byteLength < 20) //76 for raw, not sure of gzip
throw new Error( 'File to small to be mz3: b... |
bfaf52c5d3de927cd7cb48644872ff4ab7212ef3bc403412e0ded5e74c44d0ab | JavaScript | 6,256 | 1 | "function"!=typeof Object.create&&(Object.create=function(t){function o(){}return o.prototype=t,new o}),function(t,o){"use strict";var i={_positionClasses:["bottom-left","bottom-right","top-right","top-left","bottom-center","top-center","mid-center"],_defaultIcons:["success","error","info","warning"],init:function(o){t... |
5c82dc4d60650c54bc6c00d9924c246eb2739de43db748a4738b1de63e3536c2 | JavaScript | 6,382 | 193 | class BarPlot extends Plot {
constructor(dump) {
super(dump);
this.filteredSettings = [];
this.clusterSwitchClusteredActive = dump["cluster_switch_clustered_active"];
}
activeDatasetSize() {
if (this.datasets.length === 0) return 0; // no datasets
let cats = this.datasets[this.activeDatasetId... |
c67ba3f17617f33a6b166ba0763423664342097b13cecfd62ecbcc13f7bd9d64 | JavaScript | 6,633 | 210 | class BoxPlot extends Plot {
constructor(dump) {
super(dump);
this.filteredSettings = [];
this.sortSwitchSortedActive = dump["sort_switch_sorted_active"];
this.isStatsData = dump.datasets && dump.datasets.length > 0 ? dump.datasets[0].is_stats_data : false;
}
activeDatasetSize() {
if (this.da... |
d5157f75fbd472478ac33625526dc4a5eb487ac2e8f14a30e6bb15d274b92242 | JavaScript | 6,638 | 243 | const kProgressiveAttr = "data-src";
let categoriesLoaded = false;
window.quartoListingCategory = (category) => {
if (categoriesLoaded) {
activateCategory(category);
setCategoryHash(category);
}
};
window["quarto-listing-loaded"] = () => {
// Process any existing hash
const hash = getHash();
if (ha... |
9b8daf6cd7a1ac484abe931b05ac215fc5f7daf0c42fbe6609a150b84d9fc56f | JavaScript | 6,657 | 190 | class HeatmapPlot extends Plot {
constructor(dump) {
super(dump);
this.xCatsAreSamples = dump["xcats_samples"];
this.yCatsAreSamples = dump["ycats_samples"];
this.square = dump["square"];
this.filtXCatsSettings = [];
this.filtYCatsSettings = [];
this.clusterSwitchClusteredActive = dump["cl... |
1c951fd8d8a5fe993b5483bb435c8a30d1d0208b0c7094ec84c0b59d43bc7dfe | JavaScript | 6,695 | 213 | class BoxPlot extends Plot {
constructor(dump) {
super(dump);
this.filteredSettings = [];
this.sortSwitchSortedActive = dump["sort_switch_sorted_active"];
this.isStatsData = dump.datasets && dump.datasets.length > 0 ? dump.datasets[0].is_stats_data : false;
}
activeDatasetSize() {
if (this.da... |
de8e568efb0509efb9d225fcee7c488a8efae4dc7d91540cecaafea8099ae503 | JavaScript | 6,731 | 193 | class HeatmapPlot extends Plot {
constructor(dump) {
super(dump);
this.xCatsAreSamples = dump["xcats_samples"];
this.yCatsAreSamples = dump["ycats_samples"];
this.square = dump["square"];
this.filtXCatsSettings = [];
this.filtYCatsSettings = [];
this.clusterSwitchClusteredActive = dump["cl... |
0727f732b137b4e4bccde2ea06e6f6daf2e396e013b89543328ee4f127e5ba84 | JavaScript | 7,346 | 187 | /**
* Add Toggle Buttons to elements
*/
let toggleChevron = `
<svg xmlns="http://www.w3.org/2000/svg" class="tb-icon toggle-chevron-right" width="44" height="44" viewBox="0 0 24 24" stroke-width="1.5" stroke="#000000" fill="none" stroke-linecap="round" stroke-linejoin="round">
<path stroke="none" d="M0 0h24v24H0z" f... |
2985f25f79e5ddcd1ed494ca63fc85f215f79e0cd156e622ce2bf3cf2cd9445f | JavaScript | 8,171 | 264 | /*
* doctools.js
* ~~~~~~~~~~~
*
* Base JavaScript utilities for all Sphinx HTML documentation.
*
* :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
"use strict";
const _ready = (callback) => {
if (document.readyState !== "loading") {
callba... |
2678c9e9e9d6450449f5ae89ee8a859667e4de479adb0b45cccd90a2eb13b06d | JavaScript | 8,325 | 260 | ////////////////////////////////////////////////
// MultiQC Module Status Bars
// Generic status bar implementation for any module
////////////////////////////////////////////////
// Global vars for status data
let mqc_status_data = {}; // { <module_key>: { <section_key>: { <sample_name>: "pass"|"warn"|"fail" } } }
/... |
3184c6a631599a378f6b662de9a951a04df7e43c93448cdfb0db23baaaf5d6f2 | JavaScript | 8,331 | 212 | ////////////////////////////////////////////////
// MultiQC Report Toolbox - Export Functionality
////////////////////////////////////////////////
// Make functions available globally
window.initExport = function () {
// Change text on download button
$('#mqc_exportplots a[data-bs-toggle="tab"]').on("shown.bs.tab"... |
91a27497196c3062dceaad69abf358af547fc6ecc25323b65c945d3a36b7603b | JavaScript | 8,472 | 248 | // Localization support
const messages = {
'en': {
'copy': 'Copy',
'copy_to_clipboard': 'Copy to clipboard',
'copy_success': 'Copied!',
'copy_failure': 'Failed to copy',
},
'es' : {
'copy': 'Copiar',
'copy_to_clipboard': 'Copiar al portapapeles',
'copy_success': '¡Copiado!',
'copy_... |
04da61d943e0f9d16eaed11a4bb354d1e61c25ada65ccef4e82cd31b3a530116 | JavaScript | 9,573 | 254 | ////////////////////////////////////////////////
// MultiQC Report Toolbox - AI Functionality
////////////////////////////////////////////////
function updatePanel(providerId) {
const provider = AI_PROVIDERS[providerId];
// Add label dynamically
let aiModelInfo = "";
let aiApiKeyInfo = "";
// Update model ... |
a3e9c8c52dd54d783a6d9294357ef104d17d03faf0a404b592216c0d71a9f717 | JavaScript | 9,636 | 325 | const headroomChanged = new CustomEvent("quarto-hrChanged", {
detail: {},
bubbles: true,
cancelable: false,
composed: false,
});
const announceDismiss = () => {
const annEl = window.document.getElementById("quarto-announcement");
if (annEl) {
annEl.remove();
const annId = annEl.getAttribute("data-... |
974f96aa41e2ec6a2607280a1a1bc17a076ec4e8950e14d1db28fdd0ab3bc164 | JavaScript | 9,676 | 295 | (function (jtd, undefined) {
// Event handling
jtd.addEvent = function(el, type, handler) {
if (el.attachEvent) el.attachEvent('on'+type, handler); else el.addEventListener(type, handler);
}
jtd.removeEvent = function(el, type, handler) {
if (el.detachEvent) el.detachEvent('on'+type, handler); else el.removeEvent... |
576985d2b19d3730fac24dcf3e3846816b5dfed459ea2fb3e21a1452e7be9c40 | JavaScript | 9,891 | 328 | let db;
let pricing;
let user;
var dimension = [0, 0];
//$(document).ready(function() {
$(document).on('shiny:connected', function() {
// prevent browser back and forward buttons from working
history.pushState(null, null, location.href);
window.onpopstate = function () {
history.go(1);
};
$(document).on(... |
a5ccb46e4255a67b994d8292f5cfed89afc4a6afc77b89d39e48289f41b83b89 | JavaScript | 13,540 | 363 | class BarPlot extends Plot {
constructor(dump) {
super(dump);
this.filteredSettings = [];
this.groupSettingsMap = null; // For multicategory: maps original group name -> toolbox settings
}
activeDatasetSize() {
if (this.datasets.length === 0) return 0; // no datasets
let cats = this.datasets[... |
81b6e3000006e748d96056e3d5606439fb822c0777b38cd4099cc674436ab437 | JavaScript | 14,887 | 457 | /*
* Copyright 2022 Google LLC.
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* https://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in... |
e7e1e9a8626511cabf7454c563ae5ca61e87c9fbba7e2450d93ff8366ed0cb2b | JavaScript | 15,081 | 413 | class ViolinPlot extends Plot {
constructor(dump) {
super(dump);
this.violinHeight = dump["violin_height"];
this.extraHeight = dump["extra_height"];
this.showTableByDefault = dump["show_table_by_default"];
this.tableAnchor = dump["table_anchor"];
this.isDownsampled = dump["is_downsampled"];
... |
bfe96a8e735ad63a031707f6c87b51b985536e81c18c2cffc72e24a96f5e5256 | JavaScript | 15,116 | 445 | ////////////////////////////////////////////////
// MultiQC Report Toolbox - Save/Load Configurations
////////////////////////////////////////////////
// Add these helper functions
window.getConfigObject = function () {
return {
highlights_f_texts: window.mqc_highlight_f_texts,
highlights_f_cols: window.mqc_... |
d5524903f278cb336f69d8d8bd5041952e58147e83d8acd4477982779537e21c | JavaScript | 15,662 | 430 | ////////////////////////////////////////////////
// Javascript for the DRAGEN FastQC MultiQC module
////////////////////////////////////////////////
///////////////
// Per Base Sequence Content
///////////////
// Global vars
fastqc_seq_content = {}; // { <module>: { <sample>: data } }
function load_fastqc_seq_conten... |
96ef147dff6204578bea2b1f0349cee215f5e1b4aa4c6e7b7b34dbd41c4b82de | JavaScript | 16,543 | 455 | class ViolinPlot extends Plot {
constructor(dump) {
super(dump);
this.violinHeight = dump["violin_height"];
this.extraHeight = dump["extra_height"];
this.showTableByDefault = dump["show_table_by_default"];
this.tableAnchor = dump["table_anchor"];
this.isDownsampled = dump["is_downsampled"];
... |
306bb4ed7f0208f81bea031e26b9bf893360fe072a1707b04b3097dbed5d58ff | JavaScript | 17,088 | 531 | /*
* searchtools.js
* ~~~~~~~~~~~~~~~~
*
* Sphinx JavaScript utilities for the full-text search.
*
* :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
"use strict";
/**
* Simple result scoring code.
*/
if (typeof Scorer === "undefined") {
var S... |
84d657b9d7c5ea18f49998098c75d5df72a79e4eef3c2589e8ee8e3705207d7e | JavaScript | 17,244 | 520 | /*
* Copyright 2022 Google LLC.
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* https://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in... |
a5047a45d60fcfbc5a8f0a1456b036c46e3017749c5159d28b395b4b4b9d36d8 | JavaScript | 17,502 | 479 | ////////////////////////////////////////////////
// Javascript for the FastQC MultiQC module
////////////////////////////////////////////////
///////////////
// Per Base Sequence Content
///////////////
// Global vars
fastqc_seq_content = {}; // { <module>: { <sample>: data } }
function load_fastqc_seq_content() {
... |
0448c6e77b46cc9b9b138eb6b97ddee3896efddecb25dc703d1db9de99bba4f9 | JavaScript | 19,406 | 2 | var List;List=function(){var t={"./src/add-async.js":function(t){t.exports=function(t){return function e(r,n,s){var i=r.splice(0,50);s=(s=s||[]).concat(t.add(i)),r.length>0?setTimeout((function(){e(r,n,s)}),1):(t.update(),n(s))}}},"./src/filter.js":function(t){t.exports=function(t){return t.handlers.filterStart=t.handl... |
15dd220a16999cd8832c242da51adad6535176513d69bde4f482c72d145f522c | JavaScript | 19,536 | 557 | ////////////////////////////////////////////////
// Plotly Plotting Code
////////////////////////////////////////////////
// Global plot data variable. Accessed in many other JavaScript files.
let mqc_plots = {};
// Initialise the toolbox filters
window.mqc_highlight_f_texts = [];
window.mqc_highlight_f_cols = [];
wi... |
45104a2599a4571dba229c406a28ca819f3394d13b4bc3a1034ff6377300a06d | JavaScript | 21,364 | 599 | ////////////////////////////////////////////////
// MultiQC Table code
////////////////////////////////////////////////
// Execute when page load has finished loading
$(function () {
if ($(".mqc_per_sample_table").length > 0) {
// Enable tablesorter on MultiQC tables
let getSortVal = function (node) {
... |
a141365d03eb8cb42a38dcddb4218551be865a517feb841ee826ec165465f09a | JavaScript | 21,453 | 555 | ////////////////////////////////////////////////
// AI stuff
////////////////////////////////////////////////
window.continueInSeqeraChatHandler = function (event) {
let el = $(event.currentTarget);
let seqeraWebsite = el.data("seqera-website");
// Either report uuid, or encoded system and chat messages
let t... |
fa226c8e1e3556993260e6a5c1fe94e225da59b3418a06811fdc51d308f8bb43 | JavaScript | 21,479 | 2 | /*! pako 2.1.0 https://github.com/nodeca/pako @license (MIT AND Zlib) */
!function(e,t){"object"==typeof exports&&"undefined"!=typeof module?t(exports):"function"==typeof define&&define.amd?define(["exports"],t):t((e="undefined"!=typeof globalThis?globalThis:e||self).pako={})}(this,(function(e){"use strict";var t=(e,t,... |
eb83bfd1e24727d3f3daea5540d83e95f9fd18dea0908bec475e947e50c4dc15 | JavaScript | 21,877 | 570 | ////////////////////////////////////////////////
// AI stuff
////////////////////////////////////////////////
window.continueInSeqeraChatHandler = function (event) {
let el = $(event.currentTarget);
let seqeraWebsite = el.data("seqera-website");
// Either report uuid, or encoded system and chat messages
let t... |
88d2cb172e78f6f39a9c252852a110808ad526a52c19c89110c88bb3ad000fa4 | JavaScript | 22,403 | 628 | ////////////////////////////////////////////////
// MultiQC Table code
////////////////////////////////////////////////
// Execute when page load has finished loading
$(function () {
if ($(".mqc_per_sample_table").length > 0) {
// Enable tablesorter on MultiQC tables
let getSortVal = function (node) {
... |
10634f88e6e763e792b3cd131b48ac3e9d12ed40bee56b82b32321bf8dcfa01c | JavaScript | 22,626 | 667 | /*
* Copyright 2022 Google LLC.
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* https://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in... |
c57339c3fa16b1d69d9a6b46749a8139ef8d4fc9bbfe48144ff897aa7d4222ec | JavaScript | 23,539 | 9 | /**
* Fuse.js v6.6.2 - Lightweight fuzzy-search (http://fusejs.io)
*
* Copyright (c) 2022 Kiro Risk (http://kiro.me)
* All Rights Reserved. Apache Software License 2.0
*
* http://www.apache.org/licenses/LICENSE-2.0
*/
var e,t;e=this,t=function(){"use strict";function e(e,t){var n=Object.keys(e);if(Object.getOwnP... |
af87ff2b48366345922921c2f35fdaec464d79a4df10df8b7a44b2ae162a862f | JavaScript | 25,974 | 662 | function handleStreamError(error) {
if (error.toString().includes("Failed to fetch")) {
error = "Failed to connect to AI provider. Please check your internet connection and the API key, and try again.";
}
return error;
}
function isReasoningModel(model) {
if (!model) return false;
const reasoningModels =... |
84451975be26b8c8a88ad7ba23bb04771ad0649d7479a021ac76ab179974eeb4 | JavaScript | 26,271 | 667 | import DOMPurify from "dompurify";
function handleStreamError(error) {
if (error.toString().includes("Failed to fetch")) {
error = "Failed to connect to AI provider. Please check your internet connection and the API key, and try again.";
}
return error;
}
function isReasoningModel(model) {
if (!model) ret... |
f263b05369e050fa175d4ecb9c9358eb4253602d510297adfb31df48b2f1c4d5 | JavaScript | 29,369 | 3 | /*! @license DOMPurify 3.4.15 | (c) Cure53 and other contributors | Released under the Apache license 2.0 and Mozilla Public License 2.0 | github.com/cure53/DOMPurify/blob/3.4.15/LICENSE */
!function(t,e){"object"==typeof exports&&"undefined"!=typeof module?module.exports=e():"function"==typeof define&&define.amd?defin... |
b72710e13b43802c60ceb51b6ad5b404fbcd6e60008285949ea7d69dcd925f49 | JavaScript | 29,493 | 803 | ////////////////////////////////////////////////
// Plotly Plotting Code
////////////////////////////////////////////////
// Global plot data variable. Accessed in many other JavaScript files.
window.mqc_plots = {};
// Initialise the toolbox filters
window.mqc_highlight_f_texts = [];
window.mqc_highlight_f_cols = [];... |
33f0306dbfc1621f918746868e9422776ea9d5bd8e06cae4da4f7202f4313d5d | JavaScript | 29,508 | 6 | /**
* lunr - http://lunrjs.com - A bit like Solr, but much smaller and not as bright - 2.3.6
* Copyright (C) 2019 Oliver Nightingale
* @license MIT
*/
!function(){var e=function(t){var r=new e.Builder;return r.pipeline.add(e.trimmer,e.stopWordFilter,e.stemmer),r.searchPipeline.add(e.stemmer),t.call(r,r),r.build()};... |
f630c711a00d0a8356cc4effa987c78328335bf4018b915df4a1cfd6b83fe7a2 | JavaScript | 29,691 | 768 | let table;
let refreshInterval;
let setupOptionsInitialized = false;
$(document).ready(function() {
// Initialize setup filter with bootstrap-select
$('#setupFilter').selectpicker({
liveSearch: true,
actionsBox: true,
selectedTextFormat: 'count > 3',
countSelectedText: '{0} setu... |
9014294bd477f54d9dffb82309be319a8720165fdebf407f571c1a811a407569 | JavaScript | 36,315 | 7 | /*! jQuery UI - v1.12.1 - 2019-11-08
* http://jqueryui.com
* Includes: widget.js, position.js, data.js, scroll-parent.js, widgets/draggable.js, widgets/mouse.js
* Copyright jQuery Foundation and other contributors; Licensed MIT */
(function(t){"function"==typeof define&&define.amd?define(["jquery"],t):t(jQuery)})(func... |
8963bccf5b1b385956f63a879ba3c395d5dbdb009caa8de004d3d9c60fd3041b | JavaScript | 36,668 | 7 | /*! jQuery UI - v1.12.1 - 2016-12-22
* http://jqueryui.com
* Includes: widget.js, data.js, scroll-parent.js, widgets/sortable.js, widgets/mouse.js
* Copyright jQuery Foundation and other contributors; Licensed MIT */
(function(t){"function"==typeof define&&define.amd?define(["jquery"],t):t(jQuery)})(function(t){t.ui=t... |
b685d6ad9b22c04e3f55bcf54e56db7fed463bc881bc92007406e9879a0ec6be | JavaScript | 37,174 | 1,290 | const kQueryArg = "q";
const kResultsArg = "show-results";
// If items don't provide a URL, then both the navigator and the onSelect
// function aren't called (and therefore, the default implementation is used)
//
// We're using this sentinel URL to signal to those handlers that this
// item is a more item (along with... |
76d187d57700c8aa2932e8b9c76d0a9cfc6e1ae4b1f51b3aa62241ff83aabba2 | JavaScript | 44,365 | 1 | !function(e){"function"==typeof define&&define.amd?define(["jquery"],e):"object"==typeof module&&"object"==typeof module.exports?module.exports=e(require("jquery")):e(jQuery)}(function(e){return function(A){"use strict";var L=A.tablesorter={version:"2.31.3",parsers:[],widgets:[],defaults:{theme:"default",widthFixed:!1,... |
03dfe1fbce92a9f17fcd1a1501213bd820d050ab085c338419ab06a3631c9459 | JavaScript | 55,880 | 1 | !function(e,t){"object"==typeof exports&&"undefined"!=typeof module?module.exports=t():"function"==typeof define&&define.amd?define(t):(e=e||self).GLightbox=t()}(this,(function(){"use strict";function e(t){return(e="function"==typeof Symbol&&"symbol"==typeof Symbol.iterator?function(e){return typeof e}:function(e){retu... |
3da409040f90aff3b4529db7dcd5ddb13b4fe6f9547be324170c67a950648483 | JavaScript | 67,463 | 2,030 | var colors = [
'#1f77b4',
'#ff7f0e',
'#2ca02c',
'#d62728',
'#9467bd',
'#8c564b',
'#e377c2',
'#7f7f7f',
'#bcbd22',
'#17becf'
]
var colors2 = [
'#E27D60',
'#41B3A3',
'#E8A87C',
'#C38D9E',
'#7AE7C7'
]
var state = {};
state.unlocked = false;
state.token = undef... |
470ee76d0054b235f1a0f0e6745ec4c897b5ca402612c63f04098834c345546b | JavaScript | 75,208 | 3 | /*! showdown v 2.1.0 - 21-04-2022 */
!function(){function a(e){"use strict";var r={omitExtraWLInCodeBlocks:{defaultValue:!1,describe:"Omit the default extra whiteline added to code blocks",type:"boolean"},noHeaderId:{defaultValue:!1,describe:"Turn on/off generated header id",type:"boolean"},prefixHeaderId:{defaultValue... |
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